150 years of macronutrient change in unfertilized UK ecosystems:observations vs simulations

Understanding changes in plant-soil C, N and P using data alone is difficult due to the linkages between carbon, nitrogen and phosphorus cycles (C, N and P), and multiple changing long-term drivers (e.g. climate, land-use, and atmospheric N deposition). Hence, dynamic models are a vital tool for disentangling these drivers, helping us understand the dominant processes and drivers and predict future change. However, it is essential that models are tested against data if their outputs are to be concluded upon with confidence. Here, a simulation of C, N and P cycles using the N14CP model was compared with time-series observations of C, N and P in soils and biomass from the Rothamsted Research long-term experiments spanning 150 years, providing an unprecedented temporal integrated test of such a model. N14CP reproduced broad trends in soil organic matter (SOM) C, N and P, vegetation biomass and N and P leaching. Subsequently, the model was used to decouple the effects of land management and elevated nitrogen deposition in these experiments. Elevated N deposition over the last 150 years is shown to have increased net primary productivity (NPP) 4.5-fold and total carbon sequestration 5-fold at the Geescroft Wilderness experiment, which was re-wilded to woodland in 1886. In contrast, the model predicts that for cropped grassland conditions at the Park Grass site, elevated N deposition has very little effect on SOM, as increases in NPP are diverted from the soil. More broadly, these results suggest that N deposition is likely to have had a large effect on SOM and NPP in northern temperate and boreal semi-natural grasslands and forests. However, in cropped and grazed systems in the same region, whilst NPP may have been supported in part by elevated N deposition, declines in SOM may not have been appreciably counteracted by increased N availability

Resuscitation-promoting factors possess a lysozyme-like domain

The novel bacterial cytokine family – resuscitation-promoting factors (Rpfs) – share a conserved domain of uncharacterized function. Predicting the structure of this domain suggests that Rpfs possess a lysozyme-like domain. The model highlights the good conservation of residues involved in catalysis and substrate binding. A lysozyme-like function makes sense for this domain in the light of experimental characterization of the biological function of Rpfs

A study of resuscitation-promoting factors in Mycobacterium tuberculosis.

Tuberculosis is a major threat to human health. About one third of the world's population is latently infected with Mycobacterium tuberculosis . In these cases the bacillus is in a state of low metabolic activity, making eradication difficult with conventional chemotherapy, which targets actively metabolizing organisms. The mechanisms by which M. tuberculosis reactivates to cause disease are currently unknown but a better understanding could greatly improve the treatment of tuberculosis. Resuscitation-promoting factor is a protein first identified in the supernatant of stationary phase cultures of Micrococcus luteus. It is active in picomolar concentrations, increasing the number of culturable M. luteus cells from dormant populations and shortening the lag phase of growth of small inocula. Bioinformatic searches reveal over 40 examples of rpf-ke genes in the high G-C cohort of Gram-positive bacteria, including M. tuberculosis , which contains five rpf gene orthologues. The work presented here investigated aspects of the M. tuberculosis Rpfs. Improvements in solubility of recombinant mycobacterial (M. tuberculosis and M. smegmatis) Rpfs were achieved by manipulating induction times and temperatures during protein expression and by using new hosts and vectors and producing novel fusion proteins. New assays were devised to measure the biological activity of recombinant Rpfs, using ATP bioluminescence of M. luteus cultures. A phage display library for M. tuberculosis was constructed, in an attempt to identify a protein receptor for Rpf. Rpf expression in human infection was investigated for the first time, using immunocytochemistry. Anti-Rpf antibodies were applied to human tissue sections infected with M. tuberculosis. Rpf was found to be located within epithelioid giant cells and in the immediate vicinity of acid-fast bacilli in necrotic centres. The presence of Rpf in human tuberculosis infection demonstrated in this work suggests that Rpfs may have a role in controlling dormancy of the bacilli in human disease

Роздуми про музичну бібліографію

У статті розглянуто особливості розвитку музичної бібліографії в Україні – від доби “радянського часу” до сучасності. В даному контексті висвітлюється науковий доробок у цій царині А. І. Мухи.В статье рассмотрены особенности развития музыкальной библиографии в Украине, начиная с эпохи “советского времени” до современного этапа. В данном контексте освещено научное наследие в этой области А. И. Мухи.The peculiarities of music bibliography development in the Ukraine are investigated in the article (from epoch “Soviet Union” to modern period of time). Connected with music bibliography some books by A. Mukha are examined in this context

Understanding the relationship between ignition delay and burn duration in a constant volume vessel at diesel engine conditions

Experiments were performed in a constant volume vessel, with fuel sprays injected into the vessel at various different pressure and temperature conditions chosen to represent diesel engine operation at various loads. A range of diesel primary reference fuels (i.e. mixtures of cetane and heptamethylnonane) of varying cetane number (CN) were tested, and as expected lower CN fuels have longer ignition delays. Burn period was plotted against ignition delay and two distinct trends can be seen: “mainly diffusion” diesel combustion in which burn period decreases with ignition delay and “mainly pre-mixed” diesel combustion in which burn period increases with ignition delay. There is typically a minimum in plots of burn period versus ignition delay which represents the transition between the two types of combustion mode. Higher CN, higher engine load and higher boost pressure would seem to favour “mainly diffusion” combustion whilst lower CN, lower loads and non boosted conditions favour “mainly pre-mixed” combustion

A set of codes for numerical convection and geodynamo calculations

We present a set of codes for calculating and displaying solutions to diverse problems within thermal convection and magnetic field generation in rotating fluid-filled spheres and spherical shells. There are diverse programs for the kinematic dynamo problem, the onset of thermal convection, and boundary-locked thermal convection, and time-stepping codes for non-magnetic convection and the dynamo with either homogeneous or spatially varying thermal boundary conditions. Where possible, all programs have been benchmarked against other codes and tested by reproducing previously published results. Each program comes with the complete source code, a pdf instruction manual, and at least one example run with a sample input file and all necessary files for describing an initial condition. The only prerequisite for running most of the codes is a FORTRAN compiler. The plotting programs require in addition the PGPLOT graphics library. All source code, examples, input files, solutions, and instructions are available for download from github and Zenodo

Accuracy and Limitations of Fitting and Stereoscopic Methods to Determine the Direction of Coronal Mass Ejections from Heliospheric Imagers Observations

Using data from the Heliospheric Imagers (HIs) onboard STEREO, it is possible to derive the direction of propagation of coronal mass ejections (CMEs) in addition to their speed with a variety of methods. For CMEs observed by both STEREO spacecraft, it is possible to derive their direction using simultaneous observations from the twin spacecraft and also, using observations from only one spacecraft with fitting methods. This makes it possible to test and compare different analyses techniques. In this article, we propose a new fitting method based on observations from one spacecraft, which we compare to the commonly used fitting method of Sheeley et al. (1999). We also compare the results from these two fitting methods with those from two stereoscopic methods, focusing on 12 CMEs observed simultaneously by the two STEREO spacecraft in 2008 and 2009. We find evidence that the fitting method of Sheeley et al. (1999) can result in significant errors in the determination of the CME direction when the CME propagates outside of 60deg \pm 20 deg from the Sun-spacecraft line. We expect our new fitting method to be better adapted to the analysis of halo or limb CMEs with respect to the observing spacecraft. We also find some evidence that direct triangulation in the HI fields-of-view should only be applied to CMEs propagating approximatively towards Earth (\pm 20deg from the Sun-Earth line). Last, we address one of the possible sources of errors of fitting methods: the assumption of radial propagation. Using stereoscopic methods, we find that at least seven of the 12 studied CMEs had an heliospheric deflection of less than 20deg as they propagated in the HI fields-of-view, which, we believe, validates this approximation.Comment: 17 pages, 6 figures, 2 tables, accepted to Solar Physic

The problem with Kappa

It is becoming clear that traditional evaluation measures used in Computational Linguistics (including Error Rates, Accuracy, Recall, Precision and F-measure) are of limited value for unbiased evaluation of systems, and are not meaningful for comparison of algorithms unless both the dataset and algorithm parameters are strictly controlled for skew (Prevalence and Bias). The use of techniques originally designed for other purposes, in particular Receiver Operating Characteristics Area Under Curve, plus variants of Kappa, have been proposed to fill the void. This paper aims to clear up some of the confusion relating to evaluation, by demonstrating that the usefulness of each evaluation method is highly dependent on the assumptions made about the distributions of the dataset and the underlying populations. The behaviour of a number of evaluation measures is compared under common assumptions. Deploying a system in a context which has the opposite skew from its validation set can be expected to approximately negate Fleiss Kappa and halve Cohen Kappa but leave Powers Kappa unchanged. For most performance evaluation purposes, the latter is thus most appropriate, whilst for comparison of behaviour, Matthews Correlation is recommended

Speeds and arrival times of solar transients approximated by self-similar expanding circular fronts

The NASA STEREO mission opened up the possibility to forecast the arrival times, speeds and directions of solar transients from outside the Sun-Earth line. In particular, we are interested in predicting potentially geo-effective Interplanetary Coronal Mass Ejections (ICMEs) from observations of density structures at large observation angles from the Sun (with the STEREO Heliospheric Imager instrument). We contribute to this endeavor by deriving analytical formulas concerning a geometric correction for the ICME speed and arrival time for the technique introduced by Davies et al. (2012, ApJ, in press) called Self-Similar Expansion Fitting (SSEF). This model assumes that a circle propagates outward, along a plane specified by a position angle (e.g. the ecliptic), with constant angular half width (lambda). This is an extension to earlier, more simple models: Fixed-Phi-Fitting (lambda = 0 degree) and Harmonic Mean Fitting (lambda = 90 degree). This approach has the advantage that it is possible to assess clearly, in contrast to previous models, if a particular location in the heliosphere, such as a planet or spacecraft, might be expected to be hit by the ICME front. Our correction formulas are especially significant for glancing hits, where small differences in the direction greatly influence the expected speeds (up to 100-200 km/s) and arrival times (up to two days later than the apex). For very wide ICMEs (2 lambda > 120 degree), the geometric correction becomes very similar to the one derived by M\"ostl et al. (2011, ApJ, 741, id. 34) for the Harmonic Mean model. These analytic expressions can also be used for empirical or analytical models to predict the 1 AU arrival time of an ICME by correcting for effects of hits by the flank rather than the apex, if the width and direction of the ICME in a plane are known and a circular geometry of the ICME front is assumed.Comment: 15 pages, 5 figures, accepted for publication in "Solar Physics

Effect of Solar Wind Drag on the Determination of the Properties of Coronal Mass Ejections from Heliospheric Images

The Fixed-\Phi (F\Phi) and Harmonic Mean (HM) fitting methods are two methods to determine the average direction and velocity of coronal mass ejections (CMEs) from time-elongation tracks produced by Heliospheric Imagers (HIs), such as the HIs onboard the STEREO spacecraft. Both methods assume a constant velocity in their descriptions of the time-elongation profiles of CMEs, which are used to fit the observed time-elongation data. Here, we analyze the effect of aerodynamic drag on CMEs propagating through interplanetary space, and how this drag affects the result of the F\Phi and HM fitting methods. A simple drag model is used to analytically construct time-elongation profiles which are then fitted with the two methods. It is found that higher angles and velocities give rise to greater error in both methods, reaching errors in the direction of propagation of up to 15 deg and 30 deg for the F\Phi and HM fitting methods, respectively. This is due to the physical accelerations of the CMEs being interpreted as geometrical accelerations by the fitting methods. Because of the geometrical definition of the HM fitting method, it is affected by the acceleration more greatly than the F\Phi fitting method. Overall, we find that both techniques overestimate the initial (and final) velocity and direction for fast CMEs propagating beyond 90 deg from the Sun-spacecraft line, meaning that arrival times at 1 AU would be predicted early (by up to 12 hours). We also find that the direction and arrival time of a wide and decelerating CME can be better reproduced by the F\Phi due to the cancellation of two errors: neglecting the CME width and neglecting the CME deceleration. Overall, the inaccuracies of the two fitting methods are expected to play an important role in the prediction of CME hit and arrival times as we head towards solar maximum and the STEREO spacecraft further move behind the Sun.Comment: Solar Physics, Online First, 17 page