1,294 research outputs found
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
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