Causal Factors of Breeding Success and Frequency in Threatened Grassland Birds on the Ingula Nature Reserve, South Africa

The high-altitude grasslands covering the eastern escarpment of South Africa is one of the country’s most valuable habitats for biodiversity, livestock and water production. The habitat hosts several threatened bird species including endangered species such as the Rudd\u27s Lark (Heteromirafra ruddi) and Grey Crowned Crane (Balearica regulorum), and vulnerable species such as the Blue Crane (Grus paradisea), Wattled Crane (Bugeranus carunculatus), Southern Bald Ibis (Geronticus calvus), and Yellow-breasted Pipit (Anthus chloris). Avian research and monitoring have been ongoing within the recently declared Ingula Nature Reserve for more than 15 years as part of the activities of the Ingula Partnership - a partnership between BirdLife South Africa, Eskom Holdings SOC Ltd and the Middelpunt Wetland Trust - with the objective of effectively conserving birds and their habitat surrounding the Ingula Pumped Storage Scheme development. Avian monitoring on Ingula refocused in 2014 to confirm the presence of threatened species on site, followed by the determination of the breeding status of these species. An initiative was then launched to assess the breeding frequency and success of each identified species. Breeding monitoring for 13 out of the 24 occurring threatened species commenced in 2014 and was conducted for five consecutive seasons. Breeding success per season was measured in relation to the grassland management regime of that season (including both fire and grazing), as well as weather data, adjusting for dry and wet seasons. Results confirm that various grassland management regimes directly influenced the initiation of breeding activities and density of several of the species studied, while others’ breeding success and frequency were more dependent on macro-weather patterns (including climate change) and fire frequency and timing. These results have direct implications for the management of highland grasslands and associated species in the given region

Drivers of bird species richness within moist high-altitude grasslands in eastern South Africa

Moist high-altitude grasslands in South Africa are renowned for high avifaunal diversity and are priority areas for conservation. Conservation management of these areas conflicts with management for other uses, such as intensive livestock agriculture, which requires annual burning and leads to heavy grazing. Recently the area has become target for water storage schemes and renewable electricity energy projects. There is therefore an urgent need to investigate environmental factors and habitat factors that affect bird species richness in order to optimise management of those areas set aside for conservation. A particularly good opportunity to study these issues arose at Ingula in the eastern South African high-altitude grasslands. An area that had been subject to intense grazing was bought by the national power utility that constructed a pumped storage scheme on part of the land and set aside the rest for bird conservation. Since the new management took over in 2005 the area has been mostly annually burned with relatively little grazing. The new management seeks scientific advice on how to maintain avian species richness of the study area. We collected bird occurrence and vegetation data along random transects between 2006 and 2010 to monitor the impact of the new management, and to study the effect of the habitat changes on bird species richness. To achieve these, we convert bird transect data to presence only data to investigate how bird species richness were related to key transect vegetation attributes under this new grassland management. First we used generalised linear mixed models, to examine changes in vegetation grass height and cover and between burned and unburned habitats. Secondly, we examined how total bird species richness varied across seasons and years. And finally we investigated which habitat vegetation attributes were correlated with species richness of a group of grassland depended bird species only. Transects that were burned showed a larger decrease in vegetation cover compared to transects that were not burned. Grass height increased over time. Bird species richness was highest in summer compared to other seasons and increased over time. Overall bird species richness increased over the three summer surveys but species richness of birds that prefer heavily grazed habitat showed little change over the three years. Changes in bird species richness were best explained by the model with grass height for combined species richness of grassland depended birds but also for birds that prefer heavy grazing when treated alone. On one hand birds that prefer moderate grazing were best explained by a null model. However, overall bird species richness was better positively correlated to grass height than grass cover or dead grass. We conclude that frequent burning alone with relatively reduced grazing led to higher but less dense grass, which benefited some species and disadvantaged others. We suggest that management of this grassland use combination of fire and grazing and leave some areas unburned to accommodates birds of various habitat needs

Dynamical thermalization and vortex formation in stirred 2D Bose-Einstein condensates

We present a quantum mechanical treatment of the mechanical stirring of Bose-Einstein condensates using classical field techniques. In our approach the condensate and excited modes are described using a Hamiltonian classical field method in which the atom number and (rotating frame) energy are strictly conserved. We simulate a T = 0 quasi-2D condensate perturbed by a rotating anisotropic trapping potential. Vacuum fluctuations in the initial state provide an irreducible mechanism for breaking the initial symmetries of the condensate and seeding the subsequent dynamical instability. Highly turbulent motion develops and we quantify the emergence of a rotating thermal component that provides the dissipation necessary for the nucleation and motional-damping of vortices in the condensate. Vortex lattice formation is not observed, rather the vortices assemble into a spatially disordered vortex liquid state. We discuss methods we have developed to identify the condensate in the presence of an irregular distribution of vortices, determine the thermodynamic parameters of the thermal component, and extract damping rates from the classical field trajectories.Comment: 22 pages, 15 figures. v2: Minor refinements made at suggestion of referee. Discussion of other treatments revised. To appear in Phys. Rev.

Modelling diverse root density dynamics and deep nitrogen uptake — a simple approach

We present a 2-D model for simulation of root density and plant nitrogen (N) uptake for crops grown in agricultural systems, based on a modification of the root density equation originally proposed by Gerwitz and Page in J Appl Ecol 11:773–781, (1974). A root system form parameter was introduced to describe the distribution of root length vertically and horizontally in the soil profile. The form parameter can vary from 0 where root density is evenly distributed through the soil profile, to 8 where practically all roots are found near the surface. The root model has other components describing root features, such as specific root length and plant N uptake kinetics. The same approach is used to distribute root length horizontally, allowing simulation of root growth and plant N uptake in row crops. The rooting depth penetration rate and depth distribution of root density were found to be the most important parameters controlling crop N uptake from deeper soil layers. The validity of the root distribution model was tested with field data for white cabbage, red beet, and leek. The model was able to simulate very different root distributions, but it was not able to simulate increasing root density with depth as seen in the experimental results for white cabbage. The model was able to simulate N depletion in different soil layers in two field studies. One included vegetable crops with very different rooting depths and the other compared effects of spring wheat and winter wheat. In both experiments variation in spring soil N availability and depth distribution was varied by the use of cover crops. This shows the model sensitivity to the form parameter value and the ability of the model to reproduce N depletion in soil layers. This work shows that the relatively simple root model developed, driven by degree days and simulated crop growth, can be used to simulate crop soil N uptake and depletion appropriately in low N input crop production systems, with a requirement of few measured parameters

Root growth and nitrate uptake of three different catch crops in deep soil layers

Catch crops can reduce NO3 losses from leaching, but little is known about the importance of deep rooting for the efficiency of NO3 depletion. In a field experiment, we investigated the N uptake and root growth of three types of catch crops using minirhizotrons (glass tubes of 70-mm o.d.) reaching 2.4 m. Our purpose was to evaluate minirhizotron methodology and the importance of deep rooting in the ability of catch crops to take up NO3 from deep soil layers. Nitrogen uptake was studied over a 6-d period at the end of October by injection of 15NO3 at four depths in the ranges: 0.4 to 1, 0.5 to 1.4, and 1 to 2.5 m under Italian ryegrass (Lolium multiflorum Lam.), winter rye (Secale cereale L.), and fodder radish (Raphanus sativus L. var. oleiformis Pers.), respectively. The root depth of the three species were 0.6, 1.1, and more than 2.4 m, respectively. No 15N was taken up from placements below root depth, and linear relationships were found between root density and 15N uptake from different depths. Residual soil NO3 of 18, 59, and 87 kg N ha−1 was left under fodder radish, winter rye, and ryegrass, respectively. The measurements obtained with the minirhizotron method were highly relevant for evaluating N uptake from different soil layers, and root depths of the catch crops were important for N depletion. Knowledge about root growth and N uptake in deep soil layers may be utilized when designing crop rotations with improved N use efficiency. Where N has been left by a preceding crop and leached to deeper soil layers, it may be recycled by deep-rooted catch crops

Saccadic Eye Movements Minimize the Consequences of Motor Noise

The durations and trajectories of our saccadic eye movements are remarkably stereotyped. We have no voluntary control over these properties but they are determined by the movement amplitude and, to a smaller extent, also by the movement direction and initial eye orientation. Here we show that the stereotyped durations and trajectories are optimal for minimizing the variability in saccade endpoints that is caused by motor noise. The optimal duration can be understood from the nature of the motor noise, which is a combination of signal-dependent noise favoring long durations, and constant noise, which prefers short durations. The different durations of horizontal vs. vertical and of centripetal vs. centrifugal saccades, and the somewhat surprising properties of saccades in oblique directions are also accurately predicted by the principle of minimizing movement variability. The simple and sensible principle of minimizing the consequences of motor noise thus explains the full stereotypy of saccadic eye movements. This suggests that saccades are so stereotyped because that is the best strategy to minimize movement errors for an open-loop motor system

Linear ensemble-coding in midbrain superior colliculus specifies the saccade kinematics

Recently, we proposed an ensemble-coding scheme of the midbrain superior colliculus (SC) in which, during a saccade, each spike emitted by each recruited SC neuron contributes a fixed minivector to the gaze-control motor output. The size and direction of this ‘spike vector’ depend exclusively on a cell’s location within the SC motor map (Goossens and Van Opstal, in J Neurophysiol 95: 2326–2341, 2006). According to this simple scheme, the planned saccade trajectory results from instantaneous linear summation of all spike vectors across the motor map. In our simulations with this model, the brainstem saccade generator was simplified by a linear feedback system, rendering the total model (which has only three free parameters) essentially linear. Interestingly, when this scheme was applied to actually recorded spike trains from 139 saccade-related SC neurons, measured during thousands of eye movements to single visual targets, straight saccades resulted with the correct velocity profiles and nonlinear kinematic relations (‘main sequence properties– and ‘component stretching’) Hence, we concluded that the kinematic nonlinearity of saccades resides in the spatial-temporal distribution of SC activity, rather than in the brainstem burst generator. The latter is generally assumed in models of the saccadic system. Here we analyze how this behaviour might emerge from this simple scheme. In addition, we will show new experimental evidence in support of the proposed mechanism

Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Measurement of the flavour composition of dijet events in pp collisions at root s=7 TeV with the ATLAS detector

This paper describes a measurement of the flavour composition of dijet events produced in pp collisions at √s=7 TeV using the ATLAS detector. The measurement uses the full 2010 data sample, corresponding to an integrated luminosity of 39 pb−1. Six possible combinations of light, charm and bottom jets are identified in the dijet events, where the jet flavour is defined by the presence of bottom, charm or solely light flavour hadrons in the jet. Kinematic variables, based on the properties of displaced decay vertices and optimised for jet flavour identification, are used in a multidimensional template fit to measure the fractions of these dijet flavour states as functions of the leading jet transverse momentum in the range 40 GeV to 500 GeV and jet rapidity |y|<2.1. The fit results agree with the predictions of leading- and next-to-leading-order calculations, with the exception of the dijet fraction composed of bottom and light flavour jets, which is underestimated by all models at large transverse jet momenta. The ability to identify jets containing two b-hadrons, originating from e.g. gluon splitting, is demonstrated. The difference between bottom jet production rates in leading and subleading jets is consistent with the next-to-leading-order predictions