A Sixth-Order Extension to the MATLAB Package bvp4c of J. Kierzenka and L. Shampine

A new two-point boundary value problem algorithm based upon the MATLAB bvp4c package of Kierzenka and Shampine is described. The algorithm, implemented in a new package bvp6c, uses the residual control framework of bvp4c (suitably modified for a more accurate finite difference approximation) to maintain a user specified accuracy. The new package is demonstrated to be as robust as the existing software, but more efficient for most problems, requiring fewer internal mesh points and evaluations to achieve the required accuracy

High-resolution computed tomography reconstructions of invertebrate burrow systems

The architecture of biogenic structures can be highly influential in determining species contributions to major soil and sediment processes, but detailed 3-D characterisations are rare and descriptors of form and complexity are lacking. Here we provide replicate high-resolution micro-focus computed tomography (μ-CT) data for the complete burrow systems of three co-occurring, but functionally contrasting, sediment-dwelling inter-tidal invertebrates assembled alone, and in combination, in representative model aquaria. These data (≤2,000 raw image slices aquarium−1, isotropic voxel resolution, 81 μm) provide reference models that can be used for the development of novel structural analysis routines that will be of value within the fields of ecology, pedology, geomorphology, palaeobiology, ichnology and mechanical engineering. We also envisage opportunity for those investigating transport networks, vascular systems, plant rooting systems, neuron connectivity patterns, or those developing image analysis or statistics related to pattern or shape recognition. The dataset will allow investigators to develop or test novel methodology and ideas without the need to generate a complete three-dimensional computation of exemplar architecture

A review of pursuit and saccadic eye movements and their utility in stroke

The head impulse-nystagmus-test of skew (+ hearing) or HINTS+ exam is a well-established clinical bedside test used in evaluating whether patients with the acute vestibular syndrome have features concerning for a central etiology (e.g., stroke). There are other components of the ocular motor exam that are helpful in the acute setting, including smooth pursuit and saccades. We discuss the anatomy and physiology of the saccade and smooth pursuit pathways from the cortex to the infratentorial region in the context of anterior and posterior circulation strokes in general but with a particular emphasis on distinct vestibular stroke syndromes. For each stroke localization, we review the vascular supply and the expected findings on the HINTS+ exam and correlate this with the expected findings on the smooth pursuit and saccade exams to aid in bedside diagnosis

Assessing changes in structural vegetation and soil properties following riparian restoration

Efforts are underway in many areas to restore riparian zones to arrest and/or reverse their degradation and the subsequent loss of the ecosystem services they provide. Despite strong links between edaphic conditions and riparian zone function, limited research has tested how soil properties respond to restoration, especially in an experimental context. With this important knowledge gap in mind, we established a field experiment to asssess structural vegetation and soil responses in the eight years following livestock exclusion and replanting in lowland streams in south-eastern Australia. On three streams, paired restored and control sites were experimentally established and we monitored vegetation (stem density, cover of bare ground and tree canopy, and loadings of organic matter), once beforehand, and then biennually after restoration. Selected soil properties (total carbon, total nitrogen, plant-available phosphorus) were sampled once shortly after restoration, then after another five years. Significant changes in structural vegetation occurred (e.g. decreased bare ground, increased plant stem density, organic matter, and canopy cover). In contrast, those soil properties did not respond. A mega-drought occurred throughout much of the study which was immediately followed by severe flooding. The floods redistributed organic matter at our study sites, with this effect mediated by vegetation structure: the probability of organic matter retention was positively correlated with groundcover and stem density of plants. The timing of flooding was also correlated with increased soil carbon and nitrogen, which could be due to increased productivity in these systems (for the former), or potentially due to increased fertiliser inputs or increased fixation (for the latter). Our study is the first to comprehensively and experimentally test how vegetation, litter layer and surface soil properties respond following riparian restoration, and will help guide the development and implementation of other monitoring programmes.Robin Hale, Paul Reich, Tom Daniel, Philip S. Lake, Timothy R. Cavagnar

Scales that matter: guiding effective monitoring of soil properties in restored riparian zones

Considerable effort has been directed at restoring riparian zones to ensure they continue to provide ecosystem services and one of the most common aims of these activities is to reduce nutrients (in either water or soil) entering waterways. Vegetation plays a major role in nutrient interception, but nutrients in terrestrial ecosystems are strongly influenced by edaphic factors. Therefore understanding the effectiveness of riparian restoration efforts is dependent on knowledge of the complex and highly dynamic nature of nutrient cycling processes in riparian soils and their adjacent landscapes. Our primary aim was to assess the potential utility of a range of common soil indicators for monitoring responses to riparian restoration, and to use this information to provide guidance for more effective monitoring. A range of soil physiochemical properties in riparian zones and adjacent paddocks as a comparison were measured, incorporating both structural (e.g., bulk density) and functional (e.g., nitrogen) variables likely to differ in terms of both their responsiveness to restoration, and degree of natural spatial and temporal variation. Soil properties across the three spatial scales considered here (among creeks, among sites and within sites) varied considerably, particularly levels of phosphorus, ammonium and nitrate. Total organic carbon and total nitrogen were less variable and more uniform across all scales. Potential explanations for these patterns were explored by examining relationships between soil properties and vegetation measures, and between a subset of the most promising indicators (carbon, total nitrogen and bulk density, based on inherently low spatial variability) and adjacent land-use. Fertiliser inputs appear to be a strong determinant of soil phosphorus but otherwise soil properties were not strongly related to vegetation or adjacent land-use. For mineral N this is likely a reflection of the highly spatiotemporally dynamic nature of nutrient cycling in riparian zone soils. A better understanding of natural variability in soil properties will greatly aid in developing more effective monitoring programmes to assess potential changes in riparian soil properties. Management of riparian systems to recover soil ecosystem services will depend upon identifying effective ecological indicators that can be used as measures of progress towards restoration goals. This study represents a necessary first step towards guiding meaningful monitoring of soil properties at riparian zones subject to restoration efforts.Robin Hale, Paul Reicha, Tom Daniel, Philip S. Lake, Timothy R. Cavagnar

The speciation and hybridization history of the genus Salmonella.

Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella, an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B, and are both related to Selander's group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution

A note on the relationship between grid structure and metrical structure in Banawá

The stress system of Banawa ́, an endangered Arawan language spoken in the Brazilian Amazon, constitutes a puzzling case study for metrical phonology. It has been claimed that its metrical representations violate the Syllable Integrity Principle (1) (Buller, Buller, and Everett (BBE) 1993, Everett 1996, 1997), one of the core universal principles in standard metrical theory, which bans representations where a foot dis- sects a heavy syllable (e.g., *(CV.CV ́ )(V.CV ́ ), *(CV ́ .CV)(V ́ .CV), where periods indicate syllable boundaries and parentheses, foot edges)

Investigating the properties of granulation in the red giants observed by Kepler

More than 1000 red giants have been observed by NASA/Kepler mission during a nearly continuous period of ~ 13 months. The resulting high-frequency resolution (< 0.03 muHz) allows us to study the granulation parameters of these stars. The granulation pattern results from the convection motions leading to upward flows of hot plasma and downward flows of cooler plasma. We fitted Harvey-like functions to the power spectra, to retrieve the timescale and amplitude of granulation. We show that there is an anti-correlation between both of these parameters and the position of maximum power of acoustic modes, while we also find a correlation with the radius, which agrees with the theory. We finally compare our results with 3D models of the convection.Comment: 4 pages, 1 figure. To appear in the ASP proceedings of "The 61st Fujihara seminar: Progress in solar/stellar physics with helio- and asteroseismology", 13th-17th March 2011, Hakone, Japa

Snowpack Relative Permittivity and Density Derived from Near-Coincident Lidar and Ground-Penetrating Radar

Depth-based and radar-based remote sensing methods (e.g., lidar, synthetic aperture radar) are promising approaches for remotely measuring snow water equivalent (SWE) at high spatial resolution. These approaches require snow density estimates, obtained from in-situ measurements or density models, to calculate SWE. However, in-situ measurements are operationally limited, and few density models have seen extensive evaluation. Here, we combine near-coincident, lidar-measured snow depths with ground-penetrating radar (GPR) two-way travel times (twt) of snowpack thickness to derive \u3e20 km of relative permittivity estimates from nine dry and two wet snow surveys at Grand Mesa, Cameron Pass, and Ranch Creek, Colorado. We tested three equations for converting dry snow relative permittivity to snow density and found the Kovacs et al. (1995) equation to yield the best comparison with in-situ measurements (RMSE = 54 kg m−3). Variogram analyses revealed a 19 m median correlation length for relative permittivity and snow density in dry snow, which increased to \u3e 30 m in wet conditions. We compared derived densities with estimated densities from several empirical models, the Snow Data Assimilation System (SNODAS), and the physically based iSnobal model. Estimated and derived densities were combined with snow depths and twt to evaluate density model performance within SWE remote sensing methods. The Jonas et al. (2009) empirical model yielded the most accurate SWE from lidar snow depths (RMSE = 51 mm), whereas SNODAS yielded the most accurate SWE from GPR twt (RMSE = 41 mm). Densities from both models generated SWE estimates within ±10% of derived SWE when SWE averaged \u3e 400 mm, however, model uncertainty increased to \u3e 20% when SWE averaged \u3c 300 mm. The development and refinement of density models, particularly in lower SWE conditions, is a high priority to fully realize the potential of SWE remote sensing methods