Sensitivity of a hydraulic model to changes in channel erosion during extreme flooding

Recent research into flood modelling has primarily concentrated on the simulation of inundation flow without considering the influences of channel morphology. River channels are often represented by a simplified geometry that is implicitly assumed to remain unchanged during flood simulations. However, field evidence demonstrates that significant morphological changes can occur during floods to mobilise the boundary sediments. Despite this, the effect of channel morphology on model results has been largely unexplored. To address this issue, the impact of channel cross-section geometry and channel long-profile variability on flood dynamics is examined using an ensemble of a 1D-2D hydraulic model (LISFLOOD-FP) of the 1:2102 year recurrence interval floods in Cockermouth, UK, within an uncertainty framework. A series of hypothetical scenarios of channel morphology were constructed based on a simple velocity based model of critical entrainment. A Monte-Carlo simulation framework was used to quantify the effects of channel morphology together with variations in the channel and floodplain roughness coefficients, grain size characteristics, and critical shear stress on measures of flood inundation. The results showed that the bed elevation modifications generated by the simplistic equations reflected a good approximation of the observed patterns of spatial erosion despite its overestimation of erosion depths. The effect of uncertainty on channel long-profile variability only affected the local flood dynamics and did not significantly affect the friction sensitivity and flood inundation mapping. The results imply that hydraulic models generally do not need to account for within event morphodynamic changes of the type and magnitude modelled, as these have a negligible impact that is smaller than other uncertainties, e.g. boundary conditions. Instead morphodynamic change needs to happen over a series of events to become large enough to change the hydrodynamics of floods in supply limited gravel-bed rivers like the one used in this research.

Modeling plant transpiration under limited soil water: comparison of different plant and soil hydraulic parameterizations and preliminary implications for their use in land surface models

Accurate estimates of how soil water stress affects plant transpiration are crucial for reliable land surface model (LSM) predictions. Current LSMs generally use a water stress factor, β, dependent on soil moisture content, θ, that ranges linearly between β = 1 for unstressed vegetation and β = 0 when wilting point is reached. This paper explores the feasibility of replacing the current approach with equations that use soil water potential as their independent variable, or with a set of equations that involve hydraulic and chemical signaling, thereby ensuring feedbacks between the entire soil–root–xylem–leaf system. A comparison with the original linear θ-based water stress parameterization, and with its improved curvi-linear version, was conducted. Assessment of model suitability was focused on their ability to simulate the correct (as derived from experimental data) curve shape of relative transpiration versus fraction of transpirable soil water. We used model sensitivity analyses under progressive soil drying conditions, employing two commonly used approaches to calculate water retention and hydraulic conductivity curves. Furthermore, for each of these hydraulic parameterizations we used two different parameter sets, for 3 soil texture types; a total of 12 soil hydraulic permutations. Results showed that the resulting transpiration reduction functions (TRFs) varied considerably among the models. The fact that soil hydraulic conductivity played a major role in the model that involved hydraulic and chemical signaling led to unrealistic values of β, and hence TRF, for many soil hydraulic parameter sets. However, this model is much better equipped to simulate the behavior of different plant species. Based on these findings, we only recommend implementation of this approach into LSMs if great care with choice of soil hydraulic parameters is taken

Label-free enrichment of avian Leucocytozoon using flow cytometric sorting

The group of haemosporidian parasites is of general interest to basic and applied science, since several species infect mammals, leading to malaria and associated disease symptoms. Although the great majority of haemosporidian parasites appear in bird hosts, as in the case of Leucocytozoon buteonis, there is little genomic information about genetic aspects of their co-evolution with hosts. Consequently, there is a high need for parasite-enrichment strategies enabling further analyses of the genomes, namely without exposure to DNA-intercalating dyes. Here, we used flow cytometry without an additional labelling step to enrich L. buteonis from infected buzzard blood. A specific, defined area of two-dimensional scattergramms was sorted and the fraction was further analysed. The successful enrichment of L. buteonis in the sorted fraction was demonstrated by Giemsa-staining and qPCR revealing a clear increase of parasite-specific genes, while host-specific genes were significantly decreased. This is the first report describing a labelling-free enrichment approach of L. buteonis from infected buzzard blood. The enrichment of parasites presented here is free of nucleic acid-intercalating dyes which may interfere with fluorescence-based methods or subsequent sequencing approaches.

Bit-index sort: a fast non-comparison integer sorting algorithm for permutations

This paper describes a fast integer sorting algorithm, herein referred as Bit-index sort, which is a non-comparison sorting algorithm for partial per-mutations, with linear complexity order in execution time. Bit-index sort uses a bit-array to classify input sequences of distinct integers, and exploits built-in bit functions in C compilers supported by machine hardware to retrieve the ordered output sequence. Results show that Bit-index sort outperforms in execution time to quicksort and counting sort algorithms. A parallel approach for Bit-index sort using two simultaneous threads is included, which obtains speedups up to 1.6.

Commensalism in an agroecosystem: hydraulic redistribution by deep-rooted legumes improves survival of a droughted shallow-rooted legume companion

We investigated commensalism of water use among annual shallow-rooted and perennial deep-rooted pasture legumes by examining the effect of hydraulic lift by Cullen pallidum (N.T.Burb.) J.W.Grimes and Medicago sativa on growth, survival and nutrient uptake of Trifolium subterraneum L. A vertically split-root design allowed separate control of soil water in top and bottom soil. Thirty-five days after watering ceased in the top tube, but soil remained at field capacity in the bottom tube, an increase in shallow soil water content by hydraulic lift was 5.6 and 5.9 g kg−1 soil overnight for C. pallidum and M. sativa, respectively. Trifolium subterraneum in this treatment maintained higher leaf water potentials (with M. sativa) or exhibited a slower decline (with C. pallidum) than without companion perennial plants; and shoot biomass of T. subterraneum was 56% (with C. pallidum) and 67% (with M. sativa) of that when both top and bottom tubes were at field capacity. Uptake of rubidium (a potassium analog) and phosphorus by T. subterraneum was not facilitated by hydraulic lift. Interestingly, phosphorus content was threefold greater, and shoot biomass 1.5–3.3-fold greater when T. subterraneum was interplanted with C. pallidum compared with M. sativa, although dry weight of C. pallidum was much greater than that of M. sativa. This study showed that interplanting with deep-rooted perennial legumes has benefited the survival of T. subterraneum.