Urinary Calculi

The chemical composition of 256 urinary calculi on the Witwatersrand has been determined in 3 population groups. 'Calcium stones' comprised 53,1% of the total and most of the remainder were triple phosphate. The distribution of these stones in the different population groups was similar. Urinary calculi are rare in the Bantu.S. Afr. Med. J., 47, 128 (1973

Effect of root age on the biomechanics of seminal and nodal roots of barley (<i>Hordeum vulgare L.</i>) in contrasting soil environments

Acknowledgments The James Hutton Institute receives funding from the Scottish Government. The authors would also like to thank Jim McNicol from Biomathematics and Statistics Scotland for his advice on statistical analysis.Peer reviewedPostprin

Scaling of the reinforcement of soil slopes by living plants in a geotechnical centrifuge

The research described here in was funded by a EPSRC (EP/M020355/1) project in collaboration with the University of Dundee, the University of Southampton, the University of Aberdeen, the Durham University and The James Hutton Institute. The authors thank Professor Mike Humphreys (IBERS, Aberystwyth University) and Scotia seeds for providing seeds used in this study and Dr Gary Callon (University of Dundee) for arranging indoor growing area. The James Hutton Institute receives funding from the Scottish Government (Rural & Environmental Services & Analytical Services Division).Peer reviewedPublisher PD

Normalizing single-cell RNA sequencing data: challenges and opportunities

Single-cell transcriptomics is becoming an important component of the molecular biologist's toolkit. A critical step when analyzing data generated using this technology is normalization. However, normalization is typically performed using methods developed for bulk RNA sequencing or even microarray data, and the suitability of these methods for single-cell transcriptomics has not been assessed. We here discuss commonly used normalization approaches and illustrate how these can produce misleading results. Finally, we present alternative approaches and provide recommendations for single-cell RNA sequencing users

Effects of root dehydration on biomechanical properties of woody roots of <i>Ulex europaeus</i>

Aims: Effects of root water status on root tensile strength and Young’s modulus were studied in relation to root reinforcement of slopes. Methods: Biomechanical properties of woody roots, Ulex europaeus, were tested during progressive dehydration and after thirty-day moisture equilibration in soil with contrasting water contents. Root diameter, water content and water loss were recorded and root water potential versus water content relation was investigated. Tensile stresses induced by root contraction upon dehydration were measured. Results: Root tensile strength and Young’s modulus increased abruptly when root water content dropped below 0.5 g g −1. The strength increase was due to root radial and axial contraction induced by root water potential drop. Diameter decrease and strength gain were the largest for thin roots because of the relatively larger evaporative surface per volume of thin roots. Largely negative water potentials in dry soil induced root drying, affecting root biomechanical properties. Conclusion: Root water status is a factor that can cause (inappropriately) high strength values and the large variability reported in literature for thin roots. Therefore, all root diameter classes should have consistent moisture for fair comparison. Testing fully hydrated roots should be the routine protocol, given that slope instability occurs after heavy rainfall. </p

Jinn, psychiatry and contested notions of misfortune among East London Bangladeshis

This study examines understandings of misfortune among east London Bangladeshis, particularly with respect to the role of jinn spirits. It reports on the findings of ethnographic interviews among 40 members of this community. Appeal to jinn explanations is commonplace at times of psychological disturbance and unexplained physical symptoms. Resort to traditional healers is frequent. These explanations are contested by different groups in the community. The findings are examined within the context of a discourse on tradition and modernity with particular emphasis on Islam and modernity. Copyright 2008 SAGE Publications. All rights reserved. Not for commercial use or unauthorized distribution

A critical evaluation of predictive models for rooted soil strength with application to predicting the seismic deformation of rooted slopes

This paper presents a comparative study of three different classes of model for estimating the reinforcing effect of plant roots in soil, namely (i) fibre pull-out model, (ii) fibre break models (including Wu and Waldron’s Model (WWM) and the Fibre Bundle Model (FBM)) and (iii) beam bending or p-y models (specifically Beam on a Non-linear Winkler-Foundation (BNWF) models). Firstly, the prediction model of root reinforcement based on pull-out being the dominant mechanism for different potential slip plane depths was proposed. The resulting root reinforcement calculated were then compared with those derived from the other two types of models. The estimated rooted soil strength distributions were then incorporated within a fully dynamic, plane-strain continuum finite element model to assess the consequences of the selection of rooted soil strength model on the global seismic stability of a vegetated slope (assessed via accumulated slip during earthquake shaking). For the particular case considered in this paper (no roots were observed to have broken after shearing), root cohesion predicted by the pull-out model is much closer to that the BNWF model, but is largely over-predicted by the family of fibre break models. In terms of the effects on the stability of vegetated slopes, there exists a threshold value beyond which the position of the critical slip plane would bypass the rooted zones, rather than passing through them. Further increase of root cohesion beyond this value has minimal effect on the global slope behaviour. This implies that significantly over-predicted root cohesion from fibre break models when used to model roots with non-negligible bending stiffness may still provide a reasonable prediction of overall behaviour, so long as the critical failure mechanism is already bypassing the root-reinforced zones. © 2019, The Author(s)

The genomic basis of adaptive evolution in threespine sticklebacks

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.National Human Genome Research Institute (U.S.)National Human Genome Research Institute (U.S.) (NHGRI CEGS Grant P50-HG002568

Small-scale modelling of plant root systems using 3D printing, with applications to investigate the role of vegetation on earthquake-induced landslides

Vegetation has been previously proposed as a method for protecting artificial and natural slopes against shallow landslides (e.g. as may be triggered by an earthquake); however, previous research has concentrated on individual root soil interaction during shear deformation rather than the global slope behaviour due to the extreme expense and difficulty involved in conducting full-scale field tests. Geotechnical centrifuge modelling offers an opportunity to investigate in detail the engineering performance of vegetated slopes, but its application has been restricted due to the lack of availability of suitable root analogues that can repeatably replicate appropriate mechanical properties (stiffness and strength) and realistic 3-D geometry. This study employed 3-D printing to develop a representative and repeatable 1:10 scale model of a tree root cluster representing roots up to 1.5 m deep at prototype scale) that can be used within a geotechnical centrifuge to investigate the response of a vegetated slope subject to earthquake ground motion. The printed Acrylonitrile Butadiene Styrene (ABS) plastic root model was identified to be highly representative of the geometry and mechanical behaviour (stiffness and strength) of real woody root systems. A programme of large direct shear tests was also performed to evaluate the additional strength provided by the root analogues within soil that is slipping and investigate the influence of various characteristics (including root area ratio, soil confining effective stress and root morphology) on this reinforcing effect. Our results show that root reinforcement is not only a function of root mechanical properties, but also depends on factors including surrounding effective confining stress (resulting in depth dependency even for the same RAR), depth of the slip plane and root morphology. When subject to shear loading in soil, the tap root appeared to structurally transfer load within the root system, including to smaller and deeper roots which subsequently broke or were pulled out. Finally, the root analogues were added to model slopes subjected toearthquake ground motion in the centrifuge, where it was revealed that vegetation can substantially reduce earthquake-induced slope deformation in the soil conditions tested (76% reduction on crest permanent settlement during slippage). Both the realistic 3-D geometry and highly simplified root morphologies, as characterised mechanically by the shear tests, were tested in the centrifuge which, despite exhibiting very different levels of additional strength in the shear tests, resulted in very similar responses of the slopes. This suggests that once a certain minimum level of reinforcement has been reached which will alter the deformation mechanism within the slope, further increases of root contribution (e.g. due to differences in root morphology) do not have a large further effect on improving slope stability.<br/