Live Hot, Die Young: Transmission Distortion in Recombination Hotspots

There is strong evidence that hotspots of meiotic recombination in humans are transient features of the genome. For example, hotspot locations are not shared between human and chimpanzee. Biased gene conversion in favor of alleles that locally disrupt hotspots is a possible explanation of the short lifespan of hotspots. We investigate the implications of such a bias on human hotspots and their evolution. Our results demonstrate that gene conversion bias is a sufficiently strong force to produce the observed lack of sharing of intense hotspots between species, although sharing may be much more common for weaker hotspots. We investigate models of how hotspots arise, and find that only models in which hotspot alleles do not initially experience drive are consistent with observations of rather hot hotspots in the human genome. Mutations acting against drive cannot successfully introduce such hotspots into the population, even if there is direct selection for higher recombination rates, such as to ensure correct segregation during meiosis. We explore the impact of hotspot alleles on patterns of haplotype variation, and show that such alleles mask their presence in population genetic data, making them difficult to detect.</p

The influence of particle type on the mechanics of sand-rubber mixtures

Triaxial and oedometer tests were used to demonstrate that a critical state framework can be applied to sand–rubber mixtures of similar soil grain and rubber sizes. It described well the behavior of a crushable sand and a quartz sand with either rubber fibers or granules of a variety of quantities, from small to large strains. Together with additional oedometer tests on soils of a wider variety of gradings, the work enabled the influences of sand particle type, grading, and rubber shape to be established. The sand particle type, specifically whether the grains were weak or strong, was found to be a key factor. It affected the yield in compression, even when large quantities of rubber were added. It controlled the critical state stress ratio, except for those mixtures with the highest content of rubber fibers, as well as the stress strain behavior. Sand particle type also determined the critical state line (CSL) location in the volumetric plane for lower rubber contents, but at higher rubber contents the behavior tended to converge for the two sand types. The grading and rubber type were not found to affect the compression or swelling indices significantly, which were mainly controlled by rubber content. Gradings that had nonconvergent compression paths without added rubber tended to retain this feature with rubber. The addition of both types of rubber led to higher volumetric compression in isotropic or one-dimensional compression but reduced volumetric strain during shear, altering the shapes of the state boundary surfaces

Quantitative Description of Grain Contacts in a Locked Sand

Quantifying the fabric of intact soil is of great importance in both geomechanics and geology. A unique and interesting example of fabric can be found in “locked sands”. These geologically old sands are characterized by significant grain interlocking and a low cement content. They can be sampled with minimal fabric disturbance. This study analyzes images acquired by x-ray microtomography of resin impregnated samples of a natural sand, Reigate Silver Sand part of the Folkestone Bed formation from southeast England. 2D and 3D image analyses were carried out to identify the grain-grain contacts and quantify individual contact areas. In contrast to earlier studies that have focused on the coordination number, this work demonstrates that for non-punctual contacts a measure of fabric that considers the contact area may be more appropriate

Influence of Destructuration on the Compression Behaviour of a Weak Rock

The literature has highlighted the behaviour of several weak rocks and the role of structure in determining them. The need for understanding their behaviour is due to the instabilities or collapse that may involve human settlements built on these materials which are widespread all over the world. In previous studies, the authors highlighted that in Marsala, Sicily, underground calcarenite quarries have been involved in a number of collapses that have seriously damaged numerous overlying buildings. In order to investigate the influence of destructuration on the behaviour of the calcarenite of Marsala, this paper presents a preliminary investigation of the compression behaviour of the intact rock and of the same weak rock in a destructured state. A petrographic and physical characterisation of the material was carried out together with oedometer and isotropic compression tests. The investigation has highlighted behaviour not previously identified for other weak rocks in which the pores seem to play a key role; the destructured material can no longer be considered, as generally assumed for other weak rocks, as a reference

The shear stiffness characteristics of four Eocene-to-Jurassic UK stiff clays

A large proportion of the southern UK is underlain by stiff clays. Improving their geotechnical characterisation is important for many current and future infrastructure projects. This paper presents an integrated study of the complex stiffness behaviour of four key medium-plasticity, highly overconsolidated strata: the Gault, Kimmeridge, Oxford and London clays. The latter were deposited between the Jurassic and the Eocene under broadly similar marine conditions. Coordinated programmes of advanced static and dynamic laboratory measurements have been undertaken on high-quality samples, concentrating on samples taken from similar depths at inland sites and including triaxial and hollow cylinder stress path experiments employing high-resolution local strain, multi-axial bender element and resonant column techniques. A new approach was employed to interpret the hollow cylinder experiments and the laboratory measurements are examined in combination with independent field shear wave data. The clays' stiffness characteristics are shown to be markedly anisotropic, pressure dependent and highly non-linear. Synthesis allows key conclusions to be drawn regarding: the relative reliability of alternative measurement approaches; the potential spread of stiffness behaviours between the clays; and whether the clays' varying geological ages and burial depths have any systematic influence on their stiffness characteristics. The results have important geotechnical engineering implications

Image-based modelling of shelly carbonate sand for foundation design of offshore structures

For the most part, carbonate soils are of biogenic origin comprising skeleton bodies and shells of small organisms, the shelly carbonate sands. Owing to the complex microstructure of these soils, there are many uncertainties related to their mechanical behavior, in particular, regarding their high compressibility. Aside from obvious safety concerns, the inability to predict the behavior of carbonate sands involves extensive remedial measures and leads invariably to severe time delays and increased construction costs. This study makes use of 3D images of the internal structure of a shelly carbonate sand under compression on a small oedometer placed inside an x-ray scanner. The images are first used to gain insights into the grain-scale properties of the material and then the soil microstructure is virtualized and simulated within a framework of combined discrete–finite-element method. This study contributes towards a better understand the grain-scale phenomena shaping the macro response of shelly carbonate sands, which differs considerably from more commonly studied silica sands of terrigeneous origin

The role of particle mineralogy in mixtures of sands

Several recent studies on mixtures of sands of different granulometries and/or mineralogies have focused on the key factors that might lead the behaviour to change from transitional to not transitional, where a transitional behaviour is characterised by non-convergent compression paths and critical state lines that might be non-unique. The authors present a review of mixtures of different soils showing a complex pattern of compression and shearing behaviour in which transitional behaviour can be caused by relatively small varia- tions to the proportion or nature of soil particles. Laboratory investigations, carried out by means of oedometer tests, have confirmed the role of the mineralogy of the matrix composed by larger grains. This determines the mode of behaviour so that, if there is a strong and stiff matrix made of quartz sand particles, which are either larger than or at least of similar size to the other component, then non-convergent compression paths are likely to occur, no matter whether particle breakage occurs or not

Experimental investigation into the primary fabric of stress transmitting particles

Understanding the stress distribution amongst the constituent grains is fundamental to predict the response of soil and advance science-based, rather than purely empirical, constitutive models. Photoelastic experiments and discrete element method simulations have provided evidence that, upon loading, discrete force chains form in granular materials. These force chains are made up of particles transmitting relatively large stresses and they are aligned in the direction of the major principal stress. A few qualitative studies have identified the presence of these force chains in sands but direct measurements of force chains have not been previously documented and tracking stress transmission in assemblies of real soil grains remains a challenging task. The present study makes use of three dimensional micro CT images to investigate the evolution of the internal topology of a sand subjected to triaxial compression loading. The analysis of the contact normal and branch vector orientations has shown the realignment of the contact normals in the direction of the major principal stress as a clear indication of the formation of force chains in the post-peak regime. Here the extent of the non-colinearity of the branch and contact normal vectors is explored. Using the micro CT data contact force networks within and outside of shear bands are compared

Image segmentation techniques for granular materials

To improve understanding of the mechanical behavior of granular materials it is important to be able to quantify the relative arrangement of the grains, i.e. the fabric. This can be done, for example, by measuring the orientations of the particles (e.g. the long axis orientation) or by considering the orientations of the vectors normal to each grain‐grain contact. In two dimensional (2D) analyses this information can be obtained by digital image analysis of images of thin sections obtained from an optical microscope. While such data is useful, granular materials of engineering interest are three dimensional (3D) materials and quantification of the 3D fabric is necessary. Micro Computed‐Tomography (μCT) together with 3D image analysis has emerged as a promising technique for obtaining the 3D data required. This paper aims to highlight the challenges associated with using image analysis to provide quantitative information on fabric. While automated image segmentation has proved to produce reasonable results in some cases, it is sometimes less successful when dealing with highly irregular and angular soil grains. This paper evaluates the effectiveness of 2D and 3D segmentation techniques that rely on the watershed segmentation algorithm. The primary material considered is Reigate Silver Sand, a natural quartzitic sand with grain diameters in the range of 150–300 μm. While the sand considered is primarily of interest to geotechnical engineers, the results of this study will be of interest to anyone seeking to quantify granular material fabric using either 2D microscopy data or μCT 3D data sets