Improved image-based deformation measurement for geotechnical applications

This paper describes and benchmarks a new implementation of image-based deformation measurement for geotechnical applications. The updated approach combines a range of advances in image analysis algorithms and techniques best suited to geotechnical applications. Performance benchmarking of the new approach has used a series of artificial images subjected to prescribed spatially varying displacement fields. An improvement by at least a factor of 10 in measurement precision is achieved relative to the most commonly used particle image velocimetry (PIV) approach for all deformation modes, including rigid-body displacements, rotations, and strains (compressive and shear). Lastly, an example analysis of a centrifuge model test is used to demonstrate the capabilities of the new approach. The strain field generated by penetration of a flat footing and an entrapped sand plug into an underlying clay layer is computed and compared for both the current and updated algorithms. This analysis demonstrates that the enhanced measurement precision improves the clarity of the interpretation. </jats:p

Enhancement of bearing capacity from consolidation: Due to changing strength or failure mechanism?

Bearing capacity of shallow foundations is higher following preload (or self-weight)-induced consolidation because the soil strength changes, and perhaps because the failure mechanism changes. Previous studies have illustrated this effect by plotting or predicting changes in either bearing capacity factor or strength. In this study, the relative contribution of these two effects is explored. This is achieved by formalising a definition of bearing capacity factor, which is described in terms of the average strength mobilised in the deformation mechanism at failure. Using the alternative definition of bearing capacity factor, the gain in foundation capacity is shown to be almost entirely due to changes in soil strength, rather than bearing capacity factor, which remains largely unaffected by the strength gains. This observation should encourage future studies into consolidated bearing capacity to present gains in capacity in terms of changes in mobilised strength rather than changes in bearing capacity factors, and supports the use of prediction methods that focus on defining the change in soil strength.This work forms part of the activities of the Centre for Offshore Foundation Systems (COFS), supported as a node of the Australian Research Council's Centre of Excellence for Geotechnical Science and Engineering (CE110001009), and the Industrial Transformation Research Hub in Offshore Floating Facilities, supported by Shell, Woodside, Lloyds Register and Bureau Veritas (ARC grant IH140100012). The first author is supported by ARC DECRA Fellowship DE170100119. The second author is supported by the Shell EMI Chair in Offshore Engineering at the University of Western Australia. This support is gratefully acknowledged

Shallow penetrometer penetration resistance

Shallow penetrometers-such as the hemiball and toroid-were conceived as potential in situ testing devices with the ability to measure: (1) soil strength parameters during vertical penetration, (2) soil consolidation characteristics during dissipation tests postpenetration, and (3) interface friction during torsional loading. Knowledge of the response of soil to such tests is critical to the design of subsea pipelines and the ability to measure the response of soil to all three types of test using a single device in situ from a mobile testing platform, such as a remotely operated vehicle (ROV), would be highly advantageous. Potential benefits of the employment of such devices could include significant time and cost savings and improved spatial measurement density, since more tests could be conducted along the route of a pipeline if an ROV is used as a mobile in situ testing platform. This paper presents an assessment of the ability of the hemiball and toroid to measure soil strength parameters directly from their response to vertical penetration. A large deformation finite-element approach was employed to model the penetration process and initial simulations were validated against small-strain analyses published in the literature. A comprehensive parametric study was then conducted investigating the impact on normalized penetration resistance of soil unit weight, shear strength gradient and penetrometer-soil interface friction. A forward model was derived from the parametric analyses and its inverse performance (i.e., the ability to infer soil parameters from force-displacement response) was assessed using additional large deformation analyses with randomly assigned material parameters within realistic bounds. Both variants of shallow penetrometer investigated are found to be well suited to inferring soil strength parameters directly from their response to vertical penetration.</p

Enhancing accuracy and precision of transparent synthetic soil modelling

Over recent years non-intrusive modelling techniques have been developed to investigate soil-structure interaction problems of increasingly complex geometry. This paper concerns the development of a small-scale, 1 g, modelling technique using a transparent analogue for soil with particle image velocimetry for internal displacement measurement. Larger model geometry achieved in this research using fine-grained transparent synthetic soils has led to an increased need for rigorous photogrammetric correction techniques. A correction framework, based upon a modified version of the pinhole camera model, is presented that corrects for lens and camera movement induced errors as well as scaling from image space to object space. An additional statistical approach is also developed to enhance the system precision, by minimising the impact of increased non-coplanarity between the photogrammetry control plane and the target plane. The enhanced data correction and statistical precision is demonstrated using a case study examining the failure mechanism around a double helical screw pile installed in transparent synthetic soil representative of a soft clay

Selection of Suitable Reference Genes for RT-qPCR Analyses in Cyanobacteria

Cyanobacteria are a group of photosynthetic prokaryotes that have a diverse morphology, minimal nutritional requirements and metabolic plasticity that has made them attractive organisms to use in biotechnological applications. The use of these organisms as cell factories requires the knowledge of their physiology and metabolism at a systems level. For the quantification of gene transcripts real-time quantitative polymerase chain reaction (RT-qPCR) is the standard technique. However, to obtain reliable RT-qPCR results the use and validation of reference genes is mandatory. Towards this goal we have selected and analyzed twelve candidate reference genes from three morphologically distinct cyanobacteria grown under routinely used laboratory conditions. The six genes exhibiting less variation in each organism were evaluated in terms of their expression stability using geNorm, NormFinder and BestKeeper. In addition, the minimum number of reference genes required for normalization was determined. Based on the three algorithms, we provide a list of genes for cyanobacterial RT-qPCR data normalization. To our knowledge, this is the first work on the validation of reference genes for cyanobacteria constituting a valuable starting point for future works

Impact of rare variants in ARHGAP29 to the etiology of oral clefts: role of loss-of-function vs missense variants

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a prevalent, complex congenital malformation. Genome-wide association studies (GWAS) on NSCL/P have consistently identified association for the 1p22 region, in which ARHGAP29 has emerged as the main candidate gene. ARHGAP29 re-sequencing studies in NSCL/P patients have identified rare variants; however, their clinical impact is still unclear. In this study we identified 10 rare variants in ARHGAP29, including five missense, one in-frame deletion, and four loss-of-function (LoF) variants, in a cohort of 188 familial NSCL/P cases. A significant mutational burden was found for LoF (Sequence Kernel Association Test, p = 0.0005) but not for missense variants in ARHGAP29, suggesting that only LoF variants contribute to the etiology of NSCL/P. Penetrance was estimated as 59%, indicating that heterozygous LoF variants in ARHGAP29 confer a moderate risk to NSCL/P. The GWAS hits in IRF6 (rs642961) and 1p22 (rs560426 and rs4147811) do not seem to contribute to the penetrance of the phenotype, based on co-segregation analysis. Our data show that rare variants leading to haploinsufficiency of ARHGAP29 represent an important etiological clefting mechanism, and genetic testing for this gene might be taken into consideration in genetic counseling of familial cases

Anti-cyanobacterial activity of Moringa oleifera seeds

Filtrates from crushed Moringa oleifera seeds were tested for their effects on growth and Photosystem II efficiency of the common bloom-forming cyanobacterium Microcystis aeruginosa. M. aeruginosa populations exhibited good growth in controls and treatments with 4- and 8-mg crushed Moringa seeds per liter, having similar growth rates of 0.50 (±0.01) per day. In exposures of 20- to 160-mg crushed Moringa seeds L−1, growth rates were negative and on average −0.23 (±0.05) .day−1. Presumably, in the higher doses of 20- to 160-mg crushed seeds per liter, the cyanobacteria died, which was supported by a rapid drop in the Photosystem II efficiency (ΦPSII), while the ΦPSII was high and unaffected in 0, 4, and 8 mg L−1. High-density populations of M. aeruginosa (chlorophyll-a concentrations of ∼270 µg L−1) were reduced to very low levels within 2 weeks of exposure to ≥80-mg crushed seeds per liter. At the highest dosage of 160 mg L−1, the ΦPSII dropped to zero rapidly and remained nil during the course of the experiment (14 days). Hence, under laboratory conditions, a complete wipeout of the bloom could be achieved. This is the first study that yielded evidence for cyanobactericidal activity of filtrate from crushed Moringa seeds, suggesting that Moringa seed extracts might have a potential as an effect-oriented measure lessening cyanobacterial nuisance

Renewable energy from Cyanobacteria: energy production optimization by metabolic pathway engineering

The need to develop and improve sustainable energy resources is of eminent importance due to the finite nature of our fossil fuels. This review paper deals with a third generation renewable energy resource which does not compete with our food resources, cyanobacteria. We discuss the current state of the art in developing different types of bioenergy (ethanol, biodiesel, hydrogen, etc.) from cyanobacteria. The major important biochemical pathways in cyanobacteria are highlighted, and the possibility to influence these pathways to improve the production of specific types of energy forms the major part of this review

Cyanobacterial lipopolysaccharides and human health – a review

Cyanobacterial lipopolysaccharide/s (LPS) are frequently cited in the cyanobacteria literature as toxins responsible for a variety of heath effects in humans, from skin rashes to gastrointestinal, respiratory and allergic reactions. The attribution of toxic properties to cyanobacterial LPS dates from the 1970s, when it was thought that lipid A, the toxic moiety of LPS, was structurally and functionally conserved across all Gram-negative bacteria. However, more recent research has shown that this is not the case, and lipid A structures are now known to be very different, expressing properties ranging from LPS agonists, through weak endotoxicity to LPS antagonists. Although cyanobacterial LPS is widely cited as a putative toxin, most of the small number of formal research reports describe cyanobacterial LPS as weakly toxic compared to LPS from the Enterobacteriaceae. We systematically reviewed the literature on cyanobacterial LPS, and also examined the much lager body of literature relating to heterotrophic bacterial LPS and the atypical lipid A structures of some photosynthetic bacteria. While the literature on the biological activity of heterotrophic bacterial LPS is overwhelmingly large and therefore difficult to review for the purposes of exclusion, we were unable to find a convincing body of evidence to suggest that heterotrophic bacterial LPS, in the absence of other virulence factors, is responsible for acute gastrointestinal, dermatological or allergic reactions via natural exposure routes in humans. There is a danger that initial speculation about cyanobacterial LPS may evolve into orthodoxy without basis in research findings. No cyanobacterial lipid A structures have been described and published to date, so a recommendation is made that cyanobacteriologists should not continue to attribute such a diverse range of clinical symptoms to cyanobacterial LPS without research confirmation