Material model of lung parenchyma based on living precision-cut lung slice testing.

We describe a novel constitutive model of lung parenchyma, which can be used for continuum mechanics based predictive simulations. To develop this model, we experimentally determined the nonlinear material behavior of rat lung parenchyma. This was achieved via uni-axial tension tests on living precision-cut rat lung slices. The resulting force-displacement curves were then used as inputs for an inverse analysis. The Levenberg-Marquardt algorithm was utilized to optimize the material parameters of combinations and recombinations of established strain-energy density functions (SEFs). Comparing the best-fits of the tested SEFs we found Wpar = 4.1 kPa(I1-3)2 + 20.7 kPa(I1 - 3)3 + 4.1 kPa(-2 ln J + J2 - 1) to be the optimal constitutive model. This SEF consists of three summands: the first can be interpreted as the contribution of the elastin fibers and the ground substance, the second as the contribution of the collagen fibers while the third controls the volumetric change. The presented approach will help to model the behavior of the pulmonary parenchyma and to quantify the strains and stresses during ventilation.

Important aspects when modelling the interaction between surface structures and tunnelling in sand

Tunnelling in urban areas continues to increase and has highlighted the need for a better understanding of the impact of tunnel excavations on existing buildings. This paper considers the influence of surface structures on ground displacements caused by tunnelling in sand through finite element modelling and centrifuge testing. First, the importance of modelling assumptions is evaluated by comparing centrifuge modelling results to finite element modelling results for various soil constitutive models: both a Young's modulus that linearly increases with depth and a power law relation between the soil stiffness and stresses are considered. Second, the most effective soil constitutive model was used to perform a sensitivity study on the effect of different factors governing the structural response. In particular, the effect of the building stiffness and weight on the modification of soil displacements is investigated by introducing a simple surface structure. The use of a no-tension interface between the building and the soil was found to be essential to investigate the effect of weight on gap formation between the soil and the structure, as observed during the experimental tests. Results show the importance of considering the relation between the building weight and the relative stiffness between the building and the soil when assessing the structural response. © 2014 Korean Geotechnical Society.

Phase-variable surface structures are required for infection of Campylobacter jejuni by bacteriophages.

This study characterizes the interaction between Campylobacter jejuni and the 16 phages used in the United Kingdom typing scheme by screening spontaneous mutants of the phage-type strains and transposon mutants of the sequenced strain NCTC 11168. We show that the 16 typing phages fall into four groups based on their patterns of activity against spontaneous mutants. Screens of transposon and defined mutants indicate that the phage-bacterium interaction for one of these groups appears to involve the capsular polysaccharide (CPS), while two of the other three groups consist of flagellatropic phages. The expression of CPS and flagella is potentially phase variable in C. jejuni, and the implications of these findings for typing and intervention strategies are discussed.

Identification of Cj1051c as a Major determinant for the restriction barrier of Campylobacter jejuni StrainNCTC11168

Campylobacter jejuni is a leading cause of human diarrheal illness in the world, and research on it has benefitted greatly by the completion of several genome sequences and the development of molecular biology tools. However, many hurdles remain for a full understanding of this unique bacterial pathogen. One of the most commonly used strains for genetic work with C. jejuni is NCTC11168. While this strain is readily transformable with DNA for genomic recombination, transformation with plasmids is problematic. In this study, we have identified a determinant of this to be cj1051c, predicted to encode a restriction-modification type IIG enzyme. Knockout mutagenesis of this gene resulted in a strain with a 1,000-fold-enhanced transformation efficiency with a plasmid purified from a C. jejuni host. Additionally, this mutation conferred the ability to be transformed by plasmids isolated from an Escherichia coli host. Sequence analysis suggested a high level of variability of the specificity domain between strains and that this gene may be subject to phase variation. We provide evidence that cj1051c is active in NCTC11168 and behaves as expected for a type IIG enzyme. The identification of this determinant provides a greater understanding of the molecular biology of C. jejuni as well as a tool for plasmid work with strain NCTC11168. © 2012, American Society for Microbiology.

Factors affecting seismic response of submarine slopes

The response of submerged slopes on the continental shelf to seismic or storm loading has become an important element in the risk assessment for offshore structures and "local" tsunami hazards worldwide. The geological profile of these slopes typically includes normally consolidated to lightly overconsolidated soft cohesive soils with layer thickness ranging from a few meters to hundreds of meters. The factor of safety obtained from pseudo-static analyses is not always a useful measure for evaluating the slope response, since values less than one do not necessarily imply slope failure with large movements of the soil mass. This paper addresses the relative importance of different factors affecting the response of submerged slopes during seismic loading. The analyses use a dynamic finite element code which includes a constitutive law describing the anisotropic stress-strain-strength behavior of normally consolidated to lightly overconsolidated clays. The model also incorporates anisotropic hardening to describe the effect of different shear strain and stress histories as well as bounding surface principles to provide realistic descriptions of the accumulation of the plastic strains and excess pore pressure during successive loading cycles. The paper presents results from parametric site response analyses on slope geometry and layering, soil material parameters, and input ground motion characteristics. The predicted maximum shear strains, permanent deformations, displacement time histories and maximum excess pore pressure development provide insight of slope performance during a seismic event. © 2006 Author(s). This work is licensed under a Creative Commons License.

Seismic response of submarine slopes

The geological profile of submerged slopes on the continental shelf typically includes soft cohesive soils with thicknesses ranging from a few meters to tens or hundreds of meters. The response of these soils in simple shear tests is largely influenced by the presence of an initial consolidation shear stress, inducing anisotropic stress-strain-strength properties which depend also on the direction of shear. In this paper, a new simplified effective-stress-based model describing the behavior of normally to lightly overconsolidated cohesive soils is used in conjunction with a one-dimensional seismic site response analysis computer code to illustrate the importance of accounting for anisotropy and small strain nonlinearity. In particular, a simple example is carried out to compare results for different slope inclinations. Depth profiling of the maximum shear strains and permanent deformations provide insight into the mechanisms of deformation during a seismic event, and the effects of sloping ground conditions.

Modeling cyclic behavior of lightly overconsolidated clays in simple shear

Assessment of seismic performance and estimation of permanent displacements for submerged slopes require the accurate description of the soil's stress-strain-strength relationship under irregular cyclic loading. The geological profile of submerged slopes on the continental shelf typically consists of normally to lightly overconsolidated clays with depths ranging from a few meters to a few hundred meters and very low slope angles. This paper describes the formulation of a simplified effective-stress-based model, which is able to capture the key aspects of the cyclic behavior of normally consolidated clays. The proposed constitutive law incorporates anisotropic hardening and bounding surface principles to allow the user to simulate different shear strain and stress reversal histories as well as provide realistic descriptions of the accumulation of plastic shear strains and excess pore pressure during successive loading cycles. (C) 2000 Published by Elsevier Science Ltd. | Assessment of seismic performance and estimation of permanent displacements for submerged slopes require the accurate description of the soil's stress-strain-strength relationship under irregular cyclic loading. The geological profile of submerged slopes on the continental shelf typically consists of normally to lightly overconsolidated clays with depths ranging from a few meters to a few hundred meters and very low slope angles. This paper describes the formulation of a simplified effective-stress-based model, which is able to capture the key aspects of the cyclic behavior of normally consolidated clays. The proposed constitutive law incorporates anisotropic hardening and bounding surface principles to allow the user to simulate different shear strain and stress reversal histories as well as provide realistic descriptions of the accumulation of plastic shear strains and excess pore pressures during successive loading cycles.

Lymph Node Colonization Dynamics after Oral Salmonella Typhimurium Infection in Mice

An understanding of how pathogens colonize their hosts is crucial for the rational design of vaccines or therapy. While the molecular factors facilitating the invasion and systemic infection by pathogens are a central focus of research in microbiology, the population biological aspects of colonization are still poorly understood. Here, we investigated the early colonization dynamics of Salmonella enterica subspecies 1 serovar Typhimurium (S. Tm) in the streptomycin mouse model for diarrhea. We focused on the first step on the way to systemic infection - the colonization of the cecal lymph node (cLN) from the gut - and studied roles of inflammation, dendritic cells and innate immune effectors in the colonization process. To this end, we inoculated mice with mixtures of seven wild type isogenic tagged strains (WITS) of S. Tm. The experimental data were analyzed with a newly developed mathematical model describing the stochastic immigration, replication and clearance of bacteria in the cLN. We estimated that in the beginning of infection only 300 bacterial cells arrive in the cLN per day. We further found that inflammation decreases the net replication rate in the cLN by 23%. In ccr7-/- mice, in which dendritic cell movement is impaired, the bacterial migration rate was reduced 10-fold. In contrast, cybb-/- mice that cannot generate toxic reactive oxygen species displayed a 4-fold higher migration rate from gut to cLN than wild type mice. Thus, combining infections with mixed inocula of barcoded strains and mathematical analysis represents a powerful method for disentangling immigration into the cLN from replication in this compartment. The estimated parameters provide an important baseline to assess and predict the efficacy of interventions. © 2013 Kaiser et al.