Organisational resilience following the Darfield earthquake of 2010

This paper presents the preliminary findings of a study on the resilience and recovery of organisations following the Darfield earthquake in New Zealand on 4 September 2010. Sampling included organisations proximal and distal to the fault trace, organisations located within central business districts, and organisations from seven diverse industry sectors. The research captured information on the challenges to, the impacts on, and the reflections of the organisations in the first months of recovery. Organisations in central business districts and in the hospitality sector were most likely to close while organisations that had perishable stock and livestock were more heavily reliant on critical services. Staff well-being, cash flow, and customer loss were major concerns for organisations across all sectors. For all organisations, the most helpful factors in mitigating the effects of the earthquake to be their relationship with staff, the design and type of buildings, and critical service continuity or swift reinstatement of services

Holographic Scanning Laser Acoustic Microscopy (HOLOSLAM): A New QNDE Tool

Acoustic microscopy is the name given to high frequency, 10 MHz to 3 GHz ultrasonic visualization. The scanning laser acoustic microscopy (SLAM) is an important branch of acoustic microscopy which uses ultrasound in the frequency range of 10 to 200 MHz to produce high resolution ultrasonic images.1,2 In contrast to other visual observation techniques, SLAM provides direct access to the structural elastic properties of solid materials and biological tissues. By using this technique, valuable insight can be gained into mechanisms responsible for the changes of elastic architecture over areas tens of microns in diameter

Infected Cell Killing by HIV-1 Protease Promotes NF-κB Dependent HIV-1 Replication

Acute HIV-1 infection of CD4 T cells often results in apoptotic death of infected cells, yet it is unclear what evolutionary advantage this offers to HIV-1. Given the independent observations that acute T cell HIV-1 infection results in (1) NF-κB activation, (2) caspase 8 dependent apoptosis, and that (3) caspase 8 directly activates NF-κB, we questioned whether these three events might be interrelated. We first show that HIV-1 infected T cell apoptosis, NF-κB activation, and caspase 8 cleavage by HIV-1 protease are coincident. Next we show that HIV-1 protease not only cleaves procaspase 8, producing Casp8p41, but also independently stimulates NF-κB activity. Finally, we demonstrate that the HIV protease cleavage of caspase 8 is necessary for optimal NF-κB activation and that the HIV-1 protease specific cleavage fragment Casp8p41 is sufficient to stimulate HIV-1 replication through NF-κB dependent HIV-LTR activation both in vitro as well as in cells from HIV infected donors. Consequently, the molecular events which promote death of HIV-1 infected T cells function dually to promote HIV-1 replication, thereby favoring the propagation and survival of HIV-1

The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing

Peer reviewedPublisher PD

Toward a Surrogate Marker of Malaria Exposure: Modeling Longitudinal Antibody Measurements under Outbreak Conditions

Background: Biomarkers of exposure to Plasmodium falciparum would be a useful tool for the assessment of malaria burden and analysis of intervention and epidemiological studies. Antibodies to pre-erythrocytic antigens represent potential surrogates of exposure. Methods and Findings: In an outbreak cohort of U.S. Marines deployed to Liberia, we modeled pre- and post-deployment IgG against P. falciparum sporozoites by immunofluorescence antibody test, and both IgG and IgM against the P. falciparum circumsporozoite protein by enzyme-linked immunosorbant assay. Modeling seroconversion thresholds by a fixed ratio, linear regression or nonlinear regression produced sensitivity for identification of exposed U.S. Marines between 58-70% and specificities between 87-97%, compared with malaria-naïve U.S. volunteers. Exposure was predicted in 30-45% of the cohort. Conclusion: Each of the three models tested has merits in different studies, but further development and validation in endemic populations is required. Overall, these models provide support for an antibody-based surrogate marker of exposure to malaria

Foundations of Relational Particle Dynamics

Relational particle dynamics include the dynamics of pure shape and cases in which absolute scale or absolute rotation are additionally meaningful. These are interesting as regards the absolute versus relative motion debate as well as discussion of conceptual issues connected with the problem of time in quantum gravity. In spatial dimension 1 and 2 the relative configuration spaces of shapes are n-spheres and complex projective spaces, from which knowledge I construct natural mechanics on these spaces. I also show that these coincide with Barbour's indirectly-constructed relational dynamics by performing a full reduction on the latter. Then the identification of the configuration spaces as n-spheres and complex projective spaces, for which spaces much mathematics is available, significantly advances the understanding of Barbour's relational theory in spatial dimensions 1 and 2. I also provide the parallel study of a new theory for which positon and scale are purely relative but orientation is absolute. The configuration space for this is an n-sphere regardless of the spatial dimension, which renders this theory a more tractable arena for investigation of implications of scale invariance than Barbour's theory itself.Comment: Minor typos corrected; references update

Latitudinal differences in early growth of largehead hairtail (Trichiurus japonicus) in relation to environmental variables

Largehead hairtail (Trichiurus japonicus) in the China Seas shows an increasing catch trend, despite continued overexploitation, which could be attributed to improved recruitment as a result of strengthened early growth. To understand the early growth variability of largehead hairtail, we examined the linkages between early growth, as revealed by otolith microstructure, and the associated environmental variables over both spatial and temporal scales. Young‐of‐the‐Year largehead hairtail were collected from three regions in the Bohai, Yellow and East China Seas between 29° and 39° N. Daily increment widths of sagittal otoliths were measured and used as a proxy for somatic growth. We found two spawning cohorts, Spring‐ and Summer‐spawned cohorts, that showed latitudinal differences in both mean growth and growth pattern. The transition time from larval to juvenile stage was identified at around 40 days. Daily increment widths of two cohorts showed similar growth pattern in the first 40 days, while location had a marked effect on daily growth over 41–110 days. This suggests physiologically constrained growth pattern in larval stage, but more plastic growth subject to habitat‐specific influences in juvenile stage. The gradient forest analysis identified sea bottom temperature, vertical temperature gradient, and sea surface salinity, as the most important variables in determining early growth. Latitudinal differences in early growth pattern and their response to environmental variables suggest adaptive plasticity of early growth, which has notable implication for the management and sustainable utilization of this important but heavily exploited resource in the China Seas.acceptedVersio

Lack of association between polymorphisms of the IL18R1 and IL18RAP genes and cardiovascular risk: the MORGAM Project

<p>Abstract</p> <p>Background</p> <p>Interleukin-18 is a pro-inflammatory cytokine suspected to be associated with atherosclerosis and its complications. We had previously shown that one single nucleotide polymorphism (SNP) of the <it>IL18 </it>gene was associated with cardiovascular disease (CVD) through an interaction with smoking. As a further step for elucidating the contribution of the IL-18 pathway to the etiology of CVD, we here investigated the association between the genetic variability of two IL-18 receptor genes, <it>IL18R1 </it>and <it>IL18RAP</it>, with the risk of developing CVD.</p> <p>Methods</p> <p>Eleven tagging SNPs, 5 in <it>IL18R1 </it>and 6 in <it>IL18RAP</it>, characterizing the haplotypic variability of the corresponding genes; were genotyped in 5 European prospective CVD cohorts including 1416 cases and 1772 non-cases, as part of the MORGAM project. Both single-locus and haplotypes analyses were carried out to investigate the association of these SNPs with CVD.</p> <p>Results</p> <p>We did not find any significant differences in allele, genotype and haplotype frequencies between cases and non-cases for either of the two genes. Moreover, the search for interactions between SNPs located in different genes, including 5 <it>IL18 </it>SNPs previously studied in the MORGAM project, and between SNPs and environmental factors remained unfruitful.</p> <p>Conclusion</p> <p>Our analysis suggests that the variability of <it>IL18R1 </it>and <it>IL18RAP </it>genes are unlikely to contribute to modulate the risk of CVD.</p

Triangleland. I. Classical dynamics with exchange of relative angular momentum

In Euclidean relational particle mechanics, only relative times, relative angles and relative separations are meaningful. Barbour--Bertotti (1982) theory is of this form and can be viewed as a recovery of (a portion of) Newtonian mechanics from relational premises. This is of interest in the absolute versus relative motion debate and also shares a number of features with the geometrodynamical formulation of general relativity, making it suitable for some modelling of the problem of time in quantum gravity. I also study similarity relational particle mechanics (`dynamics of pure shape'), in which only relative times, relative angles and {\sl ratios of} relative separations are meaningful. This I consider firstly as it is simpler, particularly in 1 and 2 d, for which the configuration space geometry turns out to be well-known, e.g. S^2 for the `triangleland' (3-particle) case that I consider in detail. Secondly, the similarity model occurs as a sub-model within the Euclidean model: that admits a shape--scale split. For harmonic oscillator like potentials, similarity triangleland model turns out to have the same mathematics as a family of rigid rotor problems, while the Euclidean case turns out to have parallels with the Kepler--Coulomb problem in spherical and parabolic coordinates. Previous work on relational mechanics covered cases where the constituent subsystems do not exchange relative angular momentum, which is a simplifying (but in some ways undesirable) feature paralleling centrality in ordinary mechanics. In this paper I lift this restriction. In each case I reduce the relational problem to a standard one, thus obtain various exact, asymptotic and numerical solutions, and then recast these into the original mechanical variables for physical interpretation.Comment: Journal Reference added, minor updates to References and Figure

Comparative analysis of carboxysome shell proteins

Carboxysomes are metabolic modules for CO2 fixation that are found in all cyanobacteria and some chemoautotrophic bacteria. They comprise a semi-permeable proteinaceous shell that encapsulates ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase. Structural studies are revealing the integral role of the shell protein paralogs to carboxysome form and function. The shell proteins are composed of two domain classes: those with the bacterial microcompartment (BMC; Pfam00936) domain, which oligomerize to form (pseudo)hexamers, and those with the CcmL/EutN (Pfam03319) domain which form pentamers in carboxysomes. These two shell protein types are proposed to be the basis for the carboxysome’s icosahedral geometry. The shell proteins are also thought to allow the flux of metabolites across the shell through the presence of the small pore formed by their hexameric/pentameric symmetry axes. In this review, we describe bioinformatic and structural analyses that highlight the important primary, tertiary, and quaternary structural features of these conserved shell subunits. In the future, further understanding of these molecular building blocks may provide the basis for enhancing CO2 fixation in other organisms or creating novel biological nanostructures