Autoecological Approaches to Resolve Subjective Taxonomic Divisions within Arcellacea

Arcellacea (testate lobose amoebae) are important lacustrine environmental indicators that have been used in paleoclimatic reconstructions, assessing the effectiveness of mine tailings pond reclamation projects and for studying the effects of land use change in rural, industrial and urban settings. Recognition of ecophenotypically significant infra-specific ‘strains’ within arcellacean assemblages has the potential to enhance the utility of the group in characterizing contemporary and paleoenvironments. We present a novel approach which employs statistical tools to investigate the environmental and taxonomic significance of proposed strains. We test this approach on two identified strains: Difflugia protaeiformis Lamarck strain ‘acuminata’ (DPA), characterized by fine grained agglutination, and Difflugia protaeiformis Lamarck strain ‘claviformis’ (DPC), characterized by coarse grained agglutination. Redundancy analysis indicated that both organisms are associated with similar environmental variables. No relationship was observed between substrate particle size and abundance of DPC, indicating that DPC has a size preference for xenosomes during test construction. Thus DPC should not be designated as a distinct strain but rather form a species complex with DPA. This study elucidates the need to justify the designation of strains based on their autecology in addition to morphological stability.

Development of dynamic structural testing to current state-of-the-art hybrid testing

Even though computational power used for structural analysis is ever increasing, there is still a fundamental need for testing in structural engineering, either for validation of complex numerical models or to assess material behaviour. In addition to analysis of structures using scale models, many structural engineers are aware to some extent of cyclic and shake-table test methods, but less so of ‘hybrid testing’. The latter is a combination of physical testing (e.g. hydraulic
actuators) and computational modelling (e.g. finite element modelling). Over the past 40 years, hybrid testing of engineering structures has developed from concept through to maturity to become a reliable and accurate dynamic testing technique. The hybrid test method provides users with some additional benefits that standard dynamic testing methods do not, and the method is more cost-effective in comparison to shake-table testing. This article aims to provide the reader with a basic understanding of the hybrid test method, including its contextual development and potential as a dynamic testing technique.

Increased susceptibility to delayed genetic effects of low dose X-irradiation in DNA repair deficient cells

Purpose: To examine whether the levels of micronuclei induction, as a marker for genomic instability in the progeny of X-irradiated cells, correlates with DNA repair function.

Materials and methods: Two repair deficient cell lines (X-ray repair cross-complementing 1 [XRCC1] deficient cell line [EM9] and X-ray repair cross complementing 5 [XRCC5; Ku80] deficient X-ray sensitive Chinese hamster ovary [CHO] cell line [xrs5]) were used in addition to wild-type CHO cells. These cells were irradiated with low doses of X-rays (up to 1 Gy). Seven days after irradiation, micronuclei formed in binucleated cells were counted. To assess the contribution of the bystander effect micronuclei induction was measured in progeny of non-irradiated cells co-cultured with cells that had been irradiated with 1Gy.

Results: The delayed induction of micronuclei in 1 Gy-irradiated cells was observed in normal CHO and EM9 but not in xrs5. In the clone analysis, progenies of xrs5 under bystander conditions showed significantly higher levels of micronuclei, while CHO and EM9 did not.

Conclusion: Genomic instability induced by X-irradiation is associated with DSB (double-strand break) repair, even at low doses. It is also suggested that bystander signals, which lead to genomic instability, may be enhanced when DSB repair is compromised.

The performance of concrete exposed to marine environments: predictive modelling and use of laboratory/on site test methods

This paper reports an approach by which laboratory based testing and numerical modelling can be combined to predict the long term performance of a range of concretes exposed to marine environments. Firstly, a critical review of the test methods for assessing the chloride penetration resistance of concrete is given. The repeatability of the different test results is also included. In addition to the test methods, a numerical simulation model is used to explore the test data further to obtain long-term chloride ingress trends. The combined use of testing and modelling is validated with the help of long-term chloride ingress data from a North Sea exposure site. In summary, the paper outlines a methodology for determining the long term performance of concrete in marine environments.

Facile access to new C-glycosides and C-glycoside scaffolds incorporating functionalised aromatic moieties

The tandem ene/intramolecular Sakurai cyclisation (IMSC) reaction has been successfully applied to thesynthesis of a range of C-glycosides, with key intermediates offering opportunities for functionalisation ofthe glycon moiety. To demonstrate the versatility of the approach to access the 2-deoxy-C-glycoside series,we synthesised diastereomerically pure C-glucoside and galactoside derivatives incorporating functionalisedaromatic, heteroaromatic and bicyclic aromatic moieties, in addition to the C-homologue of(±)-b-2-deoxy-glucose 6-phosphate.

In utero exposure to cigarette chemicals induces sex-specific disruption of one-carbon metabolism and DNA methylation in the human fetal liver

Background: Maternal smoking is one of the most important modifiable risk factors for low birthweight, which is strongly associated with increased cardiometabolic disease risk in adulthood. Maternal smoking reduces the levels of the methyl donor vitamin B12 and is associated with altered DNA methylation at birth. Altered DNA methylation may be an important mechanism underlying increased disease susceptibility; however, the extent to which this can be induced in the developing fetus is unknown.

Methods: In this retrospective study, we measured concentrations of cobalt, vitamin B12, and mRNA transcripts encoding key enzymes in the 1-carbon cycle in 55 fetal human livers obtained from 11 to 21 weeks of gestation elective terminations and matched for gestation and maternal smoking. DNA methylation was measured at critical regions known to be susceptible to the in utero environment. Homocysteine concentrations were analyzed in plasma from 60 fetuses.

Results: In addition to identifying baseline sex differences, we found that maternal smoking was associated with sex-specific alterations of fetal liver vitamin B12, plasma homocysteine and expression of enzymes in the 1-carbon cycle in fetal liver. In the majority of the measured parameters which showed a sex difference, maternal smoking reduced the magnitude of that difference. Maternal smoking also altered DNA methylation at the imprinted gene IGF2 and the glucocorticoid receptor (GR/NR3C1).

Conclusions: Our unique data strengthen studies linking in utero exposures to altered DNA methylation by showing, for the first time, that such changes are present in fetal life and in a key metabolic target tissue, human fetal liver. Furthermore, these data propose a novel mechanism by which such changes are induced, namely through alterations in methyl donor availability and changes in 1-carbon metabolism.

Virgin Olive Oil: Losses of Antioxidant Polar Phenolic Compounds due to Storage, Packaging, and Culinary Uses

Virgin olive oil is a high quality natural product obtained only by physical means. In addition to triacylglycerols it contains nutritionally important polar and non-polar antioxidant phenols and other bioactive ingredients. The polar fraction is a complex mixture of phenolic acids, simple phenols, derivatives of the glycosides oleuropein and ligstroside, lignans, and flavonoids. These compounds contribute significantly to the stability, flavor, and biological value of virgin olive. In the various stages of production, during storage and in the culinary uses, polar phenols and other valuable bioactive ingredients may be damaged. Oxidation, photo-oxidation, enzymic hydrolysis and heating at frying temperatures have a serious adverse effect. Due to the biological importance of the oil and its unique character, analytical methods have been developed to evaluate antioxidant activity or analyse complex phenol mixtures. These are based on radical scavenging assays and chromatographic techniques. Hyphenated methods are also used including liquid chromatography-mass spectrometry and liquid chromatography-nuclear magnetic resonance spectroscopy.

Young, Old, and Weathered Carbon—Part 2: Using Radiocarbon and Stable Isotopes to Identify Terrestrial Carbon Support of the Food Web in an Alkaline, Humic Lake

Carbon (C) and nitrogen (N) stable isotope analysis (SIA) has been used to identify the terrestrial subsidy of freshwater food webs. However, SIA fails to differentiate between the contributions of old and recently fixed terrestrial C and consequently cannot fully determine the source, age, and biochemical quality of terrestrial carbon. Natural abundance radiocarbon (∆14C) was used to examine the age and origin of carbon in Lower Lough Erne, Northern Ireland. 14C and stable isotope values were obtained from invertebrate, algae, and fish samples, and the results indicate that terrestrial organic C is evident at all trophic levels. High winter δ15N values in calanoid zooplankton (δ15N = 24‰) relative to phytoplankton and particulate organic matter (δ15N = 6‰ and 12‰, respectively) may reflect several microbial trophic levels between terrestrial C and calanoid invertebrates. Winter and summer calanoid ∆14C values show a seasonal switch between autochthonous and terrestrial carbon sources. Fish ∆14C values indicate terrestrial support at the highest trophic levels in littoral and pelagic food webs. 14C therefore is useful in attributing the source of carbon in freshwater in addition to tracing the pathway of terrestrial carbon through the food web.

“If I Were Nick”: Men’s Responses to an Interactive Video Drama Series to Support Smoking Cessation

Background: Men continue to smoke in greater numbers than women; however, few interventions have been developed and tested to support men’s cessation. Men also tend to rely on quitting strategies associated with stereotypical manliness, such as willpower, stoicism and independence, but may lack the self‐efficacy skills required to sustain a quit. In this article we describe the development of and reception to an interactive video drama (IVD) series, composed of 7 brief scenarios, to support and strengthen men’s smoking cessation efforts. The value of IVD in health promotion is predicated on the evidence that viewers engage with the material when they are presented characters with whom they can personally identify. The video dramatizes the challenges unfolding in the life of the main character, Nick, on the first day of his quit and models the skills necessary to embark upon a sustainable quit. 
Objective: The objective was to describe men’s responses to the If I were Nick IVD series as part of a pilot study of QuitNow MenTM, an innovative smoking cessation website designed for men. Specific objectives were to explore the resonance of the main character of the IVD series with end‐users, and men’s perceptions of the effectiveness of the IVD series for supporting their quit self‐management. 
Methods: Seven brief IVD scenarios were developed, filmed with a professional actor and uploaded to a new online smoking cessation website, QuitNow MenTM.  A sample of 117 men who smoked were recruited into the study and provided baseline data prior to access to the QuitNow MenTM website for a 6 month period. During this time, 47 men chose to view the IVDs. Their responses to questions about the IVDs were collected in 3‐month and 6‐month online follow‐up surveys and analyzed using descriptive statistics. 
Findings: The majority of participants indicated they related to the main character, Nick. Participants who “strongly agreed” they could relate to Nick perceived significantly higher levels of support from the IVDs than the “neutral” and “disagree” groups (P <.001, d =2.0, P <.001 d =3.1). The “agree” and “neutral” groups were significantly higher on rated support from the videos than the “disagree” (P <.001 d =2.2, P =.01 d = 1.5). Participants’ perception of the main character was independent of participant age, education attainment or previous quit attempts. 
Conclusions: The findings suggest that IVD interventions may be an important addition to men’s smoking cessation programs. Given that the use of IVD scenarios in health promotion is in its infancy, the positive outcomes from this pilot study signal the potential for IVD and warrant ongoing evaluation in smoking cessation and, more generally, men’s health promotion.  

Heat transport in harmonic oscillator systems with thermal baths: application to optomechanical arrays

We investigate the transport of phonons between N harmonic oscillators in contact with independent thermal baths and coupled to a common oscillator, and derive an expression for the steady state heat flow between the oscillators in the weak coupling limit. We apply these results to an optomechanical array consisting of a pair of mechanical resonators coupled to a single quantized electromagnetic field mode by radiation pressure as well as to thermal baths with different temperatures. In the weak coupling limit this system is shown to be equivalent to two mutually-coupled harmonic oscillators in contact with an effective common thermal bath in addition to their independent baths. The steady state occupation numbers and heat flows are derived and discussed in various regimes of interest.

Stability of Short-span Bridges Subject to Overtopping during Floods: Case Studies from UK and the USA

As a consequence of increased levels of flooding, largely attributable to urbanization of watersheds (and perhaps climate change, more frequent extreme rainfall events are occurring and threatening existing critical infrastructure. Many of which are short-span bridges over relatively small waterways (e.g., small rivers, streams and canals). Whilst these short-span bridges were designed, often many years ago, to pass relatively minor the then standard return-period floods, in recenttimes the failure incidence of such short-span bridges has been noticeably increasing. This is suggestive of insufficient hydraulic capacity or alternative failure mechanism not envisaged at the time of design e.g. foundation scour or undermining. This paper presen ts, and draws lessons, from bridge failures in Ireland and the USA. For example, in November 2009, the UK and Ireland were subjected to extraordinarily severe weather conditions for several days. The resulting flooding led to the collapse of three UK bridges that were generally 19th century masonry arch bridges, withrelatively shallow foundations. Parallel failure events have been observed in the USA. To date, knowledge of the combined effect of waterway erosion, bridge submergence, and geotechnical collapse has not been adequately studied. Recent research carried out considered the hydraulic analysis of short span bridges under flood conditions, but no consideration was given towards the likely damage to these structures due to erosive coupling of hydraulic and geotechnical factors. Some work has been done to predict the discharge downstream of an inundated arch, focusing onpredicting afflux, as opposed to bridge scour, under both pressurized and free-surface flows, but no ! predictive equation for scour under pressurized conditions was ever considered. The case studies this paper presents will be augmented by the initial findings from the laboratory experiments investigating the effects of surcharged flow and subsequent scour within the vicinity of single span arch bridges. Velocities profiles will be shown within the vicinity of the arch, in addition to the depth of consequent scour, for a series of flows and model spans. The data will be presented and correlated to the most recent predictive equations for submerged contraction and abutment scour. The accuracy of these equations is examined, and the findings used as a basis for developing further studies in relation to short span bridges.

Concrete damage plasticity model for modeling FRP-to-concrete bond behavior

The technique of externally bonding fiber-reinforced polymer (FRP) composites has become very popular worldwide for retrofitting existing reinforced concrete (RC) structures. Debonding of FRP from the concrete substrate is a typical failure mode in such strengthened structures. The bond behavior between FRP and concrete thus plays a crucial role in these structures. The FRP-to-concrete bond behavior has been extensively investigated experimentally, commonly using a single or double shear test of the FRP-to-concrete bonded joint. Comparatively, much less research has been concerned with numerical simulation, chiefly due to difficulties in the accurate modeling of the complex behavior of concrete. This paper presents a simple but robust finite-element (FE) model for simulating the bond behavior in the entire debonding process for the single shear test. A concrete damage plasticity model is proposed to capture the concrete-to-FRP bond behavior. Numerical results are in close agreement with test data, validating the model. In addition to accuracy, the model has two further advantages: it only requires the basic material parameters (i.e., no arbitrary user-defined parameter such as the shear retention factor is required) and it can be directly implemented in the FE software ABAQUS.

On the Assumption of Bivariate Normality in Selection Models: A Copula Approach Applied to Estimating HIV Prevalence

Background: Heckman-type selection models have been used to control HIV prevalence estimates for selection bias when participation in HIV testing and HIV status are associated after controlling for observed variables. These models typically rely on the strong assumption that the error terms in the participation and the outcome equations that comprise the model are distributed as bivariate normal.
Methods: We introduce a novel approach for relaxing the bivariate normality assumption in selection models using copula functions. We apply this method to estimating HIV prevalence and new confidence intervals (CI) in the 2007 Zambia Demographic and Health Survey (DHS) by using interviewer identity as the selection variable that predicts participation (consent to test) but not the outcome (HIV status).
Results: We show in a simulation study that selection models can generate biased results when the bivariate normality assumption is violated. In the 2007 Zambia DHS, HIV prevalence estimates are similar irrespective of the structure of the association assumed between participation and outcome. For men, we estimate a population HIV prevalence of 21% (95% CI = 16%–25%) compared with 12% (11%–13%) among those who consented to be tested; for women, the corresponding figures are 19% (13%–24%) and 16% (15%–17%).
Conclusions: Copula approaches to Heckman-type selection models are a useful addition to the methodological toolkit of HIV epidemiology and of epidemiology in general. We develop the use of this approach to systematically evaluate the robustness of HIV prevalence estimates based on selection models, both empirically and in a simulation study.

Molecular dynamics simulation (MDS) to study nanoscale machining processes

Molecular Dynamics Simulations (MDS) are constantly being used to make important contributions to our fundamental understanding of material behaviour, at the atomic scale, for a variety of thermodynamic processes. This chapter shows that molecular dynamics simulation is a robust numerical analysis tool in addressing a range of complex nanofinishing (machining) problems that are otherwise difficult or impossible to understand using other methods. For example the mechanism of nanometric cutting of silicon carbide is influenced by a number of variables such as machine tool performance, machining conditions, material properties, and cutting tool performance (material microstructure and physical geometry of the contact) and all these variables cannot be monitored online through experimental examination. However, these could suitably be studied using an advanced simulation based approach such as MDS. This chapter details how MD simulation can be used as a research and commercial tool to understand key issues of ultra precision manufacturing research problems and a specific case was addressed by studying diamond machining of silicon carbide. While this is appreciable, there are a lot of challenges and opportunities in this fertile area. For example, the world of MD simulations is dependent on present day computers and the accuracy and reliability of potential energy functions [109]. This presents a limitation: Real-world scale simulation models are yet to be developed. The simulated length and timescales are far shorter than the experimental ones which couples further with the fact that contact loading simulations are typically done in the speed range of a few hundreds of m/sec against the experimental speed of typically about 1 m/sec [17]. Consequently, MD simulations suffer from the spurious effects of high cutting speeds and the accuracy of the simulation results has yet to be fully explored. The development of user-friendly software could help facilitate molecular dynamics as an integral part of computer-aided design and manufacturing to tackle a range of machining problems from all perspectives, including materials science (phase of the material formed due to the sub-surface deformation layer), electronics and optics (properties of the finished machined surface due to the metallurgical transformation in comparison to the bulk material), and mechanical engineering (extent of residual stresses in the machined component) [110]. Overall, this chapter provided key information concerning diamond machining of SiC which is classed as hard, brittle material. From the analysis presented in the earlier sections, MD simulation has helped in understanding the effects of crystal anisotropy in nanometric cutting of 3C-SiC by revealing the atomic-level deformation mechanisms for different crystal orientations and cutting directions. In addition to this, the MD simulation revealed that the material removal mechanism on the (111) surface of 3C-SiC (akin to diamond) is dominated by cleavage. These understandings led to the development of a new approach named the “surface defect machining” method which has the potential to be more effective to implement than ductile mode micro laser assisted machining or conventional nanometric cutting.

Using geotechnical and LIDAR spatial monitoring to determine key environmental slope instability thresholds of a Jurassic coastal landslide: Straidkilly Point, Northern Ireland, UK.

The Antrim Coast Road stretching from the seaport of Larne in the East of Northern Ireland to the famous Giant’s Causeway in the North has a well-deserved reputation for being one of the most spectacular roads in Europe (Day, 2006). At various locations along the route, fluid interactions between the problematic geology, Jurassic Lias Clay and Triassic Mudstone overlain by Cretaceous Limestone and Tertiary Basalt, and environmental variables result in frequent instances of slope instability within the vadose zone. During such instances of instability, debris flows and composite mudflows encroach on the carriageway posing a hazard to road users. This paper examines the site investigative, geotechnical and spatial analysis techniques currently being implemented to monitor slope stability for one site at Straidkilly Point, Glenarm, Northern Ireland. An in-depth understanding of the geology was obtained via boreholes, resistivity surveys and laboratory testing. Environmental variables recorded by an on-site weather station were correlated with measured pore water pressure and soil moisture infiltration dynamic data.
Terrestrial LiDAR (TLS) was applied to the slope for the monitoring of failures, with surveys carried out on a bi-monthly basis. TLS monitoring allowed for the generation of Digital Elevation Models (DEMs) of difference, highlighting areas of recent movement, erosion and deposition. Morphology parameters were generated from the DEMs and include slope, curvature and multiple measures of roughness. Changes in the structure of the slope coupled with morphological parameters are characterised and linked to progressive failures from the temporal monitoring. In addition to TLS monitoring, Aerial LiDARi datasets were used for the spatio-morphological characterisation of the slope on a macro scale. Results from the geotechnical and environmental monitoring were compared with spatial data obtained through Terrestrial and Airborne LiDAR, providing a multi-faceted approach to slope stability characterization, which facilitates more informed management of geotechnical risk by the Northern Ireland Roads Service.