Resilience to periodic disturbances and the long-term genetic stability in Acropora coral.

Climate change is restructuring natural ecosystems. The direct impacts of these events on biodiversity and community structure are widely documented, but the impacts on the genetic variation of populations remains largely unknown. We monitored populations of Acropora coral on a remote coral reef system in northwest Australia for two decades and through multiple cycles of impact and recovery. We combined these demographic data with a temporal genetic dataset of a common broadcast spawning corymbose Acropora to explore the spatial and temporal patterns of connectivity underlying recovery. Our data show that broad-scale dispersal and post-recruitment survival drive recovery from recurrent disturbances, including mass bleaching and mortality. Consequently, genetic diversity and associated patterns of connectivity are maintained through time in the broader metapopulation. The results highlight an inherent resilience in these globally threatened species of coral and showcase their ability to cope with multiple disturbances, given enough time to recover is permitted.

Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC.

An LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Inosine and mixed nucleotide bases were included at polymorphic sites. Real-time RT-qPCR and qPCR were performed on plasma viral RNA and cellular lysates. A step-up amplification approach to allow binding of primers across polymorphic regions showed improved sensitivity compared to universal cycling. Unlike a lead competing laboratory-developed assay, all major HIV-1 subtypes, and a wide range of recombinants from a 127-member diversity panel were detected and accurately quantified in spiked plasmas. Semi-nested PCR increased detection sensitivity even further. The assay was able to detect down to 88 copies/mL of HIV-1 in plasma with 95% efficiency or the equivalent of a single infected cell. The PCR assay will be valuable in studies that monitor very low viral levels including residual or break through HIV-1 in patients receiving antiretroviral therapy, in HIV-1 cure, and in other research studies.

Enhancing the hydrogen evolution activity of MoS2 basal planes and edges using tunable carbon-based supports.

The hydrogen adsorption free energy (ΔGHads) on the basal plane and edges of MoS2 is studied using periodic density functional theory, with the catalyst supported by a range of two-dimensional carbon-based materials. Understanding how ΔGHads can be tuned with support gives insight into MoS2 as a catalyst for the hydrogen evolution reaction. The supports studied here include graphene oxide materials, heteroatom doped (S, B, and N) graphene, and some insulator materials (hexagonal boron nitride and graphitic carbon nitride). For the basal plane of MoS2, a wide range of values for ΔGHads are observed (between 1.4 and 2.2 eV) depending on the support material used. It is found that ΔGHads relates directly to the energy of occupied p-orbital states in the MoS2 catalyst, which is modified by the support material. On the Mo-edge of MoS2, different supports induce smaller variations in ΔGHads, with values ranging between -0.27 and 0.09 eV. However, a graphene support doped with graphitic N atoms produces a ΔGHads value of exactly 0 eV, which is thermodynamically ideal for hydrogen evolution. Furthermore, ΔGHads is found to relate closely and linearly to the amount of charge transfer between MoS2 and support when they adhere together. The support-induced tuning of ΔGHads on MoS2 observed here provides a useful tool for improving current MoS2 catalysts, and the discovery of variables which mediate changes in ΔGHads contributes to the rational design of new hydrogen evolution catalysts.

Size-dependent trends in the hydrogen evolution activity and electronic structure of MoS2 nanotubes.

The thermodynamics of hydrogen evolution on MoS2 nanotubes is studied for the first time using periodic density functional theory calculations to obtain hydrogen adsorption free energies (ΔG Hads ) on pristine nanotubes and those with S-vacancy defects. Armchair and zigzag MoS2 nanotubes of different diameters, ranging from 12 to 22 Å, are examined. The H adsorption energy is observed to become more favourable (lower ΔG Hads ) as nanotube diameter decreases, with ΔG Hads values ranging from 1.82 to 1.39 eV on the pristine nanotubes, and from 0.03 to -0.30 eV at the nanotube S-vacancy defect sites. An ideal thermoneutral ΔG Hads value of nearly 0 eV is observed at the S-vacancy site on nanotubes around 20 to 22 Å in diameter. For the pristine nanotubes, density of states calculations reveal that electron transfer from S to Mo occurs during H adsorption, and the energy gap between these two states yields a highly reliable linear correlation with ΔG Hads , where a smaller gap leads to a more favourable hydrogen adsorption. For the S-vacancy defect site the H adsorption resembles that on a pure metallic surface, meaning that a traditional d-band centre model can be applied to explain the trends in ΔG Hads . A linear relation between the position of the Mo d-states and ΔG Hads is found, with d-states closer to the Fermi level leading to strong hydrogen adsorption. Overall this work highlights the relevance of MoS2 nanotubes as promising hydrogen evolution catalysts and explains trends in their activity using the energies of the electronic states involved in binding hydrogen.

Design of superatomic systems: exploiting favourable conditions for the delocalisation of d-electron density in transition metal doped clusters.

The incorporation of transition metals into superatomic species has led to the proposal of highly tailorable systems, with the transition metal atoms typically acting as magnetic dopants. However, the extent to which d-electrons are able to delocalise from their ionic cores has not been fully recognised. In this work a variety of systems have been explored using a range of exchange-correlation functionals commonly used to explore cluster species, to test the extent of d-electron delocalisation under favourable conditions. Early transition metals have been shown to readily delocalise their valence d-electrons for superatomic shell closing, with higher period atoms showing a greater tendency for delocalisation. Our findings also provide the framework for the design of superatomic systems with large numbers of electrons being contributed from a single atom.

5-Fold symmetry in superatomic scandium clusters: exploiting favourable orbital overlap to sequester spin.

The geometries and electronic structures of icosahedral A13C (A = Sc, Y; C = 0, ±1, ±2) clusters have been determined at a range of multiplicities at each cluster charge, using density functional theory methods. These clusters demonstrate a complex electronic structure which provides insight into the anomalously high magnetic moment of icosahedral group 3 clusters and further contextualises the role of transition metals and d-electrons within the superatomic model. Embedded deeply within the density of states for these clusters are typical superatom orbitals which are populated up to the 2S level. Above the 2S-state there are three states of apparent F symmetry, which are preferentially singly occupied, followed by an abundance of approximately degenerate P-, G-, D- and F-states at the Fermi energy, which are at most singly occupied. In spite of apparent angular symmetry and a nodal structure reminiscent of superatomic orbitals these states are actually formed from preferential overlap of the valence d-orbitals of the cluster atoms. This analysis was further contextualised through analysis of the Sc19 cluster, which shows a similar construction of Kohn-Sham states, but with the breaking of 5-fold symmetry along one of its Cartesian axes. Finally, this work clearly demonstrates the ability of d-electrons to give rise to superatomic orbitals is not just constrained by atomic species but also by the local environment of the atoms.

On the influence of exact exchange on transition metal superatoms.

The electronic structure of A7C (A = Hg, Pd, V, Cr, Mn, Fe, Ni, Cu; C = 0, ±1, ±2) clusters has been determined using density functional theory methods. The A7C (A = Hg, Pd, Cr, Cu; C = 0, ±1, ±2) clusters all conform to the existing superatomic model, with a sufficiently stabilised local structure to prevent perturbation upon the introduction of exact exchange to the exchange correlation functional. For the A7C (A = Mn, Fe, Ni; C = 0, ±1, ±2) clusters the incorporation of exact exchange separates the atomic s- and d-electrons, leading to a net increase in the number of superatomic electrons. Conversely the incorporation of exact exchange into the exchange correlation functional decreases the number of superatomic electrons for the V7C (C = 0, ±1, ±2) clusters, owing to the radial extension of the d-orbitals influencing their ability to contribute into superatomic shells.

On the involvement of d-electrons in superatomic shells: the group 3 and 4 transition metals.

The geometries and electronic structures of small M7C (M = Sc, Y, La, Ti, Zr, Hf; C = 0, ±1, ±2) clusters have been calculated at a range of multiplicities at each cluster charge, using density functional theory methods. These clusters conform to the existing superatom model, with some contextual differences. There are a range of states which are populated by the outermost s and d-electrons of the constituent atoms, with an irregular Aufbau rule for the states formed from the atomic d-electrons. The states comprised of d-electrons present themselves as two states of P-symmetry and two states of F-symmetry, which are nearly degenerate, followed by states of D-symmetry, a shell ordering which arises due to the symmetry, and favourable overlap, of the contributing states. The effect of exact exchange in modulating the localisation of these states is also discussed. In addition, this study shows pseudo-superatomic states which arise due to the 5-fold symmetry of the clusters, materialising as either a ring or plane of electron density. In summary, these observations allow for an expansion of the role that early transition metals have within the existing superatom framework.

Superatomic states in nickel clusters: Revising the prospects for transition metal based superatoms.

The geometries and electronic structures of small Ninz clusters (n = 8, 9, 10) (z = 0, ±1, 2) have been elucidated for a range of multiplicities for each cluster size and charge, using density functional theory methods. These clusters have been found to conform in part to the existing superatomic model, with each cluster having a filled superatomic S-orbital, filled or partially filled superatomic P-orbitals, and empty or partially filled superatomic D-orbitals. Despite local states of mixed symmetry being present in the immediate vicinity of the Fermi energy, the addition or removal of a single electron from these systems causes a significant shift in the relative energies of the superatomic orbitals. In addition, this study demonstrates the possibility for d-electrons to contribute into superatomic orbitals to a greater or lesser extent, depending on the local environment. In summary, these observations lead to the prospect of a predictive model for electronic shell closings in some transition metal cluster systems.

Adaptation of the animal welfare assessment grid (AWAG) for monitoring animal welfare in zoological collections.

Animal welfare monitoring is an essential part of zoo management and a legal requirement in many countries. Historically, a variety of welfare audits have been proposed to assist zoo managers. Unfortunately, there are a number of issues with these assessments, including lack of species information, validated tests and the overall complexity of these audits which make them difficult to implement in practice. The animal welfare assessment grid (AWAG) has previously been proposed as an animal welfare monitoring tool for animals used in research programmes. This computer-based system was successfully adapted for use in a zoo setting with two taxonomic groups: primates and birds. This tool is simple to use and provides continuous monitoring based on cumulative lifetime assessment. It is suggested as an alternative, practical method for welfare monitoring in zoos.

Estimating False Positive Contamination in Crater Annotations from Citizen Science Data.

Web-based citizen science often involves the classification of image features by large numbers of minimally trained volunteers, such as the identification of lunar impact craters under the Moon Zoo project. Whilst such approaches facilitate the analysis of large image data sets, the inexperience of users and ambiguity in image content can lead to contamination from false positive identifications. We give an approach, using Linear Poisson Models and image template matching, that can quantify levels of false positive contamination in citizen science Moon Zoo crater annotations. Linear Poisson Models are a form of machine learning which supports predictive error modelling and goodness-of-fits, unlike most alternative machine learning methods. The proposed supervised learning system can reduce the variability in crater counts whilst providing predictive error assessments of estimated quantities of remaining true verses false annotations. In an area of research influenced by human subjectivity, the proposed method provides a level of objectivity through the utilisation of image evidence, guided by candidate crater identifications.

A single surgeon's series of transthoracic oesophageal resections.

INTRODUCTION: Significant controversy persists over the optimum surgical management of oesophageal carcinoma. The authors report on a consecutive personal series of open transthoracic oesophageal resections. METHODS: Data relating to resections performed between mid-1993 and the end of 2010 were analysed. Patient and tumour assessment evolved over this period. Preoperative chemotherapy in appropriate cases was introduced in 2002. A laparotomy and right lateral thoracotomy approach (Ivor-Lewis) was used. In all cases the pylorus was not interfered with, no attempt was made to perform a radical lymphadenectomy but surgical strategy was focused on producing an R0 resection and a hand sewn anastomosis was fashioned. RESULTS: A total of 165 resections were performed; 130 patients (80%) were male. The median age was 66 years (range: 31-82 years). Eighty per cent had an adenocarcinoma. Sixty-four per cent of the tumours were T3/T4 and sixty-two per cent node positive. Forty patients (24%) had an involved circumferential resection margin (CRM). Five patients (3.0%) had no resection and a quarter (26%) developed morbidity of some form. There was one clinical anastomotic leak (0.6%) and three benign strictures requiring dilation (1.8%). In-hospital mortality was 3.0% (5 patients). Disease specific survival at one, two and five years was 77%, 42% and 36% respectively. Neither CRM involvement nor preoperative chemotherapy influenced survival significantly. No patient required intervention to disrupt the pylorus. CONCLUSIONS: Excellent outcomes are achievable following open transthoracic oesophagectomy without radical lymphadenectomy using a hand sewn gastro-oesophageal anastomosis and without disrupting the pylorus.

The survival of Class V restorations in general dental practice: part 3, five-year survival.

OBJECTIVE: To evaluate the survival over five years of Class V restorations placed by UK general practitioners, and to identify factors associated with increased longevity. DESIGN: Prospective longitudinal cohort multi-centre study. SETTING: UK general dental practices. MATERIALS AND METHOD: Ten general dental practitioners each placed 100 Class V restorations of varying sizes, using a range of materials and recorded selected clinical information at placement and recall visits. After five years the data were analysed using the Kaplan-Meier method, log-rank tests and Cox regressions models to identify significant associations between the time to restoration failure and different clinical factors. RESULTS: After five years 275/989 restorations had failed (27.8%), with 116 (11.7%) lost to follow-up. Cox regression analysis identified that, in combination, the practitioner, patient age, cavity size, moisture contamination and cavity preparation were found to influence the survival of the restorations. CONCLUSIONS: At least 60.5% of the restorations survived for five years. The time to failure of Class V restorations placed by this group of dentists was reduced in association with the individual practitioner, smaller cavities, glass ionomer restorations, cavities which had not been prepared with a bur, moisture contamination, increasing patient age, cavities confined to dentine and non-carious cavities.

Use of stakeholder analysis to inform risk communication and extension strategies for improved biosecurity amongst small-scale pig producers.

Extension and communication needs amongst small-scale pig producers, described as pig producers with less than 100 sows, have been previously identified. These producers, who are believed to pose a biosecurity risk to commercial livestock industries, are characterized by a lack of formal networks, mistrust of authorities, poor disease reporting behaviour and motivational diversity, and reliance on other producers, veterinarians and family for pig health and production advice. This paper applies stakeholder identification and analysis tools to determine stakeholders' influence and interest on pig producers' practices. Findings can inform a risk communication process and the development of an extension framework to increase producers' engagement with industry and their compliance with biosecurity standards and legislation in Australia. The process included identification of stakeholders, their issues of concerns regarding small-scale pig producers and biosecurity and their influence and interest in each of these issues. This exercise identified the capacity of different stakeholders to influence the outcomes for each issue and assessed their success or failure to do so. The disconnection identified between the level of interest and influence suggests that government and industry need to work with the small-scale pig producers and with those who have the capacity to influence them. Successful biosecurity risk management will depend on shared responsibility and building trust amongst stakeholders. Flow-on effects may include legitimating the importance of reporting and compliance systems and the co-management of risk. Compliance of small-scale pig producers with biosecurity industry standards and legislation will reduce the risks of entry and spread of exotic diseases in Australia.

Efficacy of intraperitoneal local anaesthetic techniques during laparoscopic cholecystectomy.

BACKGROUND: Pain following laparoscopic cholecystectomy (LC) is a barrier to early discharge. Some studies have demonstrated that local anaesthetic (LA) washed over the liver and gallbladder decreases postoperative pain. In many patients pain is partially of diaphragmatic origin which may not be treated effectively by topical wash. This study assesses the efficacy of LA injected to the peritoneum of the right hemidiaphragm or topical wash with a control group. METHODS: We performed a double-blind randomized sham controlled trial of 128 consecutive subjects who underwent elective LC. Patients received subcutaneous bupivacaine, a diaphragmatic injection of bupivacaine or sham, and topical wash over the liver/gallbladder with bupivacaine or sham depending upon allocation. The primary outcome was VAS pain scores on the ward. Secondary outcomes included VRS pain scores in theatre recovery, analgesic use, physiological observations, time to eating and ambulation, and successful day-case surgery. RESULTS: Pain scores were significantly lower in both LA groups versus control in theatre recovery but only in the subperitoneal diaphragm injection group when the patients returned to the ward. Subperitoneal diaphragm injection was associated with a reduced time in theatre recovery (p = 0.04). CONCLUSIONS: Intraperitoneal techniques of LA during LC decrease postoperative pain and shorten time in theatre recovery. Injection of LA to the right hemidiaphragm is associated with lower pain scores for a longer period following LC than a previously validated wash technique.

The survival of Class V restorations in general dental practice. Part 2, early failure.

OBJECTIVE: To evaluate Class V restorations placed by UK general practitioners comparing those failing or surviving after two years, and to identify factors associated with early failure. DESIGN: Prospective longitudinal cohort multi-centre study. Setting UK general dental practices. MATERIALS & METHODS: Ten dentists each placed 100 Class V restorations and recorded selected clinical information at placement and recall visits. Univariate associations were assessed between recorded clinical factors and whether restorations had failed or not at two years. Multi-variable binary logistic regression was also undertaken to identify which combination of factors had a significant effect on the probability of early failure. RESULTS: At two years, 156 of 989 restorations had failed (15.8%), with 40 (4%) lost to follow-up. Univariate analysis showed a significant association between restoration failure and increasing patient age, payment method, the treating practitioner, non-carious cavities, cavities involving enamel and dentine, cavity preparation and restoration material. Multi-variable analysis indicated a higher probability of early failure associated with the practitioner, older patients, glass ionomer and flowable composite, bur-preparation and moisture contamination. CONCLUSIONS: Among these practitioners, both analytic methods identified significant associations between early failure of Class V restorations and the practitioner, cavity preparation method, restoration material and patient's age.

Anomalous right coronary artery: a multimodality hunt for the origin.

Anomalous origin of the right coronary artery from the pulmonary artery (ARCAPA) is a rare congenital anomaly. Although there have been several cases of ARCAPA reported in the literature, we present a case which highlights the challenges of diagnosing this rare condition and the incremental value of using multiple imaging modalities. A healthy 48 year old female presented with angina and exertional shortness of breath. She had a normal cardiovascular examination, negative cardiac enzymes and an unremarkable chest X-ray. She did, however, have T-wave inversions in leads V1-V3. Transthoracic echocardiography (TTE), as the first imaging investigation, led to an initial provisional diagnosis of a coronary-cameral fistula. It showed unusual colour Doppler signals in the right ventricle and a prominent pattern of diastolic flow within the right ventricular myocardium, especially along the interventricular septum. A subsequent multimodality approach, correlating images from angiography, CT and MRI was instrumental in confirming the diagnosis of ARCAPA and planning for surgical correction. Cardiac CT and MRI are non-invasive, three-dimensional imaging modalities with high diagnostic accuracy for coronary artery anatomic anomalies. If echocardiography and conventional angiography have been inconclusive, cardiac CT and MRI are especially important diagnostic tools.