Chapter 19: Vulnerability of coastal and estuarine habitats in the Great Barrier Reef to climate change

This chapter attempts to address the vulnerability of the CEM in the Great Barrier Reef region to global climate change. It does not consider individual habitats (eg reefs or seagrasses) but goes beyond the individual species and habitat assessments, to consider impacts on the whole coastal marine community complex, and the ecological processes that support its functioning.This is Chapter 19 of Climate change and the Great Barrier Reef: a vulnerability assessment. The entire book can be found at http://hdl.handle.net/11017/13

Evidence for Shape Co-existence at medium spin in 76Rb

Four previously known rotational bands in 76Rb have been extended to moderate spins using the Gammasphere and Microball gamma ray and charged particle detector arrays and the 40Ca(40Ca,3pn) reaction at a beam energy of 165 MeV. The properties of two of the negative-parity bands can only readily be interpreted in terms of the highly successful Cranked Nilsson-Strutinsky model calculations if they have the same configuration in terms of the number of g9/2 particles, but they result from different nuclear shapes (one near-oblate and the other near-prolate). These data appear to constitute a unique example of shape co-existing structures at medium spins.Comment: Accepted for publication in Physics Letters

Exploring the role of E. faecalis enterococcal polysaccharide antigen (EPA) and lipoproteins in evasion of phagocytosis

Enterococcus faecalis is an opportunistic pathogen frequently causing nosocomial infections. The virulence of this organism is underpinned by its capacity to evade phagocytosis, allowing dissemination in the host. Immune evasion requires a surface polysaccharide produced by all enterococci, known as the enterococcal polysaccharide antigen (EPA). EPA consists of a cell wall-anchored rhamnose backbone substituted by strain-specific polysaccharides called ‘decorations’, essential for the biological activity of this polymer. However, the structural determinants required for innate immune evasion remain unknown, partly due to a lack of suitable validated assays. Here, we describe a quantitative, in vitro assay to investigate how EPA decorations alter phagocytosis. Using the E. faecalis model strain OG1RF, we demonstrate that a mutant with a deletion of the locus encoding EPA decorations can be used as a platform strain to express heterologous decorations, thereby providing an experimental system to investigate the inhibition of phagocytosis by strain-specific decorations. We show that the aggregation of cells lacking decorations is increasing phagocytosis and that this process does not involve the recognition of lipoproteins by macrophages. Collectively, our work provides novel insights into innate immune evasion by enterococci and paves the way for further studies to explore the structure/function relationship of EPA decorations

The ODD protocol for describing agent-based and other simulation models: A second update to improve clarity, replication, and structural realism

© 2020, University of Surrey. All rights reserved. The Overview, Design concepts and Details (ODD) protocol for describing Individual-and Agent-Based Models (ABMs) is now widely accepted and used to document such models in journal articles. As a standardized document for providing a consistent, logical and readable account of the structure and dynamics of ABMs, some research groups also find it useful as a workflow for model design. Even so, there are still limitations to ODD that obstruct its more widespread adoption. Such limitations are discussed and addressed in this paper: the limited availability of guidance on how to use ODD; the length of ODD documents; limitations of ODD for highly complex models; lack of sufficient details of many ODDs to enable reimplementation without access to the model code; and the lack of provision for sections in the document structure covering model design ratio-nale, the model’s underlying narrative, and the means by which the model’s fitness for purpose is evaluated. We document the steps we have taken to provide better guidance on: structuring complex ODDs and an ODD summary for inclusion in a journal article (with full details in supplementary material; Table 1); using ODD to point readers to relevant sections of the model code; update the document structure to include sections on model rationale and evaluation. We also further advocate the need for standard descriptions of simulation experiments and argue that ODD can in principle be used for any type of simulation model. Thereby ODD would provide a lingua franca for simulation modelling

An integrated approach to determine three‐dimensional accretion geometries of tidal point bars: Examples from the Venice Lagoon

Low rates of lateral migration (centimetres to decimetres per year) combined with relatively high rates of vertical accretion (millimetres to centimetres per year) recorded in microtidal channels of the Venice Lagoon (Italy) give rise to point‐bar geometries and internal facies arrangements that differ substantially from widely accepted models of point‐bar sedimentary architecture. In this study, field data from the Venice Lagoon are combined with a three‐dimensional forward stratigraphic model, the ‘Point‐Bar Sedimentary Architecture Numerical Deduction’ (PB‐SAND), to predict the stratal geometries of point bars formed in aggradational settings. The PB‐SAND uses a combined geometric and stochastic modelling approach that can be constrained by field evidence. The model applied determines the geometry of four point bars generated by 9 to 11 m wide channels cutting through salt marshes. An iterative best‐fit modelling approach has been used to obtain multiple simulations for each case‐study, each of which fits the observations derived from the analysis of time‐series historical aerial photographs and 44 sedimentary cores. Results demonstrate how the geometry of the bars is determined by the development of two key stratal surfaces: the point‐bar brink and channel‐thalweg surfaces. These surfaces are defined by the progressive translation and vertical shift of the point‐bar brink (i.e. break of slope between bar top and bar slope) and the channel thalweg (i.e. deepest part of the channel) during bar evolution. The approach is used to: (i) reconstruct three‐dimensional point‐bar geometries; (ii) propose alternative reconstructions; (iii) provide insight to drive the acquisition of additional data to better constrain the proposed models; and (iv) provide insight into the mechanism of bar growth for slowly migrating channels in settings subject to relatively high rates of aggradation. This study highlights how interaction between styles of planform transformation and latero‐vertical shifts of meandering channels can determine the geometry of related sedimentary bodies

A sixteen-week three-armed, randomized, controlled trial investigating clinical and biochemical effects of targeted alterations in dietary linoleic acid and n-3 EPA+DHA in adults with episodic migraine: Study protocol

Migraine is a prevalent neurological disorder, affecting over 16% of adult women and 7% of adult men in the U.S., causing significant pain, disability, and medical expense, with incomplete benefits from conventional medical management. Migraine, as a chronic pain syndrome, provides a practical model for investigating the impact of dietary modifications in omega-3 (n-3) and omega-6 (n-6) fatty acids. This paper reports the protocol of a trial to assess whether targeted dietary modifications designed to increase n-3 eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), with or without concurrent reduction in n-6 linoleic acid (LA), will alter nociceptive lipid mediators and mediate decreases in frequency and severity of migraine. This prospective, randomized, controlled trial in 153 male and female adult subjects, ages 18–99, with diagnosed and actively managed episodic migraine tests the efficacy, safety, and biochemical effects of targeted, controlled alterations in dietary omega-3 and omega-6 fatty acids. Participants are masked to diet hypotheses and all assessors are masked to treatment assignment. Following a four-week baseline period, participants with migraine headache frequency of 5–20 per month are randomized to one of three intensive dietary regimens for 16 additional weeks followed by a less intensive observation period. Dietary intervention arms include: 1) increased n-3 EPA+DHA with low n-6 linoleic acid (H3 L6); 2) increased n-3 EPA+DHA with usual US dietary intake of n-6 linoleic acid (H3 H6); and 3) usual US dietary content of n-3 and n-6 fatty acids (L3 H6). During the actual intervention, subjects receive content-specific study oils and foods sufficient for two meals and two snacks per day, as well as dietary counseling. Biochemical and clinical outcome measures are performed at intervals throughout this period. This randomized controlled trial is designed to determine whether targeted alterations in dietary n-3 and n-6 fatty acids can alter nociceptive lipid mediators in a manner that decreases headache pain and enhances quality of life and function in adults with frequent migraines. Trial registration NCT0201279

Aging-related defects in macrophage function are driven by MYC and USF1 transcriptional programs

Macrophages are central innate immune cells whose function declines with age. The molecular mechanisms underlying age-related changes remain poorly understood, particularly in human macrophages. We report a substantial reduction in phagocytosis, migration, and chemotaxis in human monocyte-derived macrophages (MDMs) from older (>50 years old) compared with younger (18–30 years old) donors, alongside downregulation of transcription factors MYC and USF1. In MDMs from young donors, knockdown of MYC or USF1 decreases phagocytosis and chemotaxis and alters the expression of associated genes, alongside adhesion and extracellular matrix remodeling. A concordant dysregulation of MYC and USF1 target genes is also seen in MDMs from older donors. Furthermore, older age and loss of either MYC or USF1 in MDMs leads to an increased cell size, altered morphology, and reduced actin content. Together, these results define MYC and USF1 as key drivers of MDM age-related functional decline and identify downstream targets to improve macrophage function in aging

A High Statistics Search for Ultra-High Energy Gamma-Ray Emission from Cygnus X-3 and Hercules X-1

We have carried out a high statistics (2 Billion events) search for ultra-high energy gamma-ray emission from the X-ray binary sources Cygnus X-3 and Hercules X-1. Using data taken with the CASA-MIA detector over a five year period (1990-1995), we find no evidence for steady emission from either source at energies above 115 TeV. The derived upper limits on such emission are more than two orders of magnitude lower than earlier claimed detections. We also find no evidence for neutral particle or gamma-ray emission from either source on time scales of one day and 0.5 hr. For Cygnus X-3, there is no evidence for emission correlated with the 4.8 hr X-ray periodicity or with the occurrence of large radio flares. Unless one postulates that these sources were very active earlier and are now dormant, the limits presented here put into question the earlier results, and highlight the difficulties that possible future experiments will have in detecting gamma-ray signals at ultra-high energies.Comment: 26 LaTeX pages, 16 PostScript figures, uses psfig.sty to be published in Physical Review

Unbalanced synaptic inhibition can create intensity-tuned auditory cortex neurons

Intensity-tuned auditory cortex neurons may be formed by intensity-tuned synaptic excitation. Synaptic inhibition has also been shown to enhance, and possibly even create intensity-tuned neurons. Here we show, using in vivo whole cell recordings in pentobarbital-anesthetized rats, that some intensity-tuned neurons are indeed created solely through disproportionally large inhibition at high intensities, without any intensity-tuned excitation. Since inhibition is essentially cortical in origin, these neurons provide examples of auditory feature-selectivity arising de novo at the cortex.Comment: 22 pages, 5 figure