Reef Cover, a coral reef classification for global habitat mapping from remote sensing

Coral reef management and conservation stand to benefit from improved high-resolution global mapping. Yet classifications underpinning large-scale reef mapping to date are typically poorly defined, not shared or region-specific, limiting end-users’ ability to interpret outputs. Here we present Reef Cover, a coral reef geomorphic zone classification, developed to support both producers and end-users of global-scale coral reef habitat maps, in a transparent and version-based framework. Scalable classes were created by focusing on attributes that can be observed remotely, but whose membership rules also reflect deep knowledge of reef form and functioning. Bridging the divide between earth observation data and geo-ecological knowledge of reefs, Reef Cover maximises the trade-off between applicability at global scales, and relevance and accuracy at local scales. Two case studies demonstrate application of the Reef Cover classification scheme and its scientific and conservation benefits: 1) detailed mapping of the Cairns Management Region of the Great Barrier Reef to support management and 2) mapping of the Caroline and Mariana Island chains in the Pacific for conservation purposes

How Much Shallow Coral Habitat Is There on the Great Barrier Reef?

Australia’s Great Barrier Reef (GBR) is a globally unique and precious national resource; however, the geomorphic and benthic composition and the extent of coral habitat per reef are greatly understudied. However, this is critical to understand the spatial extent of disturbance impacts and recovery potential. This study characterizes and quantifies coral habitat based on depth, geomorphic and benthic composition maps of more than 2164 shallow offshore GBR reefs. The mapping approach combined a Sentinel-2 satellite surface reflectance image mosaic and derived depth, wave climate, reef slope and field data in a random-forest machine learning and object-based protocol. Area calculations, for the first time, incorporated the 3D characteristic of the reef surface above 20 m. Geomorphic zonation maps (0–20 m) provided a reef extent estimate of 28,261 km2 (a 31% increase to current estimates), while benthic composition maps (0–10 m) estimated that ~10,600 km2 of reef area (~57% of shallow offshore reef area) was covered by hard substrate suitable for coral growth, the first estimate of potential coral habitat based on substrate availability. Our high-resolution maps provide valuable information for future monitoring and ecological modeling studies and constitute key tools for supporting the management, conservation and restoration efforts of the GBR

Southern right whale vocalizations on foraging grounds in South Georgia

Southern right whale vocalizations were recorded concurrently with visual observations off the sub-Antarctic Island of South Georgia, and the characteristics of these calls were described. Calls were also compared to those of humpback whales at South Georgia, to determine how the two species might reliably be distinguished acoustically. The southern right whale calls measured (which were all upcalls) had lower frequency with peak energy and were mostly shorter in duration than the calls measured from humpback whales. The frequency upsweep and the lack of harmonics of southern right whale calls were also diagnostic characteristics

A social-ecological-technological systems framework for urban ecosystem services

As rates of urbanization and climatic change soar, decision-makers are increasingly challenged to provide innovative solutions that simultaneously address climate-change impacts and risks and inclusively ensure quality of life for urban residents. Cities have turned to nature-based solutions to help address these challenges. Nature-based solutions, through the provision of ecosystem services, can yield numerous benefits for people and address multiple challenges simultaneously. Yet, efforts to mainstream nature-based solutions are impaired by the complexity of the interacting social, ecological, and technological dimensions of urban systems. This complexity must be understood and managed to ensure ecosystem-service provisioning is effective, equitable, and resilient. Here, we provide a social-ecological-technological system (SETS) framework that builds on decades of urban ecosystem services research to better understand four core challenges associated with urban nature-based solutions: multi-functionality, systemic valuation, scale mismatch of ecosystem services, and inequity and injustice. The framework illustrates the importance of coordinating natural, technological, and socio-economic systems when designing, planning, and managing urban nature-based solutions to enable optimal social-ecological outcomes

Avoiding Coral Reef Functional Collapse Requires Local and Global Action

oral reefs face multiple anthropogenic threats, from pollution and overfishing to the dual effects of greenhouse gas emissions: rising sea temperature and ocean acidification [1]. While the abundance of coral has declined in recent decades [2, 3], the implications for humanity are difficult to quantify because they depend on ecosystem function rather than the corals themselves. Most reef functions and ecosystem services are founded on the ability of reefs to maintain their three-dimensional structure through net carbonate accumulation [4]. Coral growth only constitutes part of a reef's carbonate budget; bioerosion processes are influential in determining the balance between net structural growth and disintegration [5, 6]. Here, we combine ecological models with carbonate budgets and drive the dynamics of Caribbean reefs with the latest generation of climate models. Budget reconstructions using documented ecological perturbations drive shallow (6-10 m) Caribbean forereefs toward an increasingly fragile carbonate balance. We then projected carbonate budgets toward 2080 and contrasted the benefits of local conservation and global action on climate change. Local management of fisheries (specifically, no-take marine reserves) and the watershed can delay reef loss by at least a decade under "business-as-usual" rises in greenhouse gas emissions. However, local action must be combined with a low-carbon economy to prevent degradation of reef structures and associated ecosystem services

Mapping the world's coral reefs using a global multiscale earth observation framework

Coral reefs are among the most diverse and iconic ecosystems on Earth, but a range of anthropogenic pressures are threatening their persistence. Owing to their remoteness, broad spatial coverage and cross‐jurisdictional locations, there are no high‐resolution remotely sensed maps available at the global scale. Here we present a framework that is capable of mapping coral reef habitats from individual reefs (~200 km2) to entire barrier reef systems (200 000 km2) and across vast ocean extents (>6 000 000 km2). This is the first time this has been demonstrated using a consistent and transparent remote sensing mapping framework. The ten maps that we present achieved good accuracy (78% mean overall accuracy) from multiple input image datasets and training data sources, and our framework was shown to be adaptable to either benthic or geomorphic reef features and across diverse coral reef environments. These new generation high‐resolution map data will be useful for supporting ecosystem risk assessments, detecting change in ecosystem dynamics and targeting efforts to monitor local‐scale changes in coral cover and reef health

Common polygenic variation in coeliac disease and confirmation of ZNF335 and NIFA as disease susceptibility loci

Coeliac disease (CD) is a chronic immune-mediated disease triggered by the ingestion of gluten. It has an estimated prevalence of approximately 1% in European populations. Specific HLA-DQA1 and HLA-DQB1 alleles are established coeliac susceptibility genes and are required for the presentation of gliadin to the immune system resulting in damage to the intestinal mucosa. In the largest association analysis of CD to date, 39 non-HLA risk loci were identified, 13 of which were new, in a sample of 12 014 individuals with CD and 12 228 controls using the Immunochip genotyping platform. Including the HLA, this brings the total number of known CD loci to 40. We have replicated this study in an independent Irish CD case–control population of 425 CD and 453 controls using the Immunochip platform. Using a binomial sign test, we show that the direction of the effects of previously described risk alleles were highly correlated with those reported in the Irish population, (P=2.2 × 10−16). Using the Polygene Risk Score (PRS) approach, we estimated that up to 35% of the genetic variance could be explained by loci present on the Immunochip (P=9 × 10−75). When this is limited to non-HLA loci, we explain a maximum of 4.5% of the genetic variance (P=3.6 × 10−18). Finally, we performed a meta-analysis of our data with the previous reports, identifying two further loci harbouring the ZNF335 and NIFA genes which now exceed genome-wide significance, taking the total number of CD susceptibility loci to 42

Seaview Survey Photo-quadrat and Image Classification Dataset

The primary scientific dataset arising from the XL Catlin Seaview Survey project is the “Seaview Survey Photo-quadrat and Image Classification Dataset”, consisting of: (1) over one million standardised, downward-facing “photo-quadrat” images covering approximately 1m2 of the sea floor; (2) human-classified annotations that can be used to train and validate image classifiers;\ua0(3) benthic cover data arising from the application of machine learning classifiers to the photo-quadrats; and\ua0(4)\ua0the triplets of raw images (covering 360o) from which the photo-quadrats were derived.Photo-quadrats were collected between 2012 and 2018 at 860 transect locations around the world, including: the Caribbean and Bermuda, the Indian Ocean (Maldives, Chagos Archipelago), the Coral Triangle (Indonesia, Philippines, Timor-Leste, Solomon Islands), the Great Barrier Reef, Taiwan and Hawaii.For additional information regarding methodology, data structure, organization and size, please see attached document “Dataset documentation”

DNAAF1 links heart laterality with the AAA+ ATPase RUVBL1 and ciliary intraflagellar transport

DNAAF1 (LRRC50) is a cytoplasmic protein required for dynein heavy chain assembly and cilia motility, and DNAAF1 mutations cause primary ciliary dyskinesia (PCD; MIM 613193). We describe four families with DNAAF1 mutations and complex congenital heart disease (CHD). In three families, all affected individuals have typical PCD phenotypes. However, an additional family demonstrates isolated CHD (heterotaxy) in two affected siblings, but no clinical evidence of PCD. We identified a homozygous DNAAF1 missense mutation, p.Leu191Phe, as causative for heterotaxy in this family. Genetic complementation in dnaaf1-null zebrafish embryos demonstrated the rescue of normal heart looping with wild-type human DNAAF1, but not the p.Leu191Phe variant, supporting the conserved pathogenicity of this DNAAF1 missense mutation. This observation points to a phenotypic continuum between CHD and PCD, providing new insights into the pathogenesis of isolated CHD. In further investigations of the function of DNAAF1 in dynein arm assembly, we identified interactions with members of a putative dynein arm assembly complex. These include the ciliary intraflagellar transport protein IFT88 and the AAA+ (ATPases Associated with various cellular Activities) family proteins RUVBL1 (Pontin) and RUVBL2 (Reptin). Co-localization studies support these findings, with the loss of RUVBL1 perturbing the co-localization of DNAAF1 with IFT88. We show that RUVBL1 orthologues have an asymmetric left-sided distribution at both the mouse embryonic node and the Kupffer’s vesicle in zebrafish embryos, with the latter asymmetry dependent on DNAAF1. These results suggest that DNAAF1-RUVBL1 biochemical and genetic interactions have a novel functional role in symmetry breaking and cardiac development

Development and psychometric evaluation of a new patient -reported outcome measure for stroke self -management: The Southampton Stroke Self - Management Questionnaire (SSSMQ).

BACKGROUND: Self-management is important to the recovery and quality of life of people following stroke. Many interventions to support self-management following stroke have been developed, however to date no reliable and valid outcome measure exists to support their evaluation. This study outlines the development and preliminary investigation of the psychometric performance of a newly developed patient-reported outcome measure (PROM) of self-management competency following stroke; the Southampton Stroke Self-Management Questionnaire (SSSMQ). METHODS: A convenience sample of 87 people who had had a stroke completed responses to the SSSMQ, the Stroke Self-Efficacy Questionnaire and the Stroke Impact Scale. Scaling properties were assessed using Mokken Scale Analysis. Reliability and construct validity were assessed using intra-class correlation coefficient (ICC), Mokken and Cronbach's reliability coefficients and Spearman rank order correlations with relevant measures. RESULTS: Mokken scaling refined the SSSMQ to 28 scalable items. Internal consistency reliability (Mokken r = 0.89) and test-retest reliability (ICC = 0.928) were excellent. Hypotheses of expected correlations with additional measures held, demonstrating good evidence for construct validity. CONCLUSIONS: Early findings suggest the Southampton Stroke Self-Management Questionnaire is a reliable and valid scale of self-management competency. The SSSMQ represents a potentially valid PROM for the evaluation of self-management following stroke