Establishing microbial baselines to identify indicators of coral reef health

Microorganisms make a significant contribution to reef ecosystem health and resilience via their critical role in mediating nutrient transformations, their interactions with macro-organisms and their provision of chemical cues that underpin the recruitment of diverse reef taxa. However, environmental changes often cause compositional and functional shifts in microbial communities that can have flow-on consequences for microbial-mediated processes. These microbial alterations may impact the health of specific host organisms and can have repercussions for the functioning of entire coral ecosystems. Assessing changes in reef microbial communities should therefore provide an early indicator of ecosystem impacts and would underpin the development of diagnostic tools that could help forecast shifts in coral reef health under different environmental states. Monitoring, management and active restoration efforts have recently intensified and diversified in response to global declines in coral reef health. Here we propose that regular monitoring of coral reef microorganisms could provide a rapid and sensitive platform for identifying declining ecosystem health that can complement existing management frameworks. By summarising the most common threats to coral reefs, with a particular focus on the Great Barrier Reef, and elaborating on the role of microbes in coral reef health and ecosystem stability, we highlight the diagnostic applicability of microbes in reef management programs. Fundamental to this objective is the establishment of microbial baselines for Australia's coral reefs.AIMS@JCU PhD Scholarship; GBRMPA Science Management Research Award; Advance Queensland PhD Scholarship; Portuguese Science and Technology Foundation (FCT) [SFRH/BPD/110285/2015

A-posteriori provenance-enabled linking of publications and datasets via crowdsourcing

This paper aims to share with the digital library community different opportunities to leverage crowdsourcing for a-posteriori capturing of dataset citation graphs. We describe a practical approach, which exploits one possible crowdsourcing technique to collect these graphs from domain experts and proposes their publication as Linked Data using the W3C PROV standard. Based on our findings from a study we ran during the USEWOD 2014 workshop, we propose a semi-automatic approach that generates metadata by leveraging information extraction as an additional step to crowdsourcing, to generate high-quality data citation graphs. Furthermore, we consider the design implications on our crowdsourcing approach when non-expert participants are involved in the process<br/

TOWARDS A FINANCIALLY OPTIMAL DESIGN OF IT SERVICES

The current financial crisis forces companies to allocate IT budgets more effectively and thus increases the demand for suitable methods to evaluate the financial impact of IT investments. This especially applies to service-orientation, a design paradigm which facilitates the standardisation and flexibilisation of business processes and IT applications, topics that currently are very much in vogue in science and practice. This paper focuses on the realisation of a new functionality by IT services and presents a methodology to determine their financially optimal functional scope on the continuum between realising just one IT service providing the whole functionality and realising many IT services each providing only a small share of functionality. This approach allows for a multi-period financial valuation of an uncertain demand for the new functionality, as well as of an uncertain company-wide reuse of the corresponding IT services. Finally, the methodology is evaluated by an example from a financial services provider

Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes

Microbially mediated processes contribute to coral reef resilience yet, despite extensive characterisation of microbial community variation following environmental perturbation, the effect on microbiome function is poorly understood. We undertook metagenomic sequencing of sponge, macroalgae and seawater microbiomes from a macroalgae-dominated inshore coral reef to define their functional potential and evaluate seasonal shifts in microbially mediated processes. In total, 125 high-quality metagenome-assembled genomes were reconstructed, spanning 15 bacterial and 3 archaeal phyla. Multivariate analysis of the genomes relative abundance revealed changes in the functional potential of reef microbiomes in relation to seasonal environmental fluctuations (e.g. macroalgae biomass, temperature). For example, a shift from Alphaproteobacteria to Bacteroidota-dominated seawater microbiomes occurred during summer, resulting in an increased genomic potential to degrade macroalgal-derived polysaccharides. An 85% reduction of Chloroflexota was observed in the sponge microbiome during summer, with potential consequences for nutrition, waste product removal, and detoxification in the sponge holobiont. A shift in the Firmicutes:Bacteroidota ratio was detected on macroalgae over summer with potential implications for polysaccharide degradation in macroalgal microbiomes. These results highlight that seasonal shifts in the dominant microbial taxa alter the functional repertoire of host-associated and seawater microbiomes, and highlight how environmental perturbation can affect microbially mediated processes in coral reef ecosystems.Australian Government Department of Industry, Innovation and Science; Advance Queensland PhD Scholarship Great Barrier Reef Marine Park Authority Management Award National Environmental Science Program (NESP)info:eu-repo/semantics/publishedVersio

Cross‐reactive carbohydrate determinants in atopic and healthy dogs and their influence on allergy test specificity

Background The selection of allergens for immunotherapy in atopic dogs is often based on serum allergy testing. Cross-reactive carbohydrate determinants (CCDs) are common structures in plant and insect allergens that reportedly induce polysensitisation, reduce agreement between intradermal and serum tests and complicate allergen selection. Methods Thirty-four dogs with diagnosed atopic dermatitis and 10 healthy dogs were included in the study. An intradermal test was conducted in atopic dogs, and serum samples from allergic and healthy dogs were analysed for allergen-specific immunoglobulin E (IgE) before and after inhibition of detectable anti-CCD-IgE antibodies. Results Anti-CCD-IgE antibodies were not found in any of the healthy dogs and no polysensitisation to plant and insect allergens was detected. The agreement between intradermal and serum allergy test results in the atopic dogs with anti-CCD-IgE antibodies improved from slight to fair after blocking the anti-CCD-IgE antibodies. In addition, blocking clearly reduced polysensitisation to plant allergens but not to acarid allergens. Limitations Only a limited number of healthy dogs were tested in this study. A gold standard for determining the clinical relevance of IgE sensitisation does not exist. Conclusion Inhibition of anti-CCD-IgE antibodies seems to be of importance to improve serum test specificity for allergen-specific IgE in atopic dogs in relation to intradermal allergy testing

Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopic analysis

Abstract. Manganese (Mn)-rich natural rock coatings, so-called rock varnishes, are discussed controversially regarding their genesis. Biogenic and abiogenic mechanisms, as well as a combination of both, have been proposed to be responsible for the Mn oxidation and deposition process. We conducted scanning transmission X-ray microscopy - near edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS) measurements to examine the abundance and spatial distribution of the different oxidation states of Mn within these nano- to micrometer thick crusts. Such microanalytical measurements of thin and hard rock crusts require sample preparation with minimal contamination risk. Focused ion beam (FIB) slicing, a well-established technique in geosciences, was used in this study to obtain 100–200 nm thin slices of the samples for X-ray transmission spectroscopy. However, even though this preparation is suitable to investigate element distributions and structures in rock samples, we observed that, using standard parameters, modifications of the Mn oxidation states occur in the surfaces of the FIB slices. Based on our results, the preparation technique likely causes the reduction of Mn4+ to Mn2+/3+. We draw attention to this issue, since FIB slicing, SEM imaging, and other preparation and visualization techniques operating in the keV range are well-established in geosciences, but researchers are often unaware of the potential for reduction of Mn and possibly other elements in the samples’ surface layers

Climatic controls on biophysical interactions in the Black Sea under present day conditions and a potential future (A1B) climate scenario

A dynamical downscaling approach has been applied to investigate climatic controls on biophysical interactions and lower trophic level dynamics in the Black Sea. Simulations were performed under present day conditions (1980–1999) and a potential future (2080–2099) climate scenario, based on the Intergovernmental Panel for Climate Change A1B greenhouse gas emission scenario. Simulations project a 3.7 °C increase in SST, a 25% increase in the stability of the seasonal thermocline and a 37 day increase in the duration of seasonal stratification. Increased winter temperatures inhibited the formation of Cold Intermediate Layer (CIL) waters resulting in near complete erosion of the CIL, with implications for the ventilation of intermediate water masses and the subduction of riverine nutrients. A 4% increase in nitrate availability within the upper 30 m of the water column reflected an increase in the retention time of river water within the surface mixed-layer. Changes in thermohaline structure, combined with a 27% reduction in positive wind stress curl, forced a distinct change in the structure of the basin-scale circulation. The predominantly cyclonic circulation characteristic of contemporary conditions was reversed within the southern and eastern regions of the basin, where under A1B climatic conditions, anticyclonic circulation prevailed. The change in circulation structure significantly altered the horizontal advection and dispersion of high nutrient river waters originating on the NW self. Net primary production increased by 5% on average, with much spatial variability in the response, linked to advective processes. Phytoplankton biomass also increased by 5% and the higher nutrient environment of the future scenario caused a shift in species composition in favour of larger phytoplankton. No significant change in zooplankton biomass was projected. These results constitute one of many possible future scenarios for the Black Sea, being dependent on the modelling systems employed in addition to the choice of emission scenario. Our results emphasise in particular the sensitivity of dynamical downscaling studies to the regional wind forcing fields extracted from global models (these being typically model dependent). As atmospheric warming is projected with a high degree of confidence warming of the Black Sea upper layer, increased water column stability, and erosion of the CIL are believed to be robust results of this study

Novel Use of a Social-Media-Based Survey to Detect Regional Differences in Management of Monochorionic-Diamniotic Twins.

ObjectiveThis study aims to evaluate the utility of social media to distribute a patient survey on differences in management and outcomes of monochorionic-diamniotic (MCDA) pregnancies.Study designA cross-sectional survey was posted to an English-language MCDA twins patient-centered support group within the social media site, Facebook from April 2, 2018 to June 26, 2018. Subjects were recruited through a technique called "snowballing," whereby individuals shared the survey to assist with recruiting. Patient reported data were analyzed using Chi-square and Kruskal-Wallis's tests to explore characteristics associated with surveillance and outcomes as related to region and provider type.ResultsOver 3 months, the post "reached" 14,288 Facebook users, among which 5,653 (40%) clicked on the post. A total of 2,357 respondents with MCDA pregnancies completed the survey. Total 1,928 (82%) were from the United States (US) and 419 (18%) from other countries. Total 85% of patients had co-management with maternal-fetal medicine (MFM), more in the US compared with the rest of the world (87 vs. 74%, p &lt; 0.01). MFM involvement led to increased adherence to biweekly ultrasounds (91 vs. 65%, p &lt; 0.01), diagnosis of monochorionicity by 12 weeks (74 vs. 69%, p &lt; 0.01) and better education about twin-twin transfusion syndrome (90 vs. 66%, p &lt; 0.01). Pregnancies with MFM involvement had a higher take-home baby rate for both babies (92 vs. 89%, p &lt; 0.01) or for at least one baby (98 vs. 93%, p &lt; 0.01) compared with those without MFM involvement.ConclusionA survey distributed via social media can be effective in evaluating real-life management and outcomes of an uncommon obstetrical diagnosis. This survey elucidates wide international variation in adherence to guidelines, management, and outcomes