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

Identifying news clusters using Q-analysis and modularity

With online publication and social media taking the main role in dissemination of news, and with the decline of traditional printed media, it has become necessary to devise ways to automatically extract meaningful information from the plethora of sources available and to make that information readily available to interested parties. In this paper we present a method of automated analysis of the underlying structure of online newspapers based on Q-analysis and modularity. We show how the combination of the two strategies allows for the identification of well defined news clusters that are free of noise (unrelated stories) and provide automated clustering of information on trending topics on news published online

Axonal stress kinase activation and tau misbehavior induced by kinesin-1 transport defects

Many neurodegenerative diseases exhibit axonal pathology, transport defects, and aberrant phosphorylation and aggregation of the microtubule binding protein tau. While mutant tau protein in frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP17) causes aberrant microtubule binding and assembly of tau into filaments, the pathways leading to tau-mediated neurotoxicity in Alzheimer's disease and other neurodegenerative disorders in which tau protein is not genetically modified remain unknown. To test the hypothesis that axonal transport defects alone can cause pathological abnormalities in tau protein and neurodegeneration in the absence of mutant tau or amyloid β deposits, we induced transport defects by deletion of the kinesin light chain 1 (KLC1) subunit of the anterograde motor kinesin-1. We found that upon aging, early selective axonal transport defects in mice lacking the KLC1 protein (KLC1-/-) led to axonopathies with cytoskeletal disorganization and abnormal cargo accumulation. In addition, increased c-jun N-terminal stress kinase activation colocalized with aberrant tau in dystrophic axons. Surprisingly, swollen dystrophic axons exhibited abnormal tau hyperphosphorylation and accumulation. Thus, directly interfering with axonal transport is sufficient to activate stress kinase pathways initiating a biochemical cascade that drives normal tau protein into a pathological state found in a variety of neurodegenerative disorders including Alzheimer's disease.Fil: Falzone, Tomas Luis. Howard Hughes Medical Institute; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Stokin, Gorazd B.. University Psychiatric Hospital; EsloveniaFil: Lillo, Concepción. University of California at San Diego; Estados UnidosFil: Rodrigues, Elizabeth M.. Howard Hughes Medical Institute; Estados UnidosFil: Westerman, Eileen L.. Howard Hughes Medical Institute; Estados UnidosFil: Williams, David S.. University of California at San Diego; Estados UnidosFil: Goldstein, Lawrence S. B.. Howard Hughes Medical Institute; Estados Unido

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

Discrete event simulation model for planning Level 2 “step-down” bed needs using NEMS

In highly congested hospitals it may be common for patients to overstay at Intensive Care Units (ICU) due to blockages and imbalances in capacity. This is inadequate clinically, as patients occupy a service they no longer need; operationally, as it disrupts flow from upstream units; and financially as ICU beds are more expensive than ward beds. Step-down beds, also known as Level 2 beds, have become an increasingly popular and less expensive alternative to ICU beds to deal with this issue. We developed a discrete event simulation model that estimates Level 2 bed needs for a large university hospital. The model innovates by simulating the entirety of the hospital’s inpatient flow and most importantly, the ICU’s daily stochastic flows based on a nursing workload scoring metrics called “Nine Equivalents of Nursing Manpower Use Score” (NEMS). Using data from a large academic hospital, the model shows the benefits of Level 2 beds in improving both patient flow and costs

Accelerating networks

Evolving out-of-equilibrium networks have been under intense scrutiny recently. In many real-world settings the number of links added per new node is not constant but depends on the time at which the node is introduced in the system. This simple idea gives rise to the concept of accelerating networks, for which we review an existing definition and -- after finding it somewhat constrictive -- offer a new definition. The new definition provided here views network acceleration as a time dependent property of a given system, as opposed to being a property of the specific algorithm applied to grow the network. The defnition also covers both unweighted and weighted networks. As time-stamped network data becomes increasingly available, the proposed measures may be easily carried out on empirical datasets. As a simple case study we apply the concepts to study the evolution of three different instances of Wikipedia, namely, those in English, German, and Japanese, and find that the networks undergo different acceleration regimes in their evolution.Comment: 12 pages, 8 figure

Soil Carbon in Agroforestry Systems: An Unexplored Treasure?

Soil organic matter (SOM), which contains more reactive organic carbon (C) than any other single terrestrial pool, plays a major role in determining C storage in ecosystems and regulating atmospheric concentrations of carbon dioxide (CO2)^1^. Agroforestry, the practice of growing trees and crops in interacting combinations on the same unit of land^2^, primarily by resource-poor smallholder farmers in developing countries, is recognized as a strategy for soil carbon sequestration (SCS) under the Clean Development Mechanism (CDM) of the Kyoto Protocol^3^. The understanding about C storage and dynamics under agroforestry systems (AFS), however, is minimal. Our studies under various AFS in diverse ecological conditions in five countries showed that tree-based agricultural systems, compared to treeless systems, stored more C in deeper soil layers up to 1 m depth under comparable conditions. More C is stored in soil near the tree than away from the tree; higher SOC content is associated with higher species richness and tree density; and C3 plants (trees) contribute to more C in the silt- + clay-sized (<53 µm) fractions that constitute more stable C, than C4 plants, in deeper soil profiles4 - 8. These results provide clear indications of the possibilities for climate change mitigation through SCS in AFS, and opportunities for economic benefit - through carbon trading - to millions of smallholder farmers in developing countries

Quantification of harms in cancer screening trials: literature review

Objectives To assess how often harm is quantified in randomised trials of cancer screening. Design Two authors independently extracted data on harms from randomised cancer screening trials. Binary outcomes were described as proportions and continuous outcomes with medians and interquartile ranges. Data sources For cancer screening previously assessed in a Cochrane review, we identified trials from their reference lists and updated the search in CENTRAL. For cancer screening not assessed in a Cochrane review, we searched CENTRAL, Medline, and Embase. Eligibility criteria for selecting studies Randomised trials that assessed the efficacy of cancer screening for reducing incidence of cancer, cancer specific mortality, and/or all cause mortality. Data extraction Two reviewers independently assessed articles for eligibility. Two reviewers, who were blinded to the identity of the study's authors, assessed whether absolute numbers or incidence rates of outcomes related to harm were provided separately for the screening and control groups. The outcomes were false positive findings, overdiagnosis, negative psychosocial consequences, somatic complications, invasive follow-up procedures, all cause mortality, and withdrawals because of adverse events. Results Out of 4590 articles assessed, 198 (57 trials, 10 screening technologies) matched the inclusion criteria. False positive findings were quantified in two of 57 trials (4\%, 95\% confidence interval 0\% to 12\%), overdiagnosis in four (7\%, 2\% to 18\%), negative psychosocial consequences in five (9\%, 3\% to 20\%), somatic complications in 11 (19\%, 10\% to 32\%), use of invasive follow-up procedures in 27 (47\%, 34\% to 61\%), all cause mortality in 34 (60\%, 46\% to 72\%), and withdrawals because of adverse effects in one trial (2\%, 0\% to 11\%). The median percentage of space in the results section that reported harms was 12\% (interquartile range 2-19\%). Conclusions Cancer screening trials seldom quantify the harms of screening. Of the 57 cancer screening trials examined, the most important harms of screening-overdiagnosis and false positive findings-were quantified in only 7\% and 4\%, respectively.publishersversionpublishe