Comparison of machine learning classifier models for bathing water quality exceedances in UK

The revised Bathing Water Directive (rBWD) (2006/7/EC) of the European Parliament requires monitoring of bathing water quality and, if early-warnings are provided to the public, it is permissible to discount a percentage of exceedance events from the monitoring process. This paper describes the development and implementation of both Decision Tree (DT) and Artificial Neural Network (ANN) based machine learning models for 8 beaches in south-west England, UK, as bases for early warning systems (EWS) and compares their performance for one beach. Weekly bacteria-count samples were gathered by the Environment Agency of England (EA) over a 12-year period from 2000-2011 during the 20-week bathing season and this data is used to calibrate and test the models. Daily sampling data were also collected at 5 of the beaches during the 2012 season to provide more robust validation of the models. As a benchmark, models are also compared with use of simple thresholds of antecedent rainfall to classify water quality exceedances. Evolutionary Algorithm-based optimisation of the ANN models is employed using single-objective approach using area under the Receiver Operating Characteristic (ROC) curve as fitness function. The optimum operating point is established using a weighting factor for the relative importance placed on false positives (passes) and false negatives (exceedances). The models use a number of input factors, including antecedent rainfall for the catchment adjacent to each bathing beach. A possible technique for automating selection of inputs is also discussed.Environment Agency (SW

Arabinoxylan-oligosaccharides (AXOS) affect the protein/carbohydrate fermentation balance and microbial population dynamics of the Simulator of Human Intestinal Microbial Ecosystem

Arabinoxylan-oligosaccharides (AXOS) are a recently newly discovered class of candidate prebiotics as depending on their structure - they are fermented in different regions of gastrointestinal tract. This can have an impact on the protein/carbohydrate fermentation balance in the large intestine and, thus, affect the generation of potentially toxic metabolites in the colon originating from proteolytic activity. In this study, we screened different AXOS preparations for their impact on the in vitro intestinal fermentation activity and microbial community structure. Shortterm fermentation experiments with AXOS with an average degree of polymerization (avDP) of 29 allowed part of the oligosaccharides to reach the distal colon, and decreased the concentration of proteolytic markers, whereas AXOS with lower avDP were primarily fermented in the proximal colon. Additionally, prolonged supplementation of AXOS with avDP 29 to the Simulator of Human Intestinal Microbial Ecosystem (SHIME) reactor decreased levels of the toxic proteolytic markers phenol and p-cresol in the two distal colon compartments and increased concentrations of beneficial short-chain fatty acids (SCFA) in all colon vessels (25-48%). Denaturant gradient gel electrophoresis (DGGE) analysis indicated that AXOS supplementation only slightly modified the total microbial community, implying that the observed effects on fermentation markers are mainly caused by changes in fermentation activity. Finally, specific quantitative PCR (qPCR) analysis showed that AXOS supplementation significantly increased the amount of health-promoting lactobacilli as well as of Bacteroides-Prevotella and Clostridium coccoides-Eubacterium rectale groups. These data allow concluding that AXOS are promising candidates to modulate the microbial metabolism in the distal colon

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Health care-associated Staphylococcus aureus pneumonia

INTRODUCTION: While Staphylococcus aureus is an uncommon but serious cause of traditional community-acquired pneumonia (CAP), it is a predominant cause of nosocomial pneumonia in addition to the unique clinical entity of health care-associated pneumonia (HCAP). A cohort of bacteremic S aureus pneumonia cases was reviewed to determine the role of HCAP among the cohort, and to assess for differences between CAP and HCAP

Investigating Labrador Sea's persistent surface O2 anomaly using observations and biogeochemical model results

Deviations of surface ocean dissolved oxygen (O2) from equilibrium with the atmosphere should be rectified about twenty times more quickly than deviations of dissolved carbon dioxide (CO2). Therefore, persistent O2 disequilibria in the Labrador Sea, while CO2 is close to equilibrium, has been a matter of interest to many previous works. Here we investigate this phenomenon by using a novel analytical technique, the ‘CORS (Carbon Dioxide and Oxygen Relative to Saturation) method’, and also by using more data than was available previously. We compare observations to results from a model we developed for the Labrador Sea which combines plankton ecology with biogeochemical cycling of oxygen, carbon and nitrogen. In contrast to earlier works which mostly considered individual factors in isolation, here we used the model, together with data, to distinguish between the varying influences of several processes potentially contributing to the long-lasting O2 undersaturation: mixed layer depth, duration of mixed layer deepening, convection, entrainment and bottom water O2 content. Our model experiments confirm that, for the same gas exchange rate, the effects on surface O2 concentration differ significantly among the identified drivers. Our results suggest that prolonged surface O2 undersaturation is not always dependent on the extreme winter mixed layer depths, but rather that even moderately deep mixed layers (e.g. 300m), when prolonged and in conjunction with continuous entrainment of oxygen-depleted deep water, can also drive persistent surface O2 anomalies. An implication of our results is that regions in the North Atlantic with maximum winter mixed layer depths of only a few hundred metres should also show persistent surface O2 undersaturation. We further reveal that convection in deep water formation regions produces trendlines that do not pass through the origin of a plot of CO2 vs. O2 deviations which have previously been thought to indicate erroneous data