Mining Explainable Predictive Features for Water Quality Management

With water quality management processes, identifying and interpreting relationships between features, such as location and weather variable tuples, and water quality variables, such as levels of bacteria, is key to gaining insights and identifying areas where interventions should be made. There is a need for a search process to identify the locations and types of phenomena that are influencing water quality and a need to explain how the quality is being affected and which factors are most relevant. This paper addresses both of these issues. A process is developed for collecting data for features that represent a variety of variables over a spatial region and which are used for training models and inference. An analysis of the performance of the features is undertaken using the models and Shapley values. Shapley values originated in cooperative game theory and can be used to aid in the interpretation of machine learning results. Evaluations are performed using several machine learning algorithms and water quality data from the Dublin Grand Canal basin

Implementation and integration of microbial source tracking in a river watershed monitoring plan

Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) is used to track the source of this pollution facilitating better management of pollution at the source. In this study we tested 12 MST markers to track human, ruminant, sheep, horse, pig and gull pollution to assess their usefulness as an effective management tool of water quality. First, the potential of the selected markers to track the source was evaluated using fresh fecal samples. Subsequently, we evaluated their performance in a catchment with different impacts, considering land use and environmental conditions. All MST markers showed high sensitivity and specificity, although none achieved 100% for both. Although some of the MST markers were detected in hosts other than the intended ones, their abundance in the target group was always several orders of magnitude higher than in the non-target hosts, demonstrating their suitability to distinguish between sources of pollution. The MST analysis matched the land use in the watershed allowing an accurate assessment of the main sources of pollution, in this case mainly human and ruminant pollution. Correlating environmental parameters including temperature and rainfall with MST markers provided insight into the dynamics of the pollution in the catchment. The levels of the human marker showed a significant negative correlation with rainfall in human polluted areas suggesting a dilution of the pollution, whereas at agricultural areas the ruminant marker increased with rainfall. There were no seasonal differences in the levels of human marker, indicating human pollution as a constant pressure throughout the year, whereas the levels of the ruminant marker was influenced by the seasons, being more abundant in summer and autumn. MST analysis integrated with land use and environmental data can improve the management of fecal polluted areas and set up best practice

The Use of Transport Time Scales as Indicators of Pollution Persistence in a Macro-Tidal Setting

An understanding of water exchange processes is essential for assessing water quality management issues in coastal bays. This paper evaluates the impact of water exchange processes on pollution persistence in a macro-tidal semi-closed coastal bay through two transport time scales (TTS), namely residence time and exposure time. The numerical model was calibrated against field-measured data for various tidal conditions. Simulated current speeds and directions were shown to agree well with the field data. By considering different release scenarios of a conservative tracer by the refinement of an integrated hydrodynamic and solute transport model (the EFDC), the two TTS were used for interpreting the water exchange processes in a semi-closed system, and for describing the effects of advective and dispersive processes on the transport and fate of pollutants. The results indicate that the magnitudes of river inflows to the bay, tidal ranges, and tracer release times significantly influence the residence and exposure times. Return coefficients were shown to be variable, confirming the different effects of returning water for the different conditions that were studied. For the tested river flow magnitudes and tide conditions, the exposure times were generally higher than the residence times, but particularly so for neap tide conditions. The results, therefore, highlight the risks associated with pollutants leaving a specified domain on an outgoing tide but re-entering on subsequent incoming tides. The spatial distributions of the exposure and residence times across the model domain confirmed that for the case of Dublin Bay, river inputs have a potentially greater impact on water quality on the northern side of the bay

A protein having similarity with methylmalonyl-CoA mutase is required for the assimilation of methanol and ethanol by Methylobacterium extorquens AM1

A 4.0 kb region of Methylobacterium extorquens AM1 DNA which complements three mutants unable to convert acetyl-CoA to glyoxylate (and therefore defective in the assimilation of methanol and ethanol) has been isolated and sequenced. It contains two ORFs and the 3'-end of a third one. The mutations in all three mutants mapped within the first ORF, which was designated meaA; it encodes a protein having similarity with methylmalonyl-CoA mutase. However, methylmalonyl-CoA mutase was measured in extracts of one of the mutants and the specific activity was found to be similar to that in extracts of wild-type cells. Furthermore, although the predicted meaA gene product has the proposed cobalamin-binding site, it does not contain a highly conserved sequence (RIARNT) which is present in all known methylmalonyl-CoA mutases; meaA may therefore encode a novel vitamin-B-12-dependent enzyme. The predicted polypeptide encoded by the second ORF did not have similarity with any known proteins. The partial ORF encoded a protein with similarity with the 3-oxoacyl-[acyl-carrier-protein] reductases; it was not essential for growth on methanol or ethanol

Erratum to: ‘Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis’

ErratumErratum to: ‘Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis’ -http://hdl.handle.net/11019/90

Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

Objective: This study aimed to identify the oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of 20q gain on mRNA expression of genes in this amplicon. Methods: Segmentation of DNA copy number changes on 20q was performed by array CGH (comparative genomic hybridisation) in 34 non-progressed colorectal adenomas, 41 progressed adenomas (ie, adenomas that present a focus of cancer) and 33 adenocarcinomas. Moreover, a robust analysis of altered expression of genes in these segments was performed by microarray analysis in 37 adenomas and 31 adenocarcinomas. Protein expression was evaluated by immunohistochemistry on tissue microarrays. Results: The genes C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5, mapping at 20q, were significantly overexpressed in carcinomas compared with adenomas as a consequence of copy number gain of 20q. Conclusion: This approach revealed C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5 genes to be important in chromosomal instability-related adenoma to carcinoma progression. These genes therefore may serve as highly specific biomarkers for colorectal cancer with potential clinical applications