A short review on the application of computational intelligence and machine learning in the bioenvironmental sciences

This paper aims to provide a short review on the application of computational intelligence (CI) and machine learning (ML) in the bioenvironmental sciences. To clearly illustrate the current status, we limit our focus to some key approaches, namely fuzzy systems (FSs), artificial neural networks (ANNs) and genetic algorithms (GAs) as well as some ML methods. The trends in the application studies are categorized based on the targets of the model such as animal, fish, plant, soil and water. We give an overview of specific topics in the bioenvironmental sciences on the basis of the review papers on model comparisons in the field. The summary of the modelling approaches with respect to their aim and potential application fields can promote the use of CI and ML in the bioenvironmental sciences

Tracking swimming Lefua echigonia to assess the impact of crayfish introduction

Lefua echigonia is an endangered freshwater species in Japan, whose habitats are decreasing due to urbanization and modernization of agriculture. In addition, invasion by non-native crayfish, Procambarus clarkii, is known to be a threat to L. echigonia. Whereas we observed P. clarkii at L. echigonia habitats such as large gravels, little is known about the impact of P. clarkii invasions on L. echigonia. In this study, we conducted a laboratory experiment using a 25-cm cylinder to observe swimming behaviour of L. echigonia with varying number of P. clarkii individuals and the presence/absence of a rectangular obstacle at the center. Swimming trajectories were obtained from a series of images taken 30 frames per second, based on which swimming speed, acceleration, and distance between individuals were calculated for the assessment of behavioural changes with P. clarkii introduction. No feed was given for both species during experiment. While both species moved along the wall during experiment under no obstacle condition, L. echigonia was more active than P. clarkia. Behavioural changes were observed when the obstacle was placed in the center. Foraging by P. clarkii was expected but no such a behaviour was observed even under the condition where more P. clarkii individuals were put together. Whereas no foraging behaviour was observed, some L. echigonia individuals stayed around the brick which is similar to P. clarkia. This suggests potential habitat overlaps between the two species. Further study can reveal species competition under more complex, dynamic instream conditions for which image analysis with high-speed/high-resolution cameras can be used as a tool for reliable assessment

Revisiting probabilistic neural networks: a comparative study with support vector machines and the microhabitat suitability for the Eastern Iberian chub (Squalius valentinus)

[EN] Probabilistic Neural Networks (PNNs) and Support Vector Machines (SVMs) are flexible classification techniques suited to render trustworthy species distribution and habitat suitability models. Although several alternatives to improve PNNs¿ reliability and performance and/or to reduce computational costs exist, PNNs are currently not well recognised as SVMs because the SVMs were compared with standard PNNs. To rule out this idea, the microhabitat suitability for the Eastern Iberian chub (Squalius valentinus Doadrio & Carmona, 2006) was modelled with SVMs and four types of PNNs (homoscedastic, heteroscedastic, cluster and enhanced PNNs); all of them optimised with differential evolution. The fitness function and several performance criteria (correctly classified instances, true skill statistic, specificity and sensitivity) and partial dependence plots were used to assess respectively the performance and reliability of each habitat suitability model. Heteroscedastic and enhanced PNNs achieved the highest performance in every index but specificity. However, these two PNNs rendered ecologically unreliable partial dependence plots. Conversely, homoscedastic and cluster PNNs rendered ecologically reliable partial dependence plots. Thus, Eastern Iberian chub proved to be a eurytopic species, presenting the highest suitability in microhabitats with cover present, low flow velocity (approx. 0.3 m/s), intermediate depth (approx. 0.6 m) and fine gravel (64¿256 mm). PNNs outperformed SVMs; thus, based on the results of the cluster PNN, which also showed high values of the performance criteria, we would advocate a combination of approaches (e.g., cluster & heteroscedastic or cluster & enhanced PNNs) to balance the trade-off between accuracy and reliability of habitat suitability models.The study has been partially funded by the national Research project IMPADAPT (CGL2013-48424-C2-1-R) with MINECO (Spanish Ministry of Economy) and Feder funds and by the Confederacion Hidrografica del Near (Spanish Ministry of Agriculture and Fisheries, Food and Environment). This study was also supported in part by the University Research Administration Center of the Tokyo University of Agriculture and Technology. Thanks to Maria Jose Felipe for reviewing the mathematical notation and to the two anonymous reviewers who helped to improve the manuscript.Muñoz Mas, R.; Fukuda, S.; Portolés, J.; Martinez-Capel, F. (2018). Revisiting probabilistic neural networks: a comparative study with support vector machines and the microhabitat suitability for the Eastern Iberian chub (Squalius valentinus). Ecological Informatics. 43:24-37. https://doi.org/10.1016/J.ECOINF.2017.10.008S24374

Urban Diets Linked to Gut Microbiome and Metabolome Alterations in Children: A Comparative Cross-Sectional Study in Thailand

Loss of traditional diets by food globalization may have adverse impact on the health of human being through the alteration of gut microbial ecosystem. To address this notion, we compared the gut microbiota of urban (n = 17) and rural (n = 28) school-aged children in Thailand in association with their dietary habits. Dietary records indicated that children living in urban Bangkok tended to consume modern high-fat diets, whereas children in rural Buriram tended to consume traditional vegetable-based diets. Sequencing of 16S rRNA genes amplified from stool samples showed that children in Bangkok have less Clostridiales and more Bacteroidales and Selenomonadales compared to children in Buriram and bacterial diversity is significantly less in Bangkok children than in Buriram children. In addition, fecal butyrate and propionate levels decreased in Bangkok children in association with changes in their gut microbial communities. Stool samples of these Thai children were classified into five metabolotypes (MTs) based on their metabolome profiles, each characterized by high concentrations of short and middle chain fatty acids (MT1, n = 17), amino acids (MT2, n = 7), arginine (MT3, n = 6), amino acids, and amines (MT5, n = 8), or an overall low level of metabolites (MT4, n = 4). MT1 and MT4 mainly consisted of samples from Buriram, and MT2 and MT3 mainly consisted of samples from Bangkok, whereas MT5 contained three samples from Bangkok and five from Buriram samples. According to the profiles of microbiota and diets, MT1 and MT2 are characteristic of children in Buriram and Bangkok, respectively. Predicted metagenomics indicated the underrepresentation in MT2 of eight genes involved in pathways of butyrate biosynthesis, notably including paths from glutamate as well as pyruvate. Taken together, this study shows the benefit of high-vegetable Thai traditional diets on gut microbiota and suggests that high-fat and less-vegetable urban dietary habits alter gut microbial communities in Thai children, which resulted in the reduction of colonic short chain fatty acid fermentation

A RecA-mediated exon profiling method

We have developed a RecA-mediated simple, rapid and scalable method for identifying novel alternatively spliced full-length cDNA candidates. This method is based on the principle that RecA proteins allow to carry radioisotope-labeled probe DNAs to their homologous sequences, resulting in forming triplexes. The resulting complex is easily detected by mobility difference on electrophoresis. We applied this exon profiling method to four selected mouse genes as a feasibility study. To design probes for detection, the information on known exonic regions was extracted from public database, RefSeq. Concerning the potentially transcribed novel exonic regions, RNA mapping experiment using Affymetrix tiling array was performed. As a result, we were able to identify alternative splice variants of Thioredoxin domain containing 5, Interleukin1β, Interleukin 1 family 6 and glutamine-rich hypothetical protein. In addition, full-length sequencing demonstrated that our method could profile exon structures with >90% accuracy. This reliable method can allow us to screen novel splice variants from a huge number of cDNA clone set effectively

養殖カワハギとウマヅラハギに寄生していたカイアシ類Peniculus minuticaudae

三重県南伊勢町地先の北太平洋で養殖されていたカワハギStephanolepis cirrhifer および大分県佐伯市上浦地先と蒲江地先の豊後水道でそれぞれ養殖されていたカワハギとウマヅラハギThamnaconus modestusの鰭から寄生性カイアシ類Peniculus minuticaudae Shiino, 1956の雌成虫を採集した。これは本寄生虫の養殖魚類および養殖カワハギ・ウマヅラハギからの初記録であるとともに，養殖魚類にペンネラ科カイアシ類の寄生を認めた2度目の事例である。本寄生虫は胸鰭と第2背鰭に多く見られ，次いで尾鰭と臀鰭の順に多く寄生していた。Female adult specimens of the pennellid copepod Peniculus minuticaudae Shiino, 1956 were collected from the fins of two species of monacanthid fishes, threadsail filefish (Stephanolepis cirrhifer) and black scraper (Thamnaconus modestus), cultured in floating cages in Japan. These collections represent the first records of P. minuticaudae from farmed marine fishes as well as the first records of this copepod species from farmed S. cirrhifer and T. modestus. The finding of P. minuticaudae in this study is also the second record of pennellid copepods from maricultured fishes. Both the pectoral fins and the second dorsal fin were most heavily infected, followed by the caudal fin and the anal fin

Integrated analysis of the oral and intestinal microbiome and metabolome of elderly people with more than 26 original teeth: a pilot study

Elderly subjects with more than 20 natural teeth have a higher healthy life expectancy than those with few or no teeth. The oral microbiome and its metabolome are associated with oral health, and they are also associated with systemic health via the oral-gut axis. Here, we analyzed the oral and gut microbiome and metabolome profiles of elderly subjects with more than 26 natural teeth. Salivary samples collected as mouth-rinsed water and fecal samples were obtained from 22 healthy individuals, 10 elderly individuals with more than 26 natural teeth and 24 subjects with periodontal disease. The oral microbiome and metabolome profiles of elderly individuals resembled those of subjects with periodontal disease, with the metabolome showing a more substantial differential abundance of components. Despite the distinct oral metabolome profiles, there was no differential abundance of components in the gut microbiome and metabolomes, except for enrichment of short-chain fatty acids in elderly subjects. Finally, to investigate the relationship between the oral and gut microbiome and metabolome, we analyzed bacterial coexistence in the oral cavity and gut and analyzed the correlation of metabolite levels between the oral cavity and gut. However, there were few associations between oral and gut for bacteria and metabolites in either elderly or healthy subjects. Overall, these results indicate distinct oral microbiome and metabolome profiles, as well as the lack of an oral-gut axis in elderly subjects with a high number of natural teeth