Virus Particle Detection by Convolutional Neural Network in Transmission Electron Microscopy Images

A new computational method for the detection of virus particles in transmission electron microscopy (TEM) images is presented. Our approach is to use a convolutional neural network that transforms a TEM image to a probabilistic map that indicates where virus particles exist in the image. Our proposed approach automatically and simultaneously learns both discriminative features and classifier for virus particle detection by machine learning, in contrast to existing methods that are based on handcrafted features that yield many false positives and require several postprocessing steps. The detection performance of the proposed method was assessed against a dataset of TEM images containing feline calicivirus particles and compared with several existing detection methods, and the state-of-the-art performance of the developed method for detecting virus was demonstrated. Since our method is based on supervised learning that requires both the input images and their corresponding annotations, it is basically used for detection of already-known viruses. However, the method is highly flexible, and the convolutional networks can adapt themselves to any virus particles by learning automatically from an annotated dataset.     

Evaluation of the water quality of the Hakata River based on diatoms

We investigated the epilithic diatom assemblage of samples collected from three sites of the Hakata River, Fukuoka, Japan, on November 26, 2008. Each taxon was photographed and identified. The 1747 diatom frustules collected were classified into 33 taxa belonging to 17 genera. Nitzschia fonticola was abundant at all sites. The DAIpo (the diatom assemblage index to organic water pollution) values for sites 1, 2, and 3 were 50.2, 44.1 and 48.0, respectively, indicating that the water quality of the Hakata River was at β-mesosaprobic level.     

Farmers’ attitude toward treated sludge use in the villages of West Bank,Palestine

An application of treated sewage sludge on agricultural land has been widely accepted, as this method is simple and economical for disposal of wastewater residues. When applied properly on an agricultural land, sludge can replenish organic matter and nutrients in soil. Although sewage sludge has been used in agriculture in many parts of the world, its acceptability varies with different cultures and beliefs among farmers. Farmers’ concerns on sludge use are primarily due to its anthropogenic origin, pollutants that it carries, a general perception of sewage being dirty, and its offensive odor. This paper aims to investigate farmers’ perceptions on land application of treated sewage sludge on their farm. This study targeted two farming communities, namely, Anza and Beit Dajan villages, located in Jenin and Nablus districts in the West Bank, Palestine. In this study, a sample of 106 farmers were randomly selected and surveyed through a mixture of structured and open-ended questions. Results indicated that, overall, farmers have positive perceptions on land application of sludge. A majority of the farmers are in favor of the concept of sludge use when a planned wastewater treatment plant is constructed and it becomes operational. Results also indicate that a majority of the farmers are in favor of using sludge for fertilizing fruit trees, rather than growing vegetables and other plants in a greenhouse, and that many of them have knowledge of sludge properties and advantages and disadvantages of sludge use in agriculture. Despite the positive perceptions by the majority of farmers, a small fraction of the farmers are in disfavor of the use of sludge for the following reasons: psychological and social concerns, potential health risks, and their religious beliefs. Results further suggest that the land application of treated sewage sludge can be accepted by more farmers if the consumers are willing to buy agricultural products fertilized by sludge, sludge meets the public health requirements, and sludge is available at low costs. To improve farmers’ perceptions on the land application of sludge, several measures are recommended.     

Traditional Ecological Knowledge Maintains Useful Plant Diversity in Semi-natural Grasslands in the Kiso Region,Japan

Environmental Management - Wild plant species provide a variety of ecosystem services that contribute to human well-being. However, much of the legacy of traditional ecological knowledge (TEK) in...     

Endocrine effects generated by photooxidation of coplanar biphenyls in water using titanium dioxide

The oxidative photodegradation behaviors of selected three coplanar polychlorinated biphenyls (PCBs), (CB77, CB81, and CB169) using titanium dioxide (TiO(2)) in water were investigated. The main purposes were to clarify the structural relation between the original PCBs and the intermediates derived by TiO(2) oxidation and to evaluate the estrogenic and thyroid hormonal activity in the treated three coplanar PCBs during the oxidative reactions. Approximately 90% of the three coplanar PCBs decomposed within 180 min. Intermediates from the decomposition of the three coplanar PCBs, such as some hydroxylated-PCBs (OH-PCBs), carboxylic intermediates, phenolic intermediates, and other intermediates produced by the cleavage of a benzene ring were identified and quantified. In the degradation pathways, the produced amounts of OH-PCBs increased within 60 min of irradiation time. The estrogenic activity and thyroid hormonal activity of the intermediates from the three coplanar PCBs in water at 0, 60, 120, 180 and 240 min of irradiation time were assessed by using a yeast two-hybrid assay system for human estrogen receptor alpha (hERalpha) and human thyroid hormone receptor alpha (hTRalpha). The maximal estrogenic activities were induced by the solutions of decomposed PCBs with irradiation time at 60-120 min similar and slightly lower than those after the irradiation time. We found that the solutions occuring during the irradiation times of 60-120 min contained several 4-OH-PCBs substituted with OH and Cl at para- and para'-positions having estrogenic activity. The thyroid hormonal activity was not detected in the decomposed three coplanar PCBs solutions.     

Stable isotope analysis of two species of anguilliform leptocephali (<Emphasis Type="Italic">Anguilla japonica</Emphasis> and <Emphasis Type="Italic">Ariosoma major</Emphasis>) relative to their feeding depth in the North Equatorial Current region

Anguilla japonica leptocephali are transported from their offshore spawning area to their recruitment areas in East Asia, but their depth distributions, food sources and feeding are still poorly known. This study analyzed carbon and nitrogen stable isotope ratios of leptocephali of A. japonica, Ariosoma major and Ariosoma spp., and of particulate organic matter (POM), their likely food source, at five different depths in 2004–2009. We used mixing models to show that A. japonica appeared to be feeding at depths between 5 and 50 m, but sometimes deeper. A. major appeared to have a tendency of mostly feeding at depths of 50 m or shallower. Although the A. japonica and Ariosoma spp. collected in the same area during the leptocephalus stage appeared to have different feeding ecologies possibly related to different types of POM, their different depth distributions, sizes and transport histories may also help explain these differences.     

Nematomorph parasites drive energy flow through a riparian ecosystem

Parasites are ubiquitous in natural systems and ecosystem-level effects should be proportional to the amount of biomass or energy flow altered by the parasites. Here we quantified the extent to which a manipulative parasite altered the flow of energy through a forest-stream ecosystem. In a Japanese headwater stream, camel crickets and grasshoppers (Orthoptera) were 20 times more likely to enter a stream if infected by a nematomorph parasite (Gordionus spp.), corroborating evidence that nematomorphs manipulate their hosts to seek water where the parasites emerge as free-living adults. Endangered Japanese trout (Salvelinus leucomaenis japonicus) readily ate these infected orthopterans, which due to their abundance, accounted for 60% of the annual energy intake of the trout population. Trout grew fastest in the fall, when nematomorphs were driving energy-rich orthopterans into the stream. When infected orthopterans were available, trout did not eat benthic invertebrates in proportion to their abundance, leading to the potential for cascading, indirect effects through the forest-stream ecosystem. These results provide the first quantitative evidence that a manipulative parasite can dramatically alter the flow of energy through and across ecosystems.     

Bacterial community succession during the enrichment of chemolithoautotrophic arsenite oxidizing bacteria at high arsenic concentrations

To generate cost-effective technologies for the removal of arsenic from water, we developed an enrichment culture of chemolithoautotrophic arsenite oxidizing bacteria (CAOs) that could effectively oxidize widely ranging concentrations of As(III) to As(V). In addition, we attempted to elucidate the enrichment process and characterize the microbial composition of the enrichment culture. A CAOs enrichment culture capable of stably oxidizing As(III) to As(V) was successfully constructed through repeated batch cultivation for more than 700 days, during which time the initial As(III) concentrations were increased in a stepwise manner from 1 to 10-12 mmol/L. As(III) oxidation activity of the enrichment culture gradually improved, and 10-12 mmol/L As(III) was almost completely oxidized within four days. Terminal restriction fragment length polymorphism analysis showed that the dominant bacteria in the enrichment culture varied drastically during the enrichment process depending on the As(III) concentration. Isolation and characterization of bacteria in the enrichment culture revealed that the presence of multiple CAOs with various As(III) oxidation abilities enabled the culture to adapt to a wide range of As(III) concentrations. The CAOs enrichment culture constructed here may be useful for pretreatment of water from which arsenic is being removed.     

Contributions of humic substances to the dissolved organic carbon pool in wetlands from different climates

Wetlands are an important source of DOM. However, the quantity and quality of wetlands' DOM from various climatic regions have not been studied comprehensively. The relationship between the concentrations of DOM (DOC), humic substances (HS) and non-humic substances (NHS) in wetland associated sloughs, streams and rivers, in cool temperate (Hokkaido, Japan), sub-tropical (Florida, USA), and tropical (Sarawak, Malaysia) regions was investigated. The DOC ranged from 1.0 to 15.6 mg CL(-1) in Hokkaido, 6.0-24.4 mg CL(-1) in Florida, and 18.9-75.3 mg CL(-1) in Sarawak, respectively. The relationship between DOC and HS concentrations for the whole sample set was regressed to a primary function with y-intercept of zero (P<0.005) and a slope value of 0.841. A similar correlation was observed between DOC and NHS concentrations, with a smaller slope value of 0.159. However, the correlation coefficient of the latter was much larger when the data was regressed to a logarithmic curve. These observations suggest the presence of a general tendency that the increased DOC in the river waters was mainly due to the increased supply of HS from wetland soils, whereas the rate of the increase in the NHS supply has an upper limit which may be controlled by primary productivity.