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.     

Novel enzymatic activity of cell free extract from thermophilic Geobacillus sp. UZO 3 catalyzes reductive cleavage of diaryl ether bonds of 2,7-dichlorodibenzo-p-dioxin

We characterized the ability of the cell free extract from polychlorinated dibenzo-p-dioxins degrading bacterium Geobacillus sp. UZO 3 to reduce even highly chlorinated dibenzo-p-dioxins such as octachlorodibenzo-p-dioxins in incineration fly ash. The degradation of 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD) as a model dioxin catalyzed by the cell free extract from this strain implicates that the ether bonds of 2,7-DCDD molecule undergo reductive cleavage, since 4′,5-dichloro-2-hydroxydiphenyl ether and 4-chlorophenol were detected as intermediate products of 2,7-DCDD degradation.     

Residues of pharmaceutical products in recycled organic manure produced from sewage sludge and solid waste from livestock and relationship to their fermentation level

In recent years, sludge generated in sewage treatment plants (STPs) and solid waste from livestock being utilized is useful for circulation of nourishment in farmlands as recycled organic manure (ROM). In this study, we determined the residue levels and patterns of 12 pharmaceutical products generated by human activity in the ROMs produced from human waste sludge (HWS), sewage sludge (SS), cattle manure (CM), poultry manure (PM), swine manure (SM) and horse manure (HM).The kind and number of pharmaceutical products detected in ROMs were different. Fluoroquinolones (FQs) were detected at high levels in HWS and SS samples. In addition, the detection frequency and concentration levels of sulfonamides (SAs) in PM and SM were high. Moreover, high concentrations of chlortetracycline (CTC) were found in only SM. These differences reflect specific adherence adsorption of the pharmaceutical products to different livestock and humans. Moreover, it was found that the concentrations of pharmaceutical products and fermentation levels of ROMs had significant positive correlation (r = 0.41, p = 0.024).When the fermentation test of ROM was conducted in a rotary fermentor in a lab scale test, the residue levels of pharmaceutical products decreased effectively except carbamazepine (CBZ). The rates of decrease were in the case of tetracyclines (TCs): 85-92%, FQs: 81-100%, erythromycine: 67%, SAs: 79-95%, trimethoprim: 86% and CBZ: 37% by 30 d. Pharmaceutical products that can be decomposed by fermentation process at the lowest impact of residual antibiotic activities may therefore be considered as environmentally friendly medicines.     

Ontogenetic shift in foraging habit of ocean sunfish Mola mola from dietary and behavioral studies

The ocean sunfish (Mola mola) is typically considered to feed on gelatinous zooplankton, but reports in the literature describe various benthic organisms being found in their stomachs. This might reflect ontogenetic dietary shift, as little was known about the foraging habit of this species. We examined their foraging habits using dietary analyses in combination with a behavioral study in Iwate, Japan (39°22′N, 141°58′E) from 2009 to 2010. Our stomach content analyses (n = 17, 31–250 cm total length) suggested that small sunfish (<50 cm) feed on benthic crustaceans, but large sunfish (>200 cm) feed on jellyfish. Larger sunfish showed higher values of both carbon and nitrogen stable isotope ratios. Deployment of accelerometers and animal-borne cameras on small sunfish in July (49–58 cm, n = 5) suggested their possibility of feeding, while they stayed near the seabed. This indicates that small sunfish might feed on benthic preys. Deployment of accelero-magnetometers on large sunfish in July (84–164 cm, n = 4) clarified that the large sunfish in July swam back and forth between the surface and deep water (>100 m). Temporary decelerations, which were considered to be associated with feeding of planktonic prey, were observed in deep water. Whereas deployment of accelero-magnetometers on large sunfish in November (105 cm, n = 3) showed several bursts, they swam within the mixed layer (0–100 m), which might be associated with chasing of rapid prey. These results suggest that ocean sunfish have heterogeneous diets depending on their body size and possibly season.     

Investigation of the hemolytic effects of various organophosphoric acid triesters (OPEs) and their structure‐activity relationship

The hemolytic effects of various organophosphonc acid triesters (OPEs) were investigated and they showed strong hemolyic toxicity except triethyl phosphate and tris(chloroethyl)phosphate. 2‐Ethylhexyl diphenyl phosphate (EHDP) showed the strongest toxicity. By quantitative structure‐activity relationship (QSAR) study, one‐parameter regression equation to estimate hemolysis was not obtained. But, two‐parameter regression equations were obtained which were enought to estimate EC₅₀ and EC₂₀. The correlation coefficients with the two‐parameter regression equations were 0.939 for log(l/EC₅₀) and 0.946 for log(l/EC₂₀).     

Resource utilization for decorating in three intertidal majid crabs (Brachyura: Majidae)

 For three spider crabs (Tiarinia cornigera, Micippaplatipes and Pugettia quadridens quadridens), patterns of algal utilization for decorating were compared with the dynamics of algae on an intertidal rocky shore reef where the crabs co-occurred. T. cornigera and P. quadridens quadridens were most abundant from autumn to spring when the dominant algae (Boodleacoacta, Sargassum hemiphyllum, S. thunbergii and Corallina pilulifera) occurred in high coverage, while M. platipes was most abundant from spring to autumn. Monthly change of algae used for decorating was not correlated with algae growing in the crab habitat for T. cornigera, but for M. platipes, it was positively correlated for two algal species, and for P. quadridens quadridens, negatively correlated for one algal species. Each species of the spider crabs used some algal species preferentially for decoration. Decorating preference experiments conducted in the laboratory showed that M. platipes and P. quadridens quadridens exhibited similar preference to their algal utilization in the field, whereas for T. cornigera, algal preference in the experiment differed from utilization in the field. Comparisons between materials used for decoration and gut contents revealed that T. cornigera and M. platipes used algal species differently for decorating and feeding, while P. quadridens quadridens used the same algal species for both decorating and feeding. Different tactics for camouflage are discussed in terms of algal utilizations by the three majid species. Received: 25 September 1999 / Accepted: 22 June 2000     

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.     

Prospects for a self-sustainable sewage treatment system: a case study on full-scale UASB system in India's Yamuna River Basin

The government of India decided to launch a project to implement 16 full-scale Upflow Anaerobic Sludge Blanket (UASB) reactors (with a total capacity of 598,000 m(3)/d) in the Yamuna River basin under its Yamuna Action Plan (YAP). A polishing pond called the Final Polishing Unit (FPU) was utilized for post-treatment. This paper evaluates the sewage treatment efficiency of the combined system of full-scale UASB reactors and polishing ponds under Indian climatic conditions. Results have shown that the effluent from the sewage treatment plants (STPs) investigated failed to comply with applicable discharge standards in terms of BOD, SS, and fecal coliform removal. Therefore, it is proposed that such proper operation and maintenance as removing excess sludge and scum be conducted in order to increase treatment efficiency. Moreover, trained and experienced workers are also required to operate and maintain the systems, along with a scientific approach.     

Abiotic reduction of antimony(V) by green rust (Fe(4)(II)Fe(2)(III)(OH)(12)SO(4).3H(2)O)

Green rust (Fe(4)(II)Fe(2)(III)(OH)(12)SO(4).3H(2)O) is an intermediate phase in the formation of iron (oxyhydr)oxides such as goethite, lepidocrocite, and magnetite. It is widely considered that green rust occurs in many soil and sediment systems. Green rust has been shown to reduce sorbed Se(VI), Cr(VI), and U(VI). In addition, it is also reported that green rust does not reduce As(V) to As(III). In this study, we have investigated for the first time the interaction between Sb(V) and green rust using XAFS and HPLC-ICP-MS. Most of the added Sb(V) was adsorbed on green rust, and Sb(III), a reduced form, was observed in both solid and liquid phases. Thus, it was shown that green rust has high affinity for Sb(V), and that Sb(V) was reduced to more toxic Sb(III) by green rust despite the high stability of the Sb(V) species even under reducing condition as reported in previous studies. Therefore, green rust can be one of the most important reducing agents for Sb(V), which can influence the Sb mobility in suboxic environments where green rust is formed.     

Contribution of transboundary air pollution to ionic concentrations in fog in the Kinki Region of Japan

To estimate the contribution of transboundary transported air pollutants from other Asian countries to Japan in ionic concentrations in fog water in March 2005, the Community Multiscale Air Quality (CMAQ) modeling system was utilized with meteorological fields produced by the 5th generation Mesoscale Model (MM5). For meteorological predictions, the model well reproduced the surface meteorological variables, particularly temperature and humidity, and generally captured fog occurrence. For chemical predictions, most of the model-predicted monthly mean concentrations were approximately within a factor of 2 of the observations, indicating that the model well simulated the long-range atmospheric transport from the Asian Continent to Japan. For SO₄^2?, NO₃^? and NH₄⁺, the contribution rates of the transboundary air pollution in the Kinki Region of Japan ranged from 69 to 82% for aerosols, from 47 to 87% for ionic concentrations in rain, and from 55 to 79% for ionic concentrations in fog. The study found that the transboundary air pollution also affected ionic concentrations in fog as well as aerosol concentrations and ionic concentrations in rain.