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.     

Screening of agonistic activities against four nuclear receptors in wastewater treatment plants in Japan using a yeast two-hybrid assay

To assess the potential endocrine disruptive effects through multiple nuclear receptors(NRs),especially non-steroidal NRs,in municipal wastewater,we examined the agonistic activities on four NRs(estrogen receptor α,thyroid hormone receptor α,retinoic acid receptor α and retinoid X receptor α) of untreated and treated wastewater from municipal wastewater treatment plants(WWTPs) in Japan using a yeast two-hybrid assay.Investigation of the influent and effluent of seven WWTPs revealed that agonistic activities...     

Measurements of short-lived cosmic-ray-produced radionuclides in rainwater

Cosmic-ray-produced (CP) nuclides with half-lives shorter than 21h were measured in rainwater by ultra-low-background gamma spectrometry at Ogoya Underground Laboratory. As levels of CP nuclides are extremely low and their half-lives are very short, quick sampling methods for a large volume of rainwater and rapid chemical separations by ion exchange method were developed. The nuclides measured were short-lived (24)Na, (28)Mg, (38)S, (38)Cl, (39)Cl, as well as nuclides with longer half-lives (7)Be and (22)Na. The number of atoms of CP nuclides in rainwater were evaluated to range from 30 to 1500L(-1) for (24)Na (n=16, mean; 520 [6.7mBqL(-1)]), 80 to 600L(-1) for (28)Mg (n=13, mean; 260 [2.4mBqL(-1)]), 400 to 1900L(-1) for (39)Cl (n=6, mean; 1200 [250mBqL(-1)]), 1x10(6) to 4x10(7)L(-1) for (7)Be (n=16, mean; 7x10(6) [1.05BqL(-1)]) and 2x10(3) to 1x10(5)L(-1) for (22)Na (n=9, mean; 2x10(4) [0.2mBqL(-1)]).     

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.     

Accelerated degradation of a variety of aromatic compounds by Spirodela polyrrhiza-bacterial associations and contribution of root exudates released from S. polyrrhiza

Removal experiments of phenol,aniline,2,4-dichlorophenol,nonylphenol and bisphenol A(BPA) using Spirodela polyrrhizabacterial associations revealed that all compounds but BPA underwent accelerated removal.The mechanisms differed depending on the substrates.It was found that S.polyrrhiza has a great ability to release phenolic compound-rich root exudates,and the exudates seem to stimulate bacterial degradation of a variety of aromatic compounds.     

Why did the project fail to achieve its objectives in some villages? The experience of the Upland Settlement Project (USP) in Bangladesh

By sampling an upland settlement project (USP) village, this study examined why the project failed to achieve the planned objectives in some villages, and what livelihood strategies villagers (planters) have adopted to sustain their livelihoods. The paper uses data obtained by qualitative and quantitative methods. The USP was formulated with the objectives of settling 50 landless and marginal tribal families in a project village and introducing agroforestry and rubber plantations for short- and long-term socioeconomic development of planters, in a participatory manner. There are now only 15 planters in the project village and, although agroforestry has progressed well, only 30 to 40% of poor quality rubber trees remain. Planter participation in project activities was limited to wage labour, indicating that the USP failed to adequately achieve all its proposed objectives. In the face of project failure, planters have adopted diversified strategies to maintain their livelihoods. Several shortcomings caused failure of the project, such as the inability of project staff members to organize planters, failure to create awareness among planters about project benefits, lack of regular project money disbursement, sociocultural ignorance, and lack of social capital among planters. Recommendations are made for securing effective participation of local people to assure successful and sustainable project outcomes. Lessons learned will be helpful in formulating future development programmes in this country and elsewhere.     

Nematode community composition in hydrothermal vent and adjacent non-vent fields around Myojin Knoll,a seamount on the Izu-Ogasawara Arc in the western North Pacific Ocean

In contrast to specific large benthic invertebrates in chemosynthetic ecosystems such as hydrothermal vents, meiofaunal communities in such habitats have been reported to have strong taxonomic overlap with meiofauna in the adjacent “normal” environments. However, meiofauna have only recently been included in studies of those environments and detailed information on these communities is still rare. This is especially true in the Northwest Pacific Ocean, even though there are many seamounts with active vents in the calderas of the region. Nematode community composition at the genus level in sediments from a hydrothermal vent field in the caldera of Myojin Knoll (32°06′N, 139°52′E, depth 1,300 m), a seamount on the Izu-Ogasawara Arc, Japan, was investigated for the first time and was compared with adjacent non-vent areas inside and outside the caldera. Multivariate analyses showed that the composition of nematodes in the hydrothermal field was significantly different from that in the non-hydrothermal fields around the caldera. However, the common genera, such as Oxystomina, Pareudesmoscolex, Desmoscolex, and Microlaimus were found in two, or all three vent fields while their rank contributions differed among the three fields. When the data from Myojin Knoll were compared with those from other deep-sea vent environments in different regions (e.g., North Fiji Basin, East Pacific Rise, Mid-Atlantic Ridge), the nematode composition in the vent field of the Myojin caldera was more similar to that of the non-vent fields around the caldera than the composition in vent fields of other regions. These data from the Northwest Pacific Ocean also suggest the absence of long-range transport systems and local adaptations for meiofauna in hydrothermal vent fields.     

Chlorine promotes antimony volatilization in municipal waste incineration

Antimony volatilization in municipal waste incineration was studied. Two municipal waste samples and antimony(III) oxide (Sb₄O₆) were heated to 500°C and 700°C in an air stream in a quartz furnace. The volatilization of Sb₄O₆ occurred more at 700°C that at 500°C. Conversely, antimony volatilization form municipal waste was stronger at 500°C than at 700°C. This implies that antimony from municipal waste is volatilized as chloride instead of oxide. The chlorine sources for antimony chlorination, a gas-phase reaction involving hydrochloric acid and a solid-phase reaction of inorganic chlorine, e.g., CaCl₂, were compared. Only the solid-phase reaction could offer enough active chlorine to induce chlorination of antimony oxide. Received: July 2, 1998 / Accepted: January 28, 1999     

Levels and regional trends of persistent organochlorines and polybrominated diphenyl ethers in Asian breast milk demonstrate POPs signatures unique to individual countries

Human breast milk samples collected in 2007–2008 from four countries, Vietnam (Hanoi), China (Beijing), Korea (Seoul) and Japan (Sendai, Kyoto and Takayama), were analyzed for persistent organic pollutants (POPs) such as dichlorodiphenyltrichloroethane and its metabolites (DDTs), chlordane-related compounds (CHLs), hexachlorocyclohexanes (HCHs), hexachlorobenzene (HCB), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). Comparing with previous surveys, the present study indicates that the DDTs in breast milk from China and Vietnam had gradually decreased during the last decade, but were still 5–10 times higher than those in other nations. The ratios of p,p′-DDE/p,p′-DDT and o,p′-DDT/p,p′-DDT were higher in Beijing than in the other countries, suggesting that there is less fresh intake of commercial DDT products and a possible exposure to dicofol in China. CHL and PCB levels were relatively higher in mothers from Japan, whereas β-HCH and HCB were more common in Chinese women. In Japan, it is suspected that mothers in the urban/coastal area (Sendai) were more continuously exposed to organochlorine pesticides (OCPs) than mothers in the rural/inland area (Takayama). In addition, OCP levels in primiparae were significantly higher than those in multiparae from Japan and Korea. These indicate that both parity and regional factors are major determinants of the levels of OCPs and PCBs in human milk. On the other hand, higher concentrations of PBDEs were observed in mothers' milk from Korea. The congener was dominated by BDE-47 (43–54%), followed by BDE-153 (23–33%) in all regions except for Beijing where BDE-28 (23%) was relatively abundant. In Japanese breast milk, regional and parity-dependent distributions were not observed for PBDEs. Among PBDE congeners, age-dependency was observed for BDE-153, which was negatively correlated (p < 0.05) to the age of mothers in Kyoto (17 participants were housewives), while it increased with age in Sendai (10 participants were clerks). No such correlation was seen for BDE-47, indicating that BDE-47 was ingested and assimilated via different kinetics or routes from BDE-153 in Japan.     

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.