Deep learning-based image-analysis algorithm for classification and quantification of multiple histopathological lesions in rat liver

Artificial intelligence (AI)-based image analysis is increasingly being used for preclinical safety-assessment studies in the pharmaceutical industry. In this paper, we present an AI-based solution for preclinical toxicology studies. We trained a set of algorithms to learn and quantify multiple typical histopathological findings in whole slide images (WSIs) of the livers of young Sprague Dawley rats by using a U-Net-based deep learning network. The trained algorithms were validated using 255 liver WSIs to detect, classify, and quantify seven types of histopathological findings (including vacuolation, bile duct hyperplasia, and single-cell necrosis) in the liver. The algorithms showed consistently good performance in detecting abnormal areas. Approximately 75% of all specimens could be classified as true positive or true negative. In general, findings with clear boundaries with the surrounding normal structures, such as vacuolation and single-cell necrosis, were accurately detected with high statistical scores. The results of quantitative analyses and classification of the diagnosis based on the threshold values between “no findings” and “abnormal findings” correlated well with diagnoses made by professional pathologists. However, the scores for findings ambiguous boundaries, such as hepatocellular hypertrophy, were poor. These results suggest that deep learning-based algorithms can detect, classify, and quantify multiple findings simultaneously on rat liver WSIs. Thus, it can be a useful supportive tool for a histopathological evaluation, especially for primary screening in rat toxicity studies.     

Impact of nitrogen cycling associated with production and consumption of food on nitrogen pollution of stream water

We evaluated the impact of nitrogen (N) cycling on N pollution of stream water, with emphasis on N disposed of (hereafter referred to as “disposal N”) from human and livestock excrement and the N surplus in cropland, compared to the total-N concentration of stream water, in seven zones of Asahikawa City characterized by various types of land use. In order to estimate N cycling, we used the Nitrogen Flow Model, composed of the N budgets of human, livestock, and cropland subsystems. The urban area with a population density of over 4,000 persons km^-2 generated a very large amount of disposal N (about 2,700 kg N ha^-1 cropland y^-1). Based on the amount of disposal N and the volume of domestic sewage water used, the N concentration estimated for the urban area was 34 mg N L^-1, which found in the effluent from the sewage treatment facility (24–28 mg N L^-1), regardless of the season. Thus, it was indicated that most of the disposal N in the urban area was discharged directly to streams through the sewage treatment facilities, contributing to a point source of N pollution of stream water. In addition, the disposal N from livestock facilities was larger in pig and poultry farming areas than in other farming areas, contributing to some extent to a potential source of N pollution. As a result, the concentrations increased above 1 mg N L^-1 in the urban and surrounding areas. On the other hand, the N surplus in cropland was practically determined by the N flows associated with chemical fertilizer, livestock excrement as manure, and crop uptake. The N surplus was similar among the seven zones, ranging from 69 to 99 kg N ha^-1 y^-1. The N concentration estimated from the amount of N surplus and 50% of mean annual precipitation as a discharge rate was 13.6–19.5 mg N L^-1. Most of the surplus N was indicated to be leached out. However, the total-N concentration measured in the major streams flowing through Asahikawa City was mostly below 1 mg N L^-1 except for the urban and surrounding areas. The surplus N in cropland may not reach the streams, even if N leaching occurs, probably due to N removal by plant uptake, denitrification, and sedimentation in the riparian zone and stream channels. Thus the effect of agricultural practices on N pollution of stream water was not appreciable.     

Evaluation of the utilization of heated sewage sludge for peri-urban horticulture production in the Sahel of West Africa

Shortage of organic matter hinders agricultural production in the Sahel, and this lack of enough organic matter is more severe for peri-urban horticulture, which depends heavily on it. Alternative sources of organic matter that offer new options for peri-urban horticulture can help reduce the potential for conflict over finite resources between traditional crop production and peri-urban horticulture. Both agronomic and economic evaluations of an organic amendment called heated sewage sludge (HSS) were conducted in the research station of International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)-Niamey, Niger, West Africa. For this study, HSS, a material imported from Japan, applied at a dosage application equivalent to 20.0 kg 100 m⁻² on lettuce fields led to production levels as high as those of conventional methods, and the yield became even higher than those of conventional methods when the dosage was increased to 50.0 kg 100 m⁻² and 100.0 kg 100 m⁻². Even though HSS was imported, its benefits outweighed its cost, as evidenced by the positive net returns. Since profitability in peri-urban horticulture is much higher than that of traditional crop production, the results of this study imply that if adopted, the use of HSS can lead to increased availability of organic matter for traditional cropping systems.     

Prebiotic effect of glycerol galactoside isolated from color-faded nori in rats

Glycerol galactoside (GG; floridoside: 2-O-glycerol-α-d-galactopyranoside, and isofloridoside: 1-O-glycerol-α-d-galactopyranoside) is known to be a component of edible red seaweed nori. Recently, we have found that low-quality nori (color-faded nori), which has a low protein content, contains a large quantity of GG. From further studies, we have also found that GG has prebiotic characteristics in vitro. In this study, we evaluated the in vivo prebiotic activity of GG in rats. Dietary GG selectively increased the cecal Bifidobacterium count in rats. Other indices of prebiotics, such as pH of cecal content, organic acid concentrations, and fecal weight, also supported the existence of prebiotic activity of GG. The present data will also contribute to the development of a new method of utilizing color-faded nori as a health-promoting foodstuff.     

Molecular epidemiology of avian influenza viruses circulating among healthy poultry flocks in farms in northern Vietnam

Repeated epizootics of highly pathogenic avian influenza (HPAI) virus subtype H5N1 were reported from 2003 to 2005 among poultry in Vietnam. More than 200 million birds were killed to control the spread of the disease. Human cases of H5N1 infection have been sporadically reported in an area where repeated H5N1 outbreaks among birds had occurred. Subtype H5N1 strains are established as endemic among poultry in Vietnam, however, insights into how avian influenza viruses including the H5N1 subtype are maintained in endemic areas is not clear. In order to determine the prevalence of different avian influenza viruses (AIVs), including H5N1 circulating among poultry in northern Vietnam, surveillance was conducted during the years 2006-2009. A subtype H5N1 strain was isolated from an apparently healthy duck reared on a farm in northern Vietnam in 2008 and was identified as an HPAI. Although only one H5N1 virus was isolated, it supports the view that healthy domestic ducks play a pivotal role in maintaining and transmitting H5N1 viruses which cause disease outbreaks in northern Vietnam. In addition, a total of 26 AIVs with low pathogenicity were isolated from poultry and phylogenetic analysis of all the eight gene segments revealed their diverse genetical backgrounds, implying that reassortments have occurred frequently among strains in northern Vietnam. It is, therefore, important to monitor the prevalence of influenza viruses among healthy poultry between epidemics in an area where AIVs are endemic.     

Seroprevalence of Neospora caninum in dairy and beef cattle with reproductive disorders in Japan

Serum samples from 145 dairy and 65 beef cattle with reproductive disorders and 54 normally calving dairy cattle (controls) in Japan were tested for presence of Neospora caninum antibodies by use of an indirect fluorescent antibody test (IFAT, titer 1:200). Overall, seroprevalence of N. caninum was significantly higher (P < 0.001) in dairy cattle (20.0%, 29/145) than in beef cattle (1.5%, 1/65). In cattle which aborted, seroprevalence of N. caninum was significantly higher (P = 0.041) in dairy cattle (26.1%, 23/88, compared with controls (3.7%, 2/54)) than in beef cattle (5.0%, 1/20), indicating that neosporosis might be a more common problem in dairy cattle than in beef cattle in Japan. Seropositive cattle were 9.2 times more likely to abort compared to seronegative cows. Abortions associated with N. caninum seropositivity in this study were most frequently observed in the second trimester, and the mean gestational age of the fetuses aborted from seropositive dams was 5.7 months. In conclusions, N. caninum seems to be causing serious economic losses in the dairy industry in Japan. This is the first report on an objective comparison of seroprevalence of dairy and beef cattle with reproductive disorders in Asia.     

Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses

Metagenomic approach using next-generation DNA sequencing has facilitated the detection of many pathogenic viruses from fecal samples. However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut. Here, to improve efficiency of the detection of double-stranded (ds) RNA viruses from samples, we evaluated the applicability of S1 nuclease on deep sequencing. Treating total RNA with S1 nuclease resulted in 1.5–28.4- and 10.1–208.9-fold increases in sequence reads of group A rotavirus in fecal and viral culture samples, respectively. Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software. These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.     

Sediment accretion and variability of sedimentological characteristics of a tropical estuarine mangrove: Kemaman, Terengganu, Malaysia

This paper reports on a study of accretion rate and sedimentological variability in a estuarine mangrove swamp. One hundred and sixteen stations were monitored for 2 years. In addition, surface sediment samples were collected at 52 stations during the months of May, June and July (1994) to represent the nonmonsoon sediments and November, December (1994) and January (1995) to represent the monsoon sediments. Results show that the accretion rate for the first year was 1.46±0.13cm/yr and 0.66±0.04cm/yr for the second year thus making the average accretion for the 2 years period to be 1.06cm/yr. The average accretion rate for the monsoon season (0.26 ± 0.04cm/month) was found to be significantly higher than the nonmonsoon season (0.12 ± 0.03cm/month). Nevertheless, the same is not true for the surface sediment characteristics. The sedimentological characteristics between the monsoon and the nonmonsoon sediments were not significantly different.