Ibaraki Prefecture Research Articles

Advanced mosasaurs from the Upper Cretaceous Nakaminato Group in Japan

AbstractPlotosaurus is a highly aquatically adapted mosasaur, which is supposed to inhabit the deep ocean basin. The geographic occurrence of this genus has been limited only to the west coast of North America. In this study, two Plotosaurus‐type mosasaur caudal vertebrae derived from the Upper Cretaceous Nakaminato Group in Ibaraki Prefecture, Japan, are described with discussion on the paleobiogeographic significance of the Late Cretaceous mosasaur fauna in the Northwestern Pacific region. The two specimens are an intermediate caudal vertebra found in a beach cobble, which presumably originated from the Hiraiso Formation (upper Campanian), and a terminal caudal vertebra found in situ in the lower Isoai Formation (lower Maastrichtian). Because their relative centrum lengths (ratio of centrum length/centrum height, ~0.7) are very close to that of Plotosaurus, the specimens are referred to cf. Plotosaurus sp. The two specimens provide the first evidence that highly specialized Plotosaurus‐type mosasaurs inhabited the Northwestern Pacific Ocean, suggesting that such forms had a wider distribution than previously recognized and might have existed since the late Campanian in the Northwestern Pacific Ocean.

Current State of Seedling Production for Forestry and Challenges toward Steady Supply in Ibaraki Prefecture

Current State of Seedling Production for Forestry and Challenges toward Steady Supply in Ibaraki Prefecture

Analysis of Factors of Facilitating Early Evacuation from Disaster Sites Based on Geographical Conditions: A Case Study of a Flood by Typhoon Hagibis in Mito, Ibaraki Prefecture in 2019

Analysis of Factors of Facilitating Early Evacuation from Disaster Sites Based on Geographical Conditions: A Case Study of a Flood by Typhoon Hagibis in Mito, Ibaraki Prefecture in 2019

Effect of Electric-pole Removal Projects with Trade-off between Electric-pole's Number and Trip Distance

Japan is a disaster-prone country with electric-poles distributed along most roads. The natural disasters such as typhoons, tornados and earthquakes may make electric-poles collapsed and thus closing the roads. Although electric-pole removal projects have been promoted on emergency transportation roads, route selection avoiding poles is required for secure of transportation when disaster happens. In this study, we characterize the location of electric-poles in Ibaraki prefecture of Japan by using regression models, and derived the Pareto-optimal route in geographical space. Besides, we evaluated the effect of electric-pole removal projects in emergency transportation roads with electric-pole position data in Ibaraki. Finally, we studied the basic features of the trade-off curves generated with shortest distance route and minimum existing poles route with a simple model of radial ring city.

Students\u2019 understanding of social determinants of health in a community-based curriculum: a general inductive approach for qualitative data analysis

BackgroundA community-based medical education (CBME) curriculum may provide opportunities to learn about the social determinants of health (SDH) by encouraging reflection on context, but the categories that students can learn about and their level of reflection are unclear. We aimed to analyze medical students’ understanding and level of reflection about SDH in a CBME curriculum.MethodsStudy design: General inductive approach for qualitative data analysis.Education Program: All 5th-year and 6th-year medical students at the University of Tsukuba School of Medicine in Japan who completed a mandatory 4-week clinical clerkship in general medicine and primary care during October 2018 and May 2019 were included. The curriculum included 3 weeks of rotations in community clinics and hospitals in suburban and rural areas of Ibaraki Prefecture. On the first day, students learned about SDH through a lecture and a group activity. As an SDH assignment, they were instructed to prepare a structural case description using the Solid Facts framework based on encounters during the curriculum. On the final day, they submitted the structural reflection report.Analysis: Content analysis was based on the Solid Facts framework. Levels of reflection were categorized as reflective, analytical, or descriptive.ResultsWe analyzed 113 SDH case descriptions and 118 reports. On the SDH assignments, the students frequently reported on social support (85%), stress (75%), and food (58%), but less frequently on early life (15%), unemployment (14%), and social gradient (6%). Of the 118 reports, 2 were reflective, 9 were analytical, and 36 were descriptive. The others were not evaluable.ConclusionsThe CBME curriculum enabled medical students to understand the factors of SDH to some extent. Further work is needed to deepen their levels of reflection.

Supercritical water pretreatment method for analysis of strontium and uranium in soil (Andosols)

Hydrothermal pretreatment of soils (Andosols) from Ibaraki prefecture (Japan) was used to improve methods for monitoring radioactive Sr and U. Calcined samples were pretreated with subcritical or supercritical water (SCW) followed by extraction with 0.5 M HNO3 solutions. With SCW pretreatment, recoveries of Sr and U were 70% and 40%, respectively. Experimental recoveries obtained can be described by a linear relationship in water density. The proposed method is robust and can lower environmental burden of routine analytical protocols.

<p><strong><em>Gymnosporangium raphiolepidis</em></strong><strong> <em>comb. nov. </em>(Pucciniales) for <em>Aecidium</em> <em>raphiolepidis</em> inferred from phylogenetic evidence</strong></p>

Rhaphiolepis indica (L.) Lindl. var. umbellata (Thunb.) H. Ohashi is a rosaceous shrub distributed mainly on the seashore of warm-temperate, subtropical to tropical areas of Japan, Korea, China, Philippines, and Borneo (Nakanishi 2018). This plant has been used for greenings of parks, gardens and streets in Japan. The occurrence of an aecial stage of a rust fungus on its shoots and leaves was observed near seashore of Chiba and Ibaraki Prefectures and Bonin (Ogasawara) Islands, Japan in early summer of 2017, 2019 and 2020 (Figs. 1A, B). Morphological observations were made for the identification of this rust fungus with light microscopy by the same method reported by Kasuya & Ono (2018). Spermogonia were not found on specimens. Aecia surrounded with peridia (Figs. 1C, D) were hypophyllous, often gregarious on hypertrophied lesion along veins, rounded or elliptical, cupulate, and 100–300 μm in diam. Their margins were revoluted, lacinate, and white. Peridial cells (Fig. 1E) were firmly conjunct, 20–25 × 15–20 μm in size, outer walls were striate, and 4–7 μm thick, inner walls were verrucose, and 2–3 μm thick. Aeciospores (Fig. 1F) were angularly globose, subglobose to ellipsoid, and 15–22 × 14–20 μm (av. 19 × 17 µm; n = 30) in size. Their walls were almost hyaline, finely verrucose with big granules (appendages or pore plugs), and 1–2 μm thick. The above morphological characteristics were almost identical with descriptions of Aecidium raphiolepidis Sydow (1922: 61) by Ito (1950), Sato (1975) and Hiratsuka et al. (1992) although the size of peridial cells was a little smaller than that of their descriptions. Therefore, the rust fungus on R. indica var. umbellata was identified as A. raphiolepidis. Specimens used in this observation were deposited in the Fungal Herbarium of the Department of Botany, National Museum of Nature and Science, Tsukuba, Japan (TNS).

Neogene Taga and Hitachi groups in the Kitaibaraki-Takahagi area, Ibaraki Prefecture, Japan: sedimentary complexes of shelf to slope deposits, submarine channel fills and submarine slide scar fills, reconstructed from lithostratigraphy and diatom biostratigraphy

Neogene Taga and Hitachi groups in the Kitaibaraki-Takahagi area, Ibaraki Prefecture, Japan: sedimentary complexes of shelf to slope deposits, submarine channel fills and submarine slide scar fills, reconstructed from lithostratigraphy and diatom biostratigraphy

A Knowledge-Sharing Activity on the Environmental Radiation Monitoring Results Affected by the Fukushima-Daiichi Nuclear Power Plant Accident at Tokai-Oarai Area in Ibaraki Prefecture

A Knowledge-Sharing Activity on the Environmental Radiation Monitoring Results Affected by the Fukushima-Daiichi Nuclear Power Plant Accident at Tokai-Oarai Area in Ibaraki Prefecture

Long-Term Exposure to Particulate Matter and Mortality from Cardiovascular Diseases in Japan: The Ibaraki Prefectural Health Study (IPHS).

Aim: To examine the association between long-term exposure to suspended particulate matter (SPM) and cardiovascular mortality in Japan after controlling for known major confounding factors among a large middle and elderly cohort study in Ibaraki Prefecture, Japan.Methods: We followed 91,808 residents (men 34%) who undertook a national health check-up at age 40–79 years for 17 years (1993–2010). Two different exposure indices were adopted: baseline SPM concentration (in the year 1990) and average SPM concentration for the first (average of 1990 and 1995) and the second half (average of 2005 to 2009) of the study period. Sex-specific adjusted risk ratios (RRs) for cardiovascular mortality were calculated using general mixed Poisson regression models after adjusting the age, BMI, history of diabetes mellitus and hypertension, creatinine, glutamic pyruvic transaminase, total cholesterol, high-density lipoprotein cholesterol, smoking, alcohol, and temperature. The variation between seven medical administration areas was also taken into account as a random effect.Results: Baseline SPM concentration was associated with an increased risk of mortality from all cardiovascular diseases, coronary artery disease, and stroke. The adjusted RRs (95% confidence interval [CI]) per 10 µg/m3 increase in SPM concentration for all cardiovascular mortality were 1.147 (1.014–1.300) for men and 1.097 (0.985–1.222) for women. The point estimate of RR was highest for non-hemorrhagic stroke in men (1.248 [0.991–1.571]), although CI overlapped the unity. The RRs seemed slightly lower in the second half than in the first half, though the CIs widened in the second half.Conclusion: Our results suggest that long-term exposure to SPM is associated with an increased risk of all cardiovascular mortality for men in Ibaraki, Japan.

Resistance to succinate dehydrogenase inhibitors in field isolates of Podosphaera xanthii on cucumber: Monitoring, cross-resistance patterns and molecular characterization

New succinate dehydrogenase inhibitor fungicides (SDHIs), isopyrazam, pyraziflumid and isofetamid were introduced in the Japanese market in 2017–2018 to control powdery mildew on cucumber. SDHI resistance of the disease fungus (Podosphaera xanthii) was first reported during 2008–2009 against boscalid. Then, penthiopyrad which belongs to SDHIs was introduced in 2010, but subsequent monitoring study was not performed. We investigated the sensitivity of P. xanthii field isolates from Ibaraki Prefecture, Japan, to SDHIs and SdhB, SdhC and SdhD gene mutations, using a leaf disc assay and SDH gene analysis. A total of 19 out of the 22 selected isolates showed resistance to SDHIs. The 19 isolates were phenotypically categorized into three types: Resistant I as moderately and Resistant II as highly resistant to penthiopyrad, isopyrazam and pyraziflumid but sensitive to isofetamid and Resistant III as highly resistant to isofetamid but sensitive to the other three SDHIs. SDH gene analysis revealed that Resistant I and III isolates carried a substitution in PxD-S121P and PxC-A86V, respectively. Resistant II carried three different substitutions: PxC-G151R, PxC-G172D, and PxD-H137R. Among 127 isolates sampled from 16 cucumber greenhouses, 54 exhibited Resistant I phenotype and carried only PxD-S121P. Fifty-six isolates exhibited Resistant II and carried PxC-G151R (four isolates), PxC-G172D (24), and PxD-H137R (28). Only two isolates expressed the Resistant III phenotype carrying PxC-A86V. To the best of our knowledge, this is the first report demonstrating cross-resistance patterns and the molecular characterization of SDHIs in P. xanthii.

Inbreeding between Deep-Sea Snailfishes Careproctus pellucidus and Careproctus rastrinus in the Northwestern Pacific Ocean.

Genetic deviation between two deep-sea snailfishes, Careproctus pellucidus from the Pacific Ocean and Careproctus rastrinus from the Okhotsk Sea, of the Careproctus rastrinus species complex was analyzed, based on the nucleotide sequences of the mitochondrial cytochrome b (Cytb) gene. Our sampling revealed the occurrence of individuals with C. rastrinus-type Cytb genes off northeastern Japan, in the northwestern Pacific. Most of these individuals were collected from an area off Miyagi Prefecture, while few individuals were collected from areas to its north (off Iwate Prefecture) and south (off Fukushima and Ibaraki Prefectures). Phylogeographic analyses based on nucleotide sequences of the first intron region of the nuclear S7 ribosomal protein gene (S7) and 11 microsatellite loci indicated little genetic deviation between individuals with C. pellucidus-type and C. rastrinus-type Cytb genes in the area off Miyagi Prefecture. Significant genetic differences between the Pacific Ocean and the Okhotsk Sea populations may be attributed to unidirectional migration due to a greater current from the latter to the former. In addition, peritoneum and stomach colors of 10 and 17 specimens collected from the Pacific Ocean and the Okhotsk Sea, respectively, were evaluated quantitatively. The colors were significantly different for the two populations; however, they appeared to overlap. Although only one Pacific individual with a C. rastrinus-type Cytb gene was available for color evaluation, it was more similar to Pacific individuals than to Okhotsk Sea individuals. These results suggest inbreeding between C. pellucidus and C. rastrinus in the Pacific Ocean, off Miyagi Prefecture.

Discrimination of nursery locations of juvenile Japanese flounder Paralichthys olivaceus on the Pacific coast of northern Japan based on carbon and nitrogen stable isotope ratios

To test whether stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) can be used to understand the ecological connectivity of Japanese flounder Paralichthys olivaceus, we evaluated the isotopic signatures of juvenile P. olivaceus from the Pacific coast of northern Japan (i.e., from Aomori to Ibaraki Prefectures). We measured δ13C and δ15N in muscle and collagen extracted from vertebrae and found that isotope ratios were strongly correlated in both. The discrimination models we developed for muscle and collagen proved useful in distinguishing among juvenile P. olivaceus collected from the five prefectures (Aomori, Iwate, Miyagi, Fukushima, and Ibaraki). Juveniles collected in Aomori in particular showed significantly lower values of δ13C and δ15N than those from the other prefectures, which likely reflects the greater influence of the Tsugaru Warm Current in that region. Because collagen in the vertebral centrum can be used to reconstruct annual isotopic records, our results may also assist in developing migration tracking procedures for adult P. olivaceus along the Pacific coast of northern Japan.

Risk Factors for Collisions and Near-Miss Incidents Caused by Drowsy Bus Drivers.

Serious accidents have been caused by drowsy bus drivers and have necessitated an examination of the risk factors involved. A questionnaire survey among employees of a bus company was conducted in Ibaraki Prefecture, Japan in September 2014. Respondents were asked to report details of their work and life over the preceding month. The 301 valid responses by bus drivers (295 men and 6 women) with a mean age of 51.6 years (range: 24–73 years) were used for analysis. Univariable logistic regression showed that factors affecting the incidence of collisions and near-miss incidents by drowsy drivers were continued driving when feeling sick, reporting a physical condition, number of sleep hours, time spent with family, working hours, and nutritional balance. According to a multiple regression analysis, continued driving when feeling sick (odds ratio: 3.421, 95% confidence interval: 1.618–7.231) was the only significant risk for the event. Managers should encourage drivers to voluntarily report poor health and should provide opportunities to stop driving if drivers experience physical discomfort or sleepiness. To improve road safety, educational measures are required for both drivers and managers to prevent driving under poor health conditions, although the decision to stop driving depends on drivers’ subjective judgment.

Quantifying the sources and removal of nitrate in riparian and lotic environments based on land use and topographic parameters of the watershed

Abstract In this study, the relationships between the concentration and isotopic compositions (δ15NNO3 and δ18ONO3) of nitrate in river water and the land use and topographic characteristics of the watershed were analyzed for the tributaries of two major inflow rivers (Hokota River and Tomoe River) of Lake Kitaura (Ibaraki Prefecture, Japan). Modelling by the Random Forests machine learning algorithm in combination with statistical analyses (correlation analysis and principal component analysis) revealed that crop farming in dry fields (i.e., application of chemical fertilizers and manure) and swine farming (e.g., addition of swine manure to cropland soils over the basal application rate, leakage of swine manure from the stockyard to groundwater or river) in the watershed are the main drivers for increasing nitrate concentration in the river water of the studied river basins. Based on calculations using the Random Forests models, nitrate derived from swine farming was estimated to account for up to 28% of nitrate in the river water, and its contribution was proportional to the density of farmed swine (log-transformed value). Similarly, the percentage of nitrate removed in the riparian zone and the lotic environment (e.g., bottom sediment, water column and hyporheic zone within the river flow path) was estimated to be up to 34% and was also proportional to the topographic wetness index in the riparian zone (log-transformed value). In addition, significant negative correlations between log-transformed nitrate concentration and δ15NNO3 and δ18ONO3 were recognized in the combined data for all the tributaries as well as the single data for several tributaries, suggesting that biological processes (e.g., denitrification, assimilation) contribute to the removal of nitrate and associated changes in δ15NNO3 and δ18ONO3 of residual nitrate. These findings are applicable for planning measures to control nitrogen load from the watershed and for improving the accuracy in calculating the proportions of nitrate from different sources based on the isotope mixing models.

Transcriptomics of Mature Rice (Oryza Sativa L. Koshihikari) Seed under Hot Conditions by DNA Microarray Analyses

Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. The western and central parts of Japan especially have seen record high temperatures during the past decade, resulting in the decrease of rice kernel quality. In this study, we looked at the rice harvested from a town in the central Kanto-plains (Japan) in 2010. The daytime temperatures were above the critical limits ranging from 34 to 38 °C at the final stages of seed development and maturity allowing us to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial), each with specific quality standards, were obtained from Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki Prefecture in September 2010: grade 1 (top quality, labeled as Y1), grade 2 (medium quality, labeled as Y2), and grade 3 (out-of-grade or low quality, labeled as Y3). The research objective was to examine particular alterations in genome-wide gene expression in grade 2 (Y2) and grade 3 (Y3) seeds compared to grade 1 (Y1). We followed the high-temperature spike using a high-throughput omics-approach DNA microarray (Agilent 4 × 44 K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. As expected, rice seed quality analysis revealed low quality in Y3 > Y2 over Y1 in taste, amylose, protein, and fatty acid degree, but not in water content. Differentially expressed gene (DEG) analysis from the transcriptomic profiling data revealed that there are more than one hundred upregulated (124 and 373) and downregulated (106 and 129) genes in Y2 (grade 2 rice seed) and Y3 (grade 3 rice seed), respectively. Bioinformatic analysis of DEGs selected as highly regulated differentially expressed (HRDE) genes revealed changes in function of genes related to metabolism, defense/stress response, fatty acid biosynthesis, and hormones. This research provides, for the first time, the seed transcriptome profile for the classified low grades (grade 2, and out-of-grade; i.e., grade 3) of rice under high-temperature stress condition.

Making and Maintaining Social Relationships of Foreign Residents through Religious Facilities: Case Study of Filipinos in Southern Part of Ibaraki Prefecture

Making and Maintaining Social Relationships of Foreign Residents through Religious Facilities: Case Study of Filipinos in Southern Part of Ibaraki Prefecture

Public acceptance model for siting a repository of radioactive contaminated waste

The disposal of designated radioactive contaminated waste resulting from the Fukushima nuclear accident is a primary issue in Japan. However, residents often strongly oppose siting a repository of designated waste; therefore, a possible site remains undecided. The NIMBY (Not In My Back Yard) aspect, whereby people refuse to build a repository in their hometown, has led to strong opposition. This study examined a public acceptance model for the siting investigation of a repository of designated waste. The model proposes that the antecedents of the three types of fairness, namely, procedural, distributive, and interpersonal fairness, determine public acceptance in addition to affecting evaluation of designated waste. The study investigated the differences of influences of the three types of fairness between residents in possible siting areas and in a non-siting area to compare the cognitive process toward the NIMBY issue. The respondents included 1016 residents in possible siting areas (Miyagi, Tochigi, Gunma, Ibaraki, and Chiba Prefectures), and 1006 residents in a non-siting area (the Tokyo metropolitan area). All respondents completed a web-based questionnaire. The results revealed that the influence of procedural fairness on public acceptance in the non-siting area was stronger than it was in the possible siting areas. Conversely, the influence of distributive fairness was stronger in the possible siting areas than it was in the non-siting area. Furthermore, affect evaluation through antecedents of fairness was more influential for public acceptance in the possible sites than it was in the non-siting area. Therefore, the findings suggest that the strong opposition due to the NIMBY aspect was caused by the differences between the process of fairness and the concept of fairness that people emphasize.

Research Note: Molecular and pathologic characterization of avian adenovirus isolated from the oviducts of laying hens in eastern Japan

Cases of poor egg production were investigated in 2 layer farms from Ibaraki Prefecture in eastern Japan. To identify any microbial agents that may have caused the problem, necropsy, bacterial isolation, histopathology, and virus detection were performed. Members of the avian adenoviruses was detected by PCR in oviduct samples from both farms; chicken anemia virus coinfection was also confirmed in one of the farms. Avian adenovirus was isolated from the oviducts of the affected chickens on each farm. Inoculation into chick embryos showed tropism for the chorio-allantoic membrane. Stunting and hemorrhaging was observed in all infected embryos, as well as death in a few. Inoculation of 1-day-old specific pathogen-free chicks, and 400-day-old commercial hens, did not result in any significant findings. The isolated viruses were analyzed by sequencing of the hexon gene and were confirmed as fowl adenovirus type-c serotype-4 (FAdV-4). The 2 virus strains were found to be 99.29% similar to each other. One of the strains, Japan/Ibaraki/Y-H6/2016, was 99.15% similar to the KR5 strain. The other, Japan/Ibaraki/M-HB2/2016, was 99.57% similar to the KR5 strain. Fiber-2 gene analysis confirmed the identity as FAdV-4 that is closely related to nonpathogenic strains. Although nonpathogenic to chicks and laying hens, this infection can possibly cause economic damage. Perhaps the bigger concern is the effect on infected breeder operations. Because the virus is fatal to 9.09% of infected embryos, this could translate to a considerable loss in chick production owing to embryonic death. This is the first report of detection and isolation of FAdV-4 from the chicken oviduct; however, further studies are needed to elucidate its impact on both layer and breeder flocks. Indeed, FAdV-4 has negative effects on the avian reproductive tract as well.

<i>Nerocila phaiopleura</i> (Isopoda: Cymothoidae): a new record from Ibaraki Prefecture, central Japan, with a discussion of its distribution in Japanese waters

<i>Nerocila phaiopleura</i> (Isopoda: Cymothoidae): a new record from Ibaraki Prefecture, central Japan, with a discussion of its distribution in Japanese waters