More than 400 syndromes associated with hearing loss and other symptoms have been described, corresponding to 30% of cases of hereditary hearing loss. In this study we aimed to clarify the mutation spectrum of syndromic hearing loss patients in Japan by using next-generation sequencing analysis with a multiple syndromic targeted resequencing panel (36 target genes). We analyzed single nucleotide variants, small insertions, deletions and copy number variations in the target genes. We enrolled 140 patients with any of 14 syndromes (BOR syndrome, Waardenburg syndrome, osteogenesis imperfecta, spondyloepiphyseal dysplasia congenita, Stickler syndrome, CHARGE syndrome, Jervell and Lange-Nielsen syndrome, Pendred syndrome, Klippel-Feil syndrome, Alport syndrome, Norrie disease, Treacher-Collins syndrome, Perrault syndrome and auditory neuropathy with optic atrophy) and identified the causative variants in 56% of the patients. This analysis could identify the causative variants in syndromic hearing loss patients in a short time with a high diagnostic rate. In addition, it was useful for the analysis of the cases who only partially fulfilled the diagnostic criteria.

Aggregation of volcanic ash is known to significantly impact sedimentation from volcanic plumes. The study of particle aggregates during tephra fallout is crucial to increase our understanding of both ash aggregation and sedimentation. In this work, we describe key features of ash aggregates and ash sedimentation associated with eleven Vulcanian explosions at Sakurajima Volcano (Japan) based on state-of-the-art sampling techniques. We identified five types of aggregates of both Particle Cluster (PC) and Accretionary Pellet (AP) categories. In particular, we found that PCs and the first and third type of APs can coexist within the same eruption in rainy conditions. We also found that the aerodynamic properties of aggregates (e.g., terminal velocity and density) depend on their type. In addition, grainsize analysis revealed that characteristics of the grainsize distributions (GSDs) of tephra samples correlate with the typology of the aggregates identified. In fact, bimodal GSDs correlate with the presence of cored clusters (PC3) and liquid pellets (AP3), while unimodal GSDs correlate either with the occurrence of ash clusters (PC1) or with the large particles (coarse ash) coated by fine ash (PC2).

Little is known of how fungal distribution ranges vary with elevation. We studied fungal diversity and community composition from 740 to 2940 m above sea level on Mt. Norikura, Japan, sequencing the ITS2 region. There was a clear trend, repeated across each of the fungal phyla (Basidiomycota, Ascomycota, Zygomycota, Chytridomycota and Glomeromycota), and across the whole fungal community combined, towards an increased elevational range of higher elevation OTUs, conforming to the elevational Rapoport pattern. It appears that fungi from higher elevation environments are more generalized ecologically, at least in terms of climate-related gradients. These findings add to the picture from latitudinal studies of fungal ranges, which also suggest that the classic Rapoport Rule (broader ranges at higher latitudes) applies on a geographical scale. However, there was no mid-elevation maximum in diversity in any of the phyla studied, and different diversity trends for the different phyla, when different diversity indices were used. In terms of functional guilds, on Norikura there were trends towards increased saprotrophism (Zygomycota), symbiotrophism (Basidiomycota), symbiotrophism and saprotrophism (Ascomycota) and pathotrophism (Chytridiomycota) with elevation. The causes of each of these trends require further investigation from an ecological and evolutionary viewpoint.

The spread of SARS-CoV-2 led to rapid vaccine development. However, there remains considerable vaccine hesitancy in some countries. We investigate vaccine willingness in three nations with very different vaccine histories: Israel, Japan and Hungary. Employing an ecological-systems approach we analyse associations between health status, individual cognitions, norms, trust in government, COVID-19 myths and willingness to be vaccinated, with data from three nationally representative samples (Israel, Jan. 2021, N = 1011; Japan, Feb. 2021, N = 997; Hungary, April 2021, N = 1130). Vaccine willingness was higher in Israel (74%) than Japan (51%) or Hungary (31%). In all three countries vaccine willingness was greatest amongst who would regret not being vaccinated and respondents who trusted their government. Multi-group latent class analysis identified three groups of COVID myths, with particular concern about alteration of DNA (Israel), allergies (Hungary) and infection from the vaccine (Japan). Intervention campaigns should address such cultural myths while emphasising both individual and social benefits of vaccination.

Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.

The Ryukyu Islands of Japan are a biodiversity hotspot due to geographical and historical factors. Tricyrtis formosana is a perennial herbaceous plant that commonly found in Taiwan. But only a few populations have been identified in a limited habitat on Iriomote Island, while populations of unknown origin occur near human settlements in an area on the main island of Okinawa. To better understand these populations of the phylogenetic uniqueness and intrinsic vulnerability, we conducted comparative analyses including (1) phylogeny and population structure with MIG-seq data, (2) photosynthesis-related traits of plants grown under common conditions and (3) transcriptome analysis to detect deleterious variations. Results revealed that T. formosana was split into two clades by the congeners and that Iriomote and Okinawa populations independently derived from ancestral Taiwanese populations in each clade. Photosynthetic efficiency was lowest in the Iriomote population, followed by Okinawa and Taiwan. Transcriptome analysis showed that the Iriomote population accumulated more deleterious variations, suggesting intrinsic vulnerability. These results indicate that each T. formosana population in Japan is phylogenetically unique and has been independently dispersed from Taiwan, and that the Iriomote population presents a high conservation difficulty with a unique photosynthesis-related characteristic and a larger amount of deleterious variations.

Mammalian orthoreovirus (MRV), a non-enveloped virus with a ten-segmented double-stranded RNA genome, infects virtually all mammals, including humans. Human infection with MRV seems to be common in early childhood, but is rarely symptomatic. Despite the ubiquitous presence of MRV in mammals as well as in environmental waters, the molecular characterisation of the MRV genome remains to be fully elucidated. In this study, two novel strains, MRV-2 THK0325 and MRV-1 THK0617, were unintentionally isolated from wastewater in Japan via an environmental surveillance of enteric viruses. Homology and phylogenetic analysis demonstrated that all the segments of THK0325 were closely related to the MRV-2 Osaka strains, which were recently proposed to have existed for at least two decades in Japan. Most of the segments in THK0617 also showed a close relationship with the MRV-2 Osaka strains, but the M2, S1, and S3 segments belong to another MRV cluster. According to the S1 sequence, the determinant of serotype THK0617 was classified as MRV-1, and both the M2 and S3 segments were closely related to MRV-1 and -3 from the tree shrew in China. These results suggest that the MRV-2 Osaka-like strain spread widely throughout Japan, accompanied by intertypic reassortment occurring in East Asia.

Coronavirus disease 2019 (COVID-19) has spread throughout the world. The prediction of the number of cases has become essential to governments' ability to define policies and take countermeasures in advance. The numbers of cases have been estimated using compartment models of infectious diseases such as the susceptible-infected-removed (SIR) model and its derived models. However, the required use of hypothetical future values for parameters, such as the effective reproduction number or infection rate, increases the uncertainty of the prediction results. Here, we describe our model for forecasting future COVID-19 cases based on observed data by considering the time delay (tdelay). We used machine learning to estimate the future infection rate based on real-time mobility, temperature, and relative humidity. We then used this calculation with the susceptible-exposed-infectious-removed (SEIR) model to forecast future cases with less uncertainty. The results suggest that changes in mobility affect observed infection rates with 5-10 days of time delay. This window should be accounted for in the decision-making phase especially during periods with predicted infection surges. Our prediction model helps governments and medical institutions to take targeted early countermeasures at critical decision points regarding mobility to avoid significant levels of infection rise.

In Lake Shinji, Japan, periodic outbreaks of musty odour have occurred since mid-May 2007. Although the substance responsible for the odour was identified as geosmin, the odour-producing organism was unknown. We cultivated an axenic unialgal strain and determined that a species of Coelosphaerium (Synechococcales) was responsible for the production of geosmin in Lake Shinji. Our analysis was conducted using gas chromatography/mass spectrometry to determine the odorous compound. To determine the algae species, it was observed by optical microscopy to describe its morphological characteristics and the polymerase chain reaction was used to characterise the nucleotide sequence of the 16S rRNA gene and the 16S-23S rRNA internal transcribed spacer region. In addition, we explored the relationship between the number of cells of the Coelosphaerium sp. and the concentration of geosmin. In conclusion, geosmin, the cause of the musty odour in Lake Shinji in autumn 2009, was produced by Coelosphaerium sp., and to our knowledge, this is the first report of a geosmin-producing species in the family Coelosphaeriaceae.

Intruding magma brings high temperatures close to the surface, thus offering possibilities for harnessing large amounts of heat for geothermal exploitation. Mount Aso in southern Japan showed frequent volcanic activity during 2016, accompanied by significant earthquake activities with tens of thousands of aftershocks (Kumamoto sequence). Here we investigate the influence of earthquake/volcanic activity on the future productivity of nearby geothermal power plants to determine whether the activity is detrimental or beneficial to energy exploitation. Model results show an increase in [Formula: see text] pressure and temperature with a spatio-temporal correlation between modeled earthquake locations and aftershock decay rates along the entire sequence, showing that seismic activity opened pre-existing vertical cracks providing pathways for the ascending magma. Interestingly, the minor but still significant eruption of Mount Aso in October 2021 may have enhanced future geothermal power generation, indicating a vigorous and active system, possibly increasing the future geothermal power production.

It is not known whether clustered or aligned volcanic edifices at the Earth surface have connected magmatic systems at depth. Previously suggested by geological records of paired eruptions, volcano interconnectivity still lacks proper geodetic evidence. Here we use GPS time-series and deformation modeling to show how Aira caldera and Kirishima, two adjacent volcanic centers in Kagoshima graben (southern Japan), interacted during Kirishima unrest in 2011. Whereas Aira caldera had been inflating steadily for two decades, it deflated during the eruption of Kirishima which started with a large-volume lava extrusion. This deflation, which cannot be explained by stress changes, is interpreted as the result of magma withdrawal from the Aira system during the Kirishima replenishment phase. This study highlights the behavior of connected neighboring volcanic systems before and after a large eruption, and the importance of taking into account volcano interactions in eruption probability models.

Seasonal influenza virus routinely causes epidemic infections throughout the world. Sporadic infections by H5N1, H5N6, and H7N9 viruses are also reported. To treat patients suffering from such viral infections, broadly reactive and highly sensitive influenza rapid diagnostic tests (IRDTs) are required. Here, we examined the reactivity and sensitivity of 25 IRDTs available in Japan for the detection of seasonal H1N1pdm09, H3N2, and type B viruses, as well as highly pathogenic H5 and H7 viruses. All of the IRDTs tested detected the seasonal viruses and H5 and H7 viruses albeit with different sensitivities. Several IRDTs detected the H5 and H7 viruses and the seasonal viruses with similar (high) sensitivity.

In small-breed dogs, myxomatous mitral valve disease (MMVD) is a common disease which may lead to chronic heart failure. Mitral valve repair is an optimal surgical treatment that is currently available in limited veterinary facilities globally because it requires a special surgery team and specific devices. Therefore, some dogs must travel overseas to undergo this surgery. However, a question arises regarding the safety of dogs when traveling by air with a heart disease. We aimed to evaluate the effect of flight journey on dogs with mitral valve disease, including survival rates, symptoms during the trip, laboratory test results, and operational outcomes. All dogs stayed near the owner in the cabin during the flight. The survival rate after the flight was 97.5% in 80 dogs. The surgical survival rates (96.0% and 94.3%) and hospitalization periods (7 days and 7 days) were similar between overseas and domestic dogs. This report shows that taking air flights in the cabin may not have a significant effect on dogs with MMVD, on the premise that their overall conditions are stable under cardiac medication.

Geochemical monitoring of groundwater in seismically-active regions has been carried out since 1970s. Precursors were well documented, but often criticized for anecdotal or fragmentary signals, and for lacking a clear physico-chemical explanation for these anomalies. Here we report - as potential seismic precursor - oxygen isotopic ratio anomalies of +0.24‰ relative to the local background measured in groundwater, a few months before the Tottori earthquake (M 6.6) in Southwest Japan. Samples were deep groundwater located 5 km west of the epicenter, packed in bottles and distributed as drinking water between September 2015 and July 2017, a time frame which covers the pre- and post-event. Small but substantial increase of 0.07‰ was observed soon after the earthquake. Laboratory crushing experiments of aquifer rock aimed to simulating rock deformation under strain and tensile stresses were carried out. Measured helium degassing from the rock and 18O-shift suggest that the co-seismic oxygen anomalies are directly related to volumetric strain changes. The findings provide a plausible physico-chemical basis to explain geochemical anomalies in water and may be useful in future earthquake prediction research.

The east Japan earthquake that occurred on March 11, 2011 was a big natural disaster, comprising the large earthquake shock, tsunami, and Fukushima Daiichi Nuclear Power Plant (FDNPP) accident. These disasters caused changes in the land use and land cover (LULC) in Japan's Tohoku district. While the LULC map created before the disaster is available, as yet there is no precise LULC map of the district after the disaster. In this study, we created a precise LULC map for the years 2013-2015 post-disaster with 30-m spatial resolution using the Landsat-8 with the Operational Land Imager (OLI) to evaluate the changes in LULC induced by the disaster. Our results indicate many changes in areas categorized as rice paddies primarily into grass categories along the coast damaged by the tsunami and in the evacuation zone around the FDNPP. Since there is a possibility of future LULC changes according to the change of the evacuation zone and implementation of reconstruction and revitalization efforts, we recommend continual monitoring of the changes in LULC by the use of satellite data in order to evaluate the long-term effects of the disaster.

The aims of the present study were to profile the antimicrobial susceptibility patterns of a diverse range of Nocardia species isolated in Japan, and to determine the ability of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for species/complex identification. Identification of 153 clinical isolates was performed by full-length 16S rRNA gene sequencing as a reference method to evaluate the usefulness of MALDI-TOF MS identification. Antimicrobial susceptibility testing (AST) for 14 antibiotics was performed using the broth microdilution method against 146 of the isolates. Among the total 153 clinical isolates, Nocardia farcinica complex (25%) was the most common species, followed by Nocardia cyriacigeorgica (18%), Nocardia brasiliensis (9%), Nocardia nova (8%), and Nocardia otitidiscaviarum (7%). Among 150 isolates identified to the species/complex level by 16S rRNA gene sequencing, MALDI-TOF MS with the use of a supplemental Nocardia library (JMLD library ver.ML01) correctly identified 97.3% (n = 146) to the species/complex level and 1.3% (n = 2) to the genus level. Among the 146 Nocardia isolates that underwent AST, the susceptibilities were 100% to linezolid, 96% to amikacin, 94% to trimethoprim-sulfamethoxazole, and 76% to imipenem. None of the trimethoprim-sulfamethoxazole-resistant isolates carried either plasmid-mediated sulfonamide-resistant genes (sul1, sul2) or trimethoprim-resistant genes (dfrA).

We encountered 34 Clostridioides difficile (C. difficile) infection (CDI) cases among Thoroughbred horses in Japan from 2010 to 2021. Among them, 79.4% (27/34) either died or were euthanised. The risk factors associated with CDI and mortality among Japanese Thoroughbred horses remain unclear. We used genetic methods to examine C. difficile strains and their relationships with prognosis. Twenty-two (64.7%) cases were hospitalised at the onset of colitis. Outcomes were balanced for hospitalisation rates at the onset of colitis. The mortality rates of cases treated with metronidazole (65.0%) were significantly lower than untreated cases (100%). The predominant genotype of C. difficile isolate was polymerase chain reaction ribotype (RT) 078, isolated from 12 cases (35.3%), followed by RT014 (six cases, 17.6%). Binary toxin (C. difficile transferase [CDT])-positive strains, including all RT078 strains, were isolated from 16 horses. Mortality rates in RT078 strain (75.0%) or CDT-positive strain (83.3%) cases were comparable to that in cases of other types. Sufficient infection control is needed to prevent CDI in Thoroughbred horses. A timely and prompt CDI diagnosis leading to metronidazole treatment would improve CDI outcomes.

Over the past 15 years, massive gas hydrate deposits have been studied extensively in Joetsu Basin, Japan Sea, where they are associated primarily with active gas chimney structures. Our research documents the discovery of spheroidal microdolomite aggregates found in association with other impurities inside of these massive gas hydrates. The microdolomites are often conjoined and show dark internal cores occasionally hosting saline fluid inclusions. Bacteroidetes sp. are concentrated on the inner rims of microdolomite grains, where they degrade complex petroleum-macromolecules present as an impurity within yellow methane hydrate. These oils show increasing biodegradation with depth which is consistent with the microbial activity of Bacteroidetes. Further investigation of these microdolomites and their contents can potentially yield insight into the dynamics and microbial ecology of other hydrate localities. If microdolomites are indeed found to be ubiquitous in both present and fossil hydrate settings, the materials preserved within may provide valuable insights into an unusual microhabitat which could have once fostered ancient life.

It is the conventional understanding that rain removes aerosols from the atmosphere. However, the question of whether rain plays a role in releasing aerosols to the atmosphere has recently been posed by several researchers. In the present study, we show additional evidence for rain-induced aerosol emissions in a forest environment: the occurrence of radiocaesium-bearing aerosols in a Japanese forest due to rain. We carried out general radioactive aerosol observations in a typical mountainous village area within the exclusion zone in Fukushima Prefecture to determine the impacts and major drivers of the resuspension of radiocaesium originating from the nuclear accident in March 2011. We also conducted sampling according to the weather (with and without rain conditions) in a forest to clarify the sources of atmospheric radiocaesium in the polluted forest. We found that rain induces an increase in radiocaesium in the air in forests. With further investigations, we confirmed that the fungal spore sources of resuspended radiocaesium seemed to differ between rainy weather and nonrainy weather. Larger fungal particles (possibly macroconidia) are emitted during rainy conditions than during nonrainy weather, suggesting that splash generation by rain droplets is the major mechanism of the suspension of radiocaesium-bearing mould-like fungi. The present findings indicate that radiocaesium could be used as a tracer in such research fields as forest ecology, meteorology, climatology, public health and agriculture, in which fungal spores have significance.

Dual subduction represents an unusual case of subduction where one oceanic plate subducts on top of another, creating a highly complex tectonic setting. Because of the complex interaction between the two subducted plates, the origin of seismicity in such region is still not fully understood. Here we investigate the thermal structure of dual subduction beneath Kanto, central Japan formed as a consequence of a unique case of triple trench junction. Using high-resolution three-dimensional thermo-mechanical models tailored for the specific dual subduction settings beneath Kanto, we show that, compared with single-plate subduction systems, subduction of double slabs produces a strong variation of mantle flow, thermal and fluid release pattern that strongly controls the regional seismicity distribution. Here the deepening of seismicity in the Pacific slab located under the Philippine Sea slab is explained by delaying at greater depths (~150 km depth) of the eclogitization front in this region. On the other hand, the shallower seismicity observed in the Philippine Sea slab is related to a young and warm plate subduction and probably to the presence of a hot mantle flow traveling underneath the slab and then moving upward on top of the slab.