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result(s) for
"Nagata, Kenji"
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Probabilistic estimation of model parameters through grid search approaches: applications to geomagnetic anomaly source estimations
by
Nagata, Kenji
,
Tada, Noriko
,
Ichihara, Hiroshi
in
1. Geomagnetism
,
Bayesian estimation
,
Earth and Environmental Science
2025
Model parameters, extracted from observed data that inherently contain uncertainties, necessitate estimation as probability distributions. In geophysical problem-solving, especially when dealing with a few model parameters, the conventional approach employing a grid search is widely used to determine model parameters that explain observed data. However, the metrics of the results derived from the grid search approach are predominantly based on residuals between observed data and the model’s anticipated response, such as the root mean square misfit, which lacks representation as a probability distribution. This study introduces a straightforward technique to transform the distributions of root mean square misfits acquired via grid search into probability distributions, facilitating a statistical evaluation grounded in a Bayesian framework. The outcomes of this methodology are effectively visualized through marginal probability distributions. Employing this method, we investigated synthetic geomagnetic anomaly datasets to evaluate the location and magnitude of magnetic moments of the source. The synthetic tests showed that the method is applicable not only for well-posed problems, but also for ill-posed problems, which are challenging to evaluate solely using root mean square misfits. Subsequently, we applied this methodology to real geomagnetic anomaly data reflecting temporal magnetic fluctuations induced by volcanic activity within the Nishinoshima volcano. The method’s versatility allows its broad application across various geophysical problems, including identification of earthquake epicenters, analysis of gravity anomalies and surface geodetic deformation, and their concurrent analyses. Furthermore, this approach easily utilizes prior grid search outcomes to evaluate the probability of model parameters.
Graphical Abstract
Journal Article
Bayesian active learning with model selection for spectral experiments
2024
Active learning is a common approach to improve the efficiency of spectral experiments. Model selection from the candidates and parameter estimation are often required in the analysis of spectral experiments. Therefore, we proposed an active learning with model selection method using multiple parametric models as learning models. Important points for model selection and its parameter estimation were actively measured using Bayesian posterior distribution. The present study demonstrated the effectiveness of our proposed method for spectral deconvolution and Hamiltonian selection in X-ray photoelectron spectroscopy.
Journal Article
Investigation of the relationship between ocular sarcoidosis and dry eye
2022
A relationship between ocular sarcoidosis (OcSar) and dry eye (DE) has previously been reported. Here we investigated the tear function in OcSar, and the other uveitis, Vogt–Koyanagi–Harada disease (VKH), to elucidate the association between OcSar and DE. This study involved 27 eyes of 27 female OcSar patients [mean age: 67.3 ± 13.5 (SD) years], 18 eyes of 18 female VKH patients (53.1 ± 14.1 years), and 17 eyes of 17 female healthy control subjects (59.7 ± 9.6 years). In all examined eyes, tear meniscus height (TMH, mm), fluorescein breakup time (FBUT, s), scoring of keratoconjunctival epithelial damage (ED), and the Schirmer 1 test (ST1, mm/5 min) were analyzed. In the OcSar patients, VKH patients, and control subjects, the respective TMH, FBUT, ED, and ST1 values (mean ± SD) were 0.26 ± 0.10, 0.24 ± 0.09, and 0.24 ± 0.08, 4.3 ± 2.5, 7.3 ± 2.9, and 6.3 ± 3.1, 1.1 ± 1.1, 0.7 ± 0.8, and 0.1 ± 0.3, and 12.9 ± 10.5, 21.5 ± 12.1, and 24.3 ± 10.5. Statistically, the ST1 values were significantly lower in the OcSar patients than in the VKH patients (
P
= 0.004) and control subjects (
P
= 0.001). ST1 findings revealed that the neural reflex arc and lacrimal gland system, which attenuate the vicious cycle between the tear film and ocular surface epithelium in DE, are significantly impaired in OcSar cases, thus indicating a possible association between OcSar and DE.
Journal Article
Trends in hepatocellular carcinoma incident cases in Japan between 1996 and 2019
2022
We examined the epidemiological trends, including the distribution of sex, age, and disease etiology, in HCC incident cases, over 24 years. Data of 20,547 HCC patients (1996–2019) were analyzed in this prospective study. We divided the study period into four 6-yearly quarters. HCC etiology was categorized as hepatitis B virus (HBV) infection, HBV + hepatitis C virus (HCV) infection, HCV infection, and both negative (non-BC). The incident cases of HCC per quarter of the study period were 4311 (21.0%), 5505 (26.8%), 5776 (28.1%), and 4955 (24.1%), sequentially. Overall, 14,020 (68.2%) patients were male. The number of HCC cases in patients < 60 years, 60–69 years, 70–79 years, and ≥ 80 years were 3711 (18.1%), 6652 (32.4%), 7448 (36.2%), and 2736 (13.3%), respectively. The average age of newly-diagnosed patients increased in each quarter. HCC was associated with HBV, HBV + HCV, and HCV infections and non-BC in 2997 (14.6%), 187 (0.9%), and 12,019 (58.5%), and 5344 (26.0%) cases, respectively. The number of HCV-associated cases decreased in each quarter, while that of non-BC-associated cases increased. HCC incident cases tend to increase in the elderly and in non-BC patients; in contrast, HCC incident cases due to HCV tend to decrease.
Journal Article
gene controlling the number of primary rachis branches also controls the vascular bundle formation and hence is responsible to increase the harvest index and grain yield in rice
by
Nagata, Kenji
,
Hirose, Tatsuro
,
Morino, Kazuko
in
Agricultural production
,
Agricultural research
,
Agriculture
2010
The quantitative trait locus controlling the number of primary rachis branches (PRBs) in rice was identified using backcrossed inbred lines of Sasanishiki/Habataki//Sasanishiki///Sasanishiki. The resultant gene was ABERRANT PANICLE ORGANIZATION 1 (APO1). Habataki-genotype segregated reciprocal recombinant lines for the APO1 locus increased both the number of PRB (12-13%) and the number of grains per panicle (9-12%), which increased the grain yield per plant (5-7%). Further recombination dividing this region revealed that different alleles regulated the number of PRB and the number of grains per panicle. The PRB1 allele, which includes the APO1 open reading frame (ORF) and the proximal promoter region, controlled only the number of PRB but not the number of grains per panicle. In contrast, the HI1 allele, which includes only the distal promoter region, increased the grain yield and harvest index in Habataki-genotype plants, nevertheless, the ORF expressed was Sasanishiki type. It also increased the number of large vascular bundles in the peduncle. APO1 expression occurred not only in developing panicles but also in the developing vascular bundle systems. In addition, Habataki plants displayed increased APO1 expression in comparison to Sasanishiki plants. It suggests that APO1 enhances the formation of vascular bundle systems which, consequently, promote carbohydrate translocation to panicles. The HI1 allele is suggested to regulate the amount of APO1 expression, and thereby control the development of vascular bundle systems. These findings may be useful to improve grain yield as well as quality through the improvement of translocation efficiency.
Journal Article
A universal Bayesian inference framework for complicated creep constitutive equations
2020
Evaluating the creep deformation process of heat-resistant steels is important for improving the energy efficiency of power plants by increasing the operating temperature. There is an analysis framework that estimates the rupture time of this process by regressing the strain–time relationship of the creep process using a regression model called the creep constitutive equation. Because many creep constitutive equations have been proposed, it is important to construct a framework to determine which one is best for the creep processes of different steel types at various temperatures and stresses. A Bayesian model selection framework is one of the best frameworks for evaluating the constitutive equations. In previous studies, approximate-expression methods such as the Laplace approximation were used to develop the Bayesian model selection frameworks for creep. Such frameworks are not applicable to creep constitutive equations or data that violate the assumption of the approximation. In this study, we propose a universal Bayesian model selection framework for creep that is applicable to the evaluation of various types of creep constitutive equations. Using the replica exchange Monte Carlo method, we develop a Bayesian model selection framework for creep without an approximate-expression method. To assess the effectiveness of the proposed framework, we applied it to the evaluation of a creep constitutive equation called the Kimura model, which is difficult to evaluate by existing frameworks. Through a model evaluation using the creep measurement data of Grade 91 steel, we confirmed that our proposed framework gives a more reasonable evaluation of the Kimura model than existing frameworks. Investigating the posterior distribution obtained by the proposed framework, we also found a model candidate that could improve the Kimura model.
Journal Article
Short axial length and hyperopic refractive error are risk factors of central serous chorioretinopathy
2020
Background/aimsTo evaluate the axial length (AL) and refractive status in central serous chorioretinopathy (CSC).MethodsThis retrospective observational case series involved 140 patients with CSC (180 eyes) and 78 age-matched and gender-matched control subjects. A detailed ophthalmic examination was performed, including an interferometer measurement of AL. Multimodal imaging comprised colour fundus photography, fluorescein angiography, indocyanine green angiography, fundus autofluorescence photography and spectral domain optical coherence tomography.ResultsEighty eyes of 40 patients were categorised into the bilateral-CSC (b-CSC) group and 100 eyes of 100 patients were categorised into the unilateral-CSC (u-CSC) group. AL of the b-CSC (23.19 mm) and u-CSC (23.75 mm) groups was significantly shorter than that of the control (24.85 mm) group (p<0.001 for both). Moreover, AL was significantly shorter in the b-CSC group than in the u-CSC group (p=0.020). Spherical equivalent (SE) in the b-CSC (0.25 D) group was significantly greater than in the u-CSC (−0.81 D) and control (−1.38 D) groups (p<0.001 for both). Gender (male; OR 4.55; 95% CI 1.13 to 18.40; p=0.033), AL (OR 0.38; 95% CI 0.23 to 0.63; p<0.001), area of choroidal vascular hyperpermeability (OR 1.08; 95% CI 1.03 to 1.13; p=0.002) and presence of descending tract (OR 7.22; 95% CI 1.86 to 28.00; p=0.004) were the variables found to be significantly associated with b-CSC via multiple regression analyses.ConclusionAnatomical features, such as shorter AL and greater SE, may be associated with the pathogenesis of CSC.
Journal Article
Protocol for Japan–acute retinal necrosis (J-ARN) registry: A combined prospective and retrospective cohort study
2025
Acute retinal necrosis (ARN) is a rare but vision-threatening viral retinitis that can lead to severe visual impairment or blindness if not diagnosed and treated promptly. However, due to its rarity, there are limited large-scale data on the clinical characteristics, treatment approaches, and outcomes of ARN in Japan. A nationwide registry is needed to systematically collect data on ARN cases across Japan to improve understanding of this condition and optimize patient care. We have designed a national registry that collects data of patient characteristics, diagnosis, treatment, and visual outcome to generate evidence for the management of ARN.
This research is a combined retrospective and prospective, multicenter cohort study of ARN in Japan from 1 April 2014-31 March 2029 (UMIN000056246). The registry has received Japan-wide approval from a national human research ethics committee. The following data will be collected: patient demographics, visual function at the initial visit and 6, 12, 24, and 36 months later, image data, diagnostic methods, virus analysis, indications and timing of vitrectomy, and complications. Customized software and platforms have been designed to permit data collection for a single baseline and multiple follow-up forms.
By analyzing the accumulated patient information, the results of this study will generate real-world evidence that will contribute to solve various important clinical issues in ARN. The results will be presented after data collection and analysis are completed.
Journal Article
Derived neutrophil-to-lymphocyte ratio has the potential to predict safety and outcomes of durvalumab after chemoradiation in non-small cell lung cancer
2024
The usefulness of the derived neutrophil-to-lymphocyte ratio (dNLR) and its dynamics before/after durvalumab consolidation therapy to predict safety or efficacy remains unclear. We retrospectively reviewed patients with locally advanced non-small cell lung cancer treated with durvalumab consolidation therapy after chemoradiotherapy (D group) or chemoradiotherapy alone (non-D group) at multiple institutions. We investigated the association between dNLR, or its dynamics, and pneumonitis, checkpoint inhibitor-related pneumonitis (CIP), irAEs, and efficacy. Ninety-eight and fifty-six patients were enrolled in the D and non-D groups, respectively. The dNLR at baseline was significantly lower in patients who experienced irAEs or CIP than in those who did not. The low dNLR group, 28 days following durvalumab consolidation therapy (dNLR28 ≤ 3), demonstrated longer progression-free survival (PFS) and overall survival (OS) than the high dNLR group (dNLR28 > 3) (PFS, hazard ratio [HR] 0.44, 95% confidence interval [CI] 0.22–0.88,
p
= 0.020; OS, HR 0.39, 95% CI 0.16–0.94,
p
= 0.037). Among patients with high dNLR at baseline (dNLR > 3), the dNLR28 ≤ 3 group showed longer PFS than the dNLR28 > 3 group (
p
= 0.010). The dNLR is a predictive factor for irAEs and CIP in patients receiving durvalumab consolidation therapy. The dNLR at 28 days after durvalumab consolidation therapy and its dynamics predict favorable outcomes.
Journal Article
A multicenter study of ocular inflammation after COVID-19 vaccination
2023
Purpose
To report the characteristics of a case series of ocular inflammatory events following COVID-19 vaccination in Japan.
Study design
Retrospective multicenter study
Methods
In this retrospective multicenter survey, a questionnaire was sent to 16 Japanese hospitals that had uveitis specialty clinics. Information on patients who developed ocular inflammatory events within 14 days of COVID-19 vaccination between February 2021 and December 2021 was collected.
Results
Thirty-seven patients were diagnosed with ocular inflammatory events following COVID-19 vaccination. The mean age was 53.4 ± 16.4 years (range, 26-86 years), and the mean time to onset after vaccination was 6.3 ± 4.2 days (range, 1-14 days). Vogt-Koyanagi-Harada disease (VKH) was the most common event (n = 17 patients, 46%), followed by anterior uveitis (n = 6), infectious uveitis (n = 3), acute zonal occult outer retinopathy (AZOOR) (n = 2), sarcoidosis-associated uveitis (n = 1), acute posterior multifocal placoid pigment epitheliopathy (APMPPE) (n = 1), optic neuritis (n = 1), multiple evanescent white dot syndrome (MEWDS) (n = 1), Posner-Schlossman syndrome (n = 1), and unclassified uveitis (n = 4). Twenty-eight cases occurred after BNT162b2 vaccination (Pfizer-BioNTech) and 8 after mRNA-1273 vaccination (Moderna), whilst 1 patient had no information about vaccine type.
Conclusions
COVID-19 vaccination can be related to various types of ocular inflammatory events. When we encounter patients with ocular inflammatory disease, we should consider that it may be an adverse effect of COVID-19 vaccination.
Journal Article