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  1. Article ; Online: Machine learning-based prediction of in-hospital mortality using admission laboratory data

    Tomohisa Seki / Yoshimasa Kawazoe / Kazuhiko Ohe

    PLoS ONE, Vol 16, Iss 2, p e

    A retrospective, single-site study using electronic health record data.

    2021  Volume 0246640

    Abstract: Risk assessment of in-hospital mortality of patients at the time of hospitalization is necessary for determining the scale of required medical resources for the patient depending on the patient's severity. Because recent machine learning application in ... ...

    Abstract Risk assessment of in-hospital mortality of patients at the time of hospitalization is necessary for determining the scale of required medical resources for the patient depending on the patient's severity. Because recent machine learning application in the clinical area has been shown to enhance prediction ability, applying this technique to this issue can lead to an accurate prediction model for in-hospital mortality prediction. In this study, we aimed to generate an accurate prediction model of in-hospital mortality using machine learning techniques. Patients 18 years of age or older admitted to the University of Tokyo Hospital between January 1, 2009 and December 26, 2017 were used in this study. The data were divided into a training/validation data set (n = 119,160) and a test data set (n = 33,970) according to the time of admission. The prediction target of the model was the in-hospital mortality within 14 days. To generate the prediction model, 25 variables (age, sex, 21 laboratory test items, length of stay, and mortality) were used to predict in-hospital mortality. Logistic regression, random forests, multilayer perceptron, and gradient boost decision trees were performed to generate the prediction models. To evaluate the prediction capability of the model, the model was tested using a test data set. Mean probabilities obtained from trained models with five-fold cross-validation were used to calculate the area under the receiver operating characteristic (AUROC) curve. In a test stage using the test data set, prediction models of in-hospital mortality within 14 days showed AUROC values of 0.936, 0.942, 0.942, and 0.938 for logistic regression, random forests, multilayer perceptron, and gradient boosting decision trees, respectively. Machine learning-based prediction of short-term in-hospital mortality using admission laboratory data showed outstanding prediction capability and, therefore, has the potential to be useful for the risk assessment of patients at the time of hospitalization.
    Keywords Medicine ; R ; Science ; Q
    Subject code 310
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: A clinical specific BERT developed using a huge Japanese clinical text corpus.

    Yoshimasa Kawazoe / Daisaku Shibata / Emiko Shinohara / Eiji Aramaki / Kazuhiko Ohe

    PLoS ONE, Vol 16, Iss 11, p e

    2021  Volume 0259763

    Abstract: Generalized language models that are pre-trained with a large corpus have achieved great performance on natural language tasks. While many pre-trained transformers for English are published, few models are available for Japanese text, especially in ... ...

    Abstract Generalized language models that are pre-trained with a large corpus have achieved great performance on natural language tasks. While many pre-trained transformers for English are published, few models are available for Japanese text, especially in clinical medicine. In this work, we demonstrate the development of a clinical specific BERT model with a huge amount of Japanese clinical text and evaluate it on the NTCIR-13 MedWeb that has fake Twitter messages regarding medical concerns with eight labels. Approximately 120 million clinical texts stored at the University of Tokyo Hospital were used as our dataset. The BERT-base was pre-trained using the entire dataset and a vocabulary including 25,000 tokens. The pre-training was almost saturated at about 4 epochs, and the accuracies of Masked-LM and Next Sentence Prediction were 0.773 and 0.975, respectively. The developed BERT did not show significantly higher performance on the MedWeb task than the other BERT models that were pre-trained with Japanese Wikipedia text. The advantage of pre-training on clinical text may become apparent in more complex tasks on actual clinical text, and such an evaluation set needs to be developed.
    Keywords Medicine ; R ; Science ; Q
    Subject code 410
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: A clinical specific BERT developed using a huge Japanese clinical text corpus

    Yoshimasa Kawazoe / Daisaku Shibata / Emiko Shinohara / Eiji Aramaki / Kazuhiko Ohe

    PLoS ONE, Vol 16, Iss

    2021  Volume 11

    Abstract: Generalized language models that are pre-trained with a large corpus have achieved great performance on natural language tasks. While many pre-trained transformers for English are published, few models are available for Japanese text, especially in ... ...

    Abstract Generalized language models that are pre-trained with a large corpus have achieved great performance on natural language tasks. While many pre-trained transformers for English are published, few models are available for Japanese text, especially in clinical medicine. In this work, we demonstrate the development of a clinical specific BERT model with a huge amount of Japanese clinical text and evaluate it on the NTCIR-13 MedWeb that has fake Twitter messages regarding medical concerns with eight labels. Approximately 120 million clinical texts stored at the University of Tokyo Hospital were used as our dataset. The BERT-base was pre-trained using the entire dataset and a vocabulary including 25,000 tokens. The pre-training was almost saturated at about 4 epochs, and the accuracies of Masked-LM and Next Sentence Prediction were 0.773 and 0.975, respectively. The developed BERT did not show significantly higher performance on the MedWeb task than the other BERT models that were pre-trained with Japanese Wikipedia text. The advantage of pre-training on clinical text may become apparent in more complex tasks on actual clinical text, and such an evaluation set needs to be developed.
    Keywords Medicine ; R ; Science ; Q
    Subject code 410
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Association between number of institutions with coronary computed tomography angiography and regional mortality ratio of acute myocardial infarction

    Hideaki Kawaguchi / Soichi Koike / Ryota Sakurai / Kazuhiko Ohe

    International Journal of Health Geographics, Vol 17, Iss 1, Pp 1-

    a nationwide ecological study using a spatial Bayesian model

    2018  Volume 8

    Abstract: Abstract Background Coronary computed tomography angiography (CTA) has demonstrated high diagnostic accuracy for detection of coronary artery stenosis, and healthcare providers can detect coronary artery disease in earlier stages before it develops into ... ...

    Abstract Abstract Background Coronary computed tomography angiography (CTA) has demonstrated high diagnostic accuracy for detection of coronary artery stenosis, and healthcare providers can detect coronary artery disease in earlier stages before it develops into more serious clinical conditions such as acute myocardial infarction (AMI). We hypothesized that the mortality ratio of AMI in regions with a higher density of coronary CTA is lower than that in regions with a lower density of coronary CTA. Methods This ecological and cross-sectional study using secondary data targeted all secondary medical service areas (SMSAs) in Japan (n = 349). We obtained the numbers of cardiologists, institutions with coronary CTA, and institutions with a cardiac catheterization laboratory (CCL) as medical resources, socioeconomic factors, lifestyle factors, exercise habit factors, and AMI mortality data from a Japanese national database. We evaluated the association between the number of these medical resources and the standardized mortality ratio (SMR) of AMI in each SMSA using a hierarchical Bayesian model accounting for spatial autocorrelation (i.e., a conditional autoregressive model). We assumed a Poisson distribution for the observed number of AMI-related deaths and set the expected number of AMI-related deaths as the offset variable. Results The number of institutions with coronary CTA was negatively and significantly associated with the SMR of AMI (relative risk [RR] 0.900; 95% credible interval [CI] 0.848–0.953), while the SMR in each SMSA was not significantly associated with the number of either cardiologists (RR 0.997; 95% CI 0.988–1.004) or institutions with a CCL (RR 1.026; 95% CI 0.963–1.096). Conclusions We observed a significant association between the number of institutions with coronary CTA and the SMR of AMI. Effective allocation of coronary CTA in each region is recommended, and it would be important to clarify the standing position of coronary CTA in regional networking for AMI treatment in the future.
    Keywords Coronary computed tomography angiography ; Acute myocardial infarction ; Standardized mortality ratio ; Health services research ; Healthcare access ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 610
    Language English
    Publishing date 2018-05-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Development of Graph-Based Algorithm for Differentiating Pathophysiological Conditions

    Satoshi IWAI / Tomohiro MITANI / Jin HAYAKAWA / Emiko SHINOHARA / Takeshi IMAI / Yoshimasa KAWAZOE / Kazuhiko OHE

    Applied Medical Informatics, Vol 42, Iss 2, Pp 107-

    2020  Volume 117

    Abstract: Aim: Clinical diagnostic decision support systems, which use pathophysiological information to improve diagnostic accuracy, have historically required knowledge of various relations between pathophysiological states to handle complex cases. Developing a ... ...

    Abstract Aim: Clinical diagnostic decision support systems, which use pathophysiological information to improve diagnostic accuracy, have historically required knowledge of various relations between pathophysiological states to handle complex cases. Developing a knowledge model centered on pathophysiological functions instead of pathophysiological states may reduce this unwieldiness. Materials and Methods: In this study, such a knowledge model is provided by a modified and generalized factor graph, the pathophysiological query (PPQ) graph. A PPQ algorithm that automatically suggests possible pathological conditions of patients in the form of PPQ graphs is also developed. To evaluate the model and the algorithm, a computer software that processes the PPQ algorithm and PPQ graph, which represent the acid-base regulatory functions, was developed. Four case reports were considered, and up to two-time points, used as evaluation data points, were selected for each case. The software was used to obtain the diagnoses suggested by the PPQ model, which were then compared to diagnoses formulated by three physicians. Results: The output acquired by the proposed method was in accordance with the diagnosis of the physicians in three out of the five cases. Conclusion: The PPQ model may be a valuable diagnostic tool for suggesting differential pathological conditions to physicians in complex cases.
    Keywords algorithms ; decision support techniques ; differential diagnosis ; knowledge bases system ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 006
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Survey on Usage of Medical Referral Information in Japanese Physicians

    Hiroshi Watanabe / Michio Kimura / Kazuhiko Ohe

    Healthcare Informatics Research, Vol 23, Iss 2, Pp 126-

    2017  Volume 134

    Abstract: ObjectivesThe purpose of this survey was to explore physicians' opinions to identify an adequate time range for clinical information to be provided with a referral that would help minimize wasteful retesting.MethodsIn 2011, we conducted a questionnaire ... ...

    Abstract ObjectivesThe purpose of this survey was to explore physicians' opinions to identify an adequate time range for clinical information to be provided with a referral that would help minimize wasteful retesting.MethodsIn 2011, we conducted a questionnaire survey of 193 physicians. Examining the degree of utilization of provided medical information, we determined the range of clinical information of referral documents.ResultsLess than three months of prescription history and blood sample test results in patient referral was most frequent. Less than one year of image information was most frequent. Most doctors answered there is no need to repeat the same type of blood test in their institute when they had information less than half a month old. Less than half to one month of image information was most frequent. Also, it appeared many doctors think “fundamentally they do not change their mind from their own medical department standpoint.” At the actual site, those who would even review referral clinical notes accounted for about 30% of all participants.ConclusionsMedical referral eventually takes place after the establishment of mutual communication and should consider the workflow and system environment of the receiver of the information.
    Keywords referral and consultation ; hospital information systems ; surveys and questionnaires ; statistics and numerical data ; Computer applications to medicine. Medical informatics ; R858-859.7
    Language English
    Publishing date 2017-04-01T00:00:00Z
    Publisher The Korean Society of Medical Informatics
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Feasibility of a T-Shirt-Type Wearable Electrocardiography Monitor for Detection of Covert Atrial Fibrillation in Young Healthy Adults

    Nobuaki Fukuma / Eriko Hasumi / Katsuhito Fujiu / Kayo Waki / Tsuguyoshi Toyooka / Issei Komuro / Kazuhiko Ohe

    Scientific Reports, Vol 9, Iss 1, Pp 1-

    2019  Volume 6

    Abstract: Abstract Covert atrial fibrillation (AF) accounts for cryptogenic stroke aetiology in elderly patients and in younger populations. However, asymptomatic AF is difficult to diagnose based on a short electrocardiography (ECG) recording. We evaluated the ... ...

    Abstract Abstract Covert atrial fibrillation (AF) accounts for cryptogenic stroke aetiology in elderly patients and in younger populations. However, asymptomatic AF is difficult to diagnose based on a short electrocardiography (ECG) recording. We evaluated the feasibility of a self-applied continuous ECG monitoring device that can record automatically, easily, and noninvasively in a younger population. We investigated community screening for asymptomatic AF using a wireless single-lead ECG with an electrode embedded in a T-shirt. One hundred men with a CHADS2 score ≥1 who were free from AF and <65 years of age were enrolled. We instructed the participants to wear ECG monitoring devices for at least 4 days/week over 2 months. The proportion of participants with newly detected AF (NDAF) and the monitoring time were evaluated. The mean CHADS2 score was 1.43 ± 0.62. The mean patient age was 52.5 ± 5.4 years. The mean monitoring time was 222 ± 199 hours. NDAF continuing for >30 seconds was detected in 10 participants (10.0%). AF continuing for >6 minutes was detected in 2 participants (2.0%). The T-shirt-type wearable ECG monitoring system was suitable for continuous, daily long-term use among young people with high physical activity, and it had the distinct capability of identifying covert AF.
    Keywords Medicine ; R ; Science ; Q
    Subject code 150
    Language English
    Publishing date 2019-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Disease Compass– a navigation system for disease knowledge based on ontology and linked data techniques

    Kouji Kozaki / Yuki Yamagata / Riichiro Mizoguchi / Takeshi Imai / Kazuhiko Ohe

    Journal of Biomedical Semantics, Vol 8, Iss 1, Pp 1-

    2017  Volume 18

    Abstract: Abstract Background Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases ... ...

    Abstract Abstract Background Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases are related to concepts across various medical domains. The authors developed a River Flow Model (RFM) of diseases, which captures diseases as the causal chains of abnormal states. It represents causes of diseases, disease progression, and downstream consequences of diseases, which is compliant with the intuition of medical experts. In this paper, we discuss a fact repository for causal chains of disease based on the disease ontology. It could be a valuable knowledge base for advanced medical information systems. Methods We developed the fact repository for causal chains of diseases based on our disease ontology and abnormality ontology. This section summarizes these two ontologies. It is developed as linked data so that information scientists can access it using SPARQL queries through an Resource Description Framework (RDF) model for causal chain of diseases. Results We designed the RDF model as an implementation of the RFM for the fact repository based on the ontological definitions of the RFM. 1554 diseases and 7080 abnormal states in six major clinical areas, which are extracted from the disease ontology, are published as linked data (RDF) with SPARQL endpoint (accessible API). Furthermore, the authors developed Disease Compass, a navigation system for disease knowledge. Disease Compass can browse the causal chains of a disease and obtain related information, including abnormal states, through two web services that provide general information from linked data, such as DBpedia, and 3D anatomical images. Conclusions Disease Compass can provide a complete picture of disease-associated processes in such a way that fits with a clinician’s understanding of diseases. Therefore, it supports user exploration of disease knowledge with access to pertinent information from a variety of sources.
    Keywords Disease ontology ; Definition of diseases ; River flow model of disease ; Linked data ; Navigation system ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 006
    Language English
    Publishing date 2017-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Faster R-CNN-Based Glomerular Detection in Multistained Human Whole Slide Images

    Yoshimasa Kawazoe / Kiminori Shimamoto / Ryohei Yamaguchi / Yukako Shintani-Domoto / Hiroshi Uozaki / Masashi Fukayama / Kazuhiko Ohe

    Journal of Imaging, Vol 4, Iss 7, p

    2018  Volume 91

    Abstract: The detection of objects of interest in high-resolution digital pathological images is a key part of diagnosis and is a labor-intensive task for pathologists. In this paper, we describe a Faster R-CNN-based approach for the detection of glomeruli in ... ...

    Abstract The detection of objects of interest in high-resolution digital pathological images is a key part of diagnosis and is a labor-intensive task for pathologists. In this paper, we describe a Faster R-CNN-based approach for the detection of glomeruli in multistained whole slide images (WSIs) of human renal tissue sections. Faster R-CNN is a state-of-the-art general object detection method based on a convolutional neural network, which simultaneously proposes object bounds and objectness scores at each point in an image. The method takes an image obtained from a WSI with a sliding window and classifies and localizes every glomerulus in the image by drawing the bounding boxes. We configured Faster R-CNN with a pretrained Inception-ResNet model and retrained it to be adapted to our task, then evaluated it based on a large dataset consisting of more than 33,000 annotated glomeruli obtained from 800 WSIs. The results showed the approach produces comparable or higher than average F-measures with different stains compared to other recently published approaches. This approach could have practical application in hospitals and laboratories for the quantitative analysis of glomeruli in WSIs and, potentially, lead to a better understanding of chronic glomerulonephritis.
    Keywords glomerulus detection ; digital pathology ; whole slide images ; deep neural network ; Photography ; TR1-1050 ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 006
    Language English
    Publishing date 2018-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: J-CKD-DB

    Naoki Nakagawa / Tadashi Sofue / Eiichiro Kanda / Hajime Nagasu / Kunihiro Matsushita / Masaomi Nangaku / Shoichi Maruyama / Takashi Wada / Yoshio Terada / Kunihiro Yamagata / Ichiei Narita / Motoko Yanagita / Hitoshi Sugiyama / Takashi Shigematsu / Takafumi Ito / Kouichi Tamura / Yoshitaka Isaka / Hirokazu Okada / Kazuhiko Tsuruya /
    Hitoshi Yokoyama / Naoki Nakashima / Hiromi Kataoka / Kazuhiko Ohe / Mihoko Okada / Naoki Kashihara

    Scientific Reports, Vol 10, Iss 1, Pp 1-

    a nationwide multicentre electronic health record-based chronic kidney disease database in Japan

    2020  Volume 11

    Abstract: Abstract The Japan Chronic Kidney Disease (CKD) Database (J-CKD-DB) is a large-scale, nation-wide registry based on electronic health record (EHR) data from participating university hospitals. Using a standardized exchangeable information storage, the J- ... ...

    Abstract Abstract The Japan Chronic Kidney Disease (CKD) Database (J-CKD-DB) is a large-scale, nation-wide registry based on electronic health record (EHR) data from participating university hospitals. Using a standardized exchangeable information storage, the J-CKD-DB succeeded to efficiently collect clinical data of CKD patients across hospitals despite their different EHR systems. CKD was defined as dipstick proteinuria ≥1+ and/or estimated glomerular filtration rate <60 mL/min/1.73 m2 base on both out- and inpatient laboratory data. As an initial analysis, we analyzed 39,121 CKD outpatients (median age was 71 years, 54.7% were men, median eGFR was 51.3 mL/min/1.73 m2) and observed that the number of patients with a CKD stage G1, G2, G3a, G3b, G4 and G5 were 1,001 (2.6%), 2,612 (6.7%), 23,333 (59.6%), 8,357 (21.4%), 2,710 (6.9%) and 1,108 (2.8%), respectively. According to the KDIGO risk classification, there were 30.1% and 25.5% of male and female patients with CKD at very high-risk, respectively. As the information from every clinical encounter from those participating hospitals will be continuously updated with an anonymized patient ID, the J-CKD-DB will be a dynamic registry of Japanese CKD patients by expanding and linking with other existing databases and a platform for a number of cross-sectional and prospective analyses to answer important clinical questions in CKD care.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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