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Article ; Online: Intermolecular and Electrode-Molecule Bonding in a Single Dimer Junction of Naphthalenethiol as Revealed by Surface-Enhanced Raman Scattering Combined with Transport Measurements.

Homma, Kanji / Kaneko, Satoshi / Tsukagoshi, Kazuhito / Nishino, Tomoaki

Journal of the American Chemical Society

2023 Volume 145, Issue 29, Page(s) 15788–15795

Abstract: Electron transport through noncovalent interaction is of fundamental and practical importance in nanomaterials and nanodevices. Recent single-molecule studies employing single-molecule junctions have revealed unique electron transport properties through ... ...

Abstract	Electron transport through noncovalent interaction is of fundamental and practical importance in nanomaterials and nanodevices. Recent single-molecule studies employing single-molecule junctions have revealed unique electron transport properties through noncovalent interactions, especially those through a π-π interaction. However, the relationship between the junction structure and electron transport remains elusive due to the insufficient knowledge of geometric structures. In this article, we employ surface-enhanced Raman scattering (SERS) synchronized with current-voltage (
Language	English
Publishing date	2023-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c02050
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Article ; Online: Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor.

Fukuchi, Satoshi / Noguchi, Tamotsu / Anbo, Hiroto / Homma, Keiichi

Molecular biology and evolution

2022 Volume 40, Issue 1

Abstract: Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, whereas the typical eukaryotic protein comprises multiple SDs and IDRs. How ... ...

Abstract	Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, whereas the typical eukaryotic protein comprises multiple SDs and IDRs. How eukaryotic proteins evolved to differ from prokaryotic proteins has not been fully elucidated. Here, we found that the longer the internal exons are, the more frequently they encode IDRs in eight eukaryotes including vertebrates, invertebrates, a fungus, and plants. Based on this observation, we propose the "small bang" model from the proteomic viewpoint: the protoeukaryotic genes had no introns and mostly encoded one SD each, but a majority of them were subsequently divided into multiple exons (step 1). Many exons unconstrained by SDs elongated to encode IDRs (step 2). The elongated exons encoding IDRs frequently facilitated the acquisition of multiple SDs to make the last common ancestor of eukaryotes (step 3). One prediction of the model is that long internal exons are mostly unconstrained exons. Analytical results of the eight eukaryotes are consistent with this prediction. In support of the model, we identified cases of internal exons that elongated after the rat-mouse divergence and discovered that the expanded sections are mostly in unconstrained exons and preferentially encode IDRs. The model also predicts that SDs followed by long internal exons tend to have other SDs downstream. This prediction was also verified in all the eukaryotic species analyzed. Our model accounts for the dichotomy between prokaryotic and eukaryotic proteins and proposes a selective advantage conferred by IDRs.
MeSH term(s)	Animals ; Rats ; Mice ; Eukaryota/genetics ; Proteomics ; Evolution, Molecular ; Proteins/genetics ; Exons ; Intrinsically Disordered Proteins/genetics
Chemical Substances	Proteins ; Intrinsically Disordered Proteins
Language	English
Publishing date	2022-12-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msac272
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Article ; Online: Diagnosis of skull-base invasion by nasopharyngeal tumors on CT with a deep-learning approach.

Nakagawa, Junichi / Fujima, Noriyuki / Hirata, Kenji / Harada, Taisuke / Wakabayashi, Naoto / Takano, Yuki / Homma, Akihiro / Kano, Satoshi / Minowa, Kazuyuki / Kudo, Kohsuke

Japanese journal of radiology

2024

Abstract: Purpose: To develop a convolutional neural network (CNN) model to diagnose skull-base invasion by nasopharyngeal malignancies in CT images and evaluate the model's diagnostic performance.: Materials and methods: We divided 100 malignant ... ...

Abstract	Purpose: To develop a convolutional neural network (CNN) model to diagnose skull-base invasion by nasopharyngeal malignancies in CT images and evaluate the model's diagnostic performance. Materials and methods: We divided 100 malignant nasopharyngeal tumor lesions into a training (n = 70) and a test (n = 30) dataset. Two head/neck radiologists reviewed CT and MRI images and determined the positive/negative skull-base invasion status of each case (training dataset: 29 invasion-positive and 41 invasion-negative; test dataset: 13 invasion-positive and 17 invasion-negative). Preprocessing involved extracting continuous slices of the nasopharynx and clivus. The preprocessed training dataset was used for transfer learning with Residual Neural Networks 50 to create a diagnostic CNN model, which was then tested on the preprocessed test dataset to determine the invasion status and model performance. Original CT images from the test dataset were reviewed by a radiologist with extensive head/neck imaging experience (senior reader: SR) and another less-experienced radiologist (junior reader: JR). Gradient-weighted class activation maps (Grad-CAMs) were created to visualize the explainability of the invasion status classification. Results: The CNN model's diagnostic accuracy was 0.973, significantly higher than those of the two radiologists (SR: 0.838; JR: 0.595). Receiver operating characteristic curve analysis gave an area under the curve of 0.953 for the CNN model (versus 0.832 and 0.617 for SR and JR; both p < 0.05). The Grad-CAMs suggested that the invasion-negative cases were present predominantly in bone marrow, while the invasion-positive cases exhibited osteosclerosis and nasopharyngeal masses. Conclusions: This CNN technique would be useful for CT-based diagnosis of skull-base invasion by nasopharyngeal malignancies.
Language	English
Publishing date	2024-01-27
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2488907-6
ISSN	1867-108X ; 1867-1071
ISSN (online)	1867-108X
ISSN	1867-1071
DOI	10.1007/s11604-023-01527-7
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Article: Pleiotropic Actions of Aldehyde Reductase (AKR1A).

Fujii, Junichi / Homma, Takujiro / Miyata, Satoshi / Takahashi, Motoko

Metabolites

2021 Volume 11, Issue 6

Abstract: We provide an overview of the physiological roles of aldehyde reductase (AKR1A) and also discuss the functions of aldose reductase (AKR1B) and other family members when necessary. Many types of aldehyde compounds are cytotoxic and some are even ... ...

Abstract	We provide an overview of the physiological roles of aldehyde reductase (AKR1A) and also discuss the functions of aldose reductase (AKR1B) and other family members when necessary. Many types of aldehyde compounds are cytotoxic and some are even carcinogenic. Such toxic aldehydes are detoxified via the action of AKR in an NADPH-dependent manner and the resulting products may exert anti-diabetic and anti-tumorigenic activity. AKR1A is capable of reducing 3-deoxyglucosone and methylglyoxal, which are reactive intermediates that are involved in glycation, a non-enzymatic glycosylation reaction. Accordingly, AKR1A is thought to suppress the formation of advanced glycation end products (AGEs) and prevent diabetic complications. AKR1A and, in part, AKR1B are responsible for the conversion of d-glucuronate to l-gulonate which constitutes a process for ascorbate (vitamin C) synthesis in competent animals. AKR1A is also involved in the reduction of
Language	English
Publishing date	2021-05-26
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo11060343
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Article ; Online: Consequences of a peroxiredoxin 4 (Prdx4) deficiency on learning and memory in mice.

Homma, Takujiro / Fujiwara, Hiroki / Osaki, Tsukasa / Fujii, Satoshi / Fujii, Junichi

Biochemical and biophysical research communications

2022 Volume 621, Page(s) 32–38

Abstract: Peroxiredoxin 4 (Prdx4) is responsible for the oxidative folding of new proteins that are synthesized in the endoplasmic reticulum (ER). It has recently been suggested that increased ER stress is associated with neurodegenerative diseases, including ... ...

Abstract	Peroxiredoxin 4 (Prdx4) is responsible for the oxidative folding of new proteins that are synthesized in the endoplasmic reticulum (ER). It has recently been suggested that increased ER stress is associated with neurodegenerative diseases, including Alzheimer's disease. Prdx4 is widely distributed throughout the brain, and is also expressed in hippocampal neurons and oligodendrocytes, suggesting that it is associated with learning and memory. We previously established Prdx4-knockout (KO) mice but did not examine the behavioral phenotypes. In the present study, we report on the learning and memory abilities of Prdx4-KO mice based on Morris water maze and the Y-maze tests. The findings indicate that Prdx4-KO mice showed a lower spatial memory ability in both tests. In contrast, the results of the open field test indicated that locomotor activity is significantly increased in Prdx4-KO mice. We then performed mRNA analyses of the brains of Prdx4-KO mice and found an increased expression of genes related to the ER-associated degradation (ERAD) mechanism, which is an important protein quality control system for the maintenance of ER homeostasis. Finally, proteomic analyses of the brains of Prdx4-KO mice showed an aberrant expression in the proteins, which have been suggested to be related to calcium homeostasis and synaptogenesis in neurons. Our collective results suggest that the Prdx4 ablation perturbs oxidative protein folding in the ER, thus leading to aberrant ER homeostasis in neuronal cells, ultimately leading to impaired spatial memory formation.
MeSH term(s)	Animals ; Endoplasmic Reticulum/metabolism ; Endoplasmic Reticulum Stress ; Maze Learning ; Memory ; Mice ; Mice, Knockout ; Peroxiredoxins/genetics ; Peroxiredoxins/metabolism ; Proteomics
Chemical Substances	Peroxiredoxins (EC 1.11.1.15) ; Prdx4 protein, mouse (EC 1.11.1.15)
Language	English
Publishing date	2022-07-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2022.06.096
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Article: [Patient safety and quality of medical care. Topics: I. Incident and accident in hospital: current situation; 1. Importance of an incident & occurrence-reporting system in patient safety management].

Homma, Satoshi

Nihon Naika Gakkai zasshi. The Journal of the Japanese Society of Internal Medicine

2013 Volume 101, Issue 12, Page(s) 3368–3378

MeSH term(s)	Patient Safety/standards ; Quality Control ; Risk Management ; Safety Management
Language	Japanese
Publishing date	2013-01-04
Publishing country	Japan
Document type	Journal Article
ZDB-ID	952816-7
ISSN	1883-2083 ; 0021-5384
ISSN (online)	1883-2083
ISSN	0021-5384
DOI	10.2169/naika.101.3368
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Article ; Online: Pretreatment elevated mean corpuscular volume as an indicator for high risk esophageal second primary cancer in patients with head and neck cancer.

Tsushima, Nayuta / Kano, Satoshi / Suzuki, Takayoshi / Hamada, Seijiro / Homma, Akihiro

Auris, nasus, larynx

2022 Volume 50, Issue 3, Page(s) 423–429

Abstract: Objective: Esophageal cancer is the most common second primary cancer (SPC) in patients with head and neck cancer (HNC). Esophageal SPC has a negative impact on survival. Elevated mean corpuscular volume (MCV) is an accepted predictor of esophageal ... ...

Abstract	Objective: Esophageal cancer is the most common second primary cancer (SPC) in patients with head and neck cancer (HNC). Esophageal SPC has a negative impact on survival. Elevated mean corpuscular volume (MCV) is an accepted predictor of esophageal cancer risk. The aim of this study was to elucidate the usefulness of elevated MCV as an indicator of a high risk for esophageal SPC. Methods: We retrospectively reviewed the medical records of patients with oropharyngeal, hypopharyngeal, and laryngeal squamous cell carcinoma who underwent chemoradiotherapy between 2003 and 2012. We excluded patients younger than 20 years or who had received treatment for esophageal cancer and who had a histologically unproven lesion. Patients were divided into two groups according to their MCV. The cut-off for MCV was defined by receiver operating characteristics curve analysis. The primary endpoint was the cumulative incidence of esophageal SPC. Results: A total of 295 patients were included. The median follow-up period for surviving patients was 7.4 years and the optimal cut-off point was 99.0 fL. One hundred ninety-five patients (66%) had an MCV < 99.0 fL and 100 (34%) had an MCV ≥ 99.0 fL. The 5-year cumulative incidence in patients with an MCV < 99.0 fL and ≥ 99.0 fL was 8.7% and 27%, respectively. In the multivariate analysis, an MCV ≥ 99.0 fL (HR=2.2; 95%CI, 1.1-4.2) was an independent risk factor. Conclusion: MCV ≥ 99.0 fL was found to be a risk factor for esophageal SPC. We, therefore, recommend that patients with an MCV ≥ 99.0 fL should undergo intensive monitoring.
MeSH term(s)	Humans ; Erythrocyte Indices ; Retrospective Studies ; Neoplasms, Second Primary/epidemiology ; Head and Neck Neoplasms/therapy ; Esophageal Neoplasms/therapy ; Esophageal Neoplasms/pathology
Language	English
Publishing date	2022-10-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	604552-2
ISSN	1879-1476 ; 0385-8146
ISSN (online)	1879-1476
ISSN	0385-8146
DOI	10.1016/j.anl.2022.09.009
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Article ; Online: Correction: Treatment outcomes of radiotherapy with concurrent weekly cisplatin in older patients with locally advanced head and neck squamous cell carcinoma.

Uchinami, Yusuke / Yasuda, Koichi / Kano, Satoshi / Otsuka, Manami / Hamada, Seijiro / Suzuki, Takayoshi / Tsushima, Nayuta / Takahashi, Shuhei / Fujita, Yoshihiro / Miyazaki, Tomohiko / Higaki, Hajime / Taguchi, Jun / Shimizu, Yasushi / Sakashita, Tomohiro / Homma, Akihiro / Aoyama, Hidefumi

Discover. Oncology

2024 Volume 15, Issue 1, Page(s) 18

Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Published Erratum
ISSN	2730-6011
ISSN (online)	2730-6011
DOI	10.1007/s12672-024-00868-7
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Article: Consequences of a peroxiredoxin 4 (Prdx4) deficiency on learning and memory in mice

Homma, Takujiro / Fujiwara, Hiroki / Osaki, Tsukasa / Fujii, Satoshi / Fujii, Junichi

Biochemical and biophysical research communications. 2022 Sept. 17, v. 621

2022

Abstract	Peroxiredoxin 4 (Prdx4) is responsible for the oxidative folding of new proteins that are synthesized in the endoplasmic reticulum (ER). It has recently been suggested that increased ER stress is associated with neurodegenerative diseases, including Alzheimer's disease. Prdx4 is widely distributed throughout the brain, and is also expressed in hippocampal neurons and oligodendrocytes, suggesting that it is associated with learning and memory. We previously established Prdx4-knockout (KO) mice but did not examine the behavioral phenotypes. In the present study, we report on the learning and memory abilities of Prdx4-KO mice based on Morris water maze and the Y-maze tests. The findings indicate that Prdx4-KO mice showed a lower spatial memory ability in both tests. In contrast, the results of the open field test indicated that locomotor activity is significantly increased in Prdx4-KO mice. We then performed mRNA analyses of the brains of Prdx4-KO mice and found an increased expression of genes related to the ER-associated degradation (ERAD) mechanism, which is an important protein quality control system for the maintenance of ER homeostasis. Finally, proteomic analyses of the brains of Prdx4-KO mice showed an aberrant expression in the proteins, which have been suggested to be related to calcium homeostasis and synaptogenesis in neurons. Our collective results suggest that the Prdx4 ablation perturbs oxidative protein folding in the ER, thus leading to aberrant ER homeostasis in neuronal cells, ultimately leading to impaired spatial memory formation.
Keywords	Alzheimer disease ; brain ; calcium ; endoplasmic reticulum ; homeostasis ; locomotion ; neurons ; oligodendroglia ; peroxiredoxin ; protein value ; proteomics ; quality control ; research ; spatial memory ; synaptogenesis
Language	English
Dates of publication	2022-0917
Size	p. 32-38.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	205723-2
ISSN	0006-291X ; 0006-291X
ISSN (online)	0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2022.06.096
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Article ; Online: Impact of partial pressure of arterial oxygen and radiologic findings on postoperative acute exacerbation of idiopathic interstitial pneumonia in patients with lung cancer.

Azuma, Yoko / Sakamoto, Susumu / Homma, Sakae / Sakai, Takashi / Koezuka, Satoshi / Kamemura, Megumi / Tochigi, Naobumi / Iyoda, Akira

Surgery today

2023 Volume 54, Issue 2, Page(s) 122–129

Abstract: Purpose: To establish accurate diagnostic criteria and predictors of treatment response for postoperative acute exacerbation (AE) in patients with lung cancer and idiopathic interstitial pneumonia (IIP).: Methods: Among 93 patients with IIP who ... ...

Abstract	Purpose: To establish accurate diagnostic criteria and predictors of treatment response for postoperative acute exacerbation (AE) in patients with lung cancer and idiopathic interstitial pneumonia (IIP). Methods: Among 93 patients with IIP who underwent surgery for lung cancer, suspected postoperative AE developed in 20 (21.5%). Patients were divided into a progressive AE group, comprising patients with bilateral alveolar opacities and decreasing PaO Results: The progressive AE group had significantly higher 90-day mortality (80%) than the incipient AE group (10%, P = 0.017) or the indeterminate AE group (0%, P = 0.048). Bilateral opacities may indicate advanced AE and poor prognosis, whereas unilateral opacities may indicate an early stage of AE and a good prognosis. PaO Conclusions: In patients with lung cancer and IIP, decreasing PaO
MeSH term(s)	Humans ; Lung Neoplasms/complications ; Lung Neoplasms/surgery ; Oxygen ; Partial Pressure ; Retrospective Studies ; Idiopathic Interstitial Pneumonias/diagnostic imaging ; Prognosis ; Disease Progression
Chemical Substances	Oxygen (S88TT14065)
Language	English
Publishing date	2023-06-06
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1115435-4
ISSN	1436-2813 ; 0941-1291
ISSN (online)	1436-2813
ISSN	0941-1291
DOI	10.1007/s00595-023-02711-y
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