Displaying all 14 publications

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  1. Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.
    Autophagy, 2016;12(1):1-222.
    PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
  2. Ninomiya K, Arimura H, Tanaka K, Chan WY, Kabata Y, Mizuno S, et al.
    Comput Methods Programs Biomed, 2023 Jun;236:107544.
    PMID: 37148668 DOI: 10.1016/j.cmpb.2023.107544
    OBJECTIVES: To elucidate a novel radiogenomics approach using three-dimensional (3D) topologically invariant Betti numbers (BNs) for topological characterization of epidermal growth factor receptor (EGFR) Del19 and L858R mutation subtypes.

    METHODS: In total, 154 patients (wild-type EGFR, 72 patients; Del19 mutation, 45 patients; and L858R mutation, 37 patients) were retrospectively enrolled and randomly divided into 92 training and 62 test cases. Two support vector machine (SVM) models to distinguish between wild-type and mutant EGFR (mutation [M] classification) as well as between the Del19 and L858R subtypes (subtype [S] classification) were trained using 3DBN features. These features were computed from 3DBN maps by using histogram and texture analyses. The 3DBN maps were generated using computed tomography (CT) images based on the Čech complex constructed on sets of points in the images. These points were defined by coordinates of voxels with CT values higher than several threshold values. The M classification model was built using image features and demographic parameters of sex and smoking status. The SVM models were evaluated by determining their classification accuracies. The feasibility of the 3DBN model was compared with those of conventional radiomic models based on pseudo-3D BN (p3DBN), two-dimensional BN (2DBN), and CT and wavelet-decomposition (WD) images. The validation of the model was repeated with 100 times random sampling.

    RESULTS: The mean test accuracies for M classification with 3DBN, p3DBN, 2DBN, CT, and WD images were 0.810, 0.733, 0.838, 0.782, and 0.799, respectively. The mean test accuracies for S classification with 3DBN, p3DBN, 2DBN, CT, and WD images were 0.773, 0.694, 0.657, 0.581, and 0.696, respectively.

    CONCLUSION: 3DBN features, which showed a radiogenomic association with the characteristics of the EGFR Del19/L858R mutation subtypes, yielded higher accuracy for subtype classifications in comparison with conventional features.

  3. Liu C, Hirakawa H, Tanaka K, Mohd Saaya F, Nenoi M, Fujimori A, et al.
    Dose Response, 2019 03 04;17(1):1559325819833840.
    PMID: 30858771 DOI: 10.1177/1559325819833840
    Radiotherapy (RT) treats cancer effectively with high doses of ionizing radiation (IR) to killing cancer cells and shrinking tumors while bearing the risk of developing different side effects, including secondary cancer, which is most concerning for long-term health consequences. Genomic instability (GI) is a characteristic of most cancer cells, and IR-induced GI can manifest as delayed homologous recombination (HR). Radioadaptive response (RAR) is capable of reducing genotoxicity, cell transformation, mutation, and carcinogenesis, but the rational evidence describing its contributions to the reduction of radiation risk, in particular, carcinogenesis, remains fragmented. In this work, to investigate the impact of RAR on high-dose, IR-induced GI measured as delayed HR, the frequency of recombinant cells was comparatively studied under RAR-inducible and -uninducible conditions in the nucleated cells in hematopoietic tissues (bone marrow and spleen) using the Rosa26 Direct Repeat-green fluorescent protein (RaDR-GFP) homozygote mice. Results demonstrated that the frequency of recombinant cells was significantly lower in hematopoietic tissues under RAR-inducible condition. These findings suggest that reduction in delayed HR may be at least a part of the mechanisms underlying decreased carcinogenesis by RAR, and application of RAR would contribute to a more rigorous and scientifically grounded system of radiation protection in RT.
  4. A Samad NS, Abdul-Rahim AS, Mohd Yusof MJ, Tanaka K
    Environ Sci Pollut Res Int, 2020 Apr;27(10):10367-10390.
    PMID: 31939016 DOI: 10.1007/s11356-019-07593-7
    This study assessed the economic value of public urban green spaces (UGSs) in Kuala Lumpur (KL) city by using the hedonic price method (HPM). It involves 1269 house units from eight sub-districts in KL city. Based on the hedonic price method, this study formulates a global and local model. The global model and local model are analyzed using ordinary least square (OLS) regression and geographically weighted regression (GWR). By using the hedonic price method, the house price serves as a proxy for public urban green spaces' economic value. The house price is regressed against the set of three variables which are structural characteristics, neighborhood attributes, and environmental attributes. Measurements of interest in this study are environmental characteristics, including distance to public UGSs and size of public UGSs. The results of the OLS regression illustrated that Taman Rimba Kiara and Taman Tasik Titiwangsa provide the maximum economic value. On average, reducing the distance of the house location to Taman Rimba Kiara by 10 m increased the house price by RM1700. Similarly, increasing the size of the Taman Tasik Titiwangsa by 1000 m2 increases the house price by RM60,000. The advantage of the GWR result is the economic value of public UGSs which can be analyzed by the specific location according to sub-district. From this study, the GWR result exposed that the economic values of Taman Rimba Bukit Kiara and Taman Tasik Titiwangsa were not significant in each of the sub-district within KL city. Taman Rimba Bukit Kiara was negatively significant at all sub-districts except Setapak and certain house locations located at the sub-district of KL. In contrast, Taman Tasik Titiwangsa was positively significant at all sub-districts except certain house locations at the sub-districts of Batu, KL, Setapak, and KL city center. In conclusion, results show that the house price is influenced by the environmental attribute. However, even though both of these public UGSs generate the highest economic value based on distance and size, its significant values with an expected sign are only obtained based on the specific house location as verified by the local model. In terms of model comparison, the local model was better compared with the global model.
  5. Takae S, Iwahata Y, Sugishita Y, Iwahata H, Kanamori R, Shiraishi E, et al.
    Front Endocrinol (Lausanne), 2022;13:1074603.
    PMID: 36686445 DOI: 10.3389/fendo.2022.1074603
    OBJECTIVE: To verify understanding and awareness of fertility preservation (FP) in pediatric patients undergoing FP treatments.

    METHODS: A questionnaire survey was conducted before and after explanation of fertility issues and FP treatments for patients 6-17 years old who visited or were hospitalized for the purpose of ovarian tissue cryopreservation (OTC) or oocyte cryopreservation (OC), or sperm cryopreservation between October 2018 and April 2022. This study was approved by the institutional review board at St. Marianna University School of Medicine (No. 4123, UMIN000046125).

    RESULT: Participants in the study comprised 36 children (34 girls, 2 boys). Overall mean age was 13.3 ± 3.0 years. The underlying diseases were diverse, with leukemia in 14 patients (38.9%), brain tumor in 4 patients (11.1%). The questionnaire survey before the explanation showed that 19 patients (52.8%) wanted to have children in the future, but 15 (41.7%) were unsure of future wishes to raise children. And most children expressed some degree of understanding of the treatment being planned for the underlying disease (34, 94.4%). Similarly, most children understood that the treatment would affect their fertility (33, 91.7%). When asked if they would like to hear a story about how to become a mother or father after FP which including information of FP, half answered "Don't mind" (18, 50.0%). After being provided with information about FP treatment, all participants answered that they understood the adverse effects on fertility of treatments for the underlying disease. Regarding FP treatment, 32 children (88.9%) expressed understanding for FP and 26 (72.2%) wished to receive FP. "Fear" and "Pain" and "Costs" were frequently cited as concerns about FP. Following explanations, 33 children (91.7%) answered "Happy I heard the story" and no children answered, "Wish I hadn't heard the story". Finally, 28 of the 34 girls (82.4%) underwent OTC and one girl underwent OC.

    DISCUSSION: The fact that all patients responded positively to the explanations of FP treatment is very informative. This is considered largely attributable to the patients themselves being involved in the decision-making process for FP.

    CONCLUSIONS: Explanations of FP for children appear valid if age-appropriate explanations are provided.

  6. Mori M, Sagara K, Arai K, Nakatani N, Ohira S, Toda K, et al.
    J Chromatogr A, 2016 Jan 29;1431:131-7.
    PMID: 26755416 DOI: 10.1016/j.chroma.2015.12.064
    Selective separation and sensitive detection of dissolved silicon and boron (DSi and DB) in aqueous solution was achieved by combining an electrodialytic ion isolation device (EID) as a salt remover, an ion-exclusion chromatography (IEC) column, and a corona charged aerosol detector (CCAD) in sequence. DSi and DB were separated by IEC on the H(+)-form of a cation exchange resin column using pure water eluent. DSi and DB were detected after IEC separation by the CCAD with much greater sensitivity than by conductimetric detection. The five-channel EID, which consisted of anion and cation acceptors, cathode and anode isolators, and a sample channel, removed salt from the sample prior to the IEC-CCAD. DSi and DB were scarcely attracted to the anion accepter in the EID and passed almost quantitatively through the sample channel. Thus, the coupled EID-IEC-CCAD device can isolate DSi and DB from artificial seawater and hot spring water by efficiently removing high concentrations of Cl(-) and SO4(2-) (e.g., 98% and 80% at 0.10molL(-1) each, respectively). The detection limits at a signal-to-noise ratio of 3 were 0.52μmolL(-1) for DSi and 7.1μmolL(-1) for DB. The relative standard deviations (RSD, n=5) of peak areas were 0.12% for DSi and 4.3% for DB.
  7. Hasanpourghadi M, Karthikeyan C, Pandurangan AK, Looi CY, Trivedi P, Kobayashi K, et al.
    J Exp Clin Cancer Res, 2016;35(1):58.
    PMID: 27030360 DOI: 10.1186/s13046-016-0332-0
    Microtubule Targeting Agents (MTAs) including paclitaxel, colchicine and vinca alkaloids are widely used in the treatment of various cancers. As with most chemotherapeutic agents, adverse effects and drug resistance are commonly associated with the clinical use of these agents. Methyl 2-(5-fluoro-2-hydroxyphenyl)-1H- benzo[d]imidazole-5-carboxylate (MBIC), a benzimidazole derivative displays greater toxicity against various cancer compared to normal human cell lines. The present study, focused on the cytotoxic effects of MBIC against HeLa cervical cancer cells and possible actions on the microtubule assembly.
  8. Lachs L, Johari NAM, Le DQ, Safuan CDM, Duprey NN, Tanaka K, et al.
    Mar Pollut Bull, 2019 Nov;148:85-96.
    PMID: 31422307 DOI: 10.1016/j.marpolbul.2019.07.059
    Pulau Redang and Pulau Tioman have experienced huge tourism growth over the last two decades, but minimal sewage treatment may threaten the resilience of their coral reefs. This study uses stable isotope techniques to identify suitable bioindicators of sewage nutrients (δ15N) at these islands by measuring macroalgae (Lobophora spp.), gastropods (Drupella spp.), scleractinian coral (Acropora spp.), and leather coral (Sinularia spp.). At tourist hubs using seepage septic tank systems, enrichment of Acropora δ15N (Redang, +0.7‰) and Sinularia δ15N (Tioman, +0.4‰) compared to pristine background levels indicate enhanced sewage nutrient discharge. Carbon isotopes and survey data suggest that sedimentation did not confound these δ15N trends. Potential damaging effects of sewage discharge on the coral reef communities at both islands are highlighted by strong correlations between Acropora δ15N and regional variation in coral reef community structure, and exclusive occurrence of degraded reefs at regions of high sewage influence.
  9. Siau YF, Le DQ, Suratman S, Jaaman SA, Tanaka K, Kotaro S
    Mar Pollut Bull, 2021 Jan;162:111878.
    PMID: 33341077 DOI: 10.1016/j.marpolbul.2020.111878
    Seasonal variations in total mercury concentrations [Hg] and trophic transfer through the food web were assessed using stable isotopic tracers for the Setiu Wetlands, Terengganu. The [Hg] measured in surface sediments and biota varied inversely between wet and dry seasons. Increased rainfall and water disturbance during the wet season are suggested as the main factors releasing Hg from surface sediments and enhancing the bioavailability of Hg to biota. The elevated Hg levels associated with the leaf stage suggested that litterfall and atmospheric deposition may be the main Hg inputs into mangrove food webs. The positive relationships between log [Hg] and δ15N provided evidence for Hg biomagnification, however low trophic magnification slopes in both seasons indicated that the ecological risk of Hg in the wetland would be negligible. The [Hg] in fish and commercial crabs were below the permitted limits for human consumption.
  10. Ninomiya K, Arimura H, Chan WY, Tanaka K, Mizuno S, Muhammad Gowdh NF, et al.
    PLoS One, 2021;16(1):e0244354.
    PMID: 33428651 DOI: 10.1371/journal.pone.0244354
    OBJECTIVES: To propose a novel robust radiogenomics approach to the identification of epidermal growth factor receptor (EGFR) mutations among patients with non-small cell lung cancer (NSCLC) using Betti numbers (BNs).

    MATERIALS AND METHODS: Contrast enhanced computed tomography (CT) images of 194 multi-racial NSCLC patients (79 EGFR mutants and 115 wildtypes) were collected from three different countries using 5 manufacturers' scanners with a variety of scanning parameters. Ninety-nine cases obtained from the University of Malaya Medical Centre (UMMC) in Malaysia were used for training and validation procedures. Forty-one cases collected from the Kyushu University Hospital (KUH) in Japan and fifty-four cases obtained from The Cancer Imaging Archive (TCIA) in America were used for a test procedure. Radiomic features were obtained from BN maps, which represent topologically invariant heterogeneous characteristics of lung cancer on CT images, by applying histogram- and texture-based feature computations. A BN-based signature was determined using support vector machine (SVM) models with the best combination of features that maximized a robustness index (RI) which defined a higher total area under receiver operating characteristics curves (AUCs) and lower difference of AUCs between the training and the validation. The SVM model was built using the signature and optimized in a five-fold cross validation. The BN-based model was compared to conventional original image (OI)- and wavelet-decomposition (WD)-based models with respect to the RI between the validation and the test.

    RESULTS: The BN-based model showed a higher RI of 1.51 compared with the models based on the OI (RI: 1.33) and the WD (RI: 1.29).

    CONCLUSION: The proposed model showed higher robustness than the conventional models in the identification of EGFR mutations among NSCLC patients. The results suggested the robustness of the BN-based approach against variations in image scanner/scanning parameters.

  11. Kobayashi Y, Komatsuya K, Imamura S, Nozaki T, Watanabe YI, Sato S, et al.
    Proc Natl Acad Sci U S A, 2023 Jul 11;120(28):e2214765120.
    PMID: 37406097 DOI: 10.1073/pnas.2214765120
    The malaria parasite Plasmodium falciparum has a nonphotosynthetic plastid called the apicoplast, which contains its own genome. Regulatory mechanisms for apicoplast gene expression remain poorly understood, despite this organelle being crucial for the parasite life cycle. Here, we identify a nuclear-encoded apicoplast RNA polymerase σ subunit (sigma factor) which, along with the α subunit, appears to mediate apicoplast transcript accumulation. This has a periodicity reminiscent of parasite circadian or developmental control. Expression of the apicoplast subunit gene, apSig, together with apicoplast transcripts, increased in the presence of the blood circadian signaling hormone melatonin. Our data suggest that the host circadian rhythm is integrated with intrinsic parasite cues to coordinate apicoplast genome transcription. This evolutionarily conserved regulatory system might be a future target for malaria treatment.
  12. Bono S, Kimura SS, Kuit SH, Ng JE, Tanaka K, Ichikawa K, et al.
    J Acoust Soc Am, 2021 Sep;150(3):2189.
    PMID: 34598649 DOI: 10.1121/10.0006377
    Relatively little is known about spinner dolphins in Malaysian waters and the wider Southeast Asian region. This note represents the first known acoustic recording of the species sighted opportunistically in the northern Straits of Malacca. Over a brief 20 min sighting, 46 whistles were recorded and four tonal types were detected, with 54.4% being upsweep whistles. The whistle duration ranged from 36 to 977 ms and the frequency ranged from 6.6 to 23.8 kHz. Fifty-seven click trains with a mean interclick interval of 41.5 ± 19.3 ms were detected. These findings provide a baseline for future regional acoustic research on this species.
  13. Nishi E, Abe H, Tanaka K, Jimi N, Kupriyanova EK
    Zookeys, 2022;1100:1-28.
    PMID: 36760394 DOI: 10.3897/zookeys.1100.79569
    A new species of Spirobranchus (Annelida: Serpulidae) is described based on specimens collected at the coastal Shonan area of Sagami Bay and the adjacent areas of Honshu, Japan. Spirobranchusakitsushima sp. nov. forms large aggregations in the intertidal rocky zone of warm-temperate Japanese shores. This species was referred to as Pomatoleioskraussii (Baird, 1864) until the monotypic genus Pomatoleios was synonymized with Spirobranchus. This new species is formally described based on morphologically distinct Japanese specimens with supporting DNA sequence data. The calcareous opercular endplate of Spirobranchusakitsushima sp. nov. lacks a distinct talon, but some specimens have a slight rounded swelling on the endplate underside, while in other species of the S.kraussii complex a talon is present, usually extended, and with bulges. We examined sub-fossil tube aggregations of the new species and suggest that such aggregation stranded ashore is a good indicator of vertical land movements (uplift and subsidence) resulting from past events, such as earthquakes, in Honshu, Japan.
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