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Identification of telomere maintenance gene variations related to lung adenocarcinoma risk by genome-wide association and whole genome sequencing analyses

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Cancer Communications 2024年第2期44卷 287-293页

作者： Kouya Shiraishi Atsushi Takahashi Yukihide Momozawa Yataro Daigo Syuzo Kaneko Takahisa Kawaguchi Hideo Kunitoh Shingo Matsumoto Hidehito Horinouchi Akiteru Goto Takayuki Honda Kimihiro Shimizu Masahiro Torasawa Daisuke Takayanagi Motonobu Saito Akira Saito Yuichiro Ohe Shun-ichi Watanabe Koichi Goto Masahiro Tsuboi Katsuya Tsuchihara Sadaaki Takata Tomomi Aoi Atsushi Takano Masashi Kobayashi Yohei Miyagi Kazumi Tanaka Hiroyuki Suzuki Daichi Maeda Takumi Yamaura Maiko Matsuda Yoko Shimada Takaaki Mizuno Hiromi Sakamoto Teruhiko Yoshida Yasushi Goto Tatsuya Yoshida taiki yamaji Makoto Sonobe Shinichi Toyooka Kazue Yoneda Katsuhiro Masago Fumihiro Tanaka Megumi Hara Nobuo Fuse Satoshi S.Nishizuka Noriko Motoi Norie Sawada Yuichiro Nishida Kazuki Kumada Kenji Takeuchi Kozo Tanno Yasushi Yatabe Kuniko Sunami Tomoyuki Hishida Yasunari Miyazaki Hidemi Ito Mitsuhiro Amemiya Hirohiko Totsuka Haruhiko Nakayama Tomoyuki Yokose Kazuyoshi Ishigaki Toshiteru Nagashima Yoichi Ohtaki Kazuhiro Imai Ken Takasawa Yoshihiro Minamiya Kazuma Kobayashi Kenichi Okubo Kenji Wakai Atsushi Shimizu Masayuki Yamamoto Motoki Iwasaki Koichi Matsuda Johji Inazawa Yuichi Shiraishi Hiroyoshi Nishikawa Yoshinori Murakami Michiaki Kubo Fumihiko Matsuda Yoichiro Kamatani Ryuji Hamamoto Keitaro Matsuo Takashi Kohno Division of Genome Biology National Cancer Center Research InstituteTokyoJapan Department of Clinical Genomics National Cancer Center Research InstituteTokyoJapan Laboratory for Statistical Analysis Center for Integrative Medical SciencesRIKENYokohamaJapan Department of Genomic Medicine Research InstituteNational Cerebral and Cardiovascular CenterOsakaJapan Laboratory for Genotyping Development Center for Integrative Medical SciencesRIKENYokohamaJapan Center for Antibody and Vaccine Therapy Research HospitalInstitute of Medical ScienceThe University of TokyoTokyoJapan Department of Medical Oncology and Cancer Center and Center for Advanced Medicine against CancerShiga University of Medical ScienceOtsuJapan Division of Medical AI Research and Development National Cancer Center Research InstituteTokyoJapan Center for Genomic Medicine Graduate School of MedicineKyoto UniversityKyotoJapan Department of Medical Oncology Japanese Red Cross Medical CenterTokyoJapan Department of Thoracic Oncology National Cancer Center Hospital EastJapan Department of Thoracic Oncology National Cancer Center HospitalTokyoJapan Department of Cellular and Organ Pathology Graduate School of MedicineAkita UniversityAkitaJapan Department of Respiratory Medicine Tokyo Medical and Dental UniversityBunkyo-kuTokyoJapan Division of General Thoracic Surgery Department of SurgeryShinshu University School of MedicineMatsumotoNaganoJapan Department of General Surgical Science Division of General Thoracic SurgeryGunma University Graduate School of MedicineIntegrative Center of General SurgeryGunma University HospitalGunmaJapan Department of Gastrointestinal Tract Surgery Fukushima Medical University School of MedicineFukushimaJapan StaGen Co. LtdTokyoJapan Division of Thoracic Surgery National Cancer Center HospitalTokyoJapan Department of Thoracic Surgery National Cancer Center Hospital EastChibaJapan Division of Translational Informatics Exploratory Oncology Research and Clinical Trial Center(EPOC

Dear editor,Lung carcinoma is responsible for the highest fatal-ity rate among cancer-related deaths globally,with lung adenocarcinoma(LADC)emerging as the prevailing sub-type.

关键词： adenocarcinoma lung Lung

Contour detection with bicubic spline surfaces

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International Journal of Digital Earth 2023年第1期16卷 1801-1827页

作者： Hiroyuki Goto taiki Otsuka Department of Industrial and Systems Engineering Hosei UniversityTokyoJapan Faculty of IT and Business Cyber UniversityTokyoJapan

Contour detection has a rich history in multiplefields such as geography,engineering,and earth *** predominant approach is based on piecewise planar tessellation and now being challenged concerning the extraction of contour objects for non-linear elevation functions,particularly with respect to bicubic spline functions.A storage-efficient method was developed in previous research,but the detection of the complete set of contour objects is yet to be *** intractable,theoretical underpinnings pertinent to curvature resulted in an approach to realize the complete detection of *** a digital elevation model dataset,in this study,a bicubic spline surface function wasfirst ***,candidate initial points on the edges across the region of interest were identified,and the recursive disaggregation of rectangles was repeated if the non-existence of a solution could not be assured.A developed tracking method was then *** advancement,other initial points on the same contour curve were identified and eliminated to circumvent duplicate *** completeness of the outlets provides analytical tools for elevation and other geographical *** experiments included the development of a three-dimensional contour-based network and slope *** latter application transforms the slope analysis type from raster-based to *** of a complete set of contour objects amenable to bicubic spline surfaces..Small closure inside a single patch is detectable if size exceeds the standard..Curvature&tolerances central to step length adjustment and tangent angle determination..Redundant initial points are identified and eliminated during the tracking process..Various potential applications in addition to geographical elevations.

关键词： Contour detection bicubic spline surface curvature tolerance patch disaggregation

Influence of image classification accuracy on saliency map estimation

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CAAI Transactions on Intelligence Technology 2018年第3期3卷 140-152页

作者： taiki Oyama Takao Yamanaka Department of Information and Communication Sciences Sophia University 7-1 Kioi-cho Chiyoda-ku Tokyo 102-0094 Japan

Saliency map estimation in computer vision aims to estimate the locations where people gaze in images. Since people tend to look at objects in images, the parameters of the model pre-trained on ImageNet for image classification are useful for the saliency map estimation. However, there is no research on the relationship between the image classification accuracy and the performance of the saliency map estimation. In this study, it is shown that there is a strong correlation between image classification accuracy and saliency map estimation accuracy. The authors also investigated the effective architecture based on multi-scale images and the up-sampling layers to refine the saliencymap resolution. The model achieved the state-of-the-art accuracy on the PASCAL-S, OSIE, and MIT1003 datasets. In the MIT saliency benchmark, the model achieved the best performance in some metrics and competitive results in the other metrics.

关键词：计算机视觉图像处理发展现状计算机技术

The responses of carbon-and nitrogen-acquiring enzymes to nitrogen and phosphorus additions in two plantations in southern China

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Journal of Forestry Research 2020年第4期31卷 1319-1324页

作者： Senhao Wang taiki Mori Jiangming Mo Wei Zhang Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems and Guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenChinese Academy of SciencesGuangzhou 510650GuangdongPeople’s Republic of China Graduate School of Agriculture Kyoto UniversityKitashirakawa Oiwake-choSakyo-kuKyotoJapan University of Chinese Academy of Sciences Beijing 100049People’s Republic of China

In tropical plantations,nutrients such as nitrogen(N)or phosphorus(P)are often applied as management ***,the effects of such nutrient additions on topsoil C-and N-acquiring enzymes activities are *** this study,the impacts of fertilization onβ-1,4-glucosidase(BG),β-D-cellobiosidase(CBH),β-1,4-xylosidase(BX),β-1,4-N-acetyl-glucosaminidase(NAG),and leucine amino peptidase(LAP)enzymes activities from topsoil and litter layer of two tropical plantations(Acacia auriculiformis and Eucalyptus urophylla)were *** results showed that N addition had neutral impact on topsoil enzymes,while significantly elevating the activities of BG,CBH,BX,and NAG in the litter layer.P fertilization had no impacts except for an elevation of NAG in litter *** was no interactions found between N and P additions on these enzyme *** clearer impacts of N over P fertilization were unexpected because that the study site receives a high rate of atmospheric N deposition,and has low soil P *** impact of P fertilization on hydrolytic enzyme activities may be less important compared with that of N.

关键词： Tropical tree plantation Ecoenzymes Fertilization Forest management

Water-assisted self-sustained burning of metallic single-walled carbon nanotubes for scalable transistor fabrication

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Nano Research 2017年第9期10卷 3248-3260页

作者： Keigo Otsuka taiki Inoue Yuki Shimomura Shohei Chiashi Shigeo Maruyama Department of Mechanical Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan Energy NanoEngineering Lab. National Institute of Advanced Industrial Science and Technology (AIST) 1-2-1 Namiki Tsukuba 305-8564 Japan

Although aligned arrays of semiconducting single-walled carbon nanotubes (s-SWNTs) are promising for use in next-generation electronics owing to their ultrathin bodies and ideal electrical properties, even a small portion of metallic (m-) counterparts causes excessive leakage in field-effect transistors (FETs). To fully exploit the benefits of s-SWNTs for use in large-scale systems, it is necessary to completely eliminate m-SWNTs from as-grown SWNT arrays and thereby obtain purely semiconducting large-area arrays, wherein numerous FETs can be flexibly built. In this study, we performed electrical burning of m-SWNTs assisted by water vapor and polymer coating to eliminate m-SWNTs over a long length for the scalable fabrication of transistors from the remaining s-SWNT arrays. During the electrical-breakdown process, the combination of water vapor and the polymer coating significantly enhanced the burning of the SWNTs, resulting in a self-sustained reaction along the nanotube axis. We found that m-SWNT segments partially remaining on the anode side resulted from one-way burning from the initial breakdown position, where Joule-heating-induced oxidation first occurred. The s-SWNT-enriched arrays obtained were used to fabricate multiple FETs with a high on-off current ratio. The results indicate the advantages of this approach over conventional electrical breakdown for the large-scale purification of s-SWNTs.

关键词： single-walled carbon nanotubes field-effect transistor selective removal electrical breakdown one-way burning

Psychophysical Neuroeconomics of Decision Making: Nonlinear Time Perception Commonly Explains Anomalies in Temporal and Probability Discounting

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Applied Mathematics 2013年第11期4卷 1520-1525页

作者： taiki Takahashi Ruokang Han Center for Experimental Research in Social Science Department of Behavioral Science Faculty of Letters Hokkaido University Sapporo Japan

Anomalies in decision over time (e.g., “hyperbolic time discounting”) and under risk (e.g., Allais paradox and hyperbolic probability discounting) have been attracting attention in behavioral and neuroeconomics. We have proposed that psychophysical time commonly explains anomalies in both decisions (Takahashi, 2011, Physica A;Takahashi et al., 2012, J Behav Econ & Finance). By adopting the q-exponential time and probability discounting models, our psychophysical and behavioral economic experiment confirmed that nonlinear distortion of psychophysical time is a common cause of the anomalies in decision both over time and under risk (i.e., intertemporal choice and decision under risk). Implications for psychophysical neuroeconomics and econophysics are discussed.

关键词： Psychophysics Discounting Neuroeconomics Econophysics Tsallis’ Statistics

Exploring the hepatitis C virus genome using single molecule realtime sequencing

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World Journal of Gastroenterology 2019年第32期25卷 4661-4672页

作者： Haruhiko Takeda taiki Yamashita Yoshihide Ueda Akihiro Sekine Department of Omics-based Medicine Center for Preventive Medical ScienceChiba UniversityChiba 260-0856Japan Department of Gastroenterology and Hepatology Graduate School of MedicineKyoto UniversityKyoto 606-8507Japan

Single molecular real-time(SMRT)sequencing,also called third-generation sequencing,is a novel sequencing technique capable of generating extremely long contiguous sequence *** conventional short-read sequencing cannot evaluate the linkage of nucleotide substitutions distant from one another,SMRT sequencing can directly demonstrate linkage of nucleotide changes over a span of more than 20 kbp,and thus can be applied to directly examine the haplotypes of viruses or bacteria whose genome structures are changing in real *** addition,an error correction method(circular consensus sequencing)has been established and repeated sequencing of a single-molecule DNA template can result in extremely high *** advantages of long read sequencing enable accurate determination of the haplotypes of individual viral *** sequencing has been applied in various studies of viral genomes including determination of the full-length contiguous genome sequence of hepatitis C virus(HCV),targeted deep sequencing of the HCV NS5A gene,and assessment of heterogeneity among viral ***,the emergence of multi-drug resistant HCV viruses has become a significant clinical issue and has been also demonstrated using SMRT *** this review,we introduce the novel third-generation PacBio RSII/Sequel systems,compare them with conventional next-generation sequencers,and summarize previous studies in which SMRT sequencing technology has been applied for HCV genome *** also refer to another long-read sequencing platform,nanopore sequencing technology,and discuss the advantages,limitations and future perspectives in using these thirdgeneration sequencers for HCV genome analysis.

关键词： Third generation sequencing PacBio RSII Single molecule real-time sequencing Hepatitis C virus Resistance-associated substitution Nanopore sequencer

Formation mechanism of extension fractures induced by excavation of a gallery in soft sedimentary rock,Horonobe area,Northern Japan

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Geoscience Frontiers 2013年第1期4卷 105-111页

作者： Tetsuya Tokiwa Kimikazu Tsusaka Makoto Matsubara taiki Ishikawa Daisuke Ogawa Horonobe Underground Research Unit Japan Atomic Energy AgencyHokkaido 098-3224Japan Geoscience Research Laboratory Kanagawa 242-0014Japan Mitsubishi Materials Techno Corporation Tokyo 102-8205Japan

This paper focuses on the formation mechanism of fractures induced by excavation of a gallery in soft sedimentary rocks in the Horonobe area of Japan. Detailed fracture mapping of the gallery indicates that the fractures consist of both pre-existing shear fractures and excavation damaged zone （EDZ） fractures. EDZ fractures correspond to weak planes associated with bedding planes or transgranular cracks. The EDZ fractures terminate against pre-existing shear fractures. Therefore, even for excavations in soft sedimentary rocks, formation of the EDZ fractures are controlled by pre-existing fractures and earlier weak planes.

关键词： Fracture Excavation damaged zone (EDZ)Weak plane Soft rock Excavation

Determination of persistent organic pollutants by gas chromatography/laser multiphoton ionization/time-of-flight mass spectrometry

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Frontiers of Environmental Science & Engineering 2012年第1期6卷 26-31页

作者： Osamu SHITAMICHI taiki MATSUI Yamei HUI Weiwei CHEN Totaro IMASAKA Department of Applied Chemistry Graduate School of Engineering Kyushu University Fukuoka 819-0395 Japan School of Environment Tsinghua University Beijing 100084 China Division of Translational Research Center for Future Chemistry Kyusl~u Univeresity Fukuoka 819-0395 Japan

An authentic mixture of polychlorinated biphenyls was measured using a short wide-bore capillary column for the group separation of major components present in an actual sample of Kanechlor. The limits of detection were improved by ca. 2 fold in comparison with those obtained using a conventional capillary column, since the retention time was reduced and the amount of analytes introduced into the mass spectrometer per unit time could be increased. On the other hand, surface-water and sediment samples containing polycyclic aromatic hydrocarbons （PAHs） were collected from the river located in the vicinity of a waste water treatment plant. Even acenaphthylene, a minor component of the mixture could be measured for the sediment sample, and the concentra- tions were determined for several heavy PAHs. As demonstrated, a technique involving laser multiphoton ionization/time-of-flight mass spectrometry was useful as a sensitive and selective analytical tool for the trace analysis of persistent organic pollutants in an environmental sample.

关键词： polychlorinated biphenyls (PCBs) polycyclic aromatic hydrocarbons (PAHs) laser multiphoton ioniza- tion/time-of-flight mass spectrometry (MPI/TOF-MS)