264 Works

Additional file 2 of Continuous estimation of coseismic and early postseismic slip phenomena via the GNSS carrier phase to fault slip approach: a case study of the 2011 Tohoku-Oki sequence

Yusuke Tanaka, Yusaku Ohta & Shin’ichi Miyazaki
Additional file 2. It show a full animation describing the spatio-temporal evolution of the early afterslip estimated by PTS. It uses the same expression as the snapshots in the main text, but showing temporal evolution in every 30 s.

Continuous estimation of coseismic and early postseismic slip phenomena via the GNSS carrier phase to fault slip approach: a case study of the 2011 Tohoku-Oki sequence

Yusuke Tanaka, Yusaku Ohta & Shin’ichi Miyazaki
Abstract The transition process from coseismic to early postseismic phenomena within a half-day remains a significant topic for understanding the slip budget and friction properties of the fault. However, the investigation of this phase has undergone limited advancement. This is mainly due to the lack of precision pertaining to the Global Navigation Satellite System (GNSS) analysis caused by difficulty of separation between fault slip and other unknown parameters such as tropospheric delay. Therefore, we propose...

Contrast the distribution, transformation, and degradation of dissolved and particulate organic matter in the South Yellow Sea, the East China Sea, and its adjacent Kuroshio Current

Chongxiao Ji, Gui-Peng Yang, Yan Chen, Yan Li & Lin Zhang
The detailed information of sampling stations, the carbon, nitrogen, and amino acids levels in DOM and POM, as well as other parameters including temperature, salinity, nutrients, chlorophyll-a, and biological parameters (heterotrophic bacteria, Synechococcus, and picoeukaryotes) are dispalyed in this dataset.

Contrast the distribution, transformation, and degradation of dissolved and particulate organic matter in the South Yellow Sea, the East China Sea, and its adjacent Kuroshio Current

Chongxiao Ji, Gui-Peng Yang, Yan Chen, Yan Li & Lin Zhang
The detailed information of sampling stations, the carbon, nitrogen, and amino acids levels in DOM and POM, as well as other parameters including temperature, salinity, nutrients, chlorophyll-a, and biological parameters (heterotrophic bacteria, Synechococcus, and picoeukaryotes) are dispalyed in this dataset.

Museomics contributes to the spatiotemporal assessment of genetic diversity and structure in wild and ex situ conservation organisms: a case study of three endangered coastal plants in Japan

Naoyuki Nakahama, Shuji Matsumoto, Takeshi Asai, Atsuko Takano, Nana Morita, Ayumi Matsuo, Yoshihisa Suyama & Asumo Kuroda
Understanding the extent to which genetic diversity of wild populations in ex situ conservation can be retained is crucial for the management of such populations. Wild individuals collected in the target area in the past and present can be used to estimate the number of alleles lost over time in wild populations and thereby the number of alleles whose loss could be prevented by ex situ conservation. Here, we assessed the genetic diversity of wild...

Dataset and R code from: Positive and negative effects of land abandonment on butterfly communities revealed by a hierarchical sampling design across climatic regions

Keita Fukasawa, Naoki Sugimoto, Akio Asahara, Minoru Kasada, Misako Matsuba & Tadashi Miyashita
Land abandonment may decrease biodiversity but also provides an opportunity for rewilding. It is therefore necessary to identify areas that may benefit from traditional land management practices and those that may benefit from a lack of human intervention. In this study, we conducted comparative field surveys of butterfly occurrence in abandoned and inhabited settlements in 18 regions of diverse climatic zones in Japan to test the hypotheses that species-specific responses to land abandonment correlate with...

Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish

Javier Montenegro, Shingo Fujimoto, Satoshi Ansai, Atsushi Nagano, Masahiro Sato, Yusuke Maeda, Rieko Fujitani, Kawilarang Masengi, Ryosuke Kimura, Jun Kitano & Kazunori Yamahira
Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called “pelvic-fin brooding,” wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved...

Data from: Terrigenous subsidies in lakes support zooplankton production mainly via a green food chain and not the brown food chain

Jotaro Urabe, Fumiya Hirama, Hideyuki Doi, Takehiro Kazama, Takumi Noguchi, Tyler H. Tappenbeck, Izumi Katano, Masato Yamamichi, Takehito Yoshida & James J. Elser
Terrestrial organic matter (t-OM) has been recognized as an important cross-boundary subsidy to aquatic ecosystems. However, recent evidence has shown that t-OM contributes little to promote secondary production in lakes because it is low quality food for aquatic consumers. To resolve this conflict, we performed a field experiment using leaf litter as t-OM. In the experiment, we monitored zooplankton biomass in enclosures with and without addition of leaf litter under shaded and unshaded conditions and...

Additional file 4 of Matrix Gla protein (MGP), GATA3, and TRPS1: a novel diagnostic panel to determine breast origin

Tian Du, Lu Pan, Chengyou Zheng, Keming Chen, Yuanzhong Yang, Jiewei Chen, Xue Chao, Mei Li, Jiabin Lu, Rongzhen Luo, Jinhui Zhang, Yu Wu, Jiehua He, Dongping Jiang & Peng Sun
Additional file 4. Table S3. Correlation between protein and mRNA levels of 9 candidate genes.

Additional file 1 of Matrix Gla protein (MGP), GATA3, and TRPS1: a novel diagnostic panel to determine breast origin

Tian Du, Lu Pan, Chengyou Zheng, Keming Chen, Yuanzhong Yang, Jiewei Chen, Xue Chao, Mei Li, Jiabin Lu, Rongzhen Luo, Jinhui Zhang, Yu Wu, Jiehua He, Dongping Jiang & Peng Sun
Additional file 1: Fig. S1. The mRNA levels of candidate genes in different molecular subtypes of breast cancer. ER/PR+ (ER/PR+ and HER−, n = 685), HER2+ (n = 168), and TNBC (n = 177). TCGA BRCA ER, PR, and HER2 status were retrieved from Thennavan et al. [21].

10x barcode fastq of Anolis sagrei used for Supernova de novo assembly

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
10x barcode fastq of Anolis sagrei used for Supernova de novo assembly. Paired-end short read data for Supernova de novo assembly were deposited in the DDBJ Short Read Archive database under BioProject accession number PRJDB13431.

Anolis homolechis gene annotation

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
The result of gene annotation for Anolis homolechis genome using BRAKER2.

Anolis allogus CDS

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis allogus CDS predicted using BRAKER2.

Anolis sagrei CDS

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis sagrei CDS predicted using BRAKER2.

Anolis sagrei peptide sequences

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis sagrei peptide sequences predicted using BRAKER2.

10x barcode fastq of Anolis isolepis used for Supernova de novo assembly

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi & Masakado Kawata
10x barcode fastq of Anolis isolepis used for Supernova de novo assembly. Paired-end short read data for Supernova de novo assembly were deposited in the DDBJ Short Read Archive database under BioProject accession number PRJDB13431.

Anolis homolechis CDS

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis homolechis CDS predicted using BRAKER2.

Anolis homolechis gene annotation

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
The result of gene annotation for Anolis homolechis genome using BRAKER2.

Anolis porcatus peptide sequences

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis porcatus peptide sequences predicted using BRAKER2.

Anolis isolepis draft genome (repeat-softmasked)

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Repeatitive elements annotated by RepeatMasker were softmasked.

Additional file 2 of Clinical impact of cardiac magnetic resonance in patients with suspected coronary artery disease associated with chronic kidney disease (AQUAMARINE-CKD study): study protocol for a randomized controlled trial

Teruo Noguchi, Hideki Ota, Naoya Matsumoto, Yoshiaki Morita, Akira Oshita, Eiji Kawasaki, Tomohiro Kawasaki, Kensuke Moriwaki, Shingo Kato, Kazuki Fukui, Tomoya Hoshi, Hiroaki Watabe, Tomoaki Kanaya, Yasuhide Asaumi, Yu Kataoka, Fumiyuki Otsuka, Kensuke Takagi, Shuichi Yoneda, Kenichiro Sawada, Takamasa Iwai, Hideo Matama, Satoshi Honda, Masashi Fujino, Hiroyuki Miura, Kunihiro Nishimura … & Kei Takase
Additional file 2: Supplementary Table 1. Standardized protocol for non-contrast T1-weighted imaging to assess coronary plaques: recommended protocol for CMR coronary plaque imaging.

Association between the number of remaining teeth and disability-free life expectancy, and the impact of oral self-care in older Japanese adults: a prospective cohort study

Maya Yamato, Sanae Matsuyama, Yoshitaka Murakami, Jun Aida, Yukai Lu, Yumi Sugawara & Ichiro Tsuji
Abstract Background Tooth loss has been reportedly associated with shorter disability-free life expectancy (DFLE). However, no study has explored whether oral self-care offsets reduction in DFLE. The present study aimed to assess the association between oral self-care and DFLE in older individuals with tooth loss. Methods Data on the 13-year follow-up from a cohort study of 14,206 older Japanese adults aged ≥ 65 years in 2006 were analyzed. Information on the number of remaining teeth...

Additional file 1 of Association between the number of remaining teeth and disability-free life expectancy, and the impact of oral self-care in older Japanese adults: a prospective cohort study

Maya Yamato, Sanae Matsuyama, Yoshitaka Murakami, Jun Aida, Yukai Lu, Yumi Sugawara & Ichiro Tsuji
Additional file 1: Supplementary Table 1. Baseline characteristics according to whether or not agreed to a review of their LTCI information. Supplementary Table 2. DFLE, DLE, and TLE at 65 years by the number of remaining teeth with brushing (once vs. twice or more per day). Supplementary Table 3. DFLE, DLE, and TLE at 65 years according to the number of remaining teeth stratified by smoking status. Supplementary Table 4. DFLE, DLE, and TLE at...

Metabolic syndrome and the immunogenicity of Pfizer–BioNTech vaccine: a cross-sectional study in Japanese healthcare workers

Dong Van Hoang, Shohei Yamamoto, Ami Fukunaga, Yosuke Inoue, Tetsuya Mizoue & Norio Ohmagari
Abstract Background The clustering of metabolic abnormalities may weaken vaccine-induced immunity, but epidemiological data regarding SARS-CoV-2 vaccines are scarce. The present study aimed to examine the cross-sectional association between metabolic syndrome (MetS) and humoral immune response to Pfizer–BioNTech vaccine among the staff of a research center for medical care in Japan. Methods Participants were the staff (aged 21–75 years) of the National Center of Global Health and Medicine who had completed the second dose of...

Gamma-secretase inhibitor does not induce cytotoxicity in adult T-cell leukemia cell lines despite NOTCH1 expression

Shinsuke Suzuki, Sawako Hourai, Kimiharu Uozumi, Yuichirou Uchida, Makoto Yoshimitsu, Hachiman Miho, Naomichi Arima, Shin-ichi Ueno & Kenji Ishitsuka
Abstract Background Activated mutations in NOTCH1 are drivers of T-cell type acute lymphoblastic leukemia/lymphoma. The γ-secretase inhibitor (GSI), which suppresses the function of NOTCH1, is expected to be a molecular-targeted agent. NOTCH1 is also expressed in other malignant neoplasms. We aimed to determine the function of NOTCH1 expression and the effects of GSI on adult T-cell leukemia/lymphoma (ATL) caused by long-term human T-cell leukemia virus type I (HTLV-1) infection. Methods We analyzed the expression of...

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