63 Works

Muscle systems and motility of early animals highlighted by cnidarians from the basal Cambrian

Xing Wang, Jean Vannier, Xiaoguang Yang, Lucas Leclère, Qiang Ou, Xikun Song, Tsuyoshi Komiya & Jian Han
Although fossil evidence suggests that various animal groups were able to move actively through their environment in the early stages of their evolution, virtually no direct information is available on the nature of their muscle systems. The origin of jellyfish swimming, for example, is of great interest to biologists. Exceptionally preserved muscles are described here in benthic peridermal olivooid medusozoans from the basal Cambrian of China (Kuanchuanpu Formation, ca. 535 Ma) that have direct equivalent...

Data from: A generalized distribution interpolated between the exponential and power law distributions and applied to pill bug (Armadillidium vulgare) walking data

Shuji Shinohara, Hiroshi Okamoto, Toru Moriyama, Yoshihiro Nakajima, Takaharu Shokaku, Akika Utsumi & Ung-Il Chung
The walking pattern of an organism is typically designated as either a Lévy walk or a Brownian walk based on whether the frequency distribution of its linear step lengths follows a power law distribution or an exponential distribution. However, there are many cases where actual data cannot be classified into either of these categories. In this paper, we propose a general distribution that includes the power law and exponential distributions as special cases. This distribution...

Additional file 1 of Effects of let-7a microRNA and C–C chemokine receptor type 7 expression on cellular function and prognosis in esophageal squamous cell carcinoma

Masahiro Yura, Kazumasa Fukuda, Satoru Matsuda, Tomoyuki Irino, Rieko Nakamura, Hirofumi Kawakubo, Hiroya Takeuchi & Yuko Kitagawa
Additional file 1: Table S1. Quantitative RT-PCR analysis.

Outcomes of allogeneic haematopoietic stem cell transplantation with intensity-modulated total body irradiation by helical tomotherapy: a 2-year prospective follow-up study

Tatsuya Konishi, Hiroaki Ogawa, Yuho Najima, Shinpei Hashimoto, Satoshi Kito, Yuya Atsuta, Atsushi Wada, Hiroto Adachi, Ryosuke Konuma, Yuya Kishida, Akihito Nagata, Yuta Yamada, Satoshi Kaito, Junichi Mukae, Atsushi Marumo, Yuma Noguchi, Naoki Shingai, Takashi Toya, Aiko Igarashi, Hiroaki Shimizu, Takeshi Kobayashi, Kazuteru Ohashi, Noriko Doki & Keiko Nemoto Murofushi
Intensity-modulated radiation therapy (IMRT) helps achieve good radiation dose conformity and precise dose evaluation. We conducted a single-centre prospective study to assess the safety and feasibility of total body irradiation with IMRT (IMRT-TBI) using helical tomotherapy in allogeneic haematopoietic stem cell transplantation (allo-HSCT). Thirty-nine adult patients with haematological malignancy (acute lymphoblastic leukaemia [n = 21], chronic myeloid leukaemia [n = 6], mixed phenotype acute leukaemia [n = 5], acute myeloid leukaemia [n = 4], and...

Data assimilation using high-frequency radar for tsunami early warning: A case study of the 2022 Tonga volcanic tsunami

Yuchen Wang, Kentaro Imai, Iyan E. Mulia, Keisuke Ariyoshi, Narumi Takahashi, Kenichi Sasaki, Hitoshi Kaneko & Yoshiaki Sato
Tide gauge data in Japan of the 2022 Tonga volcanic tsunami

Data assimilation using high-frequency radar for tsunami early warning: A case study of the 2022 Tonga volcanic tsunami

Yuchen Wang, Kentaro Imai, Iyan E. Mulia, Keisuke Ariyoshi, Narumi Takahashi, Kenichi Sasaki, Hitoshi Kaneko & Yoshiaki Sato
Tide gauge data in Japan of the 2022 Tonga volcanic tsunami

Positive effects of fast growth on locomotor performance in pelagic fish juveniles

Masahiro Nakamura, MIchio Yoneda, Taizo Morioka, Akinori Takasuka & Nozomi Nishiumi
Many laboratory experiments on aquatic vertebrates that inhabit closed water or coastal areas have highlighted negative effects of fast growth on swimming performance. Nonetheless, field studies on pelagic fishes have provided evidence of survival advantages of faster growing individuals. To reconcile this contradiction, we examined the relationship between growth rate and swimming performance as a continuous function for juveniles of chub mackerel (scomber japonicus) using 3D tracking analysis. For experiments, 20, 24, 27, and 30...

Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts

Yoshito Hirata, Arisa Oda, Chie Motono, Masanori Shiro & Kunihiro Ohta
These files are results obtained inImputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contactsby Yoshito Hirata, Arisa H. Oda, Chie Motono, Masanori Shiro & Kunihiro Ohta. There are 33 files for the corresponding each reconstruction of three-dimensional chromosomone structuresfor each cell.There are 3D structures for 15 GM cells and 18 PBMC cells, which are obtained from the single cell Hi-C data of Tan et al. Science (2018). For each file, there...

Data from: Evolutionary transition from a single RNA replicator to a multiple replicator network

Ryo Mizuuchi, Taro Furubayashi & Norikazu Ichihashi
In prebiotic evolution, self-replicating molecules are believed to have evolved into complex living systems by expanding their information and functions open-endedly. Theoretically, such evolutionary complexification could occur through successive appearance of novel replicators that interact with one another to form replication networks. Here we perform long-term evolution experiments of RNA that replicates using a self-encoded RNA replicase. The RNA diversifies into multiple coexisting host and parasite lineages, whose frequencies in the population initially fluctuate and...

Molasses fermentation to produce low-cost carbon source for denitrification

Chang Liu & Kai Cheng
In the present work, the fermentation of molasses using Saccharomyces cerevisiae was optimized in terms of denitrification efficiency, using the relative total nitrogen (TN) removal ratio and the C/N consumption ratio as the indicators. The denitrification efficiency in different wastewater was also measured in the presence of different carbon sources for denitrification, that is, fermentation broth, unfermented molasses, sodium acetate, ethanol and methanol. The results indicated that the optimal fermentation conditions were as follows: pH...

Molasses fermentation to produce low-cost carbon source for denitrification

Chang Liu & Kai Cheng
In the present work, the fermentation of molasses using Saccharomyces cerevisiae was optimized in terms of denitrification efficiency, using the relative total nitrogen (TN) removal ratio and the C/N consumption ratio as the indicators. The denitrification efficiency in different wastewater was also measured in the presence of different carbon sources for denitrification, that is, fermentation broth, unfermented molasses, sodium acetate, ethanol and methanol. The results indicated that the optimal fermentation conditions were as follows: pH...

Supplemental materials for utility of multimodality approach including systemic FGF23 venous sampling in localizing phosphaturic mesenchymal tumors

Hajime Kato, Minae Koga, Yuka Kinoshita, Naoko Hidaka, Yoshitomo Hoshino, Yuichi Takashi, Makoto Arai, Hiroshi Kobayashi, Masaki Katsura, Yuji Nakamoto, Naohiro Makise, Tetsuo Ushiku, Kazuto Hoshi, Masaomi Nangaku, Noriko Makita, Seiji Fukumoto & Nobuaki Ito
This is the supplemental materials for utility of multimodality approach including systemic FGF23 venous sampling in localizing phosphaturic mesenchymal tumors

Microsatellite data from: Multiple colonizations and genetic differentiation from the mainland populations in insular populations of the perennial herb Solidago virgaurea complex (Asteraceae) on recently formed nearshore oceanic islands

Takuma Kimura, Takayuki Yamada, Shota Sakaguchi, Motomi Ito & Masayuki Maki
Aim: Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands substantially far from the mainland. Except for a few examples such as the Canary Islands, endemic plants on nearshore oceanic islands have received less attention. In this study, we examined the Solidago virgaurea complex on the Japanese mainland Honshu and the adjacent Izu Islands to...

Latitudinal cline in the foraging dichotomy of loggerhead sea turtles reveals the importance of East China Sea for priority conservation

Junichi Okuyama, Akemi Watabe, Shunichi Takuma, Kentaro Tanaka, Kotaro Shirai, Naoko Murakami-Sugihara, Mamiko Arita, Kento Fujita, Hideaki Nishizawa, Tomoko Narazaki, Yoshiya Yamashita & Kazunari Kameda
Aim: Quantifying the importance of habitat areas for conservation of highly migratory marine species with complex life histories can be challenging. For example, loggerhead turtles (Caretta caretta) nesting in Japan forage both oceanically and neritically after their reproductive period. Here, we aimed to quantify the proportions of turtles using these two contrasting habitats (foraging dichotomy) to suggest priority conservation areas. Methods: We examined the occurrence of foraging dichotomy at three nesting sites (Ishigaki, Okinoerabu Islands,...

Medium-chain fatty acids prevent lipotoxicity-induced hepatic fibrosis via the immunomodulating receptor GPR84

Ryuji Ohue-Kitano, Hazuki Nonaka, Yuki Masujima, Daisuke Takahashi, Akari Nishida, Takako Ikeda, Akiharu Uwamizu, Miyako Tanaka, Motoyuki Kohjima, Miki Igarashi, Hironori Katoh, Tomohiro Tanaka, Asuka Inoue, Takayoshi Suganami, Koji Hase, Yoshihiro Ogawa, Junken Aoki & Ikuo Kimura
Medium-chain triglycerides (MCTs), which consist of medium-chain fatty acids (MCFAs), are unique forms of dietary fat with various health benefits. GPR84 acts as a receptor for MCFAs (especially C10:0 and C12:0); however, GPR84 is still considered an orphan receptor, and the nutritional signaling of endogenous and dietary MCFAs via GPR84 remains unclear. Here, we showed that endogenous MCFA-mediated GPR84-signaling protected hepatic functions from diet-induced lipotoxicity. Under high-fat diet (HFD) conditions, GPR84-deficient mice exhibited non-alcoholic steatohepatitis...

Data assimilation using high-frequency radar for tsunami early warning: A case study of the 2022 Tonga volcanic tsunami

Yuchen Wang, Kentaro Imai, Iyan E. Mulia, Keisuke Ariyoshi, Narumi Takahashi, Kenichi Sasaki, Hitoshi Kaneko & Yoshiaki Sato
Tide gauge data in Japan of the 2022 Tonga volcanic tsunami

Additional file 4 of Lithological structure of western Pacific lithosphere reconstructed from mantle xenoliths in a petit-spot volcano

Kazuto Mikuni, Naoto Hirano, Norikatsu Akizawa, Junji Yamamoto, Shiki Machida, Akihiro Tamura, Yuuki Hagiwara & Tomoaki Morishita
Additional file 4. Supplementary tables. Table S1. Major element compositions of olivine. Table S2. Major element compositions of clinopyroxene. Table S3. Major element compositions of orthopyroxene. Table S4. Major element compositions of spinel. Table S5. Trace element compositions of clinopyroxene. Table S6. Trace element compositions of orthopyroxene. Table S7. Data of Raman spectroscopy. Table S8. Average compositions of pyroxenes using the two pyroxene geothermobarometry.

Additional file 4 of Lithological structure of western Pacific lithosphere reconstructed from mantle xenoliths in a petit-spot volcano

Kazuto Mikuni, Naoto Hirano, Norikatsu Akizawa, Junji Yamamoto, Shiki Machida, Akihiro Tamura, Yuuki Hagiwara & Tomoaki Morishita
Additional file 4. Supplementary tables. Table S1. Major element compositions of olivine. Table S2. Major element compositions of clinopyroxene. Table S3. Major element compositions of orthopyroxene. Table S4. Major element compositions of spinel. Table S5. Trace element compositions of clinopyroxene. Table S6. Trace element compositions of orthopyroxene. Table S7. Data of Raman spectroscopy. Table S8. Average compositions of pyroxenes using the two pyroxene geothermobarometry.

Additional file 2 of Repression of the PRELP gene is relieved by histone deacetylase inhibitors through acetylation of histone H2B lysine 5 in bladder cancer

Kanto Shozu, Syuzo Kaneko, Norio Shinkai, Ai Dozen, Hirofumi Kosuge, Makoto Nakakido, Hidenori Machino, Ken Takasawa, Ken Asada, Masaaki Komatsu, Kouhei Tsumoto, Shin-Ichi Ohnuma & Ryuji Hamamoto
Additional file 2: It includes supplementary tables 1–4. Table S1. Individual data for the correlation between PRELP mRNA expression and somatic mutations. Table S2. Individual data for the correlation between PRELP mRNA expression and copy number aberrations. Table S3. Individual data for the correlation between PRELP mRNA expression and DNA methylation. Table S4. Information about the certified cell lines. STR method was used for certification.

Modelled fluvial flood hazard maps in Vietnam for the period 2070-2100

L. Hawker, J. Neal, K.N. Pham, Y. Hirabayashi & D. Yamazaki
This dataset contains fluvial flood maps of the present day 1 in 20 year return period, and corresponding flood extents for 3 SSP (Shared Socioeconomic Pathway)/RCP(Representative Concentration Pathway) scenarios for the future (2070-2100). Change in flood return periods are estimated using CMIP6 projections and subsequently used to extract flood maps from a global flood model.

Mass cytometry immunophenotyping data of two-week-old mouse pups' spleens depleted of maternal cells

Flore Castellan
The maternal cells transferred into the fetus during gestation persist long after birth in the progeny. These maternal cells have been hypothesized to promote the maturation of the fetal immune system in utero but there are still significant gaps in our knowledge of their potential roles after birth. To provide insights into these maternal cells' postnatal functional roles, we set up a transgenic mouse model to specifically eliminate maternal cells in the neonates by diphtheria...

Areal (+)-borneol modulates root morphology, auxin signalling and meristematic activity in Arabidopsis roots

Junji Takabayashi, Kyohei Fukuda, Masayoshi Uefune, Hidehiro Fukaki, Yasuo Yamauchi, Ikuko Hara-Nishimura, Rika Ozawa, Kenji Matsui, Kazunori Okada, Ryozo Imai, Kenshi Takahashi, Shinichi Enami, Rene Wurst & Junji Takabayashi
One of the characteristic aspects of odour sensing in humans is the activation of olfactory receptors in a slightly different manner to different enantiomers. Here, we focused on whether plants showed enantiomer-specific responses similar to that in humans. We exposed Arabidopsis seedlings to methanol (control) and (+)- or (−)-borneol, and found that only (+)-borneol reduced the root length. Furthermore, the root-tip width was more increased upon (+)-borneol exposure than upon (−)-borneol exposure. In addition, root-hair...

Data and scripts from: Exploratory analysis of multi-trait coadaptations in the light of population history

Reiichiro Nakamichi, Shuichi Kitada & Hirohisa Kishino
During the process of range expansion, populations encounter a variety of environments. They respond to the local environments by modifying their mutually interacting traits. Common approaches of landscape analysis include first focusing on the genes that undergo diversifying selection or directional selection in response to environmental variation. To understand the whole history of populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to...

Dataset from: Lung evolution in vertebrates and the water-to-land transition

Camila Cupello, Tatsuya Hirasawa, Norifumi Tatsumi, Yoshitaka Yabumoto, Pierre Gueriau, Sumio Isogai, Ryoko Matsumoto, Toshiro Saruwatari, Andrew King, Masato Hoshino, Kentaro Uesugi, Masataka Okabe & Paulo M Brito
A crucial evolutionary change in vertebrate history was the Palaeozoic (Devonian ~400 million years ago) water-to-land transition, allowed by key morphological and physiological modifications including the acquisition of lungs. Nonetheless, the origin and early evolution of vertebrate lungs remain highly controversial, particularly whether the ancestral state was paired or unpaired. Due to the rarity of fossil soft tissue preservation, lung evolution can only be traced based on the extant phylogenetic bracket. Here we investigate, for...

Additional file 1 of Effects of let-7a microRNA and C–C chemokine receptor type 7 expression on cellular function and prognosis in esophageal squamous cell carcinoma

Masahiro Yura, Kazumasa Fukuda, Satoru Matsuda, Tomoyuki Irino, Rieko Nakamura, Hirofumi Kawakubo, Hiroya Takeuchi & Yuko Kitagawa
Additional file 1: Table S1. Quantitative RT-PCR analysis.

Registration Year

  • 2022
    63

Resource Types

  • Dataset
    63

Affiliations

  • University of Tokyo
    62
  • Tohoku University
    9
  • RIKEN
    5
  • Kyoto University
    5
  • Sichuan University
    4
  • Fudan University
    4
  • Nanjing University
    4
  • Kyushu University
    3
  • Chiba Institute of Technology
    3
  • Chinese Academy of Sciences
    3