251 Works

Emergence of structures from parasitic species in a spatially distributed molecular system

Nathanael Aubert-Kato, Guillaume Gines, Yannick Rondelez & Teruo Fujii
This dataset contains microscopy images from a microfluidic setup implementing a localized autocatalytic molecular system based on the PEN DNA toolbox. Due to the enzymatic nature of the catalytic process, a variety of parasitic species eventually emerge and compete with the legitimate molecular process for fuel. The behaviors observed range from the creation of large stable structures to that of small diffusing particles. Those results, along with the modularity of the molecular system, show that...

Effects of body size divergence on male mating tactics in the ground beetle Carabus japonicus

Yutaka Okuzaki
Animal body size is involved in reproduction in various ways. Carabus japonicus exhibits considerable variation in adult body size across geographical locations depending on the larval environment. To investigate the effects of body size divergence on male mating traits, spermatophore deposition and weight, copulation duration, and post-copulatory mounting were observed using male-female pairs from C. japonicus populations with different body sizes. Then, variables with high predictive power on the mating traits were identified from individual...

Biodiversity-productivity relationships are key to nature-based climate solutions

Akira Mori, Laura Dee, Andrew Gonzalez, Haruka Ohashi, Jane Cowles, Alexandra Wright, Michel Loreau, Yann Hautier, Tim Newbold, Peter Reich, Tetsuya Matsui, Wataru Takeuchi, Kei-Ichi Okada, Rupert Seidl & Forest Isbell
The global impacts of biodiversity loss and climate change are interlinked but the feedbacks between them are rarely assessed. Areas with greater tree diversity tend to be more productive, providing a greater carbon sink, and biodiversity loss could reduce these natural C sinks. Here, we quantify how tree and shrub species richness could affect biomass production at biome, national and regional scales. We find that greenhouse gas mitigation could help maintain tree diversity and thereby...

Data from: Early origin of sweet perception in the songbird radiation

Yasuka Toda, Meng-Ching Ko, Qiaoyi Liang, Eliot Miller, Alejandro Rico-Guevara, Tomoya Nakagita, Ayano Sakakibara, Kana Uemura, Timothy Sackton, Takashi Hayakawa, Simon Yung Wa Sin, Yoshiro Ishimaru, Takumi Misaka, Pablo Oteiza, James Crall, Scott Edwards, Shuichi Matsumura & Maude Baldwin
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large radiation containing nearly half of all living birds. We demonstrate...

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: 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...

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...

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

Venus Climate Orbiter Akatsuki RS Doppler Profiles PDS3 dataset

Shin-ya Murakami, Hiroki Ando, Takeshi Imamura, Yukio Yamamoto & George L. Hashimoto
This dataset contains products acquired by radio science experiment using Ultra-Stable Oscillator (USO) onboard the Venus Climate Orbiter (VCO, also known as PLANET-C and AKATSUKI) spacecraft. This dataset conforms PDS3 Standard. This dataset uses the Committee on Data Management and Computation (CODMAC) data level numbering system. This RS OCCs Doppler data are considered Level 3 or Composite Data and are derived from Level 2. In the VCO RS level definition, this dataset is called Level...

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

Data from: Oceanic barriers promote language diversification in the Japanese Islands

Sean Lee & Toshikazu Hasegawa
Good barriers make good languages. Scholars have long speculated that geographical barriers impede linguistic contact between speech communities, and promote language diversification in a manner similar to the process of allopatric speciation. This hypothesis, however, has seldom been tested systematically and quantitatively. Here we adopt methods from evolutionary biology and attempt to quantify the influence of oceanic barriers on the degree of lexical diversity in the Japanese Islands. Measuring the degree of beta diversity from...

Data from: The Kuroshio Current influences genetic diversity and population genetic structure of a tropical seagrass, Enhalus acoroides

Yuichi Nakajima, Yu Matsuki, Chunlan Lian, Miguel D. Fortes, Wilfredo H. Uy, Wilfredo L. Campos, Masahiro Nakaoka & Kazuo Nadaoka
Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo-West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The...

Data from: Female polyandry and size-assortative mating in isolated local populations of the Japanese common toad Bufo japonicus

Kazuko Hase & Masakazu Shimada
In anurans, female polyandry under male harassment is distributed across taxa because of external aquatic fertilisation. According to the sexual selection theory, male–male competition for access to females is affected by the operational sex ratio (OSR) and population density. The Japanese common toad, Bufo japonicus, is widespread in mainland Japan, and like the European common toad, B. bufo, it engages in explosive breeding. We observed the breeding behaviour of B. japonicus in isolated local populations...

Data from: Building a responsive teacher: how temporal contingency of gaze interaction influences word learning with virtual tutors

Hanju Lee, Yasuhiro Kanakogi & Kazuo Hiraki
Animated pedagogical agents are lifelike virtual characters designed to augment learning. A review of developmental psychology literature led to the hypothesis that the temporal contingency of such agents would promote human learning. We developed a Pedagogical Agent with Gaze Interaction (PAGI), an experimental animated pedagogical agent that engages in gaze interaction with students. In this study, university students learned words of a foreign language, with temporally contingent PAGI (live group) or recorded version of PAGI...

Data from: Ocean sunfish rewarm at the surface after deep excursions to forage for siphonophores

Itsumi Nakamura, Yusuke Goto & Katsufumi Sato
1. Ocean sunfish (Mola mola) were believed to be inactive jellyfish feeders because they are often observed lying motionless at the sea surface. Recent tracking studies revealed that they are actually deep divers, but there has been no evidence of foraging in deep water. Furthermore, the surfacing behaviour of ocean sunfish was thought to be related to behavioural thermoregulation, but there was no record of sunfish body temperature. 2. Evidence of ocean sunfish feeding in...

Data from: A simple explanation for the evolution of complex song syntax in Bengalese finches

Kentaro Katahira, Kenta Suzuki, Hiroko Kagawa & Kazuo Okanoya
The songs of Bengalese finches (Lonchura striata var. domestica) have complex syntax and provide an opportunity to investigate how complex sequential behavior emerges via the evolutionary process. In the present study, we suggest that a simple mechanism, i.e., many-to-one mapping from internal states onto syllables, may underlie the emergence of apparent complex syllable sequences that have higher-order history dependencies. We analyzed the songs of Bengalese finches and of their wild ancestor, the white-rumped munia (Lonchura...

Data from: Natural allelic variations of xenobiotic metabolizing enzymes affect sexual dimorphism in Oryzias latipes

Takafumi Katsumura, Shoji Oda, Shigeki Nakagome, Tsunehiko Hanihara, Hiroshi Kataoka, Hiroshi Mitani, Shoji Kawamura & Hiroki Oota
Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection. Interestingly, sexually selected traits show geographical variations within species despite strong directional selective pressures. This paradox has eluded many evolutionary biologists for some time, and several models have been proposed (e.g. ‘indicator model’ and ‘trade-off model’). However, disentangling which of these theories explains empirical patterns remains difficult, because genetic polymorphisms that cause variation in sexual differences are still unknown. In...

Data from: Associated evolution of bipedality and cursoriality among Triassic archosaurs: a phylogenetically controlled evaluation.

Tai Kubo & Mugino O. Kubo
Bipedalism evolved more than twice among archosaurs, and it is a characteristic of basal dinosaurs and a prerequisite for avian flight. Nevertheless, the reasons for the evolution of bipedalism among archosaurs have barely been investigated. Comparative analysis using phylogenetically independent contrasts showed a significant correlation between bipedality (relative length of forelimb) and cursoriality (relative length of metatarsal III) among Triassic archosaurs. This result indicates that, among Triassic archosaurs, bipeds could run faster than quadrupeds. Bipedalism...

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