13 Works

Data from: Tracking time evolution of collective attention clusters in twitter: time evolving nonnegative matrix factorisation

Shota Saito, Yoshito Hirata, Kazutoshi Sasahara & Hideyuki Suzuki
Micro-blogging services, such as Twitter, offer opportunities to analyse user behaviour. Discovering and distinguishing behavioural patterns in micro-blogging services is valuable. However, it is difficult and challenging to distinguish users, and to track the temporal development of collective attention within distinct user groups in Twitter. In this paper, we formulate this problem as tracking matrices decomposed by Nonnegative Matrix Factorisation for time-sequential matrix data, and propose a novel extension of Nonnegative Matrix Factorisation, which we...

Data from: Convergence of soil nitrogen isotopes across global climate gradients

Joseph M. Craine, Andrew J. Elmore, Lixin Wang, Laurent Augusto, W. Troy Baisden, E. N. J. Brookshire, Michael D. Cramer, Niles J. Hasselquist, Erik A. Hobbie, Ansgar Kahmen, Keisuke Koba, J. Marty Kranabetter, Michelle C. Mack, Erika Marin-Spiotta, Jordan R. Mayor, Kendra K. McLauchlan, Anders Michelsen, Gabriela B. Nardoto, Rafael S. Oliveira, Steven S. Perakis, Pablo L. Peri, Carlos A. Quesada, Andreas Richter, Louis A. Schipper, Bryan A. Stevenson … & Bernd Zeller
Quantifying global patterns of terrestrial nitrogen (N) cycling is central to predicting future patterns of primary productivity, carbon sequestration, nutrient fluxes to aquatic systems, and climate forcing. With limited direct measures of soil N cycling at the global scale, syntheses of the 15N:14N ratio of soil organic matter across climate gradients provide key insights into understanding global patterns of N cycling. In synthesizing data from over 6000 soil samples, we show strong global relationships among...

Data from: The influence of preceding dive cycles on the foraging decisions of Antarctic fur seals

Takashi Iwata, Kentaro Q. Sakamoto, Ewan W. J. Edwards, Ian J. Staniland, Philip N. Trathan, Yusuke Goto, Katsufumi Sato, Yasuhiko Naito & Akinori Takahashi
The foraging strategy of many animals is thought to be determined by their past experiences. However, few empirical studies have investigated whether this is true in diving animals. We recorded three-dimensional movements and mouth-opening events from three Antarctic fur seals during their foraging trips to examine how they adapt their behaviour based on past experience—continuing to search for prey in the same area or moving to search in a different place. Each dive cycle was...

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: Global stability of obligate mutualistm in community modules with facultative mutualists

Gaku Takimoto & Kenta Suzuki
Mutualism is a fundamental building block of ecological communities and an important driver of biotic evolution. Classic theory suggests that a pairwise two-species obligate mutualism is fragile, with a large perturbation potentially driving both mutualist populations into extinction. In nature, however, there are many cases of pairwise obligate mutualism. Such pairwise obligate mutualisms are occasionally associated with additional interactions with facultative mutualists. Here, we use a mathematical model to show that when a two-species obligate...

Data from: Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa

Adrian Reich, Casey Dunn, Koji Akasaka & Gary Wessel
Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary...

Data from: The population demography of Betula maximowicziana, a cool temperate tree species in Japan, in relation to the last glacial period: Its admixture-like genetic structure is the result of simple population splitting not admixing

Yoshiaki T. Tsuda, Katsuhiro N. Nakao, Yuji I. Ide, Yoshihiko T. Tsumura, Y. Tsuda, Y. Tsumura & K. Nakao
Conservation of the local genetic variation and evolutionary integrity of economically and ecologically important trees is a key aspect of studies involving forest genetics, and a population demographic history of the target species provides valuable information for this purpose. Here, the genetic structure of 48 populations of Betula maximowicziana was assessed using 12 expressed sequence tag–simple sequence repeat (EST-SSR) markers. Genetic diversity was lower in northern populations than southern ones and structure analysis revealed three...

Data from: Flexibility and control of thorax deformation during hawkmoth flight

Noriyasu Ando & Ryohei Kanzaki
The interaction between neuromuscular systems and body mechanics plays an important role in the production of coordinated movements in animals. Lepidopteran insects move their wings by distortion of the thorax structure via the indirect flight muscles (IFMs), which are activated by neural signals at every stroke. However, how the action of these muscles affects thorax deformation and wing kinematics is poorly understood. We measured the deformation of the dorsal thorax (mesonotum) of tethered flying hawkmoths,...

Data from: Asymmetric dispersal structures a riverine metapopulation of the freshwater pearl mussel Margaritifera laevis

Akira Terui, Yusuke Miyazaki, Akira Yoshioka, Kenzo Kaifu, Shin-Ichiro S. Matsuzaki & Izumi Washitani
Unidirectional water flow results in the downstream-biased, asymmetric dispersal of many riverine organisms. However, little is known of how asymmetric dispersal influences riverine population structure and dynamics, limiting our ability to properly manage riverine organisms. A metapopulation of the freshwater pearl mussel Margaritifera laevis may be sensitive to river currents because mussels are repeatedly exposed to downstream drift during floods—a parasitic life stage is the only, limited period (~40 days) during which larvae (glochidia) can...

Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Masaki Miya, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Y. Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondoh & Wataru Iwasaki
We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility...

Data from: Opposite distortions in interval timing perception for visual and auditory stimuli with temporal modulations

Kenichi Yuasa & Yuko Yotsumoto
When an object is presented visually and moves or flickers, the perception of its duration tends to be overestimated. Such an overestimation is called time dilation. Perceived time can also be distorted when a stimulus is presented aurally as an auditory flutter, but the mechanisms and their relationship to visual processing remains unclear. In the present study, we measured interval timing perception while modulating the temporal characteristics of visual and auditory stimuli, and investigated whether...

Data from: A FISH-based chromosome map for the European corn borer yields insights into ancient chromosomal fusions in the silkworm

Yuji Yasukochi, Mizuki Ohno, Fukashi Shibata, Akiya Jouraku, Ryo Nakano, Yukio Ishikawa & Ken Sahara
A significant feature of the genomes of Lepidoptera, butterflies and moths, is the high conservation of chromosome organization. Recent remarkable progress in genome sequencing of Lepidoptera has revealed that syntenic gene order is extensively conserved across phylogenetically distant species. The ancestral karyotype of Lepidoptera is thought to be n = 31; however, that of the most well studied moth, Bombyx mori, is n = 28, and diverse studies suggest that three chromosomal fusion events occurred...

Data from: The landscape of realized homologous recombination in pathogenic bacteria

Koji Yahara, Xavier Didelot, Keith A. Jolley, Ichizo Kobayashi, Martin C. J. Maiden, Samuel K. Sheppard & Daniel Falush
Recombination enhances the adaptive potential of organisms by allowing genetic variants to be tested on multiple genomic backgrounds. Its distribution in the genome can provide insight into the evolutionary forces that underlie traits such as the emergence of pathogenicity. Here we examined landscapes of realized homologous recombination of 500 genomes from ten bacterial species, and found all species have ‘hot’ regions with elevated rates relative to the genome average. We examined the size, gene content...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Tokyo
  • Hokkaido University
  • National Institute for Environmental Studies
  • École Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine
  • Federal University of São Carlos
  • Ryukoku University
  • University of Waikato
  • University of Aberdeen
  • National Institute of Agrobiological Sciences
  • Copenhagen Zoo