63 Works

Data from: Patterns of pollen flow in a dense population of the insect-pollinated canopy tree species Castanopsis sieboldii

Atsushi Nakanishi, Hiroshi Yoshimaru, Nobuhiro Tomaru, Masahiro Miura, Tohru Manabe & Shin-Ichi Yamamoto
Insect pollinations of tree species with high-density populations have rarely been studied. Since the density of adults can affect effective pollen dispersal, short-distance pollination, even by insects, may frequently occur in high-density populations. To test this prediction, we investigated pollination patterns in a high-density population of the insect-pollinated canopy tree species Castanopsis sieboldii by paternity analysis using genotypes at 8 microsatellite loci of 145 adult trees and 439 seeds from 11 seed parents in a...

Data from: The effect of sitagliptin on carotid artery atherosclerosis in Type 2 Diabetes: the PROLOGUE randomized controlled trial

Jun-Ichi Oyama, Koichi Node, Atsushi Tanaka, Toyoaki Murohara, Masafumi Kitakaze, Tomoko Ishizu, Yasunori Sato, Haruo Kamiya, Masaharu Ishihara, Koji Maemura, Hirofumi Tomiyama, Yukihito Higashi, Hirotsugu Yamada, Kentaro Yamashita, Yasuko K. Bando, Shinichiro Ueda & Teruo Inoue
Background: Experimental studies have suggested that dipeptidyl peptidase-4 (DPP-4) inhibitors provide cardiovascular protective effects. We performed a randomized study to evaluate the effects of sitagliptin added on to the conventional therapy compared with conventional therapy alone (diet, exercise, and/or drugs, except for incretin-related agents) on the intima-media thickness (IMT) of the carotid artery, a surrogate marker for the evaluation of atherosclerotic cardiovascular disease, in people with type 2 diabetes mellitus (T2DM). Methods and Findings: We...

Data from: Heterogeneous genetic makeup of the Japanese house mouse (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes

Takashi Kuwayama, Mitsuo Nunome, Gohta Kinoshita, Kuniya Abe & Hitoshi Suzuki
In this study, phylogenetic analysis of relatively long sequences of mitochondrial DNA (4225 bp) in the Japanese house mouse Mus musculus provides the first evidence that both southern Asian subspecies of Mus musculus castaneus (CAS) and northern Asian subspecies of Mus musculus musculus (MUS) arrived in Japan through rapid population expansion events, from Southern China ~4000 years ago and the Korean Peninsula ~2000 years ago, respectively. Nuclear DNA haplotype structure analyses targeting a chromosome region...

Data from: Organic farming and associated management practices benefit multiple wildlife taxa: a large-scale field study in rice paddy landscapes

Naoki Katayama, Yutaka Osada, Miyuki Mashiko, Yuki G. Baba, Koichi Tanaka, Yoshinobu Kusumoto, Satoru Okubo, Hiroaki Ikeda & Yosihiro Natuhara
1. Organic farming has potential for the conservation of global biodiversity and associated ecosystem services. Despite this, knowledge of the effects of organic farming systems on farmland biodiversity is limited in Asia, the worldwide leader in rice production. 2. We conducted the first national-scale study to investigate the effects of three different rice farming systems (conventional, low-input, and organic) and specific management practices (e.g. herbicide and insecticide applications, crop rotation, and levee-vegetation management) on species...

The origin and genetic variability of vegetatively propagated clones identified from old planted trees and plantations of Thujopsis dolabrata var. hondae in Ishikawa Prefecture, Japan

Ikeda Torazo, Mishima Kentaro, Takata Katsuhiko & Tomaru Nobuhiro
Clonal plantations of Thujopsis dolabrata var. hondae have been established in Ishikawa Prefecture, Japan, since at least the 1800s. Historical planting of the species has led to the development of vegetatively propagated local cultivars, which originated from ‘donor’ trees that have often been conserved in sacred groves or avenues at shrines and temples. These donor trees must have been selected from natural populations. In this study we estimated the origin and genetic variability of clones...

Data from: Morphological and genetic divergence between two lineages of Magnolia salicifolia (Magnoliaceae) in Japan

Ichiro Tamaki, Naomichi Kawashima, Suzuki Setsuko, Akemi Itaya & Nobuhiro Tomaru
Uncovering how populations of a species differ genetically and ecologically is important for understanding evolutionary processes. We investigated genetic structure using nuclear microsatellites and chloroplast DNA sequences and geographical variation in leaf morphological traits among Magnolia salicifolia populations across its entire species range. Two distinct lineages, northern and southern lineages, were genetically detected and both lineages had substructure among populations. The width/length ratio and area of leaves showed latitudinal gradients, while the position of the...

Data from: Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana

Takashi Tsuchimatsu, Hiroyuki Kakui, Misako Yamazaki, Cindy Marona, Hiroki Tsutsui, Afif Hedhly, Dazhe Meng, Yutaka Sato, Thomas Städler, Ueli Grossniklaus, Masahiro Kanaoka, Michael Lenhard, Magnus Nordborg & Kentaro Shimizu
The number of male gametes is critical for reproductive success and varies between and within species. The evolutionary reduction of the number of pollen grains encompassing the male gametes is widespread in selfing plants. Here, we employ genome-wide association study (GWAS) to identify underlying loci and to assess the molecular signatures of selection on pollen number-associated loci in the predominantly selfing plant Arabidopsis thaliana. Regions of strong association with pollen number are enriched for signatures...

Additional file 1 of Prevalence of medical factors related to aging among older car drivers: a multicenter, cross-sectional, descriptive study

Hideharu Hagiya, Ryosuke Takase, Hiroyuki Honda, Yasuhiro Nakano, Yuki Otsuka, Hitomi Kataoka, Mika Uno, Keigo Ueda, Misa Takahashi, Hiroko Ogawa, Yoshihisa Hanayama & Fumio Otsuka
Additional file 1. Raw data for the analysis.

Liver transaminase levels during pregnancy: a Japanese multicenter study

Takafumi Ushida, Tomomi Kotani, Fumie Kinoshita, Kenji Imai, Tomoko Nakano-Kobayashi, Noriyuki Nakamura, Yoshinori Moriyama, Shigeru Yoshida, Mamoru Yamashita & Hiroaki Kajiyama
There are conflicting reports on the effect of pregnancy on liver transaminase (aspartate aminotransferase [AST] and alanine aminotransferase [ALT]) levels. In this study, we sought to investigate the trajectories of AST and ALT levels during normal pregnancy and to compare them with AST and ALT levels of matched nonpregnant controls. Our multicenter retrospective study included 34,396 women who delivered at term at 12 primary maternity care units between January 2011 and December 2018 and 57,152...

Additional file 7 of PTEN overexpression and nuclear β-catenin stabilization promote morular differentiation through induction of epithelial–mesenchymal transition and cancer stem cell-like properties in endometrial carcinoma

Ako Yokoi, Marina Minami, Miki Hashimura, Yasuko Oguri, Toshihide Matsumoto, Yoshinori Hasegawa, Mayu Nakagawa, Yu Ishibashi, Takashi Ito, Kensuke Ohhigata, Youhei Harada, Naomi Fukagawa & Makoto Saegusa
Additional file 6: Table S3. Relationship between PTEN expression and morular fomation and histological garde of endometrial carcinomas

Additional file 2 of PTEN overexpression and nuclear β-catenin stabilization promote morular differentiation through induction of epithelial–mesenchymal transition and cancer stem cell-like properties in endometrial carcinoma

Ako Yokoi, Marina Minami, Miki Hashimura, Yasuko Oguri, Toshihide Matsumoto, Yoshinori Hasegawa, Mayu Nakagawa, Yu Ishibashi, Takashi Ito, Kensuke Ohhigata, Youhei Harada, Naomi Fukagawa & Makoto Saegusa
Additional file 1: Table S1. Primer sequences used in this study

Additional file 4 of PTEN overexpression and nuclear β-catenin stabilization promote morular differentiation through induction of epithelial–mesenchymal transition and cancer stem cell-like properties in endometrial carcinoma

Ako Yokoi, Marina Minami, Miki Hashimura, Yasuko Oguri, Toshihide Matsumoto, Yoshinori Hasegawa, Mayu Nakagawa, Yu Ishibashi, Takashi Ito, Kensuke Ohhigata, Youhei Harada, Naomi Fukagawa & Makoto Saegusa
Additional file 3: Table S2. Summary of antibodies used in this study

Data from: Marmoset monkeys evaluate third-party reciprocity

Nobuyuki Kawai, Miyuki Yasue, Taku Banno & Noritaka Ichinohe
Many non-human primates have been observed to reciprocate and to understand reciprocity in one-to-one social exchanges. A recent study demonstrated that capuchin monkeys are sensitive to both third-party reciprocity and violation of reciprocity; however, whether this sensitivity is a function of general intelligence, evidenced by their larger brain size relative to other primates, remains unclear. We hypothesized that highly pro-social primates, even with a relatively smaller brain, would be sensitive to others' reciprocity. Here, we...

Data from: Patterns of geographic distribution have a considerable influence on population genetic structure in one common and two rare species of Rhododendron (Ericaceae)

Yoichi Watanabe, Nobuhiro Tomaru & Watanabe Yoichi
Genetic diversity is essential for species to sustain their populations and evolutionary potential. In order to develop effective conservation strategies for rare species, it is necessary to understand differences in patterns of genetic diversity between common and rare species. Data about population genetic structure is important to design effective conservation strategies for rare species. In this study, we compared the genetic diversity and population genetic structure of a common species, Rhododendron weyrichii, to those of...

Data from: How do growth and sibling competition affect telomere dynamics in the first month of life of long-lived seabird?

Yuichi Mizutani, Yasuaki Niizuma & Ken Yoda
Telomeres are nucleotide sequences located at the ends of chromosomes that promote genome stability. Changes in telomere length (dynamics) are related to fitness or life expectancy, and telomere dynamics during the development phase are likely to be affected by growth and stress factors. Here, we examined telomere dynamics of black-tailed gull chicks (Larus crassirostris) in nests with and without siblings. We found that the initial telomere lengths of singletons at hatching were longer than those...

Data from: Selective breeding and selection mapping using a novel wild-derived heterogeneous stock mice revealed two closely-linked loci for tameness

Yuki Matsumoto, Tatsuhiko Goto, Jo Nishino, Hirofumi Nakaoka, Akira Tanave, Toshiyuki Takano-Shimizu, Richard F. Mott & Tsuyoshi Koide
Tameness is a major behavioral factor for domestication, and can be divided into two potential components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). We identified genetic loci for active tameness through selective breeding, selection mapping, and association analysis. In previous work using laboratory and wild mouse strains, we found that laboratory strains were predominantly selected for passive tameness but not active tameness during their domestication. To identify genetic regions...

Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species

Reiko Akiyama, Jainqiang Sun, Masaomi Hatakeyama, Heidi Lischer, Roman Briskine, Angela Hay, Xiangchao Gan, Miltos Tsiantis, Hiroshi Kudoh, Masahiro Kanaoka, Jun Sese, Kentaro Shimizu & Rie Shimizu-Inatsugi
Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors. We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa...

International biological flora: Nervilia nipponica

Stephan Gale, Ayako Maeda, Ayana Miyashita, Daisuke Sugiura, Yuki Ogura-Tsujita, Akihiko Kinoshita, Shohei Fujimori, Michael Hutchings & Tomohisa Yukawa
This account presents information on all aspects of the biology of Nervilia nipponica Makino (mukago-saishin) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the International Biological Flora: distribution, habitat, communities, responses to biotic factors, responses to the environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history, conservation and global heterogeneity. Nervilia nipponica is a small, stoloniferous, seasonally dormant herb...

cGMP dynamics that underlies thermosensation in temperature-sensing neuron regulates thermotaxis behavior in C. elegans

Ichiro Aoki, Makoto Shiota, Yuki Tsukada, Shunji Nakano & Ikue Mori
Dataset

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: Revisiting the measurement of anomie

Ali Teymoori, Jolanda Jetten, Brock Bastian, Amarina Ariyanto, Frédérique Autin, Nadia Ayub, Constantina Badea, Tomasz Besta, Fabrizio Butera, Rui Costa-Lopes, Lijuan Cui, Carole Fantini, Gillian Finchilesc, Lowell Gaertner, Mario Gollwitzer, Ángel Gómez, Roberto González, Ying Yi Hong, Dorthe Høj Jensen, Minoru Karasawa, Thomas Kessler, Olivier Klein, Marcus Lima, Tuuli Anna Mähönen, Laura Megevand … & Gillian Finchilescu
Sociologists coined the term "anomie" to describe societies that are characterized by disintegration and deregulation. Extending beyond conceptualizations of anomie that conflate the measurements of anomie as 'a state of society' and as a 'state of mind', we disentangle these conceptualizations and develop an analysis and measure of this phenomenon focusing on anomie as a perception of the 'state of society'. We propose that anomie encompasses two dimensions: a perceived breakdown in social fabric (i.e.,...

Data from: Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberley M. Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T. Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F. Shibata, Shuji Shigenobu … & Mitsuyasu Hasebe
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient...

Data from: Differential clinicopathological features of EGPA-associated neuropathy with and without ANCA

Haruki Koike, Ryoji Nishi, Ken Ohyama, Yuki Fukami, Shohei Ikeda, Yuichi Kawagashira, Masahiro Iijima, Masahisa Katsuno &
Objective: To investigate the clinicopathological features of eosinophilic granulomatosis with polyangiitis (EGPA)-associated neuropathy with a focus on the presence or absence of anti-neutrophil cytoplasmic antibodies (ANCAs). Methods: We examined the clinical features and pathological findings of sural nerve biopsy specimens from 82 patients with EGPA-associated neuropathy. Of these patients, 32.9% were myeloperoxidase (MPO)-ANCA-positive, and 67.1% were MPO-ANCA-negative. PR3-ANCA was negative in all of 78 examined patients. Results: Upper-limb symptoms were more frequently reported as initial...

Explaining illness with evil: Pathogen prevalence fosters moral vitalism

Brock Bastian, Christin-Melanie Vauclair, Steve Loughnan, Paul Bain, Ashwini Ashokkumar, Maja Becker, Michal Bilewicz, Emma Collier-Baker, Carla Crespo, Paul W. Eastwick, Ronald Fischer, Malte Friese, Ángel Gómez, Valeschka M. Guerra, Jose Luis Castellanos Guevara, Katja Hanke, Nic Hooper, Li-Li Huang, Shi Junqi, Minoru Karasawa, Peter Kuppens, Siri Leknes, Müjde Peker, Cesar Pelay, Afoditi Pina … & William B. Swann
Pathogens represent a significant threat to human health leading to the emergence of strategies designed to help manage their negative impact. We examined how spiritual beliefs developed to explain and predict the devastating effects of pathogens and spread of infectious disease. Analysis of existing data in Studies 1 and 2 suggests that moral vitalism (beliefs about spiritual forces of evil) is higher in geographical regions characterized by historical higher levels of pathogens. Furthermore, drawing on...

Observation of Sublimation of Ice using Terahertz Spectroscopy

Kei Takeya, Keisuke Matsumura & Kodo Kawase
Although many studies have investigated the phase change of water, few have focused on the sublimation of ice. This study revealed that ice sublimation can be observed using terahertz (THz) spectroscopy. Ice was observed to undergo sublimation at atmospheric pressure at temperatures above 240 K, and its velocity increased in proportion to temperature. Above a certain temperature, the absorption coefficient increased during sublimation. These findings suggest that an interesting phenomenon may occur in the phase...

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