152 Works

Data from: Incorporating an ontogenetic perspective into evolutionary theory of sexual size dimorphism

Chun-Chia Chou, Yoh Iwasa & Takefumi Nakazawa
Sexual size dimorphism (SSD) describes divergent body sizes of adult males and females. While SSD has traditionally been explained by sexual and fecundity selection, recent advances in physiology and developmental biology emphasize that SSD would occur proximately because of sexual differences in ontogenetic growth trajectories (i.e., growth rate and duration). Notably, these ontogenetic traits are subject to energetic or time constraints and thus traded off with fitness components (e.g., survival and reproduction). To elucidate the...

Data from: Determining the minimum number of protein-protein interactions required to support known protein complexes

Natsu Nakajima, Morihiro Hayashida, Jesper Jansson, Osamu Maruyama & Tatsuya Akutsu
The prediction of protein complexes from protein-protein interactions (PPIs) is a well-studied problem in bioinformatics. However, the currently available PPI data is not enough to describe all known protein complexes. In this paper, we express the problem of determining the minimum number of (additional) required protein-protein interactions as a graph theoretic problem under the constraint that each complex constitutes a connected component in a PPI network. For this problem, we develop two computational methods: one...

Data from: Genome-wide sequence data suggest the possibility of pollinator sharing by host shift in dioecious figs (Moraceae, Ficus)

Nakatada Wachi, Junko Kusumi, Hsy-Yu Tzeng & Zhi-Hui Su
The obligate mutualism of figs and fig-pollinating wasps has been one of the classic models used for testing theories of co-evolution and cospeciation due to the high species-specificity of these relationships. To investigate the species-specificity between figs and fig pollinators and to further understand the speciation process in obligate mutualisms, we examined the genetic differentiation and phylogenetic relationships of four closely related fig-pollinating wasp species (Blastophaga nipponica, Blastophaga taiwanensis, Blastophaga tannoensis and Blastophaga yeni) in...

Additional file 2 of Differential associations between simple physical performance tests with global and specific cognitive functions in cognitively normal and mild cognitive impairment: a cross-sectional cohort study of Asian community-dwelling older adults

Ted Kheng Siang Ng, Madeline Fu Yun Han, Ping Yeap Loh, Ee Heok Kua, Junhong Yu, John R. Best & Rathi Mahendran
Additional file 2: Supplementary Table 1. Neurocognitive Test and its associated cognitive domain(s) and task description.

Additional file 1 of Differential associations between simple physical performance tests with global and specific cognitive functions in cognitively normal and mild cognitive impairment: a cross-sectional cohort study of Asian community-dwelling older adults

Ted Kheng Siang Ng, Madeline Fu Yun Han, Ping Yeap Loh, Ee Heok Kua, Junhong Yu, John R. Best & Rathi Mahendran
Additional file 1: Supplementary Figure 1. Fast gait speed measurement.

Differential associations between simple physical performance tests with global and specific cognitive functions in cognitively normal and mild cognitive impairment: a cross-sectional cohort study of Asian community-dwelling older adults

Ted Kheng Siang Ng, Madeline Fu Yun Han, Ping Yeap Loh, Ee Heok Kua, Junhong Yu, John R. Best & Rathi Mahendran
Abstract Background Physical performance declines and executive dysfunctions are predictors of dementia. However, their associations are not well understood in Asian older adults without dementia (cognitively normal [CN] and mild cognitive impairment [MCI]), especially in a single study. Objective Examine the associations between physical performance measures with executive function (EF)-based and non-EF-based neurocognitive tests and whether preclinical dementia cognitive status i.e., CN and MCI, moderated these associations. Methods We examined cross-sectional cohort of 716 community-dwelling...

Deep learning-based automatic-bone-destruction-evaluation system using contextual information from other joints

Kazuki Miyama, Ryoma Bise, Satoshi Ikemura, Kazuhiro Kai, Masaya Kanahori, Shinkichi Arisumi, Taisuke Uchida, Yasuharu Nakashima & Seiichi Uchida
Abstract Background X-ray images are commonly used to assess the bone destruction of rheumatoid arthritis. The purpose of this study is to propose an automatic-bone-destruction-evaluation system fully utilizing deep neural networks (DNN). This system detects all target joints of the modified Sharp/van der Heijde score (SHS) from a hand X-ray image. It then classifies every target joint as intact (SHS = 0) or non-intact (SHS ≥ 1). Methods We used 226 hand X-ray images of...

Which national park attributes attract international tourists? A Sri Lankan case study

Kanesh Suresh, Clevo Wilson, Annette Quayle, Uttam Khanal & Shunsuke Managi
This study assesses how and in what circumstances tourists’ perceived value of nature-based tourism (NBT) attributes differ among various types of national parks. A novel discrete choice experiment is used employing data collected from 343 international tourists in four national parks in Sri Lanka. We find that the improvements in frequency of large species’ encounters, habitat quality and proximity to encountered wildlife produce greater utility. A surprising finding is that tourists are shown to prefer...

Additional file 2 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 2: Fig. S1. Genome features in FSSC assemblies. Fig. S2. Multi-locus sequence typing (MLST) phylogeny tree of FSSC. Fig. S3. Genome phylogeny of Fusarium species. Fig. S4. Orthologue sharing amongst Fusarium chromosome. Fig. S5. FSSC genome synteny. Fig. S6. Synteny between F. vanettenii Fs6 and FVANE. Fig. S7. Location of FSSC-specific genes across genomes. Fig. S8. Selection level in FSSC chromosomes. Fig. S9. Orthogroup number comparison between F. falciforme Fu3 and F. oxysporum...

Additional file 2 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 2: Fig. S1. Genome features in FSSC assemblies. Fig. S2. Multi-locus sequence typing (MLST) phylogeny tree of FSSC. Fig. S3. Genome phylogeny of Fusarium species. Fig. S4. Orthologue sharing amongst Fusarium chromosome. Fig. S5. FSSC genome synteny. Fig. S6. Synteny between F. vanettenii Fs6 and FVANE. Fig. S7. Location of FSSC-specific genes across genomes. Fig. S8. Selection level in FSSC chromosomes. Fig. S9. Orthogroup number comparison between F. falciforme Fu3 and F. oxysporum...

Additional file 1 of Direct identification of HLA class I and class II-restricted T cell epitopes in pancreatic cancer tissues by mass spectrometry

Kenji Fujiwara, Yingkuan Shao, Nan Niu, Tengyi Zhang, Brian Herbst, Mackenzie Henderson, Stephen Muth, Pingbo Zhang & Lei Zheng
Additional file 1: Methods, Supplemental Figures S1–12, and Supplemental Tables S1, S3–5.

Additional file 2 of Direct identification of HLA class I and class II-restricted T cell epitopes in pancreatic cancer tissues by mass spectrometry

Kenji Fujiwara, Yingkuan Shao, Nan Niu, Tengyi Zhang, Brian Herbst, Mackenzie Henderson, Stephen Muth, Pingbo Zhang & Lei Zheng
Additional file 2: Supplemental Table S2, PDAC peptidome.

Trace-element analysis of mineral grains in Ryugu rock fragment sections by synchrotron-based confocal X-ray fluorescence

Benjamin Bazi, Pieter Tack, Miles Lindner, Bart Vekemans, Ella De Pauw, Beverley Tkalcec, Frank E. Brenker, Jan Garrevoet, Gerald Falkenberg, Hikaru Yabuta, Hisayoshi Yurimoto, Tomoki Nakamura, Kana Amano, Megumi Matsumoto, Yuri Fujioka, Yuma Enokido, Daisuke Nakashima, Masayuki Uesugi, Hiroshi Naraoka, Takaaki Noguchi, Ryuji Okazaki, Kanako Sakamoto, Toru Yada, Masahiro Nishimura, Aiko Nakato … & Laszlo Vincze
Abstract A fundamental parameter-based quantification scheme for confocal XRF was applied to sub-micron synchrotron radiation X-ray fluorescence (SR-XRF) data obtained at the beamline P06 of the Deutsches Elektronen-Synchrotron (DESY, Hamburg, Germany) from two sections C0033-01 and C0033-04 that were wet cut from rock fragment C0033 collected from Cb-type asteroid (162173) Ryugu by JAXA’s Hayabusa2 mission. Trace-element quantifications show that C0033 bulk matrix is CI-like, whereas individual mineral grains (i.e., magnetite, pyrrhotite, dolomite, apatite and breunnerite)...

Additional file 2 of Trace-element analysis of mineral grains in Ryugu rock fragment sections by synchrotron-based confocal X-ray fluorescence

Benjamin Bazi, Pieter Tack, Miles Lindner, Bart Vekemans, Ella De Pauw, Beverley Tkalcec, Frank E. Brenker, Jan Garrevoet, Gerald Falkenberg, Hikaru Yabuta, Hisayoshi Yurimoto, Tomoki Nakamura, Kana Amano, Megumi Matsumoto, Yuri Fujioka, Yuma Enokido, Daisuke Nakashima, Masayuki Uesugi, Hiroshi Naraoka, Takaaki Noguchi, Ryuji Okazaki, Kanako Sakamoto, Toru Yada, Masahiro Nishimura, Aiko Nakato … & Laszlo Vincze
Additional file 2: Monte Carlo uncertainty estimation method for the calculation of the mineral grain weight fractions.

Additional file 2 of Circulating CD8+CD122+ T cells as a prognostic indicator of pancreatic cancer

Katsuhito Teramatsu, Takamasa Oono, Koki Oyama, Nao Fujimori, Masatoshi Murakami, Sho Yasumori, Akihisa Ohno, Kazuhide Matsumoto, Ayumu Takeno, Kohei Nakata, Masafumi Nakamura & Yoshihiro Ogawa
Additional file 2.

Identification, expression, and purification of DNA cytosine 5-methyltransferases with short recognition sequences

Fumihito Miura, Miki Miura, Yukiko Shibata, Yoshikazu Furuta, Keisuke Miyamura, Yuki Ino, Asmaa M. A. Bayoumi, Utako Oba & Takashi Ito
Abstract Background DNA methyltransferases (MTases) are enzymes that induce methylation, one of the representative epigenetic modifications of DNA, and are also useful tools for analyzing epigenomes. However, regarding DNA cytosine 5-methylation, MTases identified so far have drawbacks in that their recognition sequences overlap with those for intrinsic DNA methylation in mammalian cells and/or that the recognition sequence is too long for fine epigenetic mapping. To identify MTases with short recognition sequences that never overlap with...

Additional file 1 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 1: Figure S1. Entire BSE images of the ultramafic xenolith. These were taken using SEM–EDS, Hitachi S-3400, at Tohoku University. The dark shadows are hardware artifacts. The grain cores of ultramafic xenoliths are compositionally homogeneous. Analyzed points are indicated by circles and arrows. The colors of the symbols indicate mineral species (yellow-green is olivine, green is clinopyroxene, orange is orthopyroxene, and red is spinel). (a) MPSX-PR1 peridotite, (b) MPSX-PR2 peridotite, (c) MPSX-PX1 pyroxenite,...

Additional file 1 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 1: Figure S1. Entire BSE images of the ultramafic xenolith. These were taken using SEM–EDS, Hitachi S-3400, at Tohoku University. The dark shadows are hardware artifacts. The grain cores of ultramafic xenoliths are compositionally homogeneous. Analyzed points are indicated by circles and arrows. The colors of the symbols indicate mineral species (yellow-green is olivine, green is clinopyroxene, orange is orthopyroxene, and red is spinel). (a) MPSX-PR1 peridotite, (b) MPSX-PR2 peridotite, (c) MPSX-PX1 pyroxenite,...

Additional file 9 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 8: Fig. S5. A Ishikawa cells were transfected with EBP50 reporter constructs, together with estrogen receptor α (ERα). Relative activity was determined based on arbitrary light units of luciferase activity normalized to pRL-TK activity. The activities of the reporter plus the effector relative to that of the reporter plus empty vector are shown as means ± SDs. B Ishikawa cells were transfected with Top reporter constructs, together with EBP50 and β-catenin

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
Abstract Background Although a lack of functional PTEN contributes to tumorigenesis in a wide spectrum of human malignancies, little is known about the functional role of its overexpression in the tumors. The current study focused on PTEN overexpression in endometrial carcinoma (Em Ca). Methods The functional impact of PTEN overexpression was assessed by Em Ca cell lines. Immunohistochemical analyses were also conducted using 38 Em Ca with morular lesions. Results Em Ca cell lines stably...

Additional file 10 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 9: Fig. S6. Changes in phenotypic characteristics in EBP50 knockout (KO) cells. A Left upper: western blot analysis for the indicated proteins in total lysates from H6-EBP-KO and mock cells. Left lower and right: phase contrast images of H6-EBP-KO cells. Note the changes in cell morphology toward more spread and flattened features in H6-EBP-KO cells. B Western blot analysis for the indicated proteins in total lysates from H6-EBP-KO and mock cells

Data from: Inferences of evolutionary history of a widely distributed mangrove species, Bruguiera gymnorrhiza, in the Indo-West Pacific region

Chie Urashi, Kosuke M. Teshima, Sumiko Minobe, Osamu Koizumi & Nobuyuki Inomata
Inference of genetic structure and demographic history is fundamental issue in evolutionary biology. We examined the levels and patterns of genetic variation of a widespread mangrove species in the Indo-West Pacific region, Bruguiera gymnorrhiza, using ten nuclear gene regions. Genetic variation of individual populations covering its distribution range was low, but as the entire species it was comparable to other plant species. Genetic differentiation among the investigated populations was high. They could be divided into...

Data from: Receptive females mitigate costs of sexual conflict

Tomohiro Harano
Males typically gain fitness from multiple mating, whereas females often lose fitness from numerous mating, potentially leading to sexual conflict over mating. This conflict is expected to favour the evolution of female resistance to mating. However, females may incur male harassment if they refuse to copulate; thus, greater female resistance may increase costs imposed by males. Here, I show that the evolution of resistance to mating raises fitness disadvantages of interacting with males when mating...

Data from: Parapatric speciation in three islands: dynamics of geographical configuration of allele sharing

Ryo Yamaguchi & Yoh Iwasa
We studied the time to speciation by geographical isolation for a species living on three islands connected by rare migration. We assumed that incompatibility was controlled by a number of quantitative loci and that individuals differing in loci by more than a threshold did not mix genetically with each other. For each locus, we defined the geographical configuration (GC), which specifies islands with common alleles, and traced the stochastic transitions between different GCs. From these...

Metaschoepite dissolution in sediment column systems – groundwater/soil geochemistry and uranium X-ray spectroscopy data

W. Bower, K. Morris, F.R. Livens, J.F.W. Mosselmans, C.M. Fallon, A.J. Fuller, L.S. Natrajan, C. Boothman, J.R. Lloyd, S. Utsunomia, D. Grolimund, D. Ferreira Sanchez, T. Jilbert, J.E. Parker, T. Neill & G. Law
This dataset contains the results of a laboratory study investigating the dissolution of UO3•nH2O particles in dynamic sediment/groundwater column systems, representative of the shallow subsurface at the Sellafield Ltd. site, UK. Measurements were carried out to determine the extent of uranic particle dissolution and the speciation of dissolved uranium within the columns under contrasting biogeochemical conditions (oxic and electron-donor amended). Columns effluents were analysed periodically for key biogeochemical indicators (nitrate, sulfate) and trace metals (iron,...

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