113 Works

Data from: Insecticide applications to soil contribute to development of Burkholderia mediating insecticide resistance in stinkbugs

Kanako Tago, Yoshitomo Kikuchi, Shinji Nakaoka, Chie Katsuyama, Masahito Hayatsu & Sinji Nakaoka
Some soil Burkholderia strains are capable of degrading the organophosphorus insecticide, fenitrothion, and establish symbiosis with stinkbugs, making the host insects fenitrothion-resistant. However, the ecology of the symbiotic degrading Burkholderia adapting to fenitrothion in the free-living environment is unknown. We hypothesized that fenitrothion applications affect the dynamics of fenitrothion-degrading Burkholderia, thereby controlling the transmission of symbiotic degrading Burkholderia from the soil to stinkbugs. We investigated changes in the density and diversity of culturable Burkholderia (i.e....

Data from: Within species support for the expensive tissue hypothesis: a negative association between brain size and visceral fat storage in females of the Pacific seaweed pipefish

Masahito Tsuboi, Jun Shoji, Atsushi Sogabe, Ingrid Ahnesjö & Niclas Kolm
The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the high cost of brain development and maintenance is predicted to constrain adaptive brain size evolution (the expensive tissue hypothesis, ETH). Here, we test the ETH in a teleost fish with predominant female mating competition (reversed sex roles) and male pregnancy, the pacific seaweed pipefish Syngnathus schlegeli. The relative size of the brain and other energetically expensive organs (kidney, liver,...

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: Hot spring frogs (Buergeria japonica) prefer cooler water to hot water

Shohei Komaki, Yoichi Sutoh, Kensuke Kobayashi, Shigeru Saito, Claire Saito, Takeshi Igawa & Quintin Lau
“Hot spring frog” is an informal name used for the Japanese stream tree frog (Buergeria japonica), which is widely distributed in Taiwan and the Ryukyu Archipelago in Japan. Some populations of the species are known to inhabit hot springs. However, water temperature can be extremely high around the sources of hot springs. Thus, it is questionable whether B. japonica selectively inhabits such dangerous environments. To address this question, we conducted a series of observations of...

Effect of a tailored multidimensional intervention on the care burden among family caregivers of stroke survivors: A randomised controlled trial

Mahmoud Ahmed Elsheikh, Michiko Moriyama, , Mayumi Kako, Ahmed Hashem El-Monshed, Mohamed Zoromba, Hamada Zehry, Maha Hazem Khalil, Abdel-Hady El-Gilany & Mostafa Amr
Introduction: Caring for stroke survivors at home creates high levels of care burden among family caregivers. As the nature of caregiving is multidimensional, previous initiatives at alleviating the care burden using a single approach have not been adequate. It was recommended that future studies focus on tailored interventions that address the needs of family caregivers and combine different approaches to relieve caregivers’ burden. However, there is a lack of literature regarding interventions that incorporate these...

mRNA editing analysis of Doryteuthis pealeii

Sofia Medina Ruiz, Caroline Albertin, Therese Mitros, Hannah Schmidbaur, Gustavo Sanchez, Z.Y. Wang, Jane Grimwood, Joshua Rosenthal, Clifton Ragsdale, Oleg Simakov & Daniel Rokhsar
Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid Doryteuthis (Loligo) pealeii and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring....

Number of terrestrial leeches with human-bait method and environmental variables in peninsular Malaysia

Tetsuro Hosaka, Asrulsani Jambari, Miyabi Nakabayashi & Shinya Numata
This is the data on the number of terrestrial leeches (brown Haemadipsa sp.) collected and environmental variables at the sampling site in Endau Rompin National Park in Malaysia. We investigated relative abundance of terrestrial leeches repeatedly at 99 sampling points in the tourism area of ERNP from February 2019 to September 2020. We counted the number of leeches at each sampling point based on the human-bait method, wherein the researcher is considered as the bait...

Incidence of catheter-related bloodstream infections following ultrasound-guided central venous catheterization: a systematic review and meta-analysis

Jun Takeshita, Kazuya Tachibana, Yasufumi Nakajima & Nobuaki Shime
Abstract Background Ultrasonographic guidance is widely used for central venous catheterization. Several studies have revealed that ultrasound-guided central venous catheterization increases the rate of success during the first attempt and reduces the procedural duration when compared to the anatomical landmark-guided insertion technique, which could result in protection from infectious complications. However, the effect of ultrasound-guided central venous catheterization on catheter-related bloodstream infections remains unclear. We aimed to conduct a systematic review and meta-analysis to evaluate...

Development and validation of a disease-specific quality of life scale for adult patients with Fabry disease in Japan

Yuta Koto, Wakana Yamashita, Yoko Lee, Nozomi Hadano, Chikara Kokubu & Norio Sakai
Abstract Background Fabry disease is a rare X-linked lysosomal storage disorder. It is associated with physical distress and social challenges that may affect adults differently compared to pediatric patients. However, there is no disease-specific quality of life (QOL) scale that can provide a detailed assessment of QOL for adults with Fabry disease. Therefore, we aimed to determine the factor structure and assess the validity of a scale that was created to assess the QOL of...

Additional file 1 of Potential use of EGFR-targeted molecular therapies for tumor suppressor CYLD-negative and poor prognosis oral squamous cell carcinoma with chemoresistance

Ayumi Kanemaru, Satoru Shinriki, Mimi Kai, Kanae Tsurekawa, Kazuya Ozeki, Shota Uchino, Naoki Suenaga, Kou Yonemaru, Shunsuke Miyake, Takeshi Masuda, Ryusho Kariya, Seiji Okada, Hisashi Takeshita, Yuki Seki, Hiromu Yano, Yoshihiro Komohara, Ryoji Yoshida, Hideki Nakayama, Jian-Dong Li, Hideyuki Saito & Hirofumi Jono
Additional file 1: Figure S1. CYLD-knockdown by CYLD-specific siRNA at mRNA level. Figure S2. The proteins involved in Akt and ERK signaling pathway in CYLD-negative OSCC cells. Figure S3. Cell survival rate in CYLD-knockdown OSCC cells by different siCYLD #2 and in other OSCC cells. Figure S4. Gefitinib treatment increased the expression of E-cadherin, an EMT biomarker. Figure S5. NF-κB signaling pathway does not participate in cell survival in CYLD-negative OSCC cells. Figure S6. TGF-β...

Additional file 1 of A burden of fluid, sodium, and chloride due to intravenous fluid therapy in patients with respiratory support: a post-hoc analysis of a multicenter cohort study

Masaaki Sakuraya, Shodai Yoshihiro, Kazuto Onozuka, Akihiro Takaba, Hideto Yasuda, Nobuaki Shime, Yuki Kotani, Yuki Kishihara, Natsuki Kondo, Kosuke Sekine & Keita Morikane
Additional file 1: Table S1. Daily intravenous fluid intake according to fluid type. Table S2. Daily sodium intake according to fluid type. Table S3. Daily chloride intake according to fluid type. Table S4. Estimates of the effects of covariates on the fluid volume, sodium, and chloride in the multiple linear regression models.

Additional file 4 of Senescence-accelerated mice prone 8 (SAMP8) in male as a spontaneous osteoarthritis model

Yohei Sanada, Yasunari Ikuta, Chenyang Ding, Masahiro Shinohara, Dilimulati Yimiti, Hiroyuki Ishitobi, Keita Nagira, Minjung Lee, Takayuki Akimoto, Sachi Shibata, Masakazu Ishikawa, Tomoyuki Nakasa, Kiminori Matsubara, Martin K. Lotz, Nobuo Adachi & Shigeru Miyaki
Additional file 4: Fig. S4. ADAMTS-5 and MMP-13-positive in medial and lateral compartment of the knee from SAMR1 and SAMP8.

Additional file 1 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 1: Monte Carlo uncertainty estimation method for the calculation of the elemental yields.

Additional file 3 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 3: Trace-element concentration values of matrix #6, with and without main-element randomization.

Additional file 3 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 3: Trace-element concentration values of matrix #6, with and without main-element randomization.

Additional file 5 of Trends in survival during the pandemic in patients with critical COVID-19 receiving mechanical ventilation with or without ECMO: analysis of the Japanese national registry data

Shinichiro Ohshimo, Keibun Liu, Takayuki Ogura, Yoshiaki Iwashita, Shigeki Kushimoto, Nobuaki Shime, Satoru Hashimoto, Yuji Fujino & Shinhiro Takeda
Additional file 5: Fig. S4. ROC curve analysis for predicting poor outcome in patients with critical COVID-19 receiving ECMO. (A) ROC curve for age, (B) body mass index, (C) number of ventilator days before starting ECMO, (D) number of ECMO experiences at an institution for patients with critical COVID-19, and (E) number of ECMO days. ROC, receiver operating characteristic curve; COVID-19, coronavirus disease 2019; ECMO, extracorporeal membrane oxygenation

Combined burden and functional impact tests for cancer driver discovery using DriverPower

Shimin Shuai, Federico Abascal, Samirkumar B Amin, Gary D Bader, Pratiti Bandopadhayay, Jonathan Barenboim, Rameen Beroukhim, Johanna Bertl, Keith A Boroevich, Søren Brunak, Peter J Campbell, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, Priyanka Dhingra, Klev Diamanti, Lars Feuerbach, J Lynn Fink, Nuno A Fonseca, Joan Frigola, Carlo Gambacorti-Passerini, Dale W Garsed … & L van’t Veer
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features...

Pathway and network analysis of more than 2500 whole cancer genomes

Matthew A Reyna, David Haan, Marta Paczkowska, Lieven PC Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S Lawrence, Jakob Skou Pedersen, Mark A Rubin, David A Wheeler, Søren Brunak, Jose MG Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S Cenk Sahinalp, Alfonso Valencia, Federico Abascal, Samirkumar B Amin … & L van’t Veer
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding...

Pathway and network analysis of more than 2500 whole cancer genomes

Matthew A Reyna, David Haan, Marta Paczkowska, Lieven PC Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S Lawrence, Jakob Skou Pedersen, Mark A Rubin, David A Wheeler, Søren Brunak, Jose MG Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S Cenk Sahinalp, Alfonso Valencia, Federico Abascal, Samirkumar B Amin … & L van’t Veer
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding...

Integrative pathway enrichment analysis of multivariate omics data

Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S Fox, Helen Zhu, Diala Abd-Rabbo, Miles W Mee, Paul C Boutros, Federico Abascal, Samirkumar B Amin, Gary D Bader, Rameen Beroukhim, Johanna Bertl, Keith A Boroevich, Søren Brunak, Peter J Campbell, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, Priyanka Dhingra, Klev Diamanti, Lars Feuerbach … & L van’t Veer
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated...

Data from: Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis

Takeshi Igawa, Ai Watanabe, Atsushi Suzuki, Akihiko Kashiwagi, Keiko Kashiwagi, Anna Noble, Matt Guille, David E. Simpson, Marko E. Horb, Tamotsu Fujii & Masayuki Sumida
The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains...

Raw data for the samples collected from Hole B of the ICDP DSeis project at the Moab Khotsong Gold Mine in South Africa

Takeshi Miyamoto, Tetsuro Hirono, Yuki Yokoyama, Shunya Kaneki, Yuhji Yamamoto, Tsuyoshi Ishikawa, Akira Tsuchiyama, Ikuo Katayama, Yasuo Yabe, Martin Ziegler, Raymond Durrheim & Hiroshi Ogasawara
This data set is corresponding to the Miyamoto, T. et al. “Characteristics of Seismogenic Fault Rock Related to the 2014 Orkney Earthquake (M5.5) Beneath the Moab Khotsong Gold Mine, South Africa” Geophysical Research Letters, 2022. This data set shows physical property, magnetic susceptibility, mineral assemblage, and element composition of all Hole B subsamples, and frictional properties of 5 Hole B subsamples.

Senescence-accelerated mice prone 8 (SAMP8) in male as a spontaneous osteoarthritis model

Yohei Sanada, Yasunari Ikuta, Chenyang Ding, Masahiro Shinohara, Dilimulati Yimiti, Hiroyuki Ishitobi, Keita Nagira, Minjung Lee, Takayuki Akimoto, Sachi Shibata, Masakazu Ishikawa, Tomoyuki Nakasa, Kiminori Matsubara, Martin K. Lotz, Nobuo Adachi & Shigeru Miyaki
Abstract Background Animal models of spontaneous osteoarthritis (OA) are sparse and not well characterized. The purpose of the present study is to examine OA-related changes and mechanisms in senescence-accelerated mouse prone 8 (SAMP8) that displays a phenotype of accelerated aging. Methods Knees of male SAMP8 and SAM-resistant 1 (SAMR1) mice as control from 6 to 33 weeks of age were evaluated by histological grading systems for joint tissues (cartilage, meniscus, synovium, and subchondral bone), and...

Additional file 1 of Senescence-accelerated mice prone 8 (SAMP8) in male as a spontaneous osteoarthritis model

Yohei Sanada, Yasunari Ikuta, Chenyang Ding, Masahiro Shinohara, Dilimulati Yimiti, Hiroyuki Ishitobi, Keita Nagira, Minjung Lee, Takayuki Akimoto, Sachi Shibata, Masakazu Ishikawa, Tomoyuki Nakasa, Kiminori Matsubara, Martin K. Lotz, Nobuo Adachi & Shigeru Miyaki
Additional file 1: Fig. S1. Incidence of aging-related spontaneous osteoarthritis development in knees of SAMP8 at 23 weeks of age.

Additional file 4 of Senescence-accelerated mice prone 8 (SAMP8) in male as a spontaneous osteoarthritis model

Yohei Sanada, Yasunari Ikuta, Chenyang Ding, Masahiro Shinohara, Dilimulati Yimiti, Hiroyuki Ishitobi, Keita Nagira, Minjung Lee, Takayuki Akimoto, Sachi Shibata, Masakazu Ishikawa, Tomoyuki Nakasa, Kiminori Matsubara, Martin K. Lotz, Nobuo Adachi & Shigeru Miyaki
Additional file 4: Fig. S4. ADAMTS-5 and MMP-13-positive in medial and lateral compartment of the knee from SAMR1 and SAMP8.

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Affiliations

  • Hiroshima University
    113
  • Hiroshima University Hospital
    44
  • Texas A&M University
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    31
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  • Tottori University
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