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1,006 results on '"Yoneda M"'

1. Respiratory Impedance is Associated with Ventilation and Diffusing Capacity in Patients with Idiopathic Pulmonary Fibrosis Combined with Emphysema

Author: Yamamoto Y, Hirata H, Shiroyama T, Kuge T, Matsumoto K, Yoneda M, Yamamoto M, Naito Y, Suga Y, Fukushima K, Miyake K, Koyama S, Iwahori K, Nagatomo I, Takeda Y, and Kumanogoh A
Subjects: chronic obstructive pulmonary disease, forced oscillation technique, gas exchange, idiopathic pulmonary fibrosis, ventilation, Diseases of the respiratory system, RC705-779
Abstract: Yuji Yamamoto,1 Haruhiko Hirata,1 Takayuki Shiroyama,1 Tomoki Kuge,1 Kinnosuke Matsumoto,1 Midori Yoneda,1 Makoto Yamamoto,1 Yujiro Naito,1 Yasuhiko Suga,1 Kiyoharu Fukushima,1 Kotaro Miyake,1 Shohei Koyama,1 Kota Iwahori,1 Izumi Nagatomo,1 Yoshito Takeda,1 Atsushi Kumanogoh1– 4 1Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan; 2Department of Immunopathology, WPI, Immunology Frontier Research Center (iFReC), Osaka University, Suita, Osaka, Japan; 3Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan; 4Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, JapanCorrespondence: Yuji Yamamoto, Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan, Tel +81 6-36879-3833, Fax +81 6-6879-3839, Email cyyamamoto1110@gmail.comPurpose: Pulmonary fibrosis and emphysema result in relatively maintained ventilation and reduced diffusing capacity. This pulmonary functional impairment complicates the evaluation of pulmonary function in patients with combined pulmonary fibrosis and emphysema (CPFE). Therefore, a single and easy-to-use pulmonary function index to evaluate patients with CPFE warrants further studies. Respiratory impedance can easily be provided by oscillometry and might be a candidate index to evaluate pulmonary function in patients with CPFE. As a preliminary study to assess the utility of respiratory impedance, we investigated the associations of physiological indices, including respiratory impedance, in patients with idiopathic pulmonary fibrosis (IPF) with and without emphysema.Patients and Methods: This retrospective study evaluated patients with IPF who did and did not satisfy the diagnostic criteria of CPFE. All patients underwent oscillometry, spirometry, and diffusing capacity for carbon monoxide (DLCO). Correlations of the obtained physiological indices were analyzed.Results: In total, 47 patients were included (18 and 29 patients with CPFE and IPF, respectively). Respiratory reactance (Xrs) at 5 Hz (X5) in the inspiratory phase was associated with forced vital capacity (FVC) % predicted in patients with CPFE (rS=0.576, P=0.012) and IPF (rS=0.539, P=0.003). Inspiratory X5 positively correlated with DLCO % predicted only in patients CPFE (rS=0.637, P=0.004).Conclusion: Emphysema might associate Xrs with ventilation and diffusing capacity in patients with IPF and emphysema. Given the multiple correlations of Xrs with FVC and DLCO, this study warrants further studies to verify the utility of oscillometry in a large-scale study for patients with CPFE.Keywords: chronic obstructive pulmonary disease, forced oscillation technique, gas exchange, idiopathic pulmonary fibrosis, ventilation
Published: 2022

2. Impact of glucose excursion and mean glucose concentration in oral glucose-tolerance test on oxidative stress among Japanese Americans

Author: Nakanishi S, Yoneda M, and Maeda S
Subjects: Specialties of internal medicine, RC581-951
Abstract: Shuhei Nakanishi, Masayasu Yoneda, Shusaku Maeda Department of Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan Aim: To evaluate the impact of glucose excursion (GE) and mean glucose concentration (MGC) on oxidative stress among persons with or without diabetes. Materials and methods: We examined 775 Japanese Americans who had normal glucose tolerance (NGT), impaired glucose tolerance, or diabetes according to the 75 g oral glucose-tolerance test, using fasting, 1-hour, and 2-hour glucose data. We calculated GE by subtracting the minimum from the maximum glucose level among three points and calculated MGC using these measurements. We investigated the relationship between GE or MGC and urinary isoprostane as a marker of oxidative stress. Results: According to tertiles of GE or MGC, GE was associated with isoprostane levels among subjects with NGT as well as those with diabetes (P=0.004 and 0.033 for trend, respectively). However, MGC was associated with isoprostane only among NGT subjects (P=0.001 for trend). Association between GE and isoprostane was significant when adjustment was made for age, sex, smoking status, body mass index, C-reactive protein, glucose tolerance status, and homeostatic model assessment (P=0.029), but the association with MGC was not significant. Conclusion: Our results suggest the possibility that GE might result in oxidative stress, and the relationship is stronger than that for MGC. Keywords: glucose excursion, glucose-tolerance test, oxidative stress
Published: 2013

3. Equivalence of the modified Villain formulation and the dual Hamiltonian method in the duality of the XY-plaquette model

Author: Yoneda, M.
Subjects: High Energy Physics - Theory, Condensed Matter - Statistical Mechanics, Mathematical Physics
Abstract: Regarding the duality of the XY-plaquette model in the $2+1d$ system, We compared and discussed the equivalence and difference between the modified Villain formulation, recently introduced by Gorantla et al. to study duality in exotic field theories such as fracton theory, and the standard Villain formulation and dual Hamiltonian method we introduced in our previous paper to study duality between Josephson junctions and quantum phase slips in the $1+1d$ system.
Published: 2022

4. An attempt to detect transient changes in Io's SO2 and NaCl atmosphere

Author: Roth, L., Boissier, J., Moullet, A., Sanchez-Monge, A., de Kleer, K., Yoneda, M., Hikida, R., Kita, H., Tsuchiya, F., Blcker, A., Gladstone, G. R., Grodent, D., Ivchenko, N., Lellouch, E., Retherford, K., Saur, J., Strobel, P. Schilke D., and Thorwirth, S.
Subjects: Astrophysics - Earth and Planetary Astrophysics
Abstract: Io's atmosphere is predominately SO2 sustained by a combination of volcanic outgassing and sublimation. The loss from the atmosphere is the main mass source for Jupiter's large magnetosphere. Previous studies attributed various transient phenomena in Io's environment and Jupiter's magnetosphere to a sudden change in the mass loss from the atmosphere supposedly triggered by a change in volcanic activity. Since the gas in volcanic plumes does not escape directly, such causal correlation would require a transient volcano-induced change in atmospheric abundance, which has never been observed so far. Here we report four observations of atmospheric SO2 and NaCl obtained with the IRAM NOEMA interferometer. These observations are compared to measurements of volcanic hot spots and Io's neutral and plasma environment. We find a stable NaCl column density in Io's atmosphere. The SO2 column density derived for December 2016 is about 30% lower compared to the period of March to April 2017. This increase in SO2 from December 2016 to March 2017 might be related to increasing volcanic activity observed at several sites in spring 2017, but the stability of the volcanic trace gas NaCl and resulting decrease in NaCl/SO2 ratio do not support this interpretation. Observed dimmings in both the sulfur ion torus and Na neutral cloud suggest rather a decrease in mass loading in the period of increasing SO2 abundance. The dimming Na brightness and stable atmospheric NaCl furthermore dispute an earlier suggested positive correlation of the sodium cloud and the hot spot activity at Loki Patara, which considerably increased in this period. The environment of Io overall appears to be in a quiescent state, preventing further conclusions. Only Jupiter's aurora morphology underwent several short-term changes, which are apparently unrelated to Io's quiescent environment or the relatively stable atmosphere., Comment: 19 pages, 3 figures. Paper published in Icarus. Abstract in arXiv slightly modified with respect to the published version
Published: 2020
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5. Duality between coherent quantum phase slip and Josephson junction in a nanosheet determined by the dual Hamiltonian method

Author: Yoneda, M., Niwa, M., and Motohashi, M.
Subjects: Condensed Matter - Superconductivity, High Energy Physics - Theory
Abstract: The duality between coherent quantum phase slip and Josephson junction in nanosheets was investigated using the dual Hamiltonian method. This is equivalent to the duality between superconductivity and superinsulator in the 2 + 1 dimension at zero temperature. This method proved to be reliable within the Villain approximation. The possibility of the dual Ginzburg-Landau theory, which is the phenomenology of superinsulators and the dual BCS theory, which is a microscopic theory, is also shown.
Published: 2020

6. Theoretical proposal for dual transformation between the Josephson effect and quantum phase slip in single junction systems and nanowires

Author: Yoneda, M., Niwa, M., Hirata, N., and Motohashi, M.
Subjects: Condensed Matter - Superconductivity
Abstract: A method was devised to construct a generalized dual field theory in the quantum field theory. As a simple example using this method, we examined the duality between coherent quantum phase slip and the Josephson effect in single junction systems and nanowires. The this method was proved to be reliable within the Villain approximation.
Published: 2019
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7. Electric feedback cooling of single charged nanoparticles in an optical trap

Author: Iwasaki, M., Yotsuya, T., Naruki, T., Matsuda, Y., Yoneda, M., and Aikawa, K.
Subjects: Condensed Matter - Mesoscale and Nanoscale Physics
Abstract: We demonstrate feedback cooling of the center-of-mass motion of single charged nanoparticles to millikelvin temperatures in three dimensions via applying oscillating electric fields synchronized to their optically observed motion. The observed motional temperatures at weak feedback agree with a simple model and allow us to estimate the charge number of trapped nanoparticles. The agreement between our model and experiments is confirmed by independent measurements of the charge numbers based on a shift in the oscillation frequency induced by a constant electric field. The demonstrated temperature of below 10 mK at $4 \times 10^{-3}$ Pa is lower than that with the conventional optical cooling approach at this pressure by one to two orders of magnitude. Our results form the basis of manipulating cold charged nanoparticles and paves the way to quantum mechanical studies with trapped nanoparticles near their ground state., Comment: 6 pages, 5 figures
Published: 2018
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8. Stochastic modeling of multiwavelength variability of the classical BL Lac object OJ 287 on timescales ranging from decades to hours

Author: Goyal, A., Stawarz, L., Zola, S., Marchenko, V., Soida, M., Nilsson, K., Ciprini, S., Baran, A., Ostrowski, M., Wiita, P. J., Gopal-Krishna, Siemiginowska, A., Sobolewska, M., Jorstad, S., Marscher, A., Hovatta, M. F. Aller H. D. Aller T., Caton, D. B., Reichart, D., Matsumoto, K., Sadakane, K., Gazeas, K., Kidger, M., Piirola, V., Jermak, H., Alicavus, F., Baliyan, K. S., Baransky, A., Berdyugin, A., Blay, P., Boumis, P., Boyd, D., Bufan, Y., Torrent, M. Campas, Campos, F., Gomez, J. Carrillo, Dalessio, J., Debski, B., Dimitrov, D., Drozdz, M., Er, H., Erdem, A., Perez, A. Escartin, Ramazani, V. Fallah, Filippenko, A. V., Gafton, E., Garcia, F., Godunova, V., Pinilla, F. Gomez, Gopinathan, M., Haislip, J. B., Haque, S., Harmanen, J., Hudec, R., Hurst, G., Ivarsen, K. M., Joshi, A., Kagitani, M., Karaman, N., Karjalainen, R., Kaur, N., l-Wierzbowska, D. Kozie, Kuligowska, E., Kundera, T., Kurowski, S., Kvammen, A., LaCluyze, A. P., Lee, B. C., Liakos, A., de Haro, J. Lozano, Mohammed, I., Moore, J. P., Mugrauer, M., Nogues, R. Naves, Neely, A. W., Ogloza, W., Okano, S., Pajdosz, U., Pandey, J. C., Perri, M., Poyner, G., Provencal, J., Pursimo, T., Raj, A., Rajkumar, B., Reinthal, R., Reynolds, T., Saario, J., Sadegi, S., Sakanoi, T., Gonzalez, J. L. Salto, Sameer, Heung, A., Simon, O., Siwak, M., Schweyer, T., Alfaro, F. C. Soldan, Sonbas, E., Strobl, J., Takalo, L. O., Espasa, L. Tremosa, Valdes, J. R., Vasylenko, V. V., Verrecchia, F., Webb, J. R., Yoneda, M., Zejmo, M., Zheng, W., Zielinski, P., Janik, J., Chavushyan, V., Cheung, C. C., and Giroletti, M.
Subjects: Astrophysics - High Energy Astrophysical Phenomena
Abstract: We present the results of our power spectral density analysis for the BL Lac object OJ\,287, utilizing the {\it Fermi}-LAT survey at high-energy $\gamma$-rays, {\it Swift}-XRT in X-rays, several ground-based telescopes and the {\it Kepler} satellite in the optical, and radio telescopes at GHz frequencies. The light curves are modeled in terms of continuous-time auto-regressive moving average (CARMA) processes. Owing to the inclusion of the {\it Kepler} data, we were able to construct \emph{for the first time} the optical variability power spectrum of a blazar without any gaps across $\sim6$ dex in temporal frequencies. Our analysis reveals that the radio power spectra are of a colored-noise type on timescales ranging from tens of years down to months, with no evidence for breaks or other spectral features. The overall optical power spectrum is also consistent with a colored noise on the variability timescales ranging from 117 years down to hours, with no hints of any quasi-periodic oscillations. The X-ray power spectrum resembles the radio and optical power spectra on the analogous timescales ranging from tens of years down to months. Finally, the $\gamma$-ray power spectrum is noticeably different from the radio, optical, and X-ray power spectra of the source: we have detected a characteristic relaxation timescale in the {\it Fermi}-LAT data, corresponding to $\sim 150$\,days, such that on timescales longer than this, the power spectrum is consistent with uncorrelated (white) noise, while on shorter variability timescales there is correlated (colored) noise., Comment: ApJ accepted
Published: 2017
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9. Thermal broadening of the power spectra of laser-trapped particles in vacuum

Author: Yoneda, M. and Aikawa, K.
Subjects: Condensed Matter - Mesoscale and Nanoscale Physics
Abstract: We show that at low pressures the spectral widths of the power spectra of laser-trapped particles are nearly independent from pressures and, due to the nonlinearities of the trap, reflect the thermal distribution of particles. In the experiments with nanoparticles trapped in an optical lattice, we identify two distinct features of the widths. First, the widths along an optical lattice are much broader than those in the other directions. Second, the spectral widths are narrower for larger nanoparticles. We develop a theory of thermal broadening and show that the spectral widths normalized by the frequencies of the center-of-mass motion directly reveal the ratio of the thermal energy to the trap depth. The presented model provides a good understanding of the observed features. Our model holds also for smaller particles such as atoms and molecules and can be readily extended to the general case with a single-beam optical trap., Comment: 9 pages, 9 figures
Published: 2017
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10. High-precision broad-band linear polarimetry of early-type binaries I. Discovery of variable, phase-locked polarization in HD 48099

Author: Berdyugin, A., Piirola, V., Sadegi, S., Tsygankov, S., Sakanoi, T., Kagitani, M., Yoneda, M., Okano, S., and Poutanen, J.
Subjects: Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, 85-08 (Primary)
Abstract: We investigate the structure of the O-type binary system HD 48099 by measuring linear polarization that arises due to light scattering process. Linear polarization measurements of HD 48099 in the B, V and R passbands with the high-precision Dipol-2 polarimeter have been carried out. The data have been obtained with the 60 cm KVA (Observatory Roque de los Muchachos, La Palma, Spain) and T60 (Haleakala, Hawaii, USA) remotely controlled telescopes during 31 observing nights. Polarimetry in the optical wavelengths has been complemented by observations in the X-rays with the SWIFT space observatory. Optical polarimetry revealed small intrinsic polarization in HD 48099 with 0.1% peak to peak variation over the orbital period of 3.08 days. The variability pattern is typical for binary systems, showing strong second harmonic of the orbital period. We apply our model code for the electron scattering in the circumstellar matter to put constraints on the system geometry. A good model fit is obtained for scattering of light on a cloud produced by the colliding stellar winds. The geometry of the cloud, with a broad distribution of scattering particles away from the orbital plane, helps in constraining the (low) orbital inclination. We derive from the polarization data the inclination i = 17 deg +/- 2deg and the longitude of the ascending node Omega = 82 deg +/- 1 deg of the binary orbit. The available X-ray data provide additional evidence for the existence of the colliding stellar winds in the system. Another possible source of the polarized light could be scattering from the stellar photospheres. The models with circumstellar envelopes, or matter confined to the orbital plane, do not provide good constraints on the low inclination, better than i < 27 deg, as is already suggested by the absence of eclipses., Comment: 10 pages, 9 figures to be published in Astronomy & Astrophysics
Published: 2016
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11. Primary black hole spin in OJ287 as determined by the General Relativity centenary flare

Author: Valtonen, M. J., Zola, S., Ciprini, S., Gopakumar, A., Matsumoto, K., Sadakane, K., Kidger, M., Gazeas, K., Nilsson, K., Berdyugin, A., Piirola, V., Jermak, H., Baliyan, K. S., Alicavus, F., Boyd, D., Torrent, M. Campas, Campos, F., Gomez, J. Carrillo, Caton, D. B., Chavushyan, V., Dalessio, J., Debski, B., Dimitrov, D., Drozdz, M., Er, H., Erdem, A., Perez, A. Escartin, Ramazani, V. Fallah, Filippenko, A. V., Ganesh, S., Garcia, F., Pinilla, F. Gomez, Gopinathan, M., Haislip, J. B., Hudec, R., Hurst, G., Ivarsen, K. M., Jelinek, M., Joshi, A., Kagitani, M., Kaur, N., Keel, W. C., LaCluyze, A. P., Lee, B. C., Lindfors, E., de Haro, J. Lozano, Moore, J. P., Mugrauer, M., Nogues, R. Naves, Neely, A. W., Nelson, R. H., Ogloza, W., Okano, S., Pandey, J. C., Perri, M., Pihajoki, P., Poyner, G., Provencal, J., Pursimo, T., Raj, A., Reichart, D. E., Reinthal, R., Sadegi, S., Sakanoi, T., Gonzalez, J. L. Salto, Schweyer, T., Siwak, M., Alfaro, F. C. Soldan, Sonbas, E., Steele, I., Stocke, J. T., Strobl, J., Takalo, L. O., Tomov, T., Espasa, L. Tremosa, Valdes, J. R., Perez, J. Valero, Verrecchia, F., Webb, J. R., Yoneda, M., Zejmo, M., Zheng, W., Telting, J., Saario, J., Reynolds, T., Kvammen, A., Gafton, E., Karjalainen, R., Harmanen, J., and Blay, P.
Subjects: Astrophysics - High Energy Astrophysical Phenomena
Abstract: OJ287 is a quasi-periodic quasar with roughly 12 year optical cycles. It displays prominent outbursts which are predictable in a binary black hole model. The model predicted a major optical outburst in December 2015. We found that the outburst did occur within the expected time range, peaking on 2015 December 5 at magnitude 12.9 in the optical R-band. Based on Swift/XRT satellite measurements and optical polarization data, we find that it included a major thermal component. Its timing provides an accurate estimate for the spin of the primary black hole, chi = 0.313 +- 0.01. The present outburst also confirms the established general relativistic properties of the system such as the loss of orbital energy to gravitational radiation at the 2 % accuracy level and it opens up the possibility of testing the black hole no-hair theorem with a 10 % accuracy during the present decade.
Published: 2016
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12. Physical Properties of Asteroid (308635) 2005 YU55 derived from multi-instrument infrared observations during a very close Earth-Approach

Author: Mueller, T. G., Miyata, T., Kiss, C., Gurwell, M. A., Hasegawa, S., Vilenius, E., Sako, S., Kamizuka, T., Nakamura, T., Asano, K., Uchiyama, M., Konishi, M., Yoneda, M., Ootsubo, T., Usui, F., Yoshii, Y., Kidger, M., Altieri, B., Lorente, R., Pal, A., O'Rourke, L., and Metcalfe, L.
Subjects: Astrophysics - Earth and Planetary Astrophysics
Abstract: The near-Earth asteroid (308635) 2005 YU55 is a potentially hazardous asteroid which was discovered in 2005 and passed Earth on November 8th 2011 at 0.85 lunar distances. This was the closest known approach by an asteroid of several hundred metre diameter since 1976 when a similar size object passed at 0.5 lunar distances. We observed 2005 YU55 from ground with a recently developed mid-IR camera (miniTAO/MAX38) in N- and Q-band and with the Submillimeter Array (SMA) at 1.3 mm. In addition, we obtained space observations with Herschel/PACS at 70, 100, and 160 micron. Our thermal measurements cover a wide range of wavelengths from 8.9 micron to 1.3 mm and were taken after opposition at phase angles between -97 deg and -18 deg. We performed a radiometric analysis via a thermophysical model and combined our derived properties with results from radar, adaptive optics, lightcurve observations, speckle and auxiliary thermal data. We find that (308635) 2005 YU55 has an almost spherical shape with an effective diameter of 300 to 312 m and a geometric albedo pV of 0.055 to 0.075. Its spin-axis is oriented towards celestial directions (lam_ecl, beta_ecl) = (60 deg +/- 30deg, -60 deg +/- 15 deg), which means it has a retrograde sense of rotation. The analysis of all available data combined revealed a discrepancy with the radar-derived size. Our radiometric analysis of the thermal data together with the problem to find a unique rotation period might be connected to a non-principal axis rotation. A low to intermediate level of surface roughness (r.m.s. of surface slopes in the range 0.1 - 0.3) is required to explain the available thermal measurements. We found a thermal inertia in the range 350-800 Jm^-2s^-0.5K^-1, very similar to the rubble-pile asteroid (25143) Itokawa and indicating a mixture of low conductivity fine regolith with larger rocks and boulders of high thermal inertia on the surface., Comment: Accepted for publication in Astronomy & Astrophysics, 12 pages, 10 figures
Published: 2013
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13. Three-dimensional assessment of the normal Japanese glenoid and comparison with the normal French glenoid

Author: Mizuno, N., Nonaka, S., Ozaki, R., Yoshida, M., Yoneda, M., and Walch, G.
Published: 2017
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14. A sting in the tail: An embedded stingray spine in a mid-1st millennium AD adult male skeleton from Rebun Island, Hokkaido, Japan

Author: Schulting, R, Kubo, D, Nishida, K, Braddick, I, Yoneda, M, Kato, H, and Ishida, H
Subjects: Adult, Male, Archeology, Archaeology, Japan, Radiometric Dating, Animals, Humans, Skates, Fish, Bone and Bones, Pathology and Forensic Medicine
Abstract: Objectives We report here a stingray spine (Dasyatidae) found embedded in the femur of a male skeleton from the archaeological site of Uedomari-5, Rebun Island, Hokkaido, Japan. Materials A single well-preserved but incomplete human skeleton. Methods Macroscopic observation and low power magnification, CT imaging, radiocarbon dating and stable isotope (carbon, nitrogen) analysis. Results The stingray spine is tentatively identified as Bathytoshia brevicaudata. CT imaging shows no healing, indicating that death occurred shortly afterwards. The skeleton has been directly radiocarbon dated to the Okhotsk period (cal AD 429–827), with δ13C (−13.7‰) and δ15N (19.3‰) values indicating a diet focused on marine foods. Conclusions The absence of healing in what would have been a non-lethal injury strongly suggests that the spine tipped an arrowhead, rather than being the result of an accidental encounter with a living stingray. It is possible that the injury reflects a period of increased conflict coinciding with, or following on from, the expansion of the Okhotsk culture from Sakhalin into northern Hokkaido. Significance Uedomari-5 provides the first example, to our knowledge, of a stingray spine directly embedded in human bone at an archaeological site. More widely, the finding contributes to our knowledge of conflict in northern hunter-gatherer communities. Limitations Given the early excavation date (1949–50), there is little contextual information available for the burials. Suggestions for further research ZooMS (Zooarchaeology by Mass Spectrometry) may be able to identify the stingray species. Archival research may provide more information concerning the excavations at Uedomari-5.
Published: 2022

15. Diagnostic accuracy of non-invasive tests for advanced fibrosis in patients with NAFLD : an individual patient data meta-analysis

Author: Mozes, F. E., Lee, J. A., Selvaraj, E. A., Jayaswal, A. N. A., Trauner, M., Boursier, J., Fournier, C., Staufer, K., Stauber, R. E., Bugianesi, E., Younes, R., Gaia, S., Lupsor-Platon, M., Petta, S., Shima, T., Okanoue, T., Mahadeva, S., Chan, W. -K., Eddowes, P. J., Newsome, P. N., Wong, V. W. -S., de Ledinghen, V., Fan, J., Shen, F., Cobbold, J. F., Sumida, Y., Okajima, A., Schattenberg, J. M., Labenz, C., Kim, W., Lee, M. S., Wiegand, J., Karlas, T., Yilmaz, Y., Aithal, G. P., Palaniyappan, N., Cassinotto, C., Aggarwal, S., Garg, H., Ooi, G. J., Nakajima, A., Yoneda, M., Ziol, M., Barget, N., Geier, A., Tuthill, T., Brosnan, M. J., Anstee, Q. M., Neubauer, S., Harrison, S. A., Bossuyt, P. M., Pavlides, M., Anstee, Q., Daly, A., Johnson, K., Govaere, O., Cockell, S., Tiniakos, D., Bedossa, P., Oakley, F., Cordell, H., Day, C., Wonders, K., Bossuyt, P., Zafarmand, H., Vali, Y., Lee, J., Ratziu, V., Clement, K., Pais, R., Schuppan, D., Schattenberg, J., Vidal-Puig, T., Vacca, M., Rodrigues-Cuenca, S., Allison, M., Kamzolas, I., Petsalaki, E., Oresic, M., Hyotylainen, T., Mcglinchey, A., Mato, J. M., Millet, O., Dufour, J. -F., Berzigotti, A., Harrison, S., Cobbold, J., Mozes, F., Akhtar, S., Banerjee, R., Kelly, M., Shumbayawonda, E., Dennis, A., Erpicum, C., Graham, M., Romero-Gomez, M., Gomez-Gonzalez, E., Ampuero, J., Castell, J., Gallego-Duran, R., Fernandez, I., Montero-Vallejo, R., Karsdal, M., Erhardtsen, E., Rasmussen, D., Leeming, D. J., Fisker, M. J., Sinisi, A., Musa, K., Betsou, F., Sandt, E., Tonini, M., Rosso, C., Armandi, A., Marra, F., Gastaldelli, A., Svegliati, G., Francque, S., Vonghia, L., Ekstedt, M., Kechagias, S., Yki-Jarvinen, H., Porthan, K., van Mil, S., Papatheodoridis, G., Cortez-Pinto, H., Valenti, L., Miele, L., Trautwein, C., Aithal, G., Hockings, P., Newsome, P., Wenn, D., Rodrigues, C. M. P., Chaumat, P., Hanf, R., Trylesinski, A., Ortiz, P., Duffin, K., Brosnan, J., Mcleod, E., Ertle, J., Ostroff, R., Alexander, L., Kjaer, M. S., Mikkelsen, L. F., Balp, M. -M., Brass, C., Jennings, L., Martic, M., Loeffler, J., Hanauer, G., Shankar, S., Pepin, K., Ehman, R., Myers, J., Ho, G., Torstenson, R., Myers, R., Doward, L., LITMUS Investigators, University of Denver, Medizinische Universität Wien = Medical University of Vienna, Hémodynamique, Interaction Fibrose et Invasivité tumorales Hépatiques (HIFIH), Université d'Angers (UA), SUACI Alpes du Nord, Medical University Graz, Mozes, Ferenc Emil, Lee, Jenny A., Selvaraj, Emmanuel Anandraj, Jayaswal, Arjun Narayan Ajmer, Trauner, Michael, Boursier, Jerome, Fournier, Celine, Staufer, Katharina, Stauber, Rudolf E., Bugianesi, Elisabetta, Younes, Ramy, Gaia, Silvia, Lupsor-Platon, Monica, Petta, Salvatore, Shima, Toshihide, Okanoue, Takeshi, Mahadeva, Sanjiv, Chan, Wah-Kheong, Eddowes, Peter J., Hirschfield, Gideon M., Newsome, Philip Noel, Wong, Vincent Wai-Sun, de Ledinghen, Victor, Fan, Jiangao, Shen, Feng, Cobbold, Jeremy F., Sumida, Yoshio, Okajima, Akira, Schattenberg, Joern M., Labenz, Christian, Kim, Won, Lee, Myoung Seok, Wiegand, Johannes, Karlas, Thomas, Yilmaz, Yusuf, Aithal, Guruprasad Padur, Palaniyappan, Naaventhan, Cassinotto, Christophe, Aggarwal, Sandeep, Garg, Harshit, Ooi, Geraldine J., Nakajima, Atsushi, Yoneda, Masato, Ziol, Marianne, Barget, Nathalie, Geier, Andreas, Tuthill, Theresa, Brosnan, M. Julia, Anstee, Quentin Mark, Neubauer, Stefan, Harrison, Stephen A., Bossuyt, Patrick M., Pavlides, Michael, Epidemiology and Data Science, APH - Methodology, APH - Personalized Medicine, ACS - Atherosclerosis & ischemic syndromes, APH - Aging & Later Life, ARD - Amsterdam Reproduction and Development, Graduate School, Mozes F.E., Lee J.A., Selvaraj E.A., Jayaswal A.N.A., Trauner M., Boursier J., Fournier C., Staufer K., Stauber R.E., Bugianesi E., Younes R., Gaia S., Lupsor-Platon M., Petta S., Shima T., Okanoue T., Mahadeva S., Chan W.-K., Eddowes P.J., Newsome P.N., Wong V.W.-S., de Ledinghen V., Fan J., Shen F., Cobbold J.F., Sumida Y., Okajima A., Schattenberg J.M., Labenz C., Kim W., Lee M.S., Wiegand J., Karlas T., Yilmaz Y., Aithal G.P., Palaniyappan N., Cassinotto C., Aggarwal S., Garg H., Ooi G.J., Nakajima A., Yoneda M., Ziol M., Barget N., Geier A., Tuthill T., Brosnan M.J., Anstee Q.M., Neubauer S., Harrison S.A., Bossuyt P.M., Pavlides M., Anstee Q., Daly A., Johnson K., Govaere O., Cockell S., Tiniakos D., Bedossa P., Oakley F., Cordell H., Day C., Wonders K., Bossuyt P., Zafarmand H., Vali Y., Lee J., Ratziu V., Clement K., Pais R., Schuppan D., Schattenberg J., Vidal-Puig T., Vacca M., Rodrigues-Cuenca S., Allison M., Kamzolas I., Petsalaki E., Oresic M., Hyotylainen T., McGlinchey A., Mato J.M., Millet O., Dufour J.-F., Berzigotti A., Harrison S., Cobbold J., Mozes F., Akhtar S., Banerjee R., Kelly M., Shumbayawonda E., Dennis A., Erpicum C., Graham M., Romero-Gomez M., Gomez-Gonzalez E., Ampuero J., Castell J., Gallego-Duran R., Fernandez I., Montero-Vallejo R., Karsdal M., Erhardtsen E., Rasmussen D., Leeming D.J., Fisker M.J., Sinisi A., Musa K., Betsou F., Sandt E., Tonini M., Rosso C., Armandi A., Marra F., Gastaldelli A., Svegliati G., Francque S., Vonghia L., Ekstedt M., Kechagias S., Yki-Jarvinen H., Porthan K., van Mil S., Papatheodoridis G., Cortez-Pinto H., Valenti L., Miele L., Trautwein C., Aithal G., Hockings P., Newsome P., Wenn D., Rodrigues C.M.P., Chaumat P., Hanf R., Trylesinski A., Ortiz P., Duffin K., Brosnan J., McLeod E., Ertle J., Ostroff R., Alexander L., Kjaer M.S., Mikkelsen L.F., Balp M.-M., Brass C., Jennings L., Martic M., Loeffler J., Hanauer G., Shankar S., Pepin K., Ehman R., Myers J., Ho G., Torstenson R., Myers R., and Doward L.
Subjects: Liver Cirrhosis, Male, Cirrhosis, LIVER STIFFNESS MEASUREMENT, Biopsy, [SDV]Life Sciences [q-bio], biostatistics, Gastroenterology, DISEASE, clinical decision making, fatty liver, hepatic fibrosis, 0302 clinical medicine, Non-alcoholic Fatty Liver Disease, Fibrosis, 2. Zero hunger, 0303 health sciences, medicine.diagnostic_test, NONALCOHOLIC STEATOHEPATITIS, TRANSIENT ELASTOGRAPHY, Fatty liver, CHRONIC HEPATITIS, Middle Aged, 3. Good health, Settore AGR/03 - Arboricoltura Generale E Coltivazioni Arboree, Liver, Liver biopsy, BIOPSY, Elasticity Imaging Techniques, Female, 030211 gastroenterology & hepatology, Median body, medicine.medical_specialty, CONTROLLED ATTENUATION PARAMETER, 610 Medicine & health, 03 medical and health sciences, Internal medicine, SCORE, medicine, Humans, biostatistics, clinical decision making, fatty liver, hepatic fibrosis, 030304 developmental biology, Receiver operating characteristic, business.industry, medicine.disease, Diabetes Mellitus, Type 2, XL PROBE, business, Hepatic fibrosis, Transient elastography, Biomarkers, PROSPECTIVE DERIVATION
Abstract: ObjectiveLiver biopsy is still needed for fibrosis staging in many patients with non-alcoholic fatty liver disease. The aims of this study were to evaluate the individual diagnostic performance of liver stiffness measurement by vibration controlled transient elastography (LSM-VCTE), Fibrosis-4 Index (FIB-4) and NAFLD (non-alcoholic fatty liver disease) Fibrosis Score (NFS) and to derive diagnostic strategies that could reduce the need for liver biopsies.DesignIndividual patient data meta-analysis of studies evaluating LSM-VCTE against liver histology was conducted. FIB-4 and NFS were computed where possible. Sensitivity, specificity and area under the receiver operating curve (AUROC) were calculated. Biomarkers were assessed individually and in sequential combinations.ResultsData were included from 37 primary studies (n=5735; 45% women; median age: 54 years; median body mass index: 30 kg/m2; 33% had type 2 diabetes; 30% had advanced fibrosis). AUROCs of individual LSM-VCTE, FIB-4 and NFS for advanced fibrosis were 0.85, 0.76 and 0.73. Sequential combination of FIB-4 cut-offs (ConclusionSequential combinations of markers with a lower cut-off to rule-out advanced fibrosis and a higher cut-off to rule-in cirrhosis can reduce the need for liver biopsies.
Published: 2022

16. Dynamics of M1 macrophages in oral mucosal lesions during the development of acute graft‐versus‐host disease in rats

Author: Seno, K., Yasunaga, M., Kajiya, H., Izaki‐Hagio, K., Morita, H., Yoneda, M., Hirofuji, T., and Ohno, J.
Published: 2017
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17. Common variants of the G protein-coupled receptor type 4 are associated with human essential hypertension and predict the blood pressure response to angiotensin receptor blockade

Author: Sanada, H, Yoneda, M, Yatabe, J, Williams, S M, Bartlett, J, White, M J, Gordon, L N, Felder, R A, Eisner, G M, Armando, I, and Jose, P A
Published: 2016
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18. Reconstruction of diachronic changes in human fishing activity and marine ecosystems from carbon and nitrogen stable isotope ratios of archaeological fish remains

Author: Tsutaya, T, Takahashi, T, Omori, T, Yamazaki, K, Sato, T, Yoneda, M, Schulting, RJ, Kato, H, and Weber, AW
Subjects: Earth-Surface Processes
Abstract: Stable isotope analysis is one of the most effective methods of reconstructing human fishing practices and changes in past marine ecosystems. The effectiveness of this method can be further improved when considering diachronic changes in stable isotope ratios of archaeological remains of several different fish species that exhibit different behavioral or ecological traits. In this study, diachronic changes in human fishing practices and marine ecosystems were investigated for Epi-Jomon (299–258 BC) and Okhotsk (489–1200 AD) periods in prehistoric Hokkaido, northern Japan, by utilizing the stable isotope analysis of archaeological fish bone collagen. Carbon and nitrogen stable isotope ratios of 242 fish bone samples, representing 12 taxa, excavated from the site of Hamanaka 2 on Rebun Island revealed significantly lower (p
Published: 2021

19. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Author: Grapotte M., Saraswat M., Bessiere C., Menichelli C., Ramilowski J. A., Severin J., Hayashizaki Y., Itoh M., Tagami M., Murata M., Kojima-Ishiyama M., Noma S., Noguchi S., Kasukawa T., Hasegawa A., Suzuki H., Nishiyori-Sueki H., Frith M. C., Abugessaisa I., Aitken S., Aken B. L., Alam I., Alam T., Alasiri R., Alhendi A. M. N., Alinejad-Rokny H., Alvarez M. J., Andersson R., Arakawa T., Araki M., Arbel T., Archer J., Archibald A. L., Arner E., Arner P., Asai K., Ashoor H., Astrom G., Babina M., Baillie J. K., Bajic V. B., Bajpai A., Baker S., Baldarelli R. M., Balic A., Bansal M., Batagov A. O., Batzoglou S., Beckhouse A. G., Beltrami A. P., Beltrami C. A., Bertin N., Bhattacharya S., Bickel P. J., Blake J. A., Blanchette M., Bodega B., Bonetti A., Bono H., Bornholdt J., Bttcher M., Bougouffa S., Boyd M., Breda J., Brombacher F., Brown J. B., Bult C. J., Burroughs A. M., Burt D. W., Busch A., Caglio G., Califano A., Cameron C. J., Cannistraci C. V., Carbone A., Carlisle A. J., Carninci P., Carter K. W., Cesselli D., Chang J. -C., Chen J. C., Chen Y., Chierici M., Christodoulou J., Ciani Y., Clark E. L., Coskun M., Dalby M., Dalla E., Daub C. O., Davis C. A., de Hoon M. J. L., de Rie D., Denisenko E., Deplancke B., Detmar M., Deviatiiarov R., Di Bernardo D., Diehl A. D., Dieterich L. C., Dimont E., Djebali S., Dohi T., Dostie J., Drablos F., Edge A. S. B., Edinger M., Ehrlund A., Ekwall K., Elofsson A., Endoh M., Enomoto H., Enomoto S., Faghihi M., Fagiolini M., Farach-Carson M. C., Faulkner G. J., Favorov A., Fernandes A. M., Ferrai C., Forrest A. R. R., Forrester L. M., Forsberg M., Fort A., Francescatto M., Freeman T. C., Frith M., Fukuda S., Funayama M., Furlanello C., Furuno M., Furusawa C., Gao H., Gazova I., Gebhard C., Geier F., Geijtenbeek T. B. H., Ghosh S., Ghosheh Y., Gingeras T. R., Gojobori T., Goldberg T., Goldowitz D., Gough J., Greco D., Gruber A. J., Guhl S., Guigo R., Guler R., Gusev O., Gustincich S., Ha T. J., Haberle V., Hale P., Hallstrom B. M., Hamada M., Handoko L., Hara M., Harbers M., Harrow J., Harshbarger J., Hase T., Hashimoto K., Hatano T., Hattori N., Hayashi R., Herlyn M., Hettne K., Heutink P., Hide W., Hitchens K. J., Sui S. H., 't Hoen P. A. C., Hon C. C., Hori F., Horie M., Horimoto K., Horton P., Hou R., Huang E., Huang Y., Hugues R., Hume D., Ienasescu H., Iida K., Ikawa T., Ikemura T., Ikeo K., Inoue N., Ishizu Y., Ito Y., Ivshina A. V., Jankovic B. R., Jenjaroenpun P., Johnson R., Jorgensen M., Jorjani H., Joshi A., Jurman G., Kaczkowski B., Kai C., Kaida K., Kajiyama K., Kaliyaperumal R., Kaminuma E., Kanaya T., Kaneda H., Kapranov P., Kasianov A. S., Katayama T., Kato S., Kawaguchi S., Kawai J., Kawaji H., Kawamoto H., Kawamura Y. I., Kawasaki S., Kawashima T., Kempfle J. S., Kenna T. J., Kere J., Khachigian L., Kiryu H., Kishima M., Kitajima H., Kitamura T., Kitano H., Klaric E., Klepper K., Klinken S. P., Kloppmann E., Knox A. J., Kodama Y., Kogo Y., Kojima M., Kojima S., Komatsu N., Komiyama H., Kono T., Koseki H., Koyasu S., Kratz A., Kukalev A., Kulakovskiy I., Kundaje A., Kunikata H., Kuo R., Kuo T., Kuraku S., Kuznetsov V. A., Kwon T. J., Larouche M., Lassmann T., Law A., Le-Cao K. -A., Lecellier C. -H., Lee W., Lenhard B., Lennartsson A., Li K., Li R., Lilje B., Lipovich L., Lizio M., Lopez G., Magi S., Mak G. K., Makeev V., Manabe R., Mandai M., Mar J., Maruyama K., Maruyama T., Mason E., Mathelier A., Matsuda H., Medvedeva Y. A., Meehan T. F., Mejhert N., Meynert A., Mikami N., Minoda A., Miura H., Miyagi Y., Miyawaki A., Mizuno Y., Morikawa H., Morimoto M., Morioka M., Morishita S., Moro K., Motakis E., Motohashi H., Mukarram A. K., Mummery C. L., Mungall C. J., Murakawa Y., Muramatsu M., Nagasaka K., Nagase T., Nakachi Y., Nakahara F., Nakai K., Nakamura K., Nakamura Y., Nakazawa T., Nason G. P., Nepal C., Nguyen Q. H., Nielsen L. K., Nishida K., Nishiguchi K. M., Nishiyori H., Nitta K., Notredame C., Ogishima S., Ohkura N., Ohno H., Ohshima M., Ohtsu T., Okada Y., Okada-Hatakeyama M., Okazaki Y., Oksvold P., Orlando V., Ow G. S., Ozturk M., Pachkov M., Paparountas T., Parihar S. P., Park S. -J., Pascarella G., Passier R., Persson H., Philippens I. H., Piazza S., Plessy C., Pombo A., Ponten F., Poulain S., Poulsen T. M., Pradhan S., Prezioso C., Pridans C., Qin X. -Y., Quackenbush J., Rackham O., Ramilowski J., Ravasi T., Rehli M., Rennie S., Rito T., Rizzu P., Robert C., Roos M., Rost B., Roudnicky F., Roy R., Rye M. B., Sachenkova O., Saetrom P., Sai H., Saiki S., Saito M., Saito A., Sakaguchi S., Sakai M., Sakaue S., Sakaue-Sawano A., Sandelin A., Sano H., Sasamoto Y., Sato H., Saxena A., Saya H., Schafferhans A., Schmeier S., Schmidl C., Schmocker D., Schneider C., Schueler M., Schultes E. A., Schulze-Tanzil G., Semple C. A., Seno S., Seo W., Sese J., Sheng G., Shi J., Shimoni Y., Shin J. W., SimonSanchez J., Sivertsson A., Sjostedt E., Soderhall C., Laurent G. S., Stoiber M. H., Sugiyama D., Summers K. M., Suzuki A. M., Suzuki K., Suzuki M., Suzuki N., Suzuki T., Swanson D. J., Swoboda R. K., Taguchi A., Takahashi H., Takahashi M., Takamochi K., Takeda S., Takenaka Y., Tam K. T., Tanaka H., Tanaka R., Tanaka Y., Tang D., Taniuchi I., Tanzer A., Tarui H., Taylor M. S., Terada A., Terao Y., Testa A. C., Thomas M., Thongjuea S., Tomii K., Triglia E. T., Toyoda H., Tsang H. G., Tsujikawa M., Uhlen M., Valen E., van de Wetering M., van Nimwegen E., Velmeshev D., Verardo R., Vitezic M., Vitting-Seerup K., von Feilitzen K., Voolstra C. R., Vorontsov I. E., Wahlestedt C., Wasserman W. W., Watanabe K., Watanabe S., Wells C. A., Winteringham L. N., Wolvetang E., Yabukami H., Yagi K., Yamada T., Yamaguchi Y., Yamamoto M., Yamamoto Y., Yamanaka Y., Yano K., Yasuzawa K., Yatsuka Y., Yo M., Yokokura S., Yoneda M., Yoshida E., Yoshida Y., Yoshihara M., Young R., Young R. S., Yu N. Y., Yumoto N., Zabierowski S. E., Zhang P. G., Zucchelli S., Zwahlen M., Chatelain C., Brehelin L., Grapotte, M., Saraswat, M., Bessiere, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S., Aken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-Rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Archer, J., Archibald, A. L., Arner, E., Arner, P., Asai, K., Ashoor, H., Astrom, G., Babina, M., Baillie, J. K., Bajic, V. B., Bajpai, A., Baker, S., Baldarelli, R. M., Balic, A., Bansal, M., Batagov, A. O., Batzoglou, S., Beckhouse, A. G., Beltrami, A. P., Beltrami, C. A., Bertin, N., Bhattacharya, S., Bickel, P. J., Blake, J. A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J. B., Bult, C. J., Burroughs, A. M., Burt, D. W., Busch, A., Caglio, G., Califano, A., Cameron, C. J., Cannistraci, C. V., Carbone, A., Carlisle, A. J., Carninci, P., Carter, K. W., Cesselli, D., Chang, J. -C., Chen, J. C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E. L., Coskun, M., Dalby, M., Dalla, E., Daub, C. O., Davis, C. A., de Hoon, M. J. L., de Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A. D., Dieterich, L. C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-Carson, M. C., Faulkner, G. J., Favorov, A., Fernandes, A. M., Ferrai, C., Forrest, A. R. R., Forrester, L. M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T. C., Frith, M., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T. B. H., Ghosh, S., Ghosheh, Y., Gingeras, T. R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A. J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T. J., Haberle, V., Hale, P., Hallstrom, B. M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K. J., Sui, S. H., 't Hoen, P. A. C., Hon, C. C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Ivshina, A. V., Jankovic, B. R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A. S., Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y. I., Kawasaki, S., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S. P., Kloppmann, E., Knox, A. J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V. A., Kwon, T. J., Larouche, M., Lassmann, T., Law, A., Le-Cao, K. -A., Lecellier, C. -H., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G. K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y. A., Meehan, T. F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A. K., Mummery, C. L., Mungall, C. J., Murakawa, Y., Muramatsu, M., Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakazawa, T., Nason, G. P., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Nishida, K., Nishiguchi, K. M., Nishiyori, H., Nitta, K., Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-Hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G. S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S. P., Park, S. -J., Pascarella, G., Passier, R., Persson, H., Philippens, I. H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T. M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X. -Y., Quackenbush, J., Rackham, O., Ramilowski, J., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M. B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-Sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E. A., Schulze-Tanzil, G., Semple, C. A., Seno, S., Seo, W., Sese, J., Sheng, G., Shi, J., Shimoni, Y., Shin, J. W., Simonsanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G. S., Stoiber, M. H., Sugiyama, D., Summers, K. M., Suzuki, A. M., Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D. J., Swoboda, R. K., Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K. T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M. S., Terada, A., Terao, Y., Testa, A. C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E. T., Toyoda, H., Tsang, H. G., Tsujikawa, M., Uhlen, M., Valen, E., van de Wetering, M., van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-Seerup, K., von Feilitzen, K., Voolstra, C. R., Vorontsov, I. E., Wahlestedt, C., Wasserman, W. W., Watanabe, K., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R. S., Yu, N. Y., Yumoto, N., Zabierowski, S. E., Zhang, P. G., Zucchelli, S., Zwahlen, M., Chatelain, C., Brehelin, L., Institute of Biotechnology, Biosciences, Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), National Institute of Advanced Industrial Science and Technology (AIST), SANOFI Recherche, University of British Columbia (UBC), Experimental Immunology, Infectious diseases, AII - Infectious diseases, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)
Subjects: 0301 basic medicine, General Physics and Astronomy, Genome, Mice, 0302 clinical medicine, Transcription (biology), Promoter Regions, Genetic, Transcription Initiation, Genetic, 0303 health sciences, Multidisciplinary, 1184 Genetics, developmental biology, physiology, High-Throughput Nucleotide Sequencing, Neurodegenerative Diseases, 222 Other engineering and technologies, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], humanities, Enhancer Elements, Genetic, Microsatellite Repeat, Transcription Initiation Site, Sequence motif, Transcription Initiation, Human, Enhancer Elements, Neural Networks, Science, 610 Medicine & health, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Promoter Regions, 03 medical and health sciences, Computer, Deep Learning, Tandem repeat, Genetic, Clinical Research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Machine learning, Genetics, Animals, Humans, Polymorphism, Enhancer, Transcriptomics, Gene, A549 Cell, 030304 developmental biology, Polymorphism, Genetic, Neurodegenerative Disease, Base Sequence, Animal, Genome, Human, Human Genome, Computational Biology, Promoter, General Chemistry, 113 Computer and information sciences, Cap analysis gene expression, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Cardiovascular and Metabolic Diseases, A549 Cells, Minion, Generic health relevance, 3111 Biomedicine, Neural Networks, Computer, 610 Medizin und Gesundheit, 030217 neurology & neurosurgery, FANTOM consortium, Microsatellite Repeats
Abstract: Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism., Nature Communications, 12 (1), ISSN:2041-1723
Published: 2020

20. Mercury’s exospheric He I 58.4 nm emission: Dependence on the orbital phase

Author: Yoneda, M., primary, Dima, G., additional, and Berdyugina, S. V., additional
Published: 2021
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21. Azimuthal Variation in the Io Plasma Torus Observed by the Hisaki Satellite From 2013 to 2016

Author: Steffl, A., Bagenal, F., Delamere, P., Yoneda, M., Tsuchiya, Fuminori, Arakawa, Ryo, Misawa, Hiroaki, Kagitani, Masato, Koga, Ryoichi, Suzuki, Fumiharu, Hikida, Reina, Yoshioka, Kazuo, Kimura, Tomoki, Kasaba, Yasumasa, Murakami, Go, Yoshikawa, Ichiro, and Yamazaki, Atsushi
Subjects: Physics, Azimuth, Geophysics, Space and Planetary Science, Satellite, Torus, Astrophysics, Plasma, Variation (astronomy)
Abstract: 著者人数: 17名, Accepted: 2019-04-15, 資料番号: SA1190016000
Published: 2019

22. MELAS Mutation in mtDNA Binding Site for Transcription Termination Factor Causes Defects in Protein Synthesis and in Respiration but no Change in Levels of Upstream and Downstream Mature Transcripts

Author: Chomyn, A., Martinuzzi, A., Yoneda, M., Daga, A., Hurko, O., Johns, D., Lai, S. T., Nonaka, I., Angelini, C., and Attardi, G.
Published: 1992

23. An Approach to Broad-Spectrum Cephalosporins

Author: Morita, K., Nomura, H., Numata, M., Ochiai, M., and Yoneda, M.
Published: 1980

24. Measles virus selectively blind to signaling lymphocyte activation molecule as a novel oncolytic virus for breast cancer treatment

Author: Sugiyama, T, Yoneda, M, Kuraishi, T, Hattori, S, Inoue, Y, Sato, H, and Kai, C
Published: 2013
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25. Protection from non-alcoholic steatohepatitis and liver tumourigenesis in high fat-fed insulin receptor substrate-1-knockout mice despite insulin resistance

Author: Nakamura, A., Tajima, K., Zolzaya, K., Sato, K., Inoue, R., Yoneda, M., Fujita, K., Nozaki, Y., Kubota, K. C., Haga, H., Kubota, N., Nagashima, Y., Nakajima, A., Maeda, S., Kadowaki, T., and Terauchi, Y.
Published: 2012
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26. Diagnostic accuracy of non-invasive tests for advanced fibrosis in patients with NAFLD: An individual patient data meta-analysis

Author: Mózes, F.E. Lee, J.A. Selvaraj, E.A. Jayaswal, A.N.A. Trauner, M. Boursier, J. Fournier, C. Staufer, K. Stauber, R.E. Bugianesi, E. Younes, R. Gaia, S. Lupșor-Platon, M. Petta, S. Shima, T. Okanoue, T. Mahadeva, S. Chan, W.-K. Eddowes, P.J. Newsome, P.N. Wong, V.W.-S. de Ledinghen, V. Fan, J. Shen, F. Cobbold, J.F. Sumida, Y. Okajima, A. Schattenberg, J.M. Labenz, C. Kim, W. Lee, M.S. Wiegand, J. Karlas, T. Yılmaz, Y. Aithal, G.P. Palaniyappan, N. Cassinotto, C. Aggarwal, S. Garg, H. Ooi, G.J. Nakajima, A. Yoneda, M. Ziol, M. Barget, N. Geier, A. Tuthill, T. Brosnan, M.J. Anstee, Q.M. Neubauer, S. Harrison, S.A. Bossuyt, P.M. Pavlides, M. Anstee, Q. Daly, A. Johnson, K. Govaere, O. Cockell, S. Tiniakos, D. Bedossa, P. Oakley, F. Cordell, H. Day, C. Wonders, K. Bossuyt, P. Zafarmand, H. Vali, Y. Lee, J. Ratziu, V. Clement, K. Pais, R. Schuppan, D. Schattenberg, J. Schuppan, D. Schattenberg, J. Vidal-Puig, T. Vacca, M. Rodrigues-Cuenca, S. Allison, M. Kamzolas, I. Petsalaki, E. Oresic, M. Hyötyläinen, T. McGlinchey, A. Mato, J.M. Millet, O. Dufour, J.-F. Berzigotti, A. Pavlides, M. Harrison, S. Neubauer, S. Cobbold, J. Mozes, F. Akhtar, S. Banerjee, R. Kelly, M. Shumbayawonda, E. Dennis, A. Erpicum, C. Graham, M. Romero-Gómez, M. Gómez-González, E. Ampuero, J. Castell, J. Gallego-Durán, R. Fernández, I. Montero-Vallejo, R. Karsdal, M. Erhardtsen, E. Rasmussen, D. Leeming, D.J. Fisker, M.J. Sinisi, A. Musa, K. Betsou, F. Sandt, E. Tonini, M. Bugianesi, E. Rosso, C. Armandi, A. Marra, F. Gastaldelli, A. Svegliati, G. Boursier, J. Francque, S. Vonghia, L. Ekstedt, M. Kechagias, S. Yki-Jarvinen, H. Porthan, K. van Mil, S. Papatheodoridis, G. Cortez-Pinto, H. Valenti, L. Petta, S. Miele, L. Geier, A. Trautwein, C. Aithal, G. Hockings, P. Newsome, P. Wenn, D. Rodrigues, C.M.P. Chaumat, P. Hanf, R. Trylesinski, A. Ortiz, P. Duffin, K. Brosnan, J. Tuthill, T. McLeod, E. Ertle, J. Younes, R. Ostroff, R. Alexander, L. Kjær, M.S. Mikkelsen, L.F. Balp, M.-M. Brass, C. Jennings, L. Martic, M. Loeffler, J. Hanauer, G. Shankar, S. Fournier, C. Pepin, K. Ehman, R. Myers, J. Ho, G. Torstenson, R. Myers, R. Doward, L. LITMUS Investigators
Abstract: Objective Liver biopsy is still needed for fibrosis staging in many patients with non-alcoholic fatty liver disease. The aims of this study were to evaluate the individual diagnostic performance of liver stiffness measurement by vibration controlled transient elastography (LSM-VCTE), Fibrosis-4 Index (FIB-4) and NAFLD (non-alcoholic fatty liver disease) Fibrosis Score (NFS) and to derive diagnostic strategies that could reduce the need for liver biopsies. Design Individual patient data meta-analysis of studies evaluating LSM-VCTE against liver histology was conducted. FIB-4 and NFS were computed where possible. Sensitivity, specificity and area under the receiver operating curve (AUROC) were calculated. Biomarkers were assessed individually and in sequential combinations. Results Data were included from 37 primary studies (n=5735; 45% women; median age: 54 years; median body mass index: 30 kg/m2; 33% had type 2 diabetes; 30% had advanced fibrosis). AUROCs of individual LSM-VCTE, FIB-4 and NFS for advanced fibrosis were 0.85, 0.76 and 0.73. Sequential combination of FIB-4 cut-offs (
Published: 2021

27. Effect of central corticotropin releasing factor on hepatic circulation in rats: the role of the CRF 2 receptor in the brain

Author: Yoneda, M, Nakamura, K, Nakade, Y, Tamano, M, Kono, T, Watanobe, H, Shimada, T, Hiraishi, H, and Terano, A
Subjects: Neurotransmitters -- Research, Neurotransmitters -- Analysis, Central nervous system -- Research, Health
Published: 2005

28. Transient elastography in patients with non-alcoholic fatty liver disease (NAFLD)

Author: Yoneda, M, Fujita, K, Inamori, M, Nakajima, A, Tamano, M, and Hiraishi, H
Published: 2007

29. Hashimoto’s encephalopathy presenting with progressive cerebellar ataxia

Author: Nakagawa, H, Yoneda, M, Fujii, A, Kinomoto, K, and Kuriyama, M
Published: 2007

30. Review article: regulation of TFF1 (pS2) expression in gastric epithelial cells

Author: FUJII, Y., SHIMADA, T., KOIKE, T., HOSAKA, K., TABEI, K., NAMATAME, T., TAJIMA, A., YONEDA, M., TERANO, A., and HIRAISHI, H.
Published: 2006

31. Internal carotid artery vasospasm syndrome: demonstration by neuroimaging

Author: Yokoyama, H, Yoneda, M, Abe, M, Sakai, T, Sagoh, T, Adachi, Y, and Kondo, T
Published: 2006

32. Effect of central corticotropin releasing factor on hepatic circulation in rats: the role of the CRF2 receptor in the brain

Author: Yoneda, M, Nakamura, K, Nakade, Y, Tamano, M, Kono, T, Watanobe, H, Shimada, T, Hiraishi, H, and Terano, A
Published: 2005

33. Clinical and molecular analysis of Mowat-Wilson syndrome associated with ZFHX1B mutations and deletions at 2q22–q24.1

Author: Ishihara, N, Yamada, K, Yamada, Y, Miura, K, Kato, J, Kuwabara, N, Hara, Y, Kobayashi, Y, Hoshino, K, Nomura, Y, Mimaki, M, Ohya, K, Matsushima, M, Nitta, H, Tanaka, K, Segawa, M, Ohki, T, Ezoe, T, Kumagai, T, Onuma, A, Kuroda, T, Yoneda, M, Yamanaka, T, Saeki, M, Saji, T, Nagaya, M, and Wakamatsu, N
Published: 2004

34. Up-regulation of TFF expression by PPARγ ligands in gastric epithelial cells

Author: SHIMADA, T., KOITABASHI, A., KUNIYOSHI, T., HASHIMOTO, T., YOSHIURA, K., YONEDA, M., HIRAISHI, H., and TERANO, A.
Published: 2003

35. Plasma transforming growth factor-β1 level and efficacy of α-tocopherol in patients with non-alcoholic steatohepatitis: a pilot study

Author: Hasegawa, T., Yoneda, M., Nakamura, K., Makino, I., and Terano, A.
Published: 2001

36. Stochastic Modeling of Multiwavelength Variability of the Classical BL Lac Object OJ 287 on Timescales Ranging from Decades to Hours

Author: Goyal, A. Stawarz, Ł. Zola, S. Marchenko, V. Soida, M. Nilsson, K. Ciprini, S. Baran, A. Ostrowski, M. Wiita, P.J. Gopal-Krishna Siemiginowska, A. Sobolewska, M. Jorstad, S. Marscher, A. Aller, M.F. Aller, H.D. Hovatta, T. Caton, D.B. Reichart, D. Matsumoto, K. Sadakane, K. Gazeas, K. Kidger, M. Piirola, V. Jermak, H. Alicavus, F. Baliyan, K.S. Baransky, A. Berdyugin, A. Blay, P. Boumis, P. Boyd, D. Bufan, Y. Torrent, M.C. Campos, F. Gómez, J.C. Dalessio, J. Debski, B. Dimitrov, D. Drozdz, M. Er, H. Erdem, A. Pérez, A.E. Ramazani, V.F. Filippenko, A.V. Gafton, E. Garcia, F. Godunova, V. Pinilla, F.G. Gopinathan, M. Haislip, J.B. Haque, S. Harmanen, J. Hudec, R. Hurst, G. Ivarsen, K.M. Joshi, A. Kagitani, M. Karaman, N. Karjalainen, R. Kaur, N. Kozieł-Wierzbowska, D. Kuligowska, E. Kundera, T. Kurowski, S. Kvammen, A. Lacluyze, A.P. Lee, B.C. Liakos, A. Haro, J.L.D. Moore, J.P. Mugrauer, M. Nogues, R.N. Neely, A.W. Ogloza, W. Okano, S. Pajdosz, U. Pandey, J.C. Perri, M. Poyner, G. Provencal, J. Pursimo, T. Raj, A. Rajkumar, B. Reinthal, R. Reynolds, T. Saario, J. Sadegi, S. Sakanoi, T. González, J.L.S. Sameer Simon, A.O. Siwak, M. Schweyer, T. Alfaro, F.C.S. Sonbas, E. Strobl, J. Takalo, L.O. Espasa, L.T. Valdes, J.R. Vasylenko, V.V. Verrecchia, F. Webb, J.R. Yoneda, M. Zejmo, M. Zheng, W. Zielinski, P. Janik, J. Chavushyan, V. Mohammed, I. Cheung, C.C. Giroletti, M.
Subjects: Astrophysics::High Energy Astrophysical Phenomena
Abstract: We present the results of our power spectral density analysis for the BL Lac object OJ 287, utilizing the Fermi-LAT survey at high-energy γ-rays, Swift-XRT in X-rays, several ground-based telescopes and the Kepler satellite in the optical, and radio telescopes at GHz frequencies. The light curves are modeled in terms of continuous-time autoregressive moving average (CARMA) processes. Owing to the inclusion of the Kepler data, we were able to construct for the first time the optical variability power spectrum of a blazar without any gaps across ∼6 dex in temporal frequencies. Our analysis reveals that the radio power spectra are of a colored-noise type on timescales ranging from tens of years down to months, with no evidence for breaks or other spectral features. The overall optical power spectrum is also consistent with a colored noise on the variability timescales ranging from 117 years down to hours, with no hints of any quasi-periodic oscillations. The X-ray power spectrum resembles the radio and optical power spectra on the analogous timescales ranging from tens of years down to months. Finally, the γ-ray power spectrum is noticeably different from the radio, optical, and X-ray power spectra of the source: we have detected a characteristic relaxation timescale in the Fermi-LAT data, corresponding to ∼150 days, such that on timescales longer than this, the power spectrum is consistent with uncorrelated (white) noise, while on shorter variability timescales there is correlated (colored) noise. © 2018. The American Astronomical Society. All rights reserved..
Published: 2018

37. Authenticating the Presence of a Relativistic Massive Black Hole Binary in OJ 287 Using Its General Relativity Centenary Flare: Improved Orbital Parameters

Author: Dey, L. Valtonen, M.J. Gopakumar, A. Zola, S. Hudec, R. Pihajoki, P. Ciprini, S. Matsumoto, K. Sadakane, K. Kidger, M. Nilsson, K. Mikkola, S. Sillanpää, A. Takalo, L.O. Lehto, H.J. Berdyugin, A. Piirola, V. Jermak, H. Baliyan, K.S. Pursimo, T. Caton, D.B. Alicavus, F. Baransky, A. Blay, P. Boumis, P. Boyd, D. Torrent, M.C. Campos, F. Gómez, J.C. Chandra, S. Chavushyan, V. Dalessio, J. Debski, B. Drozdz, M. Er, H. Erdem, A. Pérez, A.E. Ramazani, V.F. Filippenko, A.V. Gafton, E. Ganesh, S. Garcia, F. Gazeas, K. Godunova, V. Pinilla, F.G. Gopinathan, M. Haislip, J.B. Harmanen, J. Hurst, G. Janík, J. Jelinek, M. Joshi, A. Kagitani, M. Karjalainen, R. Kaur, N. Keel, W.C. Kouprianov, V.V. Kundera, T. Kurowski, S. Kvammen, A. Lacluyze, A.P. Lee, B.C. Liakos, A. Lindfors, E. De Haro, J.L. Mugrauer, M. Nogues, R.N. Neely, A.W. Nelson, R.H. Ogloza, W. Okano, S. Pajdosz-Śmierciak, U. Pandey, J.C. Perri, M. Poyner, G. Provencal, J. Raj, A. Reichart, D.E. Reinthal, R. Reynolds, T. Saario, J. Sadegi, S. Sakanoi, T. González, J.-L.S. Sameer Schweyer, T. Simon, A. Siwak, M. Alfaro, F.C.S. Sonbas, E. Steele, I. Stocke, J.T. Strobl, J. Tomov, T. Espasa, L.T. Valdes, J.R. Pérez, J.V. Verrecchia, F. Vasylenko, V. Webb, J.R. Yoneda, M. Zejmo, M. Zheng, W. Zielinski, P.
Subjects: Astrophysics::High Energy Astrophysical Phenomena
Abstract: Results from regular monitoring of relativistic compact binaries like PSR 1913+16 are consistent with the dominant (quadrupole) order emission of gravitational waves (GWs). We show that observations associated with the binary black hole (BBH) central engine of blazar OJ 287 demand the inclusion of gravitational radiation reaction effects beyond the quadrupolar order. It turns out that even the effects of certain hereditary contributions to GW emission are required to predict impact flare timings of OJ 287. We develop an approach that incorporates this effect into the BBH model for OJ 287. This allows us to demonstrate an excellent agreement between the observed impact flare timings and those predicted from ten orbital cycles of the BBH central engine model. The deduced rate of orbital period decay is nine orders of magnitude higher than the observed rate in PSR 1913+16, demonstrating again the relativistic nature of OJ 287's central engine. Finally, we argue that precise timing of the predicted 2019 impact flare should allow a test of the celebrated black hole "no-hair theorem" at the 10% level. © 2018. The American Astronomical Society. All rights reserved.
Published: 2018

38. Correlation between Different Type of Caesium Carrier in The Radiocaesium Interception Potential Measurement for Forest Soils

Author: Pratama, Hendra A, primary, Yoneda, M, additional, Shimada, Y, additional, Satoshi, F, additional, and Ikegami, M, additional
Published: 2019
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39. Human autologous culture expanded bone marrow mesenchymal cell transplantation for repair of cartilage defects in osteoarthritic knees

Author: Wakitani, S., Imoto, K., Yamamoto, T., Saito, M., Murata, N., and Yoneda, M.
Published: 2002
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40. Authenticating the Presence of a Relativistic Massive Black Hole Binary in OJ 287 Using Its General Relativity Centenary Flare : Improved Orbital Parameters

Author: Dey, Lankeswar, Valtonen, M. J., Gopakumar, A., Zola, S., Hudec, R., Pihajoki, P., Ciprini, S., Matsumoto, K., Sadakane, K., Kidger, M., Nilsson, K., Mikkola, S., Sillanpaa, A., Takalo, L. O., Lehto, H. J., Berdyugin, A., Piirola, V., Jermak, H., Baliyan, K. S., Pursimo, T., Caton, D. B., Alicavus, F., Baransky, A., Blay, P., Boumis, P., Boyd, D., Campas Torrent, M., Campos, F., Carrillo Gomez, J., Chandra, S., Chavushyan, V., Dalessio, J., Debski, B., Drozdz, M., Er, H., Erdem, A., Escartin Perez, A., Ramazani, V. Fallah, Filippenko, A. V., Gafton, Emanuel, Ganesh, S., Garcia, F., Gazeas, K., Godunova, V., Gomez Pinilla, F., Gopinathan, M., Haislip, J. B., Harmanen, J., Hurst, G., Janik, J., Jelinek, M., Joshi, A., Kagitani, M., Karjalainen, R., Kaur, N., Keel, W. C., Kouprianov, V. V., Kundera, T., Kurowski, S., Kvammen, A., LaCluyze, A. P., Lee, B. C., Liakos, A., Lindfors, E., Lozano de Haro, J., Mugrauer, M., Naves Nogues, R., Neely, A. W., Nelson, R. H., Ogloza, W., Okano, S., Pajdosz-Smierciak, U., Pandey, J. C., Perri, M., Poyner, G., Provencal, J., Raj, A., Reichart, D. E., Reinthal, R., Reynolds, T., Saario, J., Sadegi, S., Sakanoi, T., Salto Gonzalez, J. -L., Sameer, Schweyer, T., Simon, A., Siwak, M., Soldan Alfaro, F. C., Sonbas, E., Steele, I., Stocke, J. T., Strobl, J., Tomov, T., Tremosa Espasa, L., Valdes, J. R., Valero Perez, J., Verrecchia, F., Vasylenko, V., Webb, J. R., Yoneda, M., Zejmo, M., Zheng, W., Zielinski, P., Dey, Lankeswar, Valtonen, M. J., Gopakumar, A., Zola, S., Hudec, R., Pihajoki, P., Ciprini, S., Matsumoto, K., Sadakane, K., Kidger, M., Nilsson, K., Mikkola, S., Sillanpaa, A., Takalo, L. O., Lehto, H. J., Berdyugin, A., Piirola, V., Jermak, H., Baliyan, K. S., Pursimo, T., Caton, D. B., Alicavus, F., Baransky, A., Blay, P., Boumis, P., Boyd, D., Campas Torrent, M., Campos, F., Carrillo Gomez, J., Chandra, S., Chavushyan, V., Dalessio, J., Debski, B., Drozdz, M., Er, H., Erdem, A., Escartin Perez, A., Ramazani, V. Fallah, Filippenko, A. V., Gafton, Emanuel, Ganesh, S., Garcia, F., Gazeas, K., Godunova, V., Gomez Pinilla, F., Gopinathan, M., Haislip, J. B., Harmanen, J., Hurst, G., Janik, J., Jelinek, M., Joshi, A., Kagitani, M., Karjalainen, R., Kaur, N., Keel, W. C., Kouprianov, V. V., Kundera, T., Kurowski, S., Kvammen, A., LaCluyze, A. P., Lee, B. C., Liakos, A., Lindfors, E., Lozano de Haro, J., Mugrauer, M., Naves Nogues, R., Neely, A. W., Nelson, R. H., Ogloza, W., Okano, S., Pajdosz-Smierciak, U., Pandey, J. C., Perri, M., Poyner, G., Provencal, J., Raj, A., Reichart, D. E., Reinthal, R., Reynolds, T., Saario, J., Sadegi, S., Sakanoi, T., Salto Gonzalez, J. -L., Sameer, Schweyer, T., Simon, A., Siwak, M., Soldan Alfaro, F. C., Sonbas, E., Steele, I., Stocke, J. T., Strobl, J., Tomov, T., Tremosa Espasa, L., Valdes, J. R., Valero Perez, J., Verrecchia, F., Vasylenko, V., Webb, J. R., Yoneda, M., Zejmo, M., Zheng, W., and Zielinski, P.
Abstract: Results from regular monitoring of relativistic compact binaries like PSR 1913+16 are consistent with the dominant (quadrupole) order emission of gravitational waves (GWs). We show that observations associated with the binary black hole (BBH) central engine of blazar OJ 287 demand the inclusion of gravitational radiation reaction effects beyond the quadrupolar order. It turns out that even the effects of certain hereditary contributions to GW emission are required to predict impact flare timings of OJ 287. We develop an approach that incorporates this effect into the BBH model for OJ 287. This allows us to demonstrate an excellent agreement between the observed impact flare timings and those predicted from ten orbital cycles of the BBH central engine model. The deduced rate of orbital period decay is nine orders of magnitude higher than the observed rate in PSR 1913+16, demonstrating again the relativistic nature of OJ 287's central engine. Finally, we argue that precise timing of the predicted 2019 impact flare should allow a test of the celebrated black hole no-hair theorem at the 10% level.
Published: 2018
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41. An integrated expression atlas of miRNAs and their promoters in human and mouse

Author: De Rie D., Abugessaisa I., Alam T., Arner E., Arner P., Ashoor H., Åström G., Babina M., Bertin N., Burroughs A., Carlisle A., Daub C., Detmar M., Deviatiiarov R., Fort A., Gebhard C., Goldowitz D., Guhl S., Ha T., Harshbarger J., Hasegawa A., Hashimoto K., Herlyn M., Heutink P., Hitchens K., Hon C., Huang E., Ishizu Y., Kai C., Kasukawa T., Klinken P., Lassmann T., Lecellier C., Lee W., Lizio M., Makeev V., Mathelier A., Medvedeva Y., Mejhert N., Mungall C., Noma S., Ohshima M., Okada-Hatakeyama M., Persson H., Rizzu P., Roudnicky F., Sætrom P., Sato H., Severin J., Shin J., Swoboda R., Tarui H., Toyoda H., Vitting-Seerup K., Winteringham L., Yamaguchi Y., Yasuzawa K., Yoneda M., Yumoto N., Zabierowski S., Zhang P., Wells C., Summers K., Kawaji H., Sandelin A., Rehli M., and Hayashizaki Y.
Abstract: © 2017 Nature America, Inc., part of Springer Nature. MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.
Published: 2017

42. High-precision broad-band linear polarimetry of early-type binaries

Author: Berdyugin, A., primary, Piirola, V., additional, Sakanoi, T., additional, Kagitani, M., additional, and Yoneda, M., additional
Published: 2018
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43. Data Descriptor: FANTOM5 CAGE profiles of human and mouse samples

Author: Noguchi, S, Arakawa, T, Fukuda, S, Furuno, M, Hasegawa, A, Hori, F, Ishikawa-Kato, S, Kaida, K, Kaiho, A, Kanamori-Katayama, M, Kawashima, T, Kojima, M, Kubosaki, A, Manabe, R-I, Murata, M, Nagao-Sato, S, Nakazato, K, Ninomiya, N, Nishiyori-Sueki, H, Noma, S, Saijyo, E, Saka, A, Sakai, M, Simon, C, Suzuki, N, Tagami, M, Watanabe, S, Yoshida, S, Arner, P, Axton, RA, Babina, M, Baillie, JK, Barnett, TC, Beckhouse, AG, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Carlisle, AJ, Clevers, HC, Davis, CA, Detmar, M, Dohi, T, Edge, ASB, Edinger, M, Ehrlund, A, Ekwall, K, Endoh, M, Enomoto, H, Eslami, A, Fagiolini, M, Fairbairn, L, Farach-Carson, MC, Faulkner, GJ, Ferrai, C, Fisher, ME, Forrester, LM, Fujita, R, Furusawa, J-I, Geijtenbeek, TB, Gingeras, T, Goldowitz, D, Guhl, S, Guler, R, Gustincich, S, Ha, TJ, Hamaguchi, M, Hara, M, Hasegawa, Y, Herlyn, M, Heutink, P, Hitchens, KJ, Hume, DA, Ikawa, T, Ishizu, Y, Kai, C, Kawamoto, H, Kawamura, YI, Kempfle, JS, Kenna, TJ, Kere, J, Khachigian, LM, Kitamura, T, Klein, S, Klinken, SP, Knox, AJ, Kojima, S, Koseki, H, Koyasu, S, Lee, W, Lennartsson, A, Mackay-sim, A, Mejhert, N, Mizuno, Y, Morikawa, H, Morimoto, M, Moro, K, Morris, KJ, Motohashi, H, Mummery, CL, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nozaki, T, Ogishima, S, Ohkura, N, Ohno, H, Ohshima, M, Okada-Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, DA, Passier, R, Patrikakis, M, Pombo, A, Pradhan-Bhatt, S, Qin, X-Y, Rehli, M, Rizzu, P, Roy, S, Sajantila, A, Sakaguchi, S, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schmidl, C, Schneider, C, Schulze-Tanzil, GG, Schwegmann, A, Sheng, G, Shin, JW, Sugiyama, D, Sugiyama, T, Summers, KM, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tomoiu, A, Toyoda, H, van de Wetering, M, van den Berg, LM, Verardo, R, Vijayan, D, Wells, CA, Winteringham, LN, Wolvetang, E, Yamaguchi, Y, Yamamoto, M, Yanagi-Mizuochi, C, Yoneda, M, Yonekura, Y, Zhang, PG, Zucchelli, S, Abugessaisa, I, Arner, E, Harshbarger, J, Kondo, A, Lassmann, T, Lizio, M, Sahin, S, Sengstag, T, Severin, J, Shimoji, H, Suzuki, M, Suzuki, H, Kawai, J, Kondo, N, Itoh, M, Daub, CO, Kasukawa, T, Kawaji, H, Carninci, P, Forrest, ARR, Hayashizaki, Y, Noguchi, S, Arakawa, T, Fukuda, S, Furuno, M, Hasegawa, A, Hori, F, Ishikawa-Kato, S, Kaida, K, Kaiho, A, Kanamori-Katayama, M, Kawashima, T, Kojima, M, Kubosaki, A, Manabe, R-I, Murata, M, Nagao-Sato, S, Nakazato, K, Ninomiya, N, Nishiyori-Sueki, H, Noma, S, Saijyo, E, Saka, A, Sakai, M, Simon, C, Suzuki, N, Tagami, M, Watanabe, S, Yoshida, S, Arner, P, Axton, RA, Babina, M, Baillie, JK, Barnett, TC, Beckhouse, AG, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Carlisle, AJ, Clevers, HC, Davis, CA, Detmar, M, Dohi, T, Edge, ASB, Edinger, M, Ehrlund, A, Ekwall, K, Endoh, M, Enomoto, H, Eslami, A, Fagiolini, M, Fairbairn, L, Farach-Carson, MC, Faulkner, GJ, Ferrai, C, Fisher, ME, Forrester, LM, Fujita, R, Furusawa, J-I, Geijtenbeek, TB, Gingeras, T, Goldowitz, D, Guhl, S, Guler, R, Gustincich, S, Ha, TJ, Hamaguchi, M, Hara, M, Hasegawa, Y, Herlyn, M, Heutink, P, Hitchens, KJ, Hume, DA, Ikawa, T, Ishizu, Y, Kai, C, Kawamoto, H, Kawamura, YI, Kempfle, JS, Kenna, TJ, Kere, J, Khachigian, LM, Kitamura, T, Klein, S, Klinken, SP, Knox, AJ, Kojima, S, Koseki, H, Koyasu, S, Lee, W, Lennartsson, A, Mackay-sim, A, Mejhert, N, Mizuno, Y, Morikawa, H, Morimoto, M, Moro, K, Morris, KJ, Motohashi, H, Mummery, CL, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nozaki, T, Ogishima, S, Ohkura, N, Ohno, H, Ohshima, M, Okada-Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, DA, Passier, R, Patrikakis, M, Pombo, A, Pradhan-Bhatt, S, Qin, X-Y, Rehli, M, Rizzu, P, Roy, S, Sajantila, A, Sakaguchi, S, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schmidl, C, Schneider, C, Schulze-Tanzil, GG, Schwegmann, A, Sheng, G, Shin, JW, Sugiyama, D, Sugiyama, T, Summers, KM, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tomoiu, A, Toyoda, H, van de Wetering, M, van den Berg, LM, Verardo, R, Vijayan, D, Wells, CA, Winteringham, LN, Wolvetang, E, Yamaguchi, Y, Yamamoto, M, Yanagi-Mizuochi, C, Yoneda, M, Yonekura, Y, Zhang, PG, Zucchelli, S, Abugessaisa, I, Arner, E, Harshbarger, J, Kondo, A, Lassmann, T, Lizio, M, Sahin, S, Sengstag, T, Severin, J, Shimoji, H, Suzuki, M, Suzuki, H, Kawai, J, Kondo, N, Itoh, M, Daub, CO, Kasukawa, T, Kawaji, H, Carninci, P, Forrest, ARR, and Hayashizaki, Y
Abstract: In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
Published: 2017

44. Weakening of Jupiter's main auroral emission during January 2014

Author: Badman, S.V., Bonfond, B., Fujimoto, M., Gray, R.L., Kasaba, Y., Kasahara, S., Kimura, T., Melin, H., Nichols, J.D., Steffl, A.J., Tao, C., Tsuchiya, F., Yamazaki, A., Yoneda, M., Yoshikawa, I., and Yoshioka, K.
Subjects: field-aligned current, Jupiter, Physics::Space Physics, magnetosphere, aurora, Astrophysics::Earth and Planetary Astrophysics
Abstract: In January 2014 Jupiter's FUV main auroral oval decreased its emitted power by 70% and shifted equatorward by ∼1°. Intense, low-latitude features were also detected. The decrease in emitted power is attributed to a decrease in auroral current density rather than electron energy. This could be caused by a decrease in the source electron density, an order of magnitude increase in the source electron thermal energy, or a combination of these. Both can be explained either by expansion of the magnetosphere or by an increase in the inward transport of hot plasma through the middle magnetosphere and its interchange with cold flux tubes moving outward. In the latter case the hot plasma could have increased the electron temperature in the source region and produced the intense, low-latitude features, while the increased cold plasma transport rate produced the shift of the main oval.
Published: 2016

45. Primary black hole spin in oj 287 AS determined by the general relativity centenary flare

Author: Valtonen, M.J. Zola, S. Ciprini, S. Gopakumar, A. Matsumoto, K. Sadakane, K. Kidger, M. Gazeas, K. Nilsson, K. Berdyugin, A. Piirola, V. Jermak, H. Baliyan, K.S. Alicavus, F. Boyd, D. Torrent, M.C. Campos, F. Gómez, J.C. Caton, D.B. Chavushyan, V. Dalessio, J. Debski, B. Dimitrov, D. Drozdz, M. Er, H. Erdem, A. Pérez, A.E. Ramazani, V.F. Filippenko, A.V. Ganesh, S. Garcia, F. Gómez Pinilla, F. Gopinathan, M. Haislip, J.B. Hudec, R. Hurst, G. Ivarsen, K.M. Jelinek, M. Joshi, A. Kagitani, M. Kaur, N. Keel, W.C. Lacluyze, A.P. Lee, B.C. Lindfors, E. Lozano De Haro, J. Moore, J.P. Mugrauer, M. Naves Nogues, R. Neely, A.W. Nelson, R.H. Ogloza, W. Okano, S. Pandey, J.C. Perri, M. Pihajoki, P. Poyner, G. Provencal, J. Pursimo, T. Raj, A. Reichart, D.E. Reinthal, R. Sadegi, S. Sakanoi, T. Salto González, J.-L. Sameer Schweyer, T. Siwak, M. Soldán Alfaro, F.C. Sonbas, E. Steele, I. Stocke, J.T. Strobl, J. Takalo, L.O. Tomov, T. Tremosa Espasa, L. Valdes, J.R. Valero Pérez, J. Verrecchia, F. Webb, J.R. Yoneda, M. Zejmo, M. Zheng, W. Telting, J. Saario, J. Reynolds, T. Kvammen, A. Gafton, E. Karjalainen, R. Harmanen, J. Blay, P.
Subjects: General Relativity and Quantum Cosmology, Astrophysics::High Energy Astrophysical Phenomena
Abstract: OJ 287 is a quasi-periodic quasar with roughly 12 year optical cycles. It displays prominent outbursts that are predictable in a binary black hole model. The model predicted a major optical outburst in 2015 December. We found that the outburst did occur within the expected time range, peaking on 2015 December 5 at magnitude 12.9 in the optical R-band. Based on Swift/XRT satellite measurements and optical polarization data, we find that it included a major thermal component. Its timing provides an accurate estimate for the spin of the primary black hole, . The present outburst also confirms the established general relativistic properties of the system such as the loss of orbital energy to gravitational radiation at the 2% accuracy level, and it opens up the possibility of testing the black hole no-hair theorem with 10% accuracy during the present decade. © 2016. The American Astronomical Society. All rights reserved.
Published: 2016

46. A search for QPOs in the blazar OJ287: Preliminary results from the 2015/2016 observing campaign

Author: Zola, S. Valtonen, M. Bhatta, G. Goyal, A. Debski, B. Baran, A. Krzesinski, J. Siwak, M. Ciprini, S. Gopakumar, A. Jermak, H. Nilsson, K. Reichart, D. Matsumoto, K. Sadakane, K. Gazeas, K. Kidger, M. Piirola, V. Alicavus, F. Baliyan, K.S. Berdyugin, A. Boyd, D. Campas Torrent, M. Campos, F. Carrillo Gómez, J. Caton, D.B. Chavushyan, V. Dalessio, J. Dimitrov, D. Drozdz, M. Er, H. Erdem, A. Escartin Pérez, A. Fallah Ramazani, V. Filippenko, A.V. Garcia, F. Gómez Pinilla, F. Gopinathan, M. Haislip, J.B. Harmanen, J. Hudec, R. Hurst, G. Ivarsen, K.M. Jelinek, M. Joshi, A. Kagitani, M. Kaur, N. Keel, W.C. LaCluyze, A.P. Lee, B.C. Lindfors, E. Lozano de Haro, J. Moore, J.P. Mugrauer, M. Naves Nogues, R. Neely, A.W. Nelson, R.H. Ogloza, W. Okano, S. Pandey, J.C. Perri, M. Pihajoki, P. Poyner, G. Provencal, J. Pursimo, T. Raj, A. Reinthal, R. Sadegi, S. Sakanoi, T. Sameer González, J.-L.S. Schweyer, T. Soldán Alfaro, F.C. Karaman, N. Sonbas, E. Steele, I. Stocke, J.T. Strobl, J. Takalo, L.O. Tomov, T. Tremosa Espasa, L. Valdes, J.R. Valero Pérez, J. Verrecchia, F. Webb, J.R. Yoneda, M. Zejmo, M. Zheng, W. Telting, J. Saario, J. Reynolds, T. Kvammen, A. Gafton, E. Karjalainen, R. Blay, P.
Abstract: We analyse the light curve in the R band of the blazar OJ287, gathered during the 2015/2016 observing season. We did a search for quasi-periodic oscillations (QPOs) using several methods over a wide range of timescales. No statistically significant periods were found in the high-frequency domain both in the ground-based data and in Kepler observations. In the longer-period domain, the Lomb-Scargle periodogram revealed several peaks above the 99% significance level. The longest one-about 95 days-corresponds to the innermost stable circular orbit (ISCO) period of the more massive black hole. The 43-day period could be an alias, or it can be attributed to accretion in the form of a two-armed spiral wave. © 2016 by the authors.
Published: 2016

47. Pin1 Associates with and Induces Translocation of CRTC2 to the Cytosol, Thereby Suppressing cAMP-responsive Element Transcriptional Activity

Author: Nakatsu, Y., Sakoda, H., Kushiyama, A., Ono, H., Fujishiro, M., Horike, N., Yoneda, M., Ohno, H., Tsuchiya, Y., Kamata, H., Tahara, H., Isobe, T., Nishimura, F., Katagiri, H., Oka, Y., Fukushima, Toshiaki, Takahashi, S., Kurihara, H., Uchida, T., and Asano, T.
Subjects: Cytosol/metabolism, Transcription, Genetic, Cyclic AMP/*metabolism, Colforsin/pharmacology, Nuclear Localization Signals, Transcription Factors/genetics/*metabolism, Cell Nucleus/genetics/*metabolism, Trans-Activators/genetics/*metabolism, Biochemistry, Mice, Cytosol, Cyclic AMP, Cyclic AMP Response Element-Binding Protein, Transcription, Genetic/drug effects/*physiology, Gene knockdown, Cyclic AMP Response Element-Binding Protein/genetics/metabolism, Peptidylprolyl Isomerase/genetics/*metabolism, biology, Hep G2 Cells, Peptidylprolyl Isomerase, CREB-Binding Protein, CRTC1, CRTC2, medicine.anatomical_structure, Liver, Gene Knockdown Techniques, PIN1, Liver/metabolism, phosphoenolpyruvate carboxykinase (PEPCK), Active Transport, Cell Nucleus/drug effects/physiology, Active Transport, Cell Nucleus, CREB, Pin1, medicine, Animals, Humans, CREB-binding protein, Molecular Biology, Transcription factor, Cell Nucleus, CREB-Binding Protein/genetics/metabolism, Colforsin, Nuclear Localization Signals/genetics/*metabolism, Cell Biology, Molecular biology, NIMA-Interacting Peptidylprolyl Isomerase, Cell nucleus, Metabolism, cAMP responsive element (CRE), biology.protein, Trans-Activators, Nuclear localization sequence, Transcription Factors
Abstract: Pin1 is a unique regulator, which catalyzes the conversion of a specific phospho-Ser/Thr-Pro-containing motif in target proteins. Herein, we identified CRTC2 as a Pin1-binding protein by overexpressing Pin1 with Myc and FLAG tags in mouse livers and subsequent purification of the complex containing Pin1. The association between Pin1 and CRTC2 was observed not only in overexpression experiments but also endogenously in the mouse liver. Interestingly, Ser(136) in the nuclear localization signal of CRTC2 was shown to be involved in the association with Pin1. Pin1 overexpression in HepG2 cells attenuated forskolin- induced nuclear localization of CRTC2 and cAMP-responsive element (CRE) transcriptional activity, whereas gene knockdown of Pin1 by siRNA enhanced both. Pin1 also associated with CRTC1, leading to their cytosol localization, essentially similar to the action of CRTC2. Furthermore, it was shown that CRTC2 associated with Pin1 did not bind to CREB. Taken together, these observations indicate the association of Pin1 with CRTC2 to decrease the nuclear CBP.CRTC.CREB complex. Indeed, adenoviral gene transfer of Pin1 into diabetic mice improved hyperglycemia in conjunction with normalizing phosphoenolpyruvate carboxykinase mRNA expression levels, which is regulated by CRE transcriptional activity. In conclusion, Pin1 regulates CRE transcriptional activity, by associating with CRTC1 or CRTC2.
Published: 2010

48. Space Weathering of Super-Earths: Model Simulations of Exospheric Sodium Escape from 61 Virgo b

Author: Yoneda, M., primary, Berdyugina, S., additional, and Kuhn, J., additional
Published: 2017
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49. The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Author: Liang, C, Alam, I, Albanese, D, Altschuler, G, Andersson, R, Arakawa, T, Archer, J, Arner, E, Arner, P, Babina, M, Baillie, K, Bajic, V, Baker, S, Balic, A, Balwierz, P, Beckhouse, A, Bertin, N, Blake, Ja, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, M, Califano, A, Cannistraci, C, Carbajo, D, Carninci, P, Chen, Yang, Chierici, M, Ciani, Y, Clevers, H, Dalla, Emiliano, Daub, C, Davis, C, De Hoon, M, De Lima Morais, D, Dermar, M, Diehl, A, Dimont, E, Dohl, T, Drabros, F, Edge, A, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach Carson, Mc, Faulkner, G, Favorov, A, Fisher, M, Forrest, A, Francescatto, M, Freeman, T, Frith, M, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J, Geijtenbeek, Tb, Gibson, A, Gingeras, T, Goldowithz, D, Gough, J, Guhl, S, Guler, R, Gustincich, Stefano, Ha, T, Haberle, V, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Hayashizaki, Y, Herlyn, M, Heutink, P, Hide, W, Hitchens, K, Ho Sui, S, Hofmann, O, Hoof, I, Hori, F, Hume, D, Huminiecki, L, Iida, K, Ikawa, T, Ishizu, Y, Itoh, M, Jankovic, B, Jia, H, Jorgensen, M, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Kajiyama, K, Kanamori Katayama, M, Kasianov, A, Kasukawa, T, Katayama, S, Kato Ishikawa, S, Kawaguchi, S, Kawai, J, Kawaji, H, Kawamoto, H, Kawamura, Y, Kawashima, T, Kempfle, J, Kenna, T, Kere, J, Khachigian, L, Kitamura, T, Klinken, P, Knox, A, Kojima, M, Kojima, S, Kondo, N, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kulakovskiy, I, Kwon, At, Laros, J, Lassmann, T, Lenhard, B, Lennartsson, A, Li, K, Lilji, B, Lipovich, L, Lizio, M, Mackay Sim, A, Makeev, V, Manabe, R, Mar, J, Marchand, B, Mathelier, A, Medvedeva, Y, Meehan, Tf, Mejhert, N, Meynert, A, Mizuno, Y, Morikawa, H, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, C, Mungall, Cj, Murata, M, Nagao Sato, S, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nakazato, K, Ninomiya Fukuda, N, Nishiyori Sueki, H, Noma, S, Nozaki, T, Ogishima, S, Ohkura, N, Ohmiya, H, Ohno, H, Ohshima, M, Okada Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, D, Pain, A, Passier, R, Persson, H, Piazza, Silvano, Plessy, C, Pradhan Bhatt, S, Prendergast, J, Rackham, O, Ramilowski, J, Rashid, M, Ravasi, T, Rehli, M, Rizzu, P, Roncador, M, Roy, S, Rye, M, Saijyo, E, Sajantila, A, Saka, A, Sakaguchi, S, Sakai, M, Sandelin, A, Sato, H, Satoh, H, Suzana, S, Alka, S, Schaefer, U, Schmeier, S, Schmidl, C, Schneider, C, Schultes, Ea, Schulze Tanzil, G, Schwegmann, A, Semple, C, Sengstag, T, Severin, J, Sheng, G, Shimoji, H, Shimoni, Y, Shin, J, Simon, C, Sugiyama, D, Sugiyama, T, Summers, K, Suzuki, H, Suzuki, M, Suzuki, N, Swoboda, R, Hoen P, T, Tagami, M, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tatum, Z, Taylor, M, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, Van De Wetering, M, Van Den Berg, L, Van Nimwegen, E, Verardo, R, Vijayan, D, Vitezic, M, Vorontzov, I, Wasserman, W, Watanabe, S, Wells, C, Winteringham, L, Wolvetang, E, Wood, Ej, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Yonekura, Y, Yoshida, Shin'Ichirou, Young, R, Zabierowski, Se, Zhang, P, Zhao, X, Zucchelli, Silvia, Forrest, Ar, Wagner, Gp, Hubrecht Institute for Developmental Biology and Stem Cell Research, AII - Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology
Subjects: Cell type, General Physics and Astronomy, rna-seq data, phylogenetic networks, Biology, ENCODE, General Biochemistry, Genetics and Molecular Biology, Divergence, Transcriptome, Models, Settore BIO/13 - Biologia Applicata, Neoplasms, Humans, Genetics, Models, Statistical, Multidisciplinary, Statistical model, General Chemistry, Statistical, Biological Evolution, Body plan, Tree structure, Evolutionary biology, Cancer cell
Abstract: In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination.
Published: 2015

50. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Author: Morikawa, H, Ohkura, N, Vandenbon, A, Itoh, M, Nagao Sato, S, Kawaji, H, Lassmann, T, Carninci, P, Hayashizaki, Y, Forrest, Ar, Standley, Dm, Date, H, Sakaguchi, S, FANTOM Consortium (Forrest AR, Rehli, M, Baillie, Jk, de Hoon MJ, Haberle, V, Kulakovskiy, Iv, Lizio, M, Andersson, R, Mungall, Cj, Meehan, Tf, Schmeier, S, Bertin, N, Jørgensen, M, Dimont, E, Arner, E, Schmidl, C, Schaefer, U, Medvedeva, Ya, Plessy, C, Vitezic, M, Severin, J, Semple, Ca, Ishizu, Y, Francescatto, M, Alam, I, Albanese, D, Altschuler, Gm, Archer, Ja, Arner, P, Babina, M, Baker, S, Balwierz, Pj, Beckhouse, Ag, Pradhan Bhatt, S, Blake, Ja, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, Am, Califano, A, Cannistraci, Cv, Carbajo, D, Chen, Y, Chierici, M, Ciani, Y, Clevers, Hc, Dalla, E, Davis, Ca, Deplancke, B, Detmar, M, Diehl, Ad, Dohi, T, Drabløs, F, Edge, As, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach Carson MC, Faulkner, Gj, Favorov, Av, Fisher, Me, Frith, Mc, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J, Geijtenbeek, Tb, Gibson, A, Gingeras, T, Goldowitz, D, Gough, J, Guhl, S, Guler, R, Gustincich, Stefano, Ha, Tj, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Herlyn, M, Hitchens, Kj, Ho Sui SJ, Hofmann, Om, Hoof, I, Hori, F, Huminiecki, L, Iida, K, Ikawa, T, Jankovic, Br, Jia, H, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Kajiyama, K, Kanamori Katayama, M, Kasianov, As, Kasukawa, T, Katayama, S, Kato, S, Kawaguchi, S, Kawamoto, H, Kawamura, Yi, Kawashima, T, Kempfle, Js, Kenna, Tj, Kere, J, Khachigian, Lm, Kitamura, T, Klinken, Sp, Knox, Aj, Kojima, M, Kojima, S, Kondo, N, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kwon, At, Laros, Jf, Lee, W, Lennartsson, A, Li, K, Lilje, B, Lipovich, L, Mackay Sim, A, Manabe, R, Mar, Jc, Marchand, B, Mathelier, A, Mejhert, N, Meynert, A, Mizuno, Y, Morais, Da, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, Cl, Murata, M, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nakazato, K, van Nimwegen, E, Ninomiya, N, Nishiyori, H, Noma, S, Nozaki, T, Ogishima, S, Ohmiya, H, Ohno, H, Ohshima, M, Okada Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, Da, Pain, A, Passier, R, Patrikakis, M, Persson, H, Piazza, S, Prendergast, Jg, Rackham, Oj, Ramilowski, Ja, Rashid, M, Ravasi, T, Rizzu, P, Roncador, M, Roy, S, Rye, Mb, Saijyo, E, Sajantila, A, Saka, A, Sakai, M, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schneider, C, Schultes, Ea, Schulze Tanzil GG, Schwegmann, A, Sengstag, T, Sheng, G, Shimoji, H, Shimoni, Y, Shin, Jw, Simon, C, Sugiyama, D, Sugiyama, T, Suzuki, M, Swoboda, Rk, 't Hoen PA, Tagami, M, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tatum, Z, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, van de Wetering, M, van den Berg LM, Verardo, R, Vijayan, D, Vorontsov, Ie, Wasserman, Ww, Watanabe, S, Wells, Ca, Winteringham, Ln, Wolvetang, E, Wood, Ej, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Yonekura, Y, Yoshida, S, Zabierowski, Se, Zhang, Pg, Zhao, X, Zucchelli, S, Summers, Km, Suzuki, H, Daub, Co, Kawai, J, Heutink, P, Hide, W, Freeman, Tc, Lenhard, B, Bajic, Vb, Taylor, Ms, Makeev, Vj, Sandelin, A, Hume, Da, Hayashizaki, Y., AII - Amsterdam institute for Infection and Immunity, Infectious diseases, Experimental Immunology, and Hubrecht Institute for Developmental Biology and Stem Cell Research
Subjects: Transcription, Genetic, Regulatory T cell, T-Lymphocytes, Down-Regulation, chemical and pharmacologic phenomena, Biology, Inbred C57BL, T-Lymphocytes, Regulatory, Epigenesis, Genetic, Mice, Genetic, Settore BIO/13 - Biologia Applicata, medicine, Transcriptional regulation, Animals, Epigenetics, Gene, Inbred BALB C, Genetics, Regulation of gene expression, Mice, Inbred BALB C, Multidisciplinary, Binding Sites, FOXP3, hemic and immune systems, Forkhead Transcription Factors, DNA Methylation, Biological Sciences, Regulatory, Cap analysis gene expression, Mice, Inbred C57BL, medicine.anatomical_structure, Gene Expression Regulation, DNA methylation, Transcription, Epigenesis
Abstract: Naturally occurring regulatory T (Treg) cells, which specifically express the transcription factor forkhead box P3 (Foxp3), are engaged in the maintenance of immunological self-tolerance and homeostasis. By transcriptional start site cluster analysis, we assessed here how genome-wide patterns of DNA methylation or Foxp3 binding sites were associated with Treg-specific gene expression. We found that Treg-specific DNA hypomethylated regions were closely associated with Treg up-regulated transcriptional start site clusters, whereas Foxp3 binding regions had no significant correlation with either up- or down-regulated clusters in nonactivated Treg cells. However, in activated Treg cells, Foxp3 binding regions showed a strong correlation with down-regulated clusters. In accordance with these findings, the above two features of activation-dependent gene regulation in Treg cells tend to occur at different locations in the genome. The results collectively indicate that Treg-specific DNA hypomethylation is instrumental in gene up-regulation in steady state Treg cells, whereas Foxp3 down-regulates the expression of its target genes in activated Treg cells. Thus, the two events seem to play distinct but complementary roles in Treg-specific gene expression.
Published: 2014

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