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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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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. Noninvasive assessment of liver disease severity in patients with nonalcoholic fatty liver disease and type 2 diabetes

Author

Pennisi, G., primary, Enea, M., additional, Falco, V., additional, Aithal, G.P., additional, Palaniyappan, N., additional, Yilmaz, Y., additional, Boursier, J., additional, Cassinotto, C., additional, de Lédinghen, V., additional, Chan, W.K., additional, Mahadeva, S., additional, Eddowes, P., additional, Newsome, P., additional, Karlas, T., additional, Wiegand, J., additional, Wong, V. Wai-Sun, additional, Schattenberg, J.M., additional, Labenz, C., additional, Kim, W., additional, Lee, M.S., additional, Lupsor-Platon, M., additional, Cobbold, J.F.L., additional, Fan, J., additional, Shen, F., additional, Staufer, K., additional, Trauner, M., additional, Stauber, R., additional, Nakajima, A., additional, Yoneda, M., additional, Bugianesi, E., additional, Younes, R., additional, Gaia, S., additional, Zheng, M., additional, Cammà, C., additional, Anstee, Q.M., additional, Mózes, F.E., additional, Pavlides, M., additional, and Petta, S., additional

Published
2023
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21. 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

26. 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

28. 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

33. 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

38. 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

43. Involvement of JNK pathway in the promotion of the early stage of colorectal carcinogenesis under high-fat dietary conditions

Author

Endo, H., Hosono, K., Fujisawa, T., Takahashi, H., Sugiyama, M., Yoneda, K., Nozaki, Y., Fujita, K., Yoneda, M., Inamori, M., Wada, K., Nakagama, H., and Nakajima, A.

Subjects
Colorectal cancer -- Development and progression, Colorectal cancer -- Models, Colorectal cancer -- Research, c-Jun N-terminal kinases -- Physiological aspects, c-Jun N-terminal kinases -- Research, Dietary fat -- Health aspects, Dietary fat -- Research, Health
Published
2009

45. Effectiveness of antiplatelet drugs against experimental non-alcoholic fatty liver disease

Author

Fujita, K., Nozaki, Y., Wada, K., Yoneda, M., Endo, H., Takahashi, H., Iwasaki, T., Inamori, M., Abe, Y., Kobayashi, N., Kirikoshi, H., Kubota, K., Saito, S., Nagashima, Y., and Nakajima, A.

Subjects
Fatty liver -- Drug therapy, Fatty liver -- Research, Blood platelets -- Aggregation, Blood platelets -- Dosage and administration, Blood platelets -- Research, Health
Published
2008

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