scispace - formally typeset
Search or ask a question
Institution

Tokyo Institute of Technology

EducationTokyo, Tôkyô, Japan
About: Tokyo Institute of Technology is a education organization based out in Tokyo, Tôkyô, Japan. It is known for research contribution in the topics: Thin film & Catalysis. The organization has 46775 authors who have published 101656 publications receiving 2357893 citations. The organization is also known as: Tokyo Tech & Tokodai.


Papers
More filters
Journal ArticleDOI
12 May 2011-Nature
TL;DR: Three robust clusters (referred to as enterotypes hereafter) are identified that are not nation or continent specific and confirmed in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous.
Abstract: Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.

5,566 citations

Journal ArticleDOI
Daniel J. Klionsky1, Kotb Abdelmohsen2, Akihisa Abe3, Joynal Abedin4  +2519 moreInstitutions (695)
TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

5,187 citations

Journal ArticleDOI
TL;DR: These guidelines are presented for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

4,316 citations

Journal ArticleDOI
Y. Fukuda1, T. Hayakawa1, E. Ichihara1, Kunio Inoue1, K. Ishihara1, H. Ishino1, Yoshitaka Itow1, Takaaki Kajita1, J. Kameda1, S. Kasuga1, Ken-ichiro Kobayashi1, Yohei Kobayashi1, Yusuke Koshio1, M. Miura1, Masayuki Nakahata1, S. Nakayama1, A. Okada1, Ko Okumura1, N. Sakurai1, Masato Shiozawa1, Yoshihiro Suzuki1, Y. Takeuchi1, Y. Totsuka1, Shinya Yamada1, M. Earl2, Alec Habig2, E. Kearns2, M. D. Messier2, Kate Scholberg2, J. L. Stone2, Lawrence Sulak2, C. W. Walter2, M. Goldhaber3, T. Barszczxak4, D. Casper4, W. Gajewski4, P. G. Halverson4, J. Hsu4, W. R. Kropp4, L. R. Price4, Frederick Reines4, Michael B. Smy4, Henry W. Sobel4, Mark R. Vagins4, K. S. Ganezer5, W. E. Keig5, R. W. Ellsworth6, S. Tasaka7, J. W. Flanagan8, A. Kibayashi8, John G. Learned8, S. Matsuno8, V. J. Stenger8, D. Takemori8, T. Ishii, Junichi Kanzaki, T. Kobayashi, S. Mine, K. Nakamura, K. Nishikawa, Yuichi Oyama, A. Sakai, Makoto Sakuda, Osamu Sasaki, S. Echigo9, M. Kohama9, A. T. Suzuki9, Todd Haines10, Todd Haines4, E. Blaufuss11, B. K. Kim11, R. Sanford11, R. Svoboda11, M. L. Chen12, Z. Conner12, Z. Conner13, J. A. Goodman12, G. W. Sullivan12, J. Hill14, C. K. Jung14, K. Martens14, C. Mauger14, C. McGrew14, E. Sharkey14, B. Viren14, C. Yanagisawa14, W. Doki15, Kazumasa Miyano15, H. Okazawa15, C. Saji15, M. Takahata15, Y. Nagashima16, M. Takita16, Takashi Yamaguchi16, Minoru Yoshida16, Soo-Bong Kim17, M. Etoh18, K. Fujita18, Akira Hasegawa18, Takehisa Hasegawa18, S. Hatakeyama18, T. Iwamoto18, M. Koga18, Tomoyuki Maruyama18, Hiroshi Ogawa18, J. Shirai18, A. Suzuki18, F. Tsushima18, Masatoshi Koshiba1, M. Nemoto19, Kyoshi Nishijima19, T. Futagami20, Y. Hayato20, Y. Kanaya20, K. Kaneyuki20, Y. Watanabe20, D. Kielczewska21, D. Kielczewska4, R. A. Doyle22, J. S. George22, A. L. Stachyra22, L. Wai22, L. Wai23, R. J. Wilkes22, K. K. Young22 
Abstract: We present an analysis of atmospheric neutrino data from a 33.0 kton yr (535-day) exposure of the Super-Kamiokande detector. The data exhibit a zenith angle dependent deficit of muon neutrinos which is inconsistent with expectations based on calculations of the atmospheric neutrino flux. Experimental biases and uncertainties in the prediction of neutrino fluxes and cross sections are unable to explain our observation. The data are consistent, however, with two-flavor ${\ensuremath{ u}}_{\ensuremath{\mu}}\ensuremath{\leftrightarrow}{\ensuremath{ u}}_{\ensuremath{\tau}}$ oscillations with ${sin}^{2}2\ensuremath{\theta}g0.82$ and $5\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}4}l\ensuremath{\Delta}{m}^{2}l6\ifmmode\times\else\texttimes\fi{}1{0}^{\ensuremath{-}3}\mathrm{eV}{}^{2}$ at 90% confidence level.

3,784 citations

Journal ArticleDOI
W. B. Atwood1, A. A. Abdo2, A. A. Abdo3, Markus Ackermann4  +289 moreInstitutions (37)
TL;DR: The Large Area Telescope (Fermi/LAT) as mentioned in this paper is the primary instrument on the Fermi Gamma-ray Space Telescope, which is an imaging, wide field-of-view, high-energy gamma-ray telescope, covering the energy range from below 20 MeV to more than 300 GeV.
Abstract: (Abridged) The Large Area Telescope (Fermi/LAT, hereafter LAT), the primary instrument on the Fermi Gamma-ray Space Telescope (Fermi) mission, is an imaging, wide field-of-view, high-energy gamma-ray telescope, covering the energy range from below 20 MeV to more than 300 GeV. This paper describes the LAT, its pre-flight expected performance, and summarizes the key science objectives that will be addressed. On-orbit performance will be presented in detail in a subsequent paper. The LAT is a pair-conversion telescope with a precision tracker and calorimeter, each consisting of a 4x4 array of 16 modules, a segmented anticoincidence detector that covers the tracker array, and a programmable trigger and data acquisition system. Each tracker module has a vertical stack of 18 x,y tracking planes, including two layers (x and y) of single-sided silicon strip detectors and high-Z converter material (tungsten) per tray. Every calorimeter module has 96 CsI(Tl) crystals, arranged in an 8 layer hodoscopic configuration with a total depth of 8.6 radiation lengths. The aspect ratio of the tracker (height/width) is 0.4 allowing a large field-of-view (2.4 sr). Data obtained with the LAT are intended to (i) permit rapid notification of high-energy gamma-ray bursts (GRBs) and transients and facilitate monitoring of variable sources, (ii) yield an extensive catalog of several thousand high-energy sources obtained from an all-sky survey, (iii) measure spectra from 20 MeV to more than 50 GeV for several hundred sources, (iv) localize point sources to 0.3 - 2 arc minutes, (v) map and obtain spectra of extended sources such as SNRs, molecular clouds, and nearby galaxies, (vi) measure the diffuse isotropic gamma-ray background up to TeV energies, and (vii) explore the discovery space for dark matter.

3,666 citations


Authors

Showing all 46967 results

NameH-indexPapersCitations
Matthew Meyerson194553243726
Yury Gogotsi171956144520
Masayuki Yamamoto1711576123028
H. Eugene Stanley1541190122321
Takashi Taniguchi1522141110658
Shu-Hong Yu14479970853
Kazunori Kataoka13890870412
Osamu Jinnouchi13588586104
Hector F. DeLuca133130369395
Shlomo Havlin131101383347
Hiroyuki Iwasaki131100982739
Kazunari Domen13090877964
Hideo Hosono1281549100279
Hideyuki Okano128116967148
Andreas Strasser12850966903
Network Information
Related Institutions (5)
University of Tokyo
337.5K papers, 10.1M citations

95% related

Osaka University
185.6K papers, 5.1M citations

95% related

Kyoto University
217.2K papers, 6.5M citations

94% related

Nagoya University
128.2K papers, 3.2M citations

94% related

Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202388
2022358
20213,457
20203,694
20193,783
20183,531