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1. Full Text Visualizing cell state transition using raman spectroscopy
by Ichimura, Taro and Chiu, Liang-Da and Fujita, Katsumasa and Kawata, Satoshi and Watanabe, Tomonobu M and Yanagida, Toshio and Fujita, Hideaki
PLoS ONE, ISSN 1932-6203, 01/2014, Volume 9, Issue 1, p. e84478
System level understanding of the cell requires detailed description of the cell state, which is often characterized by the expression levels of proteins.... 
PROTEIN | NUCLEUS | MULTIDISCIPLINARY SCIENCES | EMBRYONIC STEM-CELLS | DYNAMICS | BODIES | DIFFERENTIATION | PLURIPOTENT | CYCLE | Cell Line | Mice | Spectrum Analysis, Raman - methods | Animals | Embryonic Stem Cells - cytology | Cell Differentiation - physiology | Proteins | Raman spectroscopy | Cell differentiation | Embryonic stem cells | Raman spectra | Mesenchyme | Laboratories | Change detection | Leukemia | Differentiation (biology) | Stem cell transplantation | Biochemistry | Biology | Adipocytes | Cytosol | Immunology | Allografts | Spectrum analysis | Cell cycle | DNA methylation | Deoxyribonucleic acid--DNA | Spectroscopy | Cell division | Principal components analysis | Antibiotics | Microscopy | Morphology | Stem cells | Nuclei (cytology) | Applied physics | Deoxyribonucleic acid | DNA
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2. Full Text Theoretical modeling reveals that regulatory T cells increase T cell-interaction with antigen-presenting cells for stable immune-tolerance
by Yamaguchi, Tomoyuki and Teraguchi, Shunsuke and Furusawa, Chikara and Machiyama, Hiroaki and Watanabe, Tomonobu M and Fujita, Hideaki and Sakaguchi, Shimon and Yanagida, Toshio
International immunology, ISSN 1460-2377, 05/2019, Volume 31, Issue 11, pp. 743 - 753
The immune system in tolerance maintains cell-diversity without responding to self-antigens. Foxp3-expressing CD25+CD4+ regulatory T cells (Tregs) inhibit T... 
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3. Full Text Cell type discrimination based on image features of molecular component distribution
by Germond, Arno and Ichimura, Taro and Chiu, Liang-da and Fujita, Katsumasa and Watanabe, Tomonobu M and Fujita, Hideaki
Scientific Reports, ISSN 2045-2322, 12/2018, Volume 8, Issue 1, pp. 11726 - 8
Machine learning-based cell classifiers use cell images to automate cell-type discrimination, which is increasingly becoming beneficial in biological studies... 
LABEL-FREE | RAMAN | MICROSCOPY | MULTIDISCIPLINARY SCIENCES | Learning algorithms | Spatial discrimination
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4. Full Text Flashing Brownian Ratchet Mechanism of Collective State Transition in Mouse Embryonic Stem Cell Revealed by using Single Cell Analysis
by Okamoto, Kazuko and Fujita, Hideaki and Furuwaka, Chikara and Watanabe, Tomonobu M
Biophysical Journal, ISSN 0006-3495, 02/2017, Volume 112, Issue 3, pp. 280a - 280a
Embryonic stem cells | Analysis
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5. Electrochemical aspects of ionic liquids
by Ohno, Hiroyuki
2005, 1st ed., ISBN 9780471648512, xiii, 392
Focusing on the electrochemistry of ionic liquids, Electrochemical Aspects of Ionic Liquids examines the fundamentals and electrochemical applications of ionic... 
General | Chemistry | SCIENCE | Electrochemistry | Polymerization | Ionic solutions
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6. Full Text Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation
by Okamoto, Kazuko and Germond, Arno and Fujita, Hideaki and Furusawa, Chikara and Okada, Yasushi and Watanabe, Tomonobu M
Scientific Reports, ISSN 2045-2322, 12/2018, Volume 8, Issue 1, pp. 11965 - 13
In the stem cell research field, the molecular regulatory network used to define cellular states has been extensively studied, however, the general driving... 
IN-VITRO | MULTIDISCIPLINARY SCIENCES | MOUSE EMBRYOS | BIOLOGY | TRANSCRIPTIONAL REGULATORY CIRCUITRY | SELF-RENEWAL | LEUKEMIA INHIBITORY FACTOR | PLURIPOTENCY | E-CADHERIN | ES CELLS | NANOG EXPRESSION | Stem cell transplantation | Cooperativity | Decision making | Embryos | Embryo cells | Stem cells
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7. Full Text International validation of the consensus Immunoscore for the classification of colon cancer: a prognostic and accuracy study
by Pagès, Franck and Mlecnik, Bernhard and Marliot, Florence and Bindea, Gabriela and Ou, Fang-Shu and Bifulco, Carlo and Lugli, Alessandro and Zlobec, Inti and Rau, Tilman T and Berger, Martin D and Berger, Anne and Nagtegaal, Iris D and Vink-Börger, Elisa and Hartmann, Arndt and Geppert, Carol and Kolwelter, Julie and Merkel, Susanne and Grützmann, Robert and Van den Eynde, Marc and Jouret-Mourin, Anne and Kartheuser, Alex and Léonard, Daniel and Remue, Christophe and Wang, Julia Y and Wang, Yili and Bavi, Prashant and Roehrl, Michael H A and Ohashi, Pamela S and Nguyen, Linh T and Han, SeongJun and MacGregor, Heather L and Hafezi-Bakhtiari, Sara and Wouters, Bradly G and Masucci, Giuseppe V and Andersson, Emilia K and Zavadova, Eva and Vocka, Michal and Spacek, Jan and Petruzelka, Lubos and Konopasek, Bohuslav and Dundr, Pavel and Skalova, Helena and Nemejcova, Kristyna and Botti, Gerardo and Tatangelo, Fabiana and Delrio, Paolo and Ciliberto, Gennaro and Maio, Michele and Laghi, Luigi and Grizzi, Fabio and Fredriksen, Tessa and Buttard, Bénédicte and Angelova, Mihaela and Vasaturo, Angela and Maby, Pauline and Church, Sarah E and Angell, Helen K and Lafontaine, Lucie and Bruni, Daniela and El Sissy, Carine and Haicheur, Nacilla and Kirilovsky, Amos and Lagorce, Christine and Meyers, Jeffrey P and Paustian, Christopher and Feng, Zipei and Ballesteros-Merino, Carmen and Dijkstra, Jeroen and van de Water, Carlijn and van Lent-van Vliet, Shannon and Knijn, Nikki and Mușină, Ana-Maria and Scripcariu, Dragos-Viorel and Popivanova, Boryana and Xu, Mingli and Fujita, Tomonobu and Hazama, Shoichi and Suzuki, Nobuaki and Nagano, Hiroaki and Okuno, Kiyotaka and Torigoe, Toshihiko and Sato, Noriyuki and Furuhata, Tomohisa and Takemasa, Ichiro and Itoh, Kyogo and Patel, Jayendrakumar B and Patel, Prabhu S and Vora, Hemangini H and Shah, Birva and Rajvik, Kruti N and Pandya, Shashank J and Shukla, Shilin N and Zhang, Guanjun and Kawakami, Yutaka and Marincola, Francesco M and Ascierto, Paolo A and Sargent, Daniel J and Fox, Bernard A and Galon, Jérôme
The Lancet, ISSN 0140-6736, 05/2018, Volume 391, Issue 10135, pp. 2128 - 2139
The estimation of risk of recurrence for patients with colon carcinoma must be improved. A robust immune score quantification is needed to introduce immune... 
SURVIVAL | MEDICINE, GENERAL & INTERNAL | IMPACT | IMMUNE CELLS | METASTASIS | IMMUNOTHERAPY | COLORECTAL-CANCER | MICROSATELLITE INSTABILITY | IMMUNOSURVEILLANCE | TUMORS | INFILTRATION | Reproducibility of Results | Colonic Neoplasms - classification | Prognosis | Humans | Middle Aged | Colonic Neoplasms - diagnosis | Proportional Hazards Models | Male | Neoplasm Recurrence, Local - etiology | Lymphocytes, Tumor-Infiltrating | Colonic Neoplasms - immunology | Adult | Female | Aged | Neoplasm Staging | Colon cancer | Research | Analysis | Oncology, Experimental | Cancer | Immunohistochemistry | CD8 antigen | Colorectal cancer | Cytotoxicity | Lymphocytes T | Statistical methods | Microsatellite instability | Assaying | Paraffin | Multivariate analysis | Consortia | Training | Immunology | Lymphocytes | Risk assessment | Surgery | Immunotherapy | Classification | Mathematical models | Colon | Medical research | Stability | Statistical analysis | Microsatellites | Invasiveness | Health risks | CD3 antigen | Gene expression | Patients | Reproducibility | Medical prognosis | Quality control | Tumors
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8. Full Text Phase I pilot study of Wilms tumor gene 1 peptide‐pulsed dendritic cell vaccination combined with gemcitabine in pancreatic cancer
by Mayanagi, Shuhei and Kitago, Minoru and Sakurai, Toshiharu and Matsuda, Tatsuo and Fujita, Tomonobu and Higuchi, Hajime and Taguchi, Junichi and Takeuchi, Hiroya and Itano, Osamu and Aiura, Koichi and Hamamoto, Yasuo and Takaishi, Hiromasa and Okamoto, Masato and Sunamura, Makoto and Kawakami, Yutaka and Kitagawa, Yuko
Cancer Science, ISSN 1347-9032, 04/2015, Volume 106, Issue 4, pp. 397 - 406
This study aimed to evaluate the feasibility of and immune response to Wilms tumor gene 1 (WT1) peptide‐pulsed dendritic cell vaccination combined with... 
first‐line therapy | neutrophil lymphocyte ratio | dendritic cell vaccination | Delayed‐type hypersensitivity | immunotherapy | Neutrophil lymphocyte ratio | Delayed-type hypersensitivity | Dendritic cell vaccination | First-line therapy | Immunotherapy | first-line therapy | BILIARY-TRACT CANCER | DUCTAL ADENOCARCINOMA | COMBINATION | TRIAL | THERAPY | ONCOLOGY | WT1 | SUPPRESSOR-CELLS | RESISTANT PROSTATE-CANCER | CARCINOMA | Dendritic Cells - immunology | Humans | Middle Aged | Vaccination | Male | Cancer Vaccines - therapeutic use | Deoxycytidine - therapeutic use | WT1 Proteins - pharmacology | C-Reactive Protein - metabolism | WT1 Proteins - immunology | Adult | Female | Pancreatic Neoplasms - mortality | Interleukin-8 - blood | Liver Neoplasms - secondary | Immunotherapy, Adoptive - adverse effects | Immunotherapy, Adoptive - methods | Neutrophils - immunology | Treatment Outcome | Combined Modality Therapy | Cancer Vaccines - immunology | Antimetabolites, Antineoplastic - therapeutic use | Pilot Projects | Pancreatic Neoplasms - immunology | Lymphocyte Count | Aged | CD8-Positive T-Lymphocytes - immunology | Dendritic Cells - transplantation | Deoxycytidine - analogs & derivatives | Pancreatic Neoplasms - therapy | Gemcitabine | Peptides | Hypersensitivity (delayed) | Genes | Liver | Clinical trials | Metastasis | Suppressor cells | Cancer therapies | Metastases | Liver cancer | Consent | Peripheral blood | Growth factors | Antigens | Dendritic cells | Inflammation | FDA approval | Disease control | Patients | Studies | Chemotherapy | Pancreatic cancer | Medical prognosis | Response rates | Interferon | Histocompatibility antigen HLA | Prostate cancer | Skin tests | Tumors | Original
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9. Full Text Four-Dimensional Spatial Nanometry of Single Particles in Living Cells Using Polarized Quantum Rods
by Watanabe, Tomonobu M and Fujii, Fumihiko and Jin, Takashi and Umemoto, Eiji and Miyasaka, Masayuki and Fujita, Hideaki and Yanagida, Toshio
Biophysical Journal, ISSN 0006-3495, 08/2013, Volume 105, Issue 3, pp. 555 - 564
Single particle tracking is widely used to study protein movement with high spatiotemporal resolution both in vitro and in cells. Quantum dots, which are... 
PHOTOBLEACHING KINETICS | HAND-OVER-HAND | BIOPHYSICS | IN-VIVO | VESICLE TRANSPORT | GOLD NANORODS | MYOSIN-V | MOLECULE FLUORESCENCE | ORIENTATION SENSORS | MICROSCOPY | FLUORESCENCE CORRELATION SPECTROSCOPY | Macrophages - metabolism | Optical Imaging - instrumentation | Animals | Quantum Dots - chemistry | Quantum Dots - metabolism | Imaging, Three-Dimensional - methods | Mice | Optical Imaging - methods | Fluorescence | Sects | Nanotechnology | Blends | Polymer blends | Movement | Tracking | Semiconductors | Quantum dots | Nanostructure | Three dimensional | Cell Biophysics
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10. Full Text Culturing of mouse and human cells on soft substrates promote the expression of stem cell markers
by Higuchi, Sayaka and Watanabe, Tomonobu M and Kawauchi, Keiko and Ichimura, Taro and Fujita, Hideaki
Journal of Bioscience and Bioengineering, ISSN 1389-1723, 06/2014, Volume 117, Issue 6, pp. 749 - 755
Substrate elasticity is a potent regulator of the cell state. Soft substrates have been shown to promote the homogeneous self-renewal of mouse embryonic stem... 
Actin filament | Elasticity | Fibroblasts | Reprogramming | Induced pluripotent stem cells | SURVIVAL | SOMATIC-CELLS | ROCK | FOOD SCIENCE & TECHNOLOGY | KINASE | FOCAL ADHESIONS | SHAPE | CONTRACTION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | RHO | EXTRACELLULAR-MATRIX | GENERATION | Biomarkers - metabolism | Gene Expression | Nanog Homeobox Protein | Fibroblasts - physiology | Homeodomain Proteins - metabolism | Humans | Cells, Cultured | Transcription Factors - genetics | Hardness | Homeodomain Proteins - genetics | Acrylamides - chemistry | SOXB1 Transcription Factors - metabolism | Octamer Transcription Factor-3 - genetics | Transcription Factors - metabolism | Cell Differentiation - genetics | Adult Stem Cells - metabolism | Animals | SOXB1 Transcription Factors - genetics | rho-Associated Kinases - metabolism | Octamer Transcription Factor-3 - metabolism | Mice | Cell Culture Techniques | Culture Media - chemistry | Induced Pluripotent Stem Cells - metabolism | Embryonic stem cells | Polyacrylamide | Muscle proteins
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11. Full Text SH3 Domain of C-Src Regulates its Dynamic Behavior in the Cell Membrane
by Machiyama, Hiroaki and Yamaguchi, Tomoyuki and Watanabe, Tomonobu M and Fujita, Hideaki
Biophysical Journal, ISSN 0006-3495, 01/2015, Volume 108, Issue 2, pp. 143a - 143a
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12. Full Text Glycine Insertion Makes Yellow Fluorescent Protein Sensitive to Hydrostatic Pressure
by Watanabe, Tomonobu M and Imada, Katsumi and Yoshizawa, Keiko and Nishiyama, Masayoshi and Kato, Chiaki and Abe, Fumiyoshi and Morikawa, Takamitsu J and Kinoshita, Miki and Fujita, Hideaki and Yanagida, Toshio
PLoS ONE, ISSN 1932-6203, 08/2013, Volume 8, Issue 8, p. e73212
Fluorescent protein-based indicators for intracellular environment conditions such as pH and ion concentrations are commonly used to study the status and... 
SHIFTS | TEMPERATURE | VARIANTS | STRUCTURAL BASIS | BINDING | MULTIDISCIPLINARY SCIENCES | Glycine - genetics | Glycine - metabolism | Escherichia coli - genetics | Bacterial Proteins - genetics | Escherichia coli - metabolism | Bacterial Proteins - metabolism | Luminescent Proteins - genetics | Mutation, Missense | Hydrostatic Pressure | Amino Acid Substitution | Luminescent Proteins - metabolism | Tyrosine | Fluorescence | Chromophores | Structure | Glycine | Crystals | Viscosity | Amino acids | Biology | pH effects | Crystallography | Proteins | Design engineering | Immunology | Indicators | Crystal structure | Solvents | Water chemistry | Yellow fluorescent protein | Earth science | Pressure | Biological activity | Dynamic tests | Mutagenesis | Hydrostatic pressure | Cells (biology) | Phenols | Intracellular
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13. Full Text Design and development of genetically encoded fluorescent sensors to monitor intracellular chemical and physical parameters
by Germond, Arno and Fujita, Hideaki and Ichimura, Taro and Watanabe, Tomonobu M
Biophysical Reviews, ISSN 1867-2450, 6/2016, Volume 8, Issue 2, pp. 121 - 138
Over the past decades many researchers have made major contributions towards the development of genetically encoded (GE) fluorescent sensors derived from... 
Biochemistry, general | Genetically encoded | Intracellular sensor | Probe design | Fluorescent protein | Membrane Biology | Biological Techniques | Biophysics and Biological Physics | Cell Biology | Life Sciences | Green fluorescent protein | Fluorescent measurement | Nanotechnology
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14. Full Text Simultaneous Tracking of Multiple Myosins in Sub-Diffraction Scale Based on Spectral Division
by Kakizuka, Taishi and Ichimura, Taro and Fujita, Hideaki and Watanabe, Tomonobu M
Biophysical Journal, ISSN 0006-3495, 01/2014, Volume 106, Issue 2, pp. 570a - 570a
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15. Full Text Prognostic significance of interleukin-8 and CD163-positive cell-infiltration in tumor tissues in patients with oral squamous cell carcinoma
by Fujita, Yohei and Okamoto, Masato and Goda, Hiroyuki and Tano, Tomoyuki and Nakashiro, Koh-Ichi and Sugita, Atsuro and Fujita, Tomonobu and Koido, Shigeo and Homma, Sadamu and Kawakami, Yutaka and Hamakawa, Hiroyuki
PLoS ONE, ISSN 1932-6203, 12/2014, Volume 9, Issue 12, p. e110378
Purpose: We investigated whether serum interleukin (IL)-8 reflects the tumor microenvironment and has prognostic value in patients with oral squamous cell... 
HEAD | RECURRENCE | CANCER | EXPRESSION | MULTIDISCIPLINARY SCIENCES | T-CELLS | Immunohistochemi