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Data processing pipeline for serial femtosecond crystallography at SACLA

pipeline programs

Nakane T, Joti Y, Yabashi M.
GSID: qTYff_8kHKsJ
T Nakane, Y Joti, K Tono, M Yabashi… - Journal of applied …, 2016 - scripts.iucr.org

… Since users might want to copy pipeline outputs to their home institution for analysis by their own programs, the use of a standard, widely adopted compression algorithm is an advantage. Our benchmark tests showed that compression at level...

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Nakane, T., Joti, Y., Tono, K., Yabashi, M., Nango, E., Iwata, S., ... & Nureki, O. (2016). Data processing pipeline for serial femtosecond crystallography at SACLA. Journal of applied crystallography, 49(3), 1035-1041.
Nakane, Takanori, et al. "Data processing pipeline for serial femtosecond crystallography at SACLA." Journal of applied crystallography 49.3 (2016): 1035-1041.
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Highly regioselective addition of adamantylidene carbene to Yb@C2v(3)-C80 to afford the first derivative of divalent metallofullerenes.

Angewandte Chemie (International ed. in English)

Xie Y, Suzuki M, Cai W, Mizorogi N, Nagase S, Akasaka T, Lu X.
PMID: 23576376
Angew Chem Int Ed Engl. 2013 May 03;52(19):5142-5. doi: 10.1002/anie.201210164. Epub 2013 Apr 09.

No abstract available.

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Xie Y, Suzuki M, Cai W, et al. Highly regioselective addition of adamantylidene carbene to Yb@C2v(3)-C80 to afford the first derivative of divalent metallofullerenes. Angew Chem Int Ed Engl. 2013;52(19):5142-5doi: 10.1002/anie.201210164.
Xie, Y., Suzuki, M., Cai, W., Mizorogi, N., Nagase, S., Akasaka, T., & Lu, X. (2013). Highly regioselective addition of adamantylidene carbene to Yb@C2v(3)-C80 to afford the first derivative of divalent metallofullerenes. Angewandte Chemie (International ed. in English), 52(19), 5142-5. https://doi.org/10.1002/anie.201210164
Xie, Yunpeng, et al. "Highly regioselective addition of adamantylidene carbene to Yb@C2v(3)-C80 to afford the first derivative of divalent metallofullerenes." Angewandte Chemie (International ed. in English) vol. 52,19 (2013): 5142-5. doi: https://doi.org/10.1002/anie.201210164
Xie Y, Suzuki M, Cai W, Mizorogi N, Nagase S, Akasaka T, Lu X. Highly regioselective addition of adamantylidene carbene to Yb@C2v(3)-C80 to afford the first derivative of divalent metallofullerenes. Angew Chem Int Ed Engl. 2013 May 03;52(19):5142-5. doi: 10.1002/anie.201210164. Epub 2013 Apr 09. PMID: 23576376.
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X-Ray-Induced Damage to the Submandibular Salivary Glands in Mice: An Analysis of Strain-Specific Responses.

BioResearch open access

Kamiya M, Kawase T, Hayama K, Tsuchimochi M, Okuda K, Yoshie H.
PMID: 26309806
Biores Open Access. 2015 Jun 01;4(1):307-18. doi: 10.1089/biores.2015.0017. eCollection 2015.

Radiation therapy for head and neck cancers often causes xerostomia (dry mouth) by acutely damaging the salivary glands through the induction of severe acute inflammation. By contrast, the mechanism underlying the X-ray-induced delayed salivary dysfunction is unknown and has...

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Kamiya M, Kawase T, Hayama K, et al. X-Ray-Induced Damage to the Submandibular Salivary Glands in Mice: An Analysis of Strain-Specific Responses. Biores Open Access. 2015;4(1):307-18doi: 10.1089/biores.2015.0017.
Kamiya, M., Kawase, T., Hayama, K., Tsuchimochi, M., Okuda, K., & Yoshie, H. (2015). X-Ray-Induced Damage to the Submandibular Salivary Glands in Mice: An Analysis of Strain-Specific Responses. BioResearch open access, 4(1), 307-18. https://doi.org/10.1089/biores.2015.0017
Kamiya, Mana, et al. "X-Ray-Induced Damage to the Submandibular Salivary Glands in Mice: An Analysis of Strain-Specific Responses." BioResearch open access vol. 4,1 (2015): 307-18. doi: https://doi.org/10.1089/biores.2015.0017
Kamiya M, Kawase T, Hayama K, Tsuchimochi M, Okuda K, Yoshie H. X-Ray-Induced Damage to the Submandibular Salivary Glands in Mice: An Analysis of Strain-Specific Responses. Biores Open Access. 2015 Jun 01;4(1):307-18. doi: 10.1089/biores.2015.0017. eCollection 2015. PMID: 26309806; PMCID: PMC4497710.
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Modyfied wedge osteotomy for osteoarthritis of elbow secondary to osteochondritis dissecans in adolecent with multiple epiphyseal dysplasia. A case report.

Journal of orthopaedics

Yoshida T, Kim WC, Oka Y, Nakase M, Nishida A, Wada H, Arai Y, Kubo T.
PMID: 28860685
J Orthop. 2017 Aug 10;14(4):515-519. doi: 10.1016/j.jor.2017.08.011. eCollection 2017 Dec.

Multiple epiphyseal dysplasia (MED) may be complicated by osteochondritis dissecans (OCD), most commonly reported in the knee, but involvement of the elbow is very rare. Optimal treatment for MED-associated elbow OCD and treatment outcome have not been established. This...

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Yoshida T, Kim WC, Oka Y, et al. Modyfied wedge osteotomy for osteoarthritis of elbow secondary to osteochondritis dissecans in adolecent with multiple epiphyseal dysplasia. A case report. J Orthop. 2017;14(4):515-519doi: 10.1016/j.jor.2017.08.011.
Yoshida, T., Kim, W. C., Oka, Y., Nakase, M., Nishida, A., Wada, H., Arai, Y., & Kubo, T. (2017). Modyfied wedge osteotomy for osteoarthritis of elbow secondary to osteochondritis dissecans in adolecent with multiple epiphyseal dysplasia. A case report. Journal of orthopaedics, 14(4), 515-519. https://doi.org/10.1016/j.jor.2017.08.011
Yoshida, Takashi, et al. "Modyfied wedge osteotomy for osteoarthritis of elbow secondary to osteochondritis dissecans in adolecent with multiple epiphyseal dysplasia. A case report." Journal of orthopaedics vol. 14,4 (2017): 515-519. doi: https://doi.org/10.1016/j.jor.2017.08.011
Yoshida T, Kim WC, Oka Y, Nakase M, Nishida A, Wada H, Arai Y, Kubo T. Modyfied wedge osteotomy for osteoarthritis of elbow secondary to osteochondritis dissecans in adolecent with multiple epiphyseal dysplasia. A case report. J Orthop. 2017 Aug 10;14(4):515-519. doi: 10.1016/j.jor.2017.08.011. eCollection 2017 Dec. PMID: 28860685; PMCID: PMC5568871.
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Quality Assessment of Platelet-Rich Fibrin-Like Matrix Prepared from Whole Blood Samples after Extended Storage.

Biomedicines

Kawabata H, Isobe K, Watanabe T, Okudera T, Nakamura M, Suzuki M, Ryu J, Kitamura Y, Okudera H, Okuda K, Nakata K, Kawase T.
PMID: 28926988
Biomedicines. 2017 Sep 18;5(3). doi: 10.3390/biomedicines5030057.

The platelet-rich fibrin-like matrix (PRFM) is usually prepared onsite and immediately used for regenerative therapy. Nonetheless, to meet the clinical necessity of preserving the PRFM without quality deterioration, we developed a method for preparation of PRFMs from short-term-stored whole...

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Kawabata H, Isobe K, Watanabe T, et al. Quality Assessment of Platelet-Rich Fibrin-Like Matrix Prepared from Whole Blood Samples after Extended Storage. Biomedicines. 2017;5(3)doi: 10.3390/biomedicines5030057.
Kawabata, H., Isobe, K., Watanabe, T., Okudera, T., Nakamura, M., Suzuki, M., Ryu, J., Kitamura, Y., Okudera, H., Okuda, K., Nakata, K., & Kawase, T. (2017). Quality Assessment of Platelet-Rich Fibrin-Like Matrix Prepared from Whole Blood Samples after Extended Storage. Biomedicines, 5(3), . https://doi.org/10.3390/biomedicines5030057
Kawabata, Hideo, et al. "Quality Assessment of Platelet-Rich Fibrin-Like Matrix Prepared from Whole Blood Samples after Extended Storage." Biomedicines vol. 5,3 (2017). doi: https://doi.org/10.3390/biomedicines5030057
Kawabata H, Isobe K, Watanabe T, Okudera T, Nakamura M, Suzuki M, Ryu J, Kitamura Y, Okudera H, Okuda K, Nakata K, Kawase T. Quality Assessment of Platelet-Rich Fibrin-Like Matrix Prepared from Whole Blood Samples after Extended Storage. Biomedicines. 2017 Sep 18;5(3). doi: 10.3390/biomedicines5030057. PMID: 28926988; PMCID: PMC5618315.
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A case of incarcerated umbilical hernia in an adult treated by laparoscopic surgery.

Journal of surgical case reports

Tsushimi T, Mori H, Nagase T, Harada T, Ikeda Y.
PMID: 25672973
J Surg Case Rep. 2015 Feb 10;2015(2). doi: 10.1093/jscr/rjv001.

A 42-year-old, obese woman was admitted to our hospital 3 h after the sudden development of abdominal pain. Her umbilical region was swollen and she was diagnosed with incarceration of an umbilical hernia by computed tomography. Although we tried,...

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Tsushimi T, Mori H, Nagase T, et al. A case of incarcerated umbilical hernia in an adult treated by laparoscopic surgery. J Surg Case Rep. 2015;2015(2)doi: 10.1093/jscr/rjv001.
Tsushimi, T., Mori, H., Nagase, T., Harada, T., & Ikeda, Y. (2015). A case of incarcerated umbilical hernia in an adult treated by laparoscopic surgery. Journal of surgical case reports, 2015(2), . https://doi.org/10.1093/jscr/rjv001
Tsushimi, Takaaki, et al. "A case of incarcerated umbilical hernia in an adult treated by laparoscopic surgery." Journal of surgical case reports vol. 2015,2 (2015). doi: https://doi.org/10.1093/jscr/rjv001
Tsushimi T, Mori H, Nagase T, Harada T, Ikeda Y. A case of incarcerated umbilical hernia in an adult treated by laparoscopic surgery. J Surg Case Rep. 2015 Feb 10;2015(2). doi: 10.1093/jscr/rjv001. PMID: 25672973; PMCID: PMC4323578.
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D.

Journal of the American Chemical Society

Yamada M, Tanabe Y, Dang JS, Sato S, Mizorogi N, Hachiya M, Suzuki M, Abe T, Kurihara H, Maeda Y, Zhao X, Lian Y, Nagase S, Akasaka T.
PMID: 27998084
J Am Chem Soc. 2016 Dec 21;138(50):16523-16532. doi: 10.1021/jacs.6b10751. Epub 2016 Dec 07.

We compared the chemical reactivity of D

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Yamada M, Tanabe Y, Dang JS, et al. D. J Am Chem Soc. 2016;138(50):16523-16532doi: 10.1021/jacs.6b10751.
Yamada, M., Tanabe, Y., Dang, J. S., Sato, S., Mizorogi, N., Hachiya, M., Suzuki, M., Abe, T., Kurihara, H., Maeda, Y., Zhao, X., Lian, Y., Nagase, S., & Akasaka, T. (2016). D. Journal of the American Chemical Society, 138(50), 16523-16532. https://doi.org/10.1021/jacs.6b10751
Yamada, Michio, et al. "D." Journal of the American Chemical Society vol. 138,50 (2016): 16523-16532. doi: https://doi.org/10.1021/jacs.6b10751
Yamada M, Tanabe Y, Dang JS, Sato S, Mizorogi N, Hachiya M, Suzuki M, Abe T, Kurihara H, Maeda Y, Zhao X, Lian Y, Nagase S, Akasaka T. D. J Am Chem Soc. 2016 Dec 21;138(50):16523-16532. doi: 10.1021/jacs.6b10751. Epub 2016 Dec 07. PMID: 27998084.
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Downregulation of miR-186 is associated with metastatic recurrence of gastrointestinal stromal tumors.

Oncology letters

Niinuma T, Kai M, Kitajima H, Yamamoto E, Harada T, Maruyama R, Nobuoka T, Nishida T, Kanda T, Hasegawa T, Tokino T, Sugai T, Shinomura Y, Nakase H, Suzuki H.
PMID: 29113198
Oncol Lett. 2017 Nov;14(5):5703-5710. doi: 10.3892/ol.2017.6911. Epub 2017 Sep 08.

Although dysregulation of microRNAs (miRNAs/miRs) is a common feature of human malignancies, its involvement in gastrointestinal stromal tumors (GISTs) is not fully understood. The present study aimed to identify the miRNAs that perform a role in GIST metastasis. miRNA...

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Niinuma T, Kai M, Kitajima H, et al. Downregulation of miR-186 is associated with metastatic recurrence of gastrointestinal stromal tumors. Oncol Lett. 2017;14(5):5703-5710doi: 10.3892/ol.2017.6911.
Niinuma, T., Kai, M., Kitajima, H., Yamamoto, E., Harada, T., Maruyama, R., Nobuoka, T., Nishida, T., Kanda, T., Hasegawa, T., Tokino, T., Sugai, T., Shinomura, Y., Nakase, H., & Suzuki, H. (2017). Downregulation of miR-186 is associated with metastatic recurrence of gastrointestinal stromal tumors. Oncology letters, 14(5), 5703-5710. https://doi.org/10.3892/ol.2017.6911
Niinuma, Takeshi, et al. "Downregulation of miR-186 is associated with metastatic recurrence of gastrointestinal stromal tumors." Oncology letters vol. 14,5 (2017): 5703-5710. doi: https://doi.org/10.3892/ol.2017.6911
Niinuma T, Kai M, Kitajima H, Yamamoto E, Harada T, Maruyama R, Nobuoka T, Nishida T, Kanda T, Hasegawa T, Tokino T, Sugai T, Shinomura Y, Nakase H, Suzuki H. Downregulation of miR-186 is associated with metastatic recurrence of gastrointestinal stromal tumors. Oncol Lett. 2017 Nov;14(5):5703-5710. doi: 10.3892/ol.2017.6911. Epub 2017 Sep 08. PMID: 29113198; PMCID: PMC5661378.
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Atomic structures of a liquid-phase bonded metal/nitride heterointerface.

Scientific reports

Kumamoto A, Shibata N, Nayuki K, Tohei T, Terasaki N, Nagatomo Y, Nagase T, Akiyama K, Kuromitsu Y, Ikuhara Y.
PMID: 26961157
Sci Rep. 2016 Mar 10;6:22936. doi: 10.1038/srep22936.

Liquid-phase bonding is a technologically important method to fabricate high-performance metal/ceramic heterostructures used for power electronic devices. However, the atomic-scale mechanisms of how these two dissimilar crystals specifically bond at the interfaces are still not well understood. Here we...

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Kumamoto A, Shibata N, Nayuki K, et al. Atomic structures of a liquid-phase bonded metal/nitride heterointerface. Sci Rep. 2016;6:22936doi: 10.1038/srep22936.
Kumamoto, A., Shibata, N., Nayuki, K., Tohei, T., Terasaki, N., Nagatomo, Y., Nagase, T., Akiyama, K., Kuromitsu, Y., & Ikuhara, Y. (2016). Atomic structures of a liquid-phase bonded metal/nitride heterointerface. Scientific reports, 622936. https://doi.org/10.1038/srep22936
Kumamoto, Akihito, et al. "Atomic structures of a liquid-phase bonded metal/nitride heterointerface." Scientific reports vol. 6 (2016): 22936. doi: https://doi.org/10.1038/srep22936
Kumamoto A, Shibata N, Nayuki K, Tohei T, Terasaki N, Nagatomo Y, Nagase T, Akiyama K, Kuromitsu Y, Ikuhara Y. Atomic structures of a liquid-phase bonded metal/nitride heterointerface. Sci Rep. 2016 Mar 10;6:22936. doi: 10.1038/srep22936. PMID: 26961157; PMCID: PMC4785497.
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Photoluminescence Properties of Polymorphic Modifications of Low Molecular Weight Poly(3-hexylthiophene).

Nanoscale research letters

Kobayashi T, Kinoshita K, Niwa A, Nagase T, Naito H.
PMID: 28545262
Nanoscale Res Lett. 2017 Dec;12(1):368. doi: 10.1186/s11671-017-2134-5. Epub 2017 May 23.

The structural and photoluminescence (PL) properties of thin films of poly(3-hexylthophene) (P3HT) with molecular weights (MWs) of 3000 and 13,300 have been investigated. Although high MW P3HT always self-organizes into one packing structure (form I), low MW P3HT forms...

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Kobayashi T, Kinoshita K, Niwa A, et al. Photoluminescence Properties of Polymorphic Modifications of Low Molecular Weight Poly(3-hexylthiophene). Nanoscale Res Lett. 2017;12(1):368doi: 10.1186/s11671-017-2134-5.
Kobayashi, T., Kinoshita, K., Niwa, A., Nagase, T., & Naito, H. (2017). Photoluminescence Properties of Polymorphic Modifications of Low Molecular Weight Poly(3-hexylthiophene). Nanoscale research letters, 12(1), 368. https://doi.org/10.1186/s11671-017-2134-5
Kobayashi, Takashi, et al. "Photoluminescence Properties of Polymorphic Modifications of Low Molecular Weight Poly(3-hexylthiophene)." Nanoscale research letters vol. 12,1 (2017): 368. doi: https://doi.org/10.1186/s11671-017-2134-5
Kobayashi T, Kinoshita K, Niwa A, Nagase T, Naito H. Photoluminescence Properties of Polymorphic Modifications of Low Molecular Weight Poly(3-hexylthiophene). Nanoscale Res Lett. 2017 Dec;12(1):368. doi: 10.1186/s11671-017-2134-5. Epub 2017 May 23. PMID: 28545262; PMCID: PMC5442032.
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Co-localization of iron binding on silica with p62/sequestosome1 (SQSTM1) in lung granulomas of mice with acute silicosis.

Journal of clinical biochemistry and nutrition

Shimizu Y, Dobashi K, Nagase H, Ohta K, Sano T, Matsuzaki S, Ishii Y, Satoh T, Koka M, Yokoyama A, Ohkubo T, Ishii Y, Kamiya T.
PMID: 25834305
J Clin Biochem Nutr. 2015 Jan;56(1):74-83. doi: 10.3164/jcbn.14-44. Epub 2014 Nov 28.

The cellular mechanisms involved in the development of silicosis have not been fully elucidated. This study aimed to examine influence of silica-induced lung injury on autophagy. Suspensions of crystalline silica particles were administered transnasally to C57BL/6j mice. Immunohistochemical examination...

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Shimizu Y, Dobashi K, Nagase H, et al. Co-localization of iron binding on silica with p62/sequestosome1 (SQSTM1) in lung granulomas of mice with acute silicosis. J Clin Biochem Nutr. 2014;56(1):74-83doi: 10.3164/jcbn.14-44.
Shimizu, Y., Dobashi, K., Nagase, H., Ohta, K., Sano, T., Matsuzaki, S., Ishii, Y., Satoh, T., Koka, M., Yokoyama, A., Ohkubo, T., Ishii, Y., & Kamiya, T. (2015). Co-localization of iron binding on silica with p62/sequestosome1 (SQSTM1) in lung granulomas of mice with acute silicosis. Journal of clinical biochemistry and nutrition, 56(1), 74-83. https://doi.org/10.3164/jcbn.14-44
Shimizu, Yasuo, et al. "Co-localization of iron binding on silica with p62/sequestosome1 (SQSTM1) in lung granulomas of mice with acute silicosis." Journal of clinical biochemistry and nutrition vol. 56,1 (2015): 74-83. doi: https://doi.org/10.3164/jcbn.14-44
Shimizu Y, Dobashi K, Nagase H, Ohta K, Sano T, Matsuzaki S, Ishii Y, Satoh T, Koka M, Yokoyama A, Ohkubo T, Ishii Y, Kamiya T. Co-localization of iron binding on silica with p62/sequestosome1 (SQSTM1) in lung granulomas of mice with acute silicosis. J Clin Biochem Nutr. 2015 Jan;56(1):74-83. doi: 10.3164/jcbn.14-44. Epub 2014 Nov 28. PMID: 25834305; PMCID: PMC4306660.
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Dimetallic sulfide endohedral metallofullerene Sc2S@C76: density functional theory characterization.

Journal of computational chemistry

Zhao P, Yang T, Guo YJ, Dang JS, Zhao X, Nagase S.
PMID: 24962983
J Comput Chem. 2014 Aug 15;35(22):1657-63. doi: 10.1002/jcc.23671. Epub 2014 Jun 24.

In terms of density functional theory combined with statistic mechanics computations, we investigated a dimetallic sulfide endohedral fullerene Sc2S@C76 which has been synthesized without any characterization in experiments. Our theoretical study reveals that Sc2S@Td(19151)-C76 which satisfies the isolated-pentagon rule...

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Zhao P, Yang T, Guo YJ, et al. Dimetallic sulfide endohedral metallofullerene Sc2S@C76: density functional theory characterization. J Comput Chem. 2014;35(22):1657-63doi: 10.1002/jcc.23671.
Zhao, P., Yang, T., Guo, Y. J., Dang, J. S., Zhao, X., & Nagase, S. (2014). Dimetallic sulfide endohedral metallofullerene Sc2S@C76: density functional theory characterization. Journal of computational chemistry, 35(22), 1657-63. https://doi.org/10.1002/jcc.23671
Zhao, Pei, et al. "Dimetallic sulfide endohedral metallofullerene Sc2S@C76: density functional theory characterization." Journal of computational chemistry vol. 35,22 (2014): 1657-63. doi: https://doi.org/10.1002/jcc.23671
Zhao P, Yang T, Guo YJ, Dang JS, Zhao X, Nagase S. Dimetallic sulfide endohedral metallofullerene Sc2S@C76: density functional theory characterization. J Comput Chem. 2014 Aug 15;35(22):1657-63. doi: 10.1002/jcc.23671. Epub 2014 Jun 24. PMID: 24962983.
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Showing 1 to 12 of 1165 entries