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Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction

pipeline programs

Jain A, Kagaya Y, Terashi G.
GSID: Ywp51u3Q3i8J
A Jain, G Terashi, Y Kagaya… - Scientific Reports, 2021 - nature.com

Protein 3D structure prediction has advanced significantly in recent years due to improving contact prediction accuracy. This improvement has been largely due to deep learning …

Molecular dynamics analysis of multiphase interfaces based on in situ extraction of the pressure distribution of a liquid droplet on a solid surface.

The Journal of chemical physics

Nishida S, Surblys D, Yamaguchi Y, Kuroda K, Kagawa M, Nakajima T, Fujimura H.
PMID: 24559360
J Chem Phys. 2014 Feb 21;140(7):074707. doi: 10.1063/1.4865254.

Molecular dynamics simulations of a nanoscale liquid droplet on a solid surface are carried out in order to examine the pressure tensor field around the multiphase interfaces, and to explore the validity of Young's equation. By applying the virial...

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Nishida S, Surblys D, Yamaguchi Y, et al. Molecular dynamics analysis of multiphase interfaces based on in situ extraction of the pressure distribution of a liquid droplet on a solid surface. J Chem Phys. 2014;140(7):074707doi: 10.1063/1.4865254.
Nishida, S., Surblys, D., Yamaguchi, Y., Kuroda, K., Kagawa, M., Nakajima, T., & Fujimura, H. (2014). Molecular dynamics analysis of multiphase interfaces based on in situ extraction of the pressure distribution of a liquid droplet on a solid surface. The Journal of chemical physics, 140(7), 074707. https://doi.org/10.1063/1.4865254
Nishida, S, et al. "Molecular dynamics analysis of multiphase interfaces based on in situ extraction of the pressure distribution of a liquid droplet on a solid surface." The Journal of chemical physics vol. 140,7 (2014): 074707. doi: https://doi.org/10.1063/1.4865254
Nishida S, Surblys D, Yamaguchi Y, Kuroda K, Kagawa M, Nakajima T, Fujimura H. Molecular dynamics analysis of multiphase interfaces based on in situ extraction of the pressure distribution of a liquid droplet on a solid surface. J Chem Phys. 2014 Feb 21;140(7):074707. doi: 10.1063/1.4865254. PMID: 24559360.
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Membranous nephropathy associated with type 1 autoimmune pancreatitis and dominant glomerular IgG4 deposit.

CEN case reports

Sueta S, Kondo M, Matsubara T, Yasuhara Y, Akiyama S, Imai E, Amaike H, Tagawa M.
PMID: 28509238
CEN Case Rep. 2014 May;3(1):18-23. doi: 10.1007/s13730-013-0077-y. Epub 2013 May 03.

We report a case of membranous nephropathy associated with type 1 autoimmune pancreatitis. A 58-year-old man presented with anorexia. Work-up revealed a mass in the pancreatic head, which was subsequently resected. Pathological examination showed diffuse infiltration of immunoglobulin (Ig)...

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Sueta S, Kondo M, Matsubara T, et al. Membranous nephropathy associated with type 1 autoimmune pancreatitis and dominant glomerular IgG4 deposit. CEN Case Rep. 2013;3(1):18-23doi: 10.1007/s13730-013-0077-y.
Sueta, S., Kondo, M., Matsubara, T., Yasuhara, Y., Akiyama, S., Imai, E., Amaike, H., & Tagawa, M. (2014). Membranous nephropathy associated with type 1 autoimmune pancreatitis and dominant glomerular IgG4 deposit. CEN case reports, 3(1), 18-23. https://doi.org/10.1007/s13730-013-0077-y
Sueta, Shinichi, et al. "Membranous nephropathy associated with type 1 autoimmune pancreatitis and dominant glomerular IgG4 deposit." CEN case reports vol. 3,1 (2014): 18-23. doi: https://doi.org/10.1007/s13730-013-0077-y
Sueta S, Kondo M, Matsubara T, Yasuhara Y, Akiyama S, Imai E, Amaike H, Tagawa M. Membranous nephropathy associated with type 1 autoimmune pancreatitis and dominant glomerular IgG4 deposit. CEN Case Rep. 2014 May;3(1):18-23. doi: 10.1007/s13730-013-0077-y. Epub 2013 May 03. PMID: 28509238; PMCID: PMC5411534.
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Investigation of optical and thermal properties of N-(alkyl-substituted) maleimides for use in zero-zero-birefringence polymer.

Applied optics

Beppu S, Hotta H, Shafiee H, Tagaya A, Koike Y.
PMID: 25967788
Appl Opt. 2015 Feb 01;54(4):779-88. doi: 10.1364/AO.54.000779.

N-(alkyl-substituted) maleimides (RMIs) were proposed as materials useful for the development of a zero-zero-birefringence polymer that exhibits no birefringence. We analyzed the optical and thermal properties of poly(RMI)s, such as the refractive index, birefringence, and glass transition temperature. The...

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Beppu S, Hotta H, Shafiee H, et al. Investigation of optical and thermal properties of N-(alkyl-substituted) maleimides for use in zero-zero-birefringence polymer. Appl Opt. 2015;54(4):779-88doi: 10.1364/AO.54.000779.
Beppu, S., Hotta, H., Shafiee, H., Tagaya, A., & Koike, Y. (2015). Investigation of optical and thermal properties of N-(alkyl-substituted) maleimides for use in zero-zero-birefringence polymer. Applied optics, 54(4), 779-88. https://doi.org/10.1364/AO.54.000779
Beppu, Shotaro, et al. "Investigation of optical and thermal properties of N-(alkyl-substituted) maleimides for use in zero-zero-birefringence polymer." Applied optics vol. 54,4 (2015): 779-88. doi: https://doi.org/10.1364/AO.54.000779
Beppu S, Hotta H, Shafiee H, Tagaya A, Koike Y. Investigation of optical and thermal properties of N-(alkyl-substituted) maleimides for use in zero-zero-birefringence polymer. Appl Opt. 2015 Feb 01;54(4):779-88. doi: 10.1364/AO.54.000779. PMID: 25967788.
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Selective breeding of mice for different susceptibilities to high fat diet-induced glucose intolerance: Development of two novel mouse lines, Selectively bred Diet-induced Glucose intolerance-Prone and -Resistant.

Journal of diabetes investigation

Nagao M, Asai A, Kawahara M, Nakajima Y, Sato Y, Tanimura K, Okajima F, Takaya M, Sudo M, Takemitsu S, Harada T, Sugihara H, Oikawa S.
PMID: 24843572
J Diabetes Investig. 2012 Jun 06;3(3):245-51. doi: 10.1111/j.2040-1124.2011.00175.x.

UNLABELLED: Aims/Introduction:  The development of type 2 diabetes is primarily due to lifestyle and environmental factors, as well as genetics, as shown by familial clustering. To establish mouse lines for evaluating heritable factors determining susceptibility to diet-induced diabetes, we...

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Nagao M, Asai A, Kawahara M, et al. Selective breeding of mice for different susceptibilities to high fat diet-induced glucose intolerance: Development of two novel mouse lines, Selectively bred Diet-induced Glucose intolerance-Prone and -Resistant. J Diabetes Investig. 2012;3(3):245-51doi: 10.1111/j.2040-1124.2011.00175.x.
Nagao, M., Asai, A., Kawahara, M., Nakajima, Y., Sato, Y., Tanimura, K., Okajima, F., Takaya, M., Sudo, M., Takemitsu, S., Harada, T., Sugihara, H., & Oikawa, S. (2012). Selective breeding of mice for different susceptibilities to high fat diet-induced glucose intolerance: Development of two novel mouse lines, Selectively bred Diet-induced Glucose intolerance-Prone and -Resistant. Journal of diabetes investigation, 3(3), 245-51. https://doi.org/10.1111/j.2040-1124.2011.00175.x
Nagao, Mototsugu, et al. "Selective breeding of mice for different susceptibilities to high fat diet-induced glucose intolerance: Development of two novel mouse lines, Selectively bred Diet-induced Glucose intolerance-Prone and -Resistant." Journal of diabetes investigation vol. 3,3 (2012): 245-51. doi: https://doi.org/10.1111/j.2040-1124.2011.00175.x
Nagao M, Asai A, Kawahara M, Nakajima Y, Sato Y, Tanimura K, Okajima F, Takaya M, Sudo M, Takemitsu S, Harada T, Sugihara H, Oikawa S. Selective breeding of mice for different susceptibilities to high fat diet-induced glucose intolerance: Development of two novel mouse lines, Selectively bred Diet-induced Glucose intolerance-Prone and -Resistant. J Diabetes Investig. 2012 Jun 06;3(3):245-51. doi: 10.1111/j.2040-1124.2011.00175.x. PMID: 24843572; PMCID: PMC4014945.
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Salvaging science.

Science (New York, N.Y.)

Bawaya M.
PMID: 25574002
Science. 2015 Jan 09;347(6218):117-9. doi: 10.1126/science.347.6218.117.

No abstract available.

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Bawaya M. Salvaging science. Science. 2015;347(6218):117-9doi: 10.1126/science.347.6218.117.
Bawaya, M. (2015). Salvaging science. Science (New York, N.Y.), 347(6218), 117-9. https://doi.org/10.1126/science.347.6218.117
Bawaya, Michael. "Salvaging science." Science (New York, N.Y.) vol. 347,6218 (2015): 117-9. doi: https://doi.org/10.1126/science.347.6218.117
Bawaya M. Salvaging science. Science. 2015 Jan 09;347(6218):117-9. doi: 10.1126/science.347.6218.117. PMID: 25574002.
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A clinical protocol to inhibit the HGF/c-Met pathway for malignant mesothelioma with an intrapleural injection of adenoviruses expressing the NK4 gene.

SpringerPlus

Tada Y, Hiroshima K, Shimada H, Morishita N, Shirakawa T, Matsumoto K, Shingyoji M, Sekine I, Tatsumi K, Tagawa M.
PMID: 26191485
Springerplus. 2015 Jul 16;4:358. doi: 10.1186/s40064-015-1123-3. eCollection 2015.

BACKGROUND: The hepatocyte growth factor (HGF)/c-Met signal pathway is up-regulated in human mesothelioma and suppression of the HGF/c-Met signaling with a competitive inhibitor, NK4 homologous to HGF in the structure, produced anti-tumor effects to mesothelioma in a preclinical study....

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Tada Y, Hiroshima K, Shimada H, et al. A clinical protocol to inhibit the HGF/c-Met pathway for malignant mesothelioma with an intrapleural injection of adenoviruses expressing the NK4 gene. Springerplus. 2015;4:358doi: 10.1186/s40064-015-1123-3.
Tada, Y., Hiroshima, K., Shimada, H., Morishita, N., Shirakawa, T., Matsumoto, K., Shingyoji, M., Sekine, I., Tatsumi, K., & Tagawa, M. (2015). A clinical protocol to inhibit the HGF/c-Met pathway for malignant mesothelioma with an intrapleural injection of adenoviruses expressing the NK4 gene. SpringerPlus, 4358. https://doi.org/10.1186/s40064-015-1123-3
Tada, Yuji, et al. "A clinical protocol to inhibit the HGF/c-Met pathway for malignant mesothelioma with an intrapleural injection of adenoviruses expressing the NK4 gene." SpringerPlus vol. 4 (2015): 358. doi: https://doi.org/10.1186/s40064-015-1123-3
Tada Y, Hiroshima K, Shimada H, Morishita N, Shirakawa T, Matsumoto K, Shingyoji M, Sekine I, Tatsumi K, Tagawa M. A clinical protocol to inhibit the HGF/c-Met pathway for malignant mesothelioma with an intrapleural injection of adenoviruses expressing the NK4 gene. Springerplus. 2015 Jul 16;4:358. doi: 10.1186/s40064-015-1123-3. eCollection 2015. PMID: 26191485; PMCID: PMC4503710.
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Thyroid hormone concentrations in the gonads of wild chum salmon during maturation.

Fish physiology and biochemistry

Tagawa M, Ogasawara T, Sakamoto T, Miura T, Yamauchi K, Hirano T.
PMID: 24198193
Fish Physiol Biochem. 1994 Jul;13(3):233-40. doi: 10.1007/BF00004361.

Changes in gonadal and plasma concentrations of thyroid hormones were examined at various stages of maturation in chum salmon (Oncorhynchus keta) caught in the Bering Sea and the Bay of Alaska. Plasma concentrations of thyroxine (T4) were less than...

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Tagawa M, Ogasawara T, Sakamoto T, et al. Thyroid hormone concentrations in the gonads of wild chum salmon during maturation. Fish Physiol Biochem. 1994;13(3):233-40doi: 10.1007/BF00004361.
Tagawa, M., Ogasawara, T., Sakamoto, T., Miura, T., Yamauchi, K., & Hirano, T. (1994). Thyroid hormone concentrations in the gonads of wild chum salmon during maturation. Fish physiology and biochemistry, 13(3), 233-40. https://doi.org/10.1007/BF00004361
Tagawa, M, et al. "Thyroid hormone concentrations in the gonads of wild chum salmon during maturation." Fish physiology and biochemistry vol. 13,3 (1994): 233-40. doi: https://doi.org/10.1007/BF00004361
Tagawa M, Ogasawara T, Sakamoto T, Miura T, Yamauchi K, Hirano T. Thyroid hormone concentrations in the gonads of wild chum salmon during maturation. Fish Physiol Biochem. 1994 Jul;13(3):233-40. doi: 10.1007/BF00004361. PMID: 24198193.
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Risperidone treatment of neuroleptic-induced tardive extrapyramidal symptoms.

International journal of psychiatry in clinical practice

Suenaga T, Tawara Y, Goto S, Kouhata S, Kagaya A, Horiguchi J, Yamanaka Y, Yamawaki S.
PMID: 24927461
Int J Psychiatry Clin Pract. 2000;4(3):241-3. doi: 10.1080/13651500050518154.

Tardive extrapyramidal symptoms (EPS) induced by neuroleptic treatment, and particularly EPS which persist after withdrawal of the drugs, are clinically serious problems. We describe a patient with four types of tardive and persistent EPS such as dystonia, dyskinesia, choreatic...

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Suenaga T, Tawara Y, Goto S, et al. Risperidone treatment of neuroleptic-induced tardive extrapyramidal symptoms. Int J Psychiatry Clin Pract. 2000;4(3):241-3doi: 10.1080/13651500050518154.
Suenaga, T., Tawara, Y., Goto, S., Kouhata, S., Kagaya, A., Horiguchi, J., Yamanaka, Y., & Yamawaki, S. (2000). Risperidone treatment of neuroleptic-induced tardive extrapyramidal symptoms. International journal of psychiatry in clinical practice, 4(3), 241-3. https://doi.org/10.1080/13651500050518154
Suenaga, T, et al. "Risperidone treatment of neuroleptic-induced tardive extrapyramidal symptoms." International journal of psychiatry in clinical practice vol. 4,3 (2000): 241-3. doi: https://doi.org/10.1080/13651500050518154
Suenaga T, Tawara Y, Goto S, Kouhata S, Kagaya A, Horiguchi J, Yamanaka Y, Yamawaki S. Risperidone treatment of neuroleptic-induced tardive extrapyramidal symptoms. Int J Psychiatry Clin Pract. 2000;4(3):241-3. doi: 10.1080/13651500050518154. PMID: 24927461.
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The Valence-Detrapping Phase Transition in a Crystal of the Mixed-Valence Trinuclear Iron Cyanoacetate Complex [Fe(3)O(O(2)CCH(2)CN)(6)(H(2)O)(3)].

Inorganic chemistry

Nakamoto T, Hanaya M, Katada M, Endo K, Kitagawa S, Sano H.
PMID: 11670092
Inorg Chem. 1997 Sep 24;36(20):4347-4359. doi: 10.1021/ic961438w.

A mixed-valence trinuclear iron cyanoacetate complex, [Fe(3)O(O(2)CCH(2)CN)(6)(H(2)O)(3)] (1), was prepared, and the nature of the electron-detrapping phase transition was studied by a multitemperature single-crystal X-ray structure determination (296, 135, and 100 K) and calorimetry by comparison with an isostructural...

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Nakamoto T, Hanaya M, Katada M, et al. The Valence-Detrapping Phase Transition in a Crystal of the Mixed-Valence Trinuclear Iron Cyanoacetate Complex [Fe(3)O(O(2)CCH(2)CN)(6)(H(2)O)(3)]. Inorg Chem. 1997;36(20):4347-4359doi: 10.1021/ic961438w.
Nakamoto, T., Hanaya, M., Katada, M., Endo, K., Kitagawa, S., & Sano, H. (1997). The Valence-Detrapping Phase Transition in a Crystal of the Mixed-Valence Trinuclear Iron Cyanoacetate Complex [Fe(3)O(O(2)CCH(2)CN)(6)(H(2)O)(3)]. Inorganic chemistry, 36(20), 4347-4359. https://doi.org/10.1021/ic961438w
Nakamoto, Tadahiro, et al. "The Valence-Detrapping Phase Transition in a Crystal of the Mixed-Valence Trinuclear Iron Cyanoacetate Complex [Fe(3)O(O(2)CCH(2)CN)(6)(H(2)O)(3)]." Inorganic chemistry vol. 36,20 (1997): 4347-4359. doi: https://doi.org/10.1021/ic961438w
Nakamoto T, Hanaya M, Katada M, Endo K, Kitagawa S, Sano H. The Valence-Detrapping Phase Transition in a Crystal of the Mixed-Valence Trinuclear Iron Cyanoacetate Complex [Fe(3)O(O(2)CCH(2)CN)(6)(H(2)O)(3)]. Inorg Chem. 1997 Sep 24;36(20):4347-4359. doi: 10.1021/ic961438w. PMID: 11670092.
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Synthesis of branched polysaccharides by polymerization of 6-O-t-butyldimethylsilyl-D-glucal through stereoregular haloglycosylation.

Carbohydrate letters

Kadokawa JI, Yamamoto M, Tagaya H, Chiba K.
PMID: 11506164
Carbohydr Lett. 2001;4(2):97-101.

In this letter, we report synthesis of branched polysaccharide 2 by glycosylation of glucal-type monomer 1 with two free hydroxy groups at position 3 and 4. Monomer 1 polymerized with N-halosuccinimide promoter in acetonitrile solvent at room temperature--50 degrees...

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Kadokawa JI, Yamamoto M, Tagaya H, et al. Synthesis of branched polysaccharides by polymerization of 6-O-t-butyldimethylsilyl-D-glucal through stereoregular haloglycosylation. Carbohydr Lett. 2001;4(2):97-101
Kadokawa, J. I., Yamamoto, M., Tagaya, H., & Chiba, K. (2001). Synthesis of branched polysaccharides by polymerization of 6-O-t-butyldimethylsilyl-D-glucal through stereoregular haloglycosylation. Carbohydrate letters, 4(2), 97-101.
Kadokawa, J I, et al. "Synthesis of branched polysaccharides by polymerization of 6-O-t-butyldimethylsilyl-D-glucal through stereoregular haloglycosylation." Carbohydrate letters vol. 4,2 (2001): 97-101.
Kadokawa JI, Yamamoto M, Tagaya H, Chiba K. Synthesis of branched polysaccharides by polymerization of 6-O-t-butyldimethylsilyl-D-glucal through stereoregular haloglycosylation. Carbohydr Lett. 2001;4(2):97-101. PMID: 11506164.
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Compensation of the birefringence of a polymer by a birefringent crystal.

Science (New York, N.Y.)

Tagaya A, Ohkita H, Mukoh M, Sakaguchi R, Koike Y.
PMID: 12907795
Science. 2003 Aug 08;301(5634):812-4. doi: 10.1126/science.1086966.

We report a method for compensating the birefringence of optical polymers by doping them with inorganic birefringent crystals. In this method, an inorganic birefringent material is chosen that has the opposite birefringence to that of the polymer and has...

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Tagaya A, Ohkita H, Mukoh M, et al. Compensation of the birefringence of a polymer by a birefringent crystal. Science. 2003;301(5634):812-4doi: 10.1126/science.1086966.
Tagaya, A., Ohkita, H., Mukoh, M., Sakaguchi, R., & Koike, Y. (2003). Compensation of the birefringence of a polymer by a birefringent crystal. Science (New York, N.Y.), 301(5634), 812-4. https://doi.org/10.1126/science.1086966
Tagaya, Akihiro, et al. "Compensation of the birefringence of a polymer by a birefringent crystal." Science (New York, N.Y.) vol. 301,5634 (2003): 812-4. doi: https://doi.org/10.1126/science.1086966
Tagaya A, Ohkita H, Mukoh M, Sakaguchi R, Koike Y. Compensation of the birefringence of a polymer by a birefringent crystal. Science. 2003 Aug 08;301(5634):812-4. doi: 10.1126/science.1086966. PMID: 12907795.
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Showing 1 to 12 of 378 entries