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Items: 1 to 50 of 135

1.

Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design.

Kuroda D, Tsumoto K.

J Pharm Sci. 2020 Jan 17. pii: S0022-3549(20)30016-2. doi: 10.1016/j.xphs.2020.01.011. [Epub ahead of print] Review.

PMID:
31958430
2.

Per-Residue Program of Multiple Backbone Dihedral Angles of β-Peptoids via Backbone Substitutions.

Morimoto J, Kim J, Kuroda D, Nagatoishi S, Tsumoto K, Sando S.

J Am Chem Soc. 2020 Jan 21. doi: 10.1021/jacs.9b10496. [Epub ahead of print]

PMID:
31917919
3.

Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16.

Kondo HX, Kiribayashi R, Kuroda D, Kohda J, Kugimiya A, Nakano Y, Tsumoto K, Takano Y.

Sci Rep. 2019 Dec 27;9(1):19840. doi: 10.1038/s41598-019-56154-y.

4.

How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations.

Kawade R, Kuroda D, Tsumoto K.

FEBS Lett. 2019 Nov 12. doi: 10.1002/1873-3468.13674. [Epub ahead of print]

PMID:
31713840
5.

Structure and Dynamics of the Lithium-Ion Solvation Shell in Ureas.

Chen X, Fulfer KD, Woodard KT, Kuroda DG.

J Phys Chem B. 2019 Nov 21;123(46):9889-9898. doi: 10.1021/acs.jpcb.9b07623. Epub 2019 Nov 11.

PMID:
31657571
6.

Naples Prognostic Score Is a Useful Prognostic Marker in Patients With Metastatic Colorectal Cancer.

Miyamoto Y, Hiyoshi Y, Daitoku N, Okadome K, Sakamoto Y, Yamashita K, Kuroda D, Sawayama H, Iwatsuki M, Baba Y, Yoshida N, Baba H.

Dis Colon Rectum. 2019 Dec;62(12):1485-1493. doi: 10.1097/DCR.0000000000001484.

PMID:
31567920
7.

[Preoperative Chemotherapy with DCF for Advanced Esophageal Cancer].

Murata K, Kuroda D, Okamoto S, Fujinaka R, Arai K, Otowa Y, Mii Y, Kakinoki K, Mani M, Oka S.

Gan To Kagaku Ryoho. 2019 Aug;46(8):1337-1339. Japanese.

PMID:
31501384
8.

[Adjuvant Chemotherapy for High-Risk Stage Ⅱ Colon Cancer].

Fujinaka R, Otowa Y, Yokoo H, Arai K, Murata K, Mii Y, Kakinoki K, Oka S, Kuroda D.

Gan To Kagaku Ryoho. 2019 Aug;46(8):1327-1329. Japanese.

PMID:
31501381
9.

Case of resected multiple hepatocellular adenomas in a young man with severe obesity.

Oji K, Urade T, Iwatani Y, Tanaka K, Hirano H, Sanuki T, Tomita M, Yamamoto Y, Zen Y, Kuroda D.

Surg Case Rep. 2019 Aug 13;5(1):131. doi: 10.1186/s40792-019-0689-3.

10.

A Peptoid with Extended Shape in Water.

Morimoto J, Fukuda Y, Kuroda D, Watanabe T, Yoshida F, Asada M, Nakamura T, Senoo A, Nagatoishi S, Tsumoto K, Sando S.

J Am Chem Soc. 2019 Sep 18;141(37):14612-14623. doi: 10.1021/jacs.9b04371. Epub 2019 Aug 23.

PMID:
31405271
11.

Feasibility and Effectiveness of Gastrectomy for Elderly Gastric Cancer Patients.

Otowa Y, Okamoto S, Fujinaka R, Arai K, Murata K, Mii Y, Kakinoki K, Oka S, Kuroda D.

In Vivo. 2019 Jul-Aug;33(4):1307-1311. doi: 10.21873/invivo.11604.

13.

Laparoscopic anatomical liver resection using indocyanine green fluorescence imaging.

Urade T, Sawa H, Iwatani Y, Abe T, Fujinaka R, Murata K, Mii Y, Man-I M, Oka S, Kuroda D.

Asian J Surg. 2020 Jan;43(1):362-368. doi: 10.1016/j.asjsur.2019.04.008. Epub 2019 Apr 28.

14.

Molecularly Heterogeneous Structure of a Nonionic Deep Eutectic Solvent Composed of N-Methylacetamide and Lauric Acid.

Cui Y, Rushing JC, Seifert S, Bedford NM, Kuroda DG.

J Phys Chem B. 2019 May 9;123(18):3984-3993. doi: 10.1021/acs.jpcb.8b11732. Epub 2019 Apr 29.

PMID:
30978021
15.

Preservation of physiological passage through the remnant stomach prevents postoperative malnutrition after proximal gastrectomy with double tract reconstruction.

Yamashita K, Iwatsuki M, Koga Y, Toihata T, Kiyozumi Y, Kuroda D, Eto K, Hiyoshi Y, Iwagami S, Baba Y, Miyamoto Y, Yoshida N, Baba H.

Surg Today. 2019 Sep;49(9):748-754. doi: 10.1007/s00595-019-01799-5. Epub 2019 Mar 30.

PMID:
30929080
16.

An epitope-directed antibody affinity maturation system utilizing mammalian cell survival as readout.

Eguchi A, Nakakido M, Nagatoishi S, Kuroda D, Tsumoto K, Nagamune T, Kawahara M.

Biotechnol Bioeng. 2019 Jul;116(7):1742-1751. doi: 10.1002/bit.26965. Epub 2019 Mar 29.

PMID:
30883677
17.

Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations.

Yoshida K, Kuroda D, Kiyoshi M, Nakakido M, Nagatoishi S, Soga S, Shirai H, Tsumoto K.

Sci Rep. 2019 Mar 14;9(1):4482. doi: 10.1038/s41598-019-40461-5.

18.

Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium.

Yoshida K, Nagatoishi S, Kuroda D, Suzuki N, Murata T, Tsumoto K.

Biochemistry. 2019 Feb 12;58(6):504-508. doi: 10.1021/acs.biochem.8b01194. Epub 2019 Jan 14.

PMID:
30618239
19.

Multiple Primary Cancers in Patients with Pancreatic Cancer.

Yamamura K, Hashimoto D, Kitano Y, Kuroda D, Eto T, Arima K, Kaida T, Miyata T, Nakagawa S, Imai K, Yamashita YI, Chikamoto A, Matsumura F, Baba H.

Am Surg. 2018 Dec 1;84(12):e514-e516. Review. No abstract available.

PMID:
30606360
20.

Molecular structure and ultrafast dynamics of sodium thiocyanate ion pairs formed in glymes of different lengths.

Galle Kankanamge SR, Kuroda DG.

Phys Chem Chem Phys. 2019 Jan 2;21(2):833-841. doi: 10.1039/c8cp06869k.

PMID:
30556086
21.

Nickel-catalyzed intermolecular carboiodination of alkynes with aryl iodides.

Takahashi T, Kuroda D, Kuwano T, Yoshida Y, Kurahashi T, Matsubara S.

Chem Commun (Camb). 2018 Nov 8;54(90):12750-12753. doi: 10.1039/c8cc07560c.

PMID:
30361734
22.

Thermodynamic and computational analyses reveal the functional roles of the galloyl group of tea catechins in molecular recognition.

Takahashi T, Nagatoishi S, Kuroda D, Tsumoto K.

PLoS One. 2018 Oct 11;13(10):e0204856. doi: 10.1371/journal.pone.0204856. eCollection 2018.

23.

Intraoperative ultrasonic navigation for laparoscopic colorectal surgery with preservation of the left colic artery.

Urade T, Fujinaka R, Abe T, Murata K, Mii Y, Sawa H, Man-I M, Oka S, Iwatani Y, Kuroda D.

Tech Coloproctol. 2018 Sep;22(9):703-708. doi: 10.1007/s10151-018-1853-7. Epub 2018 Sep 18. No abstract available.

PMID:
30229329
24.

Antibody Affinity Maturation by Computational Design.

Kuroda D, Tsumoto K.

Methods Mol Biol. 2018;1827:15-34. doi: 10.1007/978-1-4939-8648-4_2.

PMID:
30196490
25.

Ion speciation of lithium hexafluorophosphate in dimethyl carbonate solutions: an infrared spectroscopy study.

Fulfer KD, Kuroda DG.

Phys Chem Chem Phys. 2018 Sep 12;20(35):22710-22718. doi: 10.1039/c8cp03315c.

PMID:
30137084
26.

A resected case of gallbladder metastasis with symptoms of acute cholecystitis in multiple metastatic ductal carcinoma of the breast.

Urade T, Oka S, Iimori S, Man-I M, Abe T, Sawa H, Iwatani Y, Morinaga Y, Kuroda D.

Clin J Gastroenterol. 2019 Feb;12(1):52-56. doi: 10.1007/s12328-018-0892-y. Epub 2018 Aug 14.

PMID:
30109570
27.

The association of the lymph node ratio and serum carbohydrate antigen 19-9 with early recurrence after curative gastrectomy for gastric cancer.

Sawayama H, Iwatsuki M, Kuroda D, Toihata T, Uchihara T, Koga Y, Yagi T, Kiyozumi Y, Eto T, Hiyoshi Y, Ishimoto T, Baba Y, Miyamoto Y, Yoshida N, Baba H.

Surg Today. 2018 Nov;48(11):994-1003. doi: 10.1007/s00595-018-1684-1. Epub 2018 Jun 20.

PMID:
29926189
28.

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.

Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K.

J Biochem. 2018 Jul 1;164(1):65-76. doi: 10.1093/jb/mvy032.

PMID:
29924367
29.

Clinical utility of exhaled carbon monoxide in assessing preoperative smoking status and risks of postoperative morbidity after esophagectomy.

Yoshida N, Baba Y, Kuroda D, Miyamoto Y, Iwatsuki M, Hiyoshi Y, Ishimoto T, Sawayama H, Imamura Y, Watanabe M, Baba H.

Dis Esophagus. 2018 Sep 1;31(9). doi: 10.1093/dote/doy024.

PMID:
29893796
30.

Total iron-binding capacity is a novel prognostic marker after curative gastrectomy for gastric cancer.

Sawayama H, Iwatsuki M, Kuroda D, Toihata T, Uchihara T, Koga Y, Yagi T, Kiyozumi Y, Eto T, Hiyoshi Y, Ishimoto T, Baba Y, Miyamoto Y, Yoshida N, Baba H.

Int J Clin Oncol. 2018 Aug;23(4):671-680. doi: 10.1007/s10147-018-1274-7. Epub 2018 Apr 9.

PMID:
29633053
31.

Omental abscess due to a spilled gallstone after laparoscopic cholecystectomy.

Urade T, Sawa H, Murata K, Mii Y, Iwatani Y, Futai R, Abe S, Sanuki T, Morinaga Y, Kuroda D.

Clin J Gastroenterol. 2018 Oct;11(5):433-436. doi: 10.1007/s12328-018-0853-5. Epub 2018 Mar 21.

PMID:
29564813
32.

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification.

Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ.

Front Immunol. 2018 Mar 2;9:413. doi: 10.3389/fimmu.2018.00413. eCollection 2018.

33.

Preoperative Smoking Cessation is Integral to the Prevention of Postoperative Morbidities in Minimally Invasive Esophagectomy.

Yoshida N, Nakamura K, Kuroda D, Baba Y, Miyamoto Y, Iwatsuki M, Hiyoshi Y, Ishimoto T, Imamura Y, Watanabe M, Baba H.

World J Surg. 2018 Sep;42(9):2902-2909. doi: 10.1007/s00268-018-4572-3.

PMID:
29532141
34.

Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column.

Kiyoshi M, Caaveiro JMM, Tada M, Tamura H, Tanaka T, Terao Y, Morante K, Harazono A, Hashii N, Shibata H, Kuroda D, Nagatoishi S, Oe S, Ide T, Tsumoto K, Ishii-Watabe A.

Sci Rep. 2018 Mar 2;8(1):3955. doi: 10.1038/s41598-018-22199-8.

35.

Structures of the prefusion form of measles virus fusion protein in complex with inhibitors.

Hashiguchi T, Fukuda Y, Matsuoka R, Kuroda D, Kubota M, Shirogane Y, Watanabe S, Tsumoto K, Kohda D, Plemper RK, Yanagi Y.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2496-2501. doi: 10.1073/pnas.1718957115. Epub 2018 Feb 20.

36.

Minimally invasive esophagectomy may contribute to long-term respiratory function after esophagectomy for esophageal cancer.

Kosumi K, Yoshida N, Okadome K, Eto T, Kuroda D, Ohuchi M, Kiyozumi Y, Nakamura K, Izumi D, Tokunaga R, Harada K, Mima K, Sawayama H, Ishimoto T, Iwatsuki M, Baba Y, Miyamoto Y, Watanabe M, Baba H.

Dis Esophagus. 2018 Jun 1;31(6). doi: 10.1093/dote/dox153.

PMID:
29444214
37.

Laparoscopic transabdominal preperitoneal approach for giant inguinal hernias.

Fujinaka R, Urade T, Fukuoka E, Murata K, Mii Y, Sawa H, Man-I M, Oka S, Iwatani Y, Kuroda D.

Asian J Surg. 2019 Jan;42(1):414-419. doi: 10.1016/j.asjsur.2017.12.004. Epub 2018 Jan 20.

38.

[A case of intracholecystic papillary neoplasm of the gallbladder (ICPN) examined using contrast-enhanced endoscopic ultrasonography].

Futai R, Sanuki T, Sawa H, Sasaki A, Tanaka K, Yoshie T, Oose T, Kuroda D, Morinaga Y, Zen Y.

Nihon Shokakibyo Gakkai Zasshi. 2018;115(1):117-125. doi: 10.11405/nisshoshi.115.117. Japanese.

PMID:
29353848
39.

Evidence of Molecular Heterogeneities in Amide-Based Deep Eutectic Solvents.

Cui Y, Kuroda DG.

J Phys Chem A. 2018 Feb 8;122(5):1185-1193. doi: 10.1021/acs.jpca.7b10264. Epub 2018 Jan 24.

PMID:
29307186
40.

Risk factors for pulmonary morbidities after minimally invasive esophagectomy for esophageal cancer.

Uchihara T, Yoshida N, Baba Y, Yagi T, Toihata T, Oda E, Kuroda D, Eto T, Ohuchi M, Nakamura K, Sawayama H, Kinoshita K, Iwatsuki M, Ishimoto T, Sakamoto Y, Baba H.

Surg Endosc. 2018 Jun;32(6):2852-2858. doi: 10.1007/s00464-017-5993-z. Epub 2017 Dec 22.

PMID:
29273870
41.

Synthesis-Free Phase-Selective Gelator for Oil-Spill Remediation.

Cui Y, Li MC, Wu Q, Pojman JA, Kuroda DG.

ACS Appl Mater Interfaces. 2017 Oct 4;9(39):33549-33553. doi: 10.1021/acsami.7b10009. Epub 2017 Sep 20.

PMID:
28895716
42.

A comparison of the solvation structure and dynamics of the lithium ion in linear organic carbonates with different alkyl chain lengths.

Fulfer KD, Kuroda DG.

Phys Chem Chem Phys. 2017 Sep 20;19(36):25140-25150. doi: 10.1039/c7cp05096h.

PMID:
28884183
43.

Controlling Nutritional Status (CONUT) score is a prognostic marker for gastric cancer patients after curative resection.

Kuroda D, Sawayama H, Kurashige J, Iwatsuki M, Eto T, Tokunaga R, Kitano Y, Yamamura K, Ouchi M, Nakamura K, Baba Y, Sakamoto Y, Yamashita Y, Yoshida N, Chikamoto A, Baba H.

Gastric Cancer. 2018 Mar;21(2):204-212. doi: 10.1007/s10120-017-0744-3. Epub 2017 Jun 27.

PMID:
28656485
44.

Unusual molecular mechanism behind the thermal response of polypeptoids in aqueous solutions.

Ma J, Xuan S, Guerin AC, Yu T, Zhang D, Kuroda DG.

Phys Chem Chem Phys. 2017 May 3;19(17):10878-10888. doi: 10.1039/c6cp08536a.

PMID:
28401209
45.

Activation of Transforming Growth Factor Beta 1 Signaling in Gastric Cancer-associated Fibroblasts Increases Their Motility, via Expression of Rhomboid 5 Homolog 2, and Ability to Induce Invasiveness of Gastric Cancer Cells.

Ishimoto T, Miyake K, Nandi T, Yashiro M, Onishi N, Huang KK, Lin SJ, Kalpana R, Tay ST, Suzuki Y, Cho BC, Kuroda D, Arima K, Izumi D, Iwatsuki M, Baba Y, Oki E, Watanabe M, Saya H, Hirakawa K, Baba H, Tan P.

Gastroenterology. 2017 Jul;153(1):191-204.e16. doi: 10.1053/j.gastro.2017.03.046. Epub 2017 Apr 5.

PMID:
28390866
46.

Ascending colon cancer with synchronous external iliac and inguinal lymph node metastases but without regional lymph node metastasis: a case report and brief literature review.

Kitano Y, Kuramoto M, Masuda T, Kuroda D, Yamamoto K, Ikeshima S, Iyama KI, Shimada S, Baba H.

Surg Case Rep. 2017 Dec;3(1):32. doi: 10.1186/s40792-017-0309-z. Epub 2017 Feb 20.

47.

Modeling and docking of antibody structures with Rosetta.

Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL Jr, Gray JJ.

Nat Protoc. 2017 Feb;12(2):401-416. doi: 10.1038/nprot.2016.180. Epub 2017 Jan 26.

48.

Design and Synthesis of Potent and Highly Selective Orexin 1 Receptor Antagonists with a Morphinan Skeleton and Their Pharmacologies.

Nagase H, Yamamoto N, Yata M, Ohrui S, Okada T, Saitoh T, Kutsumura N, Nagumo Y, Irukayama-Tomobe Y, Ishikawa Y, Ogawa Y, Hirayama S, Kuroda D, Watanabe Y, Gouda H, Yanagisawa M.

J Med Chem. 2017 Feb 9;60(3):1018-1040. doi: 10.1021/acs.jmedchem.6b01418. Epub 2017 Jan 18.

PMID:
28051300
49.

Solvation dynamics of an ionic probe in choline chloride-based deep eutectic solvents.

Cui Y, Fulfer KD, Ma J, Weldeghiorghis TK, Kuroda DG.

Phys Chem Chem Phys. 2016 Nov 23;18(46):31471-31479.

PMID:
27827478
50.

Pushing the Backbone in Protein-Protein Docking.

Kuroda D, Gray JJ.

Structure. 2016 Oct 4;24(10):1821-1829. doi: 10.1016/j.str.2016.06.025. Epub 2016 Aug 25.

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