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Theory and application of the vector pair correlation function for real-space crystallographic analysis of order/disorder correlations from STEM images

Theoretical frames STEM

Cabral MJ, Ophus C.
GSID: XiKIiQsXkNMJ
SD Funni, ZJ Yang, MJ Cabral, C Ophus, XM Chen… - APL …, 2021 - aip.scitation.org

… (STEM) images to quantify and analyze structural order/disorder correlations. Our STEM-… suitable for any material that can be imaged with STEM. To show the utility of our approach, …

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Funni, S. D., Yang, Z. J., Cabral, M. J., Ophus, C., Chen, X. M., & Dickey, E. C. (2021). Theory and application of the vector pair correlation function for real-space crystallographic analysis of order/disorder correlations from STEM images. APL Materials, 9(9), 091110.
Funni, Stephen D., et al. "Theory and application of the vector pair correlation function for real-space crystallographic analysis of order/disorder correlations from STEM images." APL Materials 9.9 (2021): 091110.
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A Genome-wide Association Study of Lung Cancer Identifies a Region of Chromosome 5p15 Associated with Risk for Adenocarcinoma.

American journal of human genetics

Landi MT, Chatterjee N, Yu K, Goldin LR, Goldstein AM, Rotunno M, Mirabello L, Jacobs K, Wheeler W, Yeager M, Bergen AW, Li Q, Consonni D, Pesatori AC, Wacholder S, Thun M, Diver R, Oken M, Virtamo J, Albanes D, Wang Z, Burdette L, Doheny KF, Pugh EW, Laurie C, Brennan P, Hung R, Gaborieau V, McKay JD, Lathrop M, McLaughlin J, Wang Y, Tsao MS, Spitz MR, Wang Y, Krokan H, Vatten L, Skorpen F, Arnesen E, Benhamou S, Bouchard C, Metspalu A, Vooder T, Nelis M, Välk K, Field JK, Chen C, Goodman G, Sulem P, Thorleifsson G, Rafnar T, Eisen T, Sauter W, Rosenberger A, Bickeböller H, Risch A, Chang-Claude J, Wichmann HE, Stefansson K, Houlston R, Amos CI, Fraumeni JF, Savage SA, Bertazzi PA, Tucker MA, Chanock S, Caporaso NE.
PMID: 28472664
Am J Hum Genet. 2011 Jun 10;88(6):861. doi: 10.1016/j.ajhg.2011.05.003. Epub 2011 Jun 10.

No abstract available.

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Landi MT, Chatterjee N, Yu K, et al. A Genome-wide Association Study of Lung Cancer Identifies a Region of Chromosome 5p15 Associated with Risk for Adenocarcinoma. Am J Hum Genet. 2011;88(6):861doi: 10.1016/j.ajhg.2011.05.003.
Landi, M. T., Chatterjee, N., Yu, K., Goldin, L. R., Goldstein, A. M., Rotunno, M., Mirabello, L., Jacobs, K., Wheeler, W., Yeager, M., Bergen, A. W., Li, Q., Consonni, D., Pesatori, A. C., Wacholder, S., Thun, M., Diver, R., Oken, M., Virtamo, J., Albanes, D., Wang, Z., Burdette, L., Doheny, K. F., Pugh, E. W., Laurie, C., Brennan, P., Hung, R., Gaborieau, V., McKay, J. D., Lathrop, M., McLaughlin, J., Wang, Y., Tsao, M. S., Spitz, M. R., Wang, Y., Krokan, H., Vatten, L., Skorpen, F., Arnesen, E., Benhamou, S., Bouchard, C., Metspalu, A., Vooder, T., Nelis, M., Välk, K., Field, J. K., Chen, C., Goodman, G., Sulem, P., Thorleifsson, G., Rafnar, T., Eisen, T., Sauter, W., Rosenberger, A., Bickeböller, H., Risch, A., Chang-Claude, J., Wichmann, H. E., Stefansson, K., Houlston, R., Amos, C. I., Fraumeni, J. F., Savage, S. A., Bertazzi, P. A., Tucker, M. A., Chanock, S., & Caporaso, N. E. (2011). A Genome-wide Association Study of Lung Cancer Identifies a Region of Chromosome 5p15 Associated with Risk for Adenocarcinoma. American journal of human genetics, 88(6), 861. https://doi.org/10.1016/j.ajhg.2011.05.003
Landi, Maria Teresa, et al. "A Genome-wide Association Study of Lung Cancer Identifies a Region of Chromosome 5p15 Associated with Risk for Adenocarcinoma." American journal of human genetics vol. 88,6 (2011): 861. doi: https://doi.org/10.1016/j.ajhg.2011.05.003
Landi MT, Chatterjee N, Yu K, Goldin LR, Goldstein AM, Rotunno M, Mirabello L, Jacobs K, Wheeler W, Yeager M, Bergen AW, Li Q, Consonni D, Pesatori AC, Wacholder S, Thun M, Diver R, Oken M, Virtamo J, Albanes D, Wang Z, Burdette L, Doheny KF, Pugh EW, Laurie C, Brennan P, Hung R, Gaborieau V, McKay JD, Lathrop M, McLaughlin J, Wang Y, Tsao MS, Spitz MR, Wang Y, Krokan H, Vatten L, Skorpen F, Arnesen E, Benhamou S, Bouchard C, Metspalu A, Vooder T, Nelis M, Välk K, Field JK, Chen C, Goodman G, Sulem P, Thorleifsson G, Rafnar T, Eisen T, Sauter W, Rosenberger A, Bickeböller H, Risch A, Chang-Claude J, Wichmann HE, Stefansson K, Houlston R, Amos CI, Fraumeni JF, Savage SA, Bertazzi PA, Tucker MA, Chanock S, Caporaso NE. A Genome-wide Association Study of Lung Cancer Identifies a Region of Chromosome 5p15 Associated with Risk for Adenocarcinoma. Am J Hum Genet. 2011 Jun 10;88(6):861. doi: 10.1016/j.ajhg.2011.05.003. Epub 2011 Jun 10. PMID: 28472664; PMCID: PMC3113243.
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Design, implementation and characterization of a quantum-dot-based volumetric display.

Scientific reports

Hirayama R, Naruse M, Nakayama H, Tate N, Shiraki A, Kakue T, Shimobaba T, Ohtsu M, Ito T.
PMID: 25683656
Sci Rep. 2015 Feb 16;5:8472. doi: 10.1038/srep08472.

In this study, we propose and experimentally demonstrate a volumetric display system based on quantum dots (QDs) embedded in a polymer substrate. Unlike conventional volumetric displays, our system does not require electrical wiring; thus, the heretofore unavoidable issue of...

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Hirayama R, Naruse M, Nakayama H, et al. Design, implementation and characterization of a quantum-dot-based volumetric display. Sci Rep. 2015;5:8472doi: 10.1038/srep08472.
Hirayama, R., Naruse, M., Nakayama, H., Tate, N., Shiraki, A., Kakue, T., Shimobaba, T., Ohtsu, M., & Ito, T. (2015). Design, implementation and characterization of a quantum-dot-based volumetric display. Scientific reports, 58472. https://doi.org/10.1038/srep08472
Hirayama, Ryuji, et al. "Design, implementation and characterization of a quantum-dot-based volumetric display." Scientific reports vol. 5 (2015): 8472. doi: https://doi.org/10.1038/srep08472
Hirayama R, Naruse M, Nakayama H, Tate N, Shiraki A, Kakue T, Shimobaba T, Ohtsu M, Ito T. Design, implementation and characterization of a quantum-dot-based volumetric display. Sci Rep. 2015 Feb 16;5:8472. doi: 10.1038/srep08472. PMID: 25683656; PMCID: PMC4329567.
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The Clinical Significance of Alpha-Fetoprotein mRNAs in Patients with Hepatocellular Carcinoma.

Gastrointestinal tumors

Kobayashi S, Tomokuni A, Takahashi H, Akita H, Sugimura K, Miyoshi N, Moon JH, Yasui M, Omori T, Ohue M, Fujiwara Y, Yano M, Sakon M.
PMID: 28611981
Gastrointest Tumors. 2017 Mar;3(3):141-152. doi: 10.1159/000455955. Epub 2017 Feb 08.

BACKGROUND/AIMS: Alpha-fetoprotein (AFP) mRNA-expressing cells are candidates for circulating tumor cells in hepatocellular carcinoma. We analyzed portal vein blood, peripheral blood, and peritoneal lavage samples to detect the presence of AFP mRNA-expressing cells, and explored their relationship with metastasis.METHODS:...

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Kobayashi S, Tomokuni A, Takahashi H, et al. The Clinical Significance of Alpha-Fetoprotein mRNAs in Patients with Hepatocellular Carcinoma. Gastrointest Tumors. 2017;3(3):141-152doi: 10.1159/000455955.
Kobayashi, S., Tomokuni, A., Takahashi, H., Akita, H., Sugimura, K., Miyoshi, N., Moon, J. H., Yasui, M., Omori, T., Ohue, M., Fujiwara, Y., Yano, M., & Sakon, M. (2017). The Clinical Significance of Alpha-Fetoprotein mRNAs in Patients with Hepatocellular Carcinoma. Gastrointestinal tumors, 3(3), 141-152. https://doi.org/10.1159/000455955
Kobayashi, Shogo, et al. "The Clinical Significance of Alpha-Fetoprotein mRNAs in Patients with Hepatocellular Carcinoma." Gastrointestinal tumors vol. 3,3 (2017): 141-152. doi: https://doi.org/10.1159/000455955
Kobayashi S, Tomokuni A, Takahashi H, Akita H, Sugimura K, Miyoshi N, Moon JH, Yasui M, Omori T, Ohue M, Fujiwara Y, Yano M, Sakon M. The Clinical Significance of Alpha-Fetoprotein mRNAs in Patients with Hepatocellular Carcinoma. Gastrointest Tumors. 2017 Mar;3(3):141-152. doi: 10.1159/000455955. Epub 2017 Feb 08. PMID: 28611981; PMCID: PMC5465674.
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Atomic Defects in Two Dimensional Materials.

Advanced materials (Deerfield Beach, Fla.)

Rasool HI, Ophus C, Zettl A.
PMID: 25946075
Adv Mater. 2015 Oct 14;27(38):5771-7. doi: 10.1002/adma.201500231. Epub 2015 May 06.

Atomic defects in crystalline structures have pronounced affects on their bulk properties. Aberration-corrected transmission electron microscopy has proved to be a powerful characterization tool for understanding the bonding structure of defects in materials. In this article, recent results on...

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Rasool HI, Ophus C, Zettl A. Atomic Defects in Two Dimensional Materials. Adv Mater. 2015;27(38):5771-7doi: 10.1002/adma.201500231.
Rasool, H. I., Ophus, C., & Zettl, A. (2015). Atomic Defects in Two Dimensional Materials. Advanced materials (Deerfield Beach, Fla.), 27(38), 5771-7. https://doi.org/10.1002/adma.201500231
Rasool, Haider I, et al. "Atomic Defects in Two Dimensional Materials." Advanced materials (Deerfield Beach, Fla.) vol. 27,38 (2015): 5771-7. doi: https://doi.org/10.1002/adma.201500231
Rasool HI, Ophus C, Zettl A. Atomic Defects in Two Dimensional Materials. Adv Mater. 2015 Oct 14;27(38):5771-7. doi: 10.1002/adma.201500231. Epub 2015 May 06. PMID: 25946075.
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Use of Vacuum-assisted closure in management of open abdominal wound with multiple enterocutaneous fistulae during chemotherapy: A case report.

International journal of surgery case reports

Fujino S, Miyoshi N, Ohue M, Noura S, Fukata T, Yagi T, Fujiwara Y, Yano M.
PMID: 26599504
Int J Surg Case Rep. 2015;17:112-6. doi: 10.1016/j.ijscr.2015.11.003. Epub 2015 Nov 10.

INTRODUCTION: Vacuum-assisted closure (VAC) is useful for treating complex wounds because it promotes granulation. In the present report, a successful case of VAC used for an open abdominal wound with enterocutaneous fistulae after multiple intestinal perforations during chemotherapy is...

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Fujino S, Miyoshi N, Ohue M, et al. Use of Vacuum-assisted closure in management of open abdominal wound with multiple enterocutaneous fistulae during chemotherapy: A case report. Int J Surg Case Rep. 2015;17:112-6doi: 10.1016/j.ijscr.2015.11.003.
Fujino, S., Miyoshi, N., Ohue, M., Noura, S., Fukata, T., Yagi, T., Fujiwara, Y., & Yano, M. (2015). Use of Vacuum-assisted closure in management of open abdominal wound with multiple enterocutaneous fistulae during chemotherapy: A case report. International journal of surgery case reports, 17112-6. https://doi.org/10.1016/j.ijscr.2015.11.003
Fujino, Shiki, et al. "Use of Vacuum-assisted closure in management of open abdominal wound with multiple enterocutaneous fistulae during chemotherapy: A case report." International journal of surgery case reports vol. 17 (2015): 112-6. doi: https://doi.org/10.1016/j.ijscr.2015.11.003
Fujino S, Miyoshi N, Ohue M, Noura S, Fukata T, Yagi T, Fujiwara Y, Yano M. Use of Vacuum-assisted closure in management of open abdominal wound with multiple enterocutaneous fistulae during chemotherapy: A case report. Int J Surg Case Rep. 2015;17:112-6. doi: 10.1016/j.ijscr.2015.11.003. Epub 2015 Nov 10. PMID: 26599504; PMCID: PMC4701801.
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Analysis of grain boundary dynamics using event detection and cumulative averaging.

Ultramicroscopy

Gautam A, Ophus C, Lançon F, Denes P, Dahmen U.
PMID: 25498139
Ultramicroscopy. 2015 Apr;151:78-84. doi: 10.1016/j.ultramic.2014.11.008. Epub 2014 Nov 26.

To analyze extended time series of high resolution images, we have employed automated frame-by-frame comparisons that are able to detect dynamic changes in the structure of a grain boundary in Au. Using cumulative averaging of images between events allowed...

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Gautam A, Ophus C, Lançon F, et al. Analysis of grain boundary dynamics using event detection and cumulative averaging. Ultramicroscopy. 2014;151:78-84doi: 10.1016/j.ultramic.2014.11.008.
Gautam, A., Ophus, C., Lançon, F., Denes, P., & Dahmen, U. (2015). Analysis of grain boundary dynamics using event detection and cumulative averaging. Ultramicroscopy, 15178-84. https://doi.org/10.1016/j.ultramic.2014.11.008
Gautam, A, et al. "Analysis of grain boundary dynamics using event detection and cumulative averaging." Ultramicroscopy vol. 151 (2015): 78-84. doi: https://doi.org/10.1016/j.ultramic.2014.11.008
Gautam A, Ophus C, Lançon F, Denes P, Dahmen U. Analysis of grain boundary dynamics using event detection and cumulative averaging. Ultramicroscopy. 2015 Apr;151:78-84. doi: 10.1016/j.ultramic.2014.11.008. Epub 2014 Nov 26. PMID: 25498139.
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Quantifying Changes in the Cellular Thiol-Disulfide Status during Differentiation of B Cells into Antibody-Secreting Plasma Cells.

International journal of cell biology

Hansen RE, Otsu M, Braakman I, Winther JR.
PMID: 24223594
Int J Cell Biol. 2013;2013:898563. doi: 10.1155/2013/898563. Epub 2013 Sep 24.

Plasma cells produce and secrete massive amounts of disulfide-containing antibodies. To accommodate this load on the secretory machinery, the differentiation of resting B cells into antibody-secreting plasma cells is accompanied by a preferential expansion of the secretory compartments of...

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Hansen RE, Otsu M, Braakman I, et al. Quantifying Changes in the Cellular Thiol-Disulfide Status during Differentiation of B Cells into Antibody-Secreting Plasma Cells. Int J Cell Biol. 2013;2013:898563doi: 10.1155/2013/898563.
Hansen, R. E., Otsu, M., Braakman, I., & Winther, J. R. (2013). Quantifying Changes in the Cellular Thiol-Disulfide Status during Differentiation of B Cells into Antibody-Secreting Plasma Cells. International journal of cell biology, 2013898563. https://doi.org/10.1155/2013/898563
Hansen, Rosa E, et al. "Quantifying Changes in the Cellular Thiol-Disulfide Status during Differentiation of B Cells into Antibody-Secreting Plasma Cells." International journal of cell biology vol. 2013 (2013): 898563. doi: https://doi.org/10.1155/2013/898563
Hansen RE, Otsu M, Braakman I, Winther JR. Quantifying Changes in the Cellular Thiol-Disulfide Status during Differentiation of B Cells into Antibody-Secreting Plasma Cells. Int J Cell Biol. 2013;2013:898563. doi: 10.1155/2013/898563. Epub 2013 Sep 24. PMID: 24223594; PMCID: PMC3800581.
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An assessment of the effects of ectopic gp91phox expression in XCGD iPSC-derived neutrophils.

Molecular therapy. Methods & clinical development

Lin HT, Masaki H, Yamaguchi T, Wada T, Yachie A, Nishimura K, Ohtaka M, Nakanishi M, Nakauchi H, Otsu M.
PMID: 26682238
Mol Ther Methods Clin Dev. 2015 Dec 09;2:15046. doi: 10.1038/mtm.2015.46. eCollection 2015.

For the treatment of monogenetic hematological disorders, restoration of transgene expression in affected cell populations is generally considered to have beneficial effects. However, X-linked chronic granulomatous disease (XCGD) is unique since the appearance of functional neutrophils in the peripheral...

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Lin HT, Masaki H, Yamaguchi T, et al. An assessment of the effects of ectopic gp91phox expression in XCGD iPSC-derived neutrophils. Mol Ther Methods Clin Dev. 2015;2:15046doi: 10.1038/mtm.2015.46.
Lin, H. T., Masaki, H., Yamaguchi, T., Wada, T., Yachie, A., Nishimura, K., Ohtaka, M., Nakanishi, M., Nakauchi, H., & Otsu, M. (2015). An assessment of the effects of ectopic gp91phox expression in XCGD iPSC-derived neutrophils. Molecular therapy. Methods & clinical development, 215046. https://doi.org/10.1038/mtm.2015.46
Lin, Huan-Ting, et al. "An assessment of the effects of ectopic gp91phox expression in XCGD iPSC-derived neutrophils." Molecular therapy. Methods & clinical development vol. 2 (2015): 15046. doi: https://doi.org/10.1038/mtm.2015.46
Lin HT, Masaki H, Yamaguchi T, Wada T, Yachie A, Nishimura K, Ohtaka M, Nakanishi M, Nakauchi H, Otsu M. An assessment of the effects of ectopic gp91phox expression in XCGD iPSC-derived neutrophils. Mol Ther Methods Clin Dev. 2015 Dec 09;2:15046. doi: 10.1038/mtm.2015.46. eCollection 2015. PMID: 26682238; PMCID: PMC4674005.
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Theory of High-Spin d(4) Complexes: An Angular-Overlap Model Parametrization of the Ligand Field in Vibronic-Coupling Calculations.

Journal of chemical theory and computation

Carver G, Thut M, Noble C, Tregenna-Piggott PL.
PMID: 26620935
J Chem Theory Comput. 2008 Apr;4(4):603-13. doi: 10.1021/ct7003484.

A new theoretical approach for the calculation of the electronic and molecular structures of octahedrally-coordinated high-spin d(4) complexes is described. A prescription for the construction of an effective (3)T1 + (5)E (O) Hamiltonian from the ligand-field matrices of a...

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Carver G, Thut M, Noble C, et al. Theory of High-Spin d(4) Complexes: An Angular-Overlap Model Parametrization of the Ligand Field in Vibronic-Coupling Calculations. J Chem Theory Comput. 2008;4(4):603-13doi: 10.1021/ct7003484.
Carver, G., Thut, M., Noble, C., & Tregenna-Piggott, P. L. (2008). Theory of High-Spin d(4) Complexes: An Angular-Overlap Model Parametrization of the Ligand Field in Vibronic-Coupling Calculations. Journal of chemical theory and computation, 4(4), 603-13. https://doi.org/10.1021/ct7003484
Carver, Graham, et al. "Theory of High-Spin d(4) Complexes: An Angular-Overlap Model Parametrization of the Ligand Field in Vibronic-Coupling Calculations." Journal of chemical theory and computation vol. 4,4 (2008): 603-13. doi: https://doi.org/10.1021/ct7003484
Carver G, Thut M, Noble C, Tregenna-Piggott PL. Theory of High-Spin d(4) Complexes: An Angular-Overlap Model Parametrization of the Ligand Field in Vibronic-Coupling Calculations. J Chem Theory Comput. 2008 Apr;4(4):603-13. doi: 10.1021/ct7003484. PMID: 26620935.
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Z skin incision in reduced-port surgery for colorectal cancer.

Molecular and clinical oncology

Fujino S, Miyoshi N, Ohue M, Noura S, Fujiwara Y, Higashiyama M, Yano M.
PMID: 27073675
Mol Clin Oncol. 2016 Apr;4(4):611-615. doi: 10.3892/mco.2016.757. Epub 2016 Jan 29.

Laparoscopic surgery for colorectal cancer (CRC) has recently gained in popularity due to the fewer trocars and shorter incision, leading to reduced wound pain and improved cosmetic outcome. In July, 2013, reduced-port surgery (RPS) was introduced and has been...

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Fujino S, Miyoshi N, Ohue M, et al. Z skin incision in reduced-port surgery for colorectal cancer. Mol Clin Oncol. 2016;4(4):611-615doi: 10.3892/mco.2016.757.
Fujino, S., Miyoshi, N., Ohue, M., Noura, S., Fujiwara, Y., Higashiyama, M., & Yano, M. (2016). Z skin incision in reduced-port surgery for colorectal cancer. Molecular and clinical oncology, 4(4), 611-615. https://doi.org/10.3892/mco.2016.757
Fujino, Shiki, et al. "Z skin incision in reduced-port surgery for colorectal cancer." Molecular and clinical oncology vol. 4,4 (2016): 611-615. doi: https://doi.org/10.3892/mco.2016.757
Fujino S, Miyoshi N, Ohue M, Noura S, Fujiwara Y, Higashiyama M, Yano M. Z skin incision in reduced-port surgery for colorectal cancer. Mol Clin Oncol. 2016 Apr;4(4):611-615. doi: 10.3892/mco.2016.757. Epub 2016 Jan 29. PMID: 27073675; PMCID: PMC4812501.
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A Study in the Borderland of Morality.

The Psychological clinic

Otis M.
PMID: 28909523
Psychol Clin. 1914 Dec 15;8(7):201-207.

No abstract available.

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Otis M. A Study in the Borderland of Morality. Psychol Clin. 1914;8(7):201-207
Otis, M. (1914). A Study in the Borderland of Morality. The Psychological clinic, 8(7), 201-207.
Otis, Margaret. "A Study in the Borderland of Morality." The Psychological clinic vol. 8,7 (1914): 201-207.
Otis M. A Study in the Borderland of Morality. Psychol Clin. 1914 Dec 15;8(7):201-207. PMID: 28909523; PMCID: PMC5139587.
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