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Research Output

2019

Erratum: Metformin Targets Mitochondrial Electron Transport to Reduce Air-Pollution-Induced Thrombosis (Cell Metabolism (2019) 29(2) (335–347.e5), (S1550413118305862) (10.1016/j.cmet.2018.09.019))

Soberanes, S., Misharin, A. V., Jairaman, A., Morales-Nebreda, L., McQuattie-Pimentel, A. C., Cho, T., Hamanaka, R. B., Meliton, A. Y., Reyfman, P. A., Walter, J. M., Chen, C. I., Chi, M., Chiu, S., Gonzalez-Gonzalez, F. J., Antalek, M., Abdala-Valencia, H., Chiarella, S. E., Sun, K. A., Woods, P. S., Ghio, A. J. & 12 others, Jain, M., Perlman, H., Ridge, K. M., Morimoto, R. I., Sznajder, J. I., Balch, W. E., Bhorade, S. M., Bharat, A., Prakriya, M., Chandel, N. S., Mutlu, G. M. & Budinger, G. R. S., Feb 5 2019, In : Cell Metabolism. 29, 2, 1 p.

Research output: Contribution to journalComment/debate

2 Scopus citations

Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis

Reyfman, P. A., Walter, J. M., Joshi, N., Anekalla, K. R., McQuattie-Pimentel, A. C., Chiu, S., Fernandez, R., Akbarpour, M., Chen, C. I., Ren, Z., Verma, R., Abdala-Valencia, H., Nam, K., Chi, M., Han, S. H., Gonzalez-Gonzalez, F. J., Soberanes, S., Watanabe, S., Williams, K. J. N., Flozak, A. S. & 29 others, Nicholson, T. T., Morgan, V. K., Winter, D. R., Hinchcliff, M., Hrusch, C. L., Guzy, R. D., Bonham, C. A., Sperling, A. I., Bag, R., Hamanaka, R. B., Mutlu, G. M., Yeldandi, A. V., Marshall, S. A., Shilatifard, A., Amaral, L. A. N., Perlman, H. R., Sznajder, J. I., Christine Argento, A., Gillespie, C. T., Dematte, J., Jain, M., Singer, B., Ridge, K. M., Lam, A. P., Bharat, A., Bhorade, S. M., Gottardi, C., Budinger, GR. S. & Misharin, A., Jun 15 2019, In : American Journal of Respiratory and Critical Care Medicine. 199, 12, p. 1517-1536 20 p.

Research output: Contribution to journalArticle

Open Access
65 Scopus citations
2018

A beginner’s guide to analysis of RNA sequencing data

Koch, C. M., Chiu, S. F., Akbarpour, M., Bharat, A., Ridge, K. M., Bartom, E. T. & Winter, D. R., Aug 2018, In : American journal of respiratory cell and molecular biology. 59, 2, p. 145-157 13 p.

Research output: Contribution to journalReview article

6 Scopus citations

Future research directions in pneumonia

Dela Cruz, C. S., Wunderink, R. G., Christiani, D. C., Cormier, S. A., Crothers, K., Doerschuk, C. M., Evans, S. E., Goldstein, D. R., Khatri, P., Kobzik, L., Kolls, J. K., Levy, B. D., Metersky, M. L., Niederman, M. S., Nusrat, R., Orihuela, C. J., Peyrani, P., Prince, A. S., Ramírez, J. A., Ridge, K. M. & 9 others, Sethi, S., Suratt, B. T., Sznajder, J. I., Tsalik, E. L., Walkey, A. J., Yende, S., Aggarwal, N. R., Caler, E. V. & Mizgerd, J. P., Jul 15 2018, In : American journal of respiratory and critical care medicine. 198, 2, p. 256-263 8 p.

Research output: Contribution to journalArticle

14 Scopus citations

Inflammatory monocytes drive influenza A virus-mediated lung injury in juvenile mice

Coates, B. M., Staricha, K. L., Koch, C. M., Cheng, Y., Shumaker, D. K., Budinger, G. R. S., Perlman, H., Misharin, A. V. & Ridge, K. M., Apr 1 2018, In : Journal of Immunology. 200, 7, p. 2391-2404 14 p.

Research output: Contribution to journalArticle

18 Scopus citations

Inflammatory pathways are upregulated in the nasal epithelium in patients with idiopathic pulmonary fibrosis

Sala, M. A., Balderas-Martínez, Y. I., Buendía-Roldan, I., Abdala-Valencia, H., Nam, K., Jain, M., Bhorade, S., Bharat, A., Reyfman, P. A., Ridge, K. M., Pardo, A., Sznajder, J. I., Budinger, G. R. S., Misharin, A. V. & Selman, M., Nov 26 2018, In : Respiratory Research. 19, 1, 233.

Research output: Contribution to journalArticle

Metformin Targets Mitochondrial Electron Transport to Reduce Air-Pollution-Induced Thrombosis

Soberanes, S., Misharin, A. V., Jairaman, A., Morales-Nebreda, L., McQuattie-Pimentel, A. C., Cho, T., Hamanaka, R. B., Meliton, A. Y., Reyfman, P. A., Walter, J. M., Chen, C-I., Chi, M., Chiu, S., Gonzalez-Gonzalez, F. J., Antalek, M., Abdala-Valencia, H., Chiarella, S. E., Sun, K. A., Woods, P. S., Ghio, A. J. & 12 others, Jain, M., Perlman, H., Ridge, K. M., Morimoto, R. I., Sznajder, J. I., Balch, W. E., Bhorade, S. M., Bharat, A., Prakriya, M., Chandel, N. S., Mutlu, G. M. & Budinger, G. R. S., Oct 11 2018, In : Cell Metabolism.

Research output: Contribution to journalArticle

9 Scopus citations

Vimentin expression is required for the development of EMT-related renal fibrosis following unilateral ureteral obstruction in mice

Wang, Z., Divanyan, A., Jourd’heuil, F. L., Goldman, R. D., Ridge, K. M., Jourd’heuil, D. & Lopez-Soler, R. I., Oct 2018, In : American Journal of Physiology - Renal Physiology. 315, 4, p. F769-F780

Research output: Contribution to journalArticle

7 Scopus citations
2017

Acute Lung Injury, Repair, and Remodeling: Pulmonary Endothelial and Epithelial Biology

Zhao, Y., Ridge, K. & Zhao, J., Jan 1 2017, In : Mediators of Inflammation. 2017, 9081521.

Research output: Contribution to journalEditorial

1 Scopus citations

FXYD5 is an essential mediator of the inflammatory response during lung injury

Brazee, P. L., Soni, P. N., Tokhtaeva, E., Magnani, N., Yemelyanov, A., Perlman, H. R., Ridge, K. M., Sznajder, J. I., Vagin, O. & Dada, L. A., Jun 1 2017, In : Frontiers in immunology. 8, JUN, 623.

Research output: Contribution to journalArticle

8 Scopus citations

Inhibition of the NOD-like receptor protein 3 inflammasome is protective in juvenile influenza a virus infection

Coates, B. M., Staricha, K. L., Ravindran, N., Koch, C. M., Cheng, Y., Davis, J. M., Shumaker, D. K. & Ridge, K. M., Jul 10 2017, In : Frontiers in immunology. 8, JUL, 782.

Research output: Contribution to journalArticle

22 Scopus citations
14 Scopus citations

Lung interstitial macrophages: Establishing identity and uncovering heterogeneity

Koch, C. M., Stephen, F. C., Misharin, A. V. & Ridge, K. M., Jul 2017, In : American journal of respiratory cell and molecular biology. 57, 1, p. 7-9 3 p.

Research output: Contribution to journalReview article

1 Scopus citations

Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span

Misharin, A. V., Morales-Nebreda, L., Reyfman, P. A., Cuda, C. M., Walter, J. M., McQuattie-Pimentel, A. C., Chen, C. I., Anekalla, K. R., Joshi, N., Williams, K. J. N., Abdala-Valencia, H., Yacoub, T. J., Chi, M., Chiu, S., Gonzalez-Gonzalez, F. J., Gates, K., Lam, A. P., Nicholson, T. T., Homan, P. J., Soberanes, S. & 23 others, Dominguez, S., Morgan, V. K., Saber, R., Shaffer, A., Hinchcliff, M., Marshall, S. A., Bharat, A., Berdnikovs, S., Bhorade, S. M., Bartom, E. T., Morimoto, R. I., Balch, W. E., Sznajder, J. I., Chandel, N. S., Mutlu, G. M., Jain, M., Gottardi, C. J., Singer, B. D., Ridge, K. M., Bagheri, N., Shilatifard, A., Budinger, G. R. S. & Perlman, H., Aug 1 2017, In : Journal of Experimental Medicine. 214, 8, p. 2387-2404 18 p.

Research output: Contribution to journalArticle

171 Scopus citations

SIRT3 deficiency promotes lung fibrosis by augmenting alveolar epithelial cell mitochondrial DNA damage and apoptosis

Jablonski, R. P., Kim, S. J., Cheresh, P., Williams, D. B., Morales-Nebreda, L., Cheng, Y., Yeldandi, A., Bhorade, S., Pardo, A., Selman, M., Ridge, K., Gius, D., Budinger, G. R. S. & Kamp, D. W., Jun 2017, In : FASEB Journal. 31, 6, p. 2520-2532 13 p.

Research output: Contribution to journalArticle

30 Scopus citations

The role of nucleotide-binding oligomerization domain-like receptors in pulmonary infection

Wiese, K. M., Coates, B. M. & Ridge, K. M., Aug 2017, In : American journal of respiratory cell and molecular biology. 57, 2, p. 151-161 11 p.

Research output: Contribution to journalReview article

3 Scopus citations
2016

Flow cytometry reveals similarities between lung macrophages in humans and mice

Bharat, A., Bhorade, S. M., Morales-Nebreda, L., McQuattie-Pimentel, A. C., Soberanes, S., Ridge, K., DeCamp, M. M., Mestan, K. K., Perlman, H., Budinger, G. R. S. & Misharin, A. V., Jan 2016, In : American journal of respiratory cell and molecular biology. 54, 1, p. 147-149 3 p.

Research output: Contribution to journalLetter

48 Scopus citations

Methods for Determining the Cellular Functions of Vimentin Intermediate Filaments

Ridge, K. M., Shumaker, D., Robert, A., Hookway, C., Gelfand, V. I., Janmey, P. A., Lowery, J., Guo, M., Weitz, D. A., Kuczmarski, E. & Goldman, R. D., Jan 1 2016, Methods in Enzymology. Academic Press Inc, p. 389-426 38 p. (Methods in Enzymology; vol. 568).

Research output: Chapter in Book/Report/Conference proceedingChapter

11 Scopus citations

Mitochondrial catalase overexpressed transgenic mice are protected against lung fibrosis in part via preventing alveolar epithelial cell mitochondrial DNA damage

Kim, S. J., Cheresh, P., Jablonski, R. P., Morales-Nebreda, L., Cheng, Y., Hogan, E., Yeldandi, A., Chi, M., Piseaux, R., Ridge, K., Michael Hart, C., Chandel, N., Scott Budinger, G. R. & Kamp, D. W., Dec 1 2016, In : Free Radical Biology and Medicine. 101, p. 482-490 9 p.

Research output: Contribution to journalArticle

21 Scopus citations

The O-glycosylated ectodomain of FXYD5 impairs adhesion by disrupting cell-cell trans-dimerization of Na,K-ATPase β1 subunits

Tokhtaeva, E., Sun, H., Deiss-Yehiely, N., Wen, Y., Soni, P. N., Gabrielli, N. M., Marcus, E. A., Ridge, K. M., Sachs, G., Vazquez-Levin, M., Sznajder, J. I., Vagin, O. & Dada, L. A., Jun 15 2016, In : Journal of cell science. 129, 12, p. 2394-2406 13 p.

Research output: Contribution to journalArticle

9 Scopus citations
2015

Asbestos-induced pulmonary fibrosis is augmented in 8-oxoguanine DNA glycosylase knockout mice

Cheresh, P., Morales-Nebreda, L., Kim, S. J., Yeldandi, A., Williams, D. B., Cheng, Y., Mutlu, G. M., Scott Budinger, G. R., Ridge, K., Schumacker, P. T., Bohr, V. A. & Kamp, D. W., Jan 1 2015, In : American journal of respiratory cell and molecular biology. 52, 1, p. 25-36 12 p.

Research output: Contribution to journalArticle

23 Scopus citations

Corrigendum: [The kinase Jnk2 promotes stress-induced mitophagy by targeting the small mitochondrial form of the tumor suppressor ARF for degradation (Nat. Immunol.) (2015) 16:458'466]

Zhang, Q., Kuang, H., Chen, C., Yan, J., Do-Umehara, H. C., Liu, X. Y., Dada, L., Ridge, K. M., Chandel, N. S. & Liu, J., Jul 20 2015, In : Nature Immunology. 16, 7, 1 p.

Research output: Contribution to journalComment/debate

3 Scopus citations

Influenza a virus infection, innate immunity, and childhood

Coates, B. M., Staricha, K. L., Wiese, K. M. & Ridge, K. M., Oct 1 2015, In : JAMA Pediatrics. 169, 10, p. 956-963 8 p.

Research output: Contribution to journalReview article

18 Scopus citations

Influenza virus-induced lung injury: Pathogenesis and implications for treatment

Herold, S., Becker, C., Ridge, K. M. & Budinger, G. R. S., May 1 2015, In : European Respiratory Journal. 45, 5, p. 1463-1478 16 p.

Research output: Contribution to journalArticle

78 Scopus citations

Lung-specific loss of a3 laminin worsens bleomycin-induced pulmonary fibrosis

Morales-Nebreda, L. I., Rogel, M. R., Eisenberg, J. L., Hamill, K. J., Soberanes, S., Nigdelioglu, R., Chi, M., Cho, T., Radigan, K. A., Ridge, K. M., Misharin, A. V., Woychek, A., Hopkinson, S., Perlman, H., Mutlu, G. M., Pardo, A., Selman, M., Jones, J. C. R. & Scott Budinger, G. R., Apr 1 2015, In : American journal of respiratory cell and molecular biology. 52, 4, p. 503-512 10 p.

Research output: Contribution to journalArticle

11 Scopus citations

The kinase Jnk2 promotes stress-induced mitophagy by targeting the small mitochondrial form of the tumor suppressor ARF for degradation

Zhang, Q., Kuang, H., Chen, C., Yan, J., Do-Umehara, H. C., Liu, X. Y., Dada, L., Ridge, K. M., Chandel, N. S. & Liu, J., May 28 2015, In : Nature Immunology. 16, 5, p. 458-466 9 p.

Research output: Contribution to journalArticle

38 Scopus citations

Vimentin regulates activation of the NLRP3 inflammasome

Dos Santos, G., Rogel, M. R., Baker, M. A., Troken, J. R., Urich, D., Morales-Nebreda, L., Sennello, J. A., Kutuzov, M. A., Sitikov, A., Davis, J. M., Lam, A. P., Cheresh, P., Kamp, D., Shumaker, D. K., Budinger, G. R. S. & Ridge, K. M., Mar 12 2015, In : Nature communications. 6, 6574.

Research output: Contribution to journalArticle

88 Scopus citations
2014

Impact of S-adenosylmethionine decarboxylase 1 on pulmonary vascular remodeling

Weisel, F. C., Kloepping, C., Pichl, A., Sydykov, A., Kojonazarov, B., Wilhelm, J., Roth, M., Ridge, K. M., Igarashi, K., Nishimura, K., Maison, W., Wackendorff, C., Klepetko, W., Jaksch, P., Ghofrani, H. A., Grimminger, F., Seeger, W., Schermuly, R. T., Weissmann, N. & Kwapiszewska, G., Apr 8 2014, In : Circulation. 129, 14, p. 1510-1523 14 p.

Research output: Contribution to journalArticle

12 Scopus citations

Intratracheal administration of influenza virus is superior to intranasal administration as a model of acute lung injury

Morales-Nebreda, L., Chi, M., Lecuona, E., Chandel, N. S., Dada, L. A., Ridge, K., Soberanes, S., Nigdelioglu, R., Sznajder, J. I., Mutlu, G. M., Budinger, G. R. S. & Radigan, K. A., Dec 1 2014, In : Journal of Virological Methods. 209, p. 116-120 5 p.

Research output: Contribution to journalArticle

10 Scopus citations

Mitochondria-targeted Ogg1 and aconitase-2 prevent oxidant-induced mitochondrial DNA damage in alveolar epithelial cells

Kim, S. J., Cheresh, P., Williams, D., Cheng, Y., Ridge, K., Schumacker, P. T., Weitzman, S., Bohr, V. A. & Kamp, D. W., Feb 28 2014, In : Journal of Biological Chemistry. 289, 9, p. 6165-6176 12 p.

Research output: Contribution to journalArticle

49 Scopus citations

Structure and biomechanics of the endothelial transcellular circumferential invasion array in tumor invasion

Arvanitis, C., Khuon, S., Spann, R., Ridge, K. M. & Chew, T. L., Feb 24 2014, In : PloS one. 9, 2, e89758.

Research output: Contribution to journalArticle

11 Scopus citations

The role of Vimentin intermediate filaments in the progression of lung cancer

Kidd, M. E., Shumaker, D. K. & Ridge, K. M., Jan 1 2014, In : American journal of respiratory cell and molecular biology. 50, 1, p. 1-6 6 p.

Research output: Contribution to journalReview article

122 Scopus citations
2013

Asbestos-induced alveolar epithelial cell apoptosis: The role of endoplasmic reticulum stress response

Kamp, D. W., Liu, G., Cheresh, P., Kim, S. J., Mueller, A., Lam, A. P., Trejo, H., Williams, D., Tulasiram, S., Baker, M., Ridge, K., Chandel, N. S. & Beri, R., Dec 1 2013, In : American journal of respiratory cell and molecular biology. 49, 6, p. 892-901 10 p.

Research output: Contribution to journalArticle

38 Scopus citations

Suppression of inflammation and acute lung injury by Miz1 via repression of C/EBP-δ

Do-Umehara, H. C., Chen, C., Urich, D., Zhou, L., Qiu, J., Jang, S., Zander, A., Baker, M. A., Eilers, M., Sporn, P. H. S., Ridge, K. M., Sznajder, J. I., Budinger, G. R. S., Mutlu, G. M., Lin, A. & Liu, J., May 1 2013, In : Nature Immunology. 14, 5, p. 461-469 9 p.

Research output: Contribution to journalArticle

46 Scopus citations
2012

Particulate matter air pollution induces hypermethylation of the p16 promoter Via a mitochondrial ROS-JNK-DNMT1 pathway

Soberanes, S., Gonzalez, A., Urich, D., Chiarella, S. E., Radigan, K. A., Osornio-Vargas, A., Joseph, J., Kalyanaraman, B., Ridge, K. M., Chandel, N. S., Mutlu, G. M., De Vizcaya-Ruiz, A. & Budinger, G. R. S., Apr 19 2012, In : Scientific reports. 2, 275.

Research output: Contribution to journalArticle

60 Scopus citations

The inflammasome in lung diseases

dos Santos, G., Kutuzov, M. A. & Ridge, K. M., Oct 26 2012, In : American Journal of Physiology - Lung Cellular and Molecular Physiology. 303, 8

Research output: Contribution to journalReview article

100 Scopus citations
2011

Vimentin is sufficient and required for wound repair and remodeling in alveolar epithelial cells

Rogel, M. R., Soni, P. N., Troken, J. R., Sitikov, A., Trejo, H. E. & Ridge, K. M., Nov 1 2011, In : FASEB Journal. 25, 11, p. 3873-3883 11 p.

Research output: Contribution to journalArticle

63 Scopus citations
2010

Mitochondrial reactive oxygen species are required for hypoxia-induced degradation of keratin intermediate filaments

Na, N., Chandel, N. S., Litvan, J. & Ridge, K. M., Mar 1 2010, In : FASEB Journal. 24, 3, p. 799-809 11 p.

Research output: Contribution to journalArticle

23 Scopus citations

The role of the ubiquitin proteasome pathway in keratin intermediate filament protein degradation

Rogel, M. R., Jaitovich, A. & Ridge, K. M., Feb 15 2010, In : Proceedings of the American Thoracic Society. 7, 1, p. 71-76 6 p.

Research output: Contribution to journalReview article

32 Scopus citations
2009

Mitochondrial complex III-generated oxidants activate ASK1 and JNK to induce alveolar epithelial cell death following exposure to particulate matter air pollution

Soberanes, S., Urich, D., Baker, C. M., Burgess, Z., Chiarella, S. E., Bell, E. L., Ghio, A. J., De Vizcaya-Ruiz, A., Liu, J., Ridge, K. M., Kamp, D. W., Chandel, N. S., Schumacker, P. T., Mutlu, G. M. & Budinger, G. R. S., Jan 23 2009, In : Journal of Biological Chemistry. 284, 4, p. 2176-2186 11 p.

Research output: Contribution to journalArticle

91 Scopus citations

Proapoptotic Noxa is required for particulate matterinduced cell death and lung inflammation

Urich, D., Soberanes, S., Burgess, Z., Chiarella, S. E., Ghio, A. J., Ridge, K. M., Kamp, D. W., Chandel, N. S., Mutlu, G. M. & Budinger, G. R. S., Jul 1 2009, In : FASEB Journal. 23, 7, p. 2055-2064 10 p.

Research output: Contribution to journalArticle

25 Scopus citations

Shear stress induced reorganization of the keratin intermediate filament network requires phosphorylation by protein kinase C ζ

Sivaramakrishnan, S., Schneider, J. L., Sitikov, A., Goldman, R. D. & Ridge, K. M., Jun 1 2009, In : Molecular biology of the cell. 20, 11, p. 2755-2765 11 p.

Research output: Contribution to journalArticle

51 Scopus citations
2008

Micromechanical properties of keratin intermediate filament networks

Sivaramakrishnan, S., DeGiulio, J. V., Lorand, L., Goldman, R. D. & Ridge, K. M., Jan 22 2008, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 3, p. 889-894 6 p.

Research output: Contribution to journalArticle

66 Scopus citations

Overexpression of the Na-K-ATPase α2-subunit improves lung liquid clearance during ventilation-induced lung injury

Adir, Y., Welch, L. C., Dumasius, V., Factor, P., Sznajder, J. I. & Ridge, K. M., Jun 1 2008, In : American Journal of Physiology - Lung Cellular and Molecular Physiology. 294, 6, p. L1233-L1237

Research output: Contribution to journalArticle

16 Scopus citations

Ubiquitin-proteasome-mediated degradation of keratin intermediate filaments in mechanically stimulated A549 cells

Jaitovich, A., Mehta, S., Na, N., Ciechanover, A., Goldman, R. D. & Ridge, K. M., Sep 12 2008, In : Journal of Biological Chemistry. 283, 37, p. 25348-25355 8 p.

Research output: Contribution to journalArticle

37 Scopus citations
2006

Differential binding of plasminogen, plasmin, and Angiostatin4.5 to cell surface β-actin: Implications for cancer-mediated angiogenesis

Wang, H., Doll, J. A., Jiang, K., Cundiff, D. L., Czarnecki, J. S., Wilson, M., Ridge, K. M. & Soff, G. A., Jul 15 2006, In : Cancer Research. 66, 14, p. 7211-7215 5 p.

Research output: Contribution to journalArticle

26 Scopus citations

Laminin-311 (laminin-6) fiber assembly by type I-like alveolar cells

DeBiase, P. J., Lane, K., Budinger, S., Ridge, K., Wilson, M. & Jones, J. C. R., Jun 1 2006, In : Journal of Histochemistry and Cytochemistry. 54, 6, p. 665-672 8 p.

Research output: Contribution to journalArticle

12 Scopus citations

Proapoptotic Bid is required for pulmonary fibrosis

Budinger, G. R. S., Mutlu, G. M., Eisenbart, J., Fuller, A. C., Bellmeyer, A. A., Baker, C. M., Wilson, M., Ridge, K., Barrett, T. A., Lee, V. Y. & Chandel, N. S., Mar 21 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 12, p. 4604-4609 6 p.

Research output: Contribution to journalArticle

80 Scopus citations
45 Scopus citations
2005

Hypocapnic but not metabolic alkalosis impairs alveolar fluid reabsorption

Myrianthefs, P. M., Briva, A., Lecuona, E., Dumasius, V., Rutschman, D. H., Ridge, K. M., Baltopoulos, G. J. & Sznajder, J. I., Jun 1 2005, In : American journal of respiratory and critical care medicine. 171, 11, p. 1267-1271 5 p.

Research output: Contribution to journalArticle

20 Scopus citations