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Vargas J, Modrego A, Canabal H, Martin-Benito J. Semantic segmentation-based detection algorithm for challenging cryo-electron microscopy RNP samples. Front Mol Biosci 2024;11:1473609. [PMID: 39411403 PMCID: PMC11473350 DOI: 10.3389/fmolb.2024.1473609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 09/17/2024] [Indexed: 10/19/2024]  Open
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Russell L, Johnson TM, Lawrence Y, Reichelt B, Vanderloo N, Cufari M, Buschmann BI, Dannhoff S, DeVault A, Doeg E, Evans T, Foo BC, Frankel R, Kunimune JH, Pearcy JA, Vargas J, Gatu Johnson M, Frenje J. Quantifying the effects of neutron fluence on proton signal retention in CR-39. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024;95:103505. [PMID: 39356191 DOI: 10.1063/5.0219479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 09/17/2024] [Indexed: 10/03/2024]
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Cufari M, Vanderloo N, Buschmann BI, DeVault A, Foo BC, Vargas J, Dannhoff SG, Evans TE, Johnson TM, Kunimune J, Lawrence Y, Pearcy JA, Reichelt BL, Russell L, Wink CW, Gatu Johnson M, Petrasso RD, Frenje JA. Characterization of the image plate multi-scan response to mono-energetic x-rays. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024;95:093535. [PMID: 39315911 DOI: 10.1063/5.0219509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/18/2024] [Indexed: 09/25/2024]
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Buschmann BI, Cufari M, Vanderloo N, Vargas J, Foo BC, DeVault A, Dannhoff SG, Evans TE, Johnson TM, Kunimune JH, Lawrence Y, Pearcy JA, Reichelt BL, Wink CW, Russell L, Gatu Johnson M, Petrasso RD, Frenje JA. Characterization of the response of radiochromic film to quasi-monoenergetic x rays through a cross-calibration with image plates. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024;95:093531. [PMID: 39302171 DOI: 10.1063/5.0219340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 09/03/2024] [Indexed: 09/22/2024]
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Vanderloo N, Cufari M, Russell L, Johnson TM, Vargas J, Foo BC, Buschmann BI, Dannhoff SG, DeVault A, Evans TE, Kunimune JH, Lawrence Y, Pearcy JA, Reichelt BL, Wink CW, Gatu Johnson M, Petrasso RD, Frenje JA, Li CK. Image plate multi-scan response to fusion protons in the range of 1-14 MeV. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024;95:093536. [PMID: 39315912 DOI: 10.1063/5.0219547] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/19/2024] [Indexed: 09/25/2024]
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Garcia ME, Krikorian A, Vargas J, Rave LP, Chalarca J, Sánchez Y. Integration of Art and Humanities in Teaching/Learning in Palliative Care in Undergraduate Medicine: An International Collaborative Effort. ACADEMIC MEDICINE : JOURNAL OF THE ASSOCIATION OF AMERICAN MEDICAL COLLEGES 2023;98:S174-S175. [PMID: 37983417 DOI: 10.1097/acm.0000000000005402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
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Cardona-Maya Y, Emilio-Zapata A, Ledezma-Sillas JE, Vargas J, Meza JM, Herrera-Ramírez JM, Isaza M CA. Analysis of Aluminum-Based Metal Matrix Composite Reinforced with SiC Particles Studied by Scanning Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023;29:186-187. [PMID: 37613265 DOI: 10.1093/micmic/ozad067.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
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Vargas J, Akrami R, Marín-Alzate N, Mesa SM, Idarraga G, Isaza CA, Yang L, Meza JM. Determination of Adhesion Between Modified PLA Matrix and Natural Fibers Using SEM and Micro-Raman Spectroscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023;29:1250-1252. [PMID: 37613666 DOI: 10.1093/micmic/ozad067.641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
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Alvernia JE, Berbeo Calderón ME, Cespedes J, Vargas J, Grady M, Cadavid LC, Fonseca EO, Posada AC. Ernesto Bustamante Zuleta (1922-2021): pioneering teacher and practitioner of Colombian neurosurgery. J Neurosurg 2023;138:875-881. [PMID: 35932266 DOI: 10.3171/2022.5.jns22537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/24/2022] [Indexed: 11/06/2022]
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Osorio Fonseca E, Cadavid LC, Cespedes J, Vargas J, Grady M, Gonzalez LF, Berbeo ME, Ordóñez-Mora EG, Ordóñez-Rubiano EG, Alvernia JE. A history of Colombian neurosurgery: events, persons, and outcomes that have shaped the specialty in the country. J Neurosurg 2023;138:868-874. [PMID: 35907192 DOI: 10.3171/2022.6.jns22830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/02/2022] [Indexed: 11/06/2022]
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Klein D, Vargas J, Gaviria-Agudelo C, Panzarino VM. Renal function and injury assessment in premature infants. Am J Med Sci 2023. [DOI: 10.1016/s0002-9629(23)00625-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Sorzano COS, Vilas JL, Ramírez-Aportela E, Krieger J, Del Hoyo D, Herreros D, Fernandez-Giménez E, Marchán D, Macías JR, Sánchez I, Del Caño L, Fonseca-Reyna Y, Conesa P, García-Mena A, Burguet J, García Condado J, Méndez García J, Martínez M, Muñoz-Barrutia A, Marabini R, Vargas J, Carazo JM. Image processing tools for the validation of CryoEM maps. Faraday Discuss 2022;240:210-227. [PMID: 35861059 DOI: 10.1039/d2fd00059h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Kaur S, Kanungo R, Horiuchi W, Hagen G, Holt JD, Hu BS, Miyagi T, Suzuki T, Ameil F, Atkinson J, Ayyad Y, Bagchi S, Cortina-Gil D, Dillmann I, Estradé A, Evdokimov A, Farinon F, Geissel H, Guastalla G, Janik R, Knöbel R, Kurcewicz J, Litvinov YA, Marta M, Mostazo M, Mukha I, Nociforo C, Ong HJ, Otsuka T, Pietri S, Prochazka A, Scheidenberger C, Sitar B, Strmen P, Takechi M, Tanaka J, Tanihata I, Terashima S, Vargas J, Weick H, Winfield JS. Proton Distribution Radii of ^{16-24}O: Signatures of New Shell Closures and Neutron Skin. PHYSICAL REVIEW LETTERS 2022;129:142502. [PMID: 36240396 DOI: 10.1103/physrevlett.129.142502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/31/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
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Gomez-Blanco J, Kaur S, Strauss M, Vargas J. Hierarchical autoclassification of cryo-EM samples and macromolecular energy landscape determination. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022;216:106673. [PMID: 35149430 DOI: 10.1016/j.cmpb.2022.106673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/10/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
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Graff I, De Broucker C, Vargas J, Vanoost A, Gondry J, Foulon A. [COVID-19 and lockdown: Impact on pregnancy complications]. GYNECOLOGIE, OBSTETRIQUE, FERTILITE & SENOLOGIE 2022;50:236-239. [PMID: 34915137 PMCID: PMC8668785 DOI: 10.1016/j.gofs.2021.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/26/2022]
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Vargas J, Nuske M, Eichberger R, Hippler C, Mathey L, Hemmerich A. Orbital Many-Body Dynamics of Bosons in the Second Bloch Band of an Optical Lattice. PHYSICAL REVIEW LETTERS 2021;126:200402. [PMID: 34110197 DOI: 10.1103/physrevlett.126.200402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
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Monardes H, Herrera K, Vargas J, Steinfort K, Zaror C, Abarca J. Root Anatomy and Canal Configuration of Maxillary Premolars: A Cone-beam Computed Tomography Study. INT J MORPHOL 2021. [DOI: 10.4067/s0717-95022021000200463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Kazemi M, Sorzano COS, Carazo JM, Georges AD, Abrishami V, Vargas J. ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021;164:92-100. [PMID: 33450244 DOI: 10.1016/j.pbiomolbio.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 11/27/2022]
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Chatillon A, Taïeb J, Alvarez-Pol H, Audouin L, Ayyad Y, Bélier G, Benlliure J, Boutoux G, Caamaño M, Casarejos E, Cortina-Gil D, Ebran A, Farget F, Fernández-Domínguez B, Gorbinet T, Grente L, Heinz A, Johansson HT, Jurado B, Kelić-Heil A, Kurz N, Laurent B, Martin JF, Nociforo C, Paradela C, Pellereau E, Pietri S, Prochazka A, Rodríguez-Sánchez JL, Rossi D, Simon H, Tassan-Got L, Vargas J, Voss B, Weick H. Evidence for a New Compact Symmetric Fission Mode in Light Thorium Isotopes. PHYSICAL REVIEW LETTERS 2020;124:202502. [PMID: 32501052 DOI: 10.1103/physrevlett.124.202502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/16/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
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Kneese G, Barrera S, Castillo J, Garcia M, Ryden A, White A, Vargas J, Morrow J. ScribeMD: Mixed-methods analysis of a pen pal program in undergraduate medical education. MEDICAL TEACHER 2020;42:316-324. [PMID: 31747818 DOI: 10.1080/0142159x.2019.1686134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Vilas JL, Vargas J, Martinez M, Ramirez-Aportela E, Melero R, Jimenez-Moreno A, Garduño E, Conesa P, Marabini R, Maluenda D, Carazo JM, Sorzano COS. Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening. J Struct Biol 2020;209:107447. [PMID: 31911170 DOI: 10.1016/j.jsb.2020.107447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/29/2019] [Accepted: 01/01/2020] [Indexed: 11/24/2022]
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Vilas JL, Oton J, Messaoudi C, Melero R, Conesa P, Ramirez-Aportela E, Mota J, Martinez M, Jimenez A, Marabini R, Carazo JM, Vargas J, Sorzano COS. Measurement of local resolution in electron tomography. JOURNAL OF STRUCTURAL BIOLOGY-X 2019;4:100016. [PMID: 32647820 PMCID: PMC7337044 DOI: 10.1016/j.yjsbx.2019.100016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/13/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]
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Rahban R, Priskorn L, Senn A, Stettler E, Galli F, Vargas J, Van den Bergh M, Fusconi A, Garlantezec R, Jensen TK, Multigner L, Skakkebæk NE, Germond M, Jørgensen N, Nef S. Semen quality of young men in Switzerland: a nationwide cross-sectional population-based study. Andrology 2019;7:818-826. [PMID: 31115178 PMCID: PMC6790593 DOI: 10.1111/andr.12645] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/11/2019] [Accepted: 04/10/2019] [Indexed: 01/17/2023]
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Gomez-Blanco J, Kaur S, Ortega J, Vargas J. A robust approach to ab initio cryo-electron microscopy initial volume determination. J Struct Biol 2019;208:107397. [PMID: 31568828 DOI: 10.1016/j.jsb.2019.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
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Sorzano COS, Martínez-Muñoz L, Cascio G, García-Cuesta EM, Vargas J, Mellado M, Rodriguez Frade JM. Image Processing Protocol for the Analysis of the Diffusion and Cluster Size of Membrane Receptors by Fluorescence Microscopy. J Vis Exp 2019. [PMID: 31033950 DOI: 10.3791/59314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]  Open
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