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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
Abstract
In this study, we present a novel and robust methodology for the automatic detection of influenza A virus ribonucleoproteins (RNPs) in single-particle cryo-electron microscopy (cryo-EM) images. Utilizing a U-net architecture-a type of convolutional neural network renowned for its efficiency in biomedical image segmentation-our approach is based on a pretraining phase with a dataset annotated through visual inspection. This dataset facilitates the precise identification of filamentous RNPs, including the localization of the filaments and their terminal coordinates. A key feature of our method is the application of semantic segmentation techniques, enabling the automated categorization of micrograph pixels into distinct classifications of particle and background. This deep learning strategy allows to robustly detect these intricate particles, a crucial step in achieving high-resolution reconstructions in cryo-EM studies. To encourage collaborative advancements in the field, we have made our routines, the pretrained U-net model, and the training dataset publicly accessible. The reproducibility and accessibility of these resources aim to facilitate further research and validation in the realm of cryo-EM image analysis.
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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]
Abstract
This paper reports on investigations on the impact of higher neutron fluences on the detection efficiency of protons with CR-39, a charged particle track detector. CR-39 is widely used as a diagnostic for inertial fusion applications and is an integral component of numerous particle diagnostics at the OMEGA laser facility and National Ignition Facility. As experiments continue to produce higher and higher yields, existing diagnostics are impacted by higher particle fluences than they were originally designed for. This paper presents data from experiments measuring proton signal on pieces of CR-39 with different levels of neutron fluence with two different etch times. The experiments show a decrease in signal recovery with increased neutron fluence, which is exacerbated at longer etch times. At 3 h etch time, data suggest a 17% ± 7% signal loss at 1.3 × 105 neutron-induced tracks per cm2 and a 67% ± 21% loss at 6 h etch time. Careful signal isolation techniques can recover most of the proton tracks even with moderate neutron fluence.
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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]
Abstract
Image plates (IPs), or phosphor storage screens, are a technology employed frequently in inertial confinement fusion (ICF) and high energy density plasma (HEDP) diagnostics because of their sensitivity to many types of radiation, including, x rays, protons, alphas, beta particles, and neutrons. Prior studies characterizing IPs are predicated on the signal level remaining below the scanner saturation threshold. Since the scanning process removes some signal from the IP via photostimulated luminescence, repeatedly scanning an IP can bring the signal level below the scanner saturation threshold. This process, in turn, raises concerns about the signal response of IPs after an arbitrary number of scans and whether such a process yields, for example, a constant ratio of signal between the nth and n + 1st scan. Here, the sensitivity of IPs is investigated when scanned multiple times. It is demonstrated that the ratio of signal decay is not a constant with the number of scans and that the signal decay depends on the x-ray energy. As such, repeatedly scanning an IP with a mixture of signal types (e.g., x ray, neutron, and protons) enables ICF and HEDP diagnostics employing IPs to better isolate a particular signal type.
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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]
Abstract
Radiochromic film (RCF) and image plates (IPs) are both commonly used detectors in diagnostics fielded at inertial confinement fusion (ICF) and high-energy-density physics (HEDP) research facilities. Due to the intense x-ray background in all ICF/HEDP experiments, accurately calibrating the optical density of RCF as a function of x-ray dose, and the photostimulated luminescence per photon of IPs as a function of x-ray energy, is necessary for interpreting experimental results. Various measurements of the sensitivity curve of different IPs to x rays have been performed [Izumi et al., Proc. SPIE 8850, 885006 (2013) and Rosenberg et al., Rev. Sci. Instrum. 90(1), 013506 (2019)]; however, calibrating RCF is a tedious process that depends on factors such as the orientation in which the RCF is scanned in the film scanner and the batch of RCF used. These issues can be mitigated by cross-calibrating RCF with IPs to enable the use of IPs for the determination of dose on the RCF without scanning the RCF. Here, the first cross-calibration of RCF with IPs to quasi-monoenergetic titanium, copper, and molybdenum K-line x rays is presented. It is found that the IP-inferred dose rates on the RCF for the Ti and Mo x rays agree well with the measured dose rates, while the IP-inferred dose rate for the Cu x rays is larger than the measured dose rate by ∼2×. Explanations for this discrepancy and plans for future work are discussed.
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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]
Abstract
Image plates (IPs) are a quickly recoverable and reusable radiation detector often used to measure proton and x-ray fluence in laser-driven experiments. Recently, IPs have been used in a proton radiography detector stack on the OMEGA laser, a diagnostic historically implemented with CR-39, or radiochromic film. The IPs used in this and other diagnostics detect charged particles, neutrons, and x-rays indiscriminately. IPs detect radiation using a photo-stimulated luminescence (PSL) material, often phosphor, in which electrons are excited to metastable states by ionizing radiation. Protons at MeV energies deposit energy deeper into the IP compared with x rays below ∼20 keV due to the Bragg peak present for protons. This property is exploited to discriminate between radiation types. Doses of mono-energetic protons between 1.7 and 14 MeV are applied to IPs using the MIT linear electrostatic ion accelerator. This paper presents the results from consecutive scans of IPs irradiated with different proton energies. The PSL ratios between subsequent scans are shown to depend on proton energy, with higher energy protons having lower PSL ratios for each scan. This finding is separate from the known energy dependence in the absolute sensitivity of IPs. The results can be compared to complimentary work on x rays, showing a difference between protons and x rays, forging a path to discriminate between proton and x-ray fluence in mixed radiation environments.
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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]
Abstract
Ernesto Bustamante Zuleta (1922-2021) was an impactful Colombian neurosurgeon whose legacy is inextricably linked with the development of the neurosurgery specialty in Colombia. His detail-oriented approach to treatment complemented his reputation for mastery of the neurosciences. Never simply confined to the operating theater, this calm and considerate physician felt compelled to teach during his entire career. The result of his teaching made a lasting imprint on an entire generation of neurosurgeons who subsequently established a high standard of neurosurgical care in Colombia. A true pioneer, Bustamante comprehensively engaged in his field, from founding the country's first residency program in neurosurgery to successfully implementing technology in his procedures, performing many of Colombia's first neurosurgical interventions, and publishing extensively across various categories of medical science. This historical reflection highlights his enduring contributions to the field and considers his legacy through the witness testimony of many of his students and collaborators. The hope is that his contributions may be acknowledged in full, as he was a reserved person who never boasted of his own accomplishments. The authors also hope that those who did not have the opportunity to know him would be informed by the historical context of the development of Colombian neurosurgery and inspired by his conviction and altruism.
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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]
Abstract
The history of Colombian neurosurgery is a collective legacy of neurosurgeon-scientists, scholars, teachers, innovators, and researchers. Anchored in the country's foundational values of self-determination and adaptability, these pioneers emerged from the Spanish colonial medical tradition and forged surgical alliances abroad. From the time of Colombian independence until the end of World War I, exchanges with the French medical tradition produced an emphasis on anatomical and systematic approaches to the emerging field of neurosurgery. The onset of American neurosurgical expertise in the 1930s led to a new period of exchange, wherein technological innovations were added to the Colombian neurosurgical repertoire. This diversity of influences culminated in the 1950s with the establishment of Colombia's first in-country neurosurgery residency program. A select group of avant-garde neurosurgeons from this period expanded the domestic opportunities for patients and practitioners alike. Today, the system counts 10 recognized neurosurgery residency programs and over 500 neurosurgeons within Colombia. Although the successes of specific individuals and innovations were considered, the primary purpose of this historical survey was to glean relevant lessons from the past that can inform present challenges, inspire new opportunities, and identify professional and societal goals for the future of neurosurgical practice and specialization.
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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]
Abstract
The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.
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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]
Abstract
The root mean square radii of the proton density distribution in ^{16-24}O derived from measurements of charge changing cross sections with a carbon target at ∼900A MeV together with the matter radii portray thick neutron skin for ^{22-24}O despite ^{22,24}O being doubly magic. Imprints of the shell closures at N=14 and 16 are reflected in local minima of their proton radii that provide evidence for the tensor interaction causing them. The radii agree with ab initio calculations employing the chiral NNLO_{sat} interaction, though skin thickness predictions are challenged. Shell model predictions agree well with the data.
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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]
Abstract
BACKGROUND AND OBJECTIVE Cryo-electron microscopy using single particle analysis is a powerful technique for obtaining 3D reconstructions of macromolecules in near native conditions. One of its major advances is its capacity to reveal conformations of dynamic molecular complexes. Most popular and successful current approaches to analyzing heterogeneous complexes are founded on Bayesian inference. However, these 3D classification methods require the tuning of specific parameters by the user and the use of complicated 3D re-classification procedures for samples affected by extensive heterogeneity. Thus, the success of these approaches highly depends on the user experience. We introduce a robust approach to identify many different conformations presented in a cryo-EM dataset based on Bayesian inference through Relion classification methods that does not require tuning of parameters and reclassification strategies. METHODS The algorithm allows both 2D and 3D classification and is based on a hierarchical clustering approach that runs automatically without requiring typical inputs, such as the number of conformations present in the dataset or the required classification iterations. This approach is applied to robustly determine the energy landscapes of macromolecules. RESULTS We tested the performance of the methods proposed here using four different datasets, comprising structurally homogeneous and highly heterogeneous cases. In all cases, the approach provided excellent results. The routines are publicly available as part of the CryoMethods plugin included in the Scipion package. CONCLUSIONS Our results show that the proposed method can be used to align and classify homogeneous and heterogeneous datasets without requiring previous alignment information or any prior knowledge about the number of co-existing conformations. The approach can be used for both 2D and 3D autoclassification and only requires an initial volume. In addition, the approach is robust to the "attractor" problem providing many different conformations/views for samples affected by extensive heterogeneity. The obtained 3D classes can render high resolution 3D structures, while the obtained energy landscapes can be used to determine structural trajectories.
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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]
Abstract
OBJECTIVE The COVID-19 lockdown led to the establishment of a national lockdown in France from March 17th to May 11th, 2020. The purpose of our study is to evaluate the impact of lockdown on the rate of hospitalization for threatened preterm delivery and on the rate of preterm delivery. METHODS Multicenter retrospective epidemiological study carried out over the lockdown period from March 15th to May 31st, 2020 compared to the same period over the previous two years (2018 and 2019) in Picardy hospitals (University Hospital center Amiens Picardie, Hospital Center of Beauvais, Compiègne and Saint-Quentin). RESULTS In total, 608 patients were included. Our study shows a decrease in hospitalisations (207 in 2019 vs. 176 in 2020). We find a significant reduction in Premature Ruptures of Membranes (16.9% [73/432] in 2018/2019 vs. 9.7% [17/176] in 2020; P=0.02) and also in the preterm delivery rate (9.3% (276/2961) in 2018/2019 vs. 6.8% [96/1416] in 2020; P<0.05). CONCLUSION A reduction in the rate of preterm birth is observed during the first lockdown's period. It would also be interesting to evaluate the psychological impact of lockdown.
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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]
Abstract
We explore Josephson-like dynamics of a Bose-Einstein condensate of rubidium atoms in the second Bloch band of an optical square lattice providing a double well structure with two inequivalent, degenerate energy minima. This oscillation is a direct signature of the orbital changing collisions predicted to arise in this system in addition to the conventional on-site collisions. The observed oscillation frequency scales with the relative strength of these collisional interactions, which can be readily tuned via a distortion of the unit cell. The observations are compared to a quantum model of two single-particle modes and to a semiclassical multiband tight-binding simulation of 12×12 tubular sites of the lattice. Both models reproduce the observed oscillatory dynamics and show the correct dependence of the oscillation frequency on the ratio between the strengths of the on-site and orbital changing collision processes.
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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]
Abstract
Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, i.e., the method is restricted to small deformations and cannot determine local patterns of flexibility of small elements, such as secondary structures, which we discuss in the manuscript.
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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]
Abstract
Taking benefit of the R3B/SOFIA setup to measure the mass and the nuclear charge of both fission fragments in coincidence with the total prompt-neutron multiplicity, the scission configurations are inferred along the thorium chain, from the asymmetric fission in the heavier isotopes to the symmetric fission in the neutron-deficient thorium. Against all expectations, the symmetric scission in the light thorium isotopes shows a compact configuration, which is in total contrast to what is known in the fission of the heavier thorium isotopes and heavier actinides. This new main symmetric scission mode is characterized by a significant drop in deformation energy of the fission fragments of about 19 MeV, compared to the well-known symmetric scission in the uranium-plutonium region.
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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]
Abstract
Introduction: A growing emphasis on humanistic medical care has led to the development of programs to imbue more humanistic values into training physicians. The ScribeMD intra-class pen pal program is a narrative medicine tool designed to meet this need with a focus on the journey through medical education. This study intends to evaluate the efficacy of this novel program on the participants' professional identity formation (PIF), emotional intelligence development (EID), and narrative competency improvement (NCI).Methods: This program evaluation involved quantitative and qualitative survey solicitations from first and second-year medical student participants and controls. An efficacy-triangulation model was developed as a quantitative outcome-measuring tool linking objective, writing prompts, and survey data.Results: The quantitative results showed statistically significant improvements in line with the Efficacy Triangulation Model in the participant group. Qualitatively, reflective and insight-driven gains were elicited, as were notable themes of personal and community improvements.Conclusion: ScribeMD poses a unique avenue for the development of more humanistic physicians during their medical education. We recommend additional development of the Efficacy Triangulation Model as well as the program design itself. We also recommend the piloting of this program in other healthcare-education settings both with medical education and other health professions.
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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]
Abstract
The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the so-called B-factor correction, which applies a global filter to boost high frequencies with some dampening considerations related to noise amplification. The results are maps with a better visual aspect and a quasiflat spectrum at medium and high frequencies. This practice is so widespread that most map depositions in the Electron Microscopy Data Base (EMDB) only contain sharpened maps. Here, the use in cryoEM of global B-factor corrections is theoretically and experimentally analyzed. Results clearly illustrate that protein spectra present a falloff. Thus, spectral quasi-flattening may produce protein spectra with distortions when compared with experimental ones, this fact, combined with the practice of reporting only sharpened maps, generates a sub-optimal situation in terms of data preservation, reuse and reproducibility. Now that the field is more advanced, we put forward two suggestions: (1) to use methods which keep more faithfully the original experimental signal properties of macromolecules when "enhancing" the map, and (2) to further stress the need to deposit the original experimental maps without any postprocessing or sharpening, not only the enhanced maps. In the absence of access to these original maps data is lost, preventing their future analysis with new methods.
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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]
Abstract
Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number. However, it is known that tomogram quality is spatially variant. Still, up to our knowledge, a method to estimate local quality metrics in tomography is lacking. This work introduces MonoTomo, a method developed to estimate locally in a tomogram the highest reliable frequency component, expressed as a form of local resolution. The fundamentals lie in a local analysis of the density map via monogenic signals, which, in analogy to MonoRes, allows for local estimations. Results with experimental data show that the local resolution range that MonoTomo casts agrees with reported resolution values for experimental data sets, with the advantage of providing a local estimation. A range of applications of MonoTomo are suggested for further exploration.
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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]
Abstract
BACKGROUND Sperm counts have been steadily decreasing over the past five decades with regional differences in the Western world. The reasons behind these trends are complex, but numerous insights indicate that environmental and lifestyle factors are important players. OBJECTIVE To evaluate semen quality and male reproductive health in Switzerland. MATERIALS AND METHODS A nationwide cross-sectional study was conducted on 2523 young men coming from all regions of Switzerland, recruited during military conscription. Semen volume, sperm concentration, motility, and morphology were analyzed. Anatomy of the genital area and testicular volume was recorded. Testicular cancer incidence rates in the general population were retrieved from Swiss regional registries. RESULTS Median sperm concentration adjusted for period of sexual abstinence was 48 million/mL. Comparing with the 5th percentile of the WHO reference values for fertile men, 17% of men had sperm concentration below 15 million/mL, 25% had less than 40% motile spermatozoa, and 43% had less than 4% normal forms. Disparities in semen quality among geographic regions, urbanization rates, and linguistic areas were limited. A larger proportion of men with poor semen quality had been exposed in utero to maternal smoking. Furthermore, testicular cancer incidence rates in the Swiss general population increased significantly between 1980 and 2014. DISCUSSION For the first time, a systematic sampling among young men has confirmed that semen quality is affected on a national level. The median sperm concentration measured is among the lowest observed in Europe. No specific geographical differences could be identified. Further studies are needed to determine to what extent the fertility of Swiss men is compromised and to evaluate the impact of environmental and lifestyle factors. CONCLUSION A significant proportion of Swiss young men display suboptimal semen quality with only 38% having sperm concentration, motility, and morphology values that met WHO semen reference criteria.
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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]
Abstract
Structural information from macromolecules provides key insights into the way complexes perform their biological functions. The reconstruction process leading to the final three-dimensional (3D) map is iterative and requires an initial volume to prime the refinement procedure. Particle images are aligned to this first reference and subsequently a new map is calculated from these particles. The accurate determination of an ab initio initial volume is still a challenging and open problem in cryo-electron microscopy (cryo-EM). Different algorithms are available to estimate an initial volume from the dataset. Some of these methods provide multiple candidate initial maps and users looking for robustness typically run different approaches. In this case, users arbitrarily evaluate the different obtained candidate maps, as we lack robust methods to objectively assess the accuracy of initial references. This workflow is subjective and error-prone preventing implementation of high-throughput data processing procedures. In this work, we present a robust method to determine the best initial map or maps from a set of ab initio initial volumes obtained from one or multiple different approaches. The method is based on evaluating multiple small subsets of candidate initial volumes and particle images through reference-based 3D classifications. Obtained 3D classes of accurate initial maps will result majoritarian and the respective attracted particles will be aligned with high angular accuracies. We have tested the proposed approach with structurally homogeneous and heterogeneous datasets providing satisfactory results with both type of data.
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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
Abstract
Particle tracking on a video sequence and the posterior analysis of their trajectories is nowadays a common operation in many biological studies. Using the analysis of cell membrane receptor clusters as a model, we present a detailed protocol for this image analysis task using Fiji (ImageJ) and Matlab routines to: 1) define regions of interest and design masks adapted to these regions; 2) track the particles in fluorescence microscopy videos; 3) analyze the diffusion and intensity characteristics of selected tracks. The quantitative analysis of the diffusion coefficients, types of motion, and cluster size obtained by fluorescence microscopy and image processing provides a valuable tool to objectively determine particle dynamics and the consequences of modifying environmental conditions. In this article we present detailed protocols for the analysis of these features. The method described here not only allows single-molecule tracking detection, but also automates the estimation of lateral diffusion parameters at the cell membrane, classifies the type of trajectory and allows complete analysis thus overcoming the difficulties in quantifying spot size over its entire trajectory at the cell membrane.
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