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1. Resolving non-equilibrium shape variations amongst millions of gold nanoparticles

Author

Shen, Zhou, Awel, Salah, Barty, Anton, Bean, Richard, Bielecki, Johan, Bergemann, Martin, Daurer, Benedikt J., Ekeberg, Tomas, Estillore, Armando D., Fangohr, Hans, Giewekemeyer, Klaus, Hunter, Mark S., Karnevskiy, Mikhail, Kirian, Richard A., Kirkwood, Henry, Kim, Yoonhee, Koliyadu, Jayanath, Lange, Holger, Letrun, Romain, Lübke, Jannik, Mall, Abhishek, Michelat, Thomas, Morgan, Andrew J., Roth, Nils, Samanta, Amit K., Sato, Tokushi, Sikorski, Marcin, Schulz, Florian, Vagovic, Patrik, Wollweber, Tamme, Worbs, Lena, Xavier, Paul Lourdu, Maia, Filipe R. N. C., Horke, Daniel A., Küpper, Jochen, Mancuso, Adrian P., Chapman, Henry N., Ayyer, Kartik, and Loh, N. Duane

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with x-ray free-electron lasers (XFELs) creates unprecedented opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between $10^5$ structural models and $10^6$ XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the non-equilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable `shape envelope' amongst nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles' shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.

Published
2024

8. SARS-CoV-2 Mpro responds to oxidation by forming disulfide and NOS/SONOS bonds

Author

Reinke, Patrick Y. A., Schubert, Robin, Oberthür, Dominik, Galchenkova, Marina, Rahmani Mashhour, Aida, Günther, Sebastian, Chretien, Anaïs, Round, Adam, Seychell, Brandon Charles, Norton-Baker, Brenna, Kim, Chan, Schmidt, Christina, Koua, Faisal H. M., Tolstikova, Alexandra, Ewert, Wiebke, Peña Murillo, Gisel Esperanza, Mills, Grant, Kirkwood, Henry, Brognaro, Hévila, Han, Huijong, Koliyadu, Jayanath, Schulz, Joachim, Bielecki, Johan, Lieske, Julia, Maracke, Julia, Knoska, Juraj, Lorenzen, Kristina, Brings, Lea, Sikorski, Marcin, Kloos, Marco, Vakili, Mohammad, Vagovic, Patrik, Middendorf, Philipp, de Wijn, Raphael, Bean, Richard, Letrun, Romain, Han, Seonghyun, Falke, Sven, Geng, Tian, Sato, Tokushi, Srinivasan, Vasundara, Kim, Yoonhee, Yefanov, Oleksandr M., Gelisio, Luca, Beck, Tobias, Doré, Andrew S., Mancuso, Adrian P., Betzel, Christian, Bajt, Saša, Redecke, Lars, Chapman, Henry N., Meents, Alke, Turk, Dušan, Hinrichs, Winfried, and Lane, Thomas J.

Published
2024
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12. Association between satellite-detected tropospheric nitrogen dioxide and acute respiratory infections in children under age five in Senegal: spatio-temporal analysis

Author

Kawano, Ayako, Kim, Yoonhee, Meas, Michelle, and Sokal-Gutierrez, Karen

Subjects
Epidemiology, Health Services and Systems, Public Health, Health Sciences, Prevention, Lung, Pediatric, Clinical Research, Aetiology, 2.2 Factors relating to the physical environment, Good Health and Well Being, Air Pollutants, Air Pollution, Child, Environmental Exposure, Humans, Nitrogen Dioxide, Particulate Matter, Respiratory Tract Infections, Senegal, Spatio-Temporal Analysis, Nitrogen dioxide, Acute respiratory infections, Sentinel-5P, Sub-Saharan Africa, Public Health and Health Services, Health services and systems, Public health
Abstract

BackgroundThere is growing evidence to suggest that exposure to a high concentration of nitrogen dioxide (NO2) can lead to a higher incidence of Acute Respiratory Infections (ARIs) in children; however, such an association remains understudied in Sub-Saharan Africa due to the limited availability of exposure data. This study explored this association by using the satellite-detected tropospheric NO2 concentrations measured by Sentinel-5 Precursor and ARI symptoms in children under age five collected in the Demographic and Health Survey (DHS) in Senegal.MethodsWe matched the daily tropospheric NO2 exposure with the individual ARI symptoms according to the DHS survey clusters spatially and temporally and conducted a logistic regression analysis to estimate the association of exposure to NO2 with ARI symptoms in two preceding weeks.ResultsWe observed a positive association between exposure to continuous levels of NO2 and ARI symptoms after adjusting for confounders (OR 1.27 per 10 mol/m2, 95% CI: 1.06 - 1.52). When the association was further examined by quartile exposure categories, the 4th quartile category was positively associated with symptoms of ARI after adjusting for confounders (OR 1.71, 95% CI: 1.08-2.69). This suggests that exposure to certain high levels of NO2 is associated with the increased risk of children having symptoms of ARI in Senegal.ConclusionsThis study highlights the need for increased research on the effects of ambient NO2 exposure in Africa as well as the need for more robust, ground-based air monitoring in the region. For a country like Senegal, where more than 90% of the population lives in areas that do not meet the national air quality standards, it is urgently required to implement air pollution prevention efforts to protect children from the health hazards of air pollution.

Published
2022

13. Unsupervised learning approaches to characterize heterogeneous samples using X-ray single particle imaging

Author

Zhuang, Yulong, Awel, Salah, Barty, Anton, Bean, Richard, Bielecki, Johan, Bergemann, Martin, Daurer, Benedikt J., Ekeberg, Tomas, Estillore, Armando D., Fangohr, Hans, Giewekemeyer, Klaus, Hunter, Mark S., Karnevskiy, Mikhail, Kirian, Richard A., Kirkwood, Henry, Kim, Yoonhee, Koliyadu, Jayanath, Lange, Holger, Letrun, Romain, Lübke, Jannik, Mall, Abhishek, Michelat, Thomas, Morgan, Andrew J., Roth, Nils, Samanta, Amit K., Sato, Tokushi, Shen, Zhou, Sikorski, Marcin, Schulz, Florian, Spence, John C. H., Vagovic, Patrik, Wollweber, Tamme, Worbs, Lena, Xavier, P. Lourdu, Yefanov, Oleksandr, Maia, Filipe R. N. C., Horke, Daniel A., Küpper, Jochen, Loh, N. Duane, Mancuso, Adrian P., Chapman, Henry N., and Ayyer, Kartik

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Data Analysis, Statistics and Probability
Abstract

One of the outstanding analytical problems in X-ray single particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. We propose two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA) provides a rough classification which is essentially parameter-free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs) can generate 3D structures of the objects at any point in the structural landscape. We implement both these methods in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and demonstrate its utility by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern and recover both discrete structural classes as well as continuous deformations. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility to move beyond studying homogeneous sample sets and study open questions on topics such as nanocrystal growth and dynamics as well as phase transitions which have not been externally triggered., Comment: 29 pages, 9 figures

Published
2021

14. Temperature frequency and mortality: Assessing adaptation to local temperature

Author

Overcenco, Ala, Urban, Aleš, Schneider, Alexandra, Entezari, Alireza, Vicedo-Cabrera, Ana Maria, Zanobetti, Antonella, Analitis, Antonis, Zeka, Ariana, Tobias, Aurelio, Nunes, Baltazar, Alahmad, Barrak, Forsberg, Bertil, Íñiguez, Carmen, Ameling, Caroline, la Cruz Valencia, César De, Houthuijs, Danny, Van Dung, Do, Roye, Dominic, Indermitte, Ene, Mayvaneh, Fatemeh, Acquaotta, Fiorella, de'Donato, Francesca, Carrasco-Escobar, Gabriel, Kan, Haidong, Carlsen, Hanne Krage, Orru, Hans, Kim, Ho, Holobaca, Iulian-Horia, Kyselý, Jan, Madureira, Joana, Schwartz, Joel, Jaakkola, Jouni J.K., Katsouyanni, Klea, Diaz, Magali Hurtado, Ragettli, Martina S., Hashizume, Masahiro, Pascal, Mathilde, de Sousa Zanotti Stagliorio Coelho, Micheline, Ortega, Nicolás Valdés, Ryti, Niilo, Scovronick, Noah, Michelozzi, Paola, Correa, Patricia Matus, Goodman, Patrick, Nascimento Saldiva, Paulo Hilario, Raz, Raanan, Abrutzky, Rosana, Osorio, Samuel, Pan, Shih-Chun, Rao, Shilpa, Tong, Shilu, Achilleos, Souzana, Dang, Tran Ngoc, Colistro, Valentina, Huber, Veronika, Lee, Whanhee, Seposo, Xerxes, Honda, Yasushi, Kim, Yoonhee, Guo, Yue Leon, Li, Shanshan, Guo, Yuming, Wu, Yao, Wen, Bo, Gasparrini, Antonio, Armstrong, Ben, Sera, Francesco, and Lavigne, Eric

Published
2024
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15. Comparison for the effects of different components of temperature variability on mortality: A multi-country time-series study

Author

Wen, Bo, Wu, Yao, Guo, Yuming, Gasparrini, Antonio, Tong, Shilu, Overcenco, Ala, Urban, Aleš, Schneider, Alexandra, Entezari, Alireza, Vicedo-Cabrera, Ana Maria, Zanobetti, Antonella, Analitis, Antonis, Zeka, Ariana, Tobias, Aurelio, Nunes, Baltazar, Alahmad, Barrak, Armstrong, Ben, Forsberg, Bertil, Pan, Shih-Chun, Íñiguez, Carmen, Ameling, Caroline, Valencia, César De la Cruz, Åström, Christofer, Houthuijs, Danny, Van Dung, Do, Royé, Dominic, Indermitte, Ene, Lavigne, Eric, Mayvaneh, Fatemeh, Acquaotta, Fiorella, de’Donato, Francesca, Rao, Shilpa, Sera, Francesco, Carrasco-Escobar, Gabriel, Kan, Haidong, Orru, Hans, Kim, Ho, Holobaca, Iulian-Horia, Kyselý, Jan, Madureira, Joana, Schwartz, Joel, Jaakkola, Jouni J.K., Katsouyanni, Klea, Diaz, Magali Hurtado, Ragettli, Martina S., Hashizume, Masahiro, Pascal, Mathilde, Coélho, Micheline de Sousa Zanotti Stagliorio, Ortega, Nicolás Valdés, Ryti, Niilo, Scovronick, Noah, Michelozzi, Paola, Matus Correa, Patricia, Goodman, Patrick, Saldiva, Paulo Hilario Nascimento, Raz, Raanan, Abrutzky, Rosana, Osorio, Samuel, Dang, Tran Ngoc, Colistro, Valentina, Huber, Veronika, Lee, Whanhee, Seposo, Xerxes, Honda, Yasushi, Kim, Yoonhee, Guo, Yue Leon, Bell, Michelle L., and Li, Shanshan

Published
2024
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18. Advances in methylation analysis of liquid biopsy in early cancer detection of colorectal and lung cancer

Author

Kwon, Hyuk-Jung, Shin, Sun Hye, Kim, Hyun Ho, Min, Na Young, Lim, YuGyeong, Joo, Tae-woon, Lee, Kyoung Joo, Jeong, Min-Seon, Kim, Hyojung, Yun, Seon-young, Kim, YoonHee, Park, Dabin, Joo, Joungsu, Bae, Jin-Sik, Lee, Sunghoon, Jeong, Byeong-Ho, Lee, Kyungjong, Lee, Hayemin, Kim, Hong Kwan, Kim, Kyongchol, Um, Sang-Won, An, Changhyeok, and Lee, Min Seob

Published
2023
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19. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS)

Author

Blanchet, Clement E., Round, Adam, Mertens, Haydyn D. T., Ayyer, Kartik, Graewert, Melissa, Awel, Salah, Franke, Daniel, Dörner, Katerina, Bajt, Saša, Bean, Richard, Custódio, Tânia F., de Wijn, Raphael, Juncheng, E., Henkel, Alessandra, Gruzinov, Andrey, Jeffries, Cy M., Kim, Yoonhee, Kirkwood, Henry, Kloos, Marco, Knoška, Juraj, Koliyadu, Jayanath, Letrun, Romain, Löw, Christian, Makroczyova, Jana, Mall, Abhishek, Meijers, Rob, Pena Murillo, Gisel Esperanza, Oberthür, Dominik, Round, Ekaterina, Seuring, Carolin, Sikorski, Marcin, Vagovic, Patrik, Valerio, Joana, Wollweber, Tamme, Zhuang, Yulong, Schulz, Joachim, Haas, Heinrich, Chapman, Henry N., Mancuso, Adrian P., and Svergun, Dmitri

Published
2023
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20. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

Author

Holmes, Susannah, Kirkwood, Henry J, Bean, Richard, Giewekemeyer, Klaus, Martin, Andrew V, Hadian-Jazi, Marjan, Wiedorn, Max O, Oberthür, Dominik, Marman, Hugh, Adriano, Luigi, Al-Qudami, Nasser, Bajt, Saša, Barák, Imrich, Bari, Sadia, Bielecki, Johan, Brockhauser, Sandor, Coleman, Mathew A, Cruz-Mazo, Francisco, Danilevski, Cyril, Dörner, Katerina, Gañán-Calvo, Alfonso M, Graceffa, Rita, Fanghor, Hans, Heymann, Michael, Frank, Matthias, Kaukher, Alexander, Kim, Yoonhee, Kobe, Bostjan, Knoška, Juraj, Laurus, Torsten, Letrun, Romain, Maia, Luis, Messerschmidt, Marc, Metz, Markus, Michelat, Thomas, Mills, Grant, Molodtsov, Serguei, Monteiro, Diana CF, Morgan, Andrew J, Münnich, Astrid, Peña Murillo, Gisel E, Previtali, Gianpietro, Round, Adam, Sato, Tokushi, Schubert, Robin, Schulz, Joachim, Shelby, Megan, Seuring, Carolin, Sellberg, Jonas A, Sikorski, Marcin, Silenzi, Alessandro, Stern, Stephan, Sztuk-Dambietz, Jola, Szuba, Janusz, Trebbin, Martin, Vagovic, Patrick, Ve, Thomas, Weinhausen, Britta, Wrona, Krzysztof, Xavier, Paul Lourdu, Xu, Chen, Yefanov, Oleksandr, Nugent, Keith A, Chapman, Henry N, Mancuso, Adrian P, Barty, Anton, Abbey, Brian, and Darmanin, Connie

Subjects
Inorganic Chemistry, Chemical Sciences, Physical Sciences, Biological Sciences, Crystallography, X-Ray, Electrons, Lasers, Radiography, X-Rays
Abstract

The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by

Published
2022

22. Fluctuating risk of acute kidney injury-related mortality for four weeks after exposure to air pollution: A multi-country time-series study in 6 countries

Author

Min, Jieun, Kang, Duk-Hee, Kang, Cinoo, Bell, Michelle L., Kim, Ho, Yang, Juyeon, Gasparrini, Antonio, Lavigne, Eric, Hashizume, Masahiro, Kim, Yoonhee, Fook Sheng Ng, Chris, Honda, Yasushi, das Neves Pereira da Silva, Susana, Madureira, Joana, Leon Guo, Yue, Pan, Shih-Chun, Armstrong, Ben, Sera, Francesco, Masselot, Pierre, Schwartz, Joel, Maria Vicedo-Cabrera, Ana, Pyo Lee, Jung, Al-Aly, Ziyad, Won Lee, Jung, Kwag, Youngrin, Ha, Eunhee, and Lee, Whanhee

Published
2024
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23. 3D diffractive imaging of nanoparticle ensembles using an X-ray laser

Author

Ayyer, Kartik, Xavier, P. Lourdu, Bielecki, Johan, Shen, Zhou, Daurer, Benedikt J., Samanta, Amit K., Awel, Salah, Bean, Richard, Barty, Anton, Ekeberg, Tomas, Estillore, Armando D., Giewekemeyer, Klaus, Hunter, Mark S., Kirian, Richard A., Kirkwood, Henry, Kim, Yoonhee, Koliyadu, Jayanath, Lange, Holger, Letruin, Romain, Lübke, Jannik, Morgan, Andrew J., Roth, Nils, Sato, Tokushi, Sikorski, Marcin, Schulz, Florian, Spence, John C. H., Vagovic, Patrik, Wollweber, Tamme, Worbs, Lena, Yefanov, Oleksandr, Zhuang, Yulong, Maia, Filipe R. N. C., Horke, Daniel A., Küpper, Jochen, Loh, N. Duane, Mancuso, Adrian P., and Chapman, Henry N.

Subjects
Physics - Applied Physics, Electrical Engineering and Systems Science - Image and Video Processing, Physics - Optics
Abstract

We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 times the amount of data in any single prior SPI experiment, using the new capabilities of the European X-ray free electron laser which allow measurements of 1500 frames per second. A classification and structural sorting method was developed to disentangle the heterogeneity of the particles and to obtain a resolution of better than 3 nm. With these new experimental and analytical developments, we have entered a new era for the SPI method and the path towards close-to-atomic resolution imaging of biomolecules is apparent., Comment: 25 pages, 5 main figures, 6 supplementary figures, 2 supplementary movies (link in document)

Published
2020

24. Megahertz single-particle imaging at the European XFEL

Author

Sobolev, Egor, Zolotarev, Serguey, Giewekemeyer, Klaus, Bielecki, Johan, Okamoto, Kenta, Reddy, Hemanth K. N., Andreasson, Jakob, Ayyer, Kartik, Barak, Imrich, Bari, Sadia, Barty, Anton, Bean, Richard, Bobkov, Sergey, Chapman, Henry N., Chojnowski, Grzegorz, Daurer, Benedikt J., Dörner, Katerina, Ekeberg, Tomas, Flückiger, Leonie, Galzitskaya, Oxana, Gelisio, Luca, Hauf, Steffen, Hogue, Brenda G., Horke, Daniel A., Hosseinizadeh, Ahmad, Ilyin, Vyacheslav, Jung, Chulho, Kim, Chan, Kim, Yoonhee, Kirian, Richard A., Kirkwood, Henry, Kulyk, Olena, Letrun, Romain, Loh, Duane, Messerschmidt, Marc, Mühlig, Kerstin, Ourmazd, Abbas, Raab, Natascha, Rode, Andrei V., Rose, Max, Round, Adam, Sato, Takushi, Schubert, Robin, Schwander, Peter, Sellberg, Jonas A., Sikorski, Marcin, Silenzi, Alessandro, Song, Changyong, Spence, John C. H., Stern, Stephan, Sztuk-Dambietz, Jolanta, Teslyuk, Anthon, Timneanu, Nicusor, Trebbin, Martin, Uetrecht, Charlotte, Weinhausen, Britta, Williams, Garth J., Xavier, P Lourdu, Xu, Chen, Vartanyants, Ivan, Lamzin, Victor, Mancuso, Adrian, and Maia, Filipe R. N. C.

Subjects
Physics - Instrumentation and Detectors, Physics - Biological Physics
Abstract

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL will soon provide 27,000 pulses per second, more than two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The obtained results pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

Published
2019
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26. Projections of Temperature-Related Suicide under Climate Change Scenarios in Japan

Author

Thawonmas, Ramita, Hashizume, Masahiro, and Kim, Yoonhee

Subjects
Mortality -- Japan, Mental health -- Analysis -- Models -- Health aspects, Global temperature changes -- Analysis -- Health aspects -- Models, Suicide -- Models -- Analysis -- Health aspects, Environmental issues, Health, World Health Organization
Abstract

Background: The impact of climate change on mental health largely remains to be evaluated. Although growing evidence has reported a short-term association between suicide and temperature, future projections of temperature- attributable suicide have not been thoroughly examined. Objectives: We aimed to project the excess temperature-related suicide mortality in Japan under three climate change scenarios until the 2090s. Methods: Daily time series of mean temperature and the number of suicide deaths in 1973-2015 were collected for 47 prefectures in Japan. A two-stage time-stratified case-crossover analysis was used to estimate the temperature- suicide association. We obtained the modeled daily temperature series using five general circulation models under three climate change scenarios from the latest Coupled Model Intercomparison Project Phase 6 (CMIP6) Shared Socioeconomic Pathways scenarios (SSPs): SSP1-2.6, SSP2-4.5, and SSP5-8.5. We projected the excess temperature-related suicide mortality until 2099 for each scenario and evaluated the net relative changes compared with the 2010s. Results: During 1973-2015, there was a total of 1,049,592 suicides in Japan. Net increases in temperature-related excess suicide mortality were estimated under all scenarios. The net change in 2090-2099 compared with 2010-2019 was 1.3% [95% empirical confidence interval (eCI): 0.6, 2.4] for the intermediate-emission scenario (SSP2-4.5), 0.6% (95% eCI: 0.1, 1.6) for a low-emission scenario (SSP1-2.6), and 2.4% (95% eCI: 0.7, 3.9) for the extreme scenario (SSP5-8.5). The increases were greater the more extreme the scenarios were, with the highest increase under the most extreme scenario (SSP5-8.5). Discussion: This study indicates that Japan may experience a net increase in excess temperature-related suicide mortality, especially under the intermediate and extreme scenarios. The findings underscore the importance of mitigation policies. Further investigations of the future impacts of climate change on mental health including suicide are warranted. https://doi.org/10.1289/EHP11246, Introduction Climate change is one of the most important global challenges of the 21st century (1) affecting human health. A growing number of studies have investigated the impacts of climate [...]

Published
2023
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28. Megahertz single-particle imaging at the European XFEL

Author

Sobolev, Egor, Zolotarev, Sergei, Giewekemeyer, Klaus, Bielecki, Johan, Okamoto, Kenta, Reddy, Hemanth KN, Andreasson, Jakob, Ayyer, Kartik, Barak, Imrich, Bari, Sadia, Barty, Anton, Bean, Richard, Bobkov, Sergey, Chapman, Henry N, Chojnowski, Grzegorz, Daurer, Benedikt J, Dörner, Katerina, Ekeberg, Tomas, Flückiger, Leonie, Galzitskaya, Oxana, Gelisio, Luca, Hauf, Steffen, Hogue, Brenda G, Horke, Daniel A, Hosseinizadeh, Ahmad, Ilyin, Vyacheslav, Jung, Chulho, Kim, Chan, Kim, Yoonhee, Kirian, Richard A, Kirkwood, Henry, Kulyk, Olena, Küpper, Jochen, Letrun, Romain, Loh, N Duane, Lorenzen, Kristina, Messerschmidt, Marc, Mühlig, Kerstin, Ourmazd, Abbas, Raab, Natascha, Rode, Andrei V, Rose, Max, Round, Adam, Sato, Takushi, Schubert, Robin, Schwander, Peter, Sellberg, Jonas A, Sikorski, Marcin, Silenzi, Alessandro, Song, Changyong, Spence, John CH, Stern, Stephan, Sztuk-Dambietz, Jolanta, Teslyuk, Anthon, Timneanu, Nicusor, Trebbin, Martin, Uetrecht, Charlotte, Weinhausen, Britta, Williams, Garth J, Xavier, P Lourdu, Xu, Chen, Vartanyants, Ivan A, Lamzin, Victor S, Mancuso, Adrian, and Maia, Filipe RNC

Abstract

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

Published
2020

32. Time-resolved serial femtosecond crystallography at the European XFEL

Author

Pandey, Suraj, Bean, Richard, Sato, Tokushi, Poudyal, Ishwor, Bielecki, Johan, Cruz Villarreal, Jorvani, Yefanov, Oleksandr, Mariani, Valerio, White, Thomas A, Kupitz, Christopher, Hunter, Mark, Abdellatif, Mohamed H, Bajt, Saša, Bondar, Valerii, Echelmeier, Austin, Doppler, Diandra, Emons, Moritz, Frank, Matthias, Fromme, Raimund, Gevorkov, Yaroslav, Giovanetti, Gabriele, Jiang, Man, Kim, Daihyun, Kim, Yoonhee, Kirkwood, Henry, Klimovskaia, Anna, Knoska, Juraj, Koua, Faisal HM, Letrun, Romain, Lisova, Stella, Maia, Luis, Mazalova, Victoria, Meza, Domingo, Michelat, Thomas, Ourmazd, Abbas, Palmer, Guido, Ramilli, Marco, Schubert, Robin, Schwander, Peter, Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Tolstikova, Alexandra, Chapman, Henry N, Ros, Alexandra, Barty, Anton, Fromme, Petra, Mancuso, Adrian P, and Schmidt, Marius

Subjects
Biochemistry and Cell Biology, Biological Sciences, Bacterial Proteins, Crystallography, X-Ray, Light, Models, Molecular, Photoreceptors, Microbial, Protein Conformation, Time Factors, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

The European XFEL (EuXFEL) is a 3.4-km long X-ray source, which produces femtosecond, ultrabrilliant and spatially coherent X-ray pulses at megahertz (MHz) repetition rates. This X-ray source has been designed to enable the observation of ultrafast processes with near-atomic spatial resolution. Time-resolved crystallographic investigations on biological macromolecules belong to an important class of experiments that explore fundamental and functional structural displacements in these molecules. Due to the unusual MHz X-ray pulse structure at the EuXFEL, these experiments are challenging. Here, we demonstrate how a biological reaction can be followed on ultrafast timescales at the EuXFEL. We investigate the picosecond time range in the photocycle of photoactive yellow protein (PYP) with MHz X-ray pulse rates. We show that difference electron density maps of excellent quality can be obtained. The results connect the previously explored femtosecond PYP dynamics to timescales accessible at synchrotrons. This opens the door to a wide range of time-resolved studies at the EuXFEL.

Published
2020

33. Author Correction: Membrane protein megahertz crystallography at the European XFEL

Author

Gisriel, Chris, Coe, Jesse, Letrun, Romain, Yefanov, Oleksandr M, Luna-Chavez, Cesar, Stander, Natasha E, Lisova, Stella, Mariani, Valerio, Kuhn, Manuela, Aplin, Steve, Grant, Thomas D, Dörner, Katerina, Sato, Tokushi, Echelmeier, Austin, Villarreal, Jorvani Cruz, Hunter, Mark S, Wiedorn, Max O, Knoska, Juraj, Mazalova, Victoria, Roy-Chowdhury, Shatabdi, Yang, Jay-How, Jones, Alex, Bean, Richard, Bielecki, Johan, Kim, Yoonhee, Mills, Grant, Weinhausen, Britta, Meza, Jose D, Al-Qudami, Nasser, Bajt, Saša, Brehm, Gerrit, Botha, Sabine, Boukhelef, Djelloul, Brockhauser, Sandor, Bruce, Barry D, Coleman, Matthew A, Danilevski, Cyril, Discianno, Erin, Dobson, Zachary, Fangohr, Hans, Martin-Garcia, Jose M, Gevorkov, Yaroslav, Hauf, Steffen, Hosseinizadeh, Ahmad, Januschek, Friederike, Ketawala, Gihan K, Kupitz, Christopher, Maia, Luis, Manetti, Maurizio, Messerschmidt, Marc, Michelat, Thomas, Mondal, Jyotirmoy, Ourmazd, Abbas, Previtali, Gianpietro, Sarrou, Iosifina, Schön, Silvan, Schwander, Peter, Shelby, Megan L, Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Turcato, Monica, White, Thomas A, Wrona, Krzysztof, Xu, Chen, Abdellatif, Mohamed H, Zook, James D, Spence, John CH, Chapman, Henry N, Barty, Anton, Kirian, Richard A, Frank, Matthias, Ros, Alexandra, Schmidt, Marius, Fromme, Raimund, Mancuso, Adrian P, Fromme, Petra, and Zatsepin, Nadia A

Subjects
Biochemistry and Cell Biology, Biological Sciences
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

36. Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles

Author

Shen, Zhou, primary, Xavier, Paul Lourdu, additional, Bean, Richard, additional, Bielecki, Johan, additional, Bergemann, Martin, additional, Daurer, Benedikt J., additional, Ekeberg, Tomas, additional, Estillore, Armando D., additional, Fangohr, Hans, additional, Giewekemeyer, Klaus, additional, Karnevskiy, Mikhail, additional, Kirian, Richard A., additional, Kirkwood, Henry, additional, Kim, Yoonhee, additional, Koliyadu, Jayanath C. P., additional, Lange, Holger, additional, Letrun, Romain, additional, Lübke, Jannik, additional, Mall, Abhishek, additional, Michelat, Thomas, additional, Morgan, Andrew J., additional, Roth, Nils, additional, Samanta, Amit K., additional, Sato, Tokushi, additional, Sikorski, Marcin, additional, Schulz, Florian, additional, Vagovic, Patrik, additional, Wollweber, Tamme, additional, Worbs, Lena, additional, Maia, Filipe, additional, Horke, Daniel Alfred, additional, Küpper, Jochen, additional, Mancuso, Adrian P., additional, Chapman, Henry, additional, Ayyer, Kartik, additional, and Loh, N. Duane, additional

Published
2024
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38. Membrane protein megahertz crystallography at the European XFEL

Author

Gisriel, Chris, Coe, Jesse, Letrun, Romain, Yefanov, Oleksandr M, Luna-Chavez, Cesar, Stander, Natasha E, Lisova, Stella, Mariani, Valerio, Kuhn, Manuela, Aplin, Steve, Grant, Thomas D, Dörner, Katerina, Sato, Tokushi, Echelmeier, Austin, Cruz Villarreal, Jorvani, Hunter, Mark S, Wiedorn, Max O, Knoska, Juraj, Mazalova, Victoria, Roy-Chowdhury, Shatabdi, Yang, Jay-How, Jones, Alex, Bean, Richard, Bielecki, Johan, Kim, Yoonhee, Mills, Grant, Weinhausen, Britta, Meza, Jose D, Al-Qudami, Nasser, Bajt, Saša, Brehm, Gerrit, Botha, Sabine, Boukhelef, Djelloul, Brockhauser, Sandor, Bruce, Barry D, Coleman, Matthew A, Danilevski, Cyril, Discianno, Erin, Dobson, Zachary, Fangohr, Hans, Martin-Garcia, Jose M, Gevorkov, Yaroslav, Hauf, Steffen, Hosseinizadeh, Ahmad, Januschek, Friederike, Ketawala, Gihan K, Kupitz, Christopher, Maia, Luis, Manetti, Maurizio, Messerschmidt, Marc, Michelat, Thomas, Mondal, Jyotirmoy, Ourmazd, Abbas, Previtali, Gianpietro, Sarrou, Iosifina, Schön, Silvan, Schwander, Peter, Shelby, Megan L, Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Turcato, Monica, White, Thomas A, Wrona, Krzysztof, Xu, Chen, Abdellatif, Mohamed H, Zook, James D, Spence, John CH, Chapman, Henry N, Barty, Anton, Kirian, Richard A, Frank, Matthias, Ros, Alexandra, Schmidt, Marius, Fromme, Raimund, Mancuso, Adrian P, Fromme, Petra, and Zatsepin, Nadia A

Subjects
Biochemistry and Cell Biology, Biological Sciences, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Crystallography, Cyanobacteria, Electrons, Lasers, Membrane Proteins, Models, Molecular, Photosystem I Protein Complex, Static Electricity, Synchrotrons, Thermosynechococcus, X-Rays
Abstract

The world's first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.

Published
2019

41. A multi-million image Serial Femtosecond Crystallography dataset collected at the European XFEL

Author

Kirkwood, Henry J., de Wijn, Raphael, Mills, Grant, Letrun, Romain, Kloos, Marco, Vakili, Mohammad, Karnevskiy, Mikhail, Ahmed, Karim, Bean, Richard J., Bielecki, Johan, Dall’Antonia, Fabio, Kim, Yoonhee, Kim, Chan, Koliyadu, Jayanath, Round, Adam, Sato, Tokushi, Sikorski, Marcin, Vagovič, Patrik, Sztuk-Dambietz, Jolanta, and Mancuso, Adrian P.

Published
2022
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43. Megahertz serial crystallography

Author

Wiedorn, Max O, Oberthür, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allahgholi, Aschkan, Al-Qudami, Nasser, Andreasson, Jakob, Aplin, Steve, Awel, Salah, Ayyer, Kartik, Bajt, Saša, Barák, Imrich, Bari, Sadia, Bielecki, Johan, Botha, Sabine, Boukhelef, Djelloul, Brehm, Wolfgang, Brockhauser, Sandor, Cheviakov, Igor, Coleman, Matthew A, Cruz-Mazo, Francisco, Danilevski, Cyril, Darmanin, Connie, Doak, R Bruce, Domaracky, Martin, Dörner, Katerina, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Gañán-Calvo, Alfonso M, Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen Mary, Graafsma, Heinz, Graceffa, Rita, Greiffenberg, Dominic, Gumprecht, Lars, Göttlicher, Peter, Hajdu, Janos, Hauf, Steffen, Heymann, Michael, Holmes, Susannah, Horke, Daniel A, Hunter, Mark S, Imlau, Siegfried, Kaukher, Alexander, Kim, Yoonhee, Klyuev, Alexander, Knoška, Juraj, Kobe, Bostjan, Kuhn, Manuela, Kupitz, Christopher, Küpper, Jochen, Lahey-Rudolph, Janine Mia, Laurus, Torsten, Le Cong, Karoline, Letrun, Romain, Xavier, P Lourdu, Maia, Luis, Maia, Filipe RNC, Mariani, Valerio, Messerschmidt, Marc, Metz, Markus, Mezza, Davide, Michelat, Thomas, Mills, Grant, Monteiro, Diana CF, Morgan, Andrew, Mühlig, Kerstin, Munke, Anna, Münnich, Astrid, Nette, Julia, Nugent, Keith A, Nuguid, Theresa, Orville, Allen M, Pandey, Suraj, Pena, Gisel, Villanueva-Perez, Pablo, Poehlsen, Jennifer, Previtali, Gianpietro, Redecke, Lars, Riekehr, Winnie Maria, Rohde, Holger, Round, Adam, Safenreiter, Tatiana, Sarrou, Iosifina, Sato, Tokushi, Schmidt, Marius, Schmitt, Bernd, Schönherr, Robert, Schulz, Joachim, Sellberg, Jonas A, Seibert, M Marvin, and Seuring, Carolin

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences
Abstract

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

Published
2018

46. Global, regional, and national burden of mortality associated with cold spells during 2000–19: a three-stage modelling study

Author

Gao, Yuan, primary, Huang, Wenzhong, additional, Zhao, Qi, additional, Ryti, Niilo, additional, Armstrong, Ben, additional, Gasparrini, Antonio, additional, Tong, Shilu, additional, Pascal, Mathilde, additional, Urban, Aleš, additional, Zeka, Ariana, additional, Lavigne, Eric, additional, Madureira, Joana, additional, Goodman, Patrick, additional, Huber, Veronika, additional, Forsberg, Bertil, additional, Kyselý, Jan, additional, Sera, Francesco, additional, Guo, Yuming, additional, Li, Shanshan, additional, Gao, Yuan, additional, Bell, Michelle, additional, Hales, Simon, additional, Honda, Yasushi, additional, Jaakkola, Jouni J.K., additional, Tobias, Aurelio, additional, Vicedo-Cabrera, Ana Maria, additional, Abrutzky, Rosana, additional, Coelho, Micheline de Sousa Zanotti Stagliorio, additional, Saldiva, Paulo Hilario Nascimento, additional, Correa, Patricia Matus, additional, Ortega, Nicolás Valdés, additional, Kan, Haidong, additional, Osorio, Samuel, additional, Roye, Dominic, additional, Orru, Hans, additional, Indermitte, Ene, additional, Schneider, Alexandra, additional, Katsouyanni, Klea, additional, Analitis, Antonis, additional, Carlsen, Hanne Krage, additional, Mayvaneh, Fatemeh, additional, Roradeh, Hematollah, additional, Raz, Raanan, additional, Michelozzi, Paola, additional, de'Donato, Francesca, additional, Hashizume, Masahiro, additional, Kim, Yoonhee, additional, Alahmad, Barrak, additional, Cauchy, John Paul, additional, Diaz, Magali Hurtado, additional, Arellano, Eunice Elizabeth Félix, additional, Valencia, César De la Cruz, additional, Overcenco, Ala, additional, Houthuijs, Danny, additional, Ameling, Caroline, additional, Rao, Shilpa, additional, Carrasco, Gabriel, additional, Seposo, Xerxes, additional, Chua, Paul Lester Carlos, additional, Silva, Susana das Neves Pereira da, additional, Nunes, Baltazar, additional, Holobaca, Iulian-Horia, additional, Cvijanovic, Ivana, additional, Mistry, Malcolm, additional, Scovronick, Noah, additional, Acquaotta, Fiorella, additional, Kim, Ho, additional, Lee, Whanhee, additional, Íñiguez, Carmen, additional, Åström, Christofer, additional, Ragettli, Martina S., additional, Guo, Yue Leon, additional, Pan, Shih-Chun, additional, Colistro, Valentina, additional, Zanobetti, Antonella, additional, Schwartz, Joel, additional, Dang, Tran Ngoc, additional, and Dung, Do Van, additional

Published
2024
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47. Seasonality of mortality under climate change: a multicountry projection study

Author

Madaniyazi, Lina, primary, Armstrong, Ben, additional, Tobias, Aurelio, additional, Mistry, Malcolm N, additional, Bell, Michelle L, additional, Urban, Aleš, additional, Kyselý, Jan, additional, Ryti, Niilo, additional, Cvijanovic, Ivana, additional, Ng, Chris Fook Sheng, additional, Roye, Dominic, additional, Vicedo-Cabrera, Ana Maria, additional, Tong, Shilu, additional, Lavigne, Eric, additional, Íñiguez, Carmen, additional, da Silva, Susana das Neves Pereira, additional, Madureira, Joana, additional, Jaakkola, Jouni J K, additional, Sera, Francesco, additional, Honda, Yasushi, additional, Gasparrini, Antonio, additional, Hashizume, Masahiro, additional, Abrutzky, Rosana, additional, Acquaotta, Fiorella, additional, Alahmad, Barrak, additional, Analitis, Antonis, additional, Carlsen, Hanne Krage, additional, Carrasco-Escobar, Gabriel, additional, de Sousa Zanotti Stagliorio Coelho, Micheline, additional, Colistro, Valentina, additional, Matus Correa, Patricia, additional, Dang, Tran Ngoc, additional, de'Donato, Francesca, additional, Hurtado Diaz, Magali, additional, Dung, Do Van, additional, Entezari, Alireza, additional, Forsberg, Bertil, additional, Goodman, Patrick, additional, Guo, Yue Leon, additional, Guo, Yuming, additional, Holobaca, Iulian-Horia, additional, Houthuijs, Danny, additional, Huber, Veronika, additional, Indermitte, Ene, additional, Kan, Haidong, additional, Katsouyanni, Klea, additional, Kim, Yoonhee, additional, Kim, Ho, additional, Lee, Whanhee, additional, Li, Shanshan, additional, Mayvaneh, Fatemeh, additional, Michelozzi, Paola, additional, Orru, Hans, additional, Valdés Ortega, Nicolás, additional, Osorio, Samuel, additional, Overcenco, Ala, additional, Pan, Shih-Chun, additional, Pascal, Mathilde, additional, Ragettli, Martina S., additional, Rao, Shilpa, additional, Raz, Raanan, additional, Saldiva, Paulo Hilario Nascimento, additional, Schneider, Alexandra, additional, Schwartz, Joel, additional, Scovronick, Noah, additional, Seposo, Xerxes, additional, De la Cruz Valencia, César, additional, Zanobetti, Antonella, additional, and Zeka, Ariana, additional

Published
2024
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49. Emergence of anomalous dynamics in soft matter probed at the European XFEL

Author

Lehmkühler, Felix, Dallari, Francesco, Jain, Avni, Sikorski, Marcin, Möller, Johannes, Frenzel, Lara, Lokteva, Irina, Mills, Grant, Walther, Michael, Sinn, Harald, Schulz, Florian, Dartsch, Michael, Markmann, Verena, Bean, Richard, Kim, Yoonhee, Vagovic, Patrik, Madsen, Anders, Mancuso, Adrian P., and Grübel, Gerhard

Published
2020

50. Projections of excess mortality related to diurnal temperature range under climate change scenarios: a multi-country modelling study

Author

Lee, Whanhee, Kim, Yoonhee, Sera, Francesco, Gasparrini, Antonio, Park, Rokjin, Michelle Choi, Hayon, Prifti, Kristi, Bell, Michelle L, Abrutzky, Rosana, Guo, Yuming, Tong, Shilu, de Sousa Zanotti Stagliorio Coelho, Micheline, Nascimento Saldiva, Paulo Hilario, Lavigne, Eric, Orru, Hans, Indermitte, Ene, Jaakkola, Jouni J K, Ryti, Niilo R I, Pascal, Mathilde, Goodman, Patrick, Zeka, Ariana, Hashizume, Masahiro, Honda, Yasushi, Hurtado Diaz, Magali, César Cruz, Julio, Overcenco, Ala, Nunes, Baltazar, Madureira, Joana, Scovronick, Noah, Acquaotta, Fiorella, Tobias, Aurelio, Vicedo-Cabrera, Ana Maria, Ragettli, Martina S, Guo, Yue-Liang Leon, Chen, Bing-Yu, Li, Shanshan, Armstrong, Ben, Zanobetti, Antonella, Schwartz, Joel, and Kim, Ho

Published
2020
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