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Your search keyword '"Yaroslav Gevorkov"' showing total 11 results
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11 results on '"Yaroslav Gevorkov"'

1. The effects of age on dyspnea and respiratory mechanical and neural responses to exercise in healthy men

Author

William MacAskill, Ben Hoffman, Michael A. Johnson, Graham R. Sharpe, Joshua Rands, Shoena E. Wotherspoon, Yaroslav Gevorkov, Tracy L. Kolbe‐Alexander, and Dean E. Mills

Subjects
aging, dyspnea, exercise, mechanical, neural, Physiology, QP1-981
Abstract

Abstract The respiratory muscle pressure generation and inspiratory and expiratory neuromuscular recruitment patterns in younger and older men were compared during exercise, alongside descriptors of dyspnea. Healthy younger (n = 8, 28 ± 5 years) and older (n = 8, 68 ± 4 years) men completed a maximal incremental cycling test. Esophageal, gastric (Pga) and transdiaphragmatic pressures, and electromyography (EMG) of the crural diaphragm were measured using a micro‐transducer and EMG catheter. EMG of the parasternal intercostals, sternocleidomastoids, and rectus abdominis were measured using skin surface electrodes. After the exercise test, participants completed a questionnaire to evaluate descriptors of dyspnea. Pga at end‐expiration, Pga expiratory tidal swings, and the gastric pressure–time product (PTPga) at absolute and relative minute ventilation were higher (p

Published
2023
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2. FDIP—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments

Author

Yaroslav Gevorkov, Marina Galchenkova, Valerio Mariani, Anton Barty, Thomas A. White, Henry N. Chapman, and Oleksandr Yefanov

Subjects
serial crystallography, masking artefacts, peak finding algorithm, real-time feedback, Crystallography, QD901-999
Abstract

Serial crystallography (SX) is a cutting-edge technique in structural biology, involving the systematic collection of X-ray diffraction data from numerous randomly oriented microcrystals. To extract comprehensive three-dimensional information about the studied system, SX utilises thousands of measured diffraction patterns. As such, SX takes advantages of the properties of modern X-ray sources, including Free Electron Lasers (FELs) and third and fourth generation synchrotrons, as well as contemporary high-repetition-rate detectors. Efficient analysis of the extensive datasets generated during SX experiments demands fast and effective algorithms. The FDIP library offers meticulously optimised functions tailored for preprocessing data obtained in SX experiments. This encompasses tasks such as background subtraction, identification and masking of parasitic streaks, elimination of unwanted powder diffraction (e.g., from ice or salt crystals), and pinpointing useful Bragg peaks in each diffraction pattern. The library is equipped with a user-friendly graphical interface for facile parameter adjustment tailored to specific datasets. Compatible with popular SX processing software like OnDA, Cheetah, CrystFEL, and Merge3D, the FDIP library enhances the capabilities of these tools for streamlined and precise serial crystallography analyses.

Published
2024
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3. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser

Author

Karol Nass, Camila Bacellar, Claudio Cirelli, Florian Dworkowski, Yaroslav Gevorkov, Daniel James, Philip J. M. Johnson, Demet Kekilli, Gregor Knopp, Isabelle Martiel, Dmitry Ozerov, Alexandra Tolstikova, Laura Vera, Tobias Weinert, Oleksandr Yefanov, Jörg Standfuss, Sven Reiche, and Christopher J. Milne

Subjects
pink beams, serial femtosecond crystallography, de novo protein structure determination, single-wavelength anomalous diffraction, xfels, large bandwidths, data-quality indicators, Crystallography, QD901-999
Abstract

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [Δλ/λ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs.

Published
2021
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4. Segmented flow generator for serial crystallography at the European X-ray free electron laser

Author

Austin Echelmeier, Jorvani Cruz Villarreal, Marc Messerschmidt, Daihyun Kim, Jesse D. Coe, Darren Thifault, Sabine Botha, Ana Egatz-Gomez, Sahir Gandhi, Gerrit Brehm, Chelsie E. Conrad, Debra T. Hansen, Caleb Madsen, Saša Bajt, J. Domingo Meza-Aguilar, Dominik Oberthür, Max O. Wiedorn, Holger Fleckenstein, Derek Mendez, Juraj Knoška, Jose M. Martin-Garcia, Hao Hu, Stella Lisova, Aschkan Allahgholi, Yaroslav Gevorkov, Kartik Ayyer, Steve Aplin, Helen Mary Ginn, Heinz Graafsma, Andrew J. Morgan, Dominic Greiffenberg, Alexander Klujev, Torsten Laurus, Jennifer Poehlsen, Ulrich Trunk, Davide Mezza, Bernd Schmidt, Manuela Kuhn, Raimund Fromme, Jolanta Sztuk-Dambietz, Natascha Raab, Steffen Hauf, Alessandro Silenzi, Thomas Michelat, Chen Xu, Cyril Danilevski, Andrea Parenti, Leonce Mekinda, Britta Weinhausen, Grant Mills, Patrik Vagovic, Yoonhee Kim, Henry Kirkwood, Richard Bean, Johan Bielecki, Stephan Stern, Klaus Giewekemeyer, Adam R. Round, Joachim Schulz, Katerina Dörner, Thomas D. Grant, Valerio Mariani, Anton Barty, Adrian P. Mancuso, Uwe Weierstall, John C. H. Spence, Henry N. Chapman, Nadia Zatsepin, Petra Fromme, Richard A. Kirian, and Alexandra Ros

Subjects
Science
Abstract

Due to the pulsed nature of X-ray free electron laser (XFEL) instruments the majority of protein crystals, which are injected using continuous jet injection techniques are wasted. Here, the authors present a microfluidic device to deliver aqueous protein crystal laden droplets segmented with an immiscible oil and demonstrate that with this device an approx. 60% reduction in sample waste was achieved for data collection of 3-deoxy-D-manno-octulosonate 8-phosphate synthase crystals at the EuXFEL.

Published
2020
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5. Serial protein crystallography in an electron microscope

Author

Robert Bücker, Pascal Hogan-Lamarre, Pedram Mehrabi, Eike C. Schulz, Lindsey A. Bultema, Yaroslav Gevorkov, Wolfgang Brehm, Oleksandr Yefanov, Dominik Oberthür, Günther H. Kassier, and R. J. Dwayne Miller

Subjects
Science
Abstract

For conventional three-dimensional microcrystal electron diffraction (3D ED/MicroED), a crystal is slowly rotated under an electron beam, leading to inevitable accumulation of radiation damage during data collection. In this work, the authors present a serial electron diffraction method, where still diffraction patterns from many protein nanocrystals are rapidly recorded and merged, which minimises radiation damage and only requires a slightly modified standard scanning transmission electron microscope.

Published
2020
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6. Membrane protein megahertz crystallography at the European XFEL

Author

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

Subjects
Science
Abstract

The European X-ray free-electron laser (EuXFEL) in Hamburg is the first XFEL with a megahertz repetition rate. Here the authors present the 2.9 Å structure of the large membrane protein complex Photosystem I from T. elongatus that was determined at the EuXFEL.

Published
2019
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7. Megahertz serial crystallography

Author

Max O. Wiedorn, Dominik Oberthür, Richard Bean, Robin Schubert, Nadine Werner, Brian Abbey, Martin Aepfelbacher, Luigi Adriano, Aschkan Allahgholi, Nasser Al-Qudami, Jakob Andreasson, Steve Aplin, Salah Awel, Kartik Ayyer, Saša Bajt, Imrich Barák, Sadia Bari, Johan Bielecki, Sabine Botha, Djelloul Boukhelef, Wolfgang Brehm, Sandor Brockhauser, Igor Cheviakov, Matthew A. Coleman, Francisco Cruz-Mazo, Cyril Danilevski, Connie Darmanin, R. Bruce Doak, Martin Domaracky, Katerina Dörner, Yang Du, Hans Fangohr, Holger Fleckenstein, Matthias Frank, Petra Fromme, Alfonso M. Gañán-Calvo, Yaroslav Gevorkov, Klaus Giewekemeyer, Helen Mary Ginn, Heinz Graafsma, Rita Graceffa, Dominic Greiffenberg, Lars Gumprecht, Peter Göttlicher, Janos Hajdu, Steffen Hauf, Michael Heymann, Susannah Holmes, Daniel A. Horke, Mark S. Hunter, Siegfried Imlau, Alexander Kaukher, Yoonhee Kim, Alexander Klyuev, Juraj Knoška, Bostjan Kobe, Manuela Kuhn, Christopher Kupitz, Jochen Küpper, Janine Mia Lahey-Rudolph, Torsten Laurus, Karoline Le Cong, Romain Letrun, P. Lourdu Xavier, Luis Maia, Filipe R. N. C. Maia, Valerio Mariani, Marc Messerschmidt, Markus Metz, Davide Mezza, Thomas Michelat, Grant Mills, Diana C. F. Monteiro, Andrew Morgan, Kerstin Mühlig, Anna Munke, Astrid Münnich, Julia Nette, Keith A. Nugent, Theresa Nuguid, Allen M. Orville, Suraj Pandey, Gisel Pena, Pablo Villanueva-Perez, Jennifer Poehlsen, Gianpietro Previtali, Lars Redecke, Winnie Maria Riekehr, Holger Rohde, Adam Round, Tatiana Safenreiter, Iosifina Sarrou, Tokushi Sato, Marius Schmidt, Bernd Schmitt, Robert Schönherr, Joachim Schulz, Jonas A. Sellberg, M. Marvin Seibert, Carolin Seuring, Megan L. Shelby, Robert L. Shoeman, Marcin Sikorski, Alessandro Silenzi, Claudiu A. Stan, Xintian Shi, Stephan Stern, Jola Sztuk-Dambietz, Janusz Szuba, Aleksandra Tolstikova, Martin Trebbin, Ulrich Trunk, Patrik Vagovic, Thomas Ve, Britta Weinhausen, Thomas A. White, Krzysztof Wrona, Chen Xu, Oleksandr Yefanov, Nadia Zatsepin, Jiaguo Zhang, Markus Perbandt, Adrian P. Mancuso, Christian Betzel, Henry Chapman, and Anton Barty

Subjects
Science
Abstract

The new European X-Ray Free-Electron Laser (EuXFEL) is the first XFEL that generates X-ray pulses with a megahertz inter-pulse spacing. Here the authors demonstrate that high-quality and damage-free protein structures can be obtained with the currently available 1.1 MHz repetition rate pulses using lysozyme as a test case and furthermore present a β-lactamase structure.

Published
2018
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8. Rapid sample delivery for megahertz serial crystallography at X-ray FELs

Author

Max O. Wiedorn, Salah Awel, Andrew J. Morgan, Kartik Ayyer, Yaroslav Gevorkov, Holger Fleckenstein, Nils Roth, Luigi Adriano, Richard Bean, Kenneth R. Beyerlein, Joe Chen, Jesse Coe, Francisco Cruz-Mazo, Tomas Ekeberg, Rita Graceffa, Michael Heymann, Daniel A. Horke, Juraj Knoška, Valerio Mariani, Reza Nazari, Dominik Oberthür, Amit K. Samanta, Raymond G. Sierra, Claudiu A. Stan, Oleksandr Yefanov, Dimitrios Rompotis, Jonathan Correa, Benjamin Erk, Rolf Treusch, Joachim Schulz, Brenda G. Hogue, Alfonso M. Gañán-Calvo, Petra Fromme, Jochen Küpper, Andrei V. Rode, Saša Bajt, Richard A. Kirian, and Henry N. Chapman

Subjects
X-ray free-electron lasers, FELs, X-ray FEL pulse trains, megahertz repetition rates, Crystallography, QD901-999
Abstract

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s−1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.

Published
2018
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9. Evaluation of serial crystallographic structure determination within megahertz pulse trains

Author

Oleksandr Yefanov, Dominik Oberthür, Richard Bean, Max O. Wiedorn, Juraj Knoska, Gisel Pena, Salah Awel, Lars Gumprecht, Martin Domaracky, Iosifina Sarrou, P. Lourdu Xavier, Markus Metz, Saša Bajt, Valerio Mariani, Yaroslav Gevorkov, Thomas A. White, Aleksandra Tolstikova, Pablo Villanueva-Perez, Carolin Seuring, Steve Aplin, Armando D. Estillore, Jochen Küpper, Alexander Klyuev, Manuela Kuhn, Torsten Laurus, Heinz Graafsma, Diana C. F. Monteiro, Martin Trebbin, Filipe R. N. C. Maia, Francisco Cruz-Mazo, Alfonso M. Gañán-Calvo, Michael Heymann, Connie Darmanin, Brian Abbey, Marius Schmidt, Petra Fromme, Klaus Giewekemeyer, Marcin Sikorski, Rita Graceffa, Patrik Vagovic, Thomas Kluyver, Martin Bergemann, Hans Fangohr, Jolanta Sztuk-Dambietz, Steffen Hauf, Natascha Raab, Valerii Bondar, Adrian P. Mancuso, Henry Chapman, and Anton Barty

Subjects
Crystallography, QD901-999
Abstract

The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible results in unwanted structural changes due to either radiation damage or systematic effects on data quality. Here, separate structures from the first and subsequent pulses in the European XFEL pulse train were determined, showing that there is essentially no difference between structures determined from different pulses under currently available operating conditions at the European XFEL.

Published
2019
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10. Author Correction: Membrane protein megahertz crystallography at the European XFEL

Author

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

Subjects
Science
Abstract

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

Published
2020
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