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Genomic-Phenomic Reciprocal Illumination: Desyopone hereon gen. et sp. nov., an Exceptional Aneuretine-like Fossil Ant from Ethiopian Amber

Fossils are critical for understanding the evolutionary diversification, turnover, and morphological disparification of extant lineages. While fossils cannot be sequenced, phenome-scale data may be generated using micro-computed tomography (μ-CT), thus revealing hidden structures and
internal anatomy, when preserved. Here, we adduce the male caste of a new fossil ant species from Miocene Ethiopian amber that resembles members of the Aneuretinae, matching the operational definition of the subfamily. Through the use of synchrotron radiation for μ-CT, we critically test the aneuretine-identity hypothesis. Our results indicate that the new fossils do not belong to the Aneuretinae, but rather the Ponerini (Ponerinae). Informed by recent phylogenomic studies, we were able to place the fossils close to the extant genus Cryptopone based on logical character analysis, with the two uniquely sharing absence of the subpetiolar process among all ponerine genera. Consequently, we: (1) revise the male-based key to the global ant subfamilies; (2) revise the definitions of Aneuretinae, Ponerinae, Platythyreini, and Ponerini; (3) discuss the evolution of ant mandibles; and (4) describe the fossils as †Desyopone hereon gen. et sp. nov. Our study highlights the value of males
for ant systematics and the tremendous potential of phenomic imaging technologies for the study of ant evolution

 Insects 2022, 13, 796. https://doi.org/10.3390/insects13090796 

Boudinot, B.E.; Richter, A.K.; Hammel, J.U.; Szwedo, J.; Bojarski, B.; Perrichot, V. 
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Rapid aberration correction for diffractive X-ray optics by additive manufacturing

Photophoretic forces are induced when light causes a net momentum exchange between a particle and a surrounding gas. Such forces have been shown to be a robust means for trapping and guiding particles in air over long distances. Here, we apply the concept of an optical funnel for the delivery of bioparticles to the focus of an x-ray free-electron laser (XFEL) for femtosecond x-ray diffractive imaging. We provide the experimental demonstration of transversely compressing a high-speed beam of aerosolized viruses via photophoretic forces in a low-pressure gas environment. Relative temperature gradients induced on the viruses by the laser are estimated via particle-velocimetry measurements. The results demonstrate the potential for an optical funnel to improve particle-delivery efficiency in XFEL imaging and spectroscopy.

Opt. Express 30, 31519-31529 (2022) 

Frank Seiboth, Adam Kubec, Andreas Schropp, Sven Niese, Peter Gawlitza, Jan Garrevoet, Vanessa Galbierz, Silvio Achilles, Svenja Patjens, Michael E. Stuckelberger, Christian David, and Christian G. Schroer 
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  • 1 min read

Optical Funnel to Guide and Focus Virus Particles for X-Ray Diffractive Imaging

Photophoretic forces are induced when light causes a net momentum exchange between a particle and a surrounding gas. Such forces have been shown to be a robust means for trapping and guiding particles in air over long distances. Here, we apply the concept of an optical funnel for the delivery of bioparticles to the focus of an x-ray free-electron laser (XFEL) for femtosecond x-ray diffractive imaging. We provide the experimental demonstration of transversely compressing a high-speed beam of aerosolized viruses via photophoretic forces in a low-pressure gas environment. Relative temperature gradients induced on the viruses by the laser are estimated via particle-velocimetry measurements. The results demonstrate the potential for an optical funnel to improve particle-delivery efficiency in XFEL imaging and spectroscopy.
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Recovery time of a plasma-wakefield accelerator

The interaction of intense particle bunches with plasma can give rise to plasma wakes1,2 capable of sustaining gigavolt-per-metre electric fields3,4, which are orders of magnitude higher than provided by state-of-the-art radio-frequency technology5. Plasma wakefields can, therefore, strongly accelerate charged particles and offer the opportunity to reach higher particle energies with smaller and hence more widely available accelerator facilities. However, the luminosity and brilliance demands of high-energy physics and photon science require particle bunches to be accelerated at repetition rates of thousands or even millions per second, which are orders of magnitude higher than demonstrated with plasma-wakefield technology6,7. Here we investigate the upper limit on repetition rates of beam-driven plasma accelerators by measuring the time it takes for the plasma to recover to its initial state after perturbation by a wakefield. The many-nanosecond-level recovery time measured establishes the in-principle attainability of megahertz rates of acceleration in plasmas. The experimental signatures of the perturbation are well described by simulations of a temporally evolving parabolic ion channel, transferring energy from the collapsing wake to the surrounding media. This result establishes that plasma-wakefield modules could be developed as feasible high-repetition-rate energy boosters at current and future particle-physics and photon-science facilities.

Nature 603, 58–62

D’Arcy, R., Chappell, J., Beinortaite, J. et al.
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Scaling the U-net: segmentation of biodegradable bone implants in high-resolution synchrotron radiation microtomograms

Highly accurate segmentation of large 3D volumes is a demanding task. Challenging applications like the segmentation of synchrotron radiation microtomograms (SRμCT) at high-resolution, which suffer from low contrast, high spatial variability and measurement artifacts, readily exceed the capacities of conventional segmentation methods, including the manual segmentation by human experts. The quantitative characterization of the osseointegration and spatio-temporal biodegradation process of bone implants requires reliable, and very precise segmentation. We investigated the scaling of 2D U-net for high resolution grayscale volumes by three crucial model hyper-parameters (i.e., the model width, depth, and input size). To leverage the 3D information of high-resolution SRμCT, common three axes prediction fusing is extended, investigating the effect of adding more than three axes prediction. In a systematic evaluation we compare the performance of scaling the U-net by intersection over union (IoU) and quantitative measurements of osseointegration and degradation parameters. Overall, we observe that a compound scaling of the U-net and multi-axes prediction fusing with soft voting yields the highest IoU for the class “degradation layer”. Finally, the quantitative analysis showed that the parameters calculated with model segmentation deviated less from the high quality results than those obtained by a semi-automatic segmentation method.

Sci Rep 11, 24237 (2021).

Baltruschat, I.M., Ćwieka, H., Krüger, D. et al.
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Helical reconstruction of Salmonella and Shigella needle filaments attached to type 3 basal bodies

Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a long helical needle filament that protrudes from the bacterial surface and connects the cytoplasms of the bacterium and the eukaryotic cell. Previous structural research was predominantly focused on reconstituted type 3 needle filaments, which lacked the biological context. In this work we introduce a facile procedure to obtain high-resolution cryo-EM structure of needle filaments attached to the basal body of type 3 secretion systems. We validate our approach by solving the structure of Salmonella PrgI filament and demonstrate its utility by obtaining the first high-resolution cryo-EM reconstruction of Shigella MxiH filament. Our work paves the way to systematic structural characterization of attached type 3 needle filaments in the context of mutagenesis studies, protein structural evolution and drug development.

Biochemistry and Biophysics Reports 27, 2021, 101039

Vadim Kotov, Michele Lunelli, Jiri Wald, Michael Kolbe, Thomas C. Marlovits,
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Heterogeneity in the Fragmentation of Ziegler Catalyst Particles during Ethylene Polymerization Quantified by X-ray Nanotomography

Ziegler-type catalysts are the grand old workhorse of the polyolefin industry, yet their hierarchically complex nature complicates polymerization activity–catalyst structure relationships. In this work, the degree of catalyst framework fragmentation of a high-density polyethylene (HDPE) Ziegler-type catalyst was studied using ptychography X-ray-computed nanotomography (PXCT) in the early stages of ethylene polymerization under mild reaction conditions. An ensemble consisting of 434 fully reconstructed ethylene prepolymerized Ziegler catalyst particles prepared at a polymer yield of 3.4 g HDPE/g catalyst was imaged. This enabled a statistical route to study the heterogeneity in the degree of particle fragmentation and therefore local polymerization activity at an achieved 3-D spatial resolution of 74 nm without requiring invasive imaging tools. To study the degree of catalyst fragmentation within the ensemble, a fragmentation parameter was constructed based on a k-means clustering algorithm that relates the quantity of polyethylene formed to the average size of the spatially resolved catalyst fragments. With this classification method, we have identified particles that exhibit weak, moderate, and strong degrees of catalyst fragmentation, showing that there is a strong heterogeneity in the overall catalyst particle fragmentation and thus polymerization activity within the entire ensemble. This hints toward local mass transfer limitations or other deactivation phenomena. The methodology used here can be applied to all polyolefin catalysts, including metallocene and the Phillips catalysts to gain statistically relevant fundamental insights in the fragmentation behavior of an ensemble of catalyst particles.

JACS Au 2021 1 (6), 852-864

Koen W. Bossers, Roozbeh Valadian, Jan Garrevoet, Stijn van Malderen, Robert Chan, Nic Friederichs, John Severn, Arnold Wilbers, Silvia Zanoni, Maarten K. Jongkind, Bert M. Weckhuysen, and Florian Meirer
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  • 1 min read

3-D X-ray Nanotomography Reveals Different Carbon Deposition Mechanisms in a Single Catalyst Particle

Catalyst deactivation involves a complex interplay of processes taking place at different length and time scales. Understanding this phenomenon is one of the grand challenges in solid catalyst characterization. A process contributing to deactivation is carbon deposition (i. e., coking), which reduces catalyst activity by limiting diffusion and blocking active sites. However, characterizing coke formation and its effects remains challenging as it involves both the organic and inorganic phase of the catalytic process and length scales from the atomic scale to the scale of the catalyst body. Here we present a combination of hard X-ray imaging techniques able to visualize in 3-D the distribution, effect and nature of carbon deposits in the macro-pore space of an entire industrially used catalyst particle. Our findings provide direct evidence for coke promoting effects of metal poisons, pore clogging by coke, and a correlation between carbon nature and its location. These results provide a better understanding of the coking process, its relation to catalyst deactivation and new insights into the efficiency of the industrial scale process of fluid catalytic cracking.

ChemCatChem 2021, 13, 2494.

M. Veselý, R. Valadian, L. Merten Lohse, M. Toepperwien, K. Spiers, J. Garrevoet, E. T. C. Vogt, T. Salditt, B. M. Weckhuysen, F. Meirer
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Interactive analysis notebooks on DESY batch resources

Batch scheduling systems are usually designed to maximise fair resource utilisation and efficiency, but are less well designed for demanding interactive processing, which requires fast access to resources while low upstart latency is only of secondary significance for high throughput of high performance computing scheduling systems. The computing clusters at DESY are intended as batch systems for end users to run massive analysis and simulation jobs enabling fast turnaround systems, in particular when processing is expected to feed back to operation of instruments in near real-time. The continuously increasing popularity of Jupyter Notebooks for interactive and online processing made an integration of this technology into the DESY batch systems indispensable. We present here our approach to utilise the HTCondor and SLURM backends to integrate Jupyter Notebook servers and the techniques involved to provide fast access. The chosen approach offers a smooth user experience allowing users to customize resource allocation tailored to their computational requirements. In addition, we outline the differences between the HPC and the HTC implementations and give an overview of the experience of running Jupyter Notebook services.

Comput Softw Big Sci 5, 16 (2021).
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Pump-probe X-ray holographic imaging of laser-induced cavitation bubbles with femtosecond FEL pulses

Cavitation bubbles can be seeded from a plasma following optical breakdown, by focusing an intense laser in water. The fast dynamics are associated with extreme states of gas and liquid, especially in the nascent state. This offers a unique setting to probe water and water vapor far-from equilibrium. However, current optical techniques cannot quantify these early states due to contrast and resolution limitations. X-ray holography with single X-ray free-electron laser pulses has now enabled a quasi-instantaneous high resolution structural probe with contrast proportional to the electron density of the object. In this work, we demonstrate cone-beam holographic flash imaging of laser-induced cavitation bubbles in water with nanofocused X-ray free-electron laser pulses. We quantify the spatial and temporal pressure distribution of the shockwave surrounding the expanding cavitation bubble at time delays shortly after seeding and compare the results to numerical simulations.

Vassholz, M., Hoeppe, H.P., Hagemann, J. et al.

Nat Commun 12, 3468 (2021).