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Tausch, Simon H. ; Loka, Tobias P. ; Schulze, Jakob M. ; Andrusch, Andreas ; Klenner, Jeanette ; Dabrowski, Piotr Wojciech ; Lindner, Martin S. ; Nitsche, Andreas ; Renard, Bernhard Y.
Over the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics.
Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing has finished. The interpretation of results can further be challenged by contaminations, clinically irrelevant sequences, and the sheer amount and complexity of the data.
We implemented PathoLive, a real-time diagnostics pipeline for the detection of pathogens from clinical samples hours before sequencing has finished.
Based on real-time alignment with HiLive2, mappings are scored with respect to common contaminations, low-entropy areas, and sequences of widespread, non-pathogenic organisms.
The results are visualized using an interactive taxonomic tree that provides an easily interpretable overview of the relevance of hits. For a human plasma sample that was spiked in vitro with six pathogenic viruses, all agents were clearly detected after only 40 of 200 sequencing cycles.
For a real-world sample from Sudan, the results correctly indicated the presence of Crimean-Congo hemorrhagic fever virus. In a second real-world dataset from the 2019 SARS-CoV-2 outbreak in Wuhan, we found the presence of a SARS coronavirus as the most relevant hit without the novel virus reference genome being included in the database.
For all samples, clinically irrelevant hits were correctly de-emphasized.
Our approach is valuable to obtain fast and accurate NGS-based pathogen identifications and correctly prioritize and visualize them based on their clinical significance: PathoLive is open source and available on GitLab and BioConda.
Bernardi, Rafael L. ; Berdja, Amokrane ; Guzman, Christian Dani ; Torres-Torriti, Miguel ; Roth, Martin M.
Convolutional neural networks (CNNs) have been used for a wide range of applications in astronomy, including for the restoration of degraded images using a spatially invariant point spread function (PSF) across the field of view. Most existing development techniques use a single PSF in the deconvolution process, which is unrealistic when spatially variable PSFs are present in real observation conditions. Such conditions are simulated in this work to yield more realistic data samples. We propose a method that uses a simulated spatially variable PSF for the T80-South (T80-S) telescope, an 80-cm survey imager at Cerro Tololo (Chile). The synthetic data use real parameters from the detector noise and atmospheric seeing to recreate the T80-S observational conditions for the CNN training. The method is tested on real astronomical data from the T80-S telescope. We present the simulation and training methods, the results from real T80-S image CNN prediction, and a comparison with space observatory Gaia. A CNN can fix optical aberrations, which include image distortion, PSF size and profile, and the field position variation while preserving the source's flux. The proposed restoration approach can be applied to other optical systems and to post-process adaptive optics static residual aberrations in large-diameter telescopes.
Terbishalieva, Baiansuluu ; Timmerman, Martin Jan ; Mikolaichuk, Alexander ; Altenberger, Uwe ; Slama, Jiri ; Schleicher, Anja M. ; Sudo, Masafumi ; Sobel, Edward ; Cichy, Sarah Bettina
The Big Naryn Complex (BNC) in the East Djetim-Too Range of the Kyrgyz Middle Tianshan block is a tectonized, at least 2 km thick sequence of predominantly felsic to intermediate volcanic rocks intruded by porphyric rhyolite sills. It overlies a basement of metamorphic rocks and is overlain by late Neoproterozoic Djetim-Too Formation sediments; these also occur as tectonic intercalations in the BNC. The up to ca. 1100 m thick Lower Member is composed of predominantly rhyolites-to-dacites and minor basalts, while the at least 900 m thick pyroclastic Upper Member is dominated by rhyolitic-to-dacitic ignimbrites. Porphyric rhyolite sills are concentrated at the top of the Lower Member. A Lower Member rhyolite and a sill sample have LA-ICP-MS U-Pb zircon crystallization ages of 726.1 +/- 2.2 Ma and 720.3 +/- 6.5 Ma, respectively, showing that most of the magmatism occurred within a short time span in the late Tonian-early Cryogenian. Inherited zircons in the sill sample have Neoarchean (2.63, 2.64 Ga), Paleo- (2.33-1.81 Ga), Meso- (1.55 Ga), and Neoproterozoic (ca. 815 Ma) ages, and were derived from a heterogeneous Kuilyu Complex basement. A 1751 +/- 7 Ma Ar-40/Ar-39 age for amphibole from metagabbro is the age of cooling subsequent to Paleoproterozoic metamorphism of the Kuilyu Complex. The large amount of pyroclastic rocks, and their major and trace element compositions, the presence of Neoarchean to Neoproterozoic inherited zircons and a depositional basement of metamorphic rocks point to formation of the BNC in a continental magmatic arc setting.
Toy, Virginia Gail ; Sutherland, Rupert ; Townend, John ; Allen, Michael J. ; Becroft, Leeza ; Boles, Austin ; Boulton, Carolyn ; Carpenter, Brett ; Cooper, Alan ; Cox, Simon C. ; Daube, Christopher ; Faulkner, D. R. ; Halfpenny, Angela ; Kato, Naoki ; Keys, Stephen ; Kirilova, Martina ; Kometani, Yusuke ; Little, Timothy ; Mariani, Elisabetta ; Melosh, Benjamin ; Menzies, Catriona D. ; Morales, Luiz ; Morgan, Chance ; Mori, Hiroshi ; Niemeijer, Andre ; Norris, Richard ; Prior, David ; Sauer, Katrina ; Schleicher, Anja M. ; Shigematsu, Norio ; Teagle, Damon A. H. ; Tobin, Harold ; Valdez, Robert ; Williams, Jack ; Yeo, Samantha ; Baratin, Laura-May ; Barth, Nicolas ; Benson, Adrian ; Boese, Carolin ; Célérier, Bernard ; Chamberlain, Calum J. ; Conze, Ronald ; Coussens, Jamie ; Craw, Lisa ; Doan, Mai-Linh ; Eccles, Jennifer ; Grieve, Jason ; Grochowski, Julia ; Gulley, Anton ; Howarth, Jamie ; Jacobs, Katrina ; Janku-Capova, Lucie ; Jeppson, Tamara ; Langridge, Robert ; Mallyon, Deirdre ; Marx, Ray ; Massiot, Cécile ; Mathewson, Loren ; Moore, Josephine ; Nishikawa, Osamu ; Pooley, Brent ; Pyne, Alex ; Savage, Martha K. ; Schmitt, Doug ; Taylor-Offord, Sam ; Upton, Phaedra ; Weaver, Konrad C. ; Wiersberg, Thomas ; Zimmer, Martin
During the second phase of the Alpine Fault, Deep Fault Drilling Project (DFDP) in the Whataroa River, South Westland, New Zealand, bedrock was encountered in the DFDP-2B borehole from 238.5–893.2 m Measured Depth (MD). Continuous sampling and meso- to microscale characterisation of whole rock cuttings established that, in sequence, the borehole sampled amphibolite facies, Torlesse Composite Terrane-derived schists, protomylonites and mylonites, terminating 200–400 m above an Alpine Fault Principal Slip Zone (PSZ) with a maximum dip of 62°. The most diagnostic structural features of increasing PSZ proximity were the occurrence of shear bands and reduction in mean quartz grain sizes. A change in composition to greater mica:quartz + feldspar, most markedly below c. 700 m MD, is inferred to result from either heterogeneous sampling or a change in lithology related to alteration. Major oxide variations suggest the fault-proximal Alpine Fault alteration zone, as previously defined in DFDP-1 core, was not sampled.
Terbishalieva, Baiansuluu ; Timmerman, Martin Jan ; Mikolaichuk, Alexander ; Altenberger, Uwe ; Slama, Jiri ; Schleicher, Anja M. ; Sudo, Masafumi ; Sobel, Edward ; Cichy, Sarah Bettina
The Big Naryn Complex (BNC) in the East Djetim-Too Range of the Kyrgyz Middle Tianshan block is a tectonized, at least 2 km thick sequence of predominantly felsic to intermediate volcanic rocks intruded by porphyric rhyolite sills. It overlies a basement of metamorphic rocks and is overlain by late Neoproterozoic Djetim-Too Formation sediments; these also occur as tectonic intercalations in the BNC. The up to ca. 1100 m thick Lower Member is composed of predominantly rhyolites-to-dacites and minor basalts, while the at least 900 m thick pyroclastic Upper Member is dominated by rhyolitic-to-dacitic ignimbrites. Porphyric rhyolite sills are concentrated at the top of the Lower Member. A Lower Member rhyolite and a sill sample have LA-ICP-MS U-Pb zircon crystallization ages of 726.1 +/- 2.2 Ma and 720.3 +/- 6.5 Ma, respectively, showing that most of the magmatism occurred within a short time span in the late Tonian-early Cryogenian. Inherited zircons in the sill sample have Neoarchean (2.63, 2.64 Ga), Paleo- (2.33-1.81 Ga), Meso- (1.55 Ga), and Neoproterozoic (ca. 815 Ma) ages, and were derived from a heterogeneous Kuilyu Complex basement. A 1751 +/- 7 Ma Ar-40/Ar-39 age for amphibole from metagabbro is the age of cooling subsequent to Paleoproterozoic metamorphism of the Kuilyu Complex. The large amount of pyroclastic rocks, and their major and trace element compositions, the presence of Neoarchean to Neoproterozoic inherited zircons and a depositional basement of metamorphic rocks point to formation of the BNC in a continental magmatic arc setting.
Rezaei, Leila ; Timmerman, Martin Jan ; Moazzen, Mohssen ; Altenberger, Uwe ; Sláma, Jiří ; Sudo, Masafumi ; Günter, Christina ; Wilke, Franziska Daniela Helena ; Schleicher, Anja M.
In the Gasht-Masuleh area in the Alborz Mountains, gabbroic magma intruded Palaeozoic metasediments and Mesozoic sediments and crystallised as isotropic and cumulate gabbros. LREE enrichment points to relatively low degrees of mantle melting and depletion of Ti, Nb and Ta relative to primitive mantle points to an arc related component in the magma. Clinopyroxene compositions indicate MORB to arc signatures. U–Pb zircon crystallisation ages of 99.5 ± 0.6 Ma and 99.4 ± 0.6 Ma and phlogopite 40Ar/39Ar ages of 97.1 ± 0.4 Ma, 97.5 ± 0.4 Ma, 97.1 ± 0.1 Ma, within 2σ error, indicate that gabbro intrusion occurred in the (Albian-)Cenomanian (mid-Cretaceous). As active subduction did not take place in the Cretaceous in North Iran, the small volume mafic magmatism in the Gasht-Masuleh area must be due to local, extension-related mantle melting. Melting was most likely caused by far field effects triggered by roll-back of the Neo-Tethys subducting slab. As subduction took place at a distance of ~ 400 km (present distance) from the Alborz Mountains, the observed arc geochemical signatures must be inherited from a previous subduction event and concomitant mantle metasomatism, possibly in combination with contamination of the magma by crustal material.
Heinze, Johannes ; Simons, Nadja K. ; Seibold, Sebastian ; Wacker, Alexander ; Weithoff, Guntram ; Gossner, Martin M. ; Prati, Daniel ; Bezemer, T. Martijn ; Joshi, Jasmin Radha
Under natural conditions, aboveground herbivory and plant-soil feedbacks (PSFs) are omnipresent interactions strongly affecting individual plant performance. While recent research revealed that aboveground insect herbivory generally impacts the outcome of PSFs, no study tested to what extent the intensity of herbivory affects the outcome. This, however, is essential to estimate the contribution of PSFs to plant performance under natural conditions in the field. Here, we tested PSF effects both with and without exposure to aboveground herbivory for four common grass species in nine grasslands that formed a gradient of aboveground invertebrate herbivory. Without aboveground herbivores, PSFs for each of the four grass species were similar in each of the nine grasslands-both in direction and in magnitude. In the presence of herbivores, however, the PSFs differed from those measured under herbivory exclusion, and depended on the intensity of herbivory. At low levels of herbivory, PSFs were similar in the presence and absence of herbivores, but differed at high herbivory levels. While PSFs without herbivores remained similar along the gradient of herbivory intensity, increasing herbivory intensity mostly resulted in neutral PSFs in the presence of herbivores. This suggests that the relative importance of PSFs for plant-species performance in grassland communities decreases with increasing intensity of herbivory. Hence, PSFs might be more important for plant performance in ecosystems with low herbivore pressure than in ecosystems with large impacts of insect herbivores.
Laucht, Manfred ; Esser, Günter ; Schmidt, Martin H. ; Stöhr, R.-M. ; Weindrich, D. ; Ihle, Wolfgang ; Marcus, A.
A very small fraction of (runaway) massive stars have masses exceeding 60-70 M-circle dot and are predicted to evolve as luminous blue variable and Wolf-Rayet stars before ending their lives as core-collapse supernovae. Our 2D axisymmetric hydrodynamical simulations explore how a fast wind (2000 km s(-1)) and high mass-loss rate (10(-5)M(circle dot) yr(-1)) can impact the morphology of the circumstellar medium. It is shaped as 100 pc-scale wind nebula that can be pierced by the driving star when it supersonically moves with velocity 20-40 km s(-1) through the interstellar medium (ISM) in the Galactic plane. The motion of such runaway stars displaces the position of the supernova explosion out of their bow shock nebula, imposing asymmetries to the eventual shock wave expansion and engendering Cygnus-loop-like supernova remnants. We conclude that the size (up to more than 200 pc) of the filamentary wind cavity in which the chemically enriched supernova ejecta expand, mixing efficiently the wind and ISM materials by at least 10 per cent in number density, can be used as a tracer of the runaway nature of the very massive progenitors of such 0.1Myr old remnants. Our results motivate further observational campaigns devoted to the bow shock of the very massive stars BD+43 degrees 3654 and to the close surroundings of the synchrotron-emitting Wolf-Rayet shell G2.4+1.4.
Küken, Anika ; Sommer, Frederik ; Yaneva-Roder, Liliya ; Mackinder, Luke C.M. ; Höhne, Melanie ; Geimer, Stefan ; Jonikas, Martin C. ; Schroda, Michael ; Stitt, Mark ; Nikoloski, Zoran ; Mettler-Altmann, Tabea
Cells and organelles are not homogeneous but include microcompartments that alter the spatiotemporal characteristics of cellular processes. The effects of microcompartmentation on metabolic pathways are however difficult to study experimentally. The pyrenoid is a microcompartment that is essential for a carbon concentrating mechanism (CCM) that improves the photosynthetic performance of eukaryotic algae. Using Chlamydomonas reinhardtii, we obtained experimental data on photosynthesis, metabolites, and proteins in CCM-induced and CCM-suppressed cells. We then employed a computational strategy to estimate how fluxes through the Calvin-Benson cycle are compartmented between the pyrenoid and the stroma. Our model predicts that ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco, and 3-phosphoglycerate (3PGA), its product, diffuse in and out of the pyrenoid, respectively, with higher fluxes in CCM-induced cells. It also indicates that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Our computational approach represents a stepping stone to understanding microcompartmentalized CCM in other organisms.
Core-collapse supernova remnants are structures of the interstellar medium (ISM) left behind the explosive death of most massive stars ( ?40 M-?). Since they result in the expansion of the supernova shock wave into the gaseous environment shaped by the star's wind history, their morphology constitutes an insight into the past evolution of their progenitor star. Particularly, fast-mo ving massiv e stars can produce asymmetric core-collapse superno va remnants. We inv estigate the mixing of materials in core-collapse supernova remnants generated by a moving massive 35 M-? star, in a magnetized ISM. Stellar rotation and the wind magnetic field are time-dependently included into the models which follow the entire evolution of the stellar surroundings from the zero-age main-sequence to 80 kyr after the supernova explosion. It is found that very little main-sequence material is present in remnants from moving stars, that the Wolf-Rayet wind mixes very efficiently within the 10 kyr after the explosion, while the red supergiant material is still unmixed by 30 per cent within 50 kyr after the supernova. Our results indicate that the faster the stellar motion, the more complex the internal organization of the supernova remnant and the more ef fecti ve the mixing of ejecta therein. In contrast, the mixing of stellar wind material is only weakly affected by progenitor motion, if at all.