Understanding the dynamics of photoionization-induced solitons in gas-filled hollow-core photonic crystal fibers

We present in detail our developed model [Saleh et al., Phys. Rev. Lett. 107] that governs pulse propagation in hollow-core photonic crystal fibers filled by an ionizing gas. By using perturbative methods, we find that the photoionization process induces the opposite phenomenon of the well-known Raman self-frequency red-shift of solitons in solid-core glass fibers, as was recently experimentally demonstrated [Hoelzer et al., Phys. Rev. Lett. 107]. This process is only limited by ionization losses, and leads to a constant acceleration of solitons in the time domain with a continuous blue-shift in the frequency domain. By applying the Gagnon-B\'{e}langer gauge transformation, multi-peak `inverted gravity-like' solitary waves are predicted. We also demonstrate that the pulse dynamics shows the ejection of solitons during propagation in such fibers, analogous to what happens in conventional solid-core fibers. Moreover, unconventional long-range non-local interactions between temporally distant solitons, unique of gas plasma systems, are predicted and studied. Finally, the effects of higher-order dispersion coefficients and the shock operator on the pulse dynamics are investigated, showing that the resonant radiation in the UV [Joly et al., Phys. Rev. Lett. 106] can be improved via plasma formation.Comment: 9 pages, 10 figure

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

Background: Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches. Results: Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. Conclusions: Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future

Pressure induced high-spin to low-spin transition in FeS evidenced by x-ray emission spectroscopy

We report the observation of the pressure-induced high-spin to low-spin transition in FeS using new high-pressure synchrotron x-ray emission spectroscopy techniques. The transition is evidenced by the disappearance of the low-energy satellite in the Fe K$\beta$ emission spectrum of FeS. Moreover, the phase transition is reversible and closely related to the structural phase transition from a manganese phosphide-like phase to a monoclinic phase. The study opens new opportunities for investigating the electronic properties of materials under pressure.Comment: ReVTeX, 4 pages, 3 figures inserted with epsfig. minor modifications before submission to PR

First measurement of kaonic helium-3 X-rays

The first observation of the kaonic 3He 3d - 2p transition was made using slow K- mesons stopped in a gaseous 3He target. The kaonic atom X-rays were detected with large-area silicon drift detectors using the timing information of the K+K- pairs of phi-meson decays produced by the DAFNE e+e- collider. The strong interaction shift of the kaonic 3He 2p state was determined to be -2+-2 (stat)+-4 (syst) eV.Comment: Accepted for publication in Phys. Lett.

SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities

During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cryptic lineages, but it is difficult to clearly identify and define novel lineages from wastewater (WW) alone. While WWGS has significant advantages in monitoring SARS-CoV-2 viral spread, technical challenges remain, including poor sequencing coverage and quality due to viral RNA degradation. As a result, the viral RNAs in wastewater have low concentrations and are often fragmented, making sequencing difficult. WWGS analysis requires advanced computational tools that are yet to be developed and benchmarked. The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity. Those methods were not developed for wastewater sequencing data specifically, and are not optimized to address unique challenges associated with wastewater. While specialized tools for analysis of wastewater sequencing data have also been developed recently, it remains to be seen how they will perform given the ongoing evolution of SARS-CoV-2 and the decline in testing and patient-based genomic surveillance. Here, we discuss opportunities and challenges associated with WWGS, including sample preparation, sequencing technology, and bioinformatics methods.Comment: V Munteanu and M Saldana contributed equally to this work A Smith and S Mangul jointly supervised this work For correspondence: [email protected]

Measurements of the strong-interaction widths of the kaonic 3He and 4He 2p levels

The kaonic 3He and 4He X-rays emitted in the 3d-2p transitions were measured in the SIDDHARTA experiment. The widths of the kaonic 3He and 4He 2p states were determined to be Gamma_2p(3He) = 6 \pm 6 (stat.) \pm 7 (syst.) eV, and Gamma_2p(4He) = 14 \pm 8 (stat.) \pm 5 (syst.) eV, respectively. Both results are consistent with the theoretical predictions. The width of kaonic 4He is much smaller than the value of 55 \pm 34 eV determined by the experiments performed in the 70's and 80's, while the width of kaonic 3He was determined for the first time.Comment: Accepted in Phys. Lett.