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ABSTRACT Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cramér’s V = 0.857, and Theil’s U = 0.316). For species-level community profiling, we found strong correlations (rs > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average rs = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.IMPORTANCEA quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.

Abstract Transitions from the liquid to the solid state of matter are omnipresent. They form a crucial step in the industrial solidification of metallic alloy melts and are greatly influenced by the thermophysical properties of the melt. Knowledge of the thermophysical properties of liquid metallic alloys is necessary in order to gain a tight control over the solidification pathway, and over the obtained material structure of the solid. Measurements of thermophysical properties on ground are often difficult, or even impossible, since liquids are strongly influenced by earth’s gravity. Another problem is the reactivity of melts with container materials, especially at high temperature. Finally, deep undercooling, necessary to understand nucleus formation and equilibrium as well as non-equilibrium solidification, can only be achieved in a containerless environment. Containerless experiments in microgravity allow precise benchmark measurements of thermophysical properties. The electromagnetic levitator ISS-EML on the International Space Station (ISS) offers perfect conditions for such experiments. This way, data for process simulations is obtained, and a deeper understanding of nucleation, crystal growth, microstructural evolution, and other details of the transformation from liquid to solid can be gained. Here, we address the scientific questions in detail, show highlights of recent achievements, and give an outlook on future work.

Periprosthetic joint infection (PJI) with Salmonella is rare. We therefore describe two cases of PJI with Salmonella spp. Case one is a 79-year-old female that presented with fever and acute left hip pain 16 months after revision total hip arthroplasty (THA) performed due to instability. Case two is a 82-year-old male after revision THA due to periprosthetic pseudotumor 22 years after THA. Microbiological work up of intra-operatively obtained specimen showed growth of Salmonella spp. In both patients, implant-retaining treatment was successful. Patients with PJI with Salmonella may be oligosymptomatic, potentially delaying the diagnosis. Successful implant-retraining treatment is possible.

LiNbO3 (LNO) is a material suitable for high-frequency and wideband RF filters as well as photonic applications due to its outstanding piezoelectric and optical properties. Applications such as thin-film bulk acoustic wave resonators or highly confined electro-optic modulators require thin films, which are still challenging to be obtained with the necessary crystalline quality by deposition methods. Alternatively to deposition, crystal ion-slicing (CIS) or Smart CutTM enables obtaining thin films hundreds of nanometers thick from the bulk single-crystal utilizing high-energy and dose implantation of light atoms. The price to pay is the partial degradation of the initial crystalline perfection, which translates to a degradation of the piezoelectric performance of the material if the CIS-induced damage is not eliminated.This work aims to understand the physics of the recrystallization process of the CIS-damaged LNO crystal upon thermal annealing. The study of the coherent and diffuse scattering by high-resolution X-ray diffraction, complemented by micro-Raman backscattering spectroscopy and Transmission Electron Microscopy (TEM), allowed to study the recovery of the crystallinity from the CIS-induced lattice strain and stress and the progressive reduction of the defects clusters dimension.

Background: Biologics are among the most effective therapies for psoriasis. However, many patients are only introduced to them at advanced stages of the disease course. Objectives: Our aim was to identify predictors of initiating biologic therapy in patients with psoriasis and compare patients initiating biologics early versus late in their disease course. Methods: Kaplan–Meier curves visualized time to biologic initiation, while Cox regression models further explored variables as predictors of biologic initiation. Mann–Whitney U and chi‐squared tests compared patients who started biologics early with those who began biologics later in the disease course. Results: Our primary analysis included 233 psoriasis patients. Cox regression showed that age at diagnosis (P = 0.007), general physical well‐being (P = 0.02), and nail psoriasis severity (P = 0.02) were significantly associated with time to biologic initiation. Our secondary analysis, the comparisons between patients starting biologics early versus later in the disease course, included a total of 378 patients. The median (interquartile range [IQR]) age at diagnosis was 34.5 (25.0–51.2) years for patients initiating biologics within 5 years, compared to 22.0 (15.0–32.8) years for patients initiating biologics later (P < 0.0001). The median (IQR) age at initiation was 37.0 (27.0–53.2) and 45.0 (36.0–55.0) years for patients initiating biologics earlier versus later than 5 years (P = 0.04). Conclusions: Age at diagnosis, general well‐being, and severity of nail psoriasis significantly predicted future initiation of biologic treatment. Patients initiating biologics early in their disease course were generally older at diagnosis but younger at the time of biologic initiation compared to patients initiating biologics later in their disease course. [ABSTRACT FROM AUTHOR]

Little is known about the cause of treatment failure of soil-transmitted helminth infections. Here, the authors show that pre-treatment gut microbial community composition enables predicting treatment outcome for Trichuris trichiura and hookworm infections.