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End date: 2023 × Start date: 2020 × Has files: Yes × Type: Text × WGL Institute: IPHT ×

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Now showing 1 - 10 of 263
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    Automated and rapid identification of multidrug resistant Escherichia coli against the lead drugs of acylureidopenicillins, cephalosporins, and fluoroquinolones using specific Raman marker bands
    (Weinheim : Wiley-VCH-Verl., 2020) Götz, Theresa; Dahms, Marcel; Kirchhoff, Johanna; Beleites, Claudia; Glaser, Uwe; Bohnert, Jürgen A.; Pletz, Mathias W.; Popp, Jürgen; Schlattmann, Peter; Neugebauer, Ute
    A Raman-based, strain-independent, semi-automated method is presented that allows the rapid (<3 hours) determination of antibiotic susceptibility of bacterial pathogens isolated from clinical samples. Applying a priori knowledge about the mode of action of the respective antibiotic, we identified characteristic Raman marker bands in the spectrum and calculated batch-wise weighted sum scores from standardized Raman intensity differences between spectra of antibiotic exposed and nonexposed samples of the same strains. The lead substances for three relevant antibiotic classes (fluoroquinolone ciprofloxacin, third-generation cephalosporin cefotaxime, ureidopenicillin piperacillin) against multidrug-resistant Gram-negative bacteria (MRGN) revealed a high sensitivity and specificity for the susceptibility testing of two Escherichia coli laboratory strains and 12 clinical isolates. The method benefits from the parallel incubation of control and treated samples, which reduces the variance due to alterations in cultivation conditions and the standardization of differences between batches leading to long-term comparability of Raman measurements. © 2020 The Authors. Journal of Biophotonics published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
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    Numerical and Experimental Demonstration of Intermodal Dispersive Wave Generation
    (Weinheim : Wiley VCH, 2021) Lüpken, Niklas M.; Timmerkamp, Maximilian; Scheibinger, Ramona; Schaarschmidt, Kay; Schmidt, Markus A.; Boller, Klaus‐J.; Fallnich, Carsten
    Evidence of intermodal dispersive wave generation mediated by intermodal cross-phase modulation (iXPM) between different transverse modes during supercontinuum generation in silicon nitride waveguides is presented. The formation of a higher-order soliton in one strong transverse mode leads to phase modulation of a second, weak transverse mode by iXPM. The phase modulation enables not only supercontinuum generation but also dispersive wave generation within the weak mode, that otherwise has insufficient power to facilitate dispersive wave formation. The nonlinear frequency conversion scheme presented here suggests phase-matching conditions beyond what is currently known, which can be exploited for extending the spectral bandwidth within supercontinuum generation.
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    Genotyping of methicillin resistant Staphylococcus aureus from the United Arab Emirates
    ([London] : Macmillan Publishers Limited, part of Springer Nature, 2020) Senok, Abiola; Nassar, Rania; Celiloglu, Handan; Nabi, Anju; Alfaresi, Mubarak; Weber, Stefan; Rizvi, Irfan; Müller, Elke; Reissig, Annett; Gawlik, Darius; Monecke, Stefan; Ehricht, Ralf
    Reports from Arabian Gulf countries have demonstrated emergence of novel methicillin resistant Staphylococcus aureus (MRSA) strains. To address the lack of data from the United Arab Emirates (UAE), genetic characterisation of MRSA identified between December 2017 and August 2019 was conducted using DNA microarray-based assays. The 625 MRSA isolates studied were grouped into 23 clonal complexes (CCs) and assigned to 103 strains. CC5, CC6, CC22 and CC30 represented 54.2% (n/N = 339/625) of isolates with other common CCs being CC1, CC8, CC772, CC361, CC80, CC88. Emergence of CC398 MRSA, CC5-MRSA-IV Sri Lanka Clone and ST5/ST225-MRSA-II, Rhine-Hesse EMRSA/New York-Japan Clone in our setting was detected. Variants of pandemic CC8-MRSA-[IVa + ACME I] (PVL+) USA300 were detected and majority of CC772 strains were CC772-MRSA-V (PVL+), “Bengal- Bay Clone”. Novel MRSA strains identified include CC5-MRSA-V (edinA+), CC5-MRSA-[VT + fusC], CC5-MRSA-IVa (tst1+), CC5-MRSA-[V/VT + cas + fusC + ccrA/B-1], CC8-MRSA-V/VT, CC22-MRSA-[IV + fusC + ccrAA/(C)], CC45-MRSA-[IV + fusC + tir], CC80-MRSA-IVa, CC121-MRSA-V/VT, CC152-MRSA-[V + fusC] (PVL+). Although several strains harboured SCC-borne fusidic acid resistance (fusC) (n = 181), erythromycin/clindamycin resistance (ermC) (n = 132) and gentamicin resistance (aacA-aphD) (n = 179) genes, none harboured vancomycin resistance genes while mupirocin resistance gene mupR (n = 2) and cfr gene (n = 1) were rare. An extensive MRSA repertoire including CCs previously unreported in the region and novel strains which probably arose locally suggest an evolving MRSA landscape. © 2020, The Author(s).
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    Molecular investigations on a chimeric strain of Staphylococcus aureus sequence type 80
    (San Francisco, California, US : PLOS, 2020) Gawlik, Darius; Ruppelt-Lorz, Antje; Müller, Elke; Reißig, Annett; Hotzel, Helmut; Braun, Sascha D.; Söderquist, Bo; Ziegler-Cordts, Albrecht; Stein, Claudia; Pletz, Mathias W.; Ehricht, Ralf; Monecke, Stefan
    A PVL-positive, methicillin-susceptible Staphylococcus aureus was cultured from pus from cervical lymphadenitis of a patient of East-African origin. Microarray hybridisation assigned the isolate to clonal complex (CC) 80 but revealed unusual features, including the presence of the ORF-CM14 enterotoxin homologue and of an ACME-III element as well as the absence of etD and edinB. The isolate was subjected to both, Illumina and Nanopore sequencing allowing characterisation of deviating regions within the strain´s genome. Atypical features of this strain were attributable to the presence of two genomic regions that originated from other S. aureus lineages and that comprised, respectively, 3% and 1.4% of the genome. One deviating region extended from walJ to sirB. It comprised ORF-CM14 and the ACME-III element. A homologous but larger fragment was also found in an atypical S. aureus CC1/ST567 strain whose lineage might have served as donor of this genomic region. This region itself is a chimera comprising fragments from CC1 as well as fragments of unknown origin. The other deviating region comprised the region from htsB to ecfA2, i.e., another 3% of the genome. It was very similar to CC1 sequences. Either this suggests an incorporation of CC1 DNA into the study strain, or alternatively a recombination event affecting “canonical” CC80. Thus, the study strain bears witness of several recombination events affecting supposedly core genomic genes. Although the exact mechanism is not yet clear, such chimerism seems to be an additional pathway in the evolution of S. aureus. This could facilitate also a transmission of virulence and resistance factors and therefore offer an additional evolutionary advantage.
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    Charged domains in ferroelectric, polycrystalline yttrium manganite thin films resolved with scanning electron microscopy
    (Bristol : IOP Publ., 2020) Rayapati, Venkata Rao; Bürger, Danilo; Du, Nan; Kowol, Cornelia; Blaschke, Daniel; Stöcker, Hartmut; Matthes, Patrick; Patra, Rajkumar; Skorupa, Ilona; Schulz, Stefan E.; Schmidt, Heidemarie
    We have investigated ferroelectric charged domains in polycrystalline hexagonal yttrium manganite thin films (Y1Mn1O3, Y0.95Mn1.05O3, Y1Mn0.99Ti0.01O3, and Y0.94Mn1.05Ti0.01O3) by scanning electron microscopy (SEM) in secondary electron emission mode with a small acceleration voltage. Using SEM at an acceleration voltage of 1.0 kV otherwise homogenous surface charging effects are reduced, polarization charges can be observed and polarization directions (±Pz) of the ferroelectric domains in the polycrystalline thin films can be identified. Thin films of different chemical composition have been deposited by pulsed laser deposition on Pt/SiO2/Si structures under otherwise same growth conditions. Using SEM it has been shown that different charged domain density networks are existing in polycrystalline yttrium manganite thin films. © 2020 IOP Publishing Ltd.
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    Correlations between the structure and superconducting properties of MT-YBaCuO
    (Bristol : IOP Publ., 2020) Prikhna, T.A.; Moshchill, V.E.; Rabier, J.; Chaud, X.; Joulain, A.; Pan, A.V.; Litskendorf, D.; Habisreuther, T.
    Comprehensive experimental results of fully oxidized (up to YBa2Cu3O6,9-7) melt-Textured YBaCuO materials with different microstructures are presented. These microstructures are built respectively: (1) with a high dislocations density but almost without twins (after high temperature treatment at 2 GPa) and (2) with a high twin density, but practically free from dislocations and stacking faults (after high temperature oxygenation at 10-16 MPa). It is shown that for attaining high critical current densities and fields of irreversibility (jc(H-c, 0 T)=9•104 A/cm2, H irr=9.7 T at 77 K), a high twin density in YBa2Cu3O6.9-7 matrix of MT-YBCO is required. The density of twins in fully oxidized materials depends on the distances between Y2BaCuO5 inclusions, larger twin densities are related to shorter distances between inclusions. The influence of phase composition of the initial powder mixtures on the distances between Y2BaCuO5 inclusions have been characterized and discussed. © Published under licence by IOP Publishing Ltd.
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    What the Phage: a scalable workflow for the identification and analysis of phage sequences
    (Oxford : Oxford University Press, 2022) Marquet, Mike; Hölzer, Martin; Pletz, Mathias W; Viehweger, Adrian; Makarewicz, Oliwia; Ehricht, Ralf; Brandt, Christian
    Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed "What the Phage"(WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus supporting the user's decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage).
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    Nanograting-Enhanced Optical Fibers for Visible and Infrared Light Collection at Large Input Angles
    (Basel : MDPI, 2021) Wang, Ning; Zeisberger, Matthias; Hübner, Uwe; Schmidt, Markus A.
    The efficient incoupling of light into particular fibers at large angles is essential for a multitude of applications; however, this is difficult to achieve with commonly used fibers due to low numerical aperture. Here, we demonstrate that commonly used optical fibers functionalized with arrays of metallic nanodots show substantially improved large-angle light-collection performances at multiple wavelengths. In particular, we show that at visible wavelengths, higher diffraction orders contribute significantly to the light-coupling efficiency, independent of the incident polarization, with a dominant excitation of the fundamental mode. The experimental observation is confirmed by an analytical model, which directly suggests further improvement in incoupling efficiency through the use of powerful nanostructures such as metasurface or dielectric gratings. Therefore, our concept paves the way for high-performance fiber-based optical devices and is particularly relevant within the context of endoscopic-type applications in life science and light collection within quantum technology.
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    Response of the wood-decay fungus Schizophyllum commune to co-occurring microorganisms
    (San Francisco, California, US : PLOS, 2020) Krause, Katrin; Jung, Elke-Martina; Lindner, Julia; Hardiman, Imam; Petschner, Jessica; Madhavan, Soumya; Matthäus, Christian; Kai, Marco; Menezes, Riya Christina; Popp, Jürgen; Svatoš, Aleš; Kothe, Erika
    Microorganisms are constantly interacting in a given environment by a constant exchange of signaling molecules. In timber, wood-decay fungi will come into contact with other fungi and bacteria. In naturally bleached wood, dark, pigmented lines arising from confrontation of two fungi often hint at such interactions. The metabolites (and pigment) exchange was investigated using the lignicolous basidiomycete Schizophyllum commune, and co-occurring fungi and bacteria inoculated directly on sterilized wood, or on media. In interactions with competitive wood degrading fungi, yeasts or bacteria, different competition strategies and communication types were observed, and stress reactions, as well as competitor-induced enzymes or pigments were analyzed. Melanin, indole, flavonoids and carotenoids were shown to be induced in S. commune interactions. The induced genes included multi-copper oxidases lcc1, lcc2, mco1, mco2, mco3 and mco4, possibly involved in both pigment production and lignin degradation typical for wood bleaching by wood-decay fungi.
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    Wafer-level uniformity of atomic-layer-deposited niobium nitride thin films for quantum devices
    (New York, NY : Inst., 2021) Knehr, Emanuel; Ziegler, Mario; Linzen, Sven; Ilin, Konstantin; Schanz, Patrick; Plentz, Jonathan; Diegel, Marco; Schmidt, Heidemarie; Il’iche, Evgeni; Siegel, Michael
    Superconducting niobium nitride thin films are used for a variety of photon detectors, quantum devices, and superconducting electronics. Most of these applications require highly uniform films, for instance, when moving from single-pixel detectors to arrays with a large active area. Plasma-enhanced atomic layer deposition (ALD) of superconducting niobium nitride is a feasible option to produce high-quality, conformal thin films and has been demonstrated as a film deposition method to fabricate superconducting nanowire single-photon detectors before. Here, we explore the property spread of ALD-NbN across a 6-in. wafer area. Over the equivalent area of a 2-in. wafer, we measure a maximum deviation of 1% in critical temperature and 12% in switching current. Toward larger areas, structural characterizations indicate that changes in the crystal structure seem to be the limiting factor rather than film composition or impurities. The results show that ALD is suited to fabricate NbN thin films as a material for large-area detector arrays and for new detector designs and devices requiring uniform superconducting thin films with precise thickness control.