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- ItemA Review on Data Fusion of Multidimensional Medical and Biomedical Data(Basel : MDPI, 2022) Azam, Kazi Sultana Farhana; Ryabchykov, Oleg; Bocklitz, ThomasData fusion aims to provide a more accurate description of a sample than any one source of data alone. At the same time, data fusion minimizes the uncertainty of the results by combining data from multiple sources. Both aim to improve the characterization of samples and might improve clinical diagnosis and prognosis. In this paper, we present an overview of the advances achieved over the last decades in data fusion approaches in the context of the medical and biomedical fields. We collected approaches for interpreting multiple sources of data in different combinations: image to image, image to biomarker, spectra to image, spectra to spectra, spectra to biomarker, and others. We found that the most prevalent combination is the image-to-image fusion and that most data fusion approaches were applied together with deep learning or machine learning methods.
- ItemApplication of molecular SERS nanosensors: where we stand and where we are headed towards?(Berlin ; Heidelberg : Springer, 2020) Jahn I.J.; Mühlig A.; Cialla-May D.Molecular specific and highly sensitive detection is the driving force of the surface-enhanced Raman spectroscopy (SERS) community. The technique opens the window to the undisturbed monitoring of cellular processes in situ or to the quantification of small molecular species that do not deliver Raman signals. The smart design of molecular SERS nanosensors makes it possible to indirectly but specifically detect, e.g. reactive oxygen species, carbon monoxide or potentially toxic metal ions. Detection schemes evolved over the years from simple metallic colloidal nanoparticles functionalized with sensing molecules that show uncontrolled aggregation to complex nanostructures with magnetic properties making the analysis of complex environmental samples possible. The present article gives the readership an overview of the present research advancements in the field of molecular SERS sensors, highlighting future trends. © 2020, The Author(s).
- ItemKitaev magnetism and fractionalized excitations in double perovskite Sm2ZnIrO6(College Park, ML : American Physical Society, 2020) Singh, Birender; Vogl, M.; Wurmehl, S.; Aswartham, S.; Büchner, B.; Kumar, PradeepThe quest for Kitaev spin liquids in particular three-dimensional solids is a long sought goal in condensed matter physics, as these states may give rise to exotic new types of quasiparticle excitations carrying fractional quantum numbers, namely Majorana fermionic excitations. Here we report the experimental signature of this characteristic feature of the Kitaev spin liquid via Raman measurements. Sm2ZnIrO6 is a strongly spin-orbit-coupled Mott insulator where Jeff=1/2 controls the physics, which provides striking evidence for this characteristic feature of the Kitaev spin liquid. As the temperature is lowered, we find that the spin excitations form a continuum in contrast to the conventional sharp modes expected in ordered antiferromagnets. Our observation of a broad magnetic continuum and anomalous renormalization of the phonon self-energy parameters shows the existence of fractionalization excitations in the double-perovskite structure, as theoretically conjectured in a Kitaev-Heisenberg geometrically frustrated double-perovskite system.
- ItemModified PCA and PLS: Towards a better classification in Raman spectroscopy–based biological applications(New York, NY : Wiley Interscience, 2020) Guo, Shuxia; Rösch, Petra; Popp, Jürgen; Bocklitz, ThomasRaman spectra of biological samples often exhibit variations originating from changes of spectrometers, measurement conditions, and cultivation conditions. Such unwanted variations make a classification extremely challenging, especially if they are more significant compared with the differences between groups to be separated. A classifier is prone to such unwanted variations (ie, intragroup variations) and can fail to learn the patterns that can help separate different groups (ie, intergroup differences). This often leads to a poor generalization performance and a degraded transferability of the trained model. A natural solution is to separate the intragroup variations from the intergroup differences and build the classifier based on merely the latter information, for example, by a well-designed feature extraction. This forms the idea of this contribution. Herein, we modified two commonly applied feature extraction approaches, principal component analysis (PCA) and partial least squares (PLS), in order to extract merely the features representing the intergroup differences. Both of the methods were verified with two Raman spectral datasets measured from bacterial cultures and colon tissues of mice, respectively. In comparison to ordinary PCA and PLS, the modified PCA was able to improve the prediction on the testing data that bears significant difference to the training data, while the modified PLS could help avoid overfitting and lead to a more stable classification. © 2019 The Authors. Journal of Chemometrics published by John Wiley & Sons Ltd
- ItemChemical Imaging of Mixed Metal Oxide Catalysts for Propylene Oxidation: From Model Binary Systems to Complex Multicomponent Systems(Weinheim : Wiley-VCH, 2021) Sprenger, Paul; Stehle, Matthias; Gaur, Abhijeet; Weiß, Jana; Brueckner, Dennis; Zhang, Yi; Garrevoet, Jan; Suuronen, Jussi‐Petteri; Thomann, Michael; Fischer, Achim; Grunwaldt, Jan‐Dierk; Sheppard, Thomas L.Industrially-applied mixed metal oxide catalysts often possess an ensemble of structural components with complementary functions. Characterisation of these hierarchical systems is challenging, particularly moving from binary to quaternary systems. Here a quaternary Bi−Mo−Co−Fe oxide catalyst showing significantly greater activity than binary Bi−Mo oxides for selective propylene oxidation to acrolein was studied with chemical imaging techniques from the microscale to nanoscale. Conventional techniques like XRD and Raman spectroscopy could only distinguish a small number of components. Spatially-resolved characterisation provided a clearer picture of metal oxide phase composition, starting from elemental distribution by SEM-EDX and spatially-resolved mapping of metal oxide components by 2D Raman spectroscopy. This was extended to 3D using multiscale hard X-ray tomography with fluorescence, phase, and diffraction contrast. The identification and co-localisation of phases in 2D and 3D can assist in rationalising catalytic performance during propylene oxidation, based on studies of model, binary, or ternary catalyst systems in literature. This approach is generally applicable and attractive for characterisation of complex mixed metal oxide systems. © 2021 The Authors. ChemCatChem published by Wiley-VCH GmbH
- ItemComparison of Different Label-Free Raman Spectroscopy Approaches for the Discrimination of Clinical MRSA and MSSA Isolates(Birmingham, Ala. : ASM, 2022) Pistiki, Aikaterini; Monecke, Stefan; Shen, Haodong; Ryabchykov, Oleg; Bocklitz, Thomas W.; Rösch, Petra; Ehricht, Ralf; Popp, JürgenMethicillin-resistant Staphylococcus aureus (MRSA) is classified as one of the priority pathogens that threaten human health. Resistance detection with conventional microbiological methods takes several days, forcing physicians to administer empirical antimicrobial treatment that is not always appropriate. A need exists for a rapid, accurate, and cost-effective method that allows targeted antimicrobial therapy in limited time. In this pilot study, we investigate the efficacy of three different label-free Raman spectroscopic approaches to differentiate methicillin-resistant and -susceptible clinical isolates of S. aureus (MSSA). Single-cell analysis using 532 nm excitation was shown to be the most suitable approach since it captures information on the overall biochemical composition of the bacteria, predicting 87.5% of the strains correctly. UV resonance Raman microspectroscopy provided a balanced accuracy of 62.5% and was not sensitive enough in discriminating MRSA from MSSA. Excitation of 785 nm directly on the petri dish provided a balanced accuracy of 87.5%. However, the difference between the strains was derived from the dominant staphyloxanthin bands in the MRSA, a cell component not associated with the presence of methicillin resistance. This is the first step toward the development of label-free Raman spectroscopy for the discrimination of MRSA and MSSA using single-cell analysis with 532 nm excitation. IMPORTANCE Label-free Raman spectra capture the high chemical complexity of bacterial cells. Many different Raman approaches have been developed using different excitation wavelength and cell analysis methods. This study highlights the major importance of selecting the most suitable Raman approach, capable of providing spectral features that can be associated with the cell mechanism under investigation. It is shown that the approach of choice for differentiating MRSA from MSSA should be single-cell analysis with 532 nm excitation since it captures the difference in the overall biochemical composition. These results should be taken into consideration in future studies aiming for the development of label-free Raman spectroscopy as a clinical analytical tool for antimicrobial resistance determination.
- ItemComparability of Raman Spectroscopic Configurations: A Large Scale Cross-Laboratory Study(Columbus, Ohio : American Chemical Society, 2020) Guo S.; Beleites C.; Neugebauer U.; Abalde-Cela S.; Afseth N.K.; Alsamad F.; Anand S.; Araujo-Andrade C.; Aškrabić S.; Avci E.; Baia M.; Baranska M.; Baria E.; Batista De Carvalho L.A.E.; De Bettignies P.; Bonifacio A.; Bonnier F.; Brauchle E.M.; Byrne H.J.; Chourpa I.; Cicchi R.; Cuisinier F.; Culha M.; Dahms M.; David C.; Duponchel L.; Duraipandian S.; El-Mashtoly S.F.; Ellis D.I.; Eppe G.; Falgayrac G.; Gamulin O.; Gardner B.; Gardner P.; Gerwert K.; Giamarellos-Bourboulis E.J.; Gizurarson S.; Gnyba M.; Goodacre R.; Grysan P.; Guntinas-Lichius O.; Helgadottir H.; Grošev V.M.; Kendall C.; Kiselev R.; Kölbach M.; Krafft C.; Krishnamoorthy S.; Kubryck P.; Lendl B.; Loza-Alvarez P.; Lyng F.M.; Machill S.; Malherbe C.; Marro M.; Marques M.P.M.; Matuszyk E.; Morasso C.F.; Moreau M.; Muhamadali H.; Mussi V.; Notingher I.; Pacia M.Z.; Pavone F.S.; Penel G.; Petersen D.; Piot O.; Rau J.V.; Richter M.; Rybarczyk M.K.; Salehi H.; Schenke-Layland K.; Schlücker S.; Schosserer M.; Schütze K.; Sergo V.; Sinjab F.; Smulko J.; Sockalingum G.D.; Stiebing C.; Stone N.; Untereiner V.; Vanna R.; Wieland K.; Popp J.; Bocklitz T.The variable configuration of Raman spectroscopic platforms is one of the major obstacles in establishing Raman spectroscopy as a valuable physicochemical method within real-world scenarios such as clinical diagnostics. For such real world applications like diagnostic classification, the models should ideally be usable to predict data from different setups. Whether it is done by training a rugged model with data from many setups or by a primary-replica strategy where models are developed on a 'primary' setup and the test data are generated on 'replicate' setups, this is only possible if the Raman spectra from different setups are consistent, reproducible, and comparable. However, Raman spectra can be highly sensitive to the measurement conditions, and they change from setup to setup even if the same samples are measured. Although increasingly recognized as an issue, the dependence of the Raman spectra on the instrumental configuration is far from being fully understood and great effort is needed to address the resulting spectral variations and to correct for them. To make the severity of the situation clear, we present a round robin experiment investigating the comparability of 35 Raman spectroscopic devices with different configurations in 15 institutes within seven European countries from the COST (European Cooperation in Science and Technology) action Raman4clinics. The experiment was developed in a fashion that allows various instrumental configurations ranging from highly confocal setups to fibre-optic based systems with different excitation wavelengths. We illustrate the spectral variations caused by the instrumental configurations from the perspectives of peak shifts, intensity variations, peak widths, and noise levels. We conclude this contribution with recommendations that may help to improve the inter-laboratory studies. © 2020 American Chemical Society.
- ItemCorrelation of crystal violet biofilm test results of Staphylococcus aureus clinical isolates with Raman spectroscopic read-out(Chichester [u.a.] : Wiley, 2021) Ebert, Christina; Tuchscherr, Lorena; Unger, Nancy; Pöllath, Christine; Gladigau, Frederike; Popp, Jürgen; Löffler, Bettina; Neugebauer, UteBiofilm-related infections occur quite frequently in hospital settings and require rapid diagnostic identification as they are recalcitrant to antibiotic therapy and make special treatment necessary. One of the standard microbiological in vitro tests is the crystal violet test. It indirectly determines the amount of biofilm by measuring the optical density (OD) of the crystal violet-stained biofilm matrix and cells. However, this test is quite time-consuming, as it requires bacterial cultivation up to several days. In this study, we correlate fast Raman spectroscopic read-out of clinical Staphylococcus aureus isolates from 47 patients with different disease background with their biofilm-forming characteristics. Included were low (OD < 10), medium (OD ≥ 10 and ≤20), and high (OD > 20) biofilm performers as determined by the crystal violet test. Raman spectroscopic analysis of the bacteria revealed most spectral differences between high and low biofilm performers in the fingerprint region between 750 and 1150 cm−1. Using partial least square regression (PLSR) analysis on the Raman spectra involving the three categories of biofilm formation, it was possible to obtain a slight linear correlation of the Raman spectra with the biofilm OD values. The PLSR loading coefficient highlighted spectral differences between high and low biofilm performers for Raman bands that represent nucleic acids, carbohydrates, and proteins. Our results point to a possible application of Raman spectroscopy as a fast prediction tool for biofilm formation of bacterial strains directly after isolation from the infected patient. This could help clinicians make timely and adapted therapeutic decision in future.
- ItemCompact, Watt-class 785 nm dual-wavelength master oscillator power amplifiers(Bristol ; Philadelphia, PA : IOP Publishing Ltd., 2022) Müller, André; Maiwald, Martin; Sumpf, Bernd785 nm micro-integrated, dual-wavelength master oscillator power amplifiers with a footprint of 5 mm × 25 mm are presented. They are based on Y-branch distributed Bragg reflector ridge waveguide diode lasers and anti-reflection coated tapered amplifiers. In order to reduce the impact of potential optical feedback, devices with master oscillator front facet reflectivities of 5% and 30% as well as with an integrated miniaturized optical isolator have been realized. A comparison up to 1 W shows narrowband dual wavelength laser emission with a spectral distance of 0.6 nm (10 cm−1) and individual spectral widths <20 pm. As expected, a higher front facet reflectivity leads to a significant reduction of feedback related mode hops. Longitudinal modes corresponding to the master oscillator resonator length remain within spectral windows <0.15 nm (3 cm−1), suitable for applications such as Raman spectroscopy and especially shifted excitation Raman difference spectroscopy. Integrating a compact 30 dB optical isolator completely eliminates the observed optical feedback effects. Lateral beam propagation ratios of 1.2 (1/e2) enable easy beam shaping and fiber coupling. Outside of the experimental comparison, the developed MOPAs provide up to 2.7 W of optical output power available for applications.
- ItemReal-time stimulated Raman spectroscopy with a non-collinear optical parametric oscillator(Washington, DC : Soc., 2021) Beichert, Luise; Binhammer, Yuliya; Andrade, José R. C.; Mevert, Robin; Kniggendorf, Ann-Kathrin; Roth, Bernhard; Morgner, UweUltrafast detection of microplastic particles is becoming a vital problem, as these particles are found in water sources worldwide. Ideally, a live analysis in flow is desirable to directly monitor the water quality for contaminations. Therefore, coherent Raman spectroscopy techniques require fast and broadband tunable lasers to address all relevant spectral regions of the investigated samples. In our work, we combine a high power non-collinear optical parametric oscillator with a real-time stimulated Raman scattering spectroscopy setup. The light source is continously tunable from 700 nm to 1030 nm in less than 10 ms, delivering an average output power of more than 500 mW with sub-ps pulses. We show the immediate observation of mixing processes and the detection of microplastic particles in water solution with a spectral window of more than 2000 cm-1.
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