Time-Encoded Raman: Fiber-based, hyperspectral, broadband stimulated Raman microscopy

Raman sensing and Raman microscopy are amongst the most specific optical technologies to identify the chemical compounds of unknown samples, and to enable label-free biomedical imaging with molecular contrast. However, the high cost and complexity, low speed, and incomplete spectral information provided by current technology are major challenges preventing more widespread application of Raman systems. To overcome these limitations, we developed a new method for stimulated Raman spectroscopy and Raman imaging using continuous wave (CW), rapidly wavelength swept lasers. Our all-fiber, time-encoded Raman (TICO-Raman) setup uses a Fourier Domain Mode Locked (FDML) laser source to achieve a unique combination of high speed, broad spectral coverage (750 cm-1 - 3150 cm-1) and high resolution (0.5 cm-1). The Raman information is directly encoded and acquired in time. We demonstrate quantitative chemical analysis of a solvent mixture and hyperspectral Raman microscopy with molecular contrast of plant cells.Comment: 9 pages, 4 figure

Learning Extremal Representations with Deep Archetypal Analysis

Archetypes are typical population representatives in an extremal sense, where typicality is understood as the most extreme manifestation of a trait or feature. In linear feature space, archetypes approximate the data convex hull allowing all data points to be expressed as convex mixtures of archetypes. However, it might not always be possible to identify meaningful archetypes in a given feature space. Learning an appropriate feature space and identifying suitable archetypes simultaneously addresses this problem. This paper introduces a generative formulation of the linear archetype model, parameterized by neural networks. By introducing the distance-dependent archetype loss, the linear archetype model can be integrated into the latent space of a variational autoencoder, and an optimal representation with respect to the unknown archetypes can be learned end-to-end. The reformulation of linear Archetypal Analysis as deep variational information bottleneck, allows the incorporation of arbitrarily complex side information during training. Furthermore, an alternative prior, based on a modified Dirichlet distribution, is proposed. The real-world applicability of the proposed method is demonstrated by exploring archetypes of female facial expressions while using multi-rater based emotion scores of these expressions as side information. A second application illustrates the exploration of the chemical space of small organic molecules. In this experiment, it is demonstrated that exchanging the side information but keeping the same set of molecules, e. g. using as side information the heat capacity of each molecule instead of the band gap energy, will result in the identification of different archetypes. As an application, these learned representations of chemical space might reveal distinct starting points for de novo molecular design.Comment: Under review for publication at the International Journal of Computer Vision (IJCV). Extended version of our GCPR2019 paper "Deep Archetypal Analysis

Good Online Teaching Practice from the Students’ Perspective in the First Weeks of the CoViD-19 Crisis: The Student View on ‹Good Teaching› at TU Graz in May 2020

Ende Mai 2020 wurden die Studierenden der Technischen Universität Graz im Rahmen einer studentischen Qualifizierungsarbeit zu guten Lehrerfahrungen in der der Notfall-Online-Lehre durch die CoViD-19-Pandemie im Sommersemester 2020 befragt. 137 Beispiele für gute Lehre von unterschiedlichen Teilnehmenden werden für den Beitrag ausgewertet. Die Analyse der Antworten zeigen, dass in einem Gros der Lehrveranstaltungen die als gelungen erlebt wurden, (auch) Videotechnik zum Einsatz kommt (90 %), bei mehr als der Hälfte (auch) Videos zur Verfügung gestellt werden und bei der Hälfte Live-, d. h. synchrone Veranstaltungen angeboten werden. Ein wesentliches Merkmal für gute Lehrbeispiele ist, dass Studierende etwas gelernt haben (77 % «trifft voll zu») und bei Beschreibungen der Lehrbeispiele erwähnen rund ein Drittel, dass die Umstellung der Lehrveranstaltung, die sie als gute Lehre erlebten, zügig erfolgte. Methodisch-didaktische Besonderheiten werden damit in der frühen Phase des Distance Learning eher selten (12 %) von den befragten Studierenden benannt.At the end of May 2020, students at Graz University of Technology were asked about good teaching experiences in emergency online teaching through the CoViD 19 pandemic in the summer semester 2020 within a student qualification work. 137 examples of good teaching from different participants are evaluated for the contribution. The analysis of the responses shows that video technology is (also) used in a majority of the courses that were experienced as good practice (90 %), videos are (also) made available in more than half of them, and live, i.e. synchronous, online events are offered in half of them. An essential characteristic of good teaching examples is that students have learned something (77 % «strongly agree») and in descriptions of the teaching examples around one third mention that the changeover of the course they experienced as good practice took place quickly. Students mentioned methodological-didactic features are rather rarely (12 %) in the early phase of distance learning

A Novel Rapid Sample Preparation Method for MALDI-TOF MS Permits Borrelia burgdorferi Sensu Lato Species and Isolate Differentiation

The genus Borrelia comprises vector-borne bacterial pathogens that can severely affect human and animal health. Members of the Borrelia burgdorferi sensu lato species complex can cause Lyme borreliosis, one of the most common vector-borne diseases in the Northern hemisphere. Besides, members of the relapsing fever group of spirochetes can cause tick-borne relapsing fever in humans and various febrile illnesses in animals in tropical, subtropical and temperate regions. Borrelia spp. organisms are fastidious to cultivate and to maintain in vitro, and therefore, difficult to work with in the laboratory. Currently, borrelia identification is mainly performed using PCR and DNA sequencing methods, which can be complicated/frustrating on complex DNA templates and may still be relatively expensive. Alternative techniques such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) are not well established for Borrelia spp., although this technique is currently one of the most used techniques for rapid identification of bacteria in microbiological diagnostic laboratories. This is mainly due to unsatisfactory results obtained by use of simple sample preparation techniques and medium-contamination obscuring the mass spectra. In addition, comprehensive libraries for Borrelia spp. MALDI-TOF MS have yet to be established. In this study, we developed a new filter-based chemical extraction technique that allows measurement of high quality Borrelia spp. spectra from less than 100,000 bacteria per spot in MALDI-TOF MS. We used 49 isolates of 13 different species to produce the largest mass-library for Borrelia spp. so far and to validate the protocol. The library was successfully established and identifies >96% of used isolates correctly to species level. Cluster analysis on the sum spectra was applied to all the different isolates, which resulted in tight cluster generation for most species. Comparative analysis of the generated cluster to a phylogeny based on concatenated multi-locus sequence typing genes provided a surprising homology. Our data demonstrate that the technique described here can be used for fast and reliable species and strain typing within the borrelia complex

Delayed enhancement imaging of myocardial viability: low-dose high-pitch CT versus MRI

Objectives: To evaluate the accuracy of high-pitch delayed enhancement (DE) CT for the assessment of myocardial viability with MRI as the reference standard. Methods: Twenty-four patients (mean age 66.9 ± 9.2years) with coronary artery disease underwent DE imaging with 128-slice dual-source CT (prospective electrocardiography (ECG)-triggering) and MRI at 1.5T. Two observers assessed DE transmurality per segment, and measured signal intensity (MRI) or attenuation (CT) in infarcted and healthy myocardium and noise in the left ventricular blood pool for calculating contrast-to-noise ratios (CNR). Results: 75/408 (18.4%) segments in 18/24 patients (75.0%) showed DE in MRI, of which 28 segments in 10/24 (41.7%) patients were non-viable (scar tissue transmurality >50%). Sensitivity, specificity and accuracy of CT for diagnosis of non-viability were 60.7%, 96.8% and 94.4% per segment, and 90.0%, 92.9% and 91.7% per patient. CNR was significantly higher in MR (7.4 ± 3.0 vs. 4.6 ± 1.5; p = 0.018), and image noise significantly lower (11.6 ± 5.7 vs.15.0 ± 4.5; p = 0.019). Radiation dose of DECT was 0.89 ± 0.07mSv. Conclusions: CTDE imaging in the high-pitch mode enables myocardial viability assessment at a low radiation dose and good accuracy compared with MR, although associated with a lower CNR and higher nois

Dual-step prospective ECG-triggered 128-slice dual-source CT for evaluation of coronary arteries and cardiac function without heart rate control: a technical note

Purpose: To describe prospective ECG-triggered dual-source CT dual-step pulsing (pECGdual_step) for evaluation of coronary arteries and cardiac function. Methods: Fifty-one consecutive patients pre- or post-cardiovascular surgery were examined with adaptive sequential tube current modulated (pECGdual-step) 128-slice dual-source CT without heart rate control (main padding window: 40% RR interval >65bpm/70% RR interval <65bpm). Image quality of coronary arteries was graded (4-point scale), and cardiac function was evaluated. Results: Mean HR was 68bpm. Thirty-seven patients were in stable sinus rhythm (SR); 14 had arrhythmia. Image quality of coronary arteries was diagnostic in 804/816 (98%) of segments. The number of non-diagnostic segments was higher in patients with arrhythmia as compared to those in SR (4% vs. 0.5%; p = 0.01), and there were fewer segments with excellent image quality (79% vs. 94%; p < 0.001) and more segments with impaired image quality (p < 0.001 and p = 0.002). Global and regional LV function could be evaluated in 41 (80%) and 47 (92%) patients, and valvular function in 48 (94%). In 11/14 of patients with arrhythmia, the second step switched to full mAs, increasing radiation exposure to 8.6mAs (p < 0.001). The average radiation dose was 3.8mSv (range, 1.7-7.9) in patients in SR. Conclusion: pECGdual-step128-slice DSCT is feasible for the evaluation of coronary arteries and cardiac function without heart rate control in patients in stable sinus rhythm at a low radiation dos

Applicability of Capacitive Micromachined Ultrasonic Transducers for the detection of proton-induced thermoacoustic waves

This study investigates the application of broadband capacitive micromachined ultrasonic transducers (CMUT) to ionoacoustics (i.e., the thermoacoustic emissions induced by the energy deposition of ion beam) over a wide frequency range from hundreds of kHz to a few MHz. A water tank was irradiated by a 20 MeV pulsed proton beam. The frequency and amplitude of the ionoacoustic waves were modulated by adding material before to penetrate into the water tank to change the beam energy and its spatial dimensions. The measurements were performed with a 12 MHz CMUT prototype and compared to ones obtained from commercial 3.5 MHz piezoeletric transducer as well as to in silico studies employing the k-Wave Matlab toolbox in combination with FLUKA Monte Carlo simulations to derive the dose (i.e., energy deposition per mass) and initial pressure distribution. Comparison of the experimental and in silico results show that the CMUT bandwidth is wide enough to measure the signal without any degradation or attenuation of the frequency content in the investigated frequency range, thus ensuring accurate reconstruction of the dose distribution and potential bi-modality system for the co-registration of ionoacoustic and ultrasound imaging

Comparison of Intranasal Outer Membrane Vesicles with Cholera Toxin and Injected MF59C.1 as Adjuvants for Malaria Transmission Blocking Antigens AnAPN1 and Pfs48/45

Purified protein vaccines often require adjuvants for efficient stimulation of immune responses. There is no licensed mucosal adjuvant on the market to adequately boost the immune response to purified antigens for intranasal applications in humans. Bacterial outer membrane vesicles (OMV) are attractive candidates potentially combining antigenic and adjuvant properties in one substance. To more precisely characterize the potential of Escherichia coli OMV for intranasal vaccination with heterologous antigens, immune responses for AnAPN1 and Pfs48/45 as well as ovalbumin as a reference antigen were assessed in mice. The intranasal adjuvant cholera toxin (CT) and parenteral adjuvant MF59C.1 were used in comparison. Vaccinations were administered intranasally or subcutaneously. Antibodies (total IgG and IgM as well as subclasses IgG1, IgG2a, IgG2b, and IgG3) were measured by ELISA. T cell responses (cytotoxic T cells, Th1, Th17, and regulatory T cells) were determined by flow cytometry. When OMV were used as adjuvant for intranasal immunization, antibody and cellular responses against all three antigens could be induced, comparable to cholera toxin and MF59C.1. Antigen-specific IgG titres above 1 : 10 5 could be detected in all groups. This study provides the rationale for further development of OMV as a vaccination strategy in malaria and other diseases

Comparison of Intranasal Outer Membrane Vesicles with Cholera Toxin and Injected MF59C.1 as Adjuvants for Malaria Transmission Blocking Antigens AnAPN1 and Pfs48/45

Purified protein vaccines often require adjuvants for efficient stimulation of immune responses. There is no licensed mucosal adjuvant on the market to adequately boost the immune response to purified antigens for intranasal applications in humans. Bacterial outer membrane vesicles (OMV) are attractive candidates potentially combining antigenic and adjuvant properties in one substance. To more precisely characterize the potential of Escherichia coli OMV for intranasal vaccination with heterologous antigens, immune responses for AnAPN1 and Pfs48/45 as well as ovalbumin as a reference antigen were assessed in mice. The intranasal adjuvant cholera toxin (CT) and parenteral adjuvant MF59C.1 were used in comparison. Vaccinations were administered intranasally or subcutaneously. Antibodies (total IgG and IgM as well as subclasses IgG1, IgG2a, IgG2b, and IgG3) were measured by ELISA. T cell responses (cytotoxic T cells, Th1, Th17, and regulatory T cells) were determined by flow cytometry. When OMV were used as adjuvant for intranasal immunization, antibody and cellular responses against all three antigens could be induced, comparable to cholera toxin and MF59C.1. Antigen-specific IgG titres above 1 : 10 5 could be detected in all groups. This study provides the rationale for further development of OMV as a vaccination strategy in malaria and other diseases