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7. Conditional Generative Data Augmentation for Clinical Audio Datasets

Author

Seibold, M, Hoch, A, Farshad, M, Navab, N, Fürnstahl, P, University of Zurich, and Seibold, M

Subjects
FOS: Computer and information sciences, Sound (cs.SD), Computer Science - Machine Learning, Audio and Speech Processing (eess.AS), FOS: Electrical engineering, electronic engineering, information engineering, 610 Medicine & health, 10046 Balgrist University Hospital, Swiss Spinal Cord Injury Center, 1700 General Computer Science, 2614 Theoretical Computer Science, Computer Science - Sound, Machine Learning (cs.LG), Electrical Engineering and Systems Science - Audio and Speech Processing
Abstract

In this work, we propose a novel data augmentation method for clinical audio datasets based on a conditional Wasserstein Generative Adversarial Network with Gradient Penalty (cWGAN-GP), operating on log-mel spectrograms. To validate our method, we created a clinical audio dataset which was recorded in a real-world operating room during Total Hip Arthroplasty (THA) procedures and contains typical sounds which resemble the different phases of the intervention. We demonstrate the capability of the proposed method to generate realistic class-conditioned samples from the dataset distribution and show that training with the generated augmented samples outperforms classical audio augmentation methods in terms of classification performance. The performance was evaluated using a ResNet-18 classifier which shows a mean Macro F1-score improvement of 1.70% in a 5-fold cross validation experiment using the proposed augmentation method. Because clinical data is often expensive to acquire, the development of realistic and high-quality data augmentation methods is crucial to improve the robustness and generalization capabilities of learning-based algorithms which is especially important for safety-critical medical applications. Therefore, the proposed data augmentation method is an important step towards improving the data bottleneck for clinical audio-based machine learning systems.

Published
2022

8. 397 Sinonasal epithelial functional and transcriptional responses to long-term highly effective cystic fibrosis transmembrane conductance regulator corrector therapy

Author

Vladar, E., primary, Beswick, D., additional, Gillen, A., additional, Sajuthi, S., additional, Everman, J., additional, Humphries, S., additional, Balkissoon, C., additional, Smith, P., additional, Khatiwada, A., additional, Lynch, D., additional, Hisert, K., additional, Seibold, M., additional, and Taylor-Cousar, J., additional

Published
2022
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16. SARS-CoV-2 Entry Factors are Highly Expressed in Nasal Epithelial Cells Together with Innate Immune Genes

Author

Sungnak, W., Huang, N., Becavin, C., Berg, M., Queen, R., Litvinukova, M., Talavera-Lopez, C., Maatz, H., Reichart, D., Sampaziotis, F., Worlock, K. B., Yoshida, M., Barnes, J. L., Banovich, N. E., Barbry, P., Brazma, A., Collin, J., Desai, T. J., Duong, T. E., Eickelberg, O., Falk, C., Farzan, M., Glass, I., Gupta, R. K., Haniffa, M., Horvath, P., Hubner, N., Hung, D., Kaminski, N., Krasnow, M., Kropski, J. A., Kuhnemund, M., Lako, M., Lee, H., Leroy, S., Linnarson, S., Lundeberg, J., Meyer, K. B., Miao, Z., Misharin, A. V., Nawijn, M. C., Nikolic, M. Z., Noseda, M., Ordovas-Montanes, J., Oudit, G. Y., Pe'Er, D., Powell, J., Quake, S., Rajagopal, J., Tata, P. R., Rawlins, E. L., Regev, A., Reyfman, P. A., Rozenblatt-Rosen, O., Saeb-Parsy, K., Samakovlis, C., Schiller, H. B., Schultze, J. L., Seibold, M. A., Seidman, C. E., Seidman, J. G., Shalek, A. K., Shepherd, D., Spence, J., Spira, A., Sun, X., Teichmann, S. A., Theis, F. J., Tsankov, A. M., Vallier, L., van den Berge, M., Whitsett, J., Xavier, R., Xu, Y., Zaragosi, L. -E., Zerti, D., Zhang, H., Zhang, K., Rojas, M., Figueiredo, F., Sungnak, Waradon [0000-0002-0136-4960], Bécavin, Christophe [0000-0003-1555-3153], Sampaziotis, Fotios [0000-0003-0812-7586], Yoshida, Masahiro [0000-0002-3521-5322], Apollo - University of Cambridge Repository, Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Groningen Research Institute for Asthma and COPD (GRIAC), and Institute for Molecular Medicine Finland

Subjects
PNEUMONIA, 0301 basic medicine, TRANSMISSION, viruses, [SDV]Life Sciences [q-bio], Priming (immunology), PROTEIN, CORONAVIRUS, Biology, medicine.disease_cause, TMPRSS2, CHINA, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, 0302 clinical medicine, Immune system, HCA Lung Biological Network, FUNCTIONAL RECEPTOR, Viral entry, medicine, Receptor, Gene, ComputingMilieux_MISCELLANEOUS, Coronavirus, General Medicine, 3. Good health, WUHAN, 030104 developmental biology, 030220 oncology & carcinogenesis, Immunology, Tissue tropism, 3111 Biomedicine
Abstract

The SARS-CoV-2 coronavirus, the etiologic agent responsible for COVID-19 coronavirus disease, is a global threat. To better understand viral tropism, we assessed the RNA expression of the coronavirus receptor, ACE2, as well as the viral S protein priming protease TMPRSS2 thought to govern viral entry in single-cell RNA-sequencing (scRNA-seq) datasets from healthy individuals generated by the Human Cell Atlas consortium. We found that ACE2, as well as the protease TMPRSS2, are differentially expressed in respiratory and gut epithelial cells. In-depth analysis of epithelial cells in the respiratory tree reveals that nasal epithelial cells, specifically goblet/secretory cells and ciliated cells, display the highest ACE2 expression of all the epithelial cells analyzed. The skewed expression of viral receptors/entry-associated proteins towards the upper airway may be correlated with enhanced transmissivity. Finally, we showed that many of the top genes associated with ACE2 airway epithelial expression are innate immune-associated, antiviral genes, highly enriched in the nasal epithelial cells. This association with immune pathways might have clinical implications for the course of infection and viral pathology, and highlights the specific significance of nasal epithelia in viral infection. Our findings underscore the importance of the availability of the Human Cell Atlas as a reference dataset. In this instance, analysis of the compendium of data points to a particularly relevant role for nasal goblet and ciliated cells as early viral targets and potential reservoirs of SARS-CoV-2 infection. This, in turn, serves as a biological framework for dissecting viral transmission and developing clinical strategies for prevention and therapy.

Published
2020
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33. Mineralien und Spurenelemente

Author

Schwarz, G., Burmeister, P., Chlond, H., Helwig, H., Keiderling, W., Schmid, F., Seibold, M., Opitz, H., editor, Schmid, F., editor, von Berg, W., editor, Berger, H., editor, Bettecken, F., editor, Bickel, H., editor, Bittner, J., editor, Burmeister, P., editor, Chlond, H., editor, Courtin, W., editor, Droese, W., editor, Ebel, Kl.-D., editor, Eckardt, F., editor, Ewerbeck, H., editor, Fanconi, G., editor, Felzmann, B. S., editor, Fendel, H., editor, Kiss, P. Gegesi, editor, Gerlóczy, F., editor, Giedion, A., editor, Hagge, W., editor, Haupt, H., editor, Hecker, W. Ch., editor, Heinz, E., editor, Helwig, H., editor, Hitzig, W. H., editor, Hövels, O., editor, Jochims, J., editor, Kaufmann, H. J., editor, Keiderling, W., editor, Kerpel-Fronius, E., editor, Klinke, K., editor, Kristen, K., editor, Kübler, W., editor, Lindquist, B., editor, Marget, W., editor, Marx, U., editor, Neuhäuser, G., editor, Reiss, D., editor, Sager, C.-A., editor, Schäfer, H., editor, Schiff, E., editor, Schreier, K., editor, Schriefers, H., editor, Schultze-Jena, B. S., editor, Schuster, H., editor, Schuster, W., editor, Schwarz, G., editor, Seibold, M., editor, Spranger, J., editor, Stave, U., editor, Stolley, H., editor, Thurau, R., editor, Urban, N., editor, Véghelyi, P. V., editor, Weber, H., editor, Wenz, W., editor, Wirths, W., editor, Wolf, H., editor, and Wolf, H. G., editor

Published
1965
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34. Epidemiology and in vitro susceptibility of Fusarium species from human infections in Germany - results of a retrospective multicenter study

Author

Hamprecht, A. G., Goettig, S., Haas, A., Held, J., Koeppel, M. B., Kurzai, O., Saleh, A., Seibold, M., Steinmann, J., Tintelnot, K., Walther, G., Weig, M., Rickerts, V., Hamprecht, A. G., Goettig, S., Haas, A., Held, J., Koeppel, M. B., Kurzai, O., Saleh, A., Seibold, M., Steinmann, J., Tintelnot, K., Walther, G., Weig, M., and Rickerts, V.

Published
2018

38. Maternal age and asthma in Latino populations

Author

Abid, Z., primary, Oh, S. S., additional, Hu, D., additional, Sen, S., additional, Huntsman, S., additional, Eng, C., additional, Farber, H. J., additional, Rodriguez-Cintron, W., additional, Rodriguez-Santana, J. R., additional, Serebrisky, D., additional, Avila, P. C., additional, Thyne, S. M., additional, Kim, K.-Y. A., additional, Borrell, L. N., additional, Williams, L. K., additional, Seibold, M. A., additional, Burchard, E. G., additional, and Kumar, R., additional

Published
2016
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39. Detection of in vitro triazole resistance of Aspergillus fumigatus in clinical isolates sequencing cyp51A

Author

Braun, A, Seibold, M, and Tintelnot, K

Subjects
ddc: 610, 610 Medical sciences, Medicine
Abstract

Aspergillosis due to Aspergillus fumigatus (A. fum.) is a common and life-threatening infection in immunocompromised patients. A. fum. is increasingly reported to be resistant to azoles essentially in prophylaxis and/or therapy of aspergillosis. Resistance is often associated with alterations in[for full text, please go to the a.m. URL], Frühjahrstagung der Sektion Antimykotische Chemotherapie 2014

Published
2014
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45. Tintelnotia, a new genus in Phaeosphaeriaceae harbouring agents of cornea and nail infections in humans.

Author

Ahmed, S. A., Hofmüller, W., Seibold, M., de Hoog, G. S., Harak, H., Tammer, I., van Diepeningen, A. D., and Behrens‐Baumann, W.

Subjects
PLEOSPORALES, PATHOGENIC microorganisms, ENDOPHYTES, LICHEN planus, VORICONAZOLE, ITRACONAZOLE
Abstract

Phaeosphaeriaceae is a family in the order Pleosporales containing numerous plant pathogens, endophytes, lichenised fungi, and environmental saprobes. A novel genus, Tintelnotia is introduced containing two species, one of which caused an eye infection and several nail infections in humans. All species of Tintelnotia produce conidia in soft pycnidia with a wide ostiole. The generic type species is T. opuntiae causing necrotic spots on cactus plants. The isolates of the human opportunist T. destructans showed variable susceptibility pattern to a panel of common antifungal agents. The MICs of amphotericin B, voriconazole, posaconazole and itraconazole were 1 μg/mL, complemented by an in vitro MEC of 16 μg/mL against caspofungin; the MIC of terbinafine was 0.125 μg/mL. The latter compound contributed to the successful therapy in the ocular mycosis refractory to standard antifungal therapy, the benefit of terbinafine should be highlighted as a therapeutic option especially in difficult-to-treat fungal keratitis. [ABSTRACT FROM AUTHOR]

Published
2017
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48. A review of German Scedosporium prolificans cases from 1993 to 2007

Author

Tintelnot, K., Just-Nubling, G., Horre, R., Graf, B., Sobottka, I., Seibold, M., Haas, A., Kaben, U., de Hoog, G.S., Tintelnot, K., Just-Nubling, G., Horre, R., Graf, B., Sobottka, I., Seibold, M., Haas, A., Kaben, U., and de Hoog, G.S.

Abstract

Scedosporium prolificans is one of the most life-threatening fungal opportunistic pathogens due to its high resistance to common systemic antifungal agents. While a close relative of Pseudallescheria boydii, S. prolificans has a more limited geographic range being primarily found in Australia, USA and Spain. Infections have also been reported from several other European countries and from Chile. Twenty patients with Scedosporium prolificans infection or colonization from August 1993 to May 2007 were retrospectively reviewed in Germany. They had all been identified at or reported to the Reference Laboratory for Pseudallescheria/Scedosporium spp. in Berlin. Twelve of 13 patients with haematological disorders and/or on immunosuppressive therapy developed a fatal invasive scedosporiosis. Colonization of the respiratory tract was reported for one patient after heart-lung-transplantation, all six patients with cystic fibrosis and one with chronic sinusitis. Molecular studies of the S. prolificans isolates confirmed that parts of the 18S, the Internal Transcribed Spacer (ITS) regions and the D1/D2 domain of the 28S region of rDNA are monomorphic. However, sequencing of parts of the translation elongation factor EF1-alpha (EF-1alpha) and the chitin synthase (CHS-1) genes revealed the presence of three and two distinct genotypes, respectively. Two informative mutations were found in EF-1alpha and a single nucleotide exchange in the CHS-1 gene., Scedosporium prolificans is one of the most life-threatening fungal opportunistic pathogens due to its high resistance to common systemic antifungal agents. While a close relative of Pseudallescheria boydii, S. prolificans has a more limited geographic range being primarily found in Australia, USA and Spain. Infections have also been reported from several other European countries and from Chile. Twenty patients with Scedosporium prolificans infection or colonization from August 1993 to May 2007 were retrospectively reviewed in Germany. They had all been identified at or reported to the Reference Laboratory for Pseudallescheria/Scedosporium spp. in Berlin. Twelve of 13 patients with haematological disorders and/or on immunosuppressive therapy developed a fatal invasive scedosporiosis. Colonization of the respiratory tract was reported for one patient after heart-lung-transplantation, all six patients with cystic fibrosis and one with chronic sinusitis. Molecular studies of the S. prolificans isolates confirmed that parts of the 18S, the Internal Transcribed Spacer (ITS) regions and the D1/D2 domain of the 28S region of rDNA are monomorphic. However, sequencing of parts of the translation elongation factor EF1-alpha (EF-1alpha) and the chitin synthase (CHS-1) genes revealed the presence of three and two distinct genotypes, respectively. Two informative mutations were found in EF-1alpha and a single nucleotide exchange in the CHS-1 gene.

Published
2009

49. Re-identification of clinical isolates of the Pseudallescheria boydii-complex involved in near-drowning.

Author

Tintelnot, K., Wagner, N., Seibold, M., de Hoog, G.S., Horre, R., Tintelnot, K., Wagner, N., Seibold, M., de Hoog, G.S., and Horre, R.

Abstract

Fungal infections caused by the members of the genera Pseudallescheria and/or Scedosporium are important complications in patients after near-drowning. As the taxonomy of Pseudallescheria and Scedosporium has been revised, clinical isolates from 11 patients, after near-drowning, previously identified as P. boydii or S. apiospermum had to be re-identified. S. apiospermum, now separated from P. boydii as a distinct species, was found most frequently (n = 8), while S. aurantiacum, recently described as new species and P. boydii were less common (n = 2 and n = 1, respectively). Three patients near-drowned during the Tsunami 2004 were infected by different species of the P. boydii complex. In vitro testing resulted in lowest minimal inhibitory concentration (MICs) for voriconazole (range 0.25-2.0 microg ml(-1))., Fungal infections caused by the members of the genera Pseudallescheria and/or Scedosporium are important complications in patients after near-drowning. As the taxonomy of Pseudallescheria and Scedosporium has been revised, clinical isolates from 11 patients, after near-drowning, previously identified as P. boydii or S. apiospermum had to be re-identified. S. apiospermum, now separated from P. boydii as a distinct species, was found most frequently (n = 8), while S. aurantiacum, recently described as new species and P. boydii were less common (n = 2 and n = 1, respectively). Three patients near-drowned during the Tsunami 2004 were infected by different species of the P. boydii complex. In vitro testing resulted in lowest minimal inhibitory concentration (MICs) for voriconazole (range 0.25-2.0 microg ml(-1)).

Published
2008

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