1,001 results on '"Odermatt P"'
Search Results
2. A Scalable and Transferable Time Series Prediction Framework for Demand Forecasting
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Park, Young-Jin, Kim, Donghyun, Odermatt, Frédéric, Lee, Juho, and Kim, Kyung-Min
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence - Abstract
Time series forecasting is one of the most essential and ubiquitous tasks in many business problems, including demand forecasting and logistics optimization. Traditional time series forecasting methods, however, have resulted in small models with limited expressive power because they have difficulty in scaling their model size up while maintaining high accuracy. In this paper, we propose Forecasting orchestra (Forchestra), a simple but powerful framework capable of accurately predicting future demand for a diverse range of items. We empirically demonstrate that the model size is scalable to up to 0.8 billion parameters. The proposed method not only outperforms existing forecasting models with a significant margin, but it could generalize well to unseen data points when evaluated in a zero-shot fashion on downstream datasets. Last but not least, we present extensive qualitative and quantitative studies to analyze how the proposed model outperforms baseline models and differs from conventional approaches. The original paper was presented as a full paper at ICDM 2022 and is available at: https://ieeexplore.ieee.org/document/10027662., Comment: Published as a full paper at ICDM 2022
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- 2024
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3. Assessment of the potential risk of oteseconazole and two other tetrazole antifungals to inhibit adrenal steroidogenesis and peripheral metabolism of corticosteroids.
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Jäger, Marie-Christin, González-Ruiz, Víctor, Joos, Friedrich, Winter, Denise, Boccard, Julien, Degenhardt, Thorsten, Brand, Steve, Rudaz, Serge, Thompson, George, and Odermatt, Alex
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H295R ,adverse drug reaction ,azole antifungal ,cytochrome P450 ,enzyme ,inhibition ,steroid profile ,steroidogenesis - Abstract
The triazole antifungals posaconazole and itraconazole can cause pseudohyperaldosteronism with hypertension and hypokalemia, edema, and gynecomastia by inhibiting steroid synthesis and metabolism. Mechanisms underlying pseudohyperaldosteronism include inhibition of adrenal 11β-hydroxylase cytochrome-P450 (CYP) 11B1 and 17α-hydroxylase (CYP17A1) as well as peripherally expressed 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2). To enhance specificity for fungal CYP51, tetrazoles have been developed. This study employed H295R adrenocortical cells and enzyme activity assays to assess the potential risk of oteseconazole and two other tetrazoles, VT-1598 and quilseconazole, to inhibit adrenal steroidogenesis or 11β-HSD2. Steroidomic footprint analyses of H295R cell supernatants using untargeted liquid-chromatography-high-resolution mass-spectrometry (LC-HRMS) indicated overall patterns common to oteseconazole, quilseconazole and itraconazole, as well as similarities between VT-1598 and isavuconazole. Additionally, more specific features of the steroid signatures were observed. Targeted quantification of nine adrenal steroids in supernatants from treated H295R cells revealed an overall inhibition of adrenal steroidogenesis by the three tetrazoles, itraconazole and isavuconazole, providing an explanation for their similar steroidomic pattern. Applying recombinant enzymes indicated that this effect is not due to direct inhibition of steroidogenic enzymes because no or only weak inhibition could be observed. Moreover, oteseconazole and the two other tetrazoles did not inhibit 11β-HSD2, suggesting that they do not pose a risk of pseudohyperaldosteronism. Furthermore, oteseconazole did not alter steroid concentrations in a recent clinical study. Nevertheless, follow-up studies should assess the mechanism underlying the observed overall steroidogenesis inhibition by tetrazoles, itraconazole and isavuconazole, and whether concentrations achievable in a subgroup of susceptible patients might cause adrenal insufficiency and hyperplasia.
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- 2024
4. EZH2 specifically regulates ISL1 during embryonic urinary tract formation
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Mingardo, Enrico, Kalanithy, Jeshurun C., Dworschak, Gabriel, Ishorst, Nina, Yilmaz, Öznur, Lindenberg, Tobias, Hollstein, Ronja, Felger, Tim, Angrand, Pierre-Olivier, Reutter, Heiko, and Odermatt, Benjamin
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- 2024
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5. Integrated Eco-Health approach significantly reduces helminth infections in endemic Khong islands with emphasis on Schistosoma mekongi
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Sayasone, Somphou, Vonghachack, Youthanavanh, Xia, Shang, Lv, Shan, Zhou, Xiao-Nong, and Odermatt, Peter
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- 2024
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6. Combined Earth observations reveal the sequence of conditions leading to a large algal bloom in Lake Geneva
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Irani Rahaghi, Abolfazl, Odermatt, Daniel, Anneville, Orlane, Sepúlveda Steiner, Oscar, Reiss, Rafael Sebastian, Amadori, Marina, Toffolon, Marco, Jacquet, Stéphan, Harmel, Tristan, Werther, Mortimer, Soulignac, Frédéric, Dambrine, Etienne, Jézéquel, Didier, Hatté, Christine, Tran-Khac, Viet, Rasconi, Serena, Rimet, Frédéric, and Bouffard, Damien
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- 2024
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7. Bi-allelic variants in CELSR3 are implicated in central nervous system and urinary tract anomalies
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Stegmann, Jil D., Kalanithy, Jeshurun C., Dworschak, Gabriel C., Ishorst, Nina, Mingardo, Enrico, Lopes, Filipa M., Ho, Yee Mang, Grote, Phillip, Lindenberg, Tobias T., Yilmaz, Öznur, Channab, Khadija, Seltzsam, Steve, Shril, Shirlee, Hildebrandt, Friedhelm, Boschann, Felix, Heinen, André, Jolly, Angad, Myers, Katherine, McBride, Kim, Bekheirnia, Mir Reza, Bekheirnia, Nasim, Scala, Marcello, Morleo, Manuela, Nigro, Vincenzo, Torella, Annalaura, Pinelli, Michele, Capra, Valeria, Accogli, Andrea, Maitz, Silvia, Spano, Alice, Olson, Rory J., Klee, Eric W., Lanpher, Brendan C., Jang, Se Song, Chae, Jong-Hee, Steinbauer, Philipp, Rieder, Dietmar, Janecke, Andreas R., Vodopiutz, Julia, Vogel, Ida, Blechingberg, Jenny, Cohen, Jennifer L., Riley, Kacie, Klee, Victoria, Walsh, Laurence E., Begemann, Matthias, Elbracht, Miriam, Eggermann, Thomas, Stoppe, Arzu, Stuurman, Kyra, van Slegtenhorst, Marjon, Barakat, Tahsin Stefan, Mulhern, Maureen S., Sands, Tristan T., Cytrynbaum, Cheryl, Weksberg, Rosanna, Isidori, Federica, Pippucci, Tommaso, Severi, Giulia, Montanari, Francesca, Kruer, Michael C., Bakhtiari, Somayeh, Darvish, Hossein, Reutter, Heiko, Hagelueken, Gregor, Geyer, Matthias, Woolf, Adrian S., Posey, Jennifer E., Lupski, James R., Odermatt, Benjamin, and Hilger, Alina C.
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- 2024
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8. Gradient descent-based programming of analog in-memory computing cores
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Büchel, Julian, Vasilopoulos, Athanasios, Kersting, Benedikt, Odermatt, Frederic, Brew, Kevin, Ok, Injo, Choi, Sam, Saraf, Iqbal, Chan, Victor, Philip, Timothy, Saulnier, Nicole, Narayanan, Vijay, Gallo, Manuel Le, and Sebastian, Abu
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Computer Science - Hardware Architecture - Abstract
The precise programming of crossbar arrays of unit-cells is crucial for obtaining high matrix-vector-multiplication (MVM) accuracy in analog in-memory computing (AIMC) cores. We propose a radically different approach based on directly minimizing the MVM error using gradient descent with synthetic random input data. Our method significantly reduces the MVM error compared with conventional unit-cell by unit-cell iterative programming. It also eliminates the need for high-resolution analog-to-digital converters (ADCs) to read the small unit-cell conductance during programming. Our method improves the experimental inference accuracy of ResNet-9 implemented on two phase-change memory (PCM)-based AIMC cores by 1.26%.
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- 2023
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9. Cascaded Beam Search: Plug-and-Play Terminology-Forcing For Neural Machine Translation
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Odermatt, Frédéric, Egressy, Béni, and Wattenhofer, Roger
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
This paper presents a plug-and-play approach for translation with terminology constraints. Terminology constraints are an important aspect of many modern translation pipelines. In both specialized domains and newly emerging domains (such as the COVID-19 pandemic), accurate translation of technical terms is crucial. Recent approaches often train models to copy terminologies from the input into the output sentence by feeding the target terminology along with the input. But this requires expensive training whenever the underlying language model is changed or the system should specialize to a new domain. We propose Cascade Beam Search, a plug-and-play terminology-forcing approach that requires no training. Cascade Beam Search has two parts: 1) logit manipulation to increase the probability of target terminologies and 2) a cascading beam setup based on grid beam search, where beams are grouped by the number of terminologies they contain. We evaluate the performance of our approach by competing against the top submissions of the WMT21 terminology translation task. Our plug-and-play approach performs on par with the winning submissions without using a domain-specific language model and with no additional training., Comment: 14 pages, 7 figures
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- 2023
10. Hardware-aware training for large-scale and diverse deep learning inference workloads using in-memory computing-based accelerators
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Rasch, Malte J., Mackin, Charles, Gallo, Manuel Le, Chen, An, Fasoli, Andrea, Odermatt, Frederic, Li, Ning, Nandakumar, S. R., Narayanan, Pritish, Tsai, Hsinyu, Burr, Geoffrey W., Sebastian, Abu, and Narayanan, Vijay
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Computer Science - Machine Learning ,Computer Science - Emerging Technologies - Abstract
Analog in-memory computing (AIMC) -- a promising approach for energy-efficient acceleration of deep learning workloads -- computes matrix-vector multiplications (MVMs) but only approximately, due to nonidealities that often are non-deterministic or nonlinear. This can adversely impact the achievable deep neural network (DNN) inference accuracy as compared to a conventional floating point (FP) implementation. While retraining has previously been suggested to improve robustness, prior work has explored only a few DNN topologies, using disparate and overly simplified AIMC hardware models. Here, we use hardware-aware (HWA) training to systematically examine the accuracy of AIMC for multiple common artificial intelligence (AI) workloads across multiple DNN topologies, and investigate sensitivity and robustness to a broad set of nonidealities. By introducing a new and highly realistic AIMC crossbar-model, we improve significantly on earlier retraining approaches. We show that many large-scale DNNs of various topologies, including convolutional neural networks (CNNs), recurrent neural networks (RNNs), and transformers, can in fact be successfully retrained to show iso-accuracy on AIMC. Our results further suggest that AIMC nonidealities that add noise to the inputs or outputs, not the weights, have the largest impact on DNN accuracy, and that RNNs are particularly robust to all nonidealities., Comment: 35 pages, 7 figures, 5 tables
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- 2023
11. Author Correction: GLORIA - A globally representative hyperspectral in situ dataset for optical sensing of water quality
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Lehmann, Moritz K, Gurlin, Daniela, Pahlevan, Nima, Alikas, Krista, Conroy, Ted, Anstee, Janet, Balasubramanian, Sundarabalan V, Barbosa, Cláudio CF, Binding, Caren, Bracher, Astrid, Bresciani, Mariano, Burtner, Ashley, Cao, Zhigang, Dekker, Arnold G, Di Vittorio, Courtney, Drayson, Nathan, Errera, Reagan M, Fernandez, Virginia, Ficek, Dariusz, Fichot, Cédric G, Gege, Peter, Giardino, Claudia, Gitelson, Anatoly A, Greb, Steven R, Henderson, Hayden, Higa, Hiroto, Rahaghi, Abolfazl Irani, Jamet, Cédric, Jiang, Dalin, Jordan, Thomas, Kangro, Kersti, Kravitz, Jeremy A, Kristoffersen, Arne S, Kudela, Raphael, Li, Lin, Ligi, Martin, Loisel, Hubert, Lohrenz, Steven, Ma, Ronghua, Maciel, Daniel A, Malthus, Tim J, Matsushita, Bunkei, Matthews, Mark, Minaudo, Camille, Mishra, Deepak R, Mishra, Sachidananda, Moore, Tim, Moses, Wesley J, Nguyễn, Hà, Novo, Evlyn MLM, Novoa, Stéfani, Odermatt, Daniel, O’Donnell, David M, Olmanson, Leif G, Ondrusek, Michael, Oppelt, Natascha, Ouillon, Sylvain, Pereira Filho, Waterloo, Plattner, Stefan, Verdú, Antonio Ruiz, Salem, Salem I, Schalles, John F, Simis, Stefan GH, Siswanto, Eko, Smith, Brandon, Somlai-Schweiger, Ian, Soppa, Mariana A, Spyrakos, Evangelos, Tessin, Elinor, van der Woerd, Hendrik J, Vander Woude, Andrea, Vandermeulen, Ryan A, Vantrepotte, Vincent, Wernand, Marcel R, Werther, Mortimer, Young, Kyana, and Yue, Linwei
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Data Management and Data Science ,Information and Computing Sciences - Published
- 2023
12. Spatial distribution of jets in solar active regions
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Odermatt, Jonas, Barczynski, Krzysztof, Harra, Louise K., Schwanitz, Conrad, and Krucker, Säm
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Astrophysics - Solar and Stellar Astrophysics - Abstract
Context. Solar active regions are known to have jets. These jets are associated with heating and the release of particles into the solar wind. Aim. Our aim is to understand the spatial distribution of coronal jets within active regions to understand if there is a preferential location for them to occur. Methods. We analysed five active regions using Solar Dynamics Observatory Atmospheric Imaging Assembly data over a period of 2-3.5 days when the active regions were close to disk centre. Each active region had a different age, magnetic field strength, and topology. We developed a methodology for determining the position and length of the jets. Results. Jets are observed more frequently at the edges of the active regions and are more densely located around a strong leading sunspot. The number of coronal jets for our active regions is dependent on the age of the active region. The older active regions produce more jets than younger ones. Jets were observed dominantly at the edges of the active regions, and not as frequently in the centre. The number of jets is independent of the average unsigned magnetic field and total flux density in the whole active region. The jets are located around the edges of the strong leading sunspot., Comment: 8 pages, 8 figures, accepted for publication in A&A
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- 2022
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13. GLORIA - A globally representative hyperspectral in situ dataset for optical sensing of water quality
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Lehmann, Moritz K, Gurlin, Daniela, Pahlevan, Nima, Alikas, Krista, Conroy, Ted, Anstee, Janet, Balasubramanian, Sundarabalan V, Barbosa, Cláudio CF, Binding, Caren, Bracher, Astrid, Bresciani, Mariano, Burtner, Ashley, Cao, Zhigang, Dekker, Arnold G, Di Vittorio, Courtney, Drayson, Nathan, Errera, Reagan M, Fernandez, Virginia, Ficek, Dariusz, Fichot, Cédric G, Gege, Peter, Giardino, Claudia, Gitelson, Anatoly A, Greb, Steven R, Henderson, Hayden, Higa, Hiroto, Rahaghi, Abolfazl Irani, Jamet, Cédric, Jiang, Dalin, Jordan, Thomas, Kangro, Kersti, Kravitz, Jeremy A, Kristoffersen, Arne S, Kudela, Raphael, Li, Lin, Ligi, Martin, Loisel, Hubert, Lohrenz, Steven, Ma, Ronghua, Maciel, Daniel A, Malthus, Tim J, Matsushita, Bunkei, Matthews, Mark, Minaudo, Camille, Mishra, Deepak R, Mishra, Sachidananda, Moore, Tim, Moses, Wesley J, Nguyễn, Hà, Novo, Evlyn MLM, Novoa, Stéfani, Odermatt, Daniel, O’Donnell, David M, Olmanson, Leif G, Ondrusek, Michael, Oppelt, Natascha, Ouillon, Sylvain, Pereira Filho, Waterloo, Plattner, Stefan, Verdú, Antonio Ruiz, Salem, Salem I, Schalles, John F, Simis, Stefan GH, Siswanto, Eko, Smith, Brandon, Somlai-Schweiger, Ian, Soppa, Mariana A, Spyrakos, Evangelos, Tessin, Elinor, van der Woerd, Hendrik J, Vander Woude, Andrea, Vandermeulen, Ryan A, Vantrepotte, Vincent, Wernand, Marcel R, Werther, Mortimer, Young, Kyana, and Yue, Linwei
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Earth Sciences ,Geomatic Engineering ,Engineering - Abstract
The development of algorithms for remote sensing of water quality (RSWQ) requires a large amount of in situ data to account for the bio-geo-optical diversity of inland and coastal waters. The GLObal Reflectance community dataset for Imaging and optical sensing of Aquatic environments (GLORIA) includes 7,572 curated hyperspectral remote sensing reflectance measurements at 1 nm intervals within the 350 to 900 nm wavelength range. In addition, at least one co-located water quality measurement of chlorophyll a, total suspended solids, absorption by dissolved substances, and Secchi depth, is provided. The data were contributed by researchers affiliated with 59 institutions worldwide and come from 450 different water bodies, making GLORIA the de-facto state of knowledge of in situ coastal and inland aquatic optical diversity. Each measurement is documented with comprehensive methodological details, allowing users to evaluate fitness-for-purpose, and providing a reference for practitioners planning similar measurements. We provide open and free access to this dataset with the goal of enabling scientific and technological advancement towards operational regional and global RSWQ monitoring.
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- 2023
14. What drives health care spending in Switzerland? Findings from a decomposition by disease, health service, sex, and age
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Stucki, Michael, Schärer, Xavier, Trottmann, Maria, Scholz-Odermatt, Stefan, and Wieser, Simon
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- 2023
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15. Hydrodynamic regimes modulate nitrogen fixation and the mode of diazotrophy in Lake Tanganyika
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Ehrenfels, Benedikt, Baumann, Kathrin B. L., Niederdorfer, Robert, Mbonde, Athanasio S., Kimirei, Ismael A., Kuhn, Thomas, Magyar, Paul M., Odermatt, Daniel, Schubert, Carsten J., Bürgmann, Helmut, Lehmann, Moritz F., Wehrli, Bernhard, and Callbeck, Cameron M.
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- 2023
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16. Sex-specific differences in metabolic hormone and adipose tissue dynamics induced by moderate low-carbohydrate and ketogenic diet
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Smolensky, Ilya, Zajac-Bakri, Kilian, Odermatt, Timothy Sasha, Brégère, Catherine, Cryan, John F., Guzman, Raphael, Timper, Katharina, and Inta, Dragos
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- 2023
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17. Intestinal helminth infections and associated risk factors among adults in the Lao People’s Democratic Republic
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Phonekeo, Sengaloun, Kounnavong, Sengchanh, Vonglokham, Manithong, Siengsounthone, Latsamy, Homsana, Anousin, Gummin, Sascha, Vounatsu, Penelope, Nittiyanant, Prawat, Worawichawong, Suchin, Aekplakorn, Wichai, Odermatt, Peter, and Sayasone, Somphou
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- 2023
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18. Modelling human lower urinary tract malformations in zebrafish
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Kolvenbach, Caroline M., Dworschak, Gabriel C., Rieke, Johanna M., Woolf, Adrian S., Reutter, Heiko, Odermatt, Benjamin, and Hilger, Alina C.
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- 2023
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19. What drives health care spending in Switzerland? Findings from a decomposition by disease, health service, sex, and age
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Michael Stucki, Xavier Schärer, Maria Trottmann, Stefan Scholz-Odermatt, and Simon Wieser
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Health care spending ,Spending growth ,Cost-of-illness ,Switzerland ,Spending decomposition ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background High and increasing spending dominates the public discussion on healthcare in Switzerland. However, the drivers of the spending increase are poorly understood. This study decomposes health care spending by diseases and other perspectives and estimates the contribution of single cost drivers to overall healthcare spending growth in Switzerland between 2012 and 2017. Methods We decompose total healthcare spending according to National Health Accounts by 48 major diseases, injuries, and other conditions, 20 health services, 21 age groups, and sex of patients. This decomposition is based on micro-data from a multitude of data sources such as the hospital inpatient registry, health and accident insurance claims data, and population surveys. We identify the contribution of four main drivers of spending: population growth, change in population structure (age/sex distribution), changes in disease prevalence, and changes in spending per prevalent patient. Results Mental disorders were the most expensive major disease group in both 2012 and 2017, followed by musculoskeletal disorders and neurological disorders. Total health care spending increased by 19.7% between 2012 and 2017. An increase in spending per prevalent patient was the most important spending driver (43.5% of total increase), followed by changes in population size (29.8%), in population structure (14.5%), and in disease prevalence (12.2%). Conclusions A large part of the recent health care spending growth in Switzerland was associated with increases in spending per patient. This may indicate an increase in the treatment intensity. Future research should show if the spending increases were cost-effective.
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- 2023
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20. Hydrodynamic regimes modulate nitrogen fixation and the mode of diazotrophy in Lake Tanganyika
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Benedikt Ehrenfels, Kathrin B. L. Baumann, Robert Niederdorfer, Athanasio S. Mbonde, Ismael A. Kimirei, Thomas Kuhn, Paul M. Magyar, Daniel Odermatt, Carsten J. Schubert, Helmut Bürgmann, Moritz F. Lehmann, Bernhard Wehrli, and Cameron M. Callbeck
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Science - Abstract
Abstract The factors that govern the geographical distribution of nitrogen fixation are fundamental to providing accurate nitrogen budgets in aquatic environments. Model-based insights have demonstrated that regional hydrodynamics strongly impact nitrogen fixation. However, the mechanisms establishing this physical-biological coupling have yet to be constrained in field surveys. Here, we examine the distribution of nitrogen fixation in Lake Tanganyika – a model system with well-defined hydrodynamic regimes. We report that nitrogen fixation is five times higher under stratified than under upwelling conditions. Under stratified conditions, the limited resupply of inorganic nitrogen to surface waters, combined with greater light penetration, promotes the activity of bloom-forming photoautotrophic diazotrophs. In contrast, upwelling conditions support predominantly heterotrophic diazotrophs, which are uniquely suited to chemotactic foraging in a more dynamic nutrient landscape. We suggest that these hydrodynamic regimes (stratification versus mixing) play an important role in governing both the rates and the mode of nitrogen fixation.
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- 2023
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21. Sex-specific differences in metabolic hormone and adipose tissue dynamics induced by moderate low-carbohydrate and ketogenic diet
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Ilya Smolensky, Kilian Zajac-Bakri, Timothy Sasha Odermatt, Catherine Brégère, John F. Cryan, Raphael Guzman, Katharina Timper, and Dragos Inta
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Medicine ,Science - Abstract
Abstract Low-carbohydrates diets are increasingly used to treat obesity and metabolic disorders. A very low-carbohydrate, ketogenic diet is hard to follow and, due to the very high fat content, linked to severe side effects, like hyperlipidemia and atherogenesis. Therefore, a less restrictive, unsaturated fat-based low-carbohydrate diet appears as a promising alternative. Since neither sex differences, nor their effect on specific metabolic hormones and adipose tissue compartments have been investigated thoroughly in these diets, we aimed to analyze their dynamics and metabolic factors in mice. We found a significant sexual dimorphism with decreased body weight and subcutaneous fat only in males on ketogenic diet, while diminished insulin, elevated ghrelin and FGF-21 were present with a differential time course in both sexes. The non-ketogenic moderate low-carbohydrate diet increased body weight and perigonadal fat in females, but induced leptin elevation in males. Both diets enhanced transiently TNFɑ only in males and had no impact on behavior. Altogether, these results reveal complex sex-dependent effect of dietary interventions, indicating unexpectedly females as more prone to unfavorable metabolic effects of low-carbohydrate diets.
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- 2023
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22. A Resilient Punching Bag: A Defense of a Character-Evaluation Account of Blame
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Odermatt, Zachary
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- 2023
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23. Hardware-aware training for large-scale and diverse deep learning inference workloads using in-memory computing-based accelerators
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Malte J. Rasch, Charles Mackin, Manuel Le Gallo, An Chen, Andrea Fasoli, Frédéric Odermatt, Ning Li, S. R. Nandakumar, Pritish Narayanan, Hsinyu Tsai, Geoffrey W. Burr, Abu Sebastian, and Vijay Narayanan
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Science - Abstract
Abstract Analog in-memory computing—a promising approach for energy-efficient acceleration of deep learning workloads—computes matrix-vector multiplications but only approximately, due to nonidealities that often are non-deterministic or nonlinear. This can adversely impact the achievable inference accuracy. Here, we develop an hardware-aware retraining approach to systematically examine the accuracy of analog in-memory computing across multiple network topologies, and investigate sensitivity and robustness to a broad set of nonidealities. By introducing a realistic crossbar model, we improve significantly on earlier retraining approaches. We show that many larger-scale deep neural networks—including convnets, recurrent networks, and transformers—can in fact be successfully retrained to show iso-accuracy with the floating point implementation. Our results further suggest that nonidealities that add noise to the inputs or outputs, not the weights, have the largest impact on accuracy, and that recurrent networks are particularly robust to all nonidealities.
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- 2023
- Full Text
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24. Intestinal helminth infections and associated risk factors among adults in the Lao People’s Democratic Republic
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Sengaloun Phonekeo, Sengchanh Kounnavong, Manithong Vonglokham, Latsamy Siengsounthone, Anousin Homsana, Sascha Gummin, Penelope Vounatsu, Prawat Nittiyanant, Suchin Worawichawong, Wichai Aekplakorn, Peter Odermatt, and Somphou Sayasone
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Intestinal helminth ,Prevalence ,Risk factors ,Investigation ,Regions ,Lao PDR ,Infectious and parasitic diseases ,RC109-216 ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background Helminthiases are highly endemic in Southeast Asia, including the Lao People's Democratic Republic (Lao PDR). This study aimed to assess the current intestinal helminth infections and the associated risk factors among adults across the Lao PDR. Methods A cross-sectional survey was conducted in 165 villages across 17 provinces and the Vientiane Capital, Lao PDR. A multi-stage sampling method was employed to select the adult study participants (≥ 18 years). Data collection included (1) interview of the study participants, (2) physical measurements, and (3) a five gram of stool sample from each study participant was collected and preserved in 10% formalin solution for intestinal helminth detection using formalin-ether concentration technique (FECT). Descriptive analysis was used to describe the socio-demographic characteristics of study participants and the prevalence of intestinal helminth infections. Logistic regressions were applied to test the association between intestinal helminth infection and individual risk factors. A P-value below 0.05 was considered statistically significant. Results A total of 2800 study participants were enrolled. Their average age was 46.0 years; 57.8% were female. Overall, 30.9%, 8.6% and 1.5% of study participants were infected with one, two, or three different intestinal helminth species, respectively. Among the study participants 21.6% were infected with hookworm, 18.8% with Opisthorchis viverrini-like (Ov-like) infection, 4.8% with Strongyloides stercoralis, 2.3% with Ascaris lumbricoides, 1.5% with Trichuris trichiura, and 3.3% with Taenia spp. Ov-like infection was of high prevalence in the southern (28.8%) and central (21.3%) provinces, while hookworm (26.3%), A. lumbricoides (7.3%), T. trichiura (3.1%), and Taenia spp. (4.2%) were prevalent in the northern provinces. Risk analysis showed that men were more likely to be infected with hookworm [adjusted odds ratio (aOR) = 1.2, P = 0.019]. The Lao-Tai ethnic group had a 5.2-times (P
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- 2023
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25. Variations of intracellular density during the cell cycle arise from tip-growth regulation in fission yeast.
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Odermatt, Pascal, Miettinen, Teemu, Lemière, Joël, Kang, Joon, Bostan, Emrah, Manalis, Scott, Huang, Kerwyn, and Chang, Fred
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S. pombe ,Schizosaccharomyces pombe ,cell biology ,cell polarity ,cell-cycle arrest ,dry-mass density ,fission yeast ,physics of living systems ,polarized tip growth ,quantitative phase imaging ,Cell Cycle ,Cell Size ,Cytokinesis ,Intracellular Space ,Schizosaccharomyces ,Time-Lapse Imaging - Abstract
Intracellular density impacts the physical nature of the cytoplasm and can globally affect cellular processes, yet density regulation remains poorly understood. Here, using a new quantitative phase imaging method, we determined that dry-mass density in fission yeast is maintained in a narrow distribution and exhibits homeostatic behavior. However, density varied during the cell cycle, decreasing during G2, increasing in mitosis and cytokinesis, and dropping rapidly at cell birth. These density variations were explained by a constant rate of biomass synthesis, coupled to slowdown of volume growth during cell division and rapid expansion post-cytokinesis. Arrest at specific cell-cycle stages exacerbated density changes. Spatially heterogeneous patterns of density suggested links between density regulation, tip growth, and intracellular osmotic pressure. Our results demonstrate that systematic density variations during the cell cycle are predominantly due to modulation of volume expansion, and reveal functional consequences of density gradients and cell-cycle arrests.
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- 2021
26. Risk factors for Entamoeba histolytica infection in an agricultural community in Hanam province, Vietnam
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Nguyen-Viet Hung, Pham Duc Phuc, Hattendorf Jan, Zinsstag Jakob, Dac Cam Phung, and Odermatt Peter
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Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Entamoeba histolytica is an important protozoan intestinal infection in resource-poor settings, including Vietnam. The study objective was to assess risk factors of E. histolytica infection in a community in Vietnam, where wastewater and human excreta are used in agriculture. A case-control study was conducted among residents of Hanam province, Northern Vietnam. Cases (n = 46) infected with E. histolytica and non-infected controls (n = 138) were identified in a cross-sectional survey among 794 randomly selected individuals and matched for age, sex and place of residence. Potential risk factors including exposure to human and animal excreta and household wastewater were assessed with a questionnaire. Results People from households with an average socio-economic status had a much higher risk of E. histolytica infection (odds ratio [OR]=4.3, 95% confidence interval [CI]: 1.3-14.0) compared with those from households with a good socioeconomic status. Those individuals who never or rarely used soap for hand washing had a 3.4 times higher risk for infection (OR=3.4, 95% CI: 1.1-10.0), compared to those who used always soap. In contrast, none of the factors related to use of human or animal excreta was statistically significant associated with E. histolytica infection. People having close contact with domestic animals presented a greater risk of E. histolytica infection (OR = 5.9, 95% CI: 1.8-19.0) than those without animal contact. E. histolytica infection was not associated with direct contact with Nhue river water, pond water and household's sanitary conditions, type of latrine or water source used. Conclusions Our study suggests that in settings where human and animal excreta and Nhue River water are intensively used in agriculture, socio-economic and personal hygiene factors determine infection with E. histolytica, rather than exposure to human and animal excreta in agricultural activities.
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- 2011
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27. No Paragonimus in high-risk groups in Côte d'Ivoire, but considerable prevalence of helminths and intestinal protozoon infections
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Assoumou Aka, Adoubryn Koffi D, Aka N'da D, Utzinger Jürg, Bonfoh Bassirou, Odermatt Peter, Traoré Sylvain G, Dreyfuss Gilles, and Koussémon Marina
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Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Paragonimiasis is a neglected tropical disease caused by an infection with lung flukes that is transmitted through the consumption of undercooked crabs. The disease is often confused with tuberculosis. Paragonimiasis is thought to be endemic in south-western Côte d'Ivoire. Methods Two cross-sectional surveys were carried out in the first half of 2009 in patients attending two tuberculosis centres of Abidjan. A third cross-sectional survey was conducted in May 2010 in children of two primary schools in Dabou, where crabs are frequently consumed. Patients with chronic cough provided three sputum samples plus one stool sample. Sputum samples were examined for tuberculosis with an auramine staining technique and for Paragonimus eggs using a concentration technique. Stool samples were subjected to the Ritchie technique. Schoolchildren provided a single stool sample, and samples were subjected to the Kato-Katz and an ether-concentration technique. A pre-tested questionnaire was administered to patients and schoolchildren to investigate food consumption habits. Additionally, between June 2009 and August 2010, shellfish were purchased from markets in Abidjan and Dabou and examined for metacercariae. Results No human case of paragonimiasis was diagnosed. However, trematode infections were seen in 32 of the 272 shellfish examined (11.8%). Questionnaire results revealed that crab and pig meat is well cooked before consumption. Among the 278 patients with complete data records, 62 had tuberculosis, with a higher prevalence in males than females (28.8% vs. 13.9%, χ2 = 8.79, p = 0.003). The prevalence of helminths and intestinal protozoa was 4.6% and 16.9%, respectively. In the school survey, among 166 children with complete data records, the prevalence of helminths and intestinal protozoa was 22.3% and 48.8%, respectively. Boys had significantly higher prevalences of helminths and intestinal protozoa than girls. Hookworm was the predominant helminth species and Entamoeba coli was the most common intestinal protozoon species (13.8%). Conclusions Not a single case of Paragonimus was found in two high-risk groups of Côte d'Ivoire, most likely explained by food consumption habits. However, other helminth and intestinal protozoon infections were common.
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- 2011
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28. Access to and utilisation of GP services among Burmese migrants in London: a cross-sectional descriptive study
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Rechel Bernd, Aung Nyein, and Odermatt Peter
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Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background An estimated 10,000 Burmese migrants are currently living in London. No studies have been conducted on their access to health services. Furthermore, most studies on migrants in the United Kingdom (UK) have been conducted at the point of service provision, carrying the risk of selection bias. Our cross-sectional study explored access to and utilisation of General Practice (GP) services by Burmese migrants residing in London. Methods We used a mixed-method approach: a quantitative survey using self-administered questionnaires was complemented by qualitative in-depth interviews for developing the questionnaire and triangulating the findings of the survey. Overall, 137 questionnaires were received (a response rate of 57%) and 11 in-depth interviews conducted. The main outcome variables of the study included GP registration, barriers towards registration, GP consultations, barriers towards consultations, and knowledge on entitlements to health care. Quantitative data were analysed using descriptive statistics, association tests, and a multivariate analysis using logistic regression. The qualitative information was analysed using content analysis. Results The respondents were young, of roughly equal gender (51.5% female), well educated, and had a fair level of knowledge on health services in the UK. Although the GP registration rate was relatively high (80%, 109 out of 136), GP service utilisation during the last episode of illness, at 56.8% (54 out of 95), was low. The statistical analysis showed that age being younger than 35 years, lacking prior overseas experience, having an unstable immigration status, having a shorter duration of stay, and resorting to self-medication were the main barriers hindering Burmese migrants from accessing primary health care services. These findings were corroborated by the in-depth interviews. Conclusions Our study found that having formal access to primary health care was not sufficient to ensure GP registration and health care utilisation. Some respondents faced difficulties in registering with GP practices. Many of those who have registered prefer to forego GP services in favour of self-medication, partly due to long waiting times and language barriers. To ensure that migrants enjoy the health services they need and to which they are entitled, more proactive steps are required, including those that make health services culturally responsive.
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- 2010
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29. Survival and health status of DOTS tuberculosis patients in rural Lao PDR
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Barennes Hubert, Keophithoun Thongdam, Nguyen Tuan H, Strobel Michel, and Odermatt Peter
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Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Contact tracing of tuberculosis (TB) patients is rarely performed in low-income countries. Our objective was to assess the outcome of and compliance with directly observed treatment (DOTS) of TB patients over a 3 year period in rural Lao PDR. Methods We performed a retrospective cohort study in which we enrolled TB patients who started DOTS treatment at Attapeu Provincial Hospital. We traced, through hospital records, all patients in their residential village. We conducted a standardized questionnaire with all TB patients and performed physical and anthropometric examinations as well as evaluations of compliance through counting of treatment pills at home and at the health facilities. Results Of 172 enrolled TB patients (sex ratio female/male: 0.52, mean age: 46.9 years ± 16.9), 26 (15.1%) died. These had a lower weight at the start (34.6 vs. 40.8 kg, p < 0.001) and were less compliant (91.6% vs. 19.2%, p < 0.001) than survivors. Low compliance was associated with poor accessibility to health care (p = 0.01) and symptomatic improvement (p = 0.02). Survivors had persistently poor health status. They were underweight (54.7%), and still had clinical symptoms (53.5%), including dyspnoea (28.8%) and haemoptysis (9.5%). Conclusion Our study suggests a lower rate of survival than expected from official statistics. Additionally, it showed that follow-up of TB patients is feasible although the patients lived in very remote area of Laos. Follow-up should be strengthened as it can improve patient compliance, and allow contact tracing, detection of new cases and collection of accurate treatment outcome information.
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- 2010
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30. Modelling human lower urinary tract malformations in zebrafish
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Caroline M. Kolvenbach, Gabriel C. Dworschak, Johanna M. Rieke, Adrian S. Woolf, Heiko Reutter, Benjamin Odermatt, and Alina C. Hilger
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Pediatrics ,RJ1-570 - Abstract
Abstract Advances in molecular biology are improving our understanding of the genetic causes underlying human congenital lower urinary tract (i.e., bladder and urethral) malformations. This has recently led to the identification of the first disease-causing variants in the gene BNC2 for isolated lower urinary tract anatomical obstruction (LUTO), and of WNT3 and SLC20A1 as genes implicated in the pathogenesis of the group of conditions called bladder-exstrophy-epispadias complex (BEEC). Implicating candidate genes from human genetic data requires evidence of their influence on lower urinary tract development and evidence of the found genetic variants’ pathogenicity. The zebrafish (Danio rerio) has many advantages for use as a vertebrate model organism for the lower urinary tract. Rapid reproduction with numerous offspring, comparable anatomical kidney and lower urinary tract homology, and easy genetic manipulability by Morpholino®-based knockdown or CRISPR/Cas editing are among its advantages. In addition, established marker staining for well-known molecules involved in urinary tract development using whole-mount in situ hybridization (WISH) and the usage of transgenic lines expressing fluorescent protein under a tissue-specific promoter allow easy visualization of phenotypic abnormalities of genetically modified zebrafish. Assays to examine the functionality of the excretory organs can also be modeled in vivo with the zebrafish. The approach of using these multiple techniques in zebrafish not only enables rapid and efficient investigation of candidate genes for lower urinary tract malformations derived from human data, but also cautiously allows transferability of causality from a non-mammalian vertebrate to humans.
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- 2023
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31. Healthcare Costs, Time to Fitness for Work, and Related Factors in Chronic Complex Regional Pain Syndrome: A Comparative and Longitudinal Study of 5-Year Follow-Up
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Duong HP, Léger B, Scholz-Odermatt SM, Burrus C, Vuistiner P, Konzelmann M, and Luthi F
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complex regional pain syndrome ,healthcare costs ,biopsychosocial complexity ,work incapacity ,fitness for work ,crps ,Medicine (General) ,R5-920 - Abstract
Hong Phuoc Duong,1,* Bertrand Léger,1 Stefan Markus Scholz-Odermatt,2 Cyrille Burrus,1,3 Philippe Vuistiner,1 Michel Konzelmann,1,3 François Luthi1,3,4,* 1Department of Medical Research, Clinique romande de réadaptation, Sion, 1951, Switzerland; 2Department of Statistics, Sammelstelle für die Statistik der Unfallversicherung (SSUV), c/o Swiss Accident Insurance Fund (Suva), Lucerne, 6002 Switzerland; 3Department of Musculoskeletal Rehabilitation, Clinique Romande de Réadaptation, Sion, 1951, Switzerland; 4Department of Rheumatology and Rehabilitation, Hôpital Orthopédique, University and University Hospital of Lausanne, Lausanne, 1011, Switzerland*These authors contributed equally to this workCorrespondence: Bertrand Léger, Tel +41 27 603 2075, Email Bertrand.Leger@crr-suva.chPurpose: To assess and compare the healthcare costs, time to fitness for work (TFW) between chronic complex regional pain syndrome (CRPS) and non-CRPS; and identify factors associated with these outcomes in a comparative longitudinal study.Patients and Methods: 148 patients with chronic CRPS of the hand and 273 patients with chronic hand impairments but without CRPS (non-CRPS) were admitted at a Swiss rehabilitation clinic between 2007 and 2016. Healthcare costs and TFW were retrieved from insurance data over 5 years after the accident. Socio-demographic factors, biopsychosocial complexity measured by means of the INTERMED questionnaire, pain intensity and DASH disability scores were collected during rehabilitation. Generalized estimation equations and Cox proportional-hazards models were used to identify factors associated with outcomes.Results: Healthcare costs were increased by 20% for the CRPS versus non-CRPS group (coefficient = 1.20, 95% CI = 1.08– 1.35, p< 0.001). The median TFW was longer for CRPS than non-CRPS patients (816 vs 672 days, p = 0.02). After adjusting for covariates, TFW did not differ between the two groups (hazard ratio = 0.94, 95% CI = 0.73– 1.21, p=0.61). For CRPS patients, higher healthcare costs were associated with severe or moderate initial injury, high INTERMED or DASH disability scores. Longer TFW were associated with severe initial injury, low educational level, no work contract, and high INTERMED or DASH disability scores.Conclusion: Overall, the healthcare costs were higher for CRPS than non-CRPS patients, but the TFW was comparable. We demonstrated also the significant associations of disability and biopsychosocial factors with the healthcare costs and TFW in CRPS patients.Keywords: complex regional pain syndrome, healthcare costs, biopsychosocial complexity, work incapacity, fitness for work, CRPS
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- 2023
32. Risk of latent tuberculosis infection in children living in households with tuberculosis patients: a cross sectional survey in remote northern Lao People's Democratic Republic
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Slesak Gunther, Odermatt Peter, Nguyen Tuan H, and Barennes Hubert
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Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Tuberculosis is highly prevalent in Laos (289 per 100,000). We evaluated the risk of latent tuberculosis infection (LTBI) among children (0–15 years) living with tuberculosis patients in rural northern Laos. Methods In a cross sectional survey of 30 randomly selected villages, 72 tuberculosis patients were traced and their 317 contacts (148 were children) investigated using a questionnaire, a tuberculin skin tests (positive: > = 10 mm), a 3-day sputum examination for acid-fast bacilli (AFB), and chest radiography. Results None of the 148 contact-children received prophylaxis, one had cervical tuberculosis; the risk for LTBI was 31.0%. Awareness of the infectiousness of tuberculosis was low among patients (31%) and their contacts (31%), and risky behavior was common. After multivariate logistic analysis, increased LTBI was found in children with contact with sputum positive adults (OR: 3.3, 95% CI: 1.4–7.7), patients highly positive sputum prior to treatment (AFB >2+; OR: 4.7, 95% CI: 1.7–12.3), and living in ethnic minorities (OR: 5.4, 95% CI: 2.2–13.6). Conclusion The study supports the importance of contact tracing in remote settings with high TB prevalence. Suggestions to improve the children's detection rate, the use of existing guidelines, chemoprophylaxis of contact-children and the available interventions in Laos are discussed. Improving education and awareness of the infectiousness of TB in patients is urgently needed to reduce TB transmission.
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- 2009
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33. Gynecomastia and hypertension in a patient treated with posaconazole
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Thompson, George R, Surampudi, Prasanth N, and Odermatt, Alex
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Biomedical and Clinical Sciences ,Clinical Sciences ,11beta-hydroxylase ,adverse drug effect ,estradiol ,gynecomastia ,hypertension ,hypokalemia ,posaconazole ,11beta‐hydroxylase ,Agricultural ,veterinary and food sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Posaconazole therapy may lead to increased serum estradiol levels and development of gynecomastia. Early detection by endocrine hormone measurements may help preventing gynecomastia.
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- 2020
34. Does the Dream of Home Ownership Rest Upon Biased Beliefs? A Test Based on Predicted and Realized Life Satisfaction
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Odermatt, Reto and Stutzer, Alois
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- 2022
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35. Editorial: Return Migration and Reintegration: Discourses, Policies and Practices
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Eveline Odermatt and Luzia Jurt
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return migration ,reintegration ,Social Sciences ,Sociology (General) ,HM401-1281 - Abstract
Over the last few years, return migration has received growing attention in both academic and political discourse at the international, regional and national levels. This discourse on return migration is often linked to migrants’ safety and dignity. It was established during the development process of the Global Compact for Safe, Orderly and Regular Migration (GCM), and it helped to unify the position of the various stakeholders involved (Panizzon and Jurt 2023). Even today, it is still being maintained when it comes to supporting member states in implementing the objectives of the GCM (United Nations Network on Migration 2021).
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- 2023
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36. Posaconazole Serum Drug Levels Associated With Pseudohyperaldosteronism
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Nguyen, Minh-Vu H, Davis, Matthew R, Wittenberg, Rebecca, Mchardy, Ian, Baddley, John W, Young, Brian Y, Odermatt, Alex, and Thompson, George R
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Biomedical and Clinical Sciences ,Clinical Sciences ,Cardiovascular ,Clinical Research ,Aging ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Aged ,Antifungal Agents ,Humans ,Invasive Fungal Infections ,Retrospective Studies ,Triazoles ,toxicity ,therapeutic drug monitoring ,hypertension ,hypokalemia ,triazole ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
BackgroundPosaconazole tablets are well tolerated and efficacious in the prophylaxis and treatment of aspergillosis, mucormycosis, and other invasive fungal infections. There have been case reports of posaconazole-induced pseudohyperaldosteronism (PIPH); however, its occurrence and association with serum posaconazole drug levels have not previously been investigated.MethodsIn this single-center, retrospective, observational study, we examined the occurrence of PIPH in outpatients newly starting posaconazole and evaluated differences in serum posaconazole concentrations and clinical characteristics between those with and without this syndrome.ResultsSixty-nine patients receiving posaconazole were included, of whom 16 (23.2%) met the definition of PIPH. Patients with PIPH were significantly older (61.1 vs 44.7 years, P = .007) and more frequently had hypertension prior to starting posaconazole (68.8% vs 32.1%, P = .009). Patients with PIPH had a significantly higher median serum posaconazole level than those without PIPH (3.0 vs 1.2 µg/mL, P ≤ .0001). There was a positive correlation between serum posaconazole levels and changes in systolic blood pressure (r = .37, P = .01), a negative correlation between serum posaconazole levels and changes in serum potassium (r = -.39, P = .006), and a positive correlation between serum posaconazole levels and serum 11-deoxycortisol (r = .69, P < .0001).ConclusionsPosaconazole is associated with secondary hypertension and hypokalemia, consistent with pseudohyperaldosteronism, and development is associated with higher serum posaconazole concentrations, older age, and baseline hypertension.
- Published
- 2020
37. GLORIA - A globally representative hyperspectral in situ dataset for optical sensing of water quality
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Moritz K. Lehmann, Daniela Gurlin, Nima Pahlevan, Krista Alikas, Ted Conroy, Janet Anstee, Sundarabalan V. Balasubramanian, Cláudio C. F. Barbosa, Caren Binding, Astrid Bracher, Mariano Bresciani, Ashley Burtner, Zhigang Cao, Arnold G. Dekker, Courtney Di Vittorio, Nathan Drayson, Reagan M. Errera, Virginia Fernandez, Dariusz Ficek, Cédric G. Fichot, Peter Gege, Claudia Giardino, Anatoly A. Gitelson, Steven R. Greb, Hayden Henderson, Hiroto Higa, Abolfazl Irani Rahaghi, Cédric Jamet, Dalin Jiang, Thomas Jordan, Kersti Kangro, Jeremy A. Kravitz, Arne S. Kristoffersen, Raphael Kudela, Lin Li, Martin Ligi, Hubert Loisel, Steven Lohrenz, Ronghua Ma, Daniel A. Maciel, Tim J. Malthus, Bunkei Matsushita, Mark Matthews, Camille Minaudo, Deepak R. Mishra, Sachidananda Mishra, Tim Moore, Wesley J. Moses, Hà Nguyễn, Evlyn M. L. M. Novo, Stéfani Novoa, Daniel Odermatt, David M. O’Donnell, Leif G. Olmanson, Michael Ondrusek, Natascha Oppelt, Sylvain Ouillon, Waterloo Pereira Filho, Stefan Plattner, Antonio Ruiz Verdú, Salem I. Salem, John F. Schalles, Stefan G. H. Simis, Eko Siswanto, Brandon Smith, Ian Somlai-Schweiger, Mariana A. Soppa, Evangelos Spyrakos, Elinor Tessin, Hendrik J. van der Woerd, Andrea Vander Woude, Ryan A. Vandermeulen, Vincent Vantrepotte, Marcel R. Wernand, Mortimer Werther, Kyana Young, and Linwei Yue
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Science - Abstract
Abstract The development of algorithms for remote sensing of water quality (RSWQ) requires a large amount of in situ data to account for the bio-geo-optical diversity of inland and coastal waters. The GLObal Reflectance community dataset for Imaging and optical sensing of Aquatic environments (GLORIA) includes 7,572 curated hyperspectral remote sensing reflectance measurements at 1 nm intervals within the 350 to 900 nm wavelength range. In addition, at least one co-located water quality measurement of chlorophyll a, total suspended solids, absorption by dissolved substances, and Secchi depth, is provided. The data were contributed by researchers affiliated with 59 institutions worldwide and come from 450 different water bodies, making GLORIA the de-facto state of knowledge of in situ coastal and inland aquatic optical diversity. Each measurement is documented with comprehensive methodological details, allowing users to evaluate fitness-for-purpose, and providing a reference for practitioners planning similar measurements. We provide open and free access to this dataset with the goal of enabling scientific and technological advancement towards operational regional and global RSWQ monitoring.
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- 2023
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38. A genome-wide association study with tissue transcriptomics identifies genetic drivers for classic bladder exstrophy
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Enrico Mingardo, Glenda Beaman, Philip Grote, Agneta Nordenskjöld, William Newman, Adrian S. Woolf, Markus Eckstein, Alina C. Hilger, Gabriel C. Dworschak, Wolfgang Rösch, Anne-Karolin Ebert, Raimund Stein, Alfredo Brusco, Massimo Di Grazia, Ali Tamer, Federico M. Torres, Jose L. Hernandez, Philipp Erben, Carlo Maj, Jose M. Olmos, Jose A. Riancho, Carmen Valero, Isabel C. Hostettler, Henry Houlden, David J. Werring, Johannes Schumacher, Jan Gehlen, Ann-Sophie Giel, Benedikt C. Buerfent, Samara Arkani, Elisabeth Åkesson, Emilia Rotstein, Michael Ludwig, Gundela Holmdahl, Elisa Giorgio, Alfredo Berettini, David Keene, Raimondo M. Cervellione, Nina Younsi, Melissa Ortlieb, Josef Oswald, Bernhard Haid, Martin Promm, Claudia Neissner, Karin Hirsch, Maximilian Stehr, Frank-Mattias Schäfer, Eberhard Schmiedeke, Thomas M. Boemers, Iris A. L. M. van Rooij, Wouter F. J. Feitz, Carlo L. M. Marcelis, Martin Lacher, Jana Nelson, Benno Ure, Caroline Fortmann, Daniel P. Gale, Melanie M. Y. Chan, Kerstin U. Ludwig, Markus M. Nöthen, Stefanie Heilmann, Nadine Zwink, Ekkehart Jenetzky, Benjamin Odermatt, Michael Knapp, and Heiko Reutter
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Biology (General) ,QH301-705.5 - Abstract
A genome-wide association study on classic bladder exstrophy reveals eight genome-wide significant loci, most of which contained genes expressed in embryonic developmental bladder stages.
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- 2022
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39. Calcineurin regulates aldosterone production via dephosphorylation of NFATC4
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Mesut Berber, Sining Leng, Agnieszka Wengi, Denise V. Winter, Alex Odermatt, Felix Beuschlein, Johannes Loffing, David T. Breault, and David Penton
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Endocrinology ,Metabolism ,Medicine - Abstract
The mineralocorticoid aldosterone, secreted by the adrenal zona glomerulosa (ZG), is critical for life, maintaining ion homeostasis and blood pressure. Therapeutic inhibition of protein phosphatase 3 (calcineurin, Cn) results in inappropriately low plasma aldosterone levels despite concomitant hyperkalemia and hyperreninemia. We tested the hypothesis that Cn participates in the signal transduction pathway regulating aldosterone synthesis. Inhibition of Cn with tacrolimus abolished the potassium-stimulated (K+-stimulated) expression of aldosterone synthase, encoded by CYP11B2, in the NCI-H295R human adrenocortical cell line as well as ex vivo in mouse and human adrenal tissue. ZG-specific deletion of the regulatory Cn subunit CnB1 diminished Cyp11b2 expression in vivo and disrupted K+-mediated aldosterone synthesis. Phosphoproteomics analysis identified nuclear factor of activated T cells, cytoplasmic 4 (NFATC4), as a target for Cn-mediated dephosphorylation. Deletion of NFATC4 impaired K+-dependent stimulation of CYP11B2 expression and aldosterone production while expression of a constitutively active form of NFATC4 increased expression of CYP11B2 in NCI-H295R cells. Chromatin immunoprecipitation revealed NFATC4 directly regulated CYP11B2 expression. Thus, Cn controls aldosterone production via the Cn/NFATC4 pathway. Inhibition of Cn/NFATC4 signaling may explain low plasma aldosterone levels and hyperkalemia in patients treated with tacrolimus, and the Cn/NFATC4 pathway may provide novel molecular targets to treat primary aldosteronism.
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- 2023
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40. Editorial: Steroid hormone receptors in cardiometabolic disease
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Julie Goodwin, Alex Odermatt, Ruth Morgan, and Mark Nixon
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steroid hormone receptor ,cardiometabolic health ,cardiovascular disease risk ,steroid hormones and receptors ,steroid hormones ,Diseases of the endocrine glands. Clinical endocrinology ,RC648-665 - Published
- 2023
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41. Subacute Thyroiditis Complicating COVID-19 Infection
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Katrin Henke, Jonas Odermatt, Mairi Ziaka, and Natalia Rudovich
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Medicine (General) ,R5-920 - Abstract
Subacute thyroiditis (SAT) is a self-limited inflammatory disease and a rare cause of thyrotoxicosis. Although the exact etiology of SAT is not sufficiently understood, it is generally associated to viral infections. Current evidence highlights that SAT may be a potentially uncommon manifestation of ongoing Coronavirus disease 2019 (COVID-19) infection or a post-viral complication of the disease. Despite that SAT is a rare manifestation associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease both in ongoing and resolved COVID-19 infection, the ever-increasing numbers of COVID-19 patients strengthens the possibility that this particular disease entity will be of more immediate concern in the future. The current work aims to summarize the approach of SARS-CoV-2-associated SAT, present its pathophysiology, outline current research evidence found in the literature, and discuss potential differential diagnoses and diagnostic dilemmas through an illustrative case.
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- 2023
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42. Evaluating the food safety and risk assessment evidence-base of polyethylene terephthalate oligomers: A systematic evidence map
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Verena N. Schreier, Emre Çörek, Christian Appenzeller-Herzog, Beat J. Brüschweiler, Birgit Geueke, Martin F. Wilks, Benoit Schilter, Jane Muncke, Thomas J. Simat, Martin Smieško, Nicolas Roth, and Alex Odermatt
- Subjects
Oligomer ,Polyethylene terephthalate ,Systematic evidence map ,Health risk assessment ,Exposure ,Toxicology ,Environmental sciences ,GE1-350 - Abstract
Background: The presence of polyethylene terephthalate (PET) oligomers in food contact materials (FCMs) is well-documented. Consumers are exposed through their migration into foods and beverages; however, there is no specific guidance for their safety evaluation. Objectives: This systematic evidence map (SEM) aims to identify and organize existing knowledge and associated gaps in hazard and exposure information on 34 PET oligomers to support regulatory decision-making. Methods: The methodology for this SEM was recently registered. A systematic search in bibliographic and gray literature sources was conducted and studies evaluated for inclusion according to the Populations, Exposures, Comparators, Outcomes, and Study type (PECOS) framework. Inclusion criteria were designed to record hazard and exposure information for all 34 PET oligomers and coded into the following evidence streams: human, animal, organism (non-animal), ex vivo, in vitro, in silico, migration, hydrolysis, and absorption, distribution, metabolism, excretion/toxicokinetics/pharmacokinetics (ADME/TK/PK) studies. Relevant information was extracted from eligible studies and synthesized according to the protocol. Results: Literature searches yielded 7445 unique records, of which 96 were included. Data comprised migration (560 entries), ADME/TK/PK-related (253 entries), health/bioactivity (98 entries) and very few hydrolysis studies (7 entries). Cyclic oligomers were studied more frequently than linear PET oligomers. In vitro results indicated that hydrolysis of cyclic oligomers generated a mixture of linear oligomers, but not monomers, potentially allowing their absorption in the gastrointestinal tract. Cyclic dimers, linear trimers and the respective smaller oligomers exhibit physico-chemical properties making oral absorption more likely. Information on health/bioactivity effects of oligomers was almost non-existent, except for limited data on mutagenicity. Conclusions: This SEM revealed substantial deficiencies in the available evidence on ADME/TK/PK, hydrolysis, and health/bioactivity effects of PET oligomers, currently preventing appropriate risk assessment. It is essential to develop more systematic and tiered approaches to address the identified research needs and assess the risks of PET oligomers.
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- 2023
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43. Decoupling of Rates of Protein Synthesis from Cell Expansion Leads to Supergrowth
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Knapp, Benjamin D, Odermatt, Pascal, Rojas, Enrique R, Cheng, Wenpeng, He, Xiangwei, Huang, Kerwyn Casey, and Chang, Fred
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Biochemistry and Cell Biology ,Biological Sciences ,1.1 Normal biological development and functioning ,Underpinning research ,Generic health relevance ,Cell Cycle ,Cell Proliferation ,Homeostasis ,Protein Biosynthesis ,Proteostasis ,Schizosaccharomyces ,Schizosaccharomyces pombe Proteins ,Schizosaccharomyces pombe ,brefeldin A ,cell cycle ,cell growth ,cell size ,cytoplasmic density ,homeostasis ,osmotic stress ,Biochemistry and cell biology - Abstract
Cell growth is a complex process in which cells synthesize cellular components while they increase in size. It is generally assumed that the rate of biosynthesis must somehow be coordinated with the rate of growth in order to maintain intracellular concentrations. However, little is known about potential feedback mechanisms that could achieve proteome homeostasis or the consequences when this homeostasis is perturbed. Here, we identify conditions in which fission yeast cells are prevented from volume expansion but nevertheless continue to synthesize biomass, leading to general accumulation of proteins and increased cytoplasmic density. Upon removal of these perturbations, this biomass accumulation drove cells to undergo a multi-generational period of "supergrowth" wherein rapid volume growth outpaced biosynthesis, returning proteome concentrations back to normal within hours. These findings demonstrate a mechanism for global proteome homeostasis based on modulation of volume growth and dilution.
- Published
- 2019
44. Posaconazole-Induced Hypertension Due to Inhibition of 11β-Hydroxylase and 11β-Hydroxysteroid Dehydrogenase 2
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Thompson, George R, Beck, Katharina R, Patt, Melanie, Kratschmar, Denise V, and Odermatt, Alex
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Rare Diseases ,Cardiovascular ,Hypertension ,posaconazole ,hypertension ,beta-hydroxylase ,beta-hydroxysteroid dehydrogenase ,mineralocorticoid excess ,hypokalemia ,11β-hydroxylase ,11β-hydroxysteroid dehydrogenase - Abstract
We describe two cases of hypertension and hypokalemia due to mineralocorticoid excess caused by posaconazole treatment of coccidioidomycosis and rhinocerebral mucormycosis infections, respectively. Clinical laboratory evaluations, including a comprehensive analysis of blood and urine steroid profiles, revealed low renin and aldosterone and indicated as the underlying mechanism primarily a block of 11β-hydroxylase activity in patient 1, whereas patient 2 displayed weaker 11β-hydroxylase but more pronounced 11β-hydroxysteroid dehydrogenase 2 inhibition. The results show that both previously suggested mechanisms must be considered and emphasize significant interindividual differences in the contribution of each enzyme to the observed mineralocorticoid excess phenotype. The mineralocorticoid symptoms of patient 1 resolved after replacement of posaconazole therapy by isavoconazole, and posaconazole dosage de-escalation ameliorated the effects in patient 2. By providing a thorough analysis of the patients' blood and urine steroid metabolites, this report adds further evidence for two individually pronounced mechanisms of posaconazole-induced hypertension and hypokalemia. The elucidation of the factors responsible for the individual phenotype warrants further research.
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- 2019
45. Developing and testing a Corona VaccinE tRiAL pLatform (COVERALL) to study Covid-19 vaccine response in immunocompromised patients
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Katharina Kusejko, Frédérique Chammartin, Daniel Smith, Marc Odermatt, Julian Schuhmacher, Michael Koller, Huldrych F. Günthard, Matthias Briel, Heiner C. Bucher, Benjamin Speich, the Swiss HIV Cohort Study, and Swiss Transplant Cohort Study
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Trial platform ,SARS-CoV-2 ,Immunocompromised ,HIV ,Transplant patients ,REDCap ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background The rapid course of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic calls for fast implementation of clinical trials to assess the effects of new treatment and prophylactic interventions. Building trial platforms embedded in existing data infrastructures is an ideal way to address such questions within well-defined subpopulations. Methods We developed a trial platform building on the infrastructure of two established national cohort studies: the Swiss human immunodeficiency virus (HIV) Cohort Study (SHCS) and Swiss Transplant Cohort Study (STCS). In a pilot trial, termed Corona VaccinE tRiAL pLatform (COVERALL), we assessed the vaccine efficacy of the first two licensed SARS-CoV-2 vaccines in Switzerland and the functionality of the trial platform. Results Using Research Electronic Data Capture (REDCap), we developed a trial platform integrating the infrastructure of the SHCS and STCS. An algorithm identifying eligible patients, as well as baseline data transfer ensured a fast inclusion procedure for eligible patients. We implemented convenient re-directions between the different data entry systems to ensure intuitive data entry for the participating study personnel. The trial platform, including a randomization algorithm ensuring balance among different subgroups, was continuously adapted to changing guidelines concerning vaccination policies. We were able to randomize and vaccinate the first trial participant the same day we received ethics approval. Time to enroll and randomize our target sample size of 380 patients was 22 days. Conclusion Taking the best of each system, we were able to flag eligible patients, transfer patient information automatically, randomize and enroll the patients in an easy workflow, decreasing the administrative burden usually associated with a trial of this size.
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- 2022
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46. Das Institut der Ehe im Wandel: Legalisierung der Polygamie?
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Daniela Franziska Odermatt
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ehe ,polygamie ,wandel ,fius ,cognitio ,legal gender studies ,kritik ,monogamie ,reformbedürftigkeit ,fürsorge ,Law - Abstract
In diesem Artikel wird die aktuelle Rechtslage zur Polygamie in der Schweiz untersucht und mögliche Anknüpfungspunkte für eine Erweiterung der Ehe de lege ferenda identifiziert. Im Gegensatz zum verfassungsrechtlichen Schutzgedanke bezüglich menschlicher Netzwerke der Fürsorge ist im Zivil- und Strafrecht weiterhin das Prinzip der Monogamie zentral, weshalb die Reformbedürftigkeit aufgezeigt und für Veränderungen innerhalb dieser Rechtsbereiche argumentiert wird.
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- 2022
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47. Dynamics and consequences of nutrition-related microbial dysbiosis in early life: study protocol of the VITERBI GUT project
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Jeanne Tamarelle, Margaux M. Creze, Vanthanom Savathdy, Sengrloun Phonekeo, Jordyn Wallenborn, Latsamy Siengsounthone, Günther Fink, Peter Odermatt, Sengchanh Kounnavong, Somphou Sayasone, and Pascale Vonaesch
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overnutrition ,undernutrition ,metabolic syndrome ,epigenetics ,microbiota inheritance ,microbial succession ,Nutrition. Foods and food supply ,TX341-641 - Abstract
IntroductionEarly life under- and overnutrition (jointly termed malnutrition) is increasingly recognized as an important risk factor for adult obesity and metabolic syndrome, a diet-related cluster of conditions including high blood sugar, fat and cholesterol. Nevertheless, the exact factors linking early life malnutrition with metabolic syndrome remain poorly characterized. We hypothesize that the microbiota plays a crucial role in this trajectory and that the pathophysiological mechanisms underlying under- and overnutrition are, to some extent, shared. We further hypothesize that a “dysbiotic seed microbiota” is transmitted to children during the birth process, altering the children’s microbiota composition and metabolic health. The overall objective of this project is to understand the precise causes and biological mechanisms linking prenatal or early life under- or overnutrition with the predisposition to develop overnutrition and/or metabolic disease in later life, as well as to investigate the possibility of a dysbiotic seed microbiota inheritance in the context of maternal malnutrition.Methods/designVITERBI GUT is a prospective birth cohort allowing to study the link between early life malnutrition, the microbiota and metabolic health. VITERBI GUT will include 100 undernourished, 100 normally nourished and 100 overnourished pregnant women living in Vientiane, Lao People’s Democratic Republic (PDR). Women will be recruited during their third trimester of pregnancy and followed with their child until its second birthday. Anthropometric, clinical, metabolic and nutritional data are collected from both the mother and the child. The microbiota composition of maternal and child’s fecal and oral samples as well as maternal vaginal and breast milk samples will be determined using amplicon and shotgun metagenomic sequencing. Epigenetic modifications and lipid profiles will be assessed in the child’s blood at 2 years of age. We will investigate for possible associations between metabolic health, epigenetics, and microbial changes.DiscussionWe expect the VITERBI GUT project to contribute to the emerging literature linking the early life microbiota, epigenetic changes and growth/metabolic health. We also expect this project to give new (molecular) insights into the mechanisms linking malnutrition-induced early life dysbiosis and metabolic health in later life, opening new avenues for microbiota-engineering using microbiota-targeted interventions.
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- 2023
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48. Optical remote sensing of large-scale water pollution in Angola and DR Congo caused by the Catoca mine tailings spill
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Désirée Ruppen, James Runnalls, Raphael M. Tshimanga, Bernhard Wehrli, and Daniel Odermatt
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Mining ,Tailings dam failure ,Water quality ,Environmental pollution ,Sentinel-2 ,Optical remote sensing ,Physical geography ,GB3-5030 ,Environmental sciences ,GE1-350 - Abstract
Billions of tons of hazardous mine waste are stored in thousands of tailings storage facilities around the world. These impoundments represent one of the most important environmental risk factors of industrial mining, since occasional tailings spills or dam failures cause devastating impacts on humans and ecosystems, specifically along river corridors. In this study, we developed a satellite remote sensing methodology to assess the impacts of tailings spills on water quality focusing on the controversial incident that occurred at the Catoca diamond mine in Angola in late July 2021. The spill allegedly caused important river pollution in neighbouring Democratic Republic of the Congo (DR Congo) and led to public health concerns including the loss of human lives – however the mining company denied any responsibility. We processed high resolution imagery acquired by ESA’s Sentinel-2 satellites using the Python package Acolite for atmospheric correction and turbidity retrieval, and applied a river skeletonizing algorithm to automatically extract turbidity values for the entire river system. This allowed tracking the propagation of the pollution front from the source at the Catoca mine through the Tshikapa- and the Kasaï River during more than one month and across 1400 km, until the pollution front finally dissipated after discharging into the Congo River. We further analyzed a 6-year time series of virtual stations in the Tshikapa River located up- and downstream of the effluent discharge to compare the impacts of the tailings spill to seasonal variabilities of water quality. Turbidity values caused by the spill largely exceeded the seasonal variability in the Tshikapa River in recent years. These findings confirm that the Catoca tailings spill has significantly affected water quality of the Tshikapa- and the Kasaï River with total suspended solids concentrations that were several 10-fold above drinking water standards in Lunda Norte Province, Angola, and Kasaï Province, DR Congo, making severe public health impacts for residents and fish kills highly probable. After investigating whether this methodology could be applied to other tailings dam failures that have occurred since the Sentinel-2 mission began in 2015, we recommend to apply it to four other incidents in Mexico, Myanmar, Peru and China, respectively. Overall, this Sentinel-2 workflow provides the opportunity to assess the large-scale impacts of pollution incidents in mining areas around the world in locations where hydrological- and water quality data are scarce and monitoring capacities are limited.
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- 2023
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49. Development and validation of a diagnostic aid for convulsive epilepsy in sub-Saharan Africa: a retrospective case-control study
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Gabriel Davis Jones, MD, Symon M Kariuki, PhD, Anthony K Ngugi, PhD, Angelina Kakooza Mwesige, PhD, Honorati Masanja, PhD, Seth Owusu-Agyei, ProfPhD, Ryan Wagner, PhD, J Helen Cross, ProfMD, Josemir W Sander, ProfPhD, Charles R Newton, ProfMD, Arjune Sen, ProfPhD, Hanna Abban, Patrick Adjei, Ken Ae-Ngibise, Francis Agbokey, Lisa Aissaoui, Albert Akpalu, Bright Akpalu, Sabina Asiamah, Gershim Asiki, Mercy Atieno, Evasius Bauni, Dan Bhwana, Mary Bitta, Christian Bottomley, Martin Chabi, Eddie Chengo, Neerja Chowdhary, Myles Connor, Helen Cross, Mark Collinson, Emmanuel Darkwa, Timothy Denison, Victor Doku, Tarun Dua, Isaac Egesa, Tony Godi, F. Xavier Gómez-Olivé, Simone Grassi, Samuel Iddi, Daniel Nana Yaw Abankwah Junior, Kathleen Kahn, Angelina Kakooza, Symon Kariuki, Gathoni Kamuyu, Clarah Khalayi, Henrika Kimambo, Immo Kleinschmidt, Thomas Kwasa, Sloan Mahone, Gergana Manolova, Honorati Masanja, Alexander Mathew, William Matuja, David McDaid, Bruno Mmbando, Daniel Mtai Mwanga, Dorcas Muli, Victor Mung'ala Odera, Frederick Murunga Wekesah, Vivian Mushi, Anthony Ngugi, Peter Odermatt, Rachael Odhiambo, James O Mageto, Peter Otieno, Seth Owusu-Agyei, George Pariyo, Stefan Peterson, Josemir Sander, Arjune Sen, Cynthia Sottie, Isolide Sylvester, Stephen Tollman, Yvonne Thoya, Rhian Twine, Sonia Vallentin, Ryan Wagner, Richard Walker, and Stella Waruingi
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Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Summary: Background: Identification of convulsive epilepsy in sub-Saharan Africa relies on access to resources that are often unavailable. Infrastructure and resource requirements can further complicate case verification. Using machine-learning techniques, we have developed and tested a region-specific questionnaire panel and predictive model to identify people who have had a convulsive seizure. These findings have been implemented into a free app for health-care workers in Kenya, Uganda, Ghana, Tanzania, and South Africa. Methods: In this retrospective case-control study, we used data from the Studies of the Epidemiology of Epilepsy in Demographic Sites in Kenya, Uganda, Ghana, Tanzania, and South Africa. We randomly split these individuals using a 7:3 ratio into a training dataset and a validation dataset. We used information gain and correlation-based feature selection to identify eight binary features to predict convulsive seizures. We then assessed several machine-learning algorithms to create a multivariate prediction model. We validated the best-performing model with the internal dataset and a prospectively collected external-validation dataset. We additionally evaluated a leave-one-site-out model (LOSO), in which the model was trained on data from all sites except one that, in turn, formed the validation dataset. We used these features to develop a questionnaire-based predictive panel that we implemented into a multilingual app (the Epilepsy Diagnostic Companion) for health-care workers in each geographical region. Findings: We analysed epilepsy-specific data from 4097 people, of whom 1985 (48·5%) had convulsive epilepsy, and 2112 were controls. From 170 clinical variables, we initially identified 20 candidate predictor features. Eight features were removed, six because of negligible information gain and two following review by a panel of qualified neurologists. Correlation-based feature selection identified eight variables that demonstrated predictive value; all were associated with an increased risk of an epileptic convulsion except one. The logistic regression, support vector, and naive Bayes models performed similarly, outperforming the decision-tree model. We chose the logistic regression model for its interpretability and implementability. The area under the receiver operator curve (AUC) was 0·92 (95% CI 0·91–0·94, sensitivity 85·0%, specificity 93·7%) in the internal-validation dataset and 0·95 (0·92–0·98, sensitivity 97·5%, specificity 82·4%) in the external-validation dataset. Similar results were observed for the LOSO model (AUC 0·94, 0·93–0·96, sensitivity 88·2%, specificity 95·3%). Interpretation: On the basis of these findings, we developed the Epilepsy Diagnostic Companion as a predictive model and app offering a validated culture-specific and region-specific solution to confirm the diagnosis of a convulsive epileptic seizure in people with suspected epilepsy. The questionnaire panel is simple and accessible for health-care workers without specialist knowledge to administer. This tool can be iteratively updated and could lead to earlier, more accurate diagnosis of seizures and improve care for people with epilepsy. Funding: The Wellcome Trust, the UK National Institute of Health Research, and the Oxford NIHR Biomedical Research Centre.
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- 2023
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50. Pixel-based mapping of open field and protected agriculture using constrained Sentinel-2 data
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Daniele la Cecilia, Manu Tom, Christian Stamm, and Daniel Odermatt
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Protected agriculture ,Plastic greenhouse ,Random forest ,Sentinel-2 ,Corine ,Geography (General) ,G1-922 ,Surveying ,TA501-625 - Abstract
Protected agriculture boosts the production of vegetables, berries and fruits, and it plays a pivotal role in guaranteeing food security globally in the face of climate change. Remote sensing is proven to be useful for identifying the presence of (low-tech) plastic greenhouses and plastic mulches. However, the classification accuracy notoriously decreases in the presence of small-scale farming, heterogeneous land cover and unaccounted seasonal management of protected agriculture. Here, we present the random forest-based pixel-level Open field and Protected Agriculture land cover Classifier (OPAC) developed using Sentinel-2 L2A data. OPAC is trained using tiles from Switzerland over 2 years and the Almeria region in Spain over 1 acquisition day. OPAC classifies eight land covers typical of open field and protected agriculture (plastic mulches, low-tech greenhouses and for the first time high-tech greenhouses). Finally, we assess (1) how the land covers in OPAC are labelled in the Sentinel-2 Scene Classification Layer (SCL) and (2) the correspondence between pixels classified as protected agriculture by OPAC and by the best performing Advanced Plastic Greenhouse Index (APGI). To reduce anthropogenic land covers, we constrain the classification task to agricultural areas retrieved from cadastral data or the Corine Land Cover map. The 5-fold cross-validation reveals an overall accuracy of 92% but other classification scores are moderate when keeping the separation among the three classes of protected agriculture. However, all scores substantially improve upon grouping the three classes into one (with an Intersection Over Union of 0.58 as an average among the scores of the three classes and of 0.98 for one single class). Given the recently acknowledged importance of Sentinel-2 Band 1 (central wavelength of 443 nm), the classification accuracy of OPAC for the Swiss small-scale farming is mostly limited by the band's reduced spatial accuracy (60 m). A careful visual assessment indicates that OPAC achieves satisfactory generalization capabilities also in North European (the Netherlands) and four Mediterranean areas (Spain, Italy, Crete and Turkey) without the need of adding location and temporal specific information. There is good agreement among natural land covers classified by OPAC and the SCL. However, the SCL does not have a class for protected agriculture, the latter being often classified as clouds. APGI achieved similar to lower classification accuracies than OPAC. Importantly, the APGI classification task depends on a user-defined space- and time-specific threshold, whereas OPAC does not. Therefore, OPAC paves the way for rapid mapping of protected agriculture at continental scale.
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- 2023
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