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Brand K, Wise T, Hess AJ, Russell BR, Stephan KE, Harrison OK. Incorporating uncertainty within dynamic interoceptive learning. Front Psychol 2024; 15:1254564. [PMID: 38646115 PMCID: PMC11026658 DOI: 10.3389/fpsyg.2024.1254564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/18/2024] [Indexed: 04/23/2024] Open
Abstract
Introduction Interoception, the perception of the internal state of the body, has been shown to be closely linked to emotions and mental health. Of particular interest are interoceptive learning processes that capture associations between environmental cues and body signals as a basis for making homeostatically relevant predictions about the future. One method of measuring respiratory interoceptive learning that has shown promising results is the Breathing Learning Task (BLT). While the original BLT required binary predictions regarding the presence or absence of an upcoming inspiratory resistance, here we extended this paradigm to capture continuous measures of prediction (un)certainty. Methods Sixteen healthy participants completed the continuous version of the BLT, where they were asked to predict the likelihood of breathing resistances on a continuous scale from 0.0 to 10.0. In order to explain participants' responses, a Rescorla-Wagner model of associative learning was combined with suitable observation models for continuous or binary predictions, respectively. For validation, we compared both models against corresponding null models and examined the correlation between observed and modeled predictions. The model was additionally extended to test whether learning rates differed according to stimuli valence. Finally, summary measures of prediction certainty as well as model estimates for learning rates were considered against interoceptive and mental health questionnaire measures. Results Our results demonstrated that the continuous model fits closely captured participant behavior using empirical data, and the binarised predictions showed excellent replicability compared to previously collected data. However, the model extension indicated that there were no significant differences between learning rates for negative (i.e. breathing resistance) and positive (i.e. no breathing resistance) stimuli. Finally, significant correlations were found between fatigue severity and both prediction certainty and learning rate, as well as between anxiety sensitivity and prediction certainty. Discussion These results demonstrate the utility of gathering enriched continuous prediction data in interoceptive learning tasks, and suggest that the updated BLT is a promising paradigm for future investigations into interoceptive learning and potential links to mental health.
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Affiliation(s)
- Katja Brand
- Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Toby Wise
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Alexander J. Hess
- Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | | | - Klaas E. Stephan
- Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Olivia K. Harrison
- Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Department of Psychology, University of Otago, Dunedin, New Zealand
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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Capel-Timms I, Levinson D, Lahoorpoor B, Bonetti S, Manoli G. The angiogenic growth of cities. J R Soc Interface 2024; 21:20230657. [PMID: 38565159 PMCID: PMC10987239 DOI: 10.1098/rsif.2023.0657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Describing the space-time evolution of urban population is a fundamental challenge in the science of cities, yet a complete theoretical treatment of the underlying dynamics is still missing. Here, we first reconstruct the evolution of London (UK) over 180 years and show that urban growth consists of an initial phase of diffusion-limited growth, followed by the development of the railway transport network and a consequential shift from central to suburban living. Such dynamics-which are analogous to angiogenesis in biological systems-can be described by a minimalist reaction-diffusion model coupled with economic constraints and an adaptive transport network. We then test the generality of our approach by reproducing the evolution of Sydney, Australia, from 1851 to 2011. We show that the rail system coevolves with urban population, displaying hierarchical characteristics that remain constant over time unless large-scale interventions are put in place to alter the modes of transport. These results demonstrate that transport schemes are first-order controls of long-term urbanization patterns and efforts aimed at creating more sustainable and healthier cities require careful consideration of population-transport feedbacks.
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Affiliation(s)
- Isabella Capel-Timms
- Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK
| | - David Levinson
- School of Civil Engineering, University of Sydney, Sydney, Australia
| | - Bahman Lahoorpoor
- School of Civil Engineering, University of Sydney, Sydney, Australia
| | - Sara Bonetti
- Laboratory of Catchment Hydrology and Geomorphology, École Polytechnique Fédérale de Lausanne, Sion, Switzerland
| | - Gabriele Manoli
- Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK
- Laboratory of Urban and Environmental Systems, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Nißler R, Totter E, Walter SG, Metternich JT, Cipolato O, Nowack D, Gogos A, Herrmann IK. Material-Intrinsic NIR-Fluorescence Enables Image-Guided Surgery for Ceramic Fracture Removal. Adv Healthc Mater 2024; 13:e2302950. [PMID: 38245823 DOI: 10.1002/adhm.202302950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/10/2024] [Indexed: 01/22/2024]
Abstract
Hip arthroplasty effectively treats advanced osteoarthritis and is therefore entitled as "operation of the 20th century." With demographic shifts, the USA alone is projected to perform up to 850 000 arthroplasties annually by 2030. Many implants now feature a ceramic head, valued for strength and wear resistance. Nonetheless, a fraction, up to 0.03% may fracture during their lifespan, demanding complex removal procedures. To address this, a radiation-free, fluorescence-based image-guided surgical technique is presented. The method uses the inherent fluorescence of ceramic implant materials, demonstrated through chemical and optical analysis of prevalent implant types. Specifically, Biolox delta implants exhibited strong fluorescence around 700 nm with a 74% photoluminescence quantum yield. Emission tails are identified extending into the near-infrared (NIR-I) biological transparency range, forming a vital prerequisite for the label-free visualization of fragments. This ruby-like fluorescence could be attributed to Cr within the zirconia-toughened alumina matrix, enabling the detection of even deep-seated millimeter-sized fragments via camera-assisted techniques. Additionally, fluorescence microscopy allowed detection of µm-sized ceramic particles, enabling debris visualization in synovial fluid as well as histological samples. This label-free optical imaging approach employs readily accessible equipment and can seamlessly transition to clinical settings without significant regulatory barriers, thereby enhancing the safety, efficiency, and minimally invasive nature of fractured ceramic implant removal procedures.
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Affiliation(s)
- Robert Nißler
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
- The Ingenuity Lab, University Hospital Balgrist, University of Zurich, Forchstrasse 340, Zurich, 8008, Switzerland
| | - Elena Totter
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
| | - Sebastian G Walter
- Department of Orthopedics, Traumatology and Reconstructive Surgery, University Hospital Cologne, Joseph-Stelzmann-Str. 24, 50931, Cologne, Germany
| | - Justus T Metternich
- Physical Chemistry, Ruhr-University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
- Fraunhofer Institute for Microelectronic Circuits and Systems (IMS), Finkenstr. 61, 47057, Duisburg, Germany
| | - Oscar Cipolato
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
- The Ingenuity Lab, University Hospital Balgrist, University of Zurich, Forchstrasse 340, Zurich, 8008, Switzerland
| | - Dimitri Nowack
- Deutsches Zentrum für Orthopädie, Department of Orthopedics and Trauma Surgery, Friedrich Schiller University Jena, Eisenberg, 07743, Jena, Germany
| | - Alexander Gogos
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Inge K Herrmann
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
- The Ingenuity Lab, University Hospital Balgrist, University of Zurich, Forchstrasse 340, Zurich, 8008, Switzerland
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Nißler R, Dennebouy L, Gogos A, Gerken LRH, Dommke M, Zimmermann M, Pais MA, Neuer AL, Matter MT, Kissling VM, de Brot S, Lese I, Herrmann IK. Protein Aggregation on Metal Oxides Governs Catalytic Activity and Cellular Uptake. Small 2024:e2311115. [PMID: 38556634 DOI: 10.1002/smll.202311115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/12/2024] [Indexed: 04/02/2024]
Abstract
Engineering of catalytically active inorganic nanomaterials holds promising prospects for biomedicine. Catalytically active metal oxides show applications in enhancing wound healing but have also been employed to induce cell death in photodynamic or radiation therapy. Upon introduction into a biological system, nanomaterials are exposed to complex fluids, causing interaction and adsorption of ions and proteins. While protein corona formation on nanomaterials is acknowledged, its modulation of nanomaterial catalytic efficacy is less understood. In this study, proteomic analyses and nano-analytic methodologies quantify and characterize adsorbed proteins, correlating this protein layer with metal oxide catalytic activity in vitro and in vivo. The protein corona comprises up to 280 different proteins, constituting up to 38% by weight. Enhanced complement factors and other opsonins on nanocatalyst surfaces lead to their uptake into macrophages when applied topically, localizing >99% of the nanomaterials in tissue-resident macrophages. Initially, the formation of the protein corona significantly reduces the nanocatalysts' activity, but this activity can be partially recovered in endosomal conditions due to the proteolytic degradation of the corona. Overall, the research reveals the complex relationship between physisorbed proteins and the catalytic characteristics of specific metal oxide nanoparticles, providing design parameters for optimizing nanocatalysts in complex biological environments.
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Affiliation(s)
- Robert Nißler
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
- The Ingenuity Lab, University Hospital Balgrist, University of Zurich, Forchstrasse 340, Zurich, 8008, Switzerland
| | - Lena Dennebouy
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
| | - Alexander Gogos
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Lukas R H Gerken
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Maximilian Dommke
- Institute of Technical Chemistry and Environmental Chemistry, Friedrich Schiller University Jena, Philosophenweg 7a, 07743, Jena, Germany
| | - Monika Zimmermann
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Michael A Pais
- Department of Plastic and Hand Surgery, Inselspital, Bern University Hospital, Bern, 3010, Switzerland
| | - Anna L Neuer
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Martin T Matter
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Vera M Kissling
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Bern, 3012, Switzerland
| | - Ioana Lese
- Department of Plastic and Hand Surgery, Inselspital, Bern University Hospital, Bern, 3010, Switzerland
| | - Inge K Herrmann
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
- Particles-Biology Interactions, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland
- The Ingenuity Lab, University Hospital Balgrist, University of Zurich, Forchstrasse 340, Zurich, 8008, Switzerland
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Mountaki SA, Whitfield R, Parkatzidis K, Antonopoulou MN, Truong NP, Anastasaki A. Chemical recycling of bromine-terminated polymers synthesized by ATRP. RSC Appl Polym 2024; 2:275-283. [PMID: 38525379 PMCID: PMC10955525 DOI: 10.1039/d3lp00279a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/25/2024] [Indexed: 03/26/2024]
Abstract
Chemical recycling of polymers is one of the biggest challenges in materials science. Recently, remarkable achievements have been made by utilizing polymers prepared by controlled radical polymerization to trigger low-temperature depolymerization. However, in the case of atom transfer radical polymerization (ATRP), depolymerization has nearly exclusively focused on chlorine-terminated polymers, even though the overwhelming majority of polymeric materials synthesized with this method possess a bromine end-group. Herein, we report an efficient depolymerization strategy for bromine-terminated polymethacrylates which employs an inexpensive and environmentally friendly iron catalyst (FeBr2/L). The effect of various solvents and the concentration of metal salt and ligand on the depolymerization are judiciously explored and optimized, allowing for a depolymerization efficiency of up to 86% to be achieved in just 3 minutes. Notably, the versatility of this depolymerization is exemplified by its compatibility with chlorinated and non-chlorinated solvents, and both Fe(ii) and Fe(iii) salts. This work significantly expands the scope of ATRP materials compatible with depolymerization and creates many future opportunities in applications where the depolymerization of bromine-terminated polymers is desired.
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Affiliation(s)
- Stella Afroditi Mountaki
- Laboratory of Polymeric Materials, Department of Materials, ETH Zurich Vladimir-Prelog-Weg-5 8093 Zurich Switzerland
| | - Richard Whitfield
- Laboratory of Polymeric Materials, Department of Materials, ETH Zurich Vladimir-Prelog-Weg-5 8093 Zurich Switzerland
| | - Kostas Parkatzidis
- Laboratory of Polymeric Materials, Department of Materials, ETH Zurich Vladimir-Prelog-Weg-5 8093 Zurich Switzerland
| | - Maria-Nefeli Antonopoulou
- Laboratory of Polymeric Materials, Department of Materials, ETH Zurich Vladimir-Prelog-Weg-5 8093 Zurich Switzerland
| | - Nghia P Truong
- Laboratory of Polymeric Materials, Department of Materials, ETH Zurich Vladimir-Prelog-Weg-5 8093 Zurich Switzerland
| | - Athina Anastasaki
- Laboratory of Polymeric Materials, Department of Materials, ETH Zurich Vladimir-Prelog-Weg-5 8093 Zurich Switzerland
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Herrera-Valenzuela D, Meyer JT, Del-Ama AJ, Moreno JC, Gassert R, Lambercy O. Towards a validated glossary of usability attributes for the evaluation of wearable robotic devices. J Neuroeng Rehabil 2024; 21:30. [PMID: 38419069 PMCID: PMC10900611 DOI: 10.1186/s12984-024-01312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Despite technical advances in the field of wearable robotic devices (WRD), there is still limited user acceptance of these technologies. While usability often comes as a key factor influencing acceptance, there is a scattered landscape of definitions and scopes for the term. To advance usability evaluation, and to integrate usability features as design requirements during technology development, there is a need for benchmarks and shared terminology. These should be easily accessible and implementable by developers. METHODS An initial set of usability attributes (UA) was extracted from a literature survey on usability evaluation in WRD. The initial set of attributes was enriched and locally validated with seven developers of WRD through an online survey and a focus group. The locally validated glossary was then externally validated through a globally distributed online survey. RESULTS The result is the Robotics Usability Glossary (RUG), a comprehensive glossary of 41 UA validated by 70 WRD developers from 17 countries, ensuring its generalizability. 31 of the UA had high agreement scores among respondents and 27 were considered highly relevant in the field, but only 11 of them had been included as design criteria by the respondents. CONCLUSIONS Multiple UA ought to be considered for a comprehensive usability assessment. Usability remains inadequately incorporated into device development, indicating a need for increased awareness and end-user perspective. The RUG can be readily accessed through an online platform, the Interactive Usability Toolbox (IUT), developed to provide context-specific outcome measures and usability evaluation methods. Overall, this effort is an important step towards improving and promoting usability evaluation practices within WRD. It has the potential to pave the way for establishing usability evaluation benchmarks that further endorse the acceptance of WRD.
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Affiliation(s)
- Diana Herrera-Valenzuela
- International Doctoral School, Rey Juan Carlos University, Madrid, Spain.
- Biomechanics and Technical Aids Unit, National Hospital for Paraplegics, Toledo, Spain.
| | - Jan T Meyer
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Antonio J Del-Ama
- School of Science and Technology, Department of Applied Mathematics, Materials Science and Engineering and Electronic Technology, Rey Juan Carlos University, Móstoles, Madrid, Spain
| | - Juan C Moreno
- Neural Rehabilitation Group, Cajal Institute, CSIC-Spanish National Research Council, Madrid, Spain
- Unit of Neurorehabilitation, Biomechanics and Sensorimotor Function (HNP-SESCAM), Associated Unit of R&D&I to the CSIC, Toledo, Spain
| | - Roger Gassert
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore
| | - Olivier Lambercy
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore.
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Lizonova D, Nagarkar A, Demokritou P, Kelesidis GA. Effective density of inhaled environmental and engineered nanoparticles and its impact on the lung deposition and dosimetry. Part Fibre Toxicol 2024; 21:7. [PMID: 38368385 PMCID: PMC10874077 DOI: 10.1186/s12989-024-00567-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/07/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Airborne environmental and engineered nanoparticles (NPs) are inhaled and deposited in the respiratory system. The inhaled dose of such NPs and their deposition location in the lung determines their impact on health. When calculating NP deposition using particle inhalation models, a common approach is to use the bulk material density, ρb, rather than the effective density, ρeff. This neglects though the porous agglomerate structure of NPs and may result in a significant error of their lung-deposited dose and location. RESULTS Here, the deposition of various environmental NPs (aircraft and diesel black carbon, wood smoke) and engineered NPs (silica, zirconia) in the respiratory system of humans and mice is calculated using the Multiple-Path Particle Dosimetry model accounting for their realistic structure and effective density. This is done by measuring the NP ρeff which was found to be up to one order of magnitude smaller than ρb. Accounting for the realistic ρeff of NPs reduces their deposited mass in the pulmonary region of the respiratory system up to a factor of two in both human and mouse models. Neglecting the ρeff of NPs does not alter significantly the distribution of the deposited mass fractions in the human or mouse respiratory tract that are obtained by normalizing the mass deposited at the head, tracheobronchial and pulmonary regions by the total deposited mass. Finally, the total deposited mass fraction derived this way is in excellent agreement with those measured in human studies for diesel black carbon. CONCLUSIONS The doses of inhaled NPs are overestimated by inhalation particle deposition models when the ρb is used instead of the real-world effective density which can vary significantly due to the porous agglomerate structure of NPs. So the use of realistic ρeff, which can be measured as described here, is essential to determine the lung deposition and dosimetry of inhaled NPs and their impact on public health.
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Affiliation(s)
- Denisa Lizonova
- Nanoscience and Advanced Materials Center (NAMC), Environmental and Occupational Health Science Institute, School of Public Health, Rutgers, The State University of New Jersey, 170 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Amogh Nagarkar
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, Institute of Process Engineering, ETH Zürich, Sonneggstrasse 3, 8092, Zurich, Switzerland
| | - Philip Demokritou
- Nanoscience and Advanced Materials Center (NAMC), Environmental and Occupational Health Science Institute, School of Public Health, Rutgers, The State University of New Jersey, 170 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Georgios A Kelesidis
- Nanoscience and Advanced Materials Center (NAMC), Environmental and Occupational Health Science Institute, School of Public Health, Rutgers, The State University of New Jersey, 170 Frelinghuysen Road, Piscataway, NJ, 08854, USA.
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, Institute of Process Engineering, ETH Zürich, Sonneggstrasse 3, 8092, Zurich, Switzerland.
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Fontana GA, MacArthur MR, Rotankova N, Di Filippo M, Beer HD, Gahlon HL. The mitochondrial DNA common deletion as a potential biomarker of cancer-associated fibroblasts from skin basal and squamous cell carcinomas. Sci Rep 2024; 14:553. [PMID: 38177205 PMCID: PMC10766618 DOI: 10.1038/s41598-023-50213-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 12/16/2023] [Indexed: 01/06/2024] Open
Abstract
Cancer-associated fibroblasts (CAFs) are components of the tumor microenvironment and represent appealing therapeutic targets for translational studies. Conventional protein-based biomarkers for CAFs have been reported to be limited in their specificity, rendering difficult the identification of CAFs from normal fibroblasts (NFs) in clinical samples and dampening the development of CAF-targeted therapies to treat cancer. In this study, we propose the mitochondrial RNA and the mitochondrial DNA (mtDNA) common deletion (CD) as novel indicators of CAF identity. We found that cancer-activation correlated with decreased levels of the mtDNA CD, a condition not due to altered mitochondria count or cellular redox state, but potentially linked to the generalized overexpression of mtDNA maintenance genes in CAFs. Decreased mtDNA CD content in CAFs was associated with moderate to strong overexpression of mtDNA-encoded genes and to slightly improved mitochondrial function. We identified similar patterns of upregulation of mtDNA-encoded genes in independent single-cell RNA seq data obtained from squamous cell carcinoma (SCC) patients. By using the identified nucleic acids-based indicators, identification of CAFs from NFs could be improved, leading to potential therapeutic benefits in advancing translational and clinical studies.
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Affiliation(s)
- Gabriele A Fontana
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
- Cellvie AG, Technoparkstrasse 1, CH-8005 Zürich, Switzerland
| | - Michael R MacArthur
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Nadezhda Rotankova
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland
| | - Michela Di Filippo
- Department of Dermatology, University Hospital Zurich, 8952, Schlieren, Switzerland
- Faculty of Medicine, University of Zurich, 8032, Zurich, Switzerland
| | - Hans-Dietmar Beer
- Department of Dermatology, University Hospital Zurich, 8952, Schlieren, Switzerland
- Faculty of Medicine, University of Zurich, 8032, Zurich, Switzerland
| | - Hailey L Gahlon
- Department of Health Sciences and Technology, ETH Zurich, 8092, Zurich, Switzerland.
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9
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Nosková A, Li C, Wang X, Leonard AS, Pausch H, Kadri N. Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species. Nucleic Acids Res 2023; 51:12069-12075. [PMID: 37953306 PMCID: PMC10711541 DOI: 10.1093/nar/gkad970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/06/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
The branch point sequence is a degenerate intronic heptamer required for the assembly of the spliceosome during pre-mRNA splicing. Disruption of this motif may promote alternative splicing and eventually cause phenotype variation. Despite its functional relevance, the branch point sequence is not included in most genome annotations. Here, we predict branch point sequences in 30 plant and animal species and attempt to quantify their evolutionary constraints using public variant databases. We find an implausible variant distribution in the databases from 16 of 30 examined species. Comparative analysis of variants from whole-genome sequencing shows that variants submitted from exome sequencing or false positive variants are widespread in public databases and cause these irregularities. We then investigate evolutionary constraint with largely unbiased public variant databases in 14 species and find that the fourth and sixth position of the branch point sequence are more constrained than coding nucleotides. Our findings show that public variant databases should be scrutinized for possible biases before they qualify to analyze evolutionary constraint.
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Affiliation(s)
- Adéla Nosková
- Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Chao Li
- Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Hubert Pausch
- Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Naveen Kumar Kadri
- Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
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10
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Kesten C, Leitner V, Dora S, Sims JW, Dindas J, Zipfel C, De Moraes CM, Sanchez-Rodriguez C. Soil-borne fungi alter the apoplastic purinergic signaling in plants by deregulating the homeostasis of extracellular ATP and its metabolite adenosine. eLife 2023; 12:e92913. [PMID: 37994905 PMCID: PMC10746138 DOI: 10.7554/elife.92913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/23/2023] [Indexed: 11/24/2023] Open
Abstract
Purinergic signaling activated by extracellular nucleotides and their derivative nucleosides trigger sophisticated signaling networks. The outcome of these pathways determine the capacity of the organism to survive under challenging conditions. Both extracellular ATP (eATP) and Adenosine (eAdo) act as primary messengers in mammals, essential for immunosuppressive responses. Despite the clear role of eATP as a plant damage-associated molecular pattern, the function of its nucleoside, eAdo, and of the eAdo/eATP balance in plant stress response remain to be fully elucidated. This is particularly relevant in the context of plant-microbe interaction, where the intruder manipulates the extracellular matrix. Here, we identify Ado as a main molecule secreted by the vascular fungus Fusarium oxysporum. We show that eAdo modulates the plant's susceptibility to fungal colonization by altering the eATP-mediated apoplastic pH homeostasis, an essential physiological player during the infection of this pathogen. Our work indicates that plant pathogens actively imbalance the apoplastic eAdo/eATP levels as a virulence mechanism.
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Affiliation(s)
- Christopher Kesten
- Department of Biology and Zürich-Basel Plant Science CenterZürichSwitzerland
- Department for Plant and Environmental Sciences, University of CopenhagenCopenhagenDenmark
| | - Valentin Leitner
- Department of Biology and Zürich-Basel Plant Science CenterZürichSwitzerland
| | - Susanne Dora
- Department of Biology and Zürich-Basel Plant Science CenterZürichSwitzerland
| | - James W Sims
- Department of Environmental Systems Science, ETH ZürichZurichSwitzerland
| | - Julian Dindas
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | | | - Clara Sanchez-Rodriguez
- Department of Biology and Zürich-Basel Plant Science CenterZürichSwitzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC)Pozuelo de AlarcónSpain
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11
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Simmler P, Ioannidi EI, Mengis T, Marquart KF, Asawa S, Van-Lehmann K, Kahles A, Thomas T, Schwerdel C, Aceto N, Rätsch G, Stoffel M, Schwank G. Mutant SF3B1 promotes malignancy in PDAC. eLife 2023; 12:e80683. [PMID: 37823551 PMCID: PMC10629822 DOI: 10.7554/elife.80683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/11/2023] [Indexed: 10/13/2023] Open
Abstract
The splicing factor SF3B1 is recurrently mutated in various tumors, including pancreatic ductal adenocarcinoma (PDAC). The impact of the hotspot mutation SF3B1K700E on the PDAC pathogenesis, however, remains elusive. Here, we demonstrate that Sf3b1K700E alone is insufficient to induce malignant transformation of the murine pancreas, but that it increases aggressiveness of PDAC if it co-occurs with mutated KRAS and p53. We further show that Sf3b1K700E already plays a role during early stages of pancreatic tumor progression and reduces the expression of TGF-β1-responsive epithelial-mesenchymal transition (EMT) genes. Moreover, we found that SF3B1K700E confers resistance to TGF-β1-induced cell death in pancreatic organoids and cell lines, partly mediated through aberrant splicing of Map3k7. Overall, our findings demonstrate that SF3B1K700E acts as an oncogenic driver in PDAC, and suggest that it promotes the progression of early stage tumors by impeding the cellular response to tumor suppressive effects of TGF-β.
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Affiliation(s)
- Patrik Simmler
- Department of Biology, Institute of Molecular Health Sciences, ETH ZurichZurichSwitzerland
- Institute of Pharmacology and Toxicology, University of ZurichZurichSwitzerland
| | - Eleonora I Ioannidi
- Institute of Pharmacology and Toxicology, University of ZurichZurichSwitzerland
| | - Tamara Mengis
- Institute of Pharmacology and Toxicology, University of ZurichZurichSwitzerland
| | - Kim Fabiano Marquart
- Department of Biology, Institute of Molecular Health Sciences, ETH ZurichZurichSwitzerland
- Institute of Pharmacology and Toxicology, University of ZurichZurichSwitzerland
| | - Simran Asawa
- Department of Biology, Institute of Molecular Health Sciences, ETH ZurichZurichSwitzerland
| | - Kjong Van-Lehmann
- Department of Computer Science, Biomedical Informatics Group, ETH ZurichZurichSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Andre Kahles
- Department of Computer Science, Biomedical Informatics Group, ETH ZurichZurichSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Tinu Thomas
- Department of Computer Science, Biomedical Informatics Group, ETH ZurichZurichSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Cornelia Schwerdel
- Institute of Pharmacology and Toxicology, University of ZurichZurichSwitzerland
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, ETH ZurichZurichSwitzerland
| | - Gunnar Rätsch
- Department of Computer Science, Biomedical Informatics Group, ETH ZurichZurichSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Department of Biology, ETH ZurichZurichSwitzerland
- Biomedical Informatics Research, University Hospital ZurichZurichSwitzerland
| | - Markus Stoffel
- Department of Biology, Institute of Molecular Health Sciences, ETH ZurichZurichSwitzerland
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of ZurichZurichSwitzerland
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12
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Gerken LRH, Gerdes ME, Pruschy M, Herrmann IK. Prospects of nanoparticle-based radioenhancement for radiotherapy. Mater Horiz 2023; 10:4059-4082. [PMID: 37555747 PMCID: PMC10544071 DOI: 10.1039/d3mh00265a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Radiotherapy is a key pillar of solid cancer treatment. Despite a high level of conformal dose deposition, radiotherapy is limited due to co-irradiation of organs at risk and subsequent normal tissue toxicities. Nanotechnology offers an attractive opportunity for increasing the efficacy and safety of cancer radiotherapy. Leveraging the freedom of design and the growing synthetic capabilities of the nanomaterial-community, a variety of engineered nanomaterials have been designed and investigated as radiosensitizers or radioenhancers. While research so far has been primarily focused on gold nanoparticles and other high atomic number materials to increase the absorption cross section of tumor tissue, recent studies are challenging the traditional concept of high-Z nanoparticle radioenhancers and highlight the importance of catalytic activity. This review provides a concise overview on the knowledge of nanoparticle radioenhancement mechanisms and their quantification. It critically discusses potential radioenhancer candidate materials and general design criteria for different radiation therapy modalities, and concludes with research priorities in order to advance the development of nanomaterials, to enhance the efficacy of radiotherapy and to increase at the same time the therapeutic window.
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Affiliation(s)
- Lukas R H Gerken
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland.
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Maren E Gerdes
- Karolinska Institutet, Solnavägen 1, 171 77 Stockholm, Sweden
| | - Martin Pruschy
- Laboratory for Applied Radiobiology, Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Inge K Herrmann
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering (IEPE), Department of Mechanical and Process Engineering (D-MAVT), ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland.
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
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13
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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14
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Shekhar A, Hörtnagl L, Buchmann N, Gharun M. Long-term changes in forest response to extreme atmospheric dryness. Glob Chang Biol 2023; 29:5379-5396. [PMID: 37381105 DOI: 10.1111/gcb.16846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/01/2023] [Indexed: 06/30/2023]
Abstract
Atmospheric dryness, as indicated by vapor pressure deficit (VPD), has a strong influence on forest greenhouse gas exchange with the atmosphere. In this study, we used long-term (10-30 years) net ecosystem productivity (NEP) measurements from 60 forest sites across the world (1003 site-years) to quantify long-term changes in forest NEP resistance and NEP recovery in response to extreme atmospheric dryness. We tested two hypotheses: first, across sites differences in NEP resistance and NEP recovery of forests will depend on both the biophysical characteristics (i.e., leaf area index [LAI] and forest type) of the forest as well as on the local meteorological conditions of the site (i.e., mean VPD of the site), and second, forests experiencing an increasing trend in frequency and intensity of extreme dryness will show an increasing trend in NEP resistance and NEP recovery over time due to emergence of long-term ecological stress memory. We used a data-driven statistical learning approach to quantify NEP resistance and NEP recovery over multiple years. Our results showed that forest types, LAI, and median local VPD conditions explained over 50% of variance in both NEP resistance and NEP recovery, with drier sites showing higher NEP resistance and NEP recovery compared to sites with less atmospheric dryness. The impact of extreme atmospheric dryness events on NEP lasted for up to 3 days following most severe extreme events in most forests, indicated by an NEP recovery of less than 100%. We rejected our second hypothesis as we found no consistent relationship between trends of extreme VPD with trends in NEP resistance and NEP recovery across different forest sites, thus an increase in atmospheric dryness as it is predicted might not increase the resistance or recovery of forests in terms of NEP.
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Affiliation(s)
- Ankit Shekhar
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Lukas Hörtnagl
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Nina Buchmann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Mana Gharun
- Institute of Landscape Ecology, Faculty of Geosciences, University of Münster, Münster, Germany
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15
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Travers-Cook TJ, Jokela J, Buser CC. The evolutionary ecology of fungal killer phenotypes. Proc Biol Sci 2023; 290:20231108. [PMID: 37583325 PMCID: PMC10427833 DOI: 10.1098/rspb.2023.1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/20/2023] [Indexed: 08/17/2023] Open
Abstract
Ecological interactions influence evolutionary dynamics by selecting upon fitness variation within species. Antagonistic interactions often promote genetic and species diversity, despite the inherently suppressive effect they can have on the species experiencing them. A central aim of evolutionary ecology is to understand how diversity is maintained in systems experiencing antagonism. In this review, we address how certain single-celled and dimorphic fungi have evolved allelopathic killer phenotypes that engage in antagonistic interactions. We discuss the evolutionary pathways to the production of lethal toxins, the functions of killer phenotypes and the consequences of competition for toxin producers, their competitors and toxin-encoding endosymbionts. Killer phenotypes are powerful models because many appear to have evolved independently, enabling across-phylogeny comparisons of the origins, functions and consequences of allelopathic antagonism. Killer phenotypes can eliminate host competitors and influence evolutionary dynamics, yet the evolutionary ecology of killer phenotypes remains largely unknown. We discuss what is known and what remains to be ascertained about killer phenotype ecology and evolution, while bringing their model system properties to the reader's attention.
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Affiliation(s)
- Thomas J. Travers-Cook
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Jukka Jokela
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Claudia C. Buser
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
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16
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Bastide GMGBH, Remund AL, Oosthuizen DN, Derron N, Gerber PA, Weber IC. Handheld device quantifies breath acetone for real-life metabolic health monitoring. Sens Diagn 2023; 2:918-928. [PMID: 37465007 PMCID: PMC10351029 DOI: 10.1039/d3sd00079f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/10/2023] [Indexed: 07/20/2023]
Abstract
Non-invasive breath analysis with mobile health devices bears tremendous potential to guide therapeutic treatment and personalize lifestyle changes. Of particular interest is the breath volatile acetone, a biomarker for fat burning, that could help in understanding and treating metabolic diseases. Here, we report a hand-held (6 × 10 × 19.5 cm3), light-weight (490 g), and simple device for rapid acetone detection in breath. It comprises a tailor-made end-tidal breath sampling unit, connected to a sensor and a pump for on-demand breath sampling, all operated using a Raspberry Pi microcontroller connected with a HDMI touchscreen. Accurate acetone detection is enabled by introducing a catalytic filter and a separation column, which remove and separate undesired interferents from acetone upstream of the sensor. This way, acetone is detected selectively even in complex gas mixtures containing highly concentrated interferents. This device accurately tracks breath acetone concentrations in the exhaled breath of five volunteers during a ketogenic diet, being as high as 26.3 ppm. Most importantly, it can differentiate small acetone changes during a baseline visit as well as before and after an exercise stimulus, being as low as 0.5 ppm. It is stable for at least four months (122 days), and features excellent bias and precision of 0.03 and 0.6 ppm at concentrations below 5 ppm, as validated by proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS). Hence, this detector is highly promising for simple-in-use, non-invasive, and routine monitoring of acetone to guide therapeutic treatment and track lifestyle changes.
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Affiliation(s)
- Grégoire M G B H Bastide
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zurich CH-8092 Zurich Switzerland
- Department of Endocrinology, Diabetology, and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH) CH-8091 Zurich Switzerland
| | - Anna L Remund
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zurich CH-8092 Zurich Switzerland
- Department of Endocrinology, Diabetology, and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH) CH-8091 Zurich Switzerland
| | - Dina N Oosthuizen
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zurich CH-8092 Zurich Switzerland
- Department of Mechanical and Industrial Engineering, Northeastern University 467 Egan Center 02115 MA Boston USA
| | - Nina Derron
- Department of Endocrinology, Diabetology, and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH) CH-8091 Zurich Switzerland
| | - Philipp A Gerber
- Department of Endocrinology, Diabetology, and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH) CH-8091 Zurich Switzerland
| | - Ines C Weber
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zurich CH-8092 Zurich Switzerland
- Department of Endocrinology, Diabetology, and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH) CH-8091 Zurich Switzerland
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17
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Boontanrart MY, Mächler E, Ponta S, Nelis JC, Preiano VG, Corn JE. Engineering of the endogenous HBD promoter increases HbA2. eLife 2023; 12:e85258. [PMID: 37265399 PMCID: PMC10270685 DOI: 10.7554/elife.85258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/27/2023] [Indexed: 06/03/2023] Open
Abstract
The β-hemoglobinopathies, such as sickle cell disease and β-thalassemia, are one of the most common genetic diseases worldwide and are caused by mutations affecting the structure or production of β-globin subunits in adult hemoglobin. Many gene editing efforts to treat the β-hemoglobinopathies attempt to correct β-globin mutations or increase γ-globin for fetal hemoglobin production. δ-globin, the subunit of adult hemoglobin A2, has high homology to β-globin and is already pan-cellularly expressed at low levels in adult red blood cells. However, upregulation of δ-globin is a relatively unexplored avenue to increase the amount of functional hemoglobin. Here, we use CRISPR-Cas9 to repair non-functional transcriptional elements in the endogenous promoter region of δ-globin to increase overall expression of adult hemoglobin 2 (HbA2). We find that insertion of a KLF1 site alone is insufficient to upregulate δ-globin. Instead, multiple transcription factor elements are necessary for robust upregulation of δ-globin from the endogenous locus. Promoter edited HUDEP-2 immortalized erythroid progenitor cells exhibit striking increases of HBD transcript, from less than 5% to over 20% of total β-like globins in clonal populations. Edited CD34 +hematopoietic stem and progenitors (HSPCs) differentiated to primary human erythroblasts express up to 46% HBD in clonal populations. These findings add mechanistic insight to globin gene regulation and offer a new therapeutic avenue to treat β-hemoglobinopathies.
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Affiliation(s)
| | - Elia Mächler
- Department of Biology, ETH ZurichZurichSwitzerland
| | - Simone Ponta
- Department of Biology, ETH ZurichZurichSwitzerland
| | - Jan C Nelis
- Department of Biology, ETH ZurichZurichSwitzerland
| | | | - Jacob E Corn
- Department of Biology, ETH ZurichZurichSwitzerland
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18
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Cipolloni G, Erdős L, Schröder D. On the Spectral Form Factor for Random Matrices. Commun Math Phys 2023; 401:1665-1700. [PMID: 37397230 PMCID: PMC10313625 DOI: 10.1007/s00220-023-04692-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/13/2023] [Indexed: 07/04/2023]
Abstract
In the physics literature the spectral form factor (SFF), the squared Fourier transform of the empirical eigenvalue density, is the most common tool to test universality for disordered quantum systems, yet previous mathematical results have been restricted only to two exactly solvable models (Forrester in J Stat Phys 183:33, 2021. 10.1007/s10955-021-02767-5, Commun Math Phys 387:215-235, 2021. 10.1007/s00220-021-04193-w). We rigorously prove the physics prediction on SFF up to an intermediate time scale for a large class of random matrices using a robust method, the multi-resolvent local laws. Beyond Wigner matrices we also consider the monoparametric ensemble and prove that universality of SFF can already be triggered by a single random parameter, supplementing the recently proven Wigner-Dyson universality (Cipolloni et al. in Probab Theory Relat Fields, 2021. 10.1007/s00440-022-01156-7) to larger spectral scales. Remarkably, extensive numerics indicates that our formulas correctly predict the SFF in the entire slope-dip-ramp regime, as customarily called in physics.
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Affiliation(s)
- Giorgio Cipolloni
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ 08544 USA
| | - László Erdős
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Dominik Schröder
- Institute for Theoretical Studies, ETH Zurich, Clausiusstr. 47, 8092 Zurich, Switzerland
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19
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Bran-Anleu P, Wangler T, Nerella VN, Mechtcherine V, Trtik P, Flatt RJ. Using micro-XRF to characterize chloride ingress through cold joints in 3D printed concrete. Mater Struct 2023; 56:51. [PMID: 36909254 PMCID: PMC9988803 DOI: 10.1617/s11527-023-02132-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Digital fabrication methods with concrete have been rapidly developing, with many problems related to component production and material control being solved in recent years. These processes produce inherently layered cementitious components that are anisotropic, and in many cases, produces a weak interface between layers, which are generally referred to as cold joints. While material strength at these interfaces has been well studied in recent years, durability has received less attention, even though cold joints can function as channels for aggressive agents, such as chlorides. This work presents a method using micro-X-ray fluorescence (μXRF) to image chloride ingress into layer interfaces of 3D printed fine-grained concrete specimens produced with varying layer deposition time intervals, and also compares it to neutron imaging of moisture uptake. The results show that cold joints formed after a 1 day time interval are highly susceptible to chloride ingress, and that curing conditions play a major role in how quickly interfacial transport can take place. The μXRF method is also shown to be useful for study of transport of chlorides in cold joints, due to its spatial resolution and direct analysis of an aggressive species of interest.
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Affiliation(s)
- Paula Bran-Anleu
- Nuclear Structures and Construction Group, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Institut für Baustoffe (IfB), Physical Chemistry of Building Materials, ETH Zürich, Zurich, Switzerland
| | - Timothy Wangler
- Institut für Baustoffe (IfB), Physical Chemistry of Building Materials, ETH Zürich, Zurich, Switzerland
| | - Venkatesh N. Nerella
- TU Dresden, Institute of Construction Materials, Dresden, Germany
- Putzmeister Engineering GmbH, Max-Eyth-Str. 10, Alchtal, Germany
| | | | - Pavel Trtik
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Robert J. Flatt
- Institut für Baustoffe (IfB), Physical Chemistry of Building Materials, ETH Zürich, Zurich, Switzerland
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20
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King GA, Wettstein R, Varberg JM, Chetlapalli K, Walsh ME, Gillet LC, Hernández-Armenta C, Beltrao P, Aebersold R, Jaspersen SL, Matos J, Ünal E. Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. J Cell Biol 2023; 222:e202204039. [PMID: 36515990 PMCID: PMC9754704 DOI: 10.1083/jcb.202204039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/12/2022] [Accepted: 11/05/2022] [Indexed: 12/15/2022] Open
Abstract
Nuclear pore complexes (NPCs) are large proteinaceous assemblies that mediate nuclear compartmentalization. NPCs undergo large-scale structural rearrangements during mitosis in metazoans and some fungi. However, our understanding of NPC remodeling beyond mitosis remains limited. Using time-lapse fluorescence microscopy, we discovered that NPCs undergo two mechanistically separable remodeling events during budding yeast meiosis in which parts or all of the nuclear basket transiently dissociate from the NPC core during meiosis I and II, respectively. Meiosis I detachment, observed for Nup60 and Nup2, is driven by Polo kinase-mediated phosphorylation of Nup60 at its interface with the Y-complex. Subsequent reattachment of Nup60-Nup2 to the NPC core is facilitated by a lipid-binding amphipathic helix in Nup60. Preventing Nup60-Nup2 reattachment causes misorganization of the entire nuclear basket in gametes. Strikingly, meiotic nuclear basket remodeling also occurs in the distantly related fission yeast, Schizosaccharomyces pombe. Our study reveals a conserved and developmentally programmed aspect of NPC plasticity, providing key mechanistic insights into the nuclear basket organization.
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Affiliation(s)
- Grant A. King
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Rahel Wettstein
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | | | - Madison E. Walsh
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Ludovic C.J. Gillet
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Claudia Hernández-Armenta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Sue L. Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS
| | - Joao Matos
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
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21
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Meyer JT, Tanczak N, Kanzler CM, Pelletier C, Gassert R, Lambercy O. Design and validation of a novel online platform to support the usability evaluation of wearable robotic devices. Wearable Technol 2023; 4:e3. [PMID: 38487781 PMCID: PMC10936320 DOI: 10.1017/wtc.2022.31] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/12/2022] [Accepted: 12/05/2022] [Indexed: 03/17/2024]
Abstract
Wearable robotic devices (WRD) are still struggling to fulfill their vast potential. Inadequate daily life usability is one of the main hindrances to increased technology acceptance. Improving usability evaluation practices during the development of WRD could help address these limitations. In this work, we present the design and validation of a novel online platform aiming to fill this gap, the Interactive Usability Toolbox (IUT). This platform consists of a public website that offers an interactive, context-specific search within a database of 154 user research methods and educational information about usability. In a dedicated study, the effect of this platform to support usability evaluation was investigated. Twelve WRD experts were asked to complete the task of defining usability evaluation protocols for two specific use cases. The platform was provided to support one of the use cases. The quality and composition of the proposed protocols were assessed by (i) two blinded reviewers, (ii) the participants themselves, and (iii) the study coordinators. We showed that using the IUT significantly affected the proposed evaluation focus, shifting protocols from mainly effectiveness-oriented to more user-focused studies. The protocol quality, as rated by the external reviewers, remained equivalent to those designed with conventional strategies. A mixed-method usability evaluation of the platform yielded an overall positive image, with detailed suggestions for further improvements. The IUT is expected to positively affect the evaluation and development of WRD through its educational value, the context-specific recommendations supporting ongoing benchmarking endeavors, and highlighting the value of qualitative user research.
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Affiliation(s)
- Jan T. Meyer
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Natalie Tanczak
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore
| | - Christoph M. Kanzler
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore
| | - Colin Pelletier
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Roger Gassert
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore
| | - Olivier Lambercy
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore
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22
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Witzany C, Regoes RR, Igler C. Assessing the relative importance of bacterial resistance, persistence and hyper-mutation for antibiotic treatment failure. Proc Biol Sci 2022; 289:20221300. [PMID: 36350213 PMCID: PMC9653239 DOI: 10.1098/rspb.2022.1300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/18/2022] [Indexed: 08/01/2023] Open
Abstract
To curb the rising threat of antimicrobial resistance, we need to understand the routes to antimicrobial treatment failure. Bacteria can survive treatment by using both genetic and phenotypic mechanisms to diminish the effect of antimicrobials. We assemble empirical data showing that, for example, Pseudomonas aeruginosa infections frequently contain persisters, transiently non-growing cells unaffected by antibiotics (AB) and hyper-mutators, mutants with elevated mutation rates, and thus higher probability of genetic resistance emergence. Resistance, persistence and hyper-mutation dynamics are difficult to disentangle experimentally. Hence, we use stochastic population modelling and deterministic fitness calculations to investigate the relative importance of genetic and phenotypic mechanisms for immediate treatment failure and establishment of prolonged, chronic infections. We find that persistence causes 'hidden' treatment failure with very low cell numbers if antimicrobial concentrations prevent growth of genetically resistant cells. Persister cells can regrow after treatment is discontinued and allow for resistance evolution in the absence of AB. This leads to different mutational routes during treatment and relapse of an infection. By contrast, hyper-mutation facilitates resistance evolution during treatment, but rarely contributes to treatment failure. Our findings highlight the time and concentration dependence of different bacterial mechanisms to escape AB killing, which should be considered when designing 'failure-proof' treatments.
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Affiliation(s)
| | - Roland R. Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Claudia Igler
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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23
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Bora DK, Nadjafi M, Armutlulu A, Hosseini D, Castro-Fernández P, Toth R. Photoelectrochemical glycerol oxidation on Mo-BiVO 4 photoanodes shows high photocharging current density and enhanced H 2 evolution. Energy Adv 2022; 1:715-728. [PMID: 36324627 PMCID: PMC9558240 DOI: 10.1039/d2ya00077f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Mo-doped BiVO4's lower efficiency can be attributed in part to exciton recombination losses. Recombination losses during photoelectrochemical water oxidation can be eliminated by using glycerol as a hole acceptor. This results in an enhanced photocurrent density. In this research, we present the synthesis of a Mo-doped BiVO4 photoelectrode with a greater photocurrent density than a traditional pristine photoanode system. Increased photon exposure duration in the presence of glycerol leads to 8 mA cm-2 increase in photocurrent density due to the creation of a capacitance layer and a decrease in charge transfer resistance on the photoelectrode in a neutral-phosphate buffer solution thus confirming the photo charging effect. Glycerol photooxidation improves the photoelectrode's rate of hydrogen evolution. Research into the effects of electrolyte and electrode potential on photoelectrodes has revealed that when the applied potential increases, the light absorbance behaviour changes following its absorption distribution over the applied potential. Under a transmission electron microscope (TEM), a unique dynamical crystal fringe pattern is found in the nanoparticles scratched from the photoelectrode.
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Affiliation(s)
- Debajeet K Bora
- Laboratory of Energy Science and Engineering, Institute for Energy Technology, ETH Zurich CH-8092 Zurich Switzerland
| | - Manouchehr Nadjafi
- Laboratory of Energy Science and Engineering, Institute for Energy Technology, ETH Zurich CH-8092 Zurich Switzerland
| | - Andac Armutlulu
- Laboratory of Energy Science and Engineering, Institute for Energy Technology, ETH Zurich CH-8092 Zurich Switzerland
| | - Davood Hosseini
- Laboratory of Energy Science and Engineering, Institute for Energy Technology, ETH Zurich CH-8092 Zurich Switzerland
| | - Pedro Castro-Fernández
- Laboratory of Energy Science and Engineering, Institute for Energy Technology, ETH Zurich CH-8092 Zurich Switzerland
| | - Rita Toth
- Laboratory for High-Performance Ceramics, Empa. Swiss Federal Laboratories for Materials Science and Technology Überlandstrasse 129 CH-8600 Dübendorf Switzerland
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24
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Kehle C, Ramos JPG. Uniqueness of Solutions to Nonlinear Schrödinger Equations from their Zeros. Ann PDE 2022; 8:21. [PMID: 36119810 PMCID: PMC9470623 DOI: 10.1007/s40818-022-00138-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
We show novel types of uniqueness and rigidity results for Schrödinger equations in either the nonlinear case or in the presence of a complex-valued potential. As our main result we obtain that the trivial solution u = 0 is the only solution for which the assumptions u ( t = 0 ) | D = 0 , u ( t = T ) | D = 0 hold, where D ⊂ R d are certain subsets of codimension one. In particular, D is discrete for dimension d = 1 . Our main theorem can be seen as a nonlinear analogue of discrete Fourier uniqueness pairs such as the celebrated Radchenko-Viazovska formula in [21], and the uniqueness result of the second author and M. Sousa for powers of integers [22]. As an additional application, we deduce rigidity results for solutions to some semilinear elliptic equations from their zeros.
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Affiliation(s)
- Christoph Kehle
- Institute for Advanced Study, School of Mathematics, 1 Einstein Drive, Princeton, NJ USA
- ETH Zürich, Institute for Theoretical Studies, Clausiusstrasse 47, 8092 Zurich, Switzerland
| | - João P. G. Ramos
- ETH Zürich, Department of Mathematics, Rämisstrasse 101, 8092 Zurich, Switzerland
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25
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Konstantelos N, Rzepka AM, Burden AM, Cheung AM, Kim S, Grootendorst P, Cadarette SM. Fracture definitions in observational osteoporosis drug effects studies that leverage healthcare administrative (claims) data: a scoping review. Osteoporos Int 2022; 33:1837-1844. [PMID: 35578134 PMCID: PMC9463274 DOI: 10.1007/s00198-022-06395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/30/2022] [Indexed: 11/27/2022]
Abstract
UNLABELLED Healthcare administrative (claims) data are commonly utilized to estimate drug effects. We identified considerable heterogeneity in fracture outcome definitions in a scoping review of 57 studies that estimated osteoporosis drug effects on fracture risk. Better understanding of the impact of different fracture definitions on study results is needed. PURPOSE Healthcare administrative (claims) data are frequently used to estimate the real-world effects of drugs. Fracture incidence is a common outcome of osteoporosis drug studies. We aimed to describe how fractures are defined in studies that use claims data. METHODS We searched MEDLINE (Ovid), Embase (Ovid), CINAHL (EBSCO), and gray literature for studies published in English between 2000 and 2020 that estimated fracture effectiveness (hip, humerus, radius/ulna, vertebra) or safety (atypical fracture of the femur, AFF) of osteoporosis drugs using claims data in Canada and the USA. Literature searches, screening and data abstraction were completed independently by two reviewers. RESULTS We identified 57 eligible studies (52 effectiveness, 3 safety, 2 both). Hip fracture was the most common fracture site studied (93%), followed by humerus (66%), radius/ulna (59%), vertebra (61%), and AFF (9%). Half (n = 29) of the studies did not indicate specific data sources, codes, or cite a validation paper. Of the papers with sufficient detail, heterogeneity in fracture definitions was common. The most common definition within each fracture site was used by less than half of the studies that examined effectiveness (12 definitions in 29 hip fracture papers, 8 definitions in 17 humerus papers, 8 definitions in 13 radius/ulna papers, 9 definitions in 15 vertebra papers), and 3 definitions among 4 AFF papers. CONCLUSION There is ambiguity and heterogeneity in fracture outcome definitions in studies that leverage claims data. Better transparency in outcome reporting is needed. Future exploration of how fracture definitions impact study results is warranted.
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Affiliation(s)
- N Konstantelos
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada.
| | - A M Rzepka
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada
| | - A M Burden
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada
- ETH Zurich, Zurich, Switzerland
| | - A M Cheung
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Department of Medicine, University Health Network, University of Toronto, Toronto, Canada
| | - S Kim
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada
- Women's College Hospital, Toronto, Canada
| | - P Grootendorst
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada
- WHO Collaborating Centre for Governance, Accountability and Transparency in the Pharmaceutical Sector, Toronto, Canada
| | - S M Cadarette
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- WHO Collaborating Centre for Governance, Accountability and Transparency in the Pharmaceutical Sector, Toronto, Canada
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, USA
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26
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Glock S, Munhá Correia D, Sudakov B. The n-queens completion problem. Res Math Sci 2022; 9:41. [PMID: 35815227 PMCID: PMC9259550 DOI: 10.1007/s40687-022-00335-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
An n-queens configuration is a placement of n mutually non-attacking queens on an n × n chessboard. The n-queens completion problem, introduced by Nauck in 1850, is to decide whether a given partial configuration can be completed to an n-queens configuration. In this paper, we study an extremal aspect of this question, namely: how small must a partial configuration be so that a completion is always possible? We show that any placement of at most n/60 mutually non-attacking queens can be completed. We also provide partial configurations of roughly n/4 queens that cannot be completed and formulate a number of interesting problems. Our proofs connect the queens problem to rainbow matchings in bipartite graphs and use probabilistic arguments together with linear programming duality.
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Affiliation(s)
- Stefan Glock
- Institute for Theoretical Studies, ETH, 8092 Zurich, Switzerland
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27
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Moor L, Scheibler S, Gerken L, Scheffler K, Thieben F, Knopp T, Herrmann IK, Starsich FHL. Particle interactions and their effect on magnetic particle spectroscopy and imaging. Nanoscale 2022; 14:7163-7173. [PMID: 35343985 PMCID: PMC9119029 DOI: 10.1039/d1nr08402j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Signal stability is crucial for an accurate diagnosis via magnetic particle imaging (MPI). However, MPI-tracer nanoparticles frequently agglomerate during their in vivo applications leading to particle interactions altering the signal. Here, we investigate the influence of such magnetic coupling phenomena on the MPI signal. We prepared Zn0.4Fe2.6O4 nanoparticles by flame spray synthesis and controlled their inter-particle distance by varying SiO2 coating thickness. The silica shell affected the magnetic properties indicating stronger particle interactions for a smaller inter-particle distance. The SiO2-coated Zn0.4Fe2.6O4 outperformed the bare sample in magnetic particle spectroscopy (MPS) in terms of signal/noise, however, the shell thickness itself only weakly influenced the MPS signal. To investigate the importance of magnetic coupling effects in more detail, we benchmarked the MPS signal of the bare and SiO2-coated Zn-ferrites against commercially available PVP-coated Fe3O4 nanoparticles in water and PBS. PBS is known to destabilize nanoparticle colloids mimicking in vivo-like agglomeration. The bare and coated Zn-ferrites showed excellent signal stability, despite their agglomeration in PBS. We attribute this to their process-intrinsic aggregated morphology formed during their flame-synthesis, which generates an MPS signal only little affected by PBS. On the other hand, the MPS signal of commercial PVP-coated Fe3O4 strongly decreased in PBS compared to water, indicating strongly changed particle interactions. The relevance of this effect was further investigated in a human cell model. For PVP-coated Fe3O4, we detected a strong discrepancy between the particle concentration obtained from the MPS signal and the actual concentration determined via ICP-MS. The same trend was observed during their MPI analysis; while SiO2-coated Zn-ferrites could be precisely located in water and PBS, PVP-coated Fe3O4 could not be detected in PBS at all. This drastically limits the sensitivity and also general applicability of these commercial tracers for MPI and illustrates the advantages of our flame-made Zn-ferrites concerning signal stability and ultimately diagnostic accuracy.
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Affiliation(s)
- Lorena Moor
- Nanoparticle Systems Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland.
| | - Subas Scheibler
- Nanoparticle Systems Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland.
- Particles-Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Lukas Gerken
- Nanoparticle Systems Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland.
- Particles-Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Konrad Scheffler
- Section for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Lottestraße 55, 22529 Hamburg, Germany
- Institute for Biomedical Imaging, Hamburg University of Technology, Am Schwarzenberg-Campus 3, 21073 Hamburg, Germany
| | - Florian Thieben
- Section for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Lottestraße 55, 22529 Hamburg, Germany
- Institute for Biomedical Imaging, Hamburg University of Technology, Am Schwarzenberg-Campus 3, 21073 Hamburg, Germany
| | - Tobias Knopp
- Section for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Lottestraße 55, 22529 Hamburg, Germany
- Institute for Biomedical Imaging, Hamburg University of Technology, Am Schwarzenberg-Campus 3, 21073 Hamburg, Germany
| | - Inge K Herrmann
- Nanoparticle Systems Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland.
- Particles-Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Fabian H L Starsich
- Nanoparticle Systems Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland.
- Particles-Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
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28
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Fernandes A, Hosseini V, Vogel V, Lovchik RD. Engineering solutions for biological studies of flow-exposed endothelial cells on orbital shakers. PLoS One 2022; 17:e0262044. [PMID: 35061745 PMCID: PMC8782315 DOI: 10.1371/journal.pone.0262044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/15/2021] [Indexed: 01/01/2023] Open
Abstract
Shear stress is extremely important for endothelial cell (EC) function. The popularity of 6-well plates on orbital shakers to impose shear stress on ECs has increased among biologists due to their low cost and simplicity. One characteristic of such a platform is the heterogeneous flow profile within a well. While cells in the periphery are exposed to a laminar and high-velocity pulsatile flow that mimics physiological conditions, the flow in the center is disturbed and imposes low shear stress on the cells, which is characteristic of atheroprone regions. For studies where such heterogeneity is not desired, we present a simple cell-patterning technique to selectively prevent cell growth in the center of the well and facilitate the exclusive collection and analysis of cells in the periphery. This guarantees that cell phenotypes will not be influenced by secreted factors from cells exposed to other shear profiles nor that interesting results are obscured by mixing cells from different regions. We also present a multi-staining platform that compartmentalizes each well into 5 smaller independent regions: four at the periphery and one in the center. This is ideal for studies that aim to grow cells on the whole well surface, for comparison with previous work and minimal interference in the cell culture, but require screening of markers by immunostaining afterwards. It allows to compare different regions of the well, reduces antibody-related costs, and allows the exploration of multiple markers essential for high-content screening of cell response. By increasing the versatility of the 6-well plate on an orbital shaker system, we hope that these two solutions motivate biologists to pursue studies on EC mechanobiology and beyond.
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Affiliation(s)
- Andreia Fernandes
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Vahid Hosseini
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Viola Vogel
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
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Gantenbein J, Dittli J, Meyer JT, Gassert R, Lambercy O. Intention Detection Strategies for Robotic Upper-Limb Orthoses: A Scoping Review Considering Usability, Daily Life Application, and User Evaluation. Front Neurorobot 2022; 16:815693. [PMID: 35264940 PMCID: PMC8900616 DOI: 10.3389/fnbot.2022.815693] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Wearable robotic upper limb orthoses (ULO) are promising tools to assist or enhance the upper-limb function of their users. While the functionality of these devices has continuously increased, the robust and reliable detection of the user's intention to control the available degrees of freedom remains a major challenge and a barrier for acceptance. As the information interface between device and user, the intention detection strategy (IDS) has a crucial impact on the usability of the overall device. Yet, this aspect and the impact it has on the device usability is only rarely evaluated with respect to the context of use of ULO. A scoping literature review was conducted to identify non-invasive IDS applied to ULO that have been evaluated with human participants, with a specific focus on evaluation methods and findings related to functionality and usability and their appropriateness for specific contexts of use in daily life. A total of 93 studies were identified, describing 29 different IDS that are summarized and classified according to a four-level classification scheme. The predominant user input signal associated with the described IDS was electromyography (35.6%), followed by manual triggers such as buttons, touchscreens or joysticks (16.7%), as well as isometric force generated by residual movement in upper-limb segments (15.1%). We identify and discuss the strengths and weaknesses of IDS with respect to specific contexts of use and highlight a trade-off between performance and complexity in selecting an optimal IDS. Investigating evaluation practices to study the usability of IDS, the included studies revealed that, primarily, objective and quantitative usability attributes related to effectiveness or efficiency were assessed. Further, it underlined the lack of a systematic way to determine whether the usability of an IDS is sufficiently high to be appropriate for use in daily life applications. This work highlights the importance of a user- and application-specific selection and evaluation of non-invasive IDS for ULO. For technology developers in the field, it further provides recommendations on the selection process of IDS as well as to the design of corresponding evaluation protocols.
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Affiliation(s)
- Jessica Gantenbein
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Jan Dittli
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Jan Thomas Meyer
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Roger Gassert
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore
| | - Olivier Lambercy
- Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Future Health Technologies, Singapore-ETH Centre, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, Singapore
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Abstract
Covering: up to 2021Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a 'needle in a haystack' without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.
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Affiliation(s)
| | - Jörn Piel
- Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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Bebié P, Becker R, Commichau V, Debus J, Dissertori G, Djambazov L, Eleftheriou A, Fischer J, Fischer P, Ito M, Khateri P, Lustermann W, Ritzer C, Ritzert M, Röser U, Tsoumpas C, Warnock G, Weber B, Wyss MT, Zagozdzinska-Bochenek A. SAFIR-I: Design and Performance of a High-Rate Preclinical PET Insert for MRI. Sensors (Basel) 2021; 21:7037. [PMID: 34770344 PMCID: PMC8588038 DOI: 10.3390/s21217037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022]
Abstract
(1) Background: Small Animal Fast Insert for MRI detector I (SAFIR-I) is a preclinical Positron Emission Tomography (PET) insert for the Bruker BioSpec 70/30 Ultra Shield Refrigerated (USR) preclinical 7T Magnetic Resonance Imaging (MRI) system. It is designed explicitly for high-rate kinetic studies in mice and rats with injected activities reaching 500MBq, enabling truly simultaneous quantitative PET and Magnetic Resonance (MR) imaging with time frames of a few seconds in length. (2) Methods: SAFIR-I has an axial field of view of 54.2mm and an inner diameter of 114mm. It employs Lutetium Yttrium OxyorthoSilicate (LYSO) crystals and Multi Pixel Photon Counter (MPPC) arrays. The Position-Energy-Timing Application Specific Integrated Circuit, version 6, Single Ended (PETA6SE) digitizes the MPPC signals and provides time stamps and energy information. (3) Results: SAFIR-I is MR-compatible. The system's Coincidence Resolving Time (CRT) and energy resolution are between separate-uncertainty 209.0(3)ps and separate-uncertainty 12.41(02) Full Width at Half Maximum (FWHM) at low activity and separate-uncertainty 326.89(12)ps and separate-uncertainty 20.630(011) FWHM at 550MBq, respectively. The peak sensitivity is ∼1.6. The excellent performance facilitated the successful execution of first in vivo rat studies beyond 300MBq. Based on features visible in the acquired images, we estimate the spatial resolution to be ∼2mm in the center of the Field Of View (FOV). (4) Conclusion: The SAFIR-I PET insert provides excellent performance, permitting simultaneous in vivo small animal PET/MR image acquisitions with time frames of a few seconds in length at activities of up to 500MBq.
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Affiliation(s)
- Pascal Bebié
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Robert Becker
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Volker Commichau
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Jan Debus
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Günther Dissertori
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Lubomir Djambazov
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Afroditi Eleftheriou
- Institute of Pharmacology and Toxicology, University of Zürich, 8057 Zürich, Switzerland; (A.E.); (G.W.); (B.W.); (M.T.W.)
| | - Jannis Fischer
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Peter Fischer
- Institute of Computer Engineering, Heidelberg University, 69120 Heidelberg, Germany; (P.F.); (M.R.)
| | - Mikiko Ito
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Parisa Khateri
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Werner Lustermann
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Christian Ritzer
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Michael Ritzert
- Institute of Computer Engineering, Heidelberg University, 69120 Heidelberg, Germany; (P.F.); (M.R.)
| | - Ulf Röser
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
| | - Charalampos Tsoumpas
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK;
| | - Geoffrey Warnock
- Institute of Pharmacology and Toxicology, University of Zürich, 8057 Zürich, Switzerland; (A.E.); (G.W.); (B.W.); (M.T.W.)
| | - Bruno Weber
- Institute of Pharmacology and Toxicology, University of Zürich, 8057 Zürich, Switzerland; (A.E.); (G.W.); (B.W.); (M.T.W.)
| | - Matthias T. Wyss
- Institute of Pharmacology and Toxicology, University of Zürich, 8057 Zürich, Switzerland; (A.E.); (G.W.); (B.W.); (M.T.W.)
| | - Agnieszka Zagozdzinska-Bochenek
- Institute for Particle Physics and Astrophysics, ETH Zürich, 8093 Zürich, Switzerland; (R.B.); (V.C.); (J.D.); (G.D.); (L.D.); (J.F.); (M.I.); (P.K.); (W.L.); (C.R.); (U.R.); (A.Z.-B.)
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Lussi J, Mattmann M, Sevim S, Grigis F, De Marco C, Chautems C, Pané S, Puigmartí‐Luis J, Boehler Q, Nelson BJ. A Submillimeter Continuous Variable Stiffness Catheter for Compliance Control. Adv Sci (Weinh) 2021; 8:e2101290. [PMID: 34272935 PMCID: PMC8456283 DOI: 10.1002/advs.202101290] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/10/2021] [Indexed: 05/02/2023]
Abstract
Minimally invasive robotic surgery often requires functional tools that can change their compliance to adapt to the environment and surgical needs. This paper proposes a submillimeter continuous variable stiffness catheter equipped with a phase-change alloy that has a high stiffness variation in its different states, allowing for rapid compliance control. Variable stiffness is achieved through a variable phase boundary in the alloy due to a controlled radial temperature gradient. This catheter can be safely navigated in its soft state and rigidified to the required stiffness during operation to apply a desired force at the tip. The maximal contact force that the catheter applies to tissue can be continuously modified by a factor of 400 (≈20 mN-8 N). The catheter is equipped with a magnet and a micro-gripper to perform a fully robotic ophthalmic minimally invasive surgery on an eye phantom by means of an electromagnetic navigation system.
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Affiliation(s)
- Jonas Lussi
- Institute of Robotics and Intelligent SystemsETH ZurichZurichCH‐8092Switzerland
| | - Michael Mattmann
- Institute of Robotics and Intelligent SystemsETH ZurichZurichCH‐8092Switzerland
| | - Semih Sevim
- Institute of Chemical and BioengineeringETH ZurichVladimir Prelog Weg 1ZurichCH‐8093Switzerland
| | - Fabian Grigis
- Institute of Robotics and Intelligent SystemsETH ZurichZurichCH‐8092Switzerland
| | - Carmela De Marco
- Institute of Robotics and Intelligent SystemsETH ZurichZurichCH‐8092Switzerland
| | - Christophe Chautems
- Institute of Robotics and Intelligent SystemsETH ZurichZurichCH‐8092Switzerland
| | - Salvador Pané
- Institute of Robotics and Intelligent SystemsETH ZurichZurichCH‐8092Switzerland
| | - Josep Puigmartí‐Luis
- Departament de Ciència dels Materials i Química FísicaInstitut de Química Teòrica i ComputacionalBarcelona08028Spain
- ICREACatalan Institution for Research and Advanced StudiesPg. Lluís Companys 23Barcelona08010Spain
| | - Quentin Boehler
- Institute of Robotics and Intelligent SystemsETH ZurichZurichCH‐8092Switzerland
| | - Bradley J. Nelson
- Institute of Robotics and Intelligent SystemsETH ZurichZurichCH‐8092Switzerland
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Huh DN, Cheng Y, Frye CW, Egger DT, Tonks IA. Multicomponent syntheses of 5- and 6-membered aromatic heterocycles using group 4-8 transition metal catalysts. Chem Sci 2021; 12:9574-9590. [PMID: 34349931 PMCID: PMC8293814 DOI: 10.1039/d1sc03037j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/28/2021] [Indexed: 12/31/2022] Open
Abstract
In this Perspective, we discuss recent syntheses of 5- and 6-membered aromatic heterocycles via multicomponent reactions (MCRs) that are catalyzed by group 4-8 transition metals. These MCRs can be categorized based on the substrate components used to generate the cyclized product, as well as on common mechanistic features between the catalyst systems. These particular groupings are intended to highlight mechanistic and strategic similarities between otherwise disparate transition metals and to encourage future work exploring related systems with otherwise-overlooked elements. Importantly, in many cases these early- to mid-transition metal catalysts have been shown to be as effective for heterocycle syntheses as the later (and more commonly implemented) group 9-11 metals.
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Zehnder J, Cadalbert R, Terradot L, Ernst M, Böckmann A, Güntert P, Meier BH, Wiegand T. Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase. Chemistry 2021; 27:7745-7755. [PMID: 33822417 PMCID: PMC8252064 DOI: 10.1002/chem.202100462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg2+ cofactor with Mn2+ or Co2+ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF4 - and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies. 31 P PCSs induced in the Co2+ -containing sample are then used to localize the DNA phosphate groups on the Co2+ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.
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Affiliation(s)
- Johannes Zehnder
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Riccardo Cadalbert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Matthias Ernst
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Peter Güntert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
- Institute of Biophysical ChemistryCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt am Main60438Frankfurt am MainGermany
- Department of ChemistryTokyo Metropolitan UniversityHachiojiTokyo1920397Japan
| | - Beat H. Meier
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas Wiegand
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
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Sedda MA, Berry CPL, Jani K, Amaro-Seoane P, Auclair P, Baird J, Baker T, Berti E, Breivik K, Caprini C, Chen X, Doneva D, Ezquiaga JM, Ford KES, Katz ML, Kolkowitz S, McKernan B, Mueller G, Nardini G, Pikovski I, Rajendran S, Sesana A, Shao L, Tamanini N, Warburton N, Witek H, Wong K, Zevin M. The missing link in gravitational-wave astronomy: A summary of discoveries waiting in the decihertz range. Exp Astron (Dordr) 2021; 51:1427-1440. [PMID: 34720416 PMCID: PMC8536607 DOI: 10.1007/s10686-021-09713-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/09/2021] [Indexed: 06/13/2023]
Abstract
Since 2015 the gravitational-wave observations of LIGO and Virgo have transformed our understanding of compact-object binaries. In the years to come, ground-based gravitational-wave observatories such as LIGO, Virgo, and their successors will increase in sensitivity, discovering thousands of stellar-mass binaries. In the 2030s, the space-based LISA will provide gravitational-wave observations of massive black holes binaries. Between the ∼ 10 -103 Hz band of ground-based observatories and the ∼ 1 0 - 4 -10- 1 Hz band of LISA lies the uncharted decihertz gravitational-wave band. We propose a Decihertz Observatory to study this frequency range, and to complement observations made by other detectors. Decihertz observatories are well suited to observation of intermediate-mass ( ∼ 1 0 2 -104 M ⊙) black holes; they will be able to detect stellar-mass binaries days to years before they merge, providing early warning of nearby binary neutron star mergers and measurements of the eccentricity of binary black holes, and they will enable new tests of general relativity and the Standard Model of particle physics. Here we summarise how a Decihertz Observatory could provide unique insights into how black holes form and evolve across cosmic time, improve prospects for both multimessenger astronomy and multiband gravitational-wave astronomy, and enable new probes of gravity, particle physics and cosmology.
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Affiliation(s)
- Manuel Arca Sedda
- Astronomisches Rechen-Institut, Zentrüm für Astronomie, Universität Heidelberg, Mönchofstr. 12-14, Heidelberg, Germany
| | - Christopher P. L. Berry
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA), Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
- SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow, G12 8QQ UK
| | - Karan Jani
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37212 USA
| | - Pau Amaro-Seoane
- Universitat Politècnica de València, IGIC, Valencia, Spain
- Kavli Institute for Astronomy and Astrophysics, Peking University, Beijing, 100871 China
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, CAS, Beijing, 100190 China
- Zentrum für Astronomie und Astrophysik, TU Berlin, Hardenbergstraße 36, 10623 Berlin, Germany
| | - Pierre Auclair
- Laboratoire Astroparticule et Cosmologie, CNRS UMR 7164, Université Paris-Diderot, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France
| | - Jonathon Baird
- High Energy Physics Group, Physics Department, Imperial College London, Blackett Laboratory, Prince Consort Road, London, SW7 2BW UK
| | - Tessa Baker
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, London, E1 4NS UK
| | - Emanuele Berti
- Department of Physics and Astronomy, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218 USA
| | - Katelyn Breivik
- Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 1A7 Canada
| | - Chiara Caprini
- Laboratoire Astroparticule et Cosmologie, CNRS UMR 7164, Université Paris-Diderot, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France
| | - Xian Chen
- Kavli Institute for Astronomy and Astrophysics, Peking University, Beijing, 100871 China
- Astronomy Department, School of Physics, Peking University, Beijing, 100871 China
| | - Daniela Doneva
- Theoretical Astrophysics, Eberhard Karls University of Tübingen, Tübingen, 72076 Germany
| | - Jose M. Ezquiaga
- Kavli Institute for Cosmological Physics, Enrico Fermi Institute, The University of Chicago, Chicago, IL 60637 USA
| | - K. E. Saavik Ford
- City University of New York-BMCC, Chambers St, New York, NY 10007 USA
- Department of Astrophysics, American Museum of Natural History, New York, NY 10028 USA
| | - Michael L. Katz
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA), Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Shimon Kolkowitz
- Department of Physics, University of Wisconsin – Madison, Madison, WI 53706 USA
| | - Barry McKernan
- City University of New York-BMCC, Chambers St, New York, NY 10007 USA
- Department of Astrophysics, American Museum of Natural History, New York, NY 10028 USA
| | - Guido Mueller
- Department of Physics, University of Florida, PO Box 118440, Gainesville, Florida 32611 USA
| | - Germano Nardini
- Faculty of Science and Technology, University of Stavanger, 4036 Stavanger, Norway
| | - Igor Pikovski
- Department of Physics, Stevens Institute of Technology, Hoboken, NJ 07030 USA
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Surjeet Rajendran
- Department of Physics and Astronomy, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218 USA
| | - Alberto Sesana
- Università di Milano Bicocca, Dipartimento di Fisica G. Occhialini, Piazza della Scienza 3, I-20126 Milano, Italy
| | - Lijing Shao
- Kavli Institute for Astronomy and Astrophysics, Peking University, Beijing, 100871 China
- National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100012 China
| | - Nicola Tamanini
- Max-Planck-Institut für Gravitationsphysik (Albert-Einstein-Institut), Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Niels Warburton
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4 Ireland
| | - Helvi Witek
- Department of Physics, King’s College London, Strand, London WC2R 2LS UK
| | - Kaze Wong
- Department of Physics and Astronomy, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218 USA
| | - Michael Zevin
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA), Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
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36
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Weber IC, Wang CT, Güntner AT. Room-Temperature Catalyst Enables Selective Acetone Sensing. Materials (Basel) 2021; 14:1839. [PMID: 33917648 PMCID: PMC8067997 DOI: 10.3390/ma14081839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022]
Abstract
Catalytic packed bed filters ahead of gas sensors can drastically improve their selectivity, a key challenge in medical, food and environmental applications. Yet, such filters require high operation temperatures (usually some hundreds °C) impeding their integration into low-power (e.g., battery-driven) devices. Here, we reveal room-temperature catalytic filters that facilitate highly selective acetone sensing, a breath marker for body fat burn monitoring. Varying the Pt content between 0-10 mol% during flame spray pyrolysis resulted in Al2O3 nanoparticles decorated with Pt/PtOx clusters with predominantly 5-6 nm size, as revealed by X-ray diffraction and electron microscopy. Most importantly, Pt contents above 3 mol% removed up to 100 ppm methanol, isoprene and ethanol completely already at 40 °C and high relative humidity, while acetone was mostly preserved, as confirmed by mass spectrometry. When combined with an inexpensive, chemo-resistive sensor of flame-made Si/WO3, acetone was detected with high selectivity (≥225) over these interferants next to H2, CO, form-/acetaldehyde and 2-propanol. Such catalytic filters do not require additional heating anymore, and thus are attractive for integration into mobile health care devices to monitor, for instance, lifestyle changes in gyms, hospitals or at home.
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Affiliation(s)
- Ines C. Weber
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland; (I.C.W.); (C.-t.W.)
| | - Chang-ting Wang
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland; (I.C.W.); (C.-t.W.)
| | - Andreas T. Güntner
- Particle Technology Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland; (I.C.W.); (C.-t.W.)
- Department of Endocrinology, Diabetology, and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), CH-8091 Zurich, Switzerland
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37
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Solari SF, Kumar S, Jagielski J, Kubo NM, Krumeich F, Shih CJ. Ligand-assisted solid phase synthesis of mixed-halide perovskite nanocrystals for color-pure and efficient electroluminescence. J Mater Chem C Mater 2021; 9:5771-5778. [PMID: 33996098 PMCID: PMC8101407 DOI: 10.1039/d0tc04667a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Colloidal nanocrystals (NCs) of lead halide perovskites have generated considerable interest in the fabrication of optoelectronic devices, such as light emitting-diodes (LEDs), because of their tunable optical bandgap, narrow spectral width, and high defect tolerance. However, the inhomogeneous halide distribution within individual NCs remains a critical challenge in order to obtain color-stable electroluminescence in mixed-halide systems. Here, we demonstrate a new post-synthetic approach, ligand-assisted solid phase synthesis (LASPS), for the preparation of electroluminescent colloidal NCs of methylammonium (MA) lead halide perovskites, at room temperature. The slow reaction kinetics preserves the morphology, size, and shape in the resulting NCs whose emission covers the entire visible spectral region with photoluminescence (PL) quantum yields (QYs) of up to >90% and colloidal stability up to several months. The LEDs fabricated using the prepared mixed-halide NCs display narrowband electroluminescence (EL) ranging from 476 to 720 nm. The optimized red LEDs exhibit an external quantum efficiency, η ext, of up to 2.65%, with the CIE 1931 color coordinates of (0.705, 0.290), nearly identical to those of the red primary in the recommendation (rec.) 2020 standard (0.708, 0.292).
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Affiliation(s)
- Simon F Solari
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir Prelog Weg 1 CH-8093 Zürich Switzerland
| | - Sudhir Kumar
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir Prelog Weg 1 CH-8093 Zürich Switzerland
| | - Jakub Jagielski
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir Prelog Weg 1 CH-8093 Zürich Switzerland
| | - Nikolas M Kubo
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir Prelog Weg 1 CH-8093 Zürich Switzerland
| | - Frank Krumeich
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir Prelog Weg 1 CH-8093 Zürich Switzerland
| | - Chih-Jen Shih
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir Prelog Weg 1 CH-8093 Zürich Switzerland
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38
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Mei Y, Gamboa-Carballo JJ, Bao Y, Wu N, Le Corre G, Grützmacher H. Coordination-induced polymerization of P═C bonds leads to regular (P─C) n polycarbophosphanes. Sci Adv 2021; 7:eabf4272. [PMID: 33692112 PMCID: PMC7946365 DOI: 10.1126/sciadv.abf4272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
The replacement of carbon in (C─C) n chains of polyolefins by phosphorus leads to polycarbophosphanes (P─C) n , which may possess unique chemical and physical properties. However, macromolecules with a regular (P─C) n chain have never been unambiguously identified. Here, we demonstrate that addition polymerization, a general concept to polymerize olefins, can be extended to P═C double bonds. The polymerization of monomeric 2-phosphanaphthalenes is mediated by copper(I) halides and leads to polycarbophosphanes with an M n of 14 to 34 kDa. Each phosphorus is coordinated to Cu(I), which can be easily removed. Unlike long-term durable polyolefins, the metal-free polymers depolymerize rapidly back to monomers under sunlight or ultraviolet irradiation at λ = 365 nm. The monomers can be recycled for repolymerization, demonstrating a cradle-to-cradle life cycle for polycarbophosphanes.
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Affiliation(s)
- Yanbo Mei
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog Weg 1, 8093 Zürich, Switzerland
| | - Juan José Gamboa-Carballo
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog Weg 1, 8093 Zürich, Switzerland
- Higher Institute of Technologies and Applied Sciences (InSTEC), University of Havana, 10600 Havana, Cuba
| | - Yinyin Bao
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog Weg 1, 8093 Zürich, Switzerland
| | - Na Wu
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog Weg 1, 8093 Zürich, Switzerland
| | - Grégoire Le Corre
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog Weg 1, 8093 Zürich, Switzerland
| | - Hansjörg Grützmacher
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog Weg 1, 8093 Zürich, Switzerland.
- Lehn Institute of Functional Materials (LIFM), School of Chemistry, Sun Yat-Sen University, 510275 Guangzhou, China
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Prasad R, Sliwa-Gonzalez A, Barral Y. Mapping bilayer thickness in the ER membrane. Sci Adv 2020; 6:6/46/eaba5130. [PMID: 33177076 PMCID: PMC7673731 DOI: 10.1126/sciadv.aba5130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/23/2020] [Indexed: 05/20/2023]
Abstract
In the plasma membrane and in synthetic membranes, resident lipids may laterally unmix to form domains of distinct biophysical properties. Whether lipids also drive the lateral organization of intracellular membranes is largely unknown. Here, we describe genetically encoded fluorescent reporters visualizing local variations in bilayer thickness. Using them, we demonstrate that long-chained ceramides promote the formation of discrete domains of increased bilayer thickness in the yeast ER, particularly in the future plane of cleavage and at ER-trans-Golgi contact sites. Thickening of the ER membrane in the cleavage plane contributed to the formation of lateral diffusion barriers, which restricted the passage of short, but not long, protein transmembrane domains between the mother and bud ER compartments. Together, our data establish that the ER membrane is laterally organized and that ceramides drive this process, and provide insights into the physical nature and biophysical mechanisms of the lateral diffusion barriers that compartmentalize the ER.
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Affiliation(s)
- Rupali Prasad
- Institute of Biochemistry, Department of Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Andrzej Sliwa-Gonzalez
- Institute of Biochemistry, Department of Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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Dorodnyy A, Koepfli SM, Lochbaum A, Leuthold J. Design of CMOS-compatible metal-insulator-metal metasurfaces via extended equivalent-circuit analysis. Sci Rep 2020; 10:17941. [PMID: 33087776 PMCID: PMC7578050 DOI: 10.1038/s41598-020-74849-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/05/2020] [Indexed: 11/16/2022] Open
Abstract
Photonic metasurfaces compatible with large-scale production such as CMOS are of importance because they promise cointegration of electronics with photonics for detection, communication and sensing. The main challenges on the way of designing such metasurfaces are: (1) large variety of possible geometrical shapes of metasurface elements that makes finding the most appropriate shape difficult; (2) poor compatibility of available electronic layer stacks with photonics. In this paper we show how to address both of these challenges utilizing extended equivalent-circuit analysis. In a first step we classify the behavior of different metasurfaces using the equivalent circuit. We discover that metasurfaces that use inverted-dipole resonator type exhibit higher tolerance to dielectric spacer thickness, higher angular stability and have similar resonance quality-factor as other types. In the second step we utilize the equivalent-circuit scheme to efficiently optimize the parameters of inverted-dipole based metasurfaces for a layer stack such as given in a CMOS process. Finally, as an example we demonstrate how an inverted-cross structure can be adapted to a commercial 110 nm CMOS process with Al metal layers. We measured peak absorption above 90% at center wavelength around 4 µm with quality factor of approximately 5 and angular stability larger than 60°.
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Affiliation(s)
| | - Stefan M Koepfli
- Institute of Electromagnetic Fields, ETH Zurich, Zurich, Switzerland
| | | | - Juerg Leuthold
- Institute of Electromagnetic Fields, ETH Zurich, Zurich, Switzerland
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Vanderkelen I, Zscheischler J, Gudmundsson L, Keuler K, Rineau F, Beenaerts N, Vangronsveld J, Vicca S, Thiery W. A novel method for assessing climate change impacts in ecotron experiments. Int J Biometeorol 2020; 64:1709-1727. [PMID: 32671669 PMCID: PMC7481170 DOI: 10.1007/s00484-020-01951-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Ecotron facilities allow accurate control of many environmental variables coupled with extensive monitoring of ecosystem processes. They therefore require multivariate perturbation of climate variables, close to what is observed in the field and projections for the future. Here, we present a new method for creating realistic climate forcing for manipulation experiments and apply it to the UHasselt Ecotron experiment. The new methodology uses data derived from the best available regional climate model projection and consists of generating climate forcing along a gradient representative of increasingly high global mean air temperature anomalies. We first identified the best-performing regional climate model simulation for the ecotron site from the Coordinated Regional Downscaling Experiment in the European domain (EURO-CORDEX) ensemble based on two criteria: (i) highest skill compared to observations from a nearby weather station and (ii) representativeness of the multi-model mean in future projections. The time window is subsequently selected from the model projection for each ecotron unit based on the global mean air temperature of the driving global climate model. The ecotron units are forced with 3-hourly output from the projections of the 5-year period in which the global mean air temperature crosses the predefined values. With the new approach, Ecotron facilities become able to assess ecosystem responses on changing climatic conditions, while accounting for the co-variation between climatic variables and their projection in variability, well representing possible compound events. The presented methodology can also be applied to other manipulation experiments, aiming at investigating ecosystem responses to realistic future climate change.
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Affiliation(s)
- Inne Vanderkelen
- Department of Hydrology and Hydraulic Engineering, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Jakob Zscheischler
- Climate and Environmental Physics, University of Bern, Bern, Switzerland
- Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
| | - Lukas Gudmundsson
- Institute for Atmospheric and Climate Science, ETH Zurich, Zurich, Switzerland
| | - Klaus Keuler
- Department of Environmental Meteorology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Francois Rineau
- Centre for Environmental Sciences, UHasselt, Hasselt, Belgium
| | | | - Jaco Vangronsveld
- Centre for Environmental Sciences, UHasselt, Hasselt, Belgium
- Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Lublin, Poland
| | - Sara Vicca
- Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Wim Thiery
- Department of Hydrology and Hydraulic Engineering, Vrije Universiteit Brussel, Brussels, Belgium
- Institute for Atmospheric and Climate Science, ETH Zurich, Zurich, Switzerland
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