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2. The relationship between uremic toxins and symptoms in older men and women with advanced chronic kidney disease

Author

Massy Z. A., Chesnaye N. C., Larabi I. A., Dekker F. W., Evans M., Caskey F. J., Torino C., Porto G., Szymczak M., Drechsler C., Wanner C., Jager K. J., Alvarez J. C., Schneider A., Torp A., Iwig B., Perras B., Marx C., Blaser C., Emde C., Krieter D., Fuchs D., Irmler E., Platen E., Schmidt-Gurtler H., Schlee H., Naujoks H., Schlee I., Casar S., Beige J., Rothele J., Mazur J., Hahn K., Blouin K., Neumeier K., Anding-Rost K., Schramm L., Hopf M., Wuttke N., Frischmuth N., Ichtiaris P., Kirste P., Schulz P., Aign S., Biribauer S., Manan S., Roser S., Heidenreich S., Palm S., Schwedler S., Delrieux S., Renker S., Schattel S., Stephan T., Schmiedeke T., Weinreich T., Leimbach T., Stovesand T., Bahner U., Seeger W., Cupisti A., Sagliocca A., Ferraro A., Mele A., Naticchia A., Cosaro A., Ranghino A., Stucchi A., Pignataro A., De Blasio A., Pani A., Tsalouichos A., Bellasi A., Raffaele Di Iorio B., Butti A., Abaterusso C., Somma C., D'Alessandro C., Zullo C., Pozzi C., Bergamo D., Ciurlino D., Motta D., Russo D., Favaro E., Vigotti F., Ansali F., Conte F., Cianciotta F., Giacchino F., Cappellaio F., Pizzarelli F., Greco G., Bigatti G., Marinangeli G., Cabiddu G., Fumagalli G., Caloro G., Piccoli G., Capasso G., Gambaro G., Tognarelli G., Bonforte G., Conte G., Toscano G., Del Rosso G., Capizzi I., Baragetti I., Oldrizzi L., Gesualdo L., Biancone L., Magnano M., Ricardi M., Di Bari M., Laudato M., Luisa Sirico M., Ferraresi M., Provenzano M., Malaguti M., Palmieri N., Murrone P., Cirillo P., Dattolo P., Acampora P., Nigro R., Boero R., Scarpioni R., Sicoli R., Malandra R., Savoldi S., Bertoli S., Borrelli S., Maxia S., Maffei S., Mangano S., Cicchetti T., Rappa T., Palazzo V., De Simone W., Schrander A., Van Dam B., Siegert C., Gaillard C., Beerenhout C., Verburgh C., Janmaat C., Hoogeveen E., Hoorn E., Boots J., Boom H., Eijgenraam J. -W., Kooman J., Rotmans J., Vogt L., Raasveld M., Vervloet M., Van Buren M., Van Diepen M., Leurs P., Voskamp P., Blankestijn P., Van Esch S., Boorsma S., Berger S., Konings C., Aydin Z., Musiala A., Szymczak A., Olczyk E., Augustyniak-Bartosik H., Miskowiec-Wisniewska I., Manitius J., Pondel J., Jedrzejak K., Nowanska K., Nowak L., Durlik M., Dorota S., Nieszporek T., Heleniak Z., Jonsson A., Blom A. -L., Rogland B., Wallquist C., Vargas D., Dimeny E., Sundelin F., Uhlin F., Welander G., Bascaran Hernandez I., Grontoft K. -C., Stendahl M., Svensson M., Heimburger O., Kashioulis P., Melander S., Almquist T., Jensen U., Woodman A., McKeever A., Ullah A., McLaren B., Harron C., Barrett C., O'Toole C., Summersgill C., Geddes C., Glowski D., McGlynn D., Sands D., Roy G., Hirst G., King H., McNally H., Masri-Senghor H., Murtagh H., Rayner H., Turner J., Wilcox J., Berdeprado J., Wong J., Banda J., Jones K., Haydock L., Wilkinson L., Carmody M., Weetman M., Joinson M., Dutton M., Matthews M., Morgan N., Bleakley N., Cockwell P., Roderick P., Mason P., Kalra P., Sajith R., Chapman S., Navjee S., Crosbie S., Brown S., Tickle S., Mathavakkannan S., Kuan Y., Massy, Z. A., Chesnaye, N. C., Larabi, I. A., Dekker, F. W., Evans, M., Caskey, F. J., Torino, C., Porto, G., Szymczak, M., Drechsler, C., Wanner, C., Jager, K. J., Alvarez, J. C., Schneider, A., Torp, A., Iwig, B., Perras, B., Marx, C., Blaser, C., Emde, C., Krieter, D., Fuchs, D., Irmler, E., Platen, E., Schmidt-Gurtler, H., Schlee, H., Naujoks, H., Schlee, I., Casar, S., Beige, J., Rothele, J., Mazur, J., Hahn, K., Blouin, K., Neumeier, K., Anding-Rost, K., Schramm, L., Hopf, M., Wuttke, N., Frischmuth, N., Ichtiaris, P., Kirste, P., Schulz, P., Aign, S., Biribauer, S., Manan, S., Roser, S., Heidenreich, S., Palm, S., Schwedler, S., Delrieux, S., Renker, S., Schattel, S., Stephan, T., Schmiedeke, T., Weinreich, T., Leimbach, T., Stovesand, T., Bahner, U., Seeger, W., Cupisti, A., Sagliocca, A., Ferraro, A., Mele, A., Naticchia, A., Cosaro, A., Ranghino, A., Stucchi, A., Pignataro, A., De Blasio, A., Pani, A., Tsalouichos, A., Bellasi, A., Raffaele Di Iorio, B., Butti, A., Abaterusso, C., Somma, C., D'Alessandro, C., Zullo, C., Pozzi, C., Bergamo, D., Ciurlino, D., Motta, D., Russo, D., Favaro, E., Vigotti, F., Ansali, F., Conte, F., Cianciotta, F., Giacchino, F., Cappellaio, F., Pizzarelli, F., Greco, G., Bigatti, G., Marinangeli, G., Cabiddu, G., Fumagalli, G., Caloro, G., Piccoli, G., Capasso, G., Gambaro, G., Tognarelli, G., Bonforte, G., Conte, G., Toscano, G., Del Rosso, G., Capizzi, I., Baragetti, I., Oldrizzi, L., Gesualdo, L., Biancone, L., Magnano, M., Ricardi, M., Di Bari, M., Laudato, M., Luisa Sirico, M., Ferraresi, M., Provenzano, M., Malaguti, M., Palmieri, N., Murrone, P., Cirillo, P., Dattolo, P., Acampora, P., Nigro, R., Boero, R., Scarpioni, R., Sicoli, R., Malandra, R., Savoldi, S., Bertoli, S., Borrelli, S., Maxia, S., Maffei, S., Mangano, S., Cicchetti, T., Rappa, T., Palazzo, V., De Simone, W., Schrander, A., Van Dam, B., Siegert, C., Gaillard, C., Beerenhout, C., Verburgh, C., Janmaat, C., Hoogeveen, E., Hoorn, E., Boots, J., Boom, H., Eijgenraam, J. -W., Kooman, J., Rotmans, J., Vogt, L., Raasveld, M., Vervloet, M., Van Buren, M., Van Diepen, M., Leurs, P., Voskamp, P., Blankestijn, P., Van Esch, S., Boorsma, S., Berger, S., Konings, C., Aydin, Z., Musiala, A., Szymczak, A., Olczyk, E., Augustyniak-Bartosik, H., Miskowiec-Wisniewska, I., Manitius, J., Pondel, J., Jedrzejak, K., Nowanska, K., Nowak, L., Durlik, M., Dorota, S., Nieszporek, T., Heleniak, Z., Jonsson, A., Blom, A. -L., Rogland, B., Wallquist, C., Vargas, D., Dimeny, E., Sundelin, F., Uhlin, F., Welander, G., Bascaran Hernandez, I., Grontoft, K. -C., Stendahl, M., Svensson, M., Heimburger, O., Kashioulis, P., Melander, S., Almquist, T., Jensen, U., Woodman, A., Mckeever, A., Ullah, A., Mclaren, B., Harron, C., Barrett, C., O'Toole, C., Summersgill, C., Geddes, C., Glowski, D., Mcglynn, D., Sands, D., Roy, G., Hirst, G., King, H., Mcnally, H., Masri-Senghor, H., Murtagh, H., Rayner, H., Turner, J., Wilcox, J., Berdeprado, J., Wong, J., Banda, J., Jones, K., Haydock, L., Wilkinson, L., Carmody, M., Weetman, M., Joinson, M., Dutton, M., Matthews, M., Morgan, N., Bleakley, N., Cockwell, P., Roderick, P., Mason, P., Kalra, P., Sajith, R., Chapman, S., Navjee, S., Crosbie, S., Brown, S., Tickle, S., Mathavakkannan, S., Kuan, Y., Nephrology, ACS - Diabetes & metabolism, Medical Informatics, APH - Methodology, APH - Aging & Later Life, APH - Quality of Care, APH - Global Health, APH - Health Behaviors & Chronic Diseases, and ACS - Pulmonary hypertension & thrombosis

Subjects
Transplantation, Nephrology, uremic toxins, CKD, symptoms, symptom, elderly
Abstract

Background Patients with stage 4/5 chronic kidney disease (CKD) suffer from various symptoms. The retention of uremic solutes is thought to be associated with those symptoms. However, there are relatively few rigorous studies on the potential links between uremic toxins and symptoms in patients with CKD. Methods The EQUAL study is an ongoing observational cohort study of non-dialyzed patients with stage 4/5 CKD. EQUAL patients from Germany, Poland, Sweden and the UK were included in the present study (n = 795). Data and symptom self-report questionnaires were collected between April 2012 and September 2020. Baseline uric acid and parathyroid hormone and 10 uremic toxins were quantified. We tested the association between uremic toxins and symptoms and adjusted P-values for multiple testing. Results Symptoms were more frequent in women than in men with stage 4/5 CKD, while levels of various uremic toxins were higher in men. Only trimethylamine N-oxide (TMAO; positive association with fatigue), p-cresyl sulfate (PCS) with constipation and 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid (negative association with shortness of breath) demonstrated moderately strong associations with symptoms in adjusted analyses. The association of phenylacetylglutamine with shortness of breath was consistent in both sexes, although it only reached statistical significance in the full population. In contrast, TMAO (fatigue) and PCS and phenylacetylglutamine (constipation) were only associated with symptoms in men, who presented higher serum levels than women. Conclusion Only a limited number of toxins were associated with symptoms in persons with stage 4/5 CKD. Other uremic toxins, uremia-related factors or psychosocial factors not yet explored might contribute to symptom burden.

Published
2022
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6. Optimizing Distributed Tensor Contractions using Node-Aware Processor Grids

Author

Irmler, Andreas, Kanakagiri, Raghavendra, Ohlmann, Sebastian T., Solomonik, Edgar, and Grüneis, Andreas

Subjects
FOS: Computer and information sciences, Condensed Matter - Materials Science, Computer Science - Distributed, Parallel, and Cluster Computing, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, Distributed, Parallel, and Cluster Computing (cs.DC)
Abstract

We propose an algorithm that aims at minimizing the inter-node communication volume for distributed and memory-efficient tensor contraction schemes on modern multi-core compute nodes. The key idea is to define processor grids that optimize intra-/inter-node communication volume in the employed contraction algorithms. We present an implementation of the proposed node-aware communication algorithm into the Cyclops Tensor Framework (CTF). We demonstrate that this implementation achieves a significantly improved performance for matrix-matrix-multiplication and tensor-contractions on up to several hundreds modern compute nodes compared to conventional implementations without using node-aware processor grids. Our implementation shows good performance when compared with existing state-of-the-art parallel matrix multiplication libraries (COSMA and ScaLAPACK). In addition to the discussion of the performance for matrix-matrix-multiplication, we also investigate the performance of our node-aware communication algorithm for tensor contractions as they occur in quantum chemical coupled-cluster methods. To this end we employ a modified version of CTF in combination with a coupled-cluster code (Cc4s). Our findings show that the node-aware communication algorithm is also able to improve the performance of coupled-cluster theory calculations for real-world problems running on tens to hundreds of compute nodes., 15 pages, 4 figures

Published
2023

11. Predicting Kidney Failure, Cardiovascular Disease and Death in Advanced CKD Patients

Author

Chava L. Ramspek, Rosemarijn Boekee, Marie Evans, Olof Heimburger, Charlotte M. Snead, Fergus J. Caskey, Claudia Torino, Gaetana Porto, Maciej Szymczak, Magdalena Krajewska, Christiane Drechsler, Christoph Wanner, Nicholas C. Chesnaye, Kitty J. Jager, Friedo W. Dekker, Maarten G.J. Snoeijs, Joris I. Rotmans, Merel van Diepen, Adamasco Cupisti, Adelia Sagliocca, Alberto Ferraro, Aleksandra Musiała, Alessandra Mele, Alessandro Naticchia, Alex Còsaro, Alistair Woodman, Andrea Ranghino, Andrea Stucchi, Andreas Jonsson, Andreas Schneider, Angelo Pignataro, Anita Schrander, Anke Torp, Anna McKeever, Anna Szymczak, Anna-Lena Blom, Antonella De Blasio, Antonello Pani, Aris Tsalouichos, Asad Ullah, Barbara McLaren, Bastiaan van Dam, Beate Iwig, Bellasi Antonio, Biagio Raffaele Di Iorio, Björn Rogland, Boris Perras, Butti Alessandra, Camille Harron, Carin Wallquist, Carl Siegert, Carla Barrett, Carlo Gaillard, Carlo Garofalo, Cataldo Abaterusso, Charles Beerenhout, Charlotte O'Toole, Chiara Somma, Christian Marx, Christina Summersgill, Christof Blaser, Claudia D'alessandro, Claudia Emde, Claudia Zullo, Claudio Pozzi, Colin Geddes, Cornelis Verburgh, Daniela Bergamo, Daniele Ciurlino, Daria Motta, Deborah Glowski, Deborah McGlynn, Denes Vargas, Detlef Krieter, Domenico Russo, Dunja Fuchs, Dympna Sands, Ellen Hoogeveen, Ellen Irmler, Emöke Dimény, Enrico Favaro, Eva Platen, Ewelina Olczyk, Ewout Hoorn, Federica Vigotti, Ferruccio Ansali, Ferruccio Conte, Francesca Cianciotta, Francesca Giacchino, Francesco Cappellaio, Francesco Pizzarelli, Fredrik Sundelin, Fredrik Uhlin, Gaetano Greco, Geena Roy, Giada Bigatti, Giancarlo Marinangeli, Gianfranca Cabiddu, Gillian Hirst, Giordano Fumagalli, Giorgia Caloro, Giorgina Piccoli, Giovanbattista Capasso, Giovanni Gambaro, Giuliana Tognarelli, Giuseppe Bonforte, Giuseppe Conte, Giuseppe Toscano, Goffredo Del Rosso, Gunilla Welander, Hanna Augustyniak-Bartosik, Hans Boots, Hans Schmidt-Gürtler, Hayley King, Helen McNally, Hendrik Schlee, Henk Boom, Holger Naujoks, Houda Masri-Senghor, Hugh Murtagh, Hugh Rayner, Ilona Miśkowiec-Wiśniewska, Ines Schlee, Irene Capizzi, Isabel Bascaran Hernandez, Ivano Baragetti, Jacek Manitius, Jane Turner, Jan-Willem Eijgenraam, Jeroen Kooman, Joachim Beige, Joanna Pondel, Joanne Wilcox, Jocelyn Berdeprado, Jochen Röthele, Jonathan Wong, Joris Rotmans, Joyce Banda, Justyna Mazur, Kai Hahn, Kamila Jędrzejak, Katarzyna Nowańska, Katja Blouin, Katrin Neumeier, Kirsteen Jones, Kirsten Anding-Rost, Knut-Christian Gröntoft, Lamberto Oldrizzi, Lesley Haydock, Liffert Vogt, Lily Wilkinson, Loreto Gesualdo, Lothar Schramm, Luigi Biancone, Łukasz Nowak, Maarten Raasveld, Magdalena Durlik, Manuela Magnano, Marc Vervloet, Marco Ricardi, Margaret Carmody, Maria Di Bari, Maria Laudato, Maria Luisa Sirico, Maria Stendahl, Maria Svensson, Maria Weetman, Marjolijn van Buren, Martin Joinson, Martina Ferraresi, Mary Dutton, Michael Matthews, Michele Provenzano, Monika Hopf, Moreno Malaguti, Nadja Wuttke, Neal Morgan, Nicola Palmieri, Nikolaus Frischmuth, Nina Bleakley, Paola Murrone, Paul Cockwell, Paul Leurs, Paul Roderick, Pauline Voskamp, Pavlos Kashioulis, Pawlos Ichtiaris, Peter Blankestijn, Petra Kirste, Petra Schulz, Phil Mason, Philip Kalra, Pietro Cirillo, Pietro Dattolo, Pina Acampora, Rincy Sajith, Rita Nigro, Roberto Boero, Roberto Scarpioni, Rosa Sicoli, Rosella Malandra, Sabine Aign, Sabine Cäsar, Sadie van Esch, Sally Chapman, Sandra Biribauer, Santee Navjee, Sarah Crosbie, Sharon Brown, Sheila Tickle, Sherin Manan, Silke Röser, Silvana Savoldi, Silvio Bertoli, Silvio Borrelli, Siska Boorsma, Stefan Heidenreich, Stefan Melander, Stefania Maxia, Stefano Maffei, Stefano Mangano, Stephanie Palm, Stijn Konings, Suresh Mathavakkannan, Susanne Schwedler, Sylke Delrieux, Sylvia Renker, Sylvia Schättel, Szyszkowska Dorota, Teresa Cicchetti, Teresa Nieszporek, Theresa Stephan, Thomas Schmiedeke, Thomas Weinreich, Til Leimbach, Tiziana Rappa, Tora Almquist, Torsten Stövesand, Udo Bahner, Ulrika Jensen, Valentina Palazzo, Walter De Simone, Wolfgang Seeger, Ying Kuan, Zbigniew Heleniak, Zeynep Aydin, Vascular Surgery, MUMC+: MA Med Staf Spec Vaatchirurgie (9), RS: Carim - V03 Regenerative and reconstructive medicine vascular disease, Ramspek, C. L., Boekee, R., Evans, M., Heimburger, O., Snead, C. M., Caskey, F. J., Torino, C., Porto, G., Szymczak, M., Krajewska, M., Drechsler, C., Wanner, C., Chesnaye, N. C., Jager, K. J., Dekker, F. W., Snoeijs, M. G. J., Rotmans, J. I., van Diepen, M., Cupisti, A., Sagliocca, A., Ferraro, A., Musiala, A., Mele, A., Naticchia, A., Cosaro, A., Woodman, A., Ranghino, A., Stucchi, A., Jonsson, A., Schneider, A., Pignataro, A., Schrander, A., Torp, A., Mckeever, A., Szymczak, A., Blom, A. -L., De Blasio, A., Pani, A., Tsalouichos, A., Ullah, A., Mclaren, B., van Dam, B., Iwig, B., Antonio, B., Di Iorio, B. R., Rogland, B., Perras, B., Alessandra, B., Harron, C., Wallquist, C., Siegert, C., Barrett, C., Gaillard, C., Garofalo, C., Abaterusso, C., Beerenhout, C., O'Toole, C., Somma, C., Marx, C., Summersgill, C., Blaser, C., D'Alessandro, C., Emde, C., Zullo, C., Pozzi, C., Geddes, C., Verburgh, C., Bergamo, D., Ciurlino, D., Motta, D., Glowski, D., Mcglynn, D., Vargas, D., Krieter, D., Russo, D., Fuchs, D., Sands, D., Hoogeveen, E., Irmler, E., Dimeny, E., Favaro, E., Platen, E., Olczyk, E., Hoorn, E., Vigotti, F., Ansali, F., Conte, F., Cianciotta, F., Giacchino, F., Cappellaio, F., Pizzarelli, F., Sundelin, F., Uhlin, F., Greco, G., Roy, G., Bigatti, G., Marinangeli, G., Cabiddu, G., Hirst, G., Fumagalli, G., Caloro, G., Piccoli, G., Capasso, G., Gambaro, G., Tognarelli, G., Bonforte, G., Conte, G., Toscano, G., Del Rosso, G., Welander, G., Augustyniak-Bartosik, H., Boots, H., Schmidt-Gurtler, H., King, H., Mcnally, H., Schlee, H., Boom, H., Naujoks, H., Masri-Senghor, H., Murtagh, H., Rayner, H., Miskowiec-Wisniewska, I., Schlee, I., Capizzi, I., Hernandez, I. B., Baragetti, I., Manitius, J., Turner, J., Eijgenraam, J. -W., Kooman, J., Beige, J., Pondel, J., Wilcox, J., Berdeprado, J., Rothele, J., Wong, J., Rotmans, J., Banda, J., Mazur, J., Hahn, K., Jedrzejak, K., Nowanska, K., Blouin, K., Neumeier, K., Jones, K., Anding-Rost, K., Grontoft, K. -C., Oldrizzi, L., Haydock, L., Vogt, L., Wilkinson, L., Gesualdo, L., Schramm, L., Biancone, L., Nowak, L., Raasveld, M., Durlik, M., Magnano, M., Vervloet, M., Ricardi, M., Carmody, M., Di Bari, M., Laudato, M., Sirico, M. L., Stendahl, M., Svensson, M., Weetman, M., van Buren, M., Joinson, M., Ferraresi, M., Dutton, M., Matthews, M., Provenzano, M., Hopf, M., Malaguti, M., Wuttke, N., Morgan, N., Palmieri, N., Frischmuth, N., Bleakley, N., Murrone, P., Cockwell, P., Leurs, P., Roderick, P., Voskamp, P., Kashioulis, P., Ichtiaris, P., Blankestijn, P., Kirste, P., Schulz, P., Mason, P., Kalra, P., Cirillo, P., Dattolo, P., Acampora, P., Sajith, R., Nigro, R., Boero, R., Scarpioni, R., Sicoli, R., Malandra, R., Aign, S., Casar, S., van Esch, S., Chapman, S., Biribauer, S., Navjee, S., Crosbie, S., Brown, S., Tickle, S., Manan, S., Roser, S., Savoldi, S., Bertoli, S., Borrelli, S., Boorsma, S., Heidenreich, S., Melander, S., Maxia, S., Maffei, S., Mangano, S., Palm, S., Konings, S., Mathavakkannan, S., Schwedler, S., Delrieux, S., Renker, S., Schattel, S., Dorota, S., Cicchetti, T., Nieszporek, T., Stephan, T., Schmiedeke, T., Weinreich, T., Leimbach, T., Rappa, T., Almquist, T., Stovesand, T., Bahner, U., Jensen, U., Palazzo, V., De Simone, W., Seeger, W., Kuan, Y., Heleniak, Z., Aydin, Z., Medical Informatics, APH - Aging & Later Life, APH - Methodology, APH - Quality of Care, Nephrology, ACS - Microcirculation, APH - Health Behaviors & Chronic Diseases, APH - Global Health, ACS - Pulmonary hypertension & thrombosis, ACS - Diabetes & metabolism, and Internal Medicine

Subjects
SDG 3 - Good Health and Well-being, external validation, Nephrology, cardiovascular disease, death, CKD, kidney failure, prognostic model
Abstract

Introduction: Predicting the timing and occurrence of kidney replacement therapy (KRT), cardiovascular events, and death among patients with advanced chronic kidney disease (CKD) is clinically useful and relevant. We aimed to externally validate a recently developed CKD G4+ risk calculator for these outcomes and to assess its potential clinical impact in guiding vascular access placement. Methods: We included 1517 patients from the European Quality (EQUAL) study, a European multicentre prospective cohort study of nephrology-referred advanced CKD patients aged ≥65 years. Model performance was assessed based on discrimination and calibration. Potential clinical utility for timing of referral for vascular access placement was studied with diagnostic measures and decision curve analysis (DCA). Results: The model showed a good discrimination for KRT and “death after KRT,” with 2-year concordance (C) statistics of 0.74 and 0.76, respectively. Discrimination for cardiovascular events (2-year C-statistic: 0.70) and overall death (2-year C-statistic: 0.61) was poorer. Calibration was fairly accurate. Decision curves illustrated that using the model to guide vascular access referral would generally lead to less unused arteriovenous fistulas (AVFs) than following estimated glomerular filtration rate (eGFR) thresholds. Conclusion: This study shows moderate to good predictive performance of the model in an older cohort of nephrology-referred patients with advanced CKD. Using the model to guide referral for vascular access placement has potential in combating unnecessary vascular surgeries.

Published
2022
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13. An Eight-State Molecular Sequential Switch Featuring a Dual Single-Bond Rotation Photoreaction

Author

Marvin Irmler, Henry Dube, Aaron Gerwien, Benjamin Jehle, and Peter Mayer

Subjects
Molecular switch, Materials science, Photon, Photoswitch, General Chemistry, Rotation, Biochemistry, Molecular machine, Catalysis, Colloid and Surface Chemistry, Chemical physics, Covalent bond, Single bond, Isomerization, ddc:547
Abstract

Typical photowitches interconvert between two different states by simple isomerization reactions, which represents a fundamental limit for applications. To expand the switching capacity usually different photoswitches have to be linked together leading to strong increase in molecular weight, diminished switching function, and less precision and selectivity of switching events. Herein we present an approach for solving this essential problem with a different photoswitching concept. A basic molecular switch architecture provides precision photoswitching between eight different states via controlled rotations around three adjacent covalent bonds. All eight states can be populated one after another in an eight-step cycle by alternating between photochemical Hula-Twist isomerizations and thermal single bond rotations. By simply changing solvent and temperature the same switch can also undergo a different cycle instead interconverting just five isomers in a selective sequence. This behavior is enabled through the discovery of an unprecedented photoreaction, a one photon dual single bond rotation.

Published
2022
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14. Symptom Burden before and after Dialysis Initiation in Older Patients

Author

de Rooij, Esther N. M., Yvette, Meuleman, de Fijter, Johan W., Jager, Kitty J., Chesnaye, Nicholas C., Marie, Evans, Caskey, Fergus J., Claudia, Torino, Gaetana, Porto, Maciej, Szymczak, Christiane, Drechsler, Christoph, Wanner, Dekker, Friedo W., Hoogeveen, Ellen K., Andreas, Schneider, Anke, Torp, Beate, Iwig, Boris, Perras, Christian, Marx, Christof, Blaser, Claudia, Emde, Detlef, Krieter, Dunja, Fuchs, Ellen, Irmler, Eva, Platen, Hans, Schmidt-Gürtler, Hendrik, Schlee, Holger, Naujoks, Ines, Schlee, Sabine, Cäsar, Joachim, Beige, Jochen, Röthele, Justyna, Mazur, Kai, Hahn, Katja, Blouin, Katrin, Neumeier, Kirsten, Anding-Rost, Lothar, Schramm, Monika, Hopf, Nadja, Wuttke, Nikolaus, Frischmuth, Pawlos, Ichtiaris, Petra, Kirste, Petra, Schulz, Sabine, Aign, Sandra, Biribauer, Sherin, Manan, Silke, Röser, Stefan, Heidenreich, Stephanie, Palm, Susanne, Schwedler, Sylke, Delrieux, Sylvia, Renker, Sylvia, Schättel, Theresa, Stephan, Thomas, Schmiedeke, Thomas, Weinreich, Til, Leimbach, Torsten, Stövesand, Udo, Bahner, Wolfgang, Seeger, Cupisti, Adamasco, Adelia, Sagliocca, Alberto, Ferraro, Alessandra, Mele, Alessandro, Naticchia, Alex, Còsaro, Andrea, Ranghino, Andrea, Stucchi, Angelo, Pignataro, Antonella De Blasio, Antonello, Pani, Aris, Tsalouichos, Bellasi, Antonio, Biagio Raffaele Di Iorio, Butti, Alessandra, Cataldo, Abaterusso, Chiara, Somma, Claudia, D’Alessandro, Claudia, Zullo, Claudio, Pozzi, Daniela, Bergamo, Daniele, Ciurlino, Daria, Motta, Domenico, Russo, Enrico, Favaro, Federica, Vigotti, Ferruccio, Ansali, Ferruccio, Conte, Francesca, Cianciotta, Francesca, Giacchino, Francesco, Cappellaio, Francesco, Pizzarelli, Gaetano, Greco, Giada, Bigatti, Giancarlo, Marinangeli, Gianfranca, Cabiddu, Giordano, Fumagalli, Giorgia, Caloro, Giorgina, Piccoli, Giovanbattista, Capasso, Giovanni, Gambaro, Giuliana, Tognarelli, Giuseppe, Bonforte, Giuseppe, Conte, Giuseppe, Toscano, Goffredo Del Rosso, Irene, Capizzi, Ivano, Baragetti, Lamberto, Oldrizzi, Loreto, Gesualdo, Luigi, Biancone, Manuela, Magnano, Marco, Ricardi, Maria Di Bari, Maria, Laudato, Maria Luisa Sirico, Martina, Ferraresi, Michele, Provenzano, Moreno, Malaguti, Nicola, Palmieri, Paola, Murrone, Pietro, Cirillo, Pietro, Dattolo, Pina, Acampora, Rita, Nigro, Roberto, Boero, Roberto, Scarpioni, Rosa, Sicoli, Rosella, Malandra, Silvana, Savoldi, Silvio, Bertoli, Silvio, Borrelli, Stefania, Maxia, Stefano, Maffei, Stefano, Mangano, Teresa, Cicchetti, Tiziana, Rappa, Valentina, Palazzo, Walter De Simone, Anita, Schrander, Bastiaan van Dam, Carl, Siegert, Carlo, Gaillard, Charles, Beerenhout, Cornelis, Verburgh, Cynthia, Janmaat, Ellen, Hoogeveen, Ewout, Hoorn, Friedo, Dekker, Johannes, Boots, Henk, Boom, Jan-Willem, Eijgenraam, Jeroen, Kooman, Joris, Rotmans, Kitty, Jager, Liffert, Vogt, Maarten, Raasveld, Marc, Vervloet, Marjolijn van Buren, Merel van Diepen, Nicholas, Chesnaye, Paul, Leurs, Pauline, Voskamp, Peter, Blankestijn, Sadie van Esch, Siska, Boorsma, Stefan, Berger, Constantijn, Konings, Zeynep, Aydin, Aleksandra, Musiała, Anna, Szymczak, Ewelina, Olczyk, Hanna, Augustyniak-Bartosik, Ilona, Miśkowiec-Wiśniewska, Jacek, Manitius, Joanna, Pondel, Kamila, Jędrzejak, Katarzyna, Nowańska, Łukasz, Nowak, Magdalena, Durlik, Szyszkowska, Dorota, Teresa, Nieszporek, Zbigniew, Heleniak, Andreas, Jonsson, Anna-Lena, Blom, Björn, Rogland, Carin, Wallquist, Denes, Vargas, Emöke, Dimény, Fredrik, Sundelin, Fredrik, Uhlin, Gunilla, Welander, Isabel Bascaran Hernandez, Knut-Christian, Gröntoft, Maria, Stendahl, Maria, Svensson, Olof, Heimburger, Pavlos, Kashioulis, Stefan, Melander, Tora, Almquist, Ulrika, Jensen, Alistair, Woodman, Anna, Mckeever, Asad, Ullah, Barbara, Mclaren, Camille, Harron, Carla, Barrett, Charlotte, O'Toole, Christina, Summersgill, Colin, Geddes, Deborah, Glowski, Deborah, Mcglynn, Dympna, Sands, Fergus, Caskey, Geena, Roy, Gillian, Hirst, Hayley, King, Helen, Mcnally, Houda, Masri-Senghor, Hugh, Murtagh, Hugh, Rayner, Jane, Turner, Joanne, Wilcox, Jocelyn, Berdeprado, Jonathan, Wong, Joyce, Banda, Kirsteen, Jones, Lesley, Haydock, Lily, Wilkinson, Margaret, Carmody, Maria, Weetman, Martin, Joinson, Mary, Dutton, Michael, Matthews, Neal, Morgan, Nina, Bleakley, Paul, Cockwell, Paul, Roderick, Phil, Mason, Philip, Kalra, Rincy, Sajith, Sally, Chapman, Santee, Navjee, Sarah, Crosbie, Sharon, Brown, Sheila, Tickle, Suresh, Mathavakkannan, Ying, Kuan., Medical Informatics, APH - Aging & Later Life, APH - Quality of Care, APH - Methodology, APH - Global Health, APH - Health Behaviors & Chronic Diseases, and ACS - Pulmonary hypertension & thrombosis

Subjects
Transplantation, chronic kidney disease, dialysis, elderly, end stage kidney disease, epidemiology and outcomes, Nephrology, Epidemiology, Critical Care and Intensive Care Medicine
Abstract

Background and objectives For older patients with kidney failure, lowering symptom burden may be more important than prolonging life. Dialysis initiation may affect individual kidney failure-related symptoms differently, but the change in symptoms before and after start of dialysis has not been studied. Therefore, we investigated the course of total and individual symptom number and burden before and after starting dialysis in older patients.Design, setting, participants, & measurements The European Quality (EQUAL) study is an ongoing, prospective, multicenter study in patients >= 65 years with an incident eGFR

Published
2022
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15. Averting the infrared catastrophe in the gold standard of quantum chemistry

Author

Masios, Nikolaos, Irmler, Andreas, Schäfer, Tobias, and Grüneis, Andreas

Subjects
Condensed Matter - Materials Science, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences
Abstract

Coupled-cluster theories can be used to compute ab initio electronic correlation energies of real materials with systematically improvable accuracy. However, the widely-used coupled cluster singles and doubles plus perturbative triples (CCSD(T)) method is only applicable to insulating materials. For zero-gap materials the truncation of the underlying many-body perturbation expansion leads to an infrared catastrophe. Here, we present a novel perturbative triples formalism that yields convergent correlation energies in metallic systems. Furthermore, the computed correlation energies for the three dimensional uniform electron gas at metallic densities are in good agreement with quantum Monte Carlo results. At the same time the newly proposed method retains all desirable properties of CCSD(T) such as its accuracy for insulating systems as well as its low computational cost compared to a full inclusion of the triples. This paves the way for ab initio calculations of real metals with chemical accuracy., 6 pages, 1 figure, 1 table plus a supplemental material of 14 pages, 4 figures and 1 table

Published
2023

17. Novel ion imaging concept based on time-of-flight measurements with low gain avalanche detectors

Author

Ulrich-Pur, Felix, Bergauer, Thomas, Hirtl, Albert, Irmler, Christian, Kaser, Stefanie, Pitters, Florian, Rit, Simon, HEP, INSPIRE, GSI Helmholtzzentrum für Schwerionenforschung (GSI), Austrian Academy of Sciences (OeAW), Vienna University of Technology (TU Wien), Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-MED-PH] Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph], Physics - Instrumentation and Detectors, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, FOS: Physical sciences, Instrumentation and Detectors (physics.ins-det), Image reconstruction in medical imaging, Physics - Medical Physics, [PHYS] Physics [physics], [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, Instrumentation for hadron therapy, [PHYS.PHYS.PHYS-INS-DET] Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Accelerator applications, [PHYS.PHYS.PHYS-MED-PH]Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph], Medical Physics (physics.med-ph), [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], ddc:610, Instrumentation, Mathematical Physics
Abstract

Journal of Instrumentation 18(02), C02062 (2023). doi:10.1088/1748-0221/18/02/C02062, Published by Inst. of Physics, London

Published
2023
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19. The aminotransferase Aat initiates 3-phenyllactic acid biosynthesis in Pediococcus acidilactici

Author

Alexander Wenger, Cornelia Bär, Reto Portmann, Remo S. Schmidt, Elisabeth Eugster, Laure Weisskopf, and Stefan Irmler

Subjects
Microbiology (medical), Microbiology
Abstract

The function of the aminotransferase Aat (GenBank Protein WP_159211138) from Pediococcus acidilactici FAM 18098 was studied in vivo. For this purpose, the gene was replaced with an erythromycin resistance gene using the temperature-sensitive Escherichia coli-Pediococcus shuttle plasmid pSET4T_Δaat. The knockout was verified by PCR and genome sequencing. Subsequently, the differences between the metabolism of the knockout and of the wild-type strain were investigated by determining the free amino acids and organic acids in culture supernatants. It was found that the knockout mutant no longer synthesized 3-phenyllactic acid (PLA) and 4-hydroxyphenyllactic acid (HPLA). Additionally, the mutant strain no longer catabolized phenylalanine. Metabolic pathway analysis using the KEGG database indicate that P. acidilactici cannot synthesize α-ketoglutarate that is a predominant amino-group acceptor in many transamination reactions. To study the transfer of the amino group of phenylalanine, the wild-type strain was incubated with [15N] phenylalanine. Mass spectrometry showed that during fermentation, [15N] alanine was formed, indicating that pyruvic acid is an amino group acceptor in P. acidilactici. The present study shows that Aat plays a crucial role in PLA/HPLA biosynthesis and pyruvic acid is an amino acceptor in transamination reactions in P. acidilactici.

Published
2023
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24. Kidney failure prediction models

Author

Ramspek, Chava L, Evans, Marie, Wanner, Christoph, Drechsler, Christiane, Chesnaye, Nicholas C, Szymczak, Maciej, Krajewska, Magdalena, Torino, Claudia, Porto, Gaetana, Hayward, Samantha, Caskey, Fergus, Dekker, Friedo W, Jager, Kitty J, van Diepen, Merel, EQUAL Study Investigators: Adamasco Cupisti, Adelia Sagliocca, Alberto Ferraro, Aleksandra Musiała, Alessandra Mele, Alessandro Naticchia, Alex Còsaro, Alistair Woodman, Andrea Ranghino, Andrea Stucchi, Andreas Jonsson, Andreas Schneider, Angelo Pignataro, Anita Schrander, Anke Torp, Anna McKeever, Anna Szymczak, Anna-Lena Blom, Antonella De Blasio, Antonello Pani, Aris Tsalouichos, Asad Ullah, Barbara McLaren, Bastiaan van Dam, Beate Iwig, Bellasi Antonio, Biagio Raffaele Di Iorio, Björn Rogland, Boris Perras, Butti Alessandra, Camille Harron, Carin Wallquist, Carl Siegert, Carla Barrett, Carlo Gaillard, Carlo Garofalo, Cataldo Abaterusso, Charles Beerenhout, Charlotte O'Toole, Chiara Somma, Christian Marx, Christina Summersgill, Christof Blaser, Claudia D'alessandro, Claudia Emde, Claudia Zullo, Claudio Pozzi, Colin Geddes, Cornelis Verburgh, Daniela Bergamo, Daniele Ciurlino, Daria Motta, Deborah Glowski, Deborah McGlynn, Denes Vargas, Detlef Krieter, Domenico Russo, Dunja Fuchs, Dympna Sands, Ellen Hoogeveen, Ellen Irmler, Emöke Dimény, Enrico Favaro, Eva Platen, Ewelina Olczyk, Ewout Hoorn, Federica Vigotti, Ferruccio Ansali, Ferruccio Conte, Francesca Cianciotta, Francesca Giacchino, Francesco Cappellaio, Francesco Pizzarelli, Fredrik Sundelin, Fredrik Uhlin, Gaetano Greco, Geena Roy, Gaetana Porto, Giada Bigatti, Giancarlo Marinangeli, Gianfranca Cabiddu, Gillian Hirst, Giordano Fumagalli, Giorgia Caloro, Giorgina Piccoli, Giovanbattista Capasso, Giovanni Gambaro, Giuliana Tognarelli, Giuseppe Bonforte, Giuseppe Conte, Giuseppe Toscano, Goffredo Del Rosso, Gunilla Welander, Hanna Augustyniak-Bartosik, Hans Boots, Hans Schmidt-Gürtler, Hayley King, Helen McNally, Hendrik Schlee, Henk Boom, Holger Naujoks, Houda Masri-Senghor, Hugh Murtagh, Hugh Rayner, Ilona Miśkowiec-Wiśniewska, Ines Schlee, Irene Capizzi, Isabel Bascaran Hernandez, Ivano Baragetti, Jacek Manitius, Jane Turner, Jan-Willem Eijgenraam, Jeroen Kooman, Joachim Beige, Joanna Pondel, Joanne Wilcox, Jocelyn Berdeprado, Jochen Röthele, Jonathan Wong, Joris Rotmans, Joyce Banda, Justyna Mazur, Kai Hahn, Kamila Jędrzejak, Katarzyna Nowańska, Katja Blouin, Katrin Neumeier, Kirsteen Jones, Kirsten Anding-Rost, Knut-Christian Gröntoft, Lamberto Oldrizzi, Lesley Haydock, Liffert Vogt, Lily Wilkinson, Loreto Gesualdo, Lothar Schramm, Luigi Biancone, Łukasz Nowak, Maarten Raasveld, Magdalena Durlik, Manuela Magnano, Marc Vervloet, Marco Ricardi, Margaret Carmody, Maria Di Bari, Maria Laudato, Maria Luisa Sirico, Maria Stendahl, Maria Svensson, Maria Weetman, Marjolijn van Buren, Martin Joinson, Martina Ferraresi, Mary Dutton, Merel van Diepen, Michael Matthews, Michele Provenzano, Monika Hopf, Moreno Malaguti, Nadja Wuttke, Neal Morgan, Nicola Palmieri, Nikolaus Frischmuth, Nina Bleakley, Paola Murrone, Paul Cockwell, Paul Leurs, Paul Roderick, Pauline Voskamp, Pavlos Kashioulis, Pawlos Ichtiaris, Peter Blankestijn, Petra Kirste, Petra Schulz, Phil Mason, Philip Kalra, Pietro Cirillo, Pietro Dattolo, Pina Acampora, Rincy Sajith, Rita Nigro, Roberto Boero, Roberto Scarpioni, Rosa Sicoli, Rosella Malandra, Sabine Aign, Sabine Cäsar, Sadie van Esch, Sally Chapman, Sandra Biribauer, Santee Navjee, Sarah Crosbie, Sharon Brown, Sheila Tickle, Sherin Manan, Silke Röser, Silvana Savoldi, Silvio Bertoli, Silvio Borrelli, Siska Boorsma, Stefan Heidenreich, Stefan Melander, Stefania Maxia, Stefano Maffei, Stefano Mangano, Stephanie Palm, Stijn Konings, Suresh Mathavakkannan, Susanne Schwedler, Sylke Delrieux, Sylvia Renker, Sylvia Schättel, Szyszkowska Dorota, Teresa Cicchetti, Teresa Nieszporek, Theresa Stephan, Thomas Schmiedeke, Thomas Weinreich, Til Leimbach, Tiziana Rappa, Tora Almquist, Torsten Stövesand, Udo Bahner, Ulrika Jensen, Valentina Palazzo, Walter De Simone, Wolfgang Seeger, Ying Kuan, Zbigniew Heleniak, Zeynep Aydin, Internal Medicine, Chava L, Ramspek, Marie, Evan, Christoph, Wanner, Christiane, Drechsler, Nicholas C, Chesnaye, Maciej, Szymczak, Magdalena, Krajewska, Claudia, Torino, Gaetana, Porto, Samantha, Hayward, Fergus, Caskey, Friedo W, Dekker, Kitty J, Jager, Merel, van Diepen, Study Investigators: Adamasco Cupisti, Equal, Sagliocca, Adelia, Ferraro, Alberto, Musiała, Aleksandra, Mele, Alessandra, Naticchia, Alessandro, Còsaro, Alex, Woodman, Alistair, Ranghino, Andrea, Stucchi, Andrea, Jonsson, Andrea, Schneider, Andrea, Pignataro, Angelo, Schrander, Anita, Torp, Anke, Mckeever, Anna, Szymczak, Anna, Blom, Anna-Lena, De Blasio, Antonella, Pani, Antonello, Tsalouichos, Ari, Ullah, Asad, Mclaren, Barbara, van Dam, Bastiaan, Iwig, Beate, Antonio, Bellasi, Raffaele Di Iorio, Biagio, Rogland, Björn, Perras, Bori, Alessandra, Butti, Harron, Camille, Wallquist, Carin, Siegert, Carl, Barrett, Carla, Gaillard, Carlo, Garofalo, Carlo, Abaterusso, Cataldo, Beerenhout, Charle, O'Toole, Charlotte, Somma, Chiara, Marx, Christian, Summersgill, Christina, Blaser, Christof, D'Alessandro, Claudia, Emde, Claudia, Zullo, Claudia, Pozzi, Claudio, Geddes, Colin, Verburgh, Corneli, Bergamo, Daniela, Ciurlino, Daniele, Motta, Daria, Glowski, Deborah, Mcglynn, Deborah, Vargas, Dene, Krieter, Detlef, Russo, Domenico, Fuchs, Dunja, Sands, Dympna, Hoogeveen, Ellen, Irmler, Ellen, Dimény, Emöke, Favaro, Enrico, Platen, Eva, Olczyk, Ewelina, Hoorn, Ewout, Vigotti, Federica, Ansali, Ferruccio, Conte, Ferruccio, Cianciotta, Francesca, Giacchino, Francesca, Cappellaio, Francesco, Pizzarelli, Francesco, Sundelin, Fredrik, Uhlin, Fredrik, Greco, Gaetano, Roy, Geena, Porto, Gaetana, Bigatti, Giada, Marinangeli, Giancarlo, Cabiddu, Gianfranca, Hirst, Gillian, Fumagalli, Giordano, Caloro, Giorgia, Piccoli, Giorgina, Capasso, Giovanbattista, Gambaro, Giovanni, Tognarelli, Giuliana, Bonforte, Giuseppe, Conte, Giuseppe, Toscano, Giuseppe, Del Rosso, Goffredo, Welander, Gunilla, Augustyniak-Bartosik, Hanna, Boots, Han, Schmidt-Gürtler, Han, King, Hayley, Mcnally, Helen, Schlee, Hendrik, Boom, Henk, Naujoks, Holger, Masri-Senghor, Houda, Murtagh, Hugh, Rayner, Hugh, Miśkowiec-Wiśniewska, Ilona, Schlee, Ine, Capizzi, Irene, Bascaran Hernandez, Isabel, Baragetti, Ivano, Manitius, Jacek, Turner, Jane, Eijgenraam, Jan-Willem, Kooman, Jeroen, Beige, Joachim, Pondel, Joanna, Wilcox, Joanne, Berdeprado, Jocelyn, Röthele, Jochen, Wong, Jonathan, Rotmans, Jori, Banda, Joyce, Mazur, Justyna, Hahn, Kai, Jędrzejak, Kamila, Nowańska, Katarzyna, Blouin, Katja, Neumeier, Katrin, Jones, Kirsteen, Anding-Rost, Kirsten, Gröntoft, Knut-Christian, Oldrizzi, Lamberto, Haydock, Lesley, Vogt, Liffert, Wilkinson, Lily, Gesualdo, Loreto, Schramm, Lothar, Biancone, Luigi, Nowak, Łukasz, Raasveld, Maarten, Durlik, Magdalena, Magnano, Manuela, Vervloet, Marc, Ricardi, Marco, Carmody, Margaret, Di Bari, Maria, Laudato, Maria, Luisa Sirico, Maria, Stendahl, Maria, Svensson, Maria, Weetman, Maria, van Buren, Marjolijn, Joinson, Martin, Ferraresi, Martina, Dutton, Mary, van Diepen, Merel, Matthews, Michael, Provenzano, Michele, Hopf, Monika, Malaguti, Moreno, Wuttke, Nadja, Morgan, Neal, Palmieri, Nicola, Frischmuth, Nikolau, Bleakley, Nina, Murrone, Paola, Cockwell, Paul, Leurs, Paul, Roderick, Paul, Voskamp, Pauline, Kashioulis, Pavlo, Ichtiaris, Pawlo, Blankestijn, Peter, Kirste, Petra, Schulz, Petra, Mason, Phil, Kalra, Philip, Cirillo, Pietro, Dattolo, Pietro, Acampora, Pina, Sajith, Rincy, Nigro, Rita, Boero, Roberto, Scarpioni, Roberto, Sicoli, Rosa, Malandra, Rosella, Aign, Sabine, Cäsar, Sabine, van Esch, Sadie, Chapman, Sally, Biribauer, Sandra, Navjee, Santee, Crosbie, Sarah, Brown, Sharon, Tickle, Sheila, Manan, Sherin, Röser, Silke, Savoldi, Silvana, Bertoli, Silvio, Borrelli, Silvio, Boorsma, Siska, Heidenreich, Stefan, Melander, Stefan, Maxia, Stefania, Maffei, Stefano, Mangano, Stefano, Palm, Stephanie, Konings, Stijn, Mathavakkannan, Suresh, Schwedler, Susanne, Delrieux, Sylke, Renker, Sylvia, Schättel, Sylvia, Dorota, Szyszkowska, Cicchetti, Teresa, Nieszporek, Teresa, Stephan, Theresa, Schmiedeke, Thoma, Weinreich, Thoma, Leimbach, Til, Rappa, Tiziana, Almquist, Tora, Stövesand, Torsten, Bahner, Udo, Jensen, Ulrika, Palazzo, Valentina, De Simone, Walter, Seeger, Wolfgang, Kuan, Ying, Heleniak, Zbigniew, Aydin, Zeynep, Medical Informatics, ACS - Pulmonary hypertension & thrombosis, APH - Aging & Later Life, APH - Health Behaviors & Chronic Diseases, APH - Methodology, APH - Quality of Care, and APH - Global Health

Subjects
Male, progression of chronic renal failure, medicine.medical_specialty, Time Factors, epidemiology and outcome, 030232 urology & nephrology, Risk Assessment, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Older patients, external validation, Predictive Value of Tests, medicine, Humans, Failure risk, Clinical Epidemiology, In patient, comprehensive external validation, 030212 general & internal medicine, Statistic, Aged, Aged, 80 and over, Kidney, Models, Statistical, business.industry, External validation, General Medicine, prediction, kidney failure, Europe, prediction model, medicine.anatomical_structure, chronic kidney disease, epidemiology and outcomes, prognosis, Nephrology, Emergency medicine, Disease Progression, Kidney Failure, Chronic, Female, business, prognostic, Predictive modelling, prognosi, Cohort study
Abstract

Background Various prediction models have been developed to predict the risk of kidney failure in patients with CKD. However, guideline-recommended models have yet to be compared head to head, their validation in patients with advanced CKD is lacking, and most do not account for competing risks. Methods To externally validate 11 existing models of kidney failure, taking the competing risk of death into account, we included patients with advanced CKD from two large cohorts: the European Quality Study (EQUAL), an ongoing European prospective, multicenter cohort study of older patients with advanced CKD, and the Swedish Renal Registry (SRR), an ongoing registry of nephrology-referred patients with CKD in Sweden. The outcome of the models was kidney failure (defined as RRT-treated ESKD). We assessed model performance with discrimination and calibration. Results The study included 1580 patients from EQUAL and 13,489 patients from SRR. The average c statistic over the 11 validated models was 0.74 in EQUAL and 0.80 in SRR, compared with 0.89 in previous validations. Most models with longer prediction horizons overestimated the risk of kidney failure considerably. The 5-year Kidney Failure Risk Equation (KFRE) overpredicted risk by 10%-\18%. The four- and eight-variable 2-year KFRE and the 4-year Grams model showed excellent calibration and good discrimination in both cohorts. Conclusions Some existing models can accurately predict kidney failure in patients with advanced CKD. KFRE performed well for a shorter time frame (2 years), despite not accounting for competing events. Models predicting over a longer time frame (5 years) overestimated risk because of the competing risk of death. The Grams model, which accounts for the latter, is suitable for longer-term predictions (4 years).

Published
2021
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28. Associations between depressive symptoms and disease progression in older patients with chronic kidney disease

Author

Eveleens Maarse, Boukje C., Chesnaye, Nicholas C., Robbert, Schouten, Michels, Wieneke M., Bos, Willem Jan W., Maciej, Szymczak, Magdalena, Krajewska, Marie Evans, Olof Heimburger, Caskey, Fergus J., Christoph, Wanner, Jager, Kitty J., Dekker, Friedo W., Yvette, Meuleman, Andreas, Schneider, Anke, Torp, Beate, Iwig, Boris, Perras, Christian, Marx, Christiane, Drechsler, Christof, Blaser, Claudia, Emde, Detlef, Krieter, Dunja, Fuchs, Ellen, Irmler, Eva, Platen, Hans, Schmidt-Gürtler, Hendrik, Schlee, Holger, Naujoks, Ines, Schlee, Sabine, Cäsar, Joachim, Beige, Jochen, Röthele, Justyna, Mazur, Kai, Hahn, Katja, Blouin, Katrin, Neumeier, Kirsten, Anding-Rost, Lothar, Schramm, Monika, Hopf, Nadja, Wuttke, Nikolaus, Frischmuth, Pawlos, Ichtiaris, Petra, Kirste, Petra, Schulz, Sabine, Aign, Sandra, Biribauer, Sherin, Manan, Silke, Röser, Stefan, Heidenreich, Stephanie, Palm, Susanne, Schwedler, Sylke, Delrieux, Sylvia, Renker, Sylvia, Schättel, Theresa, Stephan, Thomas, Schmiedeke, Thomas, Weinreich, Til, Leimbach, Torsten, Stövesand, Udo, Bahner, Wolfgang, Seeger, Cupisti, Adamasco, Adelia, Sagliocca, Alberto, Ferraro, Alessandra, Mele, Alessandro, Naticchia, Alex, Còsaro, Andrea, Ranghino, Andrea, Stucchi, Angelo, Pignataro, Antonella De Blasio, Antonello, Pani, Aris, Tsalouichos, Bellasi, Antonio, Biagio Raffaele Di Iorio, Butti, Alessandra, Cataldo, Abaterusso, Chiara, Somma, Claudia, D'Alessandro, Claudia, Torino, Claudia, Zullo, Claudio, Pozzi, Daniela, Bergamo, Daniele, Ciurlino, Daria, Motta, Domenico, Russo, Enrico, Favaro, Federica, Vigotti, Ferruccio, Ansali, Ferruccio, Conte, Francesca, Cianciotta, Francesca, Giacchino, Francesco, Cappellaio, Francesco, Pizzarelli, Gaetano, Greco, Gaetana, Porto, Giada, Bigatti, Giancarlo, Marinangeli, Gianfranca, Cabiddu, Giordano, Fumagalli, Giorgia, Caloro, Giorgina, Piccoli, Giovanbattista, Capasso, Giovanni, Gambaro, Giuliana, Tognarelli, Giuseppe, Bonforte, Giuseppe, Conte, Giuseppe, Toscano, Goffredo Del Rosso, Irene, Capizzi, Ivano, Baragetti, Lamberto, Oldrizzi, Loreto, Gesualdo, Luigi, Biancone, Manuela, Magnano, Marco, Ricardi, Maria Di Bari, Maria, Laudato, Maria Luisa Sirico, Martina, Ferraresi, Maurizio, Postorino, Michele, Provenzano, Moreno, Malaguti, Nicola, Palmieri, Paola, Murrone, Pietro, Cirillo, Pietro, Dattolo, Pina, Acampora, Rita, Nigro, Roberto, Boero, Roberto, Scarpioni, Rosa, Sicoli, Rosella, Malandra, Silvana, Savoldi, Silvio, Bertoli, Silvio, Borrelli, Stefania, Maxia, Stefano, Maffei, Stefano, Mangano, Teresa, Cicchetti, Tiziana, Rappa, Valentina, Palazzo, Walter De Simone, Anita, Schrander, Bastiaan van Dam, Carl, Siegert, Carlo, Gaillard, Charles, Beerenhout, Cornelis, Verburgh, Cynthia, Janmaat, Ellen, Hoogeveen, Ewout, Hoorn, Friedo, Dekker, Johannes, Boots, Henk, Boom, Jan-Willem, Eijgenraam, Jeroen, Kooman, Joris, Rotmans, Kitty, Jager, Liffert, Vogt, Maarten, Raasveld, Marc, Vervloet, Marjolijn van Buren, Merel van Diepen, Nicholas, Chesnaye, Paul, Leurs, Pauline, Voskamp, Peter, Blankestijn, Sadie van Esch, Siska, Boorsma, Stefan, Berger, Constantijn, Konings, Zeynep, Aydin, Aleksandra, Musiała, Anna, Szymczak, Ewelina, Olczyk, Hanna, Augustyniak-Bartosik, Ilona, Miśkowiec-Wiśniewska, Jacek, Manitius, Joanna, Pondel, Kamila, Jędrzejak, Katarzyna, Nowańska, Łukasz, Nowak, Magdalena, Durlik, Szyszkowska, Dorota, Teresa, Nieszporek, Zbigniew, Heleniak, Andreas, Jonsson, Anna-Lena, Blom, Björn, Rogland, Carin, Wallquist, Denes, Vargas, Emöke, Dimény, Fredrik, Sundelin, Fredrik, Uhlin, Gunilla, Welander, Isabel Bascaran Hernandez, Knut-Christian, Gröntoft, Maria, Stendahl, Maria, Svensson, Marie, Evans, Olof, Heimburger, Pavlos, Kashioulis, Stefan, Melander, Tora, Almquist, Ulrika, Jensen, Alistair, Woodman, Anna, Mckeever, Asad, Ullah, Barbara, Mclaren, Camille, Harron, Carla, Barrett, Charlotte, O'Toole, Christina, Summersgill, Colin, Geddes, Deborah, Glowski, Deborah, Mcglynn, Dympna, Sands, Fergus, Caskey, Geena, Roy, Gillian, Hirst, Hayley, King, Helen, Mcnally, Houda, Masri-Senghor, Hugh, Murtagh, Hugh, Rayner, Jane, Turner, Joanne, Wilcox, Jocelyn, Berdeprado, Jonathan, Wong, Joyce, Banda, Kirsteen, Jones, Lesley, Haydock, Lily, Wilkinson, Margaret, Carmody, Maria, Weetman, Martin, Joinson, Mary, Dutton, Michael, Matthews, Neal, Morgan, Nina, Bleakley, Paul, Cockwell, Paul, Roderick, Phil, Mason, Philip, Kalra, Rincy, Sajith, Sally, Chapman, Santee, Navjee, Sarah, Crosbie, Sharon, Brown, Sheila, Tickle, Suresh, Mathavakkannan, Ying, Kuan, Internal medicine, Nephrology, ACS - Diabetes & metabolism, Medical Informatics, APH - Methodology, APH - Aging & Later Life, Graduate School, APH - Quality of Care, ACS - Microcirculation, APH - Health Behaviors & Chronic Diseases, APH - Global Health, ACS - Pulmonary hypertension & thrombosis, Eveleens Maarse, B. C., Chesnaye, N. C., Schouten, R., Michels, W. M., Bos, W. J. W., Szymczak, M., Krajewska, M., Evans, M., Heimburger, O., Caskey, F. J., Wanner, C., Jager, K. J., Dekker, F. W., Meuleman, Y., Schneider, A., Torp, A., Iwig, B., Perras, B., Marx, C., Drechsler, C., Blaser, C., Emde, C., Krieter, D., Fuchs, D., Irmler, E., Platen, E., Schmidt-Gurtler, H., Schlee, H., Naujoks, H., Schlee, I., Casar, S., Beige, J., Rothele, J., Mazur, J., Hahn, K., Blouin, K., Neumeier, K., Anding-Rost, K., Schramm, L., Hopf, M., Wuttke, N., Frischmuth, N., Ichtiaris, P., Kirste, P., Schulz, P., Aign, S., Biribauer, S., Manan, S., Roser, S., Heidenreich, S., Palm, S., Schwedler, S., Delrieux, S., Renker, S., Schattel, S., Stephan, T., Schmiedeke, T., Weinreich, T., Leimbach, T., Stovesand, T., Bahner, U., Seeger, W., Cupisti, A., Sagliocca, A., Ferraro, A., Mele, A., Naticchia, A., Cosaro, A., Ranghino, A., Stucchi, A., Pignataro, A., De Blasio, A., Pani, A., Tsalouichos, A., Antonio, B., Raffaele Di Iorio, B., Alessandra, B., Abaterusso, C., Somma, C., D'Alessandro, C., Torino, C., Zullo, C., Pozzi, C., Bergamo, D., Ciurlino, D., Motta, D., Russo, D., Favaro, E., Vigotti, F., Ansali, F., Conte, F., Cianciotta, F., Giacchino, F., Cappellaio, F., Pizzarelli, F., Greco, G., Porto, G., Bigatti, G., Marinangeli, G., Cabiddu, G., Fumagalli, G., Caloro, G., Piccoli, G., Capasso, G., Gambaro, G., Tognarelli, G., Bonforte, G., Conte, G., Toscano, G., Del Rosso, G., Capizzi, I., Baragetti, I., Oldrizzi, L., Gesualdo, L., Biancone, L., Magnano, M., Ricardi, M., Di Bari, M., Laudato, M., Luisa Sirico, M., Ferraresi, M., Postorino, M., Provenzano, M., Malaguti, M., Palmieri, N., Murrone, P., Cirillo, P., Dattolo, P., Acampora, P., Nigro, R., Boero, R., Scarpioni, R., Sicoli, R., Malandra, R., Savoldi, S., Bertoli, S., Borrelli, S., Maxia, S., Maffei, S., Mangano, S., Cicchetti, T., Rappa, T., Palazzo, V., De Simone, W., Schrander, A., Van Dam, B., Siegert, C., Gaillard, C., Beerenhout, C., Verburgh, C., Janmaat, C., Hoogeveen, E., Hoorn, E., Boots, J., Boom, H., Eijgenraam, J. -W., Kooman, J., Rotmans, J., Vogt, L., Raasveld, M., Vervloet, M., Van Buren, M., Van Diepen, M., Leurs, P., Voskamp, P., Blankestijn, P., Van Esch, S., Boorsma, S., Berger, S., Konings, C., Aydin, Z., Musiala, A., Szymczak, A., Olczyk, E., Augustyniak-Bartosik, H., Miskowiec-Wisniewska, I., Manitius, J., Pondel, J., Jedrzejak, K., Nowanska, K., Nowak, L., Durlik, M., Dorota, S., Nieszporek, T., Heleniak, Z., Jonsson, A., Blom, A. -L., Rogland, B., Wallquist, C., Vargas, D., Dimeny, E., Sundelin, F., Uhlin, F., Welander, G., Bascaran Hernandez, I., Grontoft, K. -C., Stendahl, M., Svensson, M., Kashioulis, P., Melander, S., Almquist, T., Jensen, U., Woodman, A., Mckeever, A., Ullah, A., Mclaren, B., Harron, C., Barrett, C., O'Toole, C., Summersgill, C., Geddes, C., Glowski, D., Mcglynn, D., Sands, D., Roy, G., Hirst, G., King, H., Mcnally, H., Masri-Senghor, H., Murtagh, H., Rayner, H., Turner, J., Wilcox, J., Berdeprado, J., Wong, J., Banda, J., Jones, K., Haydock, L., Wilkinson, L., Carmody, M., Weetman, M., Joinson, M., Dutton, M., Matthews, M., Morgan, N., Bleakley, N., Cockwell, P., Roderick, P., Mason, P., Kalra, P., Sajith, R., Chapman, S., Navjee, S., Crosbie, S., Brown, S., Tickle, S., Mathavakkannan, S., and Kuan, Y.

Subjects
Transplantation, prospective cohort study, depressive symptoms, nephrology care, Nephrology, clinical outcome, chronic kidney disease, clinical trial, epidemiology, joint model, survival analysis, depressive symptom
Abstract

Background Depressive symptoms are associated with adverse clinical outcomes in patients with end-stage kidney disease; however, few small studies have examined this association in patients with earlier phases of chronic kidney disease (CKD). We studied associations between baseline depressive symptoms and clinical outcomes in older patients with advanced CKD and examined whether these associations differed depending on sex. Methods CKD patients (≥65 years; estimated glomerular filtration rate ≤20 mL/min/1.73 m2) were included from a European multicentre prospective cohort between 2012 and 2019. Depressive symptoms were measured by the five-item Mental Health Inventory (cut-off ≤70; 0–100 scale). Cox proportional hazard analysis was used to study associations between depressive symptoms and time to dialysis initiation, all-cause mortality and these outcomes combined. A joint model was used to study the association between depressive symptoms and kidney function over time. Analyses were adjusted for potential baseline confounders. Results Overall kidney function decline in 1326 patients was –0.12 mL/min/1.73 m2/month. A total of 515 patients showed depressive symptoms. No significant association was found between depressive symptoms and kidney function over time (P = 0.08). Unlike women, men with depressive symptoms had an increased mortality rate compared with those without symptoms [adjusted hazard ratio 1.41 (95% confidence interval 1.03–1.93)]. Depressive symptoms were not significantly associated with a higher hazard of dialysis initiation, or with the combined outcome (i.e. dialysis initiation and all-cause mortality). Conclusions There was no significant association between depressive symptoms at baseline and decline in kidney function over time in older patients with advanced CKD. Depressive symptoms at baseline were associated with a higher mortality rate in men.

Published
2022
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29. The Design, Construction, Operation and Performance of the Belle II Silicon Vertex Detector

Author

Adamczyk, K., Aggarwal, L., Aihara, H., Aziz, T., Babu, V., Bacher, S., Bahinipati, S., Bari, M., Baroncelli, Ti., Baroncelli, To., Bassi, G., Batignani, G., Baudot, J., Bauer, A., Behera, P.K., Bergauer, T., Bertacchi, V., Bettarini, S., Bilka, T., Bosi, F., Bosisio, L., Bozek, A., Buchsteiner, F., Bulla, L., Casarosa, G., Cautero, G., Ceccanti, M., Chen, Y.Q., Chendvankar, S.R., Corona, L., Cristaudo, P., Czank, T., Das, S.B., Dash, N., de Marino, G., de Nuccio, M., de Pietro, G., Divekar, S.T., Dolejschi, P., Doležal, Z., Dujany, G., Dutta, D., Finck, C., Fischer, K., Forti, F., Friedl, M., Frühwirth, R., Gabrielli, A., Ganiev, E., Gfall, I., Giuressi, D., Gobbo, B., Halder, S., Hara, K., Hazra, S., Higuchi, T., Himori, S., Horiguchi, T., Irmler, C., Ishikawa, A., Jeon, H.B., Jin, Y., Joo, C., Kaleta, M., Kaliyar, A.B., Kandra, J., Kang, K.H., Kapusta, P., Kodyš, P., Kohriki, T., Kolwalkar, M.M., Komarov, I., Kumar, M., Kumar, R., Kvasnička, P., La Licata, C., Lalwani, K., Lanceri, L., Lautenbach, K., Leboucher, R., Lee, S.C., Lee, J.Y., Lettenbichler, J., Li, Y.B., Libby, J., Lueck, T., Maity, S., Mammini, P., Manfredi, R., Martel, L., Martini, A., Massaccesi, L., Mayekar, S.N., Mohanty, G.B., Mohanty, S., Grimaldo, J.A. Mora, Morii, T., Nakamura, K.R., Natkaniec, Z., Negishi, K., Nisar, N.K., Sato, N., Oberegger, M., Onuki, Y., Ostrowicz, W., Otani, F., Paladino, A., Palka, H., Paoloni, E., Park, H., Pernicka, M., Pilo, F., Pirker, J., Polat, L., Profeti, A., Rao, K.K., Rashevskaya, I., Resmi, P.K., Ripp-Baudot, I., Rizzo, G., Rout, N., Rozanska, M., Sahoo, D., Saito, T., Sandilya, S., Sasaki, J., Sato, Y., Schultschik, S., Schwanda, C., Seino, Y., Serrano, J., Koike, S., Shimasaki, T., Shimizu, N., Steininger, H., Stypula, J., Suzuki, J., Tanaka, S., Tanigawa, H., Taylor, G.N., Tenchini, F., Thalmeier, R., Thomas, R., Tiwary, R., Tsuboyama, T., Uematsu, Y., Valentan, M., Vitale, L., Volpi, M., Wan, K., Wang, Z., Watanabe, M., Watanuki, S., Watson, I.J., Webb, J., Werbycka, O., Wiechczynski, J., Williams, S., Würkner, B., Yin, H., Zanetti, A., Zani, L., Zhang, T., Adamczyk, K., Aggarwal, L., Aihara, H., Aziz, T., Babu, V., Bacher, S., Bahinipati, S., Bari, M., Baroncelli, Ti., Baroncelli, To., Bassi, G., Batignani, G., Baudot, J., Bauer, A., Behera, P. K., Bergauer, T., Bertacchi, V., Bettarini, S., Bilka, T., Bosi, F., Bosisio, L., Bozek, A., Buchsteiner, F., Bulla, L., Casarosa, G., Cautero, G., Ceccanti, M., Chen, Y. Q., Chendvankar, S. R., Corona, L., Cristaudo, P., Czank, T., Das, S. B., Dash, N., de Marino, G., De Nuccio, M., De Pietro, G., Divekar, S. T., Dolejschi, P., Dole??al, Z., Dujany, G., Dutta, D., Finck, C., Fischer, K. D., Forti, F., Friedl, M., Fr??hwirth, R., Gabrielli, A., Ganiev, E., Gfall, I., Giuressi, D., Gobbo, B., Halder, S., Hara, K., Hazra, S., Higuchi, T., Himori, S., Horiguchi, T., Irmler, C., Ishikawa, A., Jeon, H. B., Jin, Y., Joo, C., Kaleta, M., Kaliyar, A. B., Kandra, J., Kang, K. H., Kapusta, P., Kody??, P., Kohriki, T., Koike, S., Kolwalkar, M. M., Komarov, I., Kumar, M., Kumar, R., Kvasni??ka, P., La Licata, C., Lalwani, K., Lanceri, L., Lautenbach, K., Leboucher, R., Lee, S. C., Lee, J. Y., Lettenbichler, J., Li, Y. B., Libby, J., Lueck, T., Maity, S., Mammini, P., Manfredi, R., Martel, L., Martini, A., Massaccesi, L., Mayekar, S. N., Mohanty, G. B., Mohanty, S., Mora Grimaldo, J. A., Morii, T., Nakamura, K. R., Natkaniec, Z., Negishi, K., Nisar, N. K., Oberegger, M., Onuki, Y., Ostrowicz, W., Otani, F., Paladino, A., Palka, H., Paoloni, E., Park, H., Pernicka, M., Pilo, F., Pirker, J., Polat, L., Profeti, A., Rao, K. K., Rashevskaya, I., Resmi, P. K., Ripp-Baudot, I., Rizzo, G., Rout, N., Rozanska, M., Sahoo, D., Saito, T., Sandilya, S., Sasaki, J., Sato, N., Sato, Y., Schultschik, S., Schwanda, C., Seino, Y., Serrano, J., Shimasaki, T., Shimizu, N., Steininger, H., Stypula, J., Suzuki, J., Tanaka, S., Tanigawa, H., Taylor, G. N., Tenchini, F., Thalmeier, R., Thomas, R., Tiwary, R., Tsuboyama, T., Uematsu, Y., Valentan, M., Vitale, L., Volpi, M., Wan, K., Wang, Z., Watanabe, M., Watanuki, S., Watson, I. J., Webb, J., Werbycka, O., Wiechczynski, J., Williams, S., W??rkner, B., Yin, H., Zanetti, A., Zani, L., Zhang, T., Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre de Physique des Particules de Marseille (CPPM), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and Belle-II SVD

Subjects
Physics - Instrumentation and Detectors, vertex detector, FOS: Physical sciences, BELLE, fabrication, Instrumentation for particle accelerators and storage rings - high energy (linear accelerators, High Energy Physics - Experiment, High Energy Physics - Experiment (hep-ex), Detector cooling and thermo-stabilization, Detector grounding, Front-end electronics for detector readout, Particle tracking detectors, Front-end electronics for detector-readout, [PHYS.HEXP]Physics [physics]/High Energy Physics - Experiment [hep-ex], [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Solid state detectors, Detector alignment and calibration methods, Instrumentation, Instrumentation for particle accelerators and storage rings - high energy (linear accelerators, synchrotrons), activity report, detector: design, Mathematical Physics, Radiation damage to detector materials (solid state), synchrotrons), alignment, Instrumentation and Detectors (physics.ins-det), Si microstrip and pad detectors, Voltage distributions, vibration analysis etc), Particle tracking detector, Overall mechanics design (support structures and materials, quality, efficiency, Instrumentation for particle accelerators and storage rings - high energy, semiconductor detector: microstrip, Detector design and construction technologies and materials, performance
Abstract

The Silicon Vertex Detector of Belle II is a state-of-the-art tracking and vertexing system based on double-sided silicon strip sensors, designed and fabricated by a large international collaboration in the period 2012--2018. Since 2019 it has been in operation providing high quality data with a small number of defective channels (99%), a good signal-to-noise ratio (well in excess of 10 for all sensor configurations and tracks). Together with the good control over the alignment, these are all essential factors to achieve good tracking reconstruction and physics performance. In this extended paper we try to document all the aspects of the SVD challenges and achievements, in the spirit of providing information to the broader community and help the development of high quality detector systems, which are fundamental tools to carry out physics research., 199 pages, 152 figures

Published
2022
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30. Calculating 1/β2p2 for most likely path estimates for protons and helium ions using an analytical model

Author

Stefanie Kaser, Felix Ulrich-Pur, Florian Pitters, Albert Hirtl, Christian Irmler, and Thomas Bergauer

Subjects
Polynomial regression, Physics, Scattering, Gaussian, Monte Carlo method, Biophysics, General Physics and Astronomy, General Medicine, Computational physics, Ion, Momentum, Matrix (mathematics), symbols.namesake, symbols, Radiology, Nuclear Medicine and imaging, Image resolution
Abstract

In ion computed tomography, limited spatial resolution can be related to the non-straight path of ions resulting from multiple Coulomb scattering in the object to be imaged. By including sophisticated path estimates such as most likely path (MLP) or optimized cubic spline into the image reconstruction algorithm, the achieved spatial resolution can be substantially improved compared to assuming a simple straight line path only. The typically used implementation of the MLP is a matrix-based approach employing Bayesian statistics and modelling multiple Coulomb scattering as Gaussian distribution. For the elements of the scattering matrices, the term 1 / β ( w ) 2 p ( w ) 2 , depending on the momentum and velocity of an ion within a phantom depth w , has to be known and integrated along the depth w . Usually, this term is extracted from a Monte Carlo simulation and approximated by a polynomial fit to solve the integral. In the present study, an existing analytical model for ion ranges and stopping powers was used to calculate 1 / β ( w ) 2 p ( w ) 2 and the scattering matrices for the MLP and was tested for protons and helium ions. The model was investigated for 10 cm to 40 cm water targets and initial energies ranging from 150 MeV to 300 MeV for protons and 150 MeV/u to 300 MeV/u for helium ions. In all cases, the calculated value obtained for 1 / β ( w ) 2 p ( w ) 2 was compared to a GATE simulation. The difference between root-mean-square errors of MLP estimates using calculated and simulated 1 / β ( w ) 2 p ( w ) 2 values were found to be smaller than 3 μm for all investigated water targets and energies.

Published
2021
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32. Dendritic Cells or Macrophages? The Microenvironment of Human Clear Cell Renal Cell Carcinoma Imprints a Mosaic Myeloid Subtype Associated with Patient Survival

Author

Dorothee Brech, Anna S. Herbstritt, Sarah Diederich, Tobias Straub, Evangelos Kokolakis, Martin Irmler, Johannes Beckers, Florian A. Büttner, Elke Schaeffeler, Stefan Winter, Matthias Schwab, Peter J. Nelson, and Elfriede Noessner

Subjects
Biological Products, Membrane Glycoproteins, Article, mononuclear phagocyte system, macrophage plasticity, tissue macrophage, tumor microenvironment, gene expression, VSIG4, NRP1, GPNMB, Macrophages, General Medicine, Dendritic Cells, Kidney Neoplasms, ddc, Tumor Microenvironment, Humans, Carcinoma, Renal Cell, Plastics, Gene Expression, Gpnmb, Macrophage Plasticity, Mononuclear Phagocyte System, Nrp1, Tissue Macrophage, Vsig4
Abstract

Since their initial description by Elie Metchnikoff, phagocytes have sparked interest in a variety of biologic disciplines. These important cells perform central functions in tissue repair and immune activation as well as tolerance. Myeloid cells can be immunoinhibitory, particularly in the tumor microenvironment, where their presence is generally associated with poor patient prognosis. These cells are highly adaptable and plastic, and can be modulated to perform desired functions such as antitumor activity, if key programming molecules can be identified. Human clear cell renal cell carcinoma (ccRCC) is considered immunogenic; yet checkpoint blockades that target T cell dysfunction have shown limited clinical efficacy, suggesting additional layers of immunoinhibition. We previously described “enriched-in-renal cell carcinoma” (erc) DCs that were often found in tight contact with dysfunctional T cells. Using transcriptional profiling and flow cytometry, we describe here that ercDCs represent a mosaic cell type within the macrophage continuum co-expressing M1 and M2 markers. The polarization state reflects tissue-specific signals that are characteristic of RCC and renal tissue homeostasis. ErcDCs are tissue-resident with increasing prevalence related to tumor grade. Accordingly, a high ercDC score predicted poor patient survival. Within the profile, therapeutic targets (VSIG4, NRP1, GPNMB) were identified with promise to improve immunotherapy.

Published
2022

34. The Neotropical species of the genus Somoleptus Sharp, 1885 (Coleoptera: Staphylinidae: Staphylininae: Xantholinini)

Author

Irmler, Ulrich

Subjects
Pulmonary and Respiratory Medicine, new species, Neotropics, Xantholinini, Pediatrics, Perinatology and Child Health, new combinations, zoogeography
Abstract

At present, 45 Somoleptus species are known from the Neotropical region. Among these, 28 species are newly described here, whereas 18 were described in the past. The new species are: S. admirabilis spec. nov., S. andersoni spec. nov., S. ashei spec. nov., S. beniensis spec. nov., S. brevipennis spec. nov., S. breviusculus spec. nov., S. brooksi spec. nov., S. brunneus spec. nov., S. curtipennis spec. nov., S. curtulus spec. nov., S. elongatulus spec. nov., S. gigas spec. nov., S. grandiconus spec. nov., S. humicola spec. nov., S. longiceps spec. nov., S. loretensis spec. nov., S. maximus spec. nov., S. melanarius spec. nov., S. mexicanus spec. nov., S. montanus spec. nov., S. oculatus spec. nov., S. ovatus spec. nov., S. pecki spec. nov., S. peruanus spec. nov., S. recurvatus spec. nov., S. struyvei spec. nov., S. triangulus spec. nov., S. tschirnhausi spec. nov. Four species are transferred from the genus Lithocharodes. These are S. cavicola (Blackwelder, 1943) comb. nov., S. strigulata (Blackwelder 1943) comb. nov., S. longicollis (LeConte, 1863) comb. nov., and S. subtilis (Erichson, 1839) comb. nov. Somoleptus dichiformis Bernhauer, 1910 could not be assigned to either Lithocharodes or Somoleptus. Thus, this species must be treated as species incertae sedis. Two species groups could be differentiated due to the structure of the parameres and the aedeagal cones; one mainly occurs in South America, the second in Central America.

Published
2022

35. Autocrine Sfrp1 inhibits lung fibroblast invasion during transition to injury induced myofibroblasts

Author

Christoph H. Mayr, Arunima Sengupta, Meshal Ansari, Jeanine C. Pestoni, Paulina Ogar, Ilias Angelidis, Andreas Liontos, Alberto Rodriguez-Castillo, Niklas J. Lang, Maximilian Strunz, Sara Asgharpour, Diana Porras-Gonzalez, Michael Gerckens, Bettina Oehrle, Valeria Viteri-Alvarez, Isis E. Fernandez, Michelle Tallquist, Martin Irmler, Johannes Beckers, Oliver Eickelberg, Gabriel Mircea Stoleriu, Jürgen Behr, Nikolaus Kneidinger, Ali Önder Yildirim, Katrin Ahlbrecht, Rory E. Morty, Christos Samakovlis, Fabian J. Theis, Gerald Burgstaller, and Herbert B. Schiller

Abstract

Fibroblast to myofibroblast conversion is a major driver of tissue remodeling in organ fibrosis. Several distinct lineages of fibroblasts support homeostatic tissue niche functions, yet, specific activation states and phenotypic trajectories of fibroblasts during injury and repair have remained unclear. Here, we combined spatial transcriptomics, longitudinal single-cell RNA-seq and genetic lineage tracing to study fibroblast fates during mouse lung regeneration. We discovered a transitional fibroblast state characterized by high Sfrp1 expression, derived from both Tcf21-Cre lineage positive and negative cells. Sfrp1+ cells appeared early after injury in peribronchiolar, adventitial and alveolar locations and preceded the emergence of myofibroblasts. We identified lineage specific paracrine signals and inferred converging transcriptional trajectories towards Sfrp1+ transitional fibroblasts and Cthrc1+ myofibroblasts. Tgfβ1 downregulated Sfrp1 in non-invasive transitional cells and induced their switch to an invasive Cthrc1+ myofibroblast identity. Finally, using loss of function studies we showed that autocrine Sfrp1 directly inhibits fibroblast invasion by regulating the RhoA pathway. In summary, our study reveals the convergence of spatially and transcriptionally distinct fibroblast lineages into transcriptionally uniform myofibroblasts and identifies Sfrp1 as an autocrine inhibitor of fibroblast invasion during early stages of fibrogenesis.

Published
2022
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36. First application of the GPU-based software framework TIGRE for proton CT image reconstruction

Author

Thomas Bergauer, Sepideh Hatamikia, Wolfgang Birkfellner, Dietmar Georg, Florian Pitters, Alexander Burker, Christian Irmler, Stefanie Kaser, Felix Ulrich-Pur, and Albert Hirtl

Subjects
Computer science, Monte Carlo method, Biophysics, Measure (physics), General Physics and Astronomy, Iterative reconstruction, computer.software_genre, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Software, Image Processing, Computer-Assisted, Humans, Radiology, Nuclear Medicine and imaging, Projection (set theory), Proton therapy, Phantoms, Imaging, business.industry, General Medicine, Software framework, Simultaneous Algebraic Reconstruction Technique, 030220 oncology & carcinogenesis, Protons, Tomography, X-Ray Computed, business, Monte Carlo Method, computer, Algorithm, Algorithms
Abstract

In proton therapy, the knowledge of the proton stopping power, i.e. the energy deposition per unit length within human tissue, is essential for accurate treatment planning. One suitable method to directly measure the stopping power is proton computed tomography (pCT). Due to the proton interaction mechanisms in matter, pCT image reconstruction faces some challenges: the unique path of each proton has to be considered separately in the reconstruction process adding complexity to the reconstruction problem. This study shows that the GPU-based open-source software toolkit TIGRE, which was initially intended for X-ray CT reconstruction, can be applied to the pCT image reconstruction problem using a straight line approach for the proton path. This simplified approach allows for reconstructions within seconds. To validate the applicability of TIGRE to pCT, several Monte Carlo simulations modeling a pCT setup with two Catphan® modules as phantoms were performed. Ordered-Subset Simultaneous Algebraic Reconstruction Technique (OS-SART) and Adaptive-Steepest-Descent Projection Onto Convex Sets (ASD-POCS) were used for image reconstruction. Since the accuracy of the approach is limited by the straight line approximation of the proton path, requirements for further improvement of TIGRE for pCT are addressed.

Published
2021
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37. GPR101 loss promotes insulin resistance and diet-induced obesity risk

Author

Lillian Garrett, Martin Irmler, Angela Baljuls, Birgit Rathkolb, Nathalia Dragano, Raffaele Gerlini, Adrián Sanz-Moreno, Antonio Aguilar-Pimentel, Lore Becker, Markus Kraiger, Rosa Reithmeir, Johannes Beckers, Julia Calzada-Wack, Wolfgang Wurst, Helmut Fuchs, Valerie Gailus-Durner, Tina Zimmermann, Sabine M. Hölter, and Martin Hrabě de Angelis

Published
2023
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38. Inceptor counteracts insulin signalling in β-cells to control glycaemia

Author

Michal Grzybek, Matthias H. Tschöp, Oliver Plettenburg, Sara Bilekova, Lena Oppenländer, Johanna Siehler, Michael Sterr, Amir Morshedi, Sarah Homberg, Timo D. Müller, Aurelia Raducanu, Katharina Wißmiller, Felizitas Gräfin von Hahn, Ansarullah, Chirag Jain, Julius Wiener, Ünal Coskun, Johannes Beckers, Heiko Lickert, Gustav Collden, Fataneh Fathi Far, Silvia Schirge, Aimée Bastidas-Ponce, Christin Ahlbrecht, Annette Feuchtinger, Matthias Meier, Martin Irmler, and Regina Feederle

Subjects
Blood Glucose, Male, 0301 basic medicine, medicine.medical_treatment, Golgi Apparatus, Endoplasmic Reticulum, Insulin Antagonists, Mice, 0302 clinical medicine, Insulin-Secreting Cells, Insulin, Insulin-Like Growth Factor I, Receptor, Glucose tolerance test, Multidisciplinary, medicine.diagnostic_test, biology, Chemistry, Endocytosis, Neoplasm Proteins, Knockout mouse, hormones, hormone substitutes, and hormone antagonists, Signal Transduction, endocrine system, medicine.medical_specialty, 030209 endocrinology & metabolism, Cell Line, 03 medical and health sciences, Commentaries, Internal medicine, medicine, Animals, Humans, Cell Proliferation, Cell Size, Insulin-like growth factor 1 receptor, Growth factor, Insulin-like growth factor 2 receptor, Membrane Proteins, nutritional and metabolic diseases, Glucose Tolerance Test, Clathrin, Receptor, Insulin, Tamoxifen, Insulin receptor, 030104 developmental biology, Endocrinology, Commentary, biology.protein, Endocrine Cells, Lysosomes
Abstract

Resistance to insulin and insulin-like growth factor 1 (IGF1) in pancreatic β-cells causes overt diabetes in mice; thus, therapies that sensitize β-cells to insulin may protect patients with diabetes against β-cell failure1–3. Here we identify an inhibitor of insulin receptor (INSR) and IGF1 receptor (IGF1R) signalling in mouse β-cells, which we name the insulin inhibitory receptor (inceptor; encoded by the gene Iir). Inceptor contains an extracellular cysteine-rich domain with similarities to INSR and IGF1R4, and a mannose 6-phosphate receptor domain that is also found in the IGF2 receptor (IGF2R)5. Knockout mice that lack inceptor (Iir−/−) exhibit signs of hyperinsulinaemia and hypoglycaemia, and die within a few hours of birth. Molecular and cellular analyses of embryonic and postnatal pancreases from Iir−/− mice showed an increase in the activation of INSR–IGF1R in Iir−/− pancreatic tissue, resulting in an increase in the proliferation and mass of β-cells. Similarly, inducible β-cell-specific Iir−/− knockout in adult mice and in ex vivo islets led to an increase in the activation of INSR–IGF1R and increased proliferation of β-cells, resulting in improved glucose tolerance in vivo. Mechanistically, inceptor interacts with INSR–IGF1R to facilitate clathrin-mediated endocytosis for receptor desensitization. Blocking this physical interaction using monoclonal antibodies against the extracellular domain of inceptor resulted in the retention of inceptor and INSR at the plasma membrane to sustain the activation of INSR–IGF1R in β-cells. Together, our findings show that inceptor shields insulin-producing β-cells from constitutive pathway activation, and identify inceptor as a potential molecular target for INSR–IGF1R sensitization and diabetes therapy. The insulin inhibitory receptor (inceptor) is identified as a negative regulator of insulin and IGF1 signalling that could be targeted for β-cell regeneration in treatments for diabetes.

Published
2021
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39. Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates

Author

Johannes Beckers, Fabian J. Theis, Wolfgang Enard, Maren Büttner, Christoph Ziegenhain, Heiko Lickert, Fien M. Verhamme, Lena Oppenländer, Anika Böttcher, Sophie Tritschler, Oliver Eickelberg, Michael Sterr, Andrea C. Schamberger, Alexandra Aliluev, Martin Irmler, Steffen Sass, and Ingo Burtscher

Subjects
inorganic chemicals, Male, Paneth Cells, Lineage (genetic), Enteroendocrine Cells, Enteroendocrine cell, Biology, digestive system, Receptors, G-Protein-Coupled, Mice, 03 medical and health sciences, 0302 clinical medicine, Single-cell analysis, Cell polarity, medicine, Animals, Cell Lineage, Cell Self Renewal, Intestinal Mucosa, beta Catenin, 030304 developmental biology, Mice, Knockout, 0303 health sciences, Gene Expression Profiling, Stem Cells, Wnt signaling pathway, LGR5, Cell Polarity, Cell Biology, Cell biology, Mice, Inbred C57BL, Wnt Proteins, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Paneth cell, Female, Single-Cell Analysis, Stem cell
Abstract

A detailed understanding of intestinal stem cell (ISC) self-renewal and differentiation is required to treat chronic intestinal diseases. However, the different models of ISC lineage hierarchy1–6 and segregation7–12 are subject to debate. Here, we have discovered non-canonical Wnt/planar cell polarity (PCP)-activated ISCs that are primed towards the enteroendocrine or Paneth cell lineage. Strikingly, integration of time-resolved lineage labelling with single-cell gene expression analysis revealed that both lineages are directly recruited from ISCs via unipotent transition states, challenging the existence of formerly predicted bi- or multipotent secretory progenitors7–12. Transitory cells that mature into Paneth cells are quiescent and express both stem cell and secretory lineage genes, indicating that these cells are the previously described Lgr5+ label-retaining cells7. Finally, Wnt/PCP-activated Lgr5+ ISCs are molecularly indistinguishable from Wnt/β-catenin-activated Lgr5+ ISCs, suggesting that lineage priming and cell-cycle exit is triggered at the post-transcriptional level by polarity cues and a switch from canonical to non-canonical Wnt/PCP signalling. Taken together, we redefine the mechanisms underlying ISC lineage hierarchy and identify the Wnt/PCP pathway as a new niche signal preceding lateral inhibition in ISC lineage priming and segregation. Polarity cues regulate intestinal stem cell fate. Bottcher et al. demonstrate that mouse intestinal stem cells, which express the Wnt/planar cell polarity reporter Flattop, are primed either towards the enteroendocrine or Paneth cell lineage.

Published
2021
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41. Design and characterization of depleted monolithic active pixel sensors within the RD50 collaboration

Author

Patrick Sieberer, Christian Irmler, Helmut Steininger, and Thomas Bergauer

Subjects
Nuclear and High Energy Physics, WP5, Instrumentation
Abstract

The CERN RD50 CMOS working group is designing and characterizing depleted monolithic active pixel sensors (DMAPS) for use in high radiation environments fabricated in the LFoundry 150nm HV-CMOS process. The first iteration of this chip, RD50-MPW1, suffered from high leakage current, low breakdown voltage and crosstalk. In order to mitigate these shortcomings, an improved version with improved pixel geometry was designed. The RD50-MPW2 integrates a matrix of 8×8 pixels with analog front-end, but no digital readout. It was delivered in early 2020 and characterized within lab-measurements, an irradiation campaign and test beams. To read out the chips the Caribou DAQ system is used with a custom chipboard as well as specific firmware and software modules. A third iteration of the chip, the RD50-MPW3, has been submitted to LFoundry in December 2021 and is expected to be delivered in May 2022. It will keep the well working analog part of its predecessor, completed by an in-pixel digital logic and an optimized peripheral readout for effective pixel configuration and fast serial data transmission. The chip will comprise a matrix of 64×64 pixels arranged in 32 double-columns. We will present an overview of the RD50 HV-CMOS activities focusing on the measurement results of RD50-MPW2 chip, as well as the design and readout of the RD50-MPW3.

Published
2022

42. Cadaverine, putrescine, and histamine formation of Morganella morganii in raclette-type cheese

Author

Lorenz Timo Ryser, Emmanuelle Arias-Roth, Hélène Berthoud, Céline Delbès-Paus, Christophe Chassard, Rémy Bruggmann, Stefan Irmler, Agroscope, Universität Bern [Bern] (UNIBE), Unité Mixte de Recherche sur le Fromage (UMRF), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA)

Subjects
570 Life sciences, biology, Applied Microbiology and Biotechnology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract

International audience; The influence of Morganella morganii isolated from cheese on the formation of biogenic amines was studied in raclette-type cheeses. Three variants were produced. One variant containing a cadaverine-and histamine-forming strain, one variant with a putrescine-and histamine-forming strain, and a variant without M. morganii. After 130 d of ripening, live M. morganii was found in the outer layers but no longer inside the cheese. The cheeses with the cadaverine-forming strain exhibited a decreasing cadaverine gradient from the outside (on average 310 mg kg(-1)) to the inside (160 mg kg(-1)). Putrescine was present in the cheeses with the putrescine-forming strain. Its concentration averaged 59 mg kg(-1) in all layers. All cheeses with M. morganii contained also histamine with concentration less than 50 mg kg(-1). The results reveal new information on the survival of M. morganii as well as its ability to form biogenic amines in cheese.

Published
2022
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43. CMOS MAPS upgrade for the Belle II Vertex Detector

Author

M. Babeluk, M. Barbero, J. Baudot, T. Bergauer, F. Bernlochner, S. Bettarini, F. Bosi, Y. Buch, G. Casarosa, J. Dingfelder, T. Fillinger, C. Finck, A. Frey, C. Hu, C. Irmler, C. Marinas, M. Massa, L. Massaccesi, M. Minuti, H. Pham, G. Rizzo, C. Schwanda, B. Schwenker, M. Schwickardi, C. Wessel, Austrian Academy of Sciences (OeAW), Centre de Physique des Particules de Marseille (CPPM), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Universität Bonn = University of Bonn, University of Pisa - Università di Pisa, University of Goettingen, Universitat de València (UV), Belle II VTX, and European Project: 101004761,AIDAinnova

Subjects
safety, Nuclear and High Energy Physics, geometry, vertex detector, BELLE, length, Upgrade, KEK-B, pixel, VTX, structure, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Instrumentation, DMAPS, detector, background, carbon, Belle II, CMOS, tracks, matter, radiation, fibre, technology, PXD, semiconductor detector, SVD, VXD, performance
Abstract

International audience; The success of the Belle II experiment in Japan relies on the very high instantaneous luminosity, close to 6 × 1035cm−2s−1, expectedfrom the SuperKEKB collider. The corresponding beam conditions at such luminosity levels generate large rates of backgroundparticles and creates stringent constraints on the vertex detector, adding to the physics requirements. Current prospects for theoccupancy rates in the present vertex detector (VXD) at full luminosity fall close to the acceptable limits and bear large uncertainties.In this context, the Belle II collaboration is considering the possibility to install an upgraded VXD system around 2027 to providea sufficient safety margin with respect to the expected background rate and possibly enhance tracking and vertexing performance.The VTX collaboration has started the design of a fully pixelated VXD, called VTX, based on fast and highly granular DepletedMonolithic Active Pixel Sensors (DMAPS) integrated on light support structures.The two main technical features of the VTX proposal are the usage of a single sensor type over all the layers of the system and theoverall material budget below 2 % of radiation length, compared to the current VXD which has two different sensor technologiesand about 3 % of radiation length. A dedicated sensor (OBELIX), taylored to the specific needs of Belle II, is under development,evolving from the existing TJ-Monopix2 sensor. The time-stamping precision below 100 ns will allow all VTX layers to take part inthe track finding strategy contrary to the current situation. The first two detection layers are designed according to a self-supportedall-silicon ladder concept, where 4 contiguous sensors are diced out of a wafer, thinned and interconnected with post-processedredistribution layers. The outermost detection layers follow a more conventional approach with a cold plate and carbon fibresupport structure, and light flex cables interconnecting the sensors.This document will review the context, technical details and development status of the proposed Belle II VTX.

Published
2022
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44. The Use of Escape Rooms in Society and Business Environments

Author

Tanja Kranawetleitner, Heike Krebs, Diana Pistoll, and Julia Thurner-Irmler

Abstract

In recent years, the concept of gamification, and escape rooms (ER) as one of its methods, has become very popular. ER has been shown to be widely applicable for numerous target groups and contexts. This chapter presents explorative testing of two different ER contexts that have rarely been reported in the literature so far: one for needs analysis in a business setting (n = 21) and one as a tool for science communication in society (n = 63). Participants evaluated the ER with a 5-point Likert rating scale questionnaire (containing 12 respectively 11 items). The results confirm the entertaining nature of the method and show that the ER succeeded in raising awareness of the respective topics. Comparing the rooms provided valuable findings regarding different fields of application. It offers insights into developing this innovative method and conceptualizing future ER. Further implications and limitations are discussed.

Published
2022
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47. Extension of the open-source TIGRE toolbox for proton imaging

Author

Stefanie Kaser, Thomas Bergauer, Ander Biguri, Wolfgang Birkfellner, Sepideh Hatamikia, Albert Hirtl, Christian Irmler, Benjamin Kirchmayer, and Felix Ulrich-Pur

Subjects
Radiological and Ultrasound Technology, Biophysics, Radiology, Nuclear Medicine and imaging
Abstract

Proton irradiation is a well-established method to treat deep-seated tumors in radio oncology. Usually, an X-ray computed tomography (CT) scan is used for treatment planning. Since proton therapy is based on the precise knowledge of the stopping power describing the energy loss of protons in the patient tissues, the Hounsfield units of the planning CT have to be converted. This conversion introduces range errors in the treatment plan, which could be reduced, if the stopping power values were extracted directly from an image obtained using protons instead of X-rays. Since protons are affected by multiple Coulomb scattering, reconstruction of the 3D stopping power map results in limited image quality if the curved proton path is not considered. This work presents a substantial code extension of the open-source toolbox TIGRE for proton CT (pCT) image reconstruction based on proton radiographs including a curved proton path estimate. The code extension and the reconstruction algorithms are GPU-based, allowing to achieve reconstruction results within minutes. The performance of the pCT code extension was tested with Monte Carlo simulated data using three phantoms (Catphan® high resolution and sensitometry modules and a CIRS patient phantom). In the simulations, ideal and non-ideal conditions for a pCT setup were assumed. The obtained mean absolute percentage error was found to be below 1% and up to 8 lp/cm could be resolved using an idealized setup. These findings demonstrate that the presented code extension to the TIGRE toolbox offers the possibility for other research groups to use a fast and accurate open-source pCT reconstruction.

Published
2022

48. Seasonality of Carabid Beetles on an Organic Agricultural Field and Its Effect on Foraging Use

Author

Ulrich Irmler

Subjects
seasonality, organic land-use, dispersion speed, foraging effect, ground beetles, Plant Science, Agronomy and Crop Science, Food Science
Abstract

Ground beetle species from marginal areas invade organically farmed fields in a higher abundance and species richness than conventionally farmed fields. Seasonal invasion into organic fields was studied at Ritzerau Manor, converted to organic farming 18 years ago. Carabid species were explored with 123 pitfall traps within the field and in marginal near-natural habitats over the 18 years after conversion. For 56 species, seasonality could be studied in a distance gradient from the field margin to the field center. The results revealed that ground beetles from marginal habitats can use the fields differently depending on their seasonal activity. Early and fast-moving species can reach the center of the field at a 240 m distance from margin; late and slowly moving species only reach the 120 to 60 m distance level. The foraging effect of species, thus, depends on the seasonality and duration of activity. Overall, marginal species make up to 35% of the total foraging of ground beetles. Thus, organic farming not only supports a closer interaction between farmland and the adjacent near-natural landscape, but also benefits from higher biological pest control by immigrating marginal species.

Published
2022
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49. Feasibility study of a proton CT system based on 4D-tracking and residual energy determination via time-of-flight

Author

Felix Ulrich-Pur, Thomas Bergauer, Alexander Burker, Albert Hirtl, Christian Irmler, Stefanie Kaser, Florian Pitters, Simon Rit, Austrian Academy of Sciences (OeAW), Technische Universität Wien (TU), Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Léon Bérard [Lyon], and Rit, Simon

Subjects
proton computed tomography, RSP accuracy, Radiological and Ultrasound Technology, Phantoms, Imaging, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, FOS: Physical sciences, 4D-tracking detector, RSP precision, time-of-flight, Physics - Medical Physics, Disease Progression, proton therapy, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Feasibility Studies, Humans, Radiology, Nuclear Medicine and imaging, Medical Physics (physics.med-ph), Protons, low gain avalanche detector, Tomography, X-Ray Computed, Monte Carlo Method
Abstract

For dose calculations in ion beam therapy, it is vital to accurately determine the relative stopping power (RSP) distribution within the treated volume. Currently, RSP values are extrapolated from Hounsfield units (HU), measured with x-ray computed tomography (CT), which entails RSP inaccuracies due to conversion errors. A suitable method to improve the treatment plan accuracy is proton computed tomography (pCT). A typical pCT system consists of a tracking system and a separate residual energy (or range) detector to measure the RSP distribution directly. This paper introduces a novel pCT system based on a single detector technology, namely low gain avalanche detectors (LGADs). LGADs are fast 4D-tracking detectors, which can be used to simultaneously measure the particle position and time with precise timing and spatial resolution. In contrast to standard pCT systems, the residual energy is determined via a time-of-flight (TOF) measurement between different 4D-tracking stations. The design parameters for a realistic proton computed tomography system based on 4D-tracking detectors were studied and optimized using Monte Carlo simulations. The RSP accuracy and RSP resolution were measured inside the inserts of the CTP404 phantom to estimate the performance of the pCT system. After introducing a dedicated calibration procedure for the TOF calorimeter, RSP accuracies < 0.6 % could be achieved. Furthermore, the design parameters with the strongest impact on the RSP resolution were identified and a strategy to improve RSP resolution is proposed., Preprint submitted to Physics in Medicine and Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it

Published
2022
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50. The Belle II vertex detector integration

Author

H. Windel, V. Babu, S. Skambraks, P. Mammini, Ti. Baroncelli, M. Kaleta, C. Koffmane, M. Hensel, G. Batignani, J. Stypula, Prafulla Kumar Behera, V. Chekelian, C. La Licata, C. Wessel, H. Aihara, D. Münchow, F. Müller, M. Heck, J. Sanchez, F. Abudinen, AL Virto, F. Mueller, Oscar Alonso, R. Thalmeier, D. Klose, I. J. Watson, Soumen Paul, U. Packheiser, M. Ceccanti, N. Sato, Dipak Kumar Sahoo, D. Moya, B. Scavino, M. Fras, K. K. Rao, Takeo Higuchi, R. Richter, M. Albalawi, K. Nakamura, T. Kohriki, L. Zani, S. N. Mayekar, Svd Collaborations, Jakub Kandra, K. Prasanth, L. Macharski, S. Bacher, T. Morii, S. Bettarini, Jelena Ninkovic, Michael Ritzert, L. Bosisio, Jochen Dingfelder, Florian Schopper, Markus Friedl, D. Esperante, Ladislav Andricek, C. Kiesling, M. Boronat, H. Park, A. Bozek, Satoshi Tanaka, Tariq Aziz, Concettina Sfienti, C. W. Joo, R. Ayad, Seema Bahinipati, F. Lütticke, M. De Nuccio, U. Gebauer, Benjamin Schwenker, Zhiyong Liu, Steven Williams, Z. Natkaniec, Norbert Wermes, Carlos Marinas, B. Bhuyan, C. Schwanda, Shih-Chang Lee, T. Kuhr, G. Rizzo, W. Ostrowicz, S. Krivokuca, Frank Simon, B. Paschen, Maiko Takahashi, S. Vogt, H. G. Moser, R. Stever, Angel Dieguez, L. Gioi, F. Buchsteiner, Gerhard Schaller, H. Tanigawa, M. Gabriel, M. Hoek, A. Paladino, Rakesh Kumar, Gerhard Liemann, D. Getzkow, Peter Kvasnicka, B. Spruck, J.A.M. Grimaldo, Y. Onuki, K. H. Kang, T. Lueck, F. Poblotzki, S. Mccarney, P. K. Resmi, S. Schultschik, B. Gobbo, K. Lalwani, S. Rummel, D. Kittlinger, Ivan Peric, K. Gadow, Allen Caldwell, Martin Ritter, Dmytro Levit, Gagan Bihari Mohanty, To. Baroncelli, Keigo Hara, E. L. Barberio, F. Forti, L. Germic, U. Leis, A. Profeti, Tomasz Hemperek, S. Koike, B. Kisielewski, Marcel Vos, Peter Kodys, A. Bauer, P. Leitl, K. Ackermann, Ilya Komarov, Giulia Casarosa, H. Yin, Y. Soloviev, Jae-Young Lee, J. Fuster, Thomas Gessler, H. Schreeck, Phillip Urquijo, A. Martini, E. Paoloni, Carlos Lacasta, D. Červenkov, U. Stolzenberg, Pxd Belle Ii Depfet, L. Lanceri, I. Konorov, N. Dash, T. Czank, R. Blanco, G. N. Taylor, P. Wieduwilt, J. Suzuki, I. Rashevskaya, Hans Krüger, A. K. Basith, M. Rozanska, C. H. Wang, P. Kapusta, J. S. Lange, A. Rabusov, H. B. Jeon, Ivan Vila, A. Ishikawa, M. Schnecke, Filippo Bosi, T. Bilka, M. Watanabe, H. Ye, G. Caria, P. Gomis, E. Tafelmayer, M. Kumar, A. Frey, Jun Sasaki, J. Libby, K. Lautenbach, B. Deschamps, R. Sedlmeyer, Shoichi Watanuki, V. Bertacchi, Z. Doležal, S. Reiter, N. Kambara, Christian Irmler, C. Camien, T. Tsuboyama, J. Wiechczynski, Peter Fischer, W. Kun, P. Ahlburg, Wolfgang Kuhn, John Webb, L. Vitale, J. Zhao, Y. Bai, C. Niebuhr, European Commission, Ministerio de Economía y Competitividad (España), Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science, WPI Immunology Frontier Research Center (Japan), Federal Ministry of Science, Research and Economy (Austria), Australian Research Council, Ministry of Education, Youth and Sports (Czech Republic), Government of Czech Republic, Department of Science and Technology (India), Department of Atomic Energy (India), National Research Foundation of Korea, Ministry of Science and Higher Education (Poland), Federal Ministry of Science, Research and Economy (Germany), Kodyš, P., Abudinen, F., Ackermann, K., Ahlburg, P., Aihara, H., Albalawi, M., Alonso, O., Andricek, L., Ayad, R., Aziz, T., Babu, V., Bacher, S., Bahinipati, S., Bai, Y., Barberio, E., Baroncelli, Ti., Baroncelli, To., Basith, A. K., Batignani, G., Bauer, A., Behera, P. K., Bertacchi, V., Bettarini, S., Bhuyan, B., Bilka, T., Blanco, R., Bosi, F., Boronat, M., Bosisio, L., Bozek, A., Buchsteiner, F., Camien, C., Caldwell, A., Caria, G., Casarosa, G., Ceccanti, M., Červenkov, D., Chekelian, V., Czank, T., Dash, N., De Nuccio, M., Deschamps, B., Dieguez, A., Dingfelder, J., Doležal, Z., Esperante, D., Fischer, P., Forti, F., Fras, M., Frey, A., Friedl, M., Fuster, J., Gabriel, M., Gadow, K., Gebauer, U., Germic, L., Gessler, T., Getzkow, D., Gioi, L., Gobbo, B., Gomis, P., Grimaldo, J. A. M., Hara, K., Heck, M., Hemperek, T., Hensel, M., Higuchi, T., Hoek, M., Irmler, C., Ishikawa, A., Jeon, H. B., Joo, C., Kaleta, M., Kandra, J., Kambara, N., Kang, K. H., Kapusta, P., Kiesling, C., Kisielewski, B., Kittlinger, D., Klose, D., Koffmane, C., Kohriki, T., Koike, S., Komarov, I., Konorov, I., Krivokuca, S., Krüger, H., Kuhr, T., Kühn, W., Kumar, M., Kumar, R., Kun, W., Kvasnička, P., La Licata, C., Lacasta, C., Lalwani, K., Lanceri, L., Lange, J. S., Lautenbach, K., Lee, J. Y., Lee, S. C., Leis, U., Leitl, P., Levit, D., Libby, J., Liemann, G., Liu, Z., Lueck, T., Lütticke, F., Macharski, L., Mammini, P., Mariñas, C., Martini, A., Mayekar, S. N., Mccarney, S., Mohanty, G. B., Morii, T., Moser, H. G., Moya, D., Mueller, F. J., Müller, F., Münchow, D., Nakamura, K. R., Natkaniec, Z., Niebuhr, C., Ninkovic, J., Onuki, Y., Ostrowicz, W., Packheiser, U., Paladino, A., Paoloni, E., Park, H., Paschen, B., Paul, S., Peric, I., Poblotzki, F., Prasanth, K., Profeti, A., Rabusov, A., Rashevskaya, I., Rao, K. K., Reiter, S. P., P. K., Resmi, Richter, R., Ritter, M., Ritzert, M., Rizzo, G., Rozanska, M., Rummel, S., Sahoo, D., Sanchez, J. G., Sasaki, J., Sato, N., Scavino, B., Schaller, G., Schnecke, M., Schopper, F., Schreeck, H., Schultschik, S., Schwanda, C., Schwenker, B., Sedlmeyer, R., Sfienti, C., Simon, F., Skambraks, S., Soloviev, Y., Spruck, B., Stever, R., Stolzenberg, U., Stypula, J., Suzuki, J., Tafelmayer, E., Takahashi, M., Tanaka, S., Tanigawa, H., Taylor, G. N., Thalmeier, R., Tsuboyama, T., Urquijo, P., Vila, I., Virto, A. L., Vitale, L., Vogt, S., Vos, M., Wang, C., Watanuki, S., Watanabe, M., Watson, I. J., Webb, J., Wermes, N., Wessel, C., Wiechczynski, J., Wieduwilt, P., Williams, S., Windel, H., Ye, H., Yin, H., Zani, L., and Zhao, J.

Subjects
Nuclear and High Energy Physics, Physics::Instrumentation and Detectors, Silicon sensor, Phase (waves), Computer Science::Computational Geometry, 7. Clean energy, 01 natural sciences, law.invention, Nuclear physics, Belle II, Data acquisition, Pixel detector, Strip detector, Vertex detector, Instrumentation, law, 0103 physical sciences, Collider, Nuclear and High Energy Physic, Physics, Interconnection, Pixel, 010308 nuclear & particles physics, Detector, data acquisition, pixel detector, silicon sensor, strip detector, vertex detector, Upgrade, High Energy Physics::Experiment, Focus (optics)
Abstract

Belle II DEPFET, PXD, and SVD Collaborations: et al., The Belle II experiment comes with a substantial upgrade of the Belle detector and will operate at the SuperKEKB energy-asymmetric ee collider with energies tuned to ϒ(4S) resonance s=10.588 GeV. The accelerator has successfully completed the first phase of commissioning in 2016 and the first electron–positron collisions in Belle II took place in April 2018. Belle II features a newly designed silicon vertex detector based on DEPFET pixel and double-sided strip layers. Currently, a subset of the vertex detector is installed (Phase 2 of the experiment). Installation of the full detector (Phase 3) will be completed by the end of 2018. This paper describes the Phase 2 arrangement of the Belle II silicon vertex detector, with focus on the interconnection of detectors and their integration with the software framework of Belle II. Alignment issues are discussed based on detector simulations and first acquired data., This work is supported by MSCA-RISE, European Union project JENNIFER (EU grant n. 644294), MEXT, Japan, WPI, and JSPS (Japan); ARC (Australia); BMWFW (Austria); MSMT, Czech Republic, GAUK 404316 (Czech Republic); AIDA-2020 (Germany); DAE, India and DST (India); INFN (Italy); NRF-2016K1A3A7A09005605 and RSRI (Korea); MNiSW (Poland); Federal Ministry of Education and Research (BMBF, Germany); and MINECO, Spain grant FPA2015-71292-C2-1-P (Spain).

Published
2019
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