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3,033 results on '"Klein, Christoph"'

1. Understanding the Humidity Sensitivity of Sensors with TCAD Simulations

Author

Ninca, Ilona-Stefana, Bloch, Ingo, Bruers, Ben, Fadeyev, Vitaliy, Fernandez-Tejero, Xavi, Jessiman, Callan, Keller, John Stakely, Klein, Christoph Thomas, Koffas, Thomas, Lacker, Heiko Markus, Li, Peilin, Scharf, Christian, Staats, Ezekiel, Ullan, Miguel, and Unno, Yoshinobu

Subjects
Physics - Instrumentation and Detectors
Abstract

The breakdown voltage of silicon sensors without special surface is known to be affected by the ambient humidity. To understand the sensor's humidity sensitivity, Synopsys TCAD was used to simulate n-in-p test structures for different effective relative humidity. Photon emission of hot electrons was imaged with a microscope to locate breakdown in the edge-region of the sensor. The Top-Transient Current Technique was used to measure charge transport near the surface in the breakdown region of the sensor. Using the measurements and simulations, the evolution of the electric field, carrier densities and avalanche breakdown in the periphery of p-bulk silicon sensors is presented.

Published
2024

4. Generation of complex bone marrow organoids from human induced pluripotent stem cells

Author

Frenz-Wiessner, Stephanie, Fairley, Savannah D., Buser, Maximilian, Goek, Isabel, Salewskij, Kirill, Jonsson, Gustav, Illig, David, zu Putlitz, Benedicta, Petersheim, Daniel, Li, Yue, Chen, Pin-Hsuan, Kalauz, Martina, Conca, Raffaele, Sterr, Michael, Geuder, Johanna, Mizoguchi, Yoko, Megens, Remco T. A., Linder, Monika I., Kotlarz, Daniel, Rudelius, Martina, Penninger, Josef M., Marr, Carsten, and Klein, Christoph

Published
2024
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5. Enabling External Inquiries to an Existing Patient Registry by Using the Open Source Registry System for Rare Diseases: Demonstration of the System Using the European Society for Immunodeficiencies Registry

Author

Scheible, Raphael, Kadioglu, Dennis, Ehl, Stephan, Blum, Marco, Boeker, Martin, Folz, Michael, Grimbacher, Bodo, Göbel, Jens, Klein, Christoph, Nieters, Alexandra, Rusch, Stephan, Kindle, Gerhard, and Storf, Holger

Subjects
Computer applications to medicine. Medical informatics, R858-859.7
Abstract

BackgroundThe German Network on Primary Immunodeficiency Diseases (PID-NET) utilizes the European Society for Immunodeficiencies (ESID) registry as a platform for collecting data. In the context of PID-NET data, we show how registries based on custom software can be made interoperable for better collaborative access to precollected data. The Open Source Registry System for Rare Diseases (Open-Source-Registersystem für Seltene Erkrankungen [OSSE], in German) provides patient organizations, physicians, scientists, and other parties with open source software for the creation of patient registries. In addition, the necessary interoperability between different registries based on the OSSE, as well as existing registries, is supported, which allows those registries to be confederated at both the national and international levels. ObjectiveData from the PID-NET registry should be made available in an interoperable manner without losing data sovereignty by extending the existing custom software of the registry using the OSSE registry framework. MethodsThis paper describes the following: (1) the installation and configuration of the OSSE bridgehead, (2) an approach using a free toolchain to set up the required interfaces to connect a registry with the OSSE bridgehead, and (3) the decentralized search, which allows the formulation of inquiries that are sent to a selected set of registries of interest. ResultsPID-NET uses the established and highly customized ESID registry software. By setting up a so-called OSSE bridgehead, PID-NET data are made interoperable according to a federated approach, and centrally formulated inquiries for data can be received. As the first registry to use the OSSE bridgehead, the authors introduce an approach using a free toolchain to efficiently implement and maintain the required interfaces. Finally, to test and demonstrate the system, two inquiries are realized using the graphical query builder. By establishing and interconnecting an OSSE bridgehead with the underlying ESID registry, confederated queries for data can be received and, if desired, the inquirer can be contacted to further discuss any requirements for cooperation. ConclusionsThe OSSE offers an infrastructure that provides the possibility of more collaborative and transparent research. The decentralized search functionality includes registries into one search application while still maintaining data sovereignty. The OSSE bridgehead enables any registry software to be integrated into the OSSE network. The proposed toolchain to set up the required interfaces consists of freely available software components that are well documented. The use of the decentralized search is uncomplicated to use and offers a well-structured, yet still improvable, graphical user interface to formulate queries.

Published
2020
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7. Precision medicine in monogenic inflammatory bowel disease: proposed mIBD REPORT standards

Author

Uhlig, Holm H., Booth, Claire, Cho, Judy, Dubinsky, Marla, Griffiths, Anne M., Grimbacher, Bodo, Hambleton, Sophie, Huang, Ying, Jones, Kelsey, Kammermeier, Jochen, Kanegane, Hirokazu, Koletzko, Sibylle, Kotlarz, Daniel, Klein, Christoph, Lenardo, Michael J., Lo, Bernice, McGovern, Dermot P. B., Özen, Ahmet, de Ridder, Lissy, Ruemmele, Frank, Shouval, Dror S., Snapper, Scott B., Travis, Simon P., Turner, Dan, Wilson, David C., and Muise, Aleixo M.

Published
2023
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9. Democratising Knowledge Representation with BioCypher

Author

Lobentanzer, Sebastian, Aloy, Patrick, Baumbach, Jan, Bohar, Balazs, Charoentong, Pornpimol, Danhauser, Katharina, Doğan, Tunca, Dreo, Johann, Dunham, Ian, Fernandez-Torras, Adrià, Gyori, Benjamin M., Hartung, Michael, Hoyt, Charles Tapley, Klein, Christoph, Korcsmaros, Tamas, Maier, Andreas, Mann, Matthias, Ochoa, David, Pareja-Lorente, Elena, Popp, Ferdinand, Preusse, Martin, Probul, Niklas, Schwikowski, Benno, Sen, Bünyamin, Strauss, Maximilian T., Turei, Denes, Ulusoy, Erva, Wodke, Judith Andrea Heidrun, and Saez-Rodriguez, Julio

Subjects
Quantitative Biology - Molecular Networks
Abstract

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to non-specialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://biocypher.org) frees up valuable developer time; we encourage further development and usage by the community., Comment: 34 pages, 6 figures; submitted to Nature Biotechnology

Published
2022

10. Democratizing knowledge representation with BioCypher

Author

Lobentanzer, Sebastian, Aloy, Patrick, Baumbach, Jan, Bohar, Balazs, Carey, Vincent J., Charoentong, Pornpimol, Danhauser, Katharina, Doğan, Tunca, Dreo, Johann, Dunham, Ian, Farr, Elias, Fernandez-Torras, Adrià, Gyori, Benjamin M., Hartung, Michael, Hoyt, Charles Tapley, Klein, Christoph, Korcsmaros, Tamas, Maier, Andreas, Mann, Matthias, Ochoa, David, Pareja-Lorente, Elena, Popp, Ferdinand, Preusse, Martin, Probul, Niklas, Schwikowski, Benno, Sen, Bünyamin, Strauss, Maximilian T., Turei, Denes, Ulusoy, Erva, Waltemath, Dagmar, Wodke, Judith A. H., and Saez-Rodriguez, Julio

Published
2023
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13. Human Inborn Errors of Immunity: 2022 Update on the Classification from the International Union of Immunological Societies Expert Committee.

Author

Tangye, Stuart G, Al-Herz, Waleed, Bousfiha, Aziz, Cunningham-Rundles, Charlotte, Franco, Jose Luis, Holland, Steven M, Klein, Christoph, Morio, Tomohiro, Oksenhendler, Eric, Picard, Capucine, Puel, Anne, Puck, Jennifer, Seppänen, Mikko RJ, Somech, Raz, Su, Helen C, Sullivan, Kathleen E, Torgerson, Troy R, and Meyts, Isabelle

Subjects
Humans, Immune System Diseases, Immunologic Deficiency Syndromes, Phenotype, Research Report, IUIS Committee update, Inborn errors of immunity, autoinflammatory disorders, immune dysregulation, primary immunodeficiencies, Genetics, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Good Health and Well Being, Immunology
Abstract

We report the updated classification of inborn errors of immunity, compiled by the International Union of Immunological Societies Expert Committee. This report documents the key clinical and laboratory features of 55 novel monogenic gene defects, and 1 phenocopy due to autoantibodies, that have either been discovered since the previous update (published January 2020) or were characterized earlier but have since been confirmed or expanded in subsequent studies. While variants in additional genes associated with immune diseases have been reported in the literature, this update includes only those that the committee assessed that reached the necessary threshold to represent novel inborn errors of immunity. There are now a total of 485 inborn errors of immunity. These advances in discovering the genetic causes of human immune diseases continue to significantly further our understanding of molecular, cellular, and immunological mechanisms of disease pathogenesis, thereby simultaneously enhancing immunological knowledge and improving patient diagnosis and management. This report is designed to serve as a resource for immunologists and geneticists pursuing the molecular diagnosis of individuals with heritable immunological disorders and for the scientific dissection of cellular and molecular mechanisms underlying monogenic and related human immune diseases.

Published
2022

14. Transition for adolescents with a rare disease: results of a nationwide German project

Author

Grasemann, Corinna, Höppner, Jakob, Burgard, Peter, Schündeln, Michael M., Matar, Nora, Müller, Gabriele, Krude, Heiko, Berner, Reinhard, Lee-Kirsch, Min Ae, Hauck, Fabian, Wainwright, Kerstin, Baumgarten, Sylvana, Atinga, Janet, Bauer, Jens J., Manka, Eva, Körholz, Julia, Kiewert, Cordula, Heinen, André, Kretschmer, Tanita, Kurth, Tobias, Mittnacht, Janna, Schramm, Christoph, Klein, Christoph, Graessner, Holm, Hiort, Olaf, Muntau, Ania C., Grüters, Annette, Hoffmann, Georg F., and Choukair, Daniela

Published
2023
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15. Gasdermin D drives focal crystalline thrombotic microangiopathy by accelerating immunothrombosis and necroinflammation

Author

Watanabe-Kusunoki, Kanako, Li, Chenyu, Bandeira Honda, Tâmisa Seeko, Zhao, Danyang, Kusunoki, Yoshihiro, Ku, John, Long, Hao, Klaus, Martin, Han, Chao, Braun, Attila, Mammadova-Bach, Elmina, Linkermann, Andreas, Van Avondt, Kristof, Richter, Mathis, Soehnlein, Oliver, Linder, Monika I., Klein, Christoph, Steiger, Stefanie, and Anders, Hans-Joachim

Published
2024
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16. Wiskott-Aldrich syndrome: a study of 577 patients defines the genotype as a biomarker for disease severity and survival

Author

Vallée, Tanja C., Glasmacher, Jannik S., Buchner, Hannes, Arkwright, Peter D., Behrends, Uta, Bondarenko, Anastasia, Browning, Michael J., Buchbinder, David, Cattoni, Alessandro, Chernyshova, Liudmyla, Ciznar, Peter, Cole, Theresa, Czogała, Wojciech, Dueckers, Gregor, Edgar, John David M., Erbey, Fatih, Fasth, Anders, Ferrua, Francesca, Formankova, Renata, Gambineri, Eleonora, Gennery, Andrew R., Goldman, Frederick D., Gonzalez-Granado, Luis I., Heilmann, Carsten, Heiskanen-Kosma, Tarja, Juntti, Hanna, Kainulainen, Leena, Kanegane, Hirokazu, Karaca, Neslihan E., Kilic, Sara S., Klein, Christoph, Kołtan, Sylwia, Kondratenko, Irina, Meyts, Isabelle, Nasrullayeva, Gulnara M., Notarangelo, Lucia D., Pasic, Srdjan, Pellier, Isabelle, Pignata, Claudio, Misbah, Siraj, Schulz, Ansgar, Segundo, Gesmar R., Shcherbina, Anna, Slatter, Mary, Sokolic, Robert, Soler-Palacin, Pere, Stepensky, Polina, van Montfrans, Joris M., Ryhänen, Samppa, Wolska-Kuśnierz, Beata, Ziegler, John B., Zhao, Xiaodong, Aiuti, Alessandro, Ochs, Hans D., and Albert, Michael H.

Published
2024
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17. Truncating NFKB1 variants cause combined NLRP3 inflammasome activation and type I interferon signaling and predispose to necrotizing fasciitis

Author

Nurmi, Katariina, Silventoinen, Kristiina, Keskitalo, Salla, Rajamäki, Kristiina, Kouri, Vesa-Petteri, Kinnunen, Matias, Jalil, Sami, Maldonado, Rocio, Wartiovaara, Kirmo, Nievas, Elma Inés, Denita-Juárez, Silvina Paola, Duncan, Christopher J.A., Kuismin, Outi, Saarela, Janna, Romo, Inka, Martelius, Timi, Parantainen, Jukka, Beklen, Arzu, Bilicka, Marcelina, Matikainen, Sampsa, Nordström, Dan C., Kaustio, Meri, Wartiovaara-Kautto, Ulla, Kilpivaara, Outi, Klein, Christoph, Hauck, Fabian, Jahkola, Tiina, Hautala, Timo, Varjosalo, Markku, Barreto, Goncalo, Seppänen, Mikko R.J., and Eklund, Kari K.

Published
2024
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18. Clinical and functional spectrum of RAC2-related immunodeficiency

Author

Donkó, Ágnes, Sharapova, Svetlana O., Kabat, Juraj, Ganesan, Sundar, Hauck, Fabian H., Bergerson, Jenna R. E., Marois, Louis, Abbott, Jordan, Moshous, Despina, Williams, Kelli W., Campbell, Nicholas, Martin, Paul L., Lagresle-Peyrou, Chantal, Trojan, Timothy, Kuzmenko, Natalia B., Deordieva, Ekaterina A., Raykina, Elena V., Abers, Michael S., Abolhassani, Hassan, Barlogis, Vincent, Milla, Carlos, Hall, Geoffrey, Mousallem, Talal, Church, Joseph, Kapoor, Neena, Cros, Guilhem, Chapdelaine, Hugo, Franco-Jarava, Clara, Lopez-Lerma, Ingrid, Miano, Maurizio, Leiding, Jennifer W., Klein, Christoph, Stasia, Marie José, Fischer, Alain, Hsiao, Kuang-Chih, Martelius, Timi, Sepännen, Mikko R. J., Barmettler, Sara, Walter, Jolan, Masmas, Tania N., Mukhina, Anna A., Falcone, Emilia Liana, Kracker, Sven, Shcherbina, Anna, Holland, Steven M., Leto, Thomas L., and Hsu, Amy P.

Published
2024
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20. Brain expression profiles of two SCN1A antisense RNAs in children and adolescents with epilepsy

Author

Schneider Marius Frederik, Vogt Miriam, Scheuermann Johanna, Müller Veronika, Fischer-Hentrich Antje H. L., Kremer Thomas, Lugert Sebastian, Metzger Friedrich, Kudernatsch Manfred, Kluger Gerhard, Hartlieb Till, Noachtar Soheyl, Vollmar Christian, Kunz Mathias, Tonn Jörg Christian, Coras Roland, Blümcke Ingmar, Pace Claudia, Heinen Florian, Klein Christoph, Potschka Heidrun, and Borggraefe Ingo

Subjects
dravet syndrome, long non coding rna, regulatory rna, precision medicine, epilepsy, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

Heterozygous mutations within the voltage-gated sodium channel α subunit (SCN1A) are responsible for the majority of cases of Dravet syndrome (DS), a severe developmental and epileptic encephalopathy. Development of novel therapeutic approaches is mandatory in order to directly target the molecular consequences of the genetic defect. The aim of the present study was to investigate whether cis-acting long non-coding RNAs (lncRNAs) of SCN1A are expressed in brain specimens of children and adolescent with epilepsy as these molecules comprise possible targets for precision-based therapy approaches.

Published
2024
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22. C-terminal variants in CDC42 drive type I interferon-dependent autoinflammation in NOCARH syndrome reversible by ruxolitinib

Author

Kapp, Friedrich G., Kretschmer, Stefanie, Beckmann, Cora C.A., Wäsch, Lena, Molitor, Anne, Carapito, Raphaël, Schubert, Mario, Lucas, Nadja, Conrad, Solène, Poignant, Sylvaine, Isidor, Bertrand, Rohlfs, Meino, Kisaarslan, Ayşenur Paç, Schanze, Denny, Zenker, Martin, Schmitt-Graeff, Annette, Strahm, Brigitte, Peters, Anke, Yoshimi, Ayami, Driever, Wolfgang, Zillinger, Thomas, Günther, Claudia, Maharana, Shovamayee, Guan, Kaomei, Klein, Christoph, Ehl, Stephan, Niemeyer, Charlotte M., Unal, Ekrem, Bahram, Seiamak, Hauck, Fabian, Lee-Kirsch, Min Ae, and Speckmann, Carsten

Published
2023
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23. The ABC130 barrel module prototyping programme for the ATLAS strip tracker

Author

Poley, Luise, Sawyer, Craig, Addepalli, Sagar, Affolder, Anthony, Allongue, Bruno, Allport, Phil, Anderssen, Eric, Anghinolfi, Francis, Arguin, Jean-François, Arling, Jan-Hendrik, Arnaez, Olivier, Asbah, Nedaa Alexandra, Ashby, Joe, Asimakopoulou, Eleni Myrto, Atlay, Naim Bora, Bartsch, Ludwig, Basso, Matthew J., Beacham, James, Beaupré, Scott L., Beck, Graham, Beichert, Carl, Bergsten, Laura, Bernabeu, Jose, Bhattarai, Prajita, Bloch, Ingo, Blue, Andrew, Bochenek, Michal, Botte, James, Boynton, Liam, Brenner, Richard, Brueers, Ben, Buchanan, Emma, Bullard, Brendon, Capocasa, Francesca, Carr, Isabel, Carra, Sonia, Chao, Chen Wen, Chen, Jiayi, Chen, Liejian, Chen, Yebo, Chen, Xin, Cindro, Vladimir, Ciocio, Alessandra, Civera, Jose V., Cormier, Kyle, Cornell, Ella, Crick, Ben, Dabrowski, Wladyslaw, Dam, Mogens, David, Claire, Demontigny, Gabriel, Dette, Karola, DeWitt, Joel, Diez, Sergio, Doherty, Fred, Dopke, Jens, Dressnandt, Nandor, Edwards, Sam, Fadeyev, Vitaliy, Farrington, Sinead, Fawcett, William, Fernandez-Tejero, Javier, Filmer, Emily, Fleta, Celeste, Gallop, Bruce, Galloway, Zachary, Argos, Carlos Garcia, Garg, Diksha, Gignac, Matthew, Gillberg, Dag, Giovinazzo, Dena, Glover, James, Goettlicher, Peter, Gonella, Laura, Gorišek, Andrej, Grant, Charles, Grant, Fiona, Gray, Calum, Greenall, Ashley, Gregor, Ingrid-Maria, Greig, Graham, Grillo, Alexander A., Gu, Shan, Guescini, Francesco, da Costa, Joao Barreiro Guimaraes, Gunnell, Jane, Gupta, Ruchi, Haber, Carl, Halgeri, Amogh, Hamersly, Derek, Haugen, Tom-Erik, Hauser, Marc, Heim, Sarah, Heim, Timon, Helling, Cole, Herde, Hannah, Hessey, Nigel P., Hommels, Bart, Hönig, Jan Cedric, Hunter, Amelia, Jackson, Paul, Jewkes, Keith, John, Jaya John, Johnson, Thomas Allan, Jones, Tim, Kachiguin, Serguei, Kang, Nathan, Kaplon, Jan, Kareem, Mohammad, Keener, Paul, Keller, John, Key-Charriere, Michelle, Kilani, Samer, Kisliuk, Dylan, Klein, Christoph Thomas, Koffas, Thomas, Kramberger, Gregor, Krizka, Karol, Kroll, Jiri, Kuehn, Susanne, Kurth, Matthew, Labitan, Charilou, Lacasta, Carlos, Lacker, Heiko, Leitao, Pedro Vicente, León, Pablo, Li, Boyang, Li, Chenyang, Li, Yiming, Li, Zhiying, Liang, Zhijun, Liberatore, Marianna, Lister, Alison, Liu, Kai, Liu, Peilian, Lohse, Thomas, Lönker, Jonas, Lou, Xinchou, Lu, Weiguo, Luce, Zachary, Lynn, David, MacFadyen, Ross, Mägdefessel, Sven, Mahboubi, Kambiz, Malik, Usha, Mandić, Igor, La Marra, Daniel, Martin, Jean-Pierre, Martinez-Mckinney, Forest, Mikestikova, Marcela, Mikuž, Marko, Mitra, Ankush, Mladina, Evan, Montalbano, Alyssa, Monzat, David, Morii, Masahiro, Mullier, Geoffrey, Neundorf, Jonas, Newcomer, Mitch, Ng, Yanwing, Nikolica, Adrian, Nikolopoulos, Konstantinos, Oechsle, Jan, Oliver, Jason, Orr, Robert S., Ottino, Gregory, Paillard, Christian, Pani, Priscilla, Paowell, Sam, Parzefall, Ulrich, Phillips, Peter W., Platero, Adrián, Platero, Vicente, Prahl, Volker, Pyatt, Simon, Ran, Kunlin, Reardon, Nikita, Rehnisch, Laura, Renardi, Alessia, Renzmann, Martin, Rifki, Othmane, Rodriguez, Arturo Rodriguez, Rosin, Guy, Rossi, Edoardo, Ruggeri, Tristan, Rühr, Frederik, Rymaszewski, Piotr, Sadrozinski, Hartmut F. -W., Sanethavong, Phathakone, Santpur, Sai Neha, Scharf, Christian, Schillaci, Zach, Schmitt, Stefan, Sharma, Abhishek, Sciolla, Gabriella, Seiden, Abraham, Shi, Xin, Simpson-Allsop, Cameron, Snoek, Hella, Snow, Steve, Solaz, Carles, Soldevila, Urmila, Sousa, Filipe, Sperlich, Dennis, Staats, Ezekiel, Stack, Tynan Louis, Stanitzki, Marcel, Starinsky, Nikolai, Steentoft, Jonas, Stegler, Martin, Stelzer, Bernd, Stucci, Stefania, Swientek, Krzysztof, Taylor, Geoffrey N., Taylor, Wendy, Teoh, Jia Jian, Teuscher, Richard, Thomas, Jürgen, Tigchelaar, Allen, Tran, Tony, Tricoli, Alessandro, Trischuk, Dominique Anderson, Unno, Yoshinobu, van Nieuwenhuizen, Gerrit, Ullán, Miguel, Vermeulen, Jos, Vickey, Trevor, Vidal, Guillem, Vreeswijk, Marcel, Warren, Matt, Weidberg, Tony, Wiehe, Moritz, Wiglesworth, Craig, Wiik-Fuchs, Liv, Williams, Scott, Wilson, John, Witharm, Rhonda, Wizemann, Felix, Wonsak, Sven, Worm, Steve, Wormald, Mike, Xella, Stefania, Yang, Yuzhen, Yarwick, Joseph, Yu, Tang-Fai, Zhang, Dengfeng, Zhang, Kaili, Zhou, Maosen, and Zhu, Hongbo

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

For the Phase-II Upgrade of the ATLAS Detector, its Inner Detector, consisting of silicon pixel, silicon strip and transition radiation sub-detectors, will be replaced with an all new 100 % silicon tracker, composed of a pixel tracker at inner radii and a strip tracker at outer radii. The future ATLAS strip tracker will include 11,000 silicon sensor modules in the central region (barrel) and 7,000 modules in the forward region (end-caps), which are foreseen to be constructed over a period of 3.5 years. The construction of each module consists of a series of assembly and quality control steps, which were engineered to be identical for all production sites. In order to develop the tooling and procedures for assembly and testing of these modules, two series of major prototyping programs were conducted: an early program using readout chips designed using a 250 nm fabrication process (ABCN-25) and a subsequent program using a follow-up chip set made using 130 nm processing (ABC130 and HCC130 chips). This second generation of readout chips was used for an extensive prototyping program that produced around 100 barrel-type modules and contributed significantly to the development of the final module layout. This paper gives an overview of the components used in ABC130 barrel modules, their assembly procedure and findings resulting from their tests., Comment: 82 pages, 66 figures

Published
2020
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24. The Ever-Increasing Array of Novel Inborn Errors of Immunity: an Interim Update by the IUIS Committee

Author

Tangye, Stuart G, Al-Herz, Waleed, Bousfiha, Aziz, Cunningham-Rundles, Charlotte, Franco, Jose Luis, Holland, Steven M, Klein, Christoph, Morio, Tomohiro, Oksenhendler, Eric, Picard, Capucine, Puel, Anne, Puck, Jennifer, Seppänen, Mikko RJ, Somech, Raz, Su, Helen C, Sullivan, Kathleen E, Torgerson, Troy R, and Meyts, Isabelle

Subjects
Biomedical and Clinical Sciences, Immunology, Orphan Drug, Prevention, Genetics, Pediatric, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Alleles, COVID-19, Diagnosis, Differential, Disease Management, Genetic Association Studies, Genetic Predisposition to Disease, Genotype, Humans, Immunity, Inheritance Patterns, Phenotype, Primary Immunodeficiency Diseases, Public Health Surveillance, Risk Factors, Inborn errors of immunity, immune dysregulation, primary immunodeficiencies, autoinflammatory disorders
Abstract

The most recent updated classification of inborn errors of immunity/primary immunodeficiencies, compiled by the International Union of Immunological Societies Expert Committee, was published in January 2020. Within days of completing this report, it was already out of date, evidenced by the frequent publication of genetic variants proposed to cause novel inborn errors of immunity. As the next formal report from the IUIS Expert Committee will not be published until 2022, we felt it important to provide the community with a brief update of recent contributions to the field of inborn errors of immunity. Herein, we highlight studies that have identified 26 additional monogenic gene defects that reach the threshold to represent novel causes of immune defects.

Published
2021

27. Transcatheter Aortic Valve Replacement for Isolated Aortic Regurgitation Using a New Self-Expanding TAVR System

Author

Adam, Matti, Tamm, Alexander R., Wienemann, Hendrik, Unbehaun, Axel, Klein, Christoph, Arnold, Martin, Marwan, Mohamed, Theiss, Hans, Braun, Daniel, Bleiziffer, Sabine, Geyer, Martin, Goncharov, Arseniy, Kuhn, Elmar, Falk, Volkmar, von Bardeleben, Ralph Stephan, Achenbach, Stephan, Massberg, Steffen, Baldus, Stephan, Treede, Hendrik, and Rudolph, Tanja Katharina

Published
2023
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29. Metastasis founder cells activate immunosuppression early in human melanoma metastatic colonization

Author

Guetter, Severin, primary, Koenig, Courtney, additional, Koerkel-Qu, Huiqin, additional, Markiewicz, Aleksandra, additional, Scheitler, Sebastian, additional, Katzer, Marie, additional, Berneburg, Mark, additional, Renner, Philipp, additional, Cucuruz, Beatrix, additional, Guttenberger, Leonhard, additional, Naimer, Veronika, additional, Weidele, Kathrin, additional, Treitschke, Steffi, additional, Werno, Christian, additional, Jaser, Hanna, additional, Bargmann, Tonia, additional, Braun, Armin, additional, Weber, Florian, additional, Rachel, Reinhard, additional, Baumann, Felix, additional, Schmidleithner, Lisa, additional, Schambeck, Kathrin, additional, Mohammadi, Parvaneh, additional, Ulmer, Anja, additional, Haferkamp, Sebastian, additional, Klein, Christoph Andreas, additional, and Werner-Klein, Melanie, additional

Published
2024
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31. The Human Phenotype Ontology in 2021

Author

Köhler, Sebastian, Gargano, Michael, Matentzoglu, Nicolas, Carmody, Leigh C, Lewis-Smith, David, Vasilevsky, Nicole A, Danis, Daniel, Balagura, Ganna, Baynam, Gareth, Brower, Amy M, Callahan, Tiffany J, Chute, Christopher G, Est, Johanna L, Galer, Peter D, Ganesan, Shiva, Griese, Matthias, Haimel, Matthias, Pazmandi, Julia, Hanauer, Marc, Harris, Nomi L, Hartnett, Michael J, Hastreiter, Maximilian, Hauck, Fabian, He, Yongqun, Jeske, Tim, Kearney, Hugh, Kindle, Gerhard, Klein, Christoph, Knoflach, Katrin, Krause, Roland, Lagorce, David, McMurry, Julie A, Miller, Jillian A, Munoz-Torres, Monica C, Peters, Rebecca L, Rapp, Christina K, Rath, Ana M, Rind, Shahmir A, Rosenberg, Avi Z, Segal, Michael M, Seidel, Markus G, Smedley, Damian, Talmy, Tomer, Thomas, Yarlalu, Wiafe, Samuel A, Xian, Julie, Yüksel, Zafer, Helbig, Ingo, Mungall, Christopher J, Haendel, Melissa A, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Neurodegenerative, Animals, Biological Ontologies, Computational Biology, Databases, Factual, Disease, Disease Models, Animal, Genome, Genotype, Humans, Infant, Newborn, International Cooperation, Internet, Neonatal Screening, Pharmacogenetics, Phenotype, Software, Terminology as Topic, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

Published
2021

32. Investigation of performance and the influence of environmental conditions on strip detectors for the ATLAS Inner Tracker Upgrade

Author

Klein, Christoph Thomas and Hommels, Leonard

Subjects
539.7, LHC, ATLAS, ATLAS Upgrade, Inner Tracker, Silicon Strip Sensors
Abstract

With the upgrade of the Large Hadron Collider (LHC) to the High-Luminosity LHC (HL-LHC) scheduled for installation in 2024, the Inner Detector will be replaced with the new all-silicon ATLAS Inner Tracker (ITk) to maintain tracking performance in this high-occupancy environment and to cope with the increase of approximately a factor of ten in the integrated radiation dose. The outer four layers in the barrel and six disks in the end-cap region will host strip modules, built with single-sided strip sensors and glued-on hybrids carrying the front-end electronics necessary for readout. The strip sensors are manufactured as n-in-p strip sensors from high-resistivity silicon, which allow operation even after the fluences expected towards the end of the proposed lifetime of the HL-LHC. Prototypes of different sensor designs have been extensively tested electrically as well as in testbeam setups, yielding generally satisfactory results, but also revealing ongoing challenges. During electrical sensor evaluation many prototype sensors are found to not comply with specifications for stable long-term operation. This outcome was attributed to the influence of humidity, which has been subsequently investigated in great detail and will have lasting consequences for sensor production and module assembly. Repeated measurements on continuously biased sensors revealed a decrease in tracking performance and increased charge-sharing due to the accumulation of charges in the Si-SiO₂ interface. The dynamics of this effect and how it will affect operation of the finished ITk have been examined with a novel approach using the time-development of inter-strip quantities and trap energy level characterisation in SiO₂ with Deep-level Transient Spectroscopy (DLTS).

Published
2020
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33. The 2022 Update of IUIS Phenotypical Classification for Human Inborn Errors of Immunity

Author

Bousfiha, Aziz, Moundir, Abderrahmane, Tangye, Stuart G., Picard, Capucine, Jeddane, Leïla, Al-Herz, Waleed, Rundles, Charlotte C., Franco, Jose Luis, Holland, Steven M., Klein, Christoph, Morio, Tomohiro, Oksenhendler, Eric, Puel, Anne, Puck, Jennifer, Seppänen, Mikko R. J., Somech, Raz, Su, Helen C., Sullivan, Kathleen E., Torgerson, Troy R., and Meyts, Isabelle

Published
2022
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35. Hematologically important mutations: Leukocyte adhesion deficiency (second update)

Author

Roos, Dirk, van Leeuwen, Karin, Madkaikar, Manisha, Kambli, Priyanka M., Gupta, Maya, Mathews, Vikram, Rawat, Amit, Kuhns, Douglas B., Holland, Steven M., de Boer, Martin, Kanegane, Hirokazu, Parvaneh, Nima, Lorenz, Myriam, Schwarz, Klaus, Klein, Christoph, Sherkat, Roya, Jafari, Mahbube, Wolach, Baruch, den Dunnen, Johan T., Kuijpers, Taco W., and Köker, M. Yavuz

Published
2023
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36. Human genetic defects in SRP19 and SRPRA cause severe congenital neutropenia with distinctive proteome changes

Author

Linder, Monika I., Mizoguchi, Yoko, Hesse, Sebastian, Csaba, Gergely, Tatematsu, Megumi, Łyszkiewicz, Marcin, Ziȩtara, Natalia, Jeske, Tim, Hastreiter, Maximilian, Rohlfs, Meino, Liu, Yanshan, Grabowski, Piotr, Ahomaa, Kaarin, Maier-Begandt, Daniela, Schwestka, Marko, Pazhakh, Vahid, Isiaku, Abdulsalam I., Briones Miranda, Brenda, Blombery, Piers, Saito, Megumu K., Rusha, Ejona, Alizadeh, Zahra, Pourpak, Zahra, Kobayashi, Masao, Rezaei, Nima, Unal, Ekrem, Hauck, Fabian, Drukker, Micha, Walzog, Barbara, Rappsilber, Juri, Zimmer, Ralf, Lieschke, Graham J., and Klein, Christoph

Published
2023
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37. Human Inborn Errors of Immunity: 2019 Update on the Classification from the International Union of Immunological Societies Expert Committee.

Author

Tangye, Stuart G, Al-Herz, Waleed, Bousfiha, Aziz, Chatila, Talal, Cunningham-Rundles, Charlotte, Etzioni, Amos, Franco, Jose Luis, Holland, Steven M, Klein, Christoph, Morio, Tomohiro, Ochs, Hans D, Oksenhendler, Eric, Picard, Capucine, Puck, Jennifer, Torgerson, Troy R, Casanova, Jean-Laurent, and Sullivan, Kathleen E

Subjects
IUIS, autoinflammatory disorders, immune dysregulation, inborn errors of immunity, next-generation sequencing, primary immune deficiency, Immunology
Abstract

We report the updated classification of Inborn Errors of Immunity/Primary Immunodeficiencies, compiled by the International Union of Immunological Societies Expert Committee. This report documents the key clinical and laboratory features of 430 inborn errors of immunity, including 64 gene defects that have either been discovered in the past 2 years since the previous update (published January 2018) or were characterized earlier but have since been confirmed or expanded upon in subsequent studies. The application of next-generation sequencing continues to expedite the rapid identification of novel gene defects, rare or common; broaden the immunological and clinical phenotypes of conditions arising from known gene defects and even known variants; and implement gene-specific therapies. These advances are contributing to greater understanding of the molecular, cellular, and immunological mechanisms of disease, thereby enhancing immunological knowledge while improving the management of patients and their families. This report serves as a valuable resource for the molecular diagnosis of individuals with heritable immunological disorders and also for the scientific dissection of cellular and molecular mechanisms underlying inborn errors of immunity and related human diseases.

Published
2020

38. Correction to: Human Inborn Errors of Immunity: 2019 Update on the Classification from the International Union of Immunological Societies Expert Committee

Author

Tangye, Stuart G, Al-Herz, Waleed, Bousfiha, Aziz, Chatila, Talal, Cunningham-Rundles, Charlotte, Etzioni, Amos, Franco, Jose Luis, Holland, Steven M, Klein, Christoph, Morio, Tomohiro, Ochs, Hans D, Oksenhendler, Eric, Picard, Capucine, Puck, Jennifer, Torgerson, Troy R, Casanova, Jean-Laurent, and Sullivan, Kathleen E

Subjects
Biomedical and Clinical Sciences, Immunology, Biotechnology
Abstract

The original version of this article unfortunately contained mistakes in reference numbers. The in-text citations and the references were mismatched. The original article has been corrected.

Published
2020

39. Human Inborn Errors of Immunity: 2019 Update of the IUIS Phenotypical Classification

Author

Bousfiha, Aziz, Jeddane, Leila, Picard, Capucine, Al-Herz, Waleed, Ailal, Fatima, Chatila, Talal, Cunningham-Rundles, Charlotte, Etzioni, Amos, Franco, Jose Luis, Holland, Steven M, Klein, Christoph, Morio, Tomohiro, Ochs, Hans D, Oksenhendler, Eric, Puck, Jennifer, Torgerson, Troy R, Casanova, Jean-Laurent, Sullivan, Kathleen E, and Tangye, Stuart G

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Genetics, Autoimmunity, Genotype, Hereditary Autoinflammatory Diseases, Humans, Hypersensitivity, Immunity, Immunologic Deficiency Syndromes, Phenotype, IUIS, primary immune deficiency, inborn errors of immunity, immune dysregulation, autoinflammatory disorders, classification, Immunology
Abstract

Since 2013, the International Union of Immunological Societies (IUIS) expert committee (EC) on Inborn Errors of Immunity (IEI) has published an updated phenotypic classification of IEI, which accompanies and complements their genotypic classification into ten tables. This phenotypic classification is user-friendly and serves as a resource for clinicians at the bedside. There are now 430 single-gene IEI underlying phenotypes as diverse as infection, malignancy, allergy, autoimmunity, and autoinflammation. We herein report the 2019 phenotypic classification, including the 65 new conditions. The diagnostic algorithms are based on clinical and laboratory phenotypes for each of the ten broad categories of IEI.

Published
2020

40. Formalizing Atom-typing and the Dissemination of Force Fields with Foyer

Author

Klein, Christoph, Summers, Andrew Z., Thompson, Matthew W., Gilmer, Justin, McCabe, Clare, Cummings, Peter T., Sallai, Janos, and Iacovella, Christopher R.

Subjects
Physics - Computational Physics, Condensed Matter - Soft Condensed Matter
Abstract

A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models. Ambiguity in molecular models often stems from the dissemination of molecular force fields in a format that is not directly usable or is ambiguously documented via a non-machine readable mechanism. Specifically, the lack of a general tool for performing automated atom-typing under the rules of a particular force field facilitates errors in model parameterization that may go unnoticed if other researchers are unable reproduce this process. Here, we present Foyer, a Python tool that enables users to define force field atom-typing rules in a format that is both machine- and human-readable thus eliminating ambiguity in atom-typing and additionally providing a framework for force field dissemination. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type. Herein we describe the underlying methodology of the Foyer package, highlighting its advantages over typical atom-typing approaches and demonstrate is application in several use-cases., Comment: 39 Page, 4 Figures, 8 Listings

Published
2018

42. CARMIL2 Deficiency Presenting as Very Early Onset Inflammatory Bowel Disease.

Author

Magg, Thomas, Shcherbina, Anna, Arslan, Duran, Desai, Mukesh M, Wall, Sarah, Mitsialis, Vanessa, Conca, Raffaele, Unal, Ekrem, Karacabey, Neslihan, Mukhina, Anna, Rodina, Yulia, Taur, Prasad D, Illig, David, Marquardt, Benjamin, Hollizeck, Sebastian, Jeske, Tim, Gothe, Florian, Schober, Tilmann, Rohlfs, Meino, Koletzko, Sibylle, Lurz, Eberhard, Muise, Aleixo M, Snapper, Scott B, Hauck, Fabian, Klein, Christoph, and Kotlarz, Daniel

Subjects
Autoimmune Disease, Clinical Research, Genetics, Human Genome, Inflammatory Bowel Disease, Pediatric, Crohn's Disease, Digestive Diseases, 2.1 Biological and endogenous factors, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Aetiology, Inflammatory and immune system, Oral and gastrointestinal, Age of Onset, Child, Child, Preschool, Female, Genetic Predisposition to Disease, Humans, Inflammatory Bowel Diseases, Lymphocytes, Male, Microfilament Proteins, Mutation, Phenotype, Exome Sequencing, immunodeficiency, very early onset inflammatory bowel diseases, CARMIL2, Clinical Sciences, Gastroenterology & Hepatology
Abstract

BackgroundChildren with very early onset inflammatory bowel diseases (VEO-IBD) often have a refractory and severe disease course. A significant number of described VEO-IBD-causing monogenic disorders can be attributed to defects in immune-related genes. The diagnosis of the underlying primary immunodeficiency (PID) often has critical implications for the treatment of patients with IBD-like phenotypes.MethodsTo identify the molecular etiology in 5 patients from 3 unrelated kindred with IBD-like symptoms, we conducted whole exome sequencing. Immune workup confirmed an underlying PID.ResultsWhole exome sequencing revealed 3 novel CARMIL2 loss-of-function mutations in our patients. Immunophenotyping of peripheral blood mononuclear cells showed reduction of regulatory and effector memory T cells and impaired B cell class switching. The T cell proliferation and activation assays confirmed defective responses to CD28 costimulation, consistent with CARMIL2 deficiency.ConclusionOur study highlights that human CARMIL2 deficiency can manifest with IBD-like symptoms. This example illustrates that early diagnosis of underlying PID is crucial for the treatment and prognosis of children with VEO-IBD.

Published
2019

43. Biallelic variants in the calpain regulatory subunit CAPNS1 cause pulmonary arterial hypertension

Author

Postma, Alex V., Rapp, Christina K., Knoflach, Katrin, Volk, Alexander E., Lemke, Johannes R., Ackermann, Maximilian, Regamey, Nicolas, Latzin, Philipp, Celant, Lucas, Jansen, Samara M.A., Bogaard, Harm J., Ilgun, Aho, Alders, Mariëlle, van Spaendonck-Zwarts, Karin Y., Jonigk, Danny, Klein, Christoph, Gräf, Stefan, Kubisch, Christian, Houweling, Arjan C., and Griese, Matthias

Published
2023
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47. Disrupted degradative sorting of TLR7 is associated with human lupus

Author

Mishra, Harshita, primary, Schlack-Leigers, Claire, additional, Lim, Ee Lyn, additional, Thieck, Oliver, additional, Magg, Thomas, additional, Raedler, Johannes, additional, Wolf, Christine, additional, Klein, Christoph, additional, Ewers, Helge, additional, Lee-Kirsch, Min Ae, additional, Meierhofer, David, additional, Hauck, Fabian, additional, and Majer, Olivia, additional

Published
2024
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