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1. Demonstration of two-dimensional connectivity for a scalable error-corrected ion-trap quantum processor architecture

Author

Valentini, Marco, van Mourik, Martin W., Butt, Friederike, Wahl, Jakob, Dietl, Matthias, Pfeifer, Michael, Anmasser, Fabian, Colombe, Yves, Rössler, Clemens, Holz, Philip, Blatt, Rainer, Müller, Markus, Monz, Thomas, and Schindler, Philipp

Subjects
Quantum Physics
Abstract

A major hurdle for building a large-scale quantum computer is to scale up the number of qubits while maintaining connectivity between them. In trapped-ion devices, this connectivity can be provided by physically moving subregisters consisting of a few ions across the processor. The topology of the connectivity is given by the layout of the ion trap where one-dimensional and two-dimensional arrangements are possible. Here, we focus on an architecture based on a rectangular two-dimensional lattice, where each lattice site contains a subregister with a linear string of ions. We refer to this architecture as the Quantum Spring Array (QSA). Subregisters placed in neighboring lattice sites can be coupled by bringing the respective ion strings close to each other while avoiding merging them into a single trapping potential. Control of the separation of subregisters along one axis of the lattice, known as the axial direction, uses quasi-static voltages, while the second axis, the radial, requires control of radio frequency signals. In this work, we investigate key elements of the 2D lattice quantum computation architecture along both axes: We show that the coupling rate between neighboring lattice sites increases with the number of ions per site and the motion of the coupled system can be resilient to noise. The coherence of the coupling is assessed, and an entangled state of qubits in separate trapping regions along the radial axis is demonstrated. Moreover, we demonstrate control over radio frequency signals to adjust radial separation between strings, and thus tune their coupling rate. We further map the 2D lattice architecture to code primitives for fault-tolerant quantum error correction, providing a step towards a quantum processor architecture that is optimized for large-scale fault-tolerant operation., Comment: 23 pages, 19 figures (15 in main text, 4 in appendices)

Published
2024

8. Towards personalized medicine: a scoping review of immunotherapy in sepsis

Author

Slim, Marleen A., van Mourik, Niels, Bakkerus, Lieke, Fuller, Katherine, Acharya, Lydia, Giannidis, Tatiana, Dionne, Joanna C., Oczkowski, Simon J. W., Netea, Mihai G., Pickkers, Peter, Giamarellos-Bourboulis, Evangelos J., Müller, Marcella C. A., van der Poll, Tom, Wiersinga, W. Joost, Vlaar, Alexander P. J., and van Vught, Lonneke A.

Published
2024
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9. The pluripotency factor NANOG contributes to mesenchymal plasticity and is predictive for outcome in esophageal adenocarcinoma

Author

van der Zalm, Amber P., Dings, Mark P. G., Manoukian, Paul, Boersma, Hannah, Janssen, Reimer, Bailey, Peter, Koster, Jan, Zwijnenburg, Danny, Volckmann, Richard, Bootsma, Sanne, Waasdorp, Cynthia, van Mourik, Monique, Blangé, Dionne, van den Ende, Tom, Oyarce, César I., Derks, Sarah, Creemers, Aafke, Ebbing, Eva A., Hooijer, Gerrit K., Meijer, Sybren L., van Berge Henegouwen, Mark I., Medema, Jan Paul, van Laarhoven, Hanneke W. M., and Bijlsma, Maarten F.

Published
2024
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11. Federated systems for automated infection surveillance: a perspective

Author

Stephanie M. van Rooden, Suzanne D. van der Werff, Maaike S. M. van Mourik, Frederikke Lomholt, Karina Lauenborg Møller, Sarah Valk, Carolina dos Santos Ribeiro, Albert Wong, Saskia Haitjema, Michael Behnke, and Eugenia Rinaldi

Subjects
Automated surveillance, Healthcare associated infections, Severe acute respiratory infections, Federated systems, Interoperability, Standards, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Automation of surveillance of infectious diseases—where algorithms are applied to routine care data to replace manual decisions—likely reduces workload and improves quality of surveillance. However, various barriers limit large-scale implementation of automated surveillance (AS). Current implementation strategies for AS in surveillance networks include central implementation (i.e. collecting all data centrally, and central algorithm application for case ascertainment) or local implementation (i.e. local algorithm application and sharing surveillance results with the network coordinating center). In this perspective, we explore whether current challenges can be solved by federated AS. In federated AS, scripts for analyses are developed centrally and applied locally. We focus on the potential of federated AS in the context of healthcare associated infections (AS-HAI) and of severe acute respiratory illness (AS-SARI). AS-HAI and AS-SARI have common and specific requirements, but both would benefit from decreased local surveillance burden, alignment of AS and increased central and local oversight, and improved access to data while preserving privacy. Federated AS combines some benefits of a centrally implemented system, such as standardization and alignment of an easily scalable methodology, with some of the benefits of a locally implemented system including (near) real-time access to data and flexibility in algorithms, meeting different information needs and improving sustainability, and allowance of a broader range of clinically relevant case-definitions. From a global perspective, it can promote the development of automated surveillance where it is not currently possible and foster international collaboration.The necessary transformation of source data likely will place a significant burden on healthcare facilities. However, this may be outweighed by the potential benefits: improved comparability of surveillance results, flexibility and reuse of data for multiple purposes. Governance and stakeholder agreement to address accuracy, accountability, transparency, digital literacy, and data protection, warrants clear attention to create acceptance of the methodology. In conclusion, federated automated surveillance seems a potential solution for current barriers of large-scale implementation of AS-HAI and AS-SARI. Prerequisites for successful implementation include validation of results and evaluation requirements of network participants to govern understanding and acceptance of the methodology.

Published
2024
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12. Tertiary Review on Explainable Artificial Intelligence: Where Do We Stand?

Author

Frank van Mourik, Annemarie Jutte, Stijn E. Berendse, Faiza A. Bukhsh, and Faizan Ahmed

Subjects
explainable AI, computer vision, time series, neural network, deep learning, Computer engineering. Computer hardware, TK7885-7895
Abstract

Research into explainable artificial intelligence (XAI) methods has exploded over the past five years. It is essential to synthesize and categorize this research and, for this purpose, multiple systematic reviews on XAI mapped out the landscape of the existing methods. To understand how these methods have developed and been applied and what evidence has been accumulated through model training and analysis, we carried out a tertiary literature review that takes as input systematic literature reviews published between 1992 and 2023. We evaluated 40 systematic literature review papers and presented binary tabular overviews of researched XAI methods and their respective characteristics, such as the scope, scale, input data, explanation data, and machine learning models researched. We identified seven distinct characteristics and organized them into twelve specific categories, culminating in the creation of comprehensive research grids. Within these research grids, we systematically documented the presence or absence of research mentions for each pairing of characteristic and category. We identified 14 combinations that are open to research. Our findings reveal a significant gap, particularly in categories like the cross-section of feature graphs and numerical data, which appear to be notably absent or insufficiently addressed in the existing body of research and thus represent a future research road map.

Published
2024
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13. Building Parental Capacity: Outcomes of a Therapeutic Parent Group Run Concurrently with a Social Skills Group for Their Young Person

Author

Marcella van Mourik, Jenny-Maree Marshall, Liza Hopkins, Michelle Kehoe, and Richard Whitehead

Subjects
ASD, autism, parent support, parent stress, implementing parent groups, early adolescence, Psychiatry, RC435-571, Pediatrics, RJ1-570, Psychology, BF1-990
Abstract

Introduction: Raising a child with social communication and emotion regulation challenges, such as those experienced in the context of an autism spectrum disorder (ASD), is associated with family disruption and parental stress. Research shows that parents of children and young people with ASD can experience challenges in managing their child’s behaviour and experience a sense of disconnectedness, a lack of support from the “system”, and a broader lack of understanding within the community. Methods: A therapeutic parent group was held in parallel to a young person group working on social skills. The young person cohort included both boys and girls in early adolescence with neurodevelopmental diagnoses. The parent group provided a space for participants to focus on themselves, tune into their own emotions, and receive support in relation to their lived experiences of parenting. Parental outcomes were assessed using standard measures, and the experiences of the groups were captured qualitatively through focus groups with both parents and staff. Results: The project found that the therapeutic parent group was effective in supporting parents to feel less stressed and more in control, as well as less alone in their parenting journey. Qualitative data indicated that the groups filled an identified need within the service and were engaging and acceptable to parents.

Published
2024
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15. Plant Performance in Precision Horticulture: Optimal climate control under stochastic uncertainty

Author

van Mourik, Simon, Ooster, Bert van't, and Vellekoop, Michel

Subjects
Mathematics - Optimization and Control, Electrical Engineering and Systems Science - Systems and Control
Abstract

This paper presents a risk mitigating, time-varying feedback control algorithm for crop production when state dynamics are subject to uncertainty. The model based case study concerns a 40 day production round of lettuce in a greenhouse where control input consists of daily and nightly temperature set points. The control problem was formulated in terms of a stochastic Markov decision process with the objective to maximize the expected net revenue at harvest time. The importance of time-varying feedback and of risk mitigation was investigated by making a comparison with a controller that takes uncertainty into account but is static and a controller which is dynamic but ignores the uncertainty in the state dynamics. For the case of heat limited crop growth, and strict requirements on harvest weight precision, the dynamic stochastic controller outperformed the static controller in terms of both maximal expected net revenue (by 19 %) and state precision at harvest time (with 50 % less standard deviation). It also outperformed the deterministic controller for both criteria (15 % in maximal expected net revenue and 8 % less standard deviation). A detailed sensitivity analysis showed that such improvements in performance levels are robust, since they hold over large ranges of uncertainty in state dynamics, required harvest precision levels, starting days, and initial weights. The results provide insights in potential of dynamic feedback and risk mitigation strategies for high precision requirements under uncertainty. Although the results should be interpreted with caution, they illustrate the considerable potential benefit for stochastic greenhouse climate control under uncertainty when high precision is required.

Published
2023

16. Experimental realization of nonunitary multi-qubit operations

Author

van Mourik, Martin W., Zapusek, Elias, Hrmo, Pavel, Gerster, Lukas, Blatt, Rainer, Monz, Thomas, Schindler, Philipp, and Reiter, Florentin

Subjects
Quantum Physics, Physics - Atomic Physics
Abstract

We demonstrate a novel experimental toolset that enables irreversible multi-qubit operations on a quantum platform. To exemplify our approach, we realize two elementary nonunitary operations: the OR and NOR gates. The electronic states of two trapped $^{40}$Ca$^{+}$ ions encode the logical information, and a co-trapped $^{88}$Sr$^{+}$ ion provides the irreversibility of the gate by a dissipation channel through sideband cooling. We measure $87\%$ and $81\%$ success rates for the OR and NOR gates, respectively. The presented methods are a stepping stone towards other nonunitary operations such as in quantum error correction and quantum machine learning., Comment: 5 main text pages, 2 supplemental material pages, 4 main text figures, 1 supplemental material figure, 1 supplemental material table

Published
2023
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17. Comparing automated surveillance systems for detection of pathogen-related clusters in healthcare settings

Author

Jean Xiang Ying Sim, Susanne Pinto, and Maaike S. M. van Mourik

Subjects
Cluster detection, WHONET, SaTScan, Automated surveillance, Pathogen-based detection, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Detection of pathogen-related clusters within a hospital is key to early intervention to prevent onward transmission. Various automated surveillance methods for outbreak detection have been implemented in hospital settings. However, direct comparison is difficult due to heterogenicity of data sources and methodologies. In the hospital setting, we assess the performance of three different methods for identifying microbiological clusters when applied to various pathogens with distinct occurrence patterns. Methods In this retrospective cohort study we use WHONET-SaTScan, CLAR (CLuster AleRt system) and our currently used percentile-based system (P75) for the means of cluster detection. The three methods are applied to the same data curated from 1st January 2014 to 31st December 2021 from a tertiary care hospital. We show the results for the following case studies: the introduction of a new pathogen with subsequent endemicity, an endemic species, rising levels of an endemic organism, and a sporadically occurring species. Results All three cluster detection methods showed congruence only in endemic organisms. However, there was a paucity of alerts from WHONET-SaTScan (n = 9) compared to CLAR (n = 319) and the P75 system (n = 472). WHONET-SaTScan did not pick up smaller variations in baseline numbers of endemic organisms as well as sporadic organisms as compared to CLAR and the P75 system. CLAR and the P75 system revealed congruence in alerts for both endemic and sporadic organisms. Conclusions Use of statistically based automated cluster alert systems (such as CLAR and WHONET-Satscan) are comparable to rule-based alert systems only for endemic pathogens. For sporadic pathogens WHONET-SaTScan returned fewer alerts compared to rule-based alert systems. Further work is required regarding clinical relevance, timelines of cluster alerts and implementation.

Published
2024
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18. Evaluation of a multifaceted implementation strategy for semi-automated surveillance of surgical site infections after total hip or knee arthroplasty: a multicentre pilot study in the Netherlands

Author

Manon Brekelmans, Titia Hopmans, Maaike van Mourik, Sabine de Greeff, Julie Swillens, and Stephanie van Rooden

Subjects
Automated surveillance, Implementation science, Surgical site infections, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Introduction To promote the nation-wide implementation of semi-automated surveillance (AS) of surgical site infection after hip and knee arthroplasty, the Dutch National Institute for Public Health and the Environment (RIVM) deployed a decentralised multifaceted implementation strategy. This strategy consisted of a protocol specifying minimum requirements for an AS system, supported by a user manual, education module, individual guidance for hospitals and user-group meetings. This study describes an effect evaluation and process evaluation of the implementation strategy for AS in five frontrunner hospitals. Methods To evaluate the effect of the implementation strategy, the achieved phase of implementation was determined in each frontrunner hospital at the end of the study period. The process evaluation consisted of (1) an evaluation of the feasibility of strategy elements, (2) an evaluation of barriers and facilitators for implementation and (3) an evaluation of the workload for implementation. Interviews were performed as a basis for a subsequent survey quantifying the results regarding the feasibility as well as barriers and facilitators. Workload was self-monitored per profession. Qualitative data were analysed using a framework analysis, whereas quantitative data were analysed descriptively. Results One hospital finished the complete implementation process in 240 person-hours. Overall, the elements of the implementation strategy were often used, positively received and overall, the strategy was rated effective and feasible. During the implementation process, participants perceived the relative advantage of AS and had sufficient knowledge about AS. However, barriers regarding complexity of AS data extraction, data-infrastructure, and validation, lack of capacity and motivation at the IT department, and difficulties with assigning roles and responsibilities were experienced. Conclusion A decentralised multifaceted implementation strategy is suitable for the implementation of AS in hospitals. Effective local project management, including clear project leadership and ownership, obtaining commitment of higher management levels, active involvement of stakeholders, and appropriate allocation of roles and responsibilities is important for successful implementation and should be facilitated by the implementation strategy. Sufficient knowledge about AS, its requirements and the implementation process should be available among stakeholders by e.g. an education module. Furthermore, exchange of knowledge and experiences between hospitals should be encouraged in user-group meetings.

Published
2024
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19. The pluripotency factor NANOG contributes to mesenchymal plasticity and is predictive for outcome in esophageal adenocarcinoma

Author

Amber P. van der Zalm, Mark P. G. Dings, Paul Manoukian, Hannah Boersma, Reimer Janssen, Peter Bailey, Jan Koster, Danny Zwijnenburg, Richard Volckmann, Sanne Bootsma, Cynthia Waasdorp, Monique van Mourik, Dionne Blangé, Tom van den Ende, César I. Oyarce, Sarah Derks, Aafke Creemers, Eva A. Ebbing, Gerrit K. Hooijer, Sybren L. Meijer, Mark I. van Berge Henegouwen, Jan Paul Medema, Hanneke W. M. van Laarhoven, and Maarten F. Bijlsma

Subjects
Medicine
Abstract

Abstract Background Despite the advent of neoadjuvant chemoradiotherapy (CRT), overall survival rates of esophageal adenocarcinoma (EAC) remain low. A readily induced mesenchymal transition of EAC cells contributes to resistance to CRT. Methods In this study, we aimed to chart the heterogeneity in cell state transition after CRT and to identify its underpinnings. A panel of 12 esophageal cultures were treated with CRT and ranked by their relative epithelial-mesenchymal plasticity. RNA-sequencing was performed on 100 pre-treatment biopsies. After RNA-sequencing, Ridge regression analysis was applied to correlate gene expression to ranked plasticity, and models were developed to predict mesenchymal transitions in patients. Plasticity score predictions of the three highest significant predictive models were projected on the pre-treatment biopsies and related to clinical outcome data. Motif enrichment analysis of the genes associated with all three models was performed. Results This study reveals NANOG as the key associated transcription factor predicting mesenchymal plasticity in EAC. Expression of NANOG in pre-treatment biopsies is highly associated with poor response to neoadjuvant chemoradiation, the occurrence of recurrences, and median overall survival difference in EAC patients (>48 months). Perturbation of NANOG reduces plasticity and resensitizes cell lines, organoid cultures, and patient-derived in vivo grafts. Conclusions In conclusion, NANOG is a key transcription factor in mesenchymal plasticity in EAC and a promising predictive marker for outcome.

Published
2024
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20. Cartilage-derived cells display heterogeneous pericellular matrix synthesis in agarose microgels

Author

Marloes van Mourik, Bart M. Tiemeijer, Maarten van Zon, Florencia Abinzano, Jurjen Tel, Jasper Foolen, and Keita Ito

Subjects
Chondrocytes, Chondroprogenitors, Pericellular matrix, Type-VI collagen, Perlecan, Microgels, Biology (General), QH301-705.5
Abstract

The pericellular matrix (PCM) surrounding chondrocytes is essential for articular cartilage tissue engineering. As the current isolation methods to obtain chondrocytes with their PCM (chondrons) result in a heterogeneous mixture of chondrocytes and chondrons, regenerating the PCM using a tissue engineering approach could prove beneficial. In this study, we aimed to discern the behavior of articular chondrocytes (ACs) in regenerating the PCM in such an approach and whether this would also be true for articular cartilage-derived progenitor cells (ACPCs), as an alternative cell source. Bovine ACs and ACPCs were encapsulated in agarose microgels using droplet-based microfluidics. ACs were stimulated with TGF-β1 and dexamethasone and ACPCs were sequentially stimulated with BMP-9 followed by TGF-β1 and dexamethasone. After 0, 3, 5, and 10 days of culture, PCM components, type-VI collagen and perlecan, and ECM component, type-II collagen, were assessed using flow cytometry and fluorescence microscopy. Both ACs and ACPCs synthesized the PCM before the ECM. It was seen for the first time that synthesis of type-VI collagen always preceded perlecan. While the PCM synthesized by ACs resembled native chondrons after only 5 days of culture, ACPCs often made less well-structured PCMs. Both cell types showed variations between individual cells and donors. On one hand, this was more prominent in ACPCs, but also a subset of ACPCs showed superior PCM and ECM regeneration, suggesting that isolating these cells may potentially improve cartilage repair strategies.

Published
2024
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21. An Intestinal Microbiome Intervention Affects Biochemical Disease Activity in Patients with Antiphospholipid Syndrome

Author

Valérie L. B. I. Jansen, Dagmar J. M. van Mourik, Mark Davids, Kika van Bergen en Henegouwen, Tessa Noordermeer, Johannes H. M. Levels, Maarten Limper, Michiel Coppens, Max Nieuwdorp, Rolf T. Urbanus, Saskia Middeldorp, and Thijs E. van Mens

Subjects
antiphospholipid syndrome, autoimmune disease, intestinal microbiome, gut microbiome, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background The origin of autoantibodies in patients with antiphospholipid syndrome (APS) is unknown. The gut microbiome contributes to autoimmunity and contains peptide homologues to the main APS autoantigen, which affect disease activity in animal models. Alteration of the gut microbiota with vancomycin diminishes disease activity in mice but no data on the effect of gut microbiota alteration in APS patients are available to date.

Published
2024
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22. Acetylated bacterial proteins as potent antigens inducing an anti-modified protein antibody response

Author

Tom W J Huizinga, Diane van der Woude, René E M Toes, Mikhail Volkov, Peter A van Veelen, Joanneke C Kwekkeboom, Karin A J van Schie, Arieke S B Kampstra, Anouk G van Mourik, and Arnoud de Ru

Subjects
Medicine
Abstract

Objective Gut-residing bacteria, such as Escherichia coli, can acetylate their proteome under conditions of amine starvation. It is postulated that the (gut) microbiome is involved in the breach of immune tolerance to modified self-proteins leading to the anti-modified protein antibodies (AMPAs), hallmarking seropositive rheumatoid arthritis (RA). Our aim was to determine whether acetylated bacterial proteins can induce AMPA responses cross-reactive to modified self-proteins and be recognised by human AMPA (hAMPA).Methods E. coli bacteria were grown under amine starvation to generate endogenously acetylated bacterial proteins. Furthermore, E. coli proteins were acetylated chemically. Recognition of these proteins by hAMPA was analysed by western blotting and ELISA; recognition by B cells carrying a modified protein-reactive B cell receptor (BCR) was analysed by pSyk (Syk phosphorylation) activation assay. C57BL/6 mice were immunised with (modified) bacterial protein fractions, and sera were analysed by ELISA.Results Chemically modified bacterial protein fractions contained high levels of acetylated proteins and were readily recognised by hAMPA and able to activate B cells carrying modified protein-reactive BCRs. Likely due to substantially lower levels of acetylation, endogenously acetylated protein fractions were not recognised by hAMPA or hAMPA-expressing B cells. Immunising mice with chemically modified protein fractions induced a strong cross-reactive AMPA response, targeting various modified antigens including citrullinated proteins.Conclusions Acetylated bacterial proteins are recognisable by hAMPA and are capable of inducing cross-reactive AMPA in mice. These observations provide the first conceptual evidence for a novel mechanism involving the (endogenous) acetylation of the bacterial proteome, allowing a breach of tolerance to modified proteins and the formation of cross-reactive AMPA.

Published
2024
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23. Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection

Author

Astrid Marchal, Elizabeth T. Cirulli, Iva Neveux, Evangelos Bellos, Ryan S. Thwaites, Kelly M. Schiabor Barrett, Yu Zhang, Ivana Nemes-Bokun, Mariya Kalinova, Andrew Catchpole, Stuart G. Tangye, András N. Spaan, Justin B. Lack, Jade Ghosn, Charles Burdet, Guy Gorochov, Florence Tubach, Pierre Hausfater, Clifton L. Dalgard, Shen-Ying Zhang, Qian Zhang, Christopher Chiu, Jacques Fellay, Joseph J. Grzymski, Vanessa Sancho-Shimizu, Laurent Abel, Jean-Laurent Casanova, Aurélie Cobat, Alexandre Bolze, Alessandro Aiuti, Saleh Al-Muhsen, Fahd Al-Mulla, Ali Amara, Mark S. Anderson, Evangelos Andreakos, Andrés A. Arias, Lisa M. Arkin, Hagit Baris Feldman, Paul Bastard, Alexandre Belot, Catherine M. Biggs, Dusan Bogunovic, Anastasiia Bondarenko, Alessandro Borghesi, Ahmed A. Bousfiha, Petter Brodin, Yenan Bryceson, Manish J. Butte, Giorgio Casari, John Christodoulou, Roger Colobran, Antonio Condino-Neto, Stefan N. Constantinescu, Megan A. Cooper, Murkesh Desai, Beth A. Drolet, Xavier Duval, Jamila El Baghdadi, Philippine Eloy, Sara Espinosa-Padilla, Carlos Flores, José Luis Franco, Antoine Froidure, Peter K. Gregersen, Bodo Grimbacher, Filomeen Haerynck, David Hagin, Rabih Halwani, Lennart Hammarström, James R. Heath, Elena W.Y. Hsieh, Eystein Husebye, Kohsuke Imai, Yuval Itan, Emmanuelle Jouanguy, Elżbieta Kaja, Timokratis Karamitros, Kai Kisand, Cheng-Lung Ku, Yu-Lung Lau, Yun Ling, Carrie L. Lucas, Tom Maniatis, Davood Mansouri, László Maródi, France Mentré, Isabelle Meyts, Joshua D. Milner, Kristina Mironska, Trine H. Mogensen, Tomohiro Morio, Lisa F.P. Ng, Luigi D. Notarangelo, Antonio Novelli, Giuseppe Novelli, Cliona O'Farrelly, Satoshi Okada, Keisuke Okamoto, Tayfun Ozcelik, Qiang Pan-Hammarström, Jean W. Pape, Rebeca Perez de Diego, Jordi Perez-Tur, David S. Perlin, Graziano Pesole, Anna M. Planas, Carolina Prando, Aurora Pujol, Anne Puel, Lluis Quintana-Murci, Sathishkumar Ramaswamy, Laurent Renia, Igor Resnick, Carlos Rodríguez-Gallego, Anna Sediva, Mikko R.J. Seppänen, Mohammad Shahrooei, Anna Shcherbina, Ondrej Slaby, Andrew L. Snow, Pere Soler-Palacín, Vassili Soumelis, Ivan Tancevski, Ahmad Abou Tayoun, Şehime Gülsün Temel, Christian Thorball, Pierre Tiberghien, Sophie Trouillet-Assant, Stuart E. Turvey, K. M. Furkan Uddin, Mohammed J. Uddin, Diederik van de Beek, Donald C. Vinh, Horst von Bernuth, Joost Wauters, Mayana Zatz, Pawel Zawadzki, Serge Bureau, Yannick Vacher, Anne Gysembergh-Houal, Lauren Demerville, Abla Benleulmi-Chaachoua, Sebastien Abad, Radhiya Abassi, Abdelrafie Abdellaoui, Abdelkrim Abdelmalek, Hendy Abdoul, Helene Abergel, Fariza Abeud, Sophie Abgrall, Noemie Abisror, Marylise Adechian, Nordine Aderdour, Hakeem Farid Admane, Frederic Adnet, Sara Afritt, Helene Agostini, Claire Aguilar, Sophie Agut, Tommaso Francesco Aiello, Marc Ait Kaci, Hafid Ait Oufella, Gokula Ajeenthiravasan, Virginie Alauzy, Fanny Alby-Laurent, Lucie Allard, Marie-Alexandra Alyanakian, Blanca Amador Borrero, Sabrina Amam, Lucile Amrouche, Marc Andronikof, Dany Anglicheau, Nadia Anguel, Djillali Annane, Mohammed Aounzou, Caroline Aparicio, Gladys Aratus, Jean-Benoit Arlet, Jeremy Arzoine, Elisabeth Aslangul, Mona Assefi, Adeline Aubry, Laetitia Audiffred, Etienne Audureau, Christelle Nathalie Auger, Jean-Charles Auregan, Celine Awotar, Sonia Ayllon Milla, Delphine Azan, Laurene Azemar, Billal Azzouguen, Marwa Bachir Elrufaai, Aïda Badsi, Prissile Bakouboula, Coline Balcerowiak, Fanta Balde, Elodie Baldivia, Eliane-Flore Bangamingo, Amandine Baptiste, Fanny Baran-Marszak, Caroline Barau, Nathalie Barget, Flore Baronnet, Romain Barthelemy, Jean-Luc Baudel, Camille Baudry, Elodie Baudry, Laurent Beaugerie, Adel Belamri, Nicolas Belaube, Rhida Belilita, Pierre Bellassen, Rawan Belmokhtar, Isabel Beltran, Ruben Benainous, Mourad Benallaoua, Robert Benamouzig, Amélie Benbara, Jaouad Benhida, Anis Benkhelouf, Jihene Benlagha, Chahinez Benmostafa, Skander Benothmane, Miassa Bentifraouine, Laurence Berard, Quentin Bernier, Enora Berti, Astrid Bertier, Laure Berton, Simon Bessis, Alexandra Beurton, Celine Bianco, Clara Bianquis, Frank Bidar, Philippe Blanche, Clarisse Blayau, Alexandre Bleibtreu, Emmanuelle Blin, Coralie Bloch-Queyrat, Marie-Christophe Boissier, Diane Bollens, Marion Bolzoni, Rudy pierre Bompard, Nicolas Bonnet, Justine Bonnouvrier, Shirmonecrystal Botha, Wissam Boucenna, Fatiha Bouchama, Olivier Bouchaud, Hanane Bouchghoul, Taoueslylia Boudjebla, Noel Boudjema, Catherine Bouffard, Adrien Bougle, Meriem Bouguerra, Leila Bouras, Agnes Bourcier, Anne Bourgarit Durand, Anne Bourrier, Fabrice Bouscarat, Diane Bouvry, Nesrine Bouziri, Ons Bouzrara, Sarah Bribier, Delphine Brugier, Melanie Brunel, Eida Bui, Anne Buisson, Iryna Bukreyeva, Côme Bureau, Jacques Cadranel, Johann Cailhol, Ruxandra Calin, Clara Campos Vega, Pauline Canavaggio, Marta Cancella, Delphine Cantin, Albert Cao, Lionel Carbillon, Nicolas Carlier, Clementine Cassard, Guylaine Castor, Marion Cauchy, Olivier Cha, Benjamin Chaigne, Salima Challal, Karine Champion, Patrick Chariot, Julie Chas, Simon Chauveau, Anthony Chauvin, Clement Chauvin, Nathalie Chavarot, Kamélia Chebbout, Mustapha Cherai, Ilaria Cherubini, Amelie Chevalier, Thibault Chiarabini, Thierry Chinet, Richard Chocron, Pascaline Choinier, Juliette Chommeloux, Christophe Choquet, Laure Choupeaux, Benjamin Chousterman, Dragosmarius Ciocan, Ada Clarke, Gaëlle Clavere, Florian Clavier, Karine Clement, Sebastien Clerc, Yves Cohen, Fleur Cohen, Adrien Cohen, Audrey Coilly, Hester Colboc, Pauline Colin, Magalie Collet, Chloé Comarmond, Emeline Combacon, Alain Combes, Celine Comparon, Jean-Michel Constantin, Hugues Cordel, Anne-Gael Cordier, Adrien Costantini, Nathalie Costedoat Chalumeau, Camille Couffignal, Doriane Coupeau, Alain Creange, Yannie Cuvillier Lamarre, Charlène Da Silveira, Sandrine Dautheville Guibal El Kayani, Nathalie De Castro, Yann De Rycke, Lucie Del Pozo, Quentin Delannoy, Mathieu Delay, Robin Deleris, Juliette Delforge, Laëtitia Delphine, Noemie Demare, Sophie Demeret, Alexandre Demoule, Aurore Deniau, François Depret, Sophie Derolez, Ouda Derradji, Nawal Derridj, Vincent Descamps, Lydia Deschamps, Celine Desconclois, Cyrielle Desnos, Karine Desongins, Robin Dhote, Benjamin Diallo, Morgane Didier, Myriam Diemer, Stephane Diez, Juliette Djadi-Prat, Fatima-Zohra Djamouri Monnory, Siham Djebara, Naoual Djebra, Minette Djietcheu, Hadjer Djillali, Nouara Djouadi, Severine Donneger, Catarina Dos Santos, Nathalie Dournon, Martin Dres, Laura Droctove, Marie Drogrey, Margot Dropy, Elodie Drouet, Valérie Dubosq, Evelyne Dubreucq, Estelle Dubus, Boris Duchemann, Thibault Duchenoy, Emmanuel Dudoignon, Romain Dufau, Florence Dumas, Clara Duran, Emmanuelle Duron, Antoine Durrbach, Claudine Duvivier, Nathan Ebstein, Jihane El Khalifa, Alexandre Elabbadi, Caroline Elie, Gabriel Ernotte, Anne Esling, Martin Etienne, Xavier Eyer, Muriel Sarah Fartoukh, Takoua Fayali, Marion Fermaut, Arianna Fiorentino, Souha Fliss, Marie-Céline Fournier, Benjamin Fournier, Hélène Francois, Olivia Freynet, Yvann Frigout, Isaure Fromont, Axelle Fuentes, Thomas Furet, Joris Galand, Marc Garnier, Agnes Gaubert, Stéphane Gaudry, Samuel Gaugain, Damien Gauthier, Maxime Gautier, Sophie Georgin-Lavialle, Daniela Geromin, Mohamed Ghalayini, Bijan Ghaleh, Myriam Ghezal, Aude Gibelin, Linda Gimeno, Benoit Girard, Bénédicte Giroux Leprieur, Doryan Gomes, Elisabete Gomes-Pires, Anne Gouge, Amel Gouja, Helene Goulet, Sylvain Goupil, Jeanne Goupil De Bouille, Julien Gras, Segolene Greffe, Lamiae Grimaldi, Paul Guedeney, Bertrand Guidet, Matthias Guillo, Mariechristelle Gulczynski, Tassadit Hadjam, Didier Haguenauer, Soumeya Hammal, Nadjib Hammoudi, Olivier Hanon, Anarole Harrois, Coraline Hautem, Guillaume Hekimian, Nicholas Heming, Olivier Hermine, Sylvie Ho, Marie Houllier, Benjamin Huot, Tessa Huscenot, Wafa Ibn Saied, Ghilas Ikherbane, Meriem Imarazene, Patrick Ingiliz, Lina Iratni, Stephane Jaureguiberry, Jean-Francois Jean-Marc, Deleena Jeyarajasingham, Pauline Jouany, Veronique Jouis, Clement Jourdaine, Ouifiya Kafif, Rim Kallala, Sandrine Katsahian, Lilit Kelesyan, Vixra Keo, Flora Ketz, Warda Khamis, Enfel Khelili, Mehdi Khellaf, Christy Gaëlla Kotokpo Youkou, Ilias Kounis, Gaelle Kpalma, Jessica Krause, Vincent Labbe, Karine Lacombe, Jean-Marc Lacorte, Anne Gaelle Lafont, Emmanuel Lafont, Lynda Lagha, Lionel Lamhaut, Aymeric Lancelot, Cecilia Landman, Fanny Lanternier, Cecile Larcheveque, Caroline Lascoux Combe, Ludovic Lassel, Benjamin Laverdant, Christophe Lavergne, Jean-Rémi Lavillegrand, Pompilia Lazureanu, Loïc Le Guennec, Lamia Leberre, Claire Leblanc, Marion Leboyer, Francois Lecomte, Marine Lecorre, Romain Leenhardt, Marylou Lefebvre, Bénédicte Lefebvre, Paul Legendre, Anne Leger, Laurence Legros, Justyna Legrosse, Sébastien Lehuunghia, Julien Lemarec, Jeremie Leporrier-Ext, Manon Lesein, Hubert Lesur, Vincent Levy, Albert Levy, Edwige Lopes, Amanda Lopes, Vanessa Lopez, Julien Lopinto, Olivier Lortholary, Badr Louadah, Bénédicte Loze, Marie-Laure Lucas, Axelle Lucasamichi, Liem Binh Luong, Arouna Magazimama-Ext, David Maingret, Lakhdar Mameri, Philippe Manivet, Cylia Mansouri, Estelle Marcault, Jonathan Marey, Nathalie Marin, Clémence Marois, Olivier Martin, Lou Martineau, Cannelle Martinez-Lopez, Pierre Martyniuck, Pauline Mary De Farcy, Nessrine Marzouk, Rafik Masmoudi, Alexandre Mebazaa, Frédéric Mechai, Fabio Mecozzi, Chamseddine Mediouni, Bruno Megarbane, Mohamed Meghadecha, Élodie Mejean, Arsene Mekinian, Nour Mekki Abdelhadi, Rania Mekni, Thinhinan Sabrina Meliti, Breno Melo Lima, Paris Meng, Soraya Merbah, Fadhila Messani, Yasmine Messaoudi, Baboo-Irwinsingh Mewasing, Lydia Meziane, Carole Michelot-Burger, Françoise Mignot, Fadi Hillary Minka, Makoto Miyara, Pierre Moine, Jean-Michel Molina, Anaïs Montegnies-Boulet, Alexandra Monti, Claire Montlahuc, Anne-Lise Montout, Alexandre Moores, Caroline Morbieu, Helene Mortelette, Stéphane Mouly, Rosita Muzaffar, Cherifa Iness Nacerddine, Marine Nadal, Hajer Nadif, Kladoum Nassarmadji, Pierre Natella, Sandrine Ndingamondze, Stefan Neraal, Caroline Nguyen, Bao N'Guyen, Isabelle Nion Larmurier, Luc Nlomenyengue, Nicolas Noel, Hilario Nunes, Edris Omar, Zineb Ouazene, Elise Ouedraogo, Wassila Ouelaa, Anissa Oukhedouma, Yasmina Ould Amara, Herve Oya, Johanna Oziel, Thomas Padilla, Elena Paillaud, Solenne Paiva, Beatrice Parfait, Perrine Parize, Christophe Parizot, Antoine Parrot, Arthur Pavot, Laetitia Peaudecerf, Frédéric Pene, Marion Pepin, Julie Pernet, Claire Pernin, Mylène Petit, Olivier Peyrony, Marie-Pierre Pietri, Olivia Pietri, Marc Pineton De Chambrun, Michelle Pinson, Claire Pintado, Valentine Piquard, Christine Pires, Benjamin Planquette, Sandrine Poirier, Anne-Laure Pomel, Stéphanie Pons, Diane Ponscarme, Annegaelle Pourcelot, Valérie Pourcher, Anne Pouvaret, Florian Prever, Miresta Previlon, Margot Prevost, Marie-Julie Provoost, Cyril Quemeneur, Cédric Rafat, Agathe Rami, Brigitte Ranque, Maurice Raphael, Jean Herle Raphalen, Anna Rastoin, Mathieu Raux, Amani Rebai, Michael Reby, Alexis Regent, Asma Regrag, Matthieu Resche-Rigon, Quentin Ressaire, Christian Richard, Mariecaroline Richard, Maxence Robert, Benjamin Rohaut, Camille Rolland-Debord, Jacques Ropers, Anne-Marie Roque-Afonso, Charlotte Rosso, Mélanie Rousseaux, Nabila Rousseaux, Swasti Roux, Lorène Roux, Claire Rouzaud, Antoine Rozes, Emma Rubenstein, Jean-Marc Sabate, Sheila Sabet, Sophie-Caroline Sacleux, Nathalie Saidenberg Kermanach, Faouzi Saliba, Dominique Salmon, Laurent Savale, Guillaume Savary, Rebecca Sberro, Anne Scemla, Frederic Schlemmer, Mathieu Schwartz, Saïd Sedfi, Samia Sefir-Kribel, Philippe Seksik, Pierre Sellier, Agathe Selves, Nicole Sembach, Luca Semerano, Marie-Victoire Senat, Damien Sene, Alexandra Serris, Lucile Sese, Naima Sghiouar, Johanna Sigaux, Martin Siguier, Johanne Silvain, Noémie Simon, Tabassome Simon, Lina Innes Skandri, Miassa Slimani, Aurélie Snauwaert, Harry Sokol, Heithem Soliman, Nisrine Soltani, Benjamin Soyer, Gabriel Steg, Lydia Suarez, Tali-Anne Szwebel, Kossi Taffame, Yacine Tandjaoui-Lambiotte, Claire Tantet, Mariagrazia Tateo, Igor Theodose, Pierre clement Thiebaud, Caroline Thomas, Kelly Tiercelet, Julie Tisserand, Carole Tomczak, Krystel Torelino, Fatima Touam-Ext, Lilia Toumi, Gustave Toury, Mireille Toy-Miou, Olivia Tran Dinh Thanh Lien, Alexy Trandinh, Jean-Marc Treluyer, Baptiste Trinque, Jennifer Truchot, Sarah Tubiana, Simone Tunesi, Matthieu Turpin, Agathe Turpin, Tomas Urbina, Rafael Usubillaga Narvaez, Yurdagul Uzunhan, Prabakar Vaittinadaayar, Arnaud Valent, Maelle Valentian, Nadia Valin, Hélène Vallet, Marina Vaz, Miguel-Alejandro Vazquezibarra, Benoit Vedie, Laetitia Velly, Celine Verstuyft, Cedric Viallette, Eric Vicaut, Dorothee Vignes, Damien Vimpere, Myriam Virlouvet, Guillaume Voiriot, Lena Voisot, Emmanuel Weiss, Nicolas Weiss, Anaïs Winchenne, Youri Yordanov, Lara Zafrani, Mohamad Zaidan, Wissem Zaidi, Cathia Zak, Aida Zarhrate-Ghoul, Ouassila Zatout, Suzanne Zeino, Michel Zeitouni, Naïma Zemirli, Lorene Zerah, Ounsa Zia, Marianne Ziol, Oceane Zolario, Julien Zuber, Claire Andrejak, François Angoulvant, Delphine Bachelet, Marie Bartoli, Romain Basmaci, Sylvie Behillil, Marine Beluze, Dehbia Benkerrou, Krishna Bhavsar, Lila Bouadma, Sabelline Bouchez, Maude Bouscambert, Minerva Cervantes-Gonzalez, Anissa Chair, Catherine Chirouze, Alexandra Coelho, Sandrine Couffin-Cadiergues, Eric d’Ortenzio, Marie-Pierre Debray, Laurene Deconinck, Dominique Deplanque, Diane Descamps, Mathilde Desvallée, Alpha Diallo, Alphonsine Diouf, Céline Dorival, François Dubos, Brigitte Elharrar, Vincent Enouf, Hélène Esperou, Marina Esposito-Farese, Manuel Etienne, Eglantine Ferrand Devouge, Nathalie Gault, Alexandre Gaymard, Tristan Gigante, Morgane Gilg, Jérémie Guedj, Alexandre Hoctin, Isabelle Hoffmann, Ikram Houas, Jean-Sébastien Hulot, Salma Jaafoura, Florentia Kaguelidou, Sabrina Kali, Antoine Khalil, Coralie Khan, Cédric Laouénan, Samira Laribi, Minh Le, Quentin Le Hingrat, Soizic Le Mestre, Hervé Le Nagard, François-Xavier Lescure, Sophie Letrou, Yves Levy, Bruno Lina, Guillaume Lingas, Jean-Christophe Lucet, Denis Malvy, Marina Mambert, Amina Meziane, Hugo Mouquet, Jimmy Mullaert, Nadège Neant, Duc Nguyen, Marion Noret, Saad Nseir, Aurélie Papadopoulos, Christelle Paul, Nathan Peiffer-Smadja, Thomas Perpoint, Ventzislava Petrov-Sanchez, Gilles Peytavin, Huong Pham, Olivier Picone, Oriane Puéchal, Christian Rabaud, Manuel Rosa-Calatrava, Bénédicte Rossignol, Patrick Rossignol, Carine Roy, Marion Schneider, Richa Su, Coralie Tardivon, Marie-Capucine Tellier, François Téoulé, Olivier Terrier, Jean-François Timsit, Christelle Tual, Sylvie Van Der Werf, Noémie Vanel, Aurélie Veislinger, Benoit Visseaux, Aurélie Wiedemann, Yazdan Yazdanpanah, Loubna Alavoine, Charlotte Charpentier, Aline Dechanet, Jean-Luc Ecobichon, Wahiba Frezouls, Nadhira Houhou, Jonathan Lehacaut, Pauline Manchon, Mariama Nouroudine, Caroline Quintin, Michael Thy, Sylvie van der Werf, Valérie Vignali, Abir Chahine, Nawal Waucquier, Maria-Claire Migaud, Félix Djossou, Mayka Mergeay-Fabre, Aude Lucarelli, Magalie Demar, Léa Bruneau, Patrick Gérardin, Adrien Maillot, Christine Payet, Bruno Laviolle, Fabrice Laine, Christophe Paris, Mireille Desille-Dugast, Julie Fouchard, Thierry Pistone, Pauline Perreau, Valérie Gissot, Carole L.E. Goas, Samatha Montagne, Lucie Richard, Kévin Bouiller, Maxime Desmarets, Alexandre Meunier, Marilou Bourgeon, Benjamin Lefévre, Hélène Jeulin, Karine Legrand, Sandra Lomazzi, Bernard Tardy, Amandine Gagneux-Brunon, Frédérique Bertholon, Elisabeth Botelho-Nevers, Christelle Kouakam, Leturque Nicolas, Layidé Roufai, Karine Amat, Hélène Espérou, Samia Hendou, Giuseppe Foti, Giuseppe Citerio, Ernesto Contro, Alberto Pesci, Maria Grazia Valsecchi, Marina Cazzaniga, Giacomo Bellani, Jorge Abad, Giulia Accordino, Micol Angelini, Sergio Aguilera-Albesa, Aina Aguiló-Cucurull, Esra Akyüz Özkan, Ilad Alavi Darazam, Jonathan Antonio Roblero Albisures, Juan C. Aldave, Miquel Alfonso Ramos, Taj Ali Khan, Anna Aliberti, Seyed Alireza Nadji, Gulsum Alkan, Suzan A. AlKhater, Jerome Allardet-Servent, Luis M. Allende, Rebeca Alonso-Arias, Mohammed S. Alshahrani, Laia Alsina, Zahir Amoura, Arnau Antolí, Romain Arrestier, Mélodie Aubart, Teresa Auguet, Iryna Avramenko, Gökhan Aytekin, Axelle Azot, Seiamak Bahram, Fanny Bajolle, Fausto Baldanti, Aurélie Baldolli, Maite Ballester, Benoit Barrou, Federica Barzaghi, Sabrina Basso, Gulsum Iclal Bayhan, Liliana Bezrodnik, Agurtzane Bilbao, Geraldine Blanchard-Rohner, Ignacio Blanco, Adeline Blandinières, Daniel Blázquez-Gamero, Marketa Bloomfield, Mireia Bolivar-Prados, Raphael Borie, Elisabeth Botdhlo-Nevers, Aurore Bousquet, David Boutolleau, Claire Bouvattier, Oksana Boyarchuk, Juliette Bravais, M. Luisa Briones, Marie-Eve Brunner, Raffaele Bruno, Maria Rita P. Bueno, Huda Bukhari, Jacinta Bustamante, Juan José Cáceres Agra, Ruggero Capra, Raphael Carapito, Maria Carrabba, Carlos Casasnovas, Marion Caseris, Irene Cassaniti, Martin Castelle, Francesco Castelli, Martín Castillo de Vera, Mateus V. Castro, Emilie Catherinot, Jale Bengi Celik, Alessandro Ceschi, Martin Chalumeau, Bruno Charbit, Cécile Boulanger, Père Clavé, Bonaventura Clotet, Anna Codina, Cloé Comarmond, Patrizia Comoli, Angelo G. Corsico, Taner Coşkuner, Aleksandar Cvetkovski, Cyril Cyrus, David Dalmau, François Danion, David Ross Darley, Vincent Das, Nicolas Dauby, Stéphane Dauger, Paul De Munte, Loic de Pontual, Amin Dehban, Geoffroy Delplancq, Isabelle Desguerre, Antonio Di Sabatino, Jean-Luc Diehl, Stephanie Dobbelaere, Elena Domínguez-Garrido, Clément Dubost, Olov Ekwall, Şefika Elmas Bozdemir, Marwa H. Elnagdy, Melike Emiroglu, Akifumi Endo, Emine Hafize Erdeniz, Selma Erol Aytekin, Maria Pilar Etxart Lasa, Romain Euvrard, Giovanna Fabio, Laurence Faivre, Antonin Falck, Muriel Fartoukh, Morgane Faure, Miguel Fernandez Arquero, Ricard Ferrer, Jose Ferreres, Bruno Francois, Victoria Fumadó, Kitty S.C. Fung, Francesca Fusco, Alenka Gagro, Blanca Garcia Solis, Pierre Garçon, Pascale Gaussem, Zeynep Gayretli, Juana Gil-Herrera, Laurent Gilardin, Audrey Giraud Gatineau, Mònica Girona-Alarcón, Karen Alejandra Cifuentes Godínez, Jean-Christophe Goffard, Nacho Gonzales, Luis I. Gonzalez-Granado, Rafaela González-Montelongo, Antoine Guerder, Belgin Gülhan, Victor Daniel Gumucio, Leif Gunnar Hanitsch, Jan Gunst, Marta Gut, Jérôme Hadjadj, Selda Hancerli, Tetyana Hariyan, Nevin Hatipoglu, Deniz Heppekcan, Elisa Hernandez-Brito, Po-ki Ho, María Soledad Holanda-Peña, Juan P. Horcajada, Sami Hraiech, Linda Humbert, Ivan F.N. Hung, Alejandro D. Iglesias, Antonio Íñigo-Campos, Matthieu Jamme, María Jesús Arranz, Marie-Thérèse Jimeno, Iolanda Jordan, Saliha Kanık-Yüksek, Yalcin Kara, Aydın Karahan, Adem Karbuz, Kadriye Kart Yasar, Ozgur Kasapcopur, Kenichi Kashimada, Sevgi Keles, Yasemin Kendir Demirkol, Yasutoshi Kido, Can Kizil, Ahmet Osman Kılıç, Adam Klocperk, Antonia Koutsoukou, Zbigniew J. Król, Hatem Ksouri, Paul Kuentz, Arthur M.C. Kwan, Yat Wah M. Kwan, Janette S.Y. Kwok, Jean-Christophe Lagier, David S.Y. Lam, Vicky Lampropoulou, Fleur Le Bourgeois, Yee-Sin Leo, Rafael Leon Lopez, Daniel Leung, Michael Levin, Michael Levy, Romain Lévy, Zhi Li, Daniele Lilleri, Edson Jose Adrian Bolanos Lima, Agnes Linglart, Eduardo López-Collazo, José M. Lorenzo-Salazar, Céline Louapre, Catherine Lubetzki, Kwok-Cheung Lung, Charles-Edouard Luyt, David C. Lye, Cinthia Magnone, Enrico Marchioni, Carola Marioli, Majid Marjani, Laura Marques, Jesus Marquez Pereira, Andrea Martín-Nalda, David Martínez Pueyo, Javier Martinez-Picado, Iciar Marzana, Carmen Mata-Martínez, Alexis Mathian, Larissa R.B. Matos, Gail V. Matthews, Julien Mayaux, Raquel McLaughlin-Garcia, Philippe Meersseman, Jean-Louis Mège, Armand Mekontso-Dessap, Isabelle Melki, Federica Meloni, Jean-François Meritet, Paolo Merlani, Özge Metin Akcan, Mehdi Mezidi, Isabelle Migeotte, Maude Millereux, Matthieu Million, Tristan Mirault, Clotilde Mircher, Mehdi Mirsaeidi, Yoko Mizoguchi, Bhavi P. Modi, Francesco Mojoli, Elsa Moncomble, Abián Montesdeoca Melián, Antonio Morales Martinez, Francisco Morandeira, Pierre-Emmanuel Morange, Clémence Mordacq, Guillaume Morelle, Stéphane J. Mouly, Adrián Muñoz-Barrera, Cyril Nafati, Shintaro Nagashima, Yu Nakagama, Bénédicte Neven, João Farela Neves, Yuk-Yung Ng, Hubert Nielly, Yeray Novoa Medina, Esmeralda Nuñez Cuadros, Semsi Nur Karabela, J. Gonzalo Ocejo-Vinyals, Mehdi Oualha, Amani Ouedrani, Tayfun Özçelik, Aslinur Ozkaya-Parlakay, Michele Pagani, Maria Papadaki, Philippe Parola, Tiffany Pascreau, Stéphane Paul, Estela Paz-Artal, Sigifredo Pedraza, Nancy Carolina González Pellecer, Silvia Pellegrini, Rebeca Pérez de Diego, Xosé Luis Pérez-Fernández, Aurélien Philippe, Quentin Philippot, Adrien Picod, Marc Pineton de Chambrun, Antonio Piralla, Laura Planas-Serra, Dominique Ploin, Julien Poissy, Géraldine Poncelet, Garyphallia Poulakou, Marie S. Pouletty, Persia Pourshahnazari, Jia Li Qiu-Chen, Paul Quentric, Thomas Rambaud, Didier Raoult, Violette Raoult, Anne-Sophie Rebillat, Claire Redin, Léa Resmini, Pilar Ricart, Jean-Christophe Richard, Raúl Rigo-Bonnin, Nadia Rivet, Jacques G. Rivière, Gemma Rocamora-Blanch, Mathieu P. Rodero, Carlos Rodrigo, Luis Antonio Rodriguez, Carlos Rodriguez-Gallego, Agustí Rodriguez-Palmero, Carolina Soledad Romero, Anya Rothenbuhler, Damien Roux, Nikoletta Rovina, Flore Rozenberg, Yvon Ruch, Montse Ruiz, Maria Yolanda Ruiz del Prado, Juan Carlos Ruiz-Rodriguez, Joan Sabater-Riera, Kai Saks, Maria Salagianni, Oliver Sanchez, Adrián Sánchez-Montalvá, Silvia Sánchez-Ramón, Laire Schidlowski, Agatha Schluter, Julien Schmidt, Matthieu Schmidt, Catharina Schuetz, Cyril E. Schweitzer, Francesco Scolari, Luis Seijo, Analia Gisela Seminario, Piseth Seng, Sevtap Senoglu, Mikko Seppänen, Alex Serra Llovich, Virginie Siguret, Eleni Siouti, David M. Smadja, Nikaia Smith, Ali Sobh, Xavier Solanich, Jordi Solé-Violán, Catherine Soler, Betül Sözeri, Giulia Maria Stella, Yuriy Stepanovskiy, Annabelle Stoclin, Fabio Taccone, Jean-Luc Taupin, Simon J. Tavernier, Loreto Vidaur Tello, Benjamin Terrier, Guillaume Thiery, Karolina Thorn, Caroline Thumerelle, Imran Tipu, Martin Tolstrup, Gabriele Tomasoni, Julie Toubiana, Josep Trenado Alvarez, Vasiliki Triantafyllia, Jesús Troya, Owen T.Y. Tsang, Liina Tserel, Eugene Y.K. Tso, Alessandra Tucci, Şadiye Kübra Tüter Öz, Matilde Valeria Ursini, Takanori Utsumi, Pierre Vabres, Juan Valencia-Ramos, Ana Maria Van Den Rym, Isabelle Vandernoot, Valentina Velez-Santamaria, Silvia Patricia Zuniga Veliz, Mateus C. Vidigal, Sébastien Viel, Cédric Villain, Marie E. Vilaire-Meunier, Judit Villar-García, Audrey Vincent, Dimitri Van der Linden, Alla Volokha, Fanny Vuotto, Els Wauters, Alan K.L. Wu, Tak-Chiu Wu, Aysun Yahşi, Osman Yesilbas, Mehmet Yildiz, Barnaby E. Young, Ufuk Yükselmiş, Marco Zecca, Valentina Zuccaro, Jens Van Praet, Bart N. Lambrecht, Eva Van Braeckel, Cédric Bosteels, Levi Hoste, Eric Hoste, Fré Bauters, Jozefien De Clercq, Catherine Heijmans, Hans Slabbynck, Leslie Naesens, Benoit Florkin, Mary-Anne Young, Amanda Willis, Paloma Lapuente-Suanzes, Ana de Andrés-Martín, Matilda Berkell, Valerio Carelli, Alessia Fiorentino, Surbhi Malhotra, Alessandro Mattiaccio, Tommaso Pippucci, Marco Seri, Evelina Tacconelli, Michiel van Agtmael, Anne Geke Algera, Brent Appelman, Frank van Baarle, Diane Bax, Martijn Beudel, Harm Jan Bogaard, Marije Bomers, Peter Bonta, Lieuwe Bos, Michela Botta, Justin de Brabander, Godelieve de Bree, Sanne de Bruin, David T.P. Buis, Marianna Bugiani, Esther Bulle, Osoul Chouchane, Alex Cloherty, Mirjam Dijkstra, Dave A. Dongelmans, Romein W.G. Dujardin, Paul Elbers, Lucas Fleuren, Suzanne Geerlings, Theo Geijtenbeek, Armand Girbes, Bram Goorhuis, Martin P. Grobusch, Florianne Hafkamp, Laura Hagens, Jorg Hamann, Vanessa Harris, Robert Hemke, Sabine M. Hermans, Leo Heunks, Markus Hollmann, Janneke Horn, Joppe W. Hovius, Menno D. de Jong, Rutger Koning, Endry H.T. Lim, Niels van Mourik, Jeaninne Nellen, Esther J. Nossent, Frederique Paulus, Edgar Peters, Dan A.I. Pina-Fuentes, Tom van der Poll, Bennedikt Preckel, Jan M. Prins, Jorinde Raasveld, Tom Reijnders, Maurits C.F. J. de Rotte, Michiel Schinkel, Marcus J. Schultz, Femke A.P. Schrauwen, Alex Schuurmans, Jaap Schuurmans, Kim Sigaloff, Marleen A. Slim, Patrick Smeele, Marry Smit, Cornelis S. Stijnis, Willemke Stilma, Charlotte Teunissen, Patrick Thoral, Anissa M. Tsonas, Pieter R. Tuinman, Marc van der Valk, Denise P. Veelo, Carolien Volleman, Heder de Vries, Lonneke A. Vught, Michèle van Vugt, Dorien Wouters, A.H. Zwinderman, Matthijs C. Brouwer, W. Joost Wiersinga, Alexander P.J. Vlaar, Miranda F. Tompkins, Camille Alba, Daniel N. Hupalo, John Rosenberger, Gauthaman Sukumar, Matthew D. Wilkerson, Xijun Zhang, Justin Lack, Andrew J. Oler, Kerry Dobbs, Ottavia M. Delmonte, Jeffrey J. Danielson, Andrea Biondi, Laura Rachele Bettini, Mariella D’Angiò, Ilaria Beretta, Luisa Imberti, Alessandra Sottini, Virginia Quaresima, Eugenia Quiros-Roldan, Camillo Rossi, Riccardo Castagnoli, Daniela Montagna, Amelia Licari, and Gian Luigi Marseglia

Subjects
HLA, association, asymptomatic infection, COVID-19, population stratification, Genetics, QH426-470
Abstract

Summary: Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B∗15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B∗15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the United States (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B∗15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections studied, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified.

Published
2024
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24. BaIT: Barometer for Information Trustworthiness

Author

Nolan, Oisín, van Mourik, Jeroen, and Tilbury, Callum Rhys

Subjects
Computer Science - Machine Learning, Computer Science - Computation and Language
Abstract

This paper presents a new approach to the FNC-1 fake news classification task which involves employing pre-trained encoder models from similar NLP tasks, namely sentence similarity and natural language inference, and two neural network architectures using this approach are proposed. Methods in data augmentation are explored as a means of tackling class imbalance in the dataset, employing common pre-existing methods and proposing a method for sample generation in the under-represented class using a novel sentence negation algorithm. Comparable overall performance with existing baselines is achieved, while significantly increasing accuracy on an under-represented but nonetheless important class for FNC-1.

Published
2022

25. Native qudit entanglement in a trapped ion quantum processor

Author

Hrmo, Pavel, Wilhelm, Benjamin, Gerster, Lukas, van Mourik, Martin W., Huber, Marcus, Blatt, Rainer, Schindler, Philipp, Monz, Thomas, and Ringbauer, Martin

Subjects
Quantum Physics
Abstract

Quantum information carriers, just like most physical systems, naturally occupy high-dimensional Hilbert spaces. Instead of restricting them to a two-level subspace, these high-dimensional (qudit) quantum systems are emerging as a powerful resource for the next generation of quantum processors. Yet harnessing the potential of these systems requires efficient ways of generating the desired interaction between them. Here, we experimentally demonstrate an implementation of a native two-qudit entangling gate in a trapped-ion qudit system up to dimension $5$. This is achieved by generalizing a recently proposed light-shift gate mechanism to generate genuine qudit entanglement in a single application of the gate. The gate seamlessly adapts to the local dimension of the system with a calibration overhead that is independent of the dimension., Comment: 9 pages, 5 figures

Published
2022
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26. Mixed Chiral and Achiral Character in Substituted Ethane: A Next Generation QTAIM Perspective

Author

Li, Zi, Xu, Tianlv, Früchtl, Herbert, van Mourik, Tanja, Kirk, Steven Robert, and Jenkins, Samantha

Subjects
Physics - Chemical Physics
Abstract

We use the newly introduced spanning stress tensor trajectory $U_{\sigma}$-space construction within next generation quantum theory of atoms in molecules (NG-QTAIM) for a chirality investigation of singly and doubly substituted ethane with halogen substituents: F, Cl, Br. A lack of achiral character in $U_{\sigma}$-space was discovered for singly substituted ethane. The resultant axial bond critical point (BCP) sliding responded more strongly to the increase in atomic number of the substituted halogen than the chirality. The presence of the very light F atom was found responsible for a very high degree of achiral character of the doubly substituted ethane., Comment: arXiv admin note: substantial text overlap with arXiv:2203.09750

Published
2022
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27. Chiral and Steric Effects in Ethane: A Next Generation QTAIM Interpretation

Author

Li, Zi, Xu, Tianlv, Früchtl, Herbert, van Mourik, Tanja, Kirk, Steven R., and Jenkins, Samantha

Subjects
Physics - Chemical Physics
Abstract

We introduce a development of next generation quantum theory of atoms in molecules (NG-QTAIM) for an investigation of the chirality of ethane and discover a $Q_{\sigma}$ isomer in addition to $S_{\sigma}$ and $R_{\sigma}$ stereoisomers in the stress tensor trajectory $U_{\sigma}$-space. The $Q_{\sigma}$ isomer is defined to be a 'null-isomer' since the value of the chirality-helicity function $\approx 0$. The presence of chiral contributions suggests that steric effects, rather than hyper-conjugation, explain the staggered geometry of ethane. The steric effects, within the NG-QTAIM interpretation, are reduced by a factor of two using an applied electric-field directed down a C-H bond.

Published
2022
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28. Experimental Bayesian calibration of trapped ion entangling operations

Author

Gerster, Lukas, Martínez-García, Fernando, Hrmo, Pavel, van Mourik, Martin, Wilhelm, Benjamin, Vodola, Davide, Müller, Markus, Blatt, Rainer, Schindler, Philipp, and Monz, Thomas

Subjects
Quantum Physics
Abstract

The performance of quantum gate operations is experimentally determined by how correct operational parameters can be determined and set, and how stable these parameters can be maintained. In addition, gates acting on different sets of qubits require unique sets of control parameters. Thus, an efficient multi-dimensional parameter estimation procedure is crucial to calibrate even medium sized quantum processors. Here, we develop and characterize an efficient calibration protocol to automatically estimate and adjust experimental parameters of the widely used Molmer-Sorensen entangling gate operation in a trapped ion quantum information processor. The protocol exploits Bayesian parameter estimation methods which includes a stopping criterion based on a desired gate infidelity. We experimentally demonstrate a median gate infidelity of $1.3(1)\cdot10^{-3}$, requiring only $1200\pm500$ experimental cycles, while completing the entire gate calibration procedure in less than one minute. This approach is applicable to other quantum information processor architectures with known or sufficiently characterized theoretical models., Comment: 20 pages, 11 figures; Fixed typo in abstract

Published
2021
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29. Phenotypic immune characterization of gastric and esophageal adenocarcinomas reveals profound immune suppression in esophageal tumor locations

Author

Tessa S. Groen-van Schooten, Micaela Harrasser, Jens Seidel, Emma N. Bos, Tania Fleitas, Monique van Mourik, Roos E. Pouw, Ruben S. A. Goedegebuure, Benthe H. Doeve, Jasper Sanders, Joris Bos, Mark I. van Berge Henegouwen, Victor L. J. L. Thijssen, Nicole C. T. van Grieken, Hanneke W. M. van Laarhoven, Tanja D. de Gruijl, and Sarah Derks

Subjects
tumor microenvironment, single cell flow cytometry, biomarkers, HER2, MSI, Immunologic diseases. Allergy, RC581-607
Abstract

BackgroundTumors in the distal esophagus (EAC), gastro-esophageal junction including cardia (GEJAC), and stomach (GAC) develop in close proximity and show strong similarities on a molecular and cellular level. However, recent clinical data showed that the effectiveness of chemo-immunotherapy is limited to a subset of GEAC patients and that EACs and GEJACs generally benefit less from checkpoint inhibition compared to GACs. As the composition of the tumor immune microenvironment drives response to (immuno)therapy we here performed a detailed immune analysis of a large series of GEACs to facilitate the development of a more individualized immunomodulatory strategy.MethodsExtensive immunophenotyping was performed by 14-color flow cytometry in a prospective study to detail the immune composition of untreated gastro-esophageal cancers (n=104) using fresh tumor biopsies of 35 EACs, 38 GEJACs and 31 GACs. The immune cell composition of GEACs was characterized and correlated with clinicopathologic features such as tumor location, MSI and HER2 status. The spatial immune architecture of a subset of tumors (n=30) was evaluated using multiplex immunohistochemistry (mIHC) which allowed us to determine the tumor infiltration status of CD3+, CD8+, FoxP3+, CD163+ and Ki67+ cells.ResultsImmunophenotyping revealed that the tumor immune microenvironment of GEACs is heterogeneous and that immune suppressive cell populations such as monocytic myeloid-derived suppressor cells (mMDSC) are more abundant in EACs compared to GACs (p

Published
2024
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30. The augmented value of using clinical notes in semi-automated surveillance of deep surgical site infections after colorectal surgery

Author

Janneke D.M. Verberk, Suzanne D. van der Werff, Rebecka Weegar, Aron Henriksson, Milan C. Richir, Christian Buchli, Maaike S.M. van Mourik, and Pontus Nauclér

Subjects
Automated surveillance, Algorithm, Colorectal surgery, Healthcare-associated infections, Natural language processing, Surgical site infections, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background In patients who underwent colorectal surgery, an existing semi-automated surveillance algorithm based on structured data achieves high sensitivity in detecting deep surgical site infections (SSI), however, generates a significant number of false positives. The inclusion of unstructured, clinical narratives to the algorithm may decrease the number of patients requiring manual chart review. The aim of this study was to investigate the performance of this semi-automated surveillance algorithm augmented with a natural language processing (NLP) component to improve positive predictive value (PPV) and thus workload reduction (WR). Methods Retrospective, observational cohort study in patients who underwent colorectal surgery from January 1, 2015, through September 30, 2020. NLP was used to detect keyword counts in clinical notes. Several NLP-algorithms were developed with different count input types and classifiers, and added as component to the original semi-automated algorithm. Traditional manual surveillance was compared with the NLP-augmented surveillance algorithms and sensitivity, specificity, PPV and WR were calculated. Results From the NLP-augmented models, the decision tree models with discretized counts or binary counts had the best performance (sensitivity 95.1% (95%CI 83.5–99.4%), WR 60.9%) and improved PPV and WR by only 2.6% and 3.6%, respectively, compared to the original algorithm. Conclusions The addition of an NLP component to the existing algorithm had modest effect on WR (decrease of 1.4–12.5%), at the cost of sensitivity. For future implementation it will be a trade-off between optimal case-finding techniques versus practical considerations such as acceptability and availability of resources.

Published
2023
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34. RF-induced heating dynamics of non-crystallized trapped ions

Author

van Mourik, Martin W., Hrmo, Pavel, Gerster, Lukas, Wilhelm, Benjamin, Blatt, Rainer, Schindler, Philipp, and Monz, Thomas

Subjects
Physics - Atomic Physics, Quantum Physics
Abstract

We investigate the energy dynamics of non-crystallized (melted) ions, confined in a Paul trap. The non-periodic Coulomb interaction experienced by melted ions forms a medium for non-conservative energy transfer from the radio-frequency (rf) field to the ions, a process known as rf heating. We study rf heating by analyzing numerical simulations of non-crystallized ion motion in Paul trap potentials, in which the energy of the ions' secular motion changes at discrete intervals, corresponding to ion-ion collisions. The analysis of these collisions is used as a basis to derive a simplified model of rf heating energy dynamics, from which we conclude that the rf heating rate is predominantly dependent on the rf field strength. We confirm the predictability of the model experimentally: Two trapped $^{40}$Ca$^{+}$ ions are deterministically driven to melt, and their fluorescence rate is used to infer the ions' energy. From simulation and experimental results, we generalize which experimental parameters are required for efficient recrystallization of melted trapped ions.

Published
2021
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35. External validation of semi-automated surveillance algorithms for deep surgical site infections after colorectal surgery in an independent country

Author

Suzanne D. van der Werff, Janneke D.M. Verberk, Christian Buchli, Maaike S.M. van Mourik, and Pontus Nauclér

Subjects
Automated surveillance, Algorithms, Colorectal surgery, Healthcare-associated infections, Surgical site infections, Validation, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Automated surveillance methods that re-use electronic health record data are considered an attractive alternative to traditional manual surveillance. However, surveillance algorithms need to be thoroughly validated before being implemented in a clinical setting. With semi-automated surveillance patients are classified as low or high probability of having developed infection, and only high probability patients subsequently undergo manual record review. The aim of this study was to externally validate two existing semi-automated surveillance algorithms for deep SSI after colorectal surgery, developed on Spanish and Dutch data, in a Swedish setting. Methods The algorithms were validated in 225 randomly selected surgeries from Karolinska University Hospital from the period January 1, 2015 until August 31, 2020. Both algorithms were based on (re)admission and discharge data, mortality, reoperations, radiology orders, and antibiotic prescriptions, while one additionally used microbiology cultures. SSI was based on ECDC definitions. Sensitivity, specificity, positive predictive value, negative predictive value, and workload reduction were assessed compared to manual surveillance. Results Both algorithms performed well, yet the algorithm not relying on microbiological culture data had highest sensitivity (97.6, 95%CI: 87.4–99.6), which was comparable to previously published results. The latter algorithm aligned best with clinical practice and would lead to 57% records less to review. Conclusions The results highlight the importance of thorough validation before implementation in other clinical settings than in which algorithms were originally developed: the algorithm excluding microbiology cultures had highest sensitivity in this new setting and has the potential to support large-scale semi-automated surveillance of SSI after colorectal surgery.

Published
2023
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36. Behavioral patterns as indicators of resilience after parturition in dairy cows

Author

I.D.E. van Dixhoorn, R.M. de Mol, S.K. Schnabel, J.T.N. van der Werf, S. van Mourik, J.E. Bolhuis, J.M.J. Rebel, and C.G. van Reenen

Subjects
transition period, resilience, postpartum disease, sensor data, Dairy processing. Dairy products, SF250.5-275, Dairying, SF221-250
Abstract

ABSTRACT: During the transition phase, dairy cows are susceptible to develop postpartum diseases. Cows that stay healthy or recover rapidly can be considered to be more resilient in comparison to those that develop postpartum diseases. An indication of loss of resilience will allow for early intervention with preventive and supportive measures before the onset of disease. We investigated which quantitative behavioral characteristics during the dry period could be used as indicators of reduced resilience after calving, using noninvasive Smart Tag neck and Smart Tag leg sensors in dairy cows (Nedap N.V.). We followed 180 cows during 2 wk before until 6 wk after parturition at 4 farms in the Netherlands. Serving as proxy for loss of resilience, as defined by the duration and severity of disease, a clinical assessment was performed twice weekly and blood samples were taken in the first and fifth week after parturition. For each cow, clinical and serum value deviations were aggregated into a total deficit score (TDS total). We also calculated TDS values relating to inflammation, locomotion, or metabolic problems, which were further divided into macro-mineral and liver-related deviations. Smart Tag neck and leg sensors provided continuous behavioral activity signals of which we calculated the average, variance, and autocorrelation during the dry period. Diurnal patterns in the behavioral activity signals were derived by fast Fourier transformation and the calculation of the nonperiodicity. To select significant predictors of resilience, we first performed a univariate analysis with TDS as dependent variable and the behavioral characteristics that were measured during the dry period, as potential predictors with cow as experimental unit. We included parity group as fixed effect and farm as random effect. Next, we performed multivariable analysis with only significant predictors, followed by a variable selection procedure to obtain a final linear mixed model with an optimal subset of predictors with parity group as fixed effect and farm as random effect. The TDS total was best predicted by average inactive time, nonperiodicity ruminating, nonperiodicity of bouts standing up and fast Fourier transformation stand still. Average inactive time was negatively correlated with average eating time, and these 2 predictors could be exchanged with only little difference in model performance. Our best performing model predicted TDS total at a cutoff level of 60 points, with a sensitivity of 79.5% and a specificity of 73.2% with a positive predicted value of 0.69 and a negative predicted value of 0.83. The models to predict the other TDS categories showed a lower predictive performance as compared with the TDS total model, which could be related to the limited sample size and therefore, low occurrence of problems within a specific TDS category. Furthermore, more resilient dairy cows are characterized by high averages of eating time with high regularity in rumination and low averages of inactive time. They reveal high regularity in standing time and transitions from lying to standing, in the dry period. These behaviors can be used as indicators of resilience and allow for preventive intervention during the dry period in vulnerable dairy cattle. However, further examination is still required to find clues for adequate intervention strategies.

Published
2023
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38. Corrigendum: Animal-based factors prior to infection predict histological disease outcome in porcine reproductive and respiratory syndrome virus- and Actinobacillus pleuropneumoniae-infected pigs

Author

Ingrid D. E. van Dixhoorn, Dennis E. te Beest, Jantina E. Bolhuis, Hendrik K. Parmentier, Bas Kemp, Simon van Mourik, Norbert Stockhofe-Zurwieden, Cornelis G. van Reenen, and Johanna M. J. Rebel

Subjects
resilience indicators, porcine respiratory disease, PRRSV, Actinobacillus pleuropneumoniae, coping strategy, enriched housing, Veterinary medicine, SF600-1100
Published
2024
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39. Navigation and Exploration in 3D-Game Automated Play Testing

Author

Prasetya, I. S. W. B., Voshol, Maurin, Tanis, Tom, Smits, Adam, Smit, Bram, van Mourik, Jacco, Klunder, Menno, Hoogmoed, Frank, Hinlopen, Stijn, van Casteren, August, van de Berg, Jesse, Prasetya, Naraenda G. W. Y., Shirzadehhajimahmood, Samira, and Ansari, Saba Gholizadeh

Subjects
Computer Science - Software Engineering, D.2.5
Abstract

To enable automated software testing, the ability to automatically navigate to a state of interest and to explore all, or at least sufficient number of, instances of such a state is fundamental. When testing a computer game the problem has an extra dimension, namely the virtual world where the game is played on. This world often plays a dominant role in constraining which logical states are reachable, and how to reach them. So, any automated testing algorithm for computer games will inevitably need a layer that deals with navigation on a virtual world. Unlike e.g. navigating through the GUI of a typical web-based application, navigating over a virtual world is much more challenging. This paper discusses how concepts from geometry and graph-based path finding can be applied in the context of game testing to solve the problem of automated navigation and exploration. As a proof of concept, the paper also briefly discusses the implementation of the proposed approach.

Published
2020
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40. Heterogeneity in Outcomes of Repeated Instances of Percolation Experiments

Author

Kuehn, Reimer and van Mourik, Jort

Subjects
Condensed Matter - Statistical Mechanics, Condensed Matter - Disordered Systems and Neural Networks
Abstract

We investigate the heterogeneity of outcomes of repeated instances of percolation experiments in complex networks using a message passing approach to evaluate heterogeneous, node dependent probabilities of belonging to the giant or percolating cluster, i.e. the set of mutually connected nodes whose size scales linearly with the size of the system. We evaluate these both for large finite single instances, and for synthetic networks in the configuration model class in the thermodynamic limit. For the latter, we consider both Erdos-Renyi and scale free networks as examples of networks with narrow and broad degree distributions respectively. For real-world networks we use an undirected version of a Gnutella peer-to-peer file-sharing network with $N=62,568$ nodes as an example. We derive the theory for multiple instances of both uncorrelated and correlated percolation processes. For the uncorrelated case, we also obtain a closed form approximation for the large mean degree limit of Erdos-Renyi networks., Comment: 14 pages, 6 multipart figures

Published
2020
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41. Coherent rotations of qubits within a multi-species ion-trap quantum computer

Author

van Mourik, Martin W., Martinez, Esteban A., Gerster, Lukas, Hrmo, Pavel, Monz, Thomas, Schindler, Philipp, and Blatt, Rainer

Subjects
Quantum Physics
Abstract

We describe, realize, and experimentally investigate a method to perform physical rotations of ion chains, trapped in a segmented surface Paul trap, as a building block for large scale quantum computational sequences. Control of trapping potentials is achieved by parametrizing electrode voltages in terms of spherical harmonic potentials. Voltage sequences that enable crystal rotations are numerically obtained by optimizing time-dependent ion positions and motional frequencies, taking into account the effect of electrical filters in our set-up. We minimize rotation-induced heating by expanding the sequences into Fourier components, and optimizing the resulting parameters with a machine-learning approach. Optimized sequences rotate $^{40}$Ca$^+$ - $^{40}$Ca$^+$ crystals with axial heating rates of $\Delta\bar{n}_{com}=0.6^{(+3)}_{(-2)}$ and $\Delta\bar{n}_{str}=3.9(5)$ phonons per rotation for the common and stretch modes, at mode frequencies of 1.24 and 2.15 MHz. Qubit coherence loss is 0.2(2)$\%$ per rotation. We also investigate rotations of mixed species crystals ($^{40}$Ca$^+$ - $^{88}$Sr$^+$) and achieve unity success rate.

Published
2020
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45. SDG indicator 3.b.3 – an analysis of its robustness and challenges for measuring access to medicines for children

Author

I. R. Joosse, V. J. Wirtz, A. T. van Mourik, B. A. Wagner, A. K. Mantel-Teeuwisse, F. Suleman, and H. A. van den Ham

Subjects
Access to medicines, Child medicines, Child health, Sustainable development goals, Indicator, Affordability, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Sustainable Development Goal (SDG) indicator 3.b.3 monitors progress in medicines’ accessibility for adults and has significant limitations when applying to medicines for children. An adapted indicator methodology was developed to fill this gap, but no proof of its robustness exists. We provide this evidence through sensitivity analyses. Methods Data on availability and prices of child medicines from ten historical datasets were combined to create datasets for analysis: Dataset 1 (medicines selected at random) and Dataset 2 (preference given to available medicines, to better capture affordability of medicines). A base case scenario and univariate sensitivity analyses were performed to test critical components of the methodology, including the new variable of number of units needed for treatment (NUNT), disease burden (DB) weighting, and the National Poverty Line (NPL) limits. Additional analyses were run on a continuously smaller basket of medicines to explore the minimum number of medicines required. Mean facility scores for access were calculated and compared. Results The mean facility score for Dataset 1 and Dataset 2 within the base case scenario was 35.5% (range 8.0–58.8%) and 76.3% (range 57.2–90.6%). Different NUNT scenarios led to limited variations in mean facility scores of + 0.1% and -0.2%, or differences of + 4.4% and -2.1% at the more critical NPL of $5.50 (Dataset 1). For Dataset 2, variations to the NUNT generated differences of + 0.0% and -0.6%, at an NPL of $5.50 the differences were + 5.0 and -2.0%. Different approaches for weighting for DB induced considerable fluctuations of 9.0% and 11.2% respectively. Stable outcomes with less than 5% change in mean facility score were observed for a medicine basket down to 12 medicines. For smaller baskets, scores increased more rapidly with a widening range. Conclusion This study has confirmed that the proposed adaptations to make SDG indicator 3.b.3 appropriate for children are robust, indicating that they could be an important addition to the official Global Indicator Framework. At least 12 child-appropriate medicines should be surveyed to obtain meaningful outcomes. General concerns that remain about the weighting of medicines for DB and the NPL should be considered at the 2025 planned review of this framework.

Published
2023
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46. Native qudit entanglement in a trapped ion quantum processor

Author

Pavel Hrmo, Benjamin Wilhelm, Lukas Gerster, Martin W. van Mourik, Marcus Huber, Rainer Blatt, Philipp Schindler, Thomas Monz, and Martin Ringbauer

Subjects
Science
Abstract

Abstract Quantum information carriers, just like most physical systems, naturally occupy high-dimensional Hilbert spaces. Instead of restricting them to a two-level subspace, these high-dimensional (qudit) quantum systems are emerging as a powerful resource for the next generation of quantum processors. Yet harnessing the potential of these systems requires efficient ways of generating the desired interaction between them. Here, we experimentally demonstrate an implementation of a native two-qudit entangling gate up to dimension 5 in a trapped-ion system. This is achieved by generalizing a recently proposed light-shift gate mechanism to generate genuine qudit entanglement in a single application of the gate. The gate seamlessly adapts to the local dimension of the system with a calibration overhead that is independent of the dimension.

Published
2023
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49. An Event-Contingent Method to Track Disfluency Effects on the Relationship and the Self

Author

Koudenburg, Namkje, van Mourik Broekman, Aafke, and Stellingwerf, Sjoerd

Abstract

Background: Theoretically, reductions of self-esteem among people who stutter (PWS) are often explained by individual negative cognitions or emotions of the PWS or their conversation partners. We propose that the flow of a conversation can be seen as a representation of the relationship between speakers, and that by disrupting this flow, a stutter may directly threaten this relationship, and in turn affect self-esteem. Methodologically, we present a new, event-contingent, method that assesses fluctuations in self-esteem over time and thereby allows one to assess the predictive value of specific conversational experiences. Aims: To have both a theoretical and a methodological contribution on conversational disfluency. Methods & Procedures: Our focus is not on stable individual factors, but we expect that fluctuations within the flow of everyday conversations predict changes in self-esteem. We studied these fluctuations with an experience sampling method which prompted participants to answer a brief survey after each of 10 conversations in a 2-week period. Self-identified PWS (n = 58) and people who do not stutter (PWNS; n = 53) reported on their individual negative cognitions and emotions and experienced relational quality and state self-esteem in more than 1000 conversations. By assessing fluctuations in self-esteem over time, this method allows one to assess the predictive value of specific conversational experiences. Outcomes & Results: Correlational evidence demonstrates that flow disruptions are associated with temporary reductions in self-esteem. This association is mediated by increased individual negative cognitions and emotions, as well as threatened social relationships. This appeared to be true for both PWS and PWNS, although PWS experienced on average less conversational flow and lower state self-esteem. On average, PWS did not experience lower relational quality than PWNS. Conclusions & Implications: An event-contingent recording method is a useful way to assess momentary fluctuations in self-esteem. Findings are consistent with the notion that people monitor their relationship by attending to fluctuations in conversational flow; whereas a smooth conversational flow indicates a strong relationship, disruptions of flow (e.g., as caused by a stutter or other factors) signal a threat to the relationship.

Published
2022
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