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3,269 results on '"Houben P"'

1. Bayesian Inverse Graphics for Few-Shot Concept Learning

Author

Arriaga, Octavio, Guo, Jichen, Adam, Rebecca, Houben, Sebastian, and Kirchner, Frank

Subjects
Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition
Abstract

Humans excel at building generalizations of new concepts from just one single example. Contrary to this, current computer vision models typically require large amount of training samples to achieve a comparable accuracy. In this work we present a Bayesian model of perception that learns using only minimal data, a prototypical probabilistic program of an object. Specifically, we propose a generative inverse graphics model of primitive shapes, to infer posterior distributions over physically consistent parameters from one or several images. We show how this representation can be used for downstream tasks such as few-shot classification and pose estimation. Our model outperforms existing few-shot neural-only classification algorithms and demonstrates generalization across varying lighting conditions, backgrounds, and out-of-distribution shapes. By design, our model is uncertainty-aware and uses our new differentiable renderer for optimizing global scene parameters through gradient descent, sampling posterior distributions over object parameters with Markov Chain Monte Carlo (MCMC), and using a neural based likelihood function.

Published
2024
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2. Supervised Representation Learning towards Generalizable Assembly State Recognition

Author

Schoonbeek, Tim J., Balachandran, Goutham, Onvlee, Hans, Houben, Tim, Hung, Shao-Hsuan, Kustra, Jacek, de With, Peter H. N., and van der Sommen, Fons

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Assembly state recognition facilitates the execution of assembly procedures, offering feedback to enhance efficiency and minimize errors. However, recognizing assembly states poses challenges in scalability, since parts are frequently updated, and the robustness to execution errors remains underexplored. To address these challenges, this paper proposes an approach based on representation learning and the novel intermediate-state informed loss function modification (ISIL). ISIL leverages unlabeled transitions between states and demonstrates significant improvements in clustering and classification performance for all tested architectures and losses. Despite being trained exclusively on images without execution errors, thorough analysis on error states demonstrates that our approach accurately distinguishes between correct states and states with various types of execution errors. The integration of the proposed algorithm can offer meaningful assistance to workers and mitigate unexpected losses due to procedural mishaps in industrial settings. The code is available at: https://timschoonbeek.github.io/state_rec, Comment: 8 pages, 8 figures

Published
2024

3. Topotaxial Mutual-Exchange Growth of Magnetic Zintl Eu$_3$In$_2$As$_4$ Nanowires with Axion Insulator Classification

Author

Song, Man Suk, Houben, Lothar, Zhao, Yufei, Bae, Hyeonhu, Rothem, Nadav, Gupta, Ambikesh, Yan, Binghai, Kalisky, Beena, Zaluska-Kotur, Magdalena, Kacman, Perla, Shtrikman, Hadas, and Beidenkopf, Haim

Subjects
Condensed Matter - Materials Science, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Nanomaterials bring to expression unique electronic properties that promote advanced functionality and technologies. Albeit, nanoscale growth presents paramount challenges for synthesis limiting the diversity in structures and compositions. Here, we demonstrate solid-state topotactic exchange that converts Wurtzite InAs nanowires into Zintl phase Eu$_3$In$_2$As$_4$ nanowires. In situ evaporation of Eu and As over InAs nanowire cores in molecular beam epitaxy results in mutual exchange of Eu from the shell and In from the core. A continuous Eu$_3$In$_2$As$_4$ shell thereby grows that gradually consumes the InAs core and converts it into a single phase Eu$_3$In$_2$As$_4$ nanowire. Topotaxy, which facilitates the mutual exchange, is supported by the substructure of the As matrix which is similar across the Wurtzite InAs and Zintl Eu$_3$In$_2$As$_4$. We provide initial evidence of an antiferromagnetic transition at T$_N$ $\sim$ 6.5 K in the Zintl phase Eu$_3$In$_2$As$_4$ nanowires. Ab initio calculation confirms the antiferromagnetic state and classifies Eu$_3$In$_2$As$_4$ as a $C_2 T$ axion insulator hosting both chiral hinge modes and unpinned Dirac surface states. The topotactic mutual-exchange growth of Zintl Eu$_3$In$_2$As$_4$ nanowires thus enables the exploration of intricate magneto-topological states of nanomaterials. Moreover, it may open the path for topotactic mutual-exchange synthesis of nanowires made of other exotic compounds., Comment: 45 pages, 23 figures

Published
2024
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4. Robust Entropy Search for Safe Efficient Bayesian Optimization

Author

Weichert, Dorina, Kister, Alexander, Houben, Sebastian, Link, Patrick, and Ernis, Gunar

Subjects
Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

The practical use of Bayesian Optimization (BO) in engineering applications imposes special requirements: high sampling efficiency on the one hand and finding a robust solution on the other hand. We address the case of adversarial robustness, where all parameters are controllable during the optimization process, but a subset of them is uncontrollable or even adversely perturbed at the time of application. To this end, we develop an efficient information-based acquisition function that we call Robust Entropy Search (RES). We empirically demonstrate its benefits in experiments on synthetic and real-life data. The results showthat RES reliably finds robust optima, outperforming state-of-the-art algorithms.

Published
2024

5. A multi-step calibration strategy for reliable parameter determination of salt rock mechanics constitutive models

Author

Honório, Hermínio T., Houben, Maartje, Bisdom, Kevin, van der Linden, Arjan, de Borst, Karin, Sluys, Lambertus J., and Hajibeygi, Hadi

Subjects
Physics - Geophysics, Mathematics - Numerical Analysis
Abstract

Renewable hydrogen storage in salt caverns requires fast injection and production rates to cope with the imbalance between energy production and consumption. Such operational conditions raise concerns about the mechanical stability of salt caverns. Choosing an appropriate constitutive model for salt mechanics is an important step in investigating this issue, and many constitutive models with several parameters have been presented in the literature. However, a robust calibration strategy to reliably determine which model and which parameter set represent the given rock, based on stress-strain data, remains an unsolved challenge. For the first time in the community, we present a multi-step strategy to determine a single parameter set based on many deformation datasets for salt rocks. Towards this end, we first develop a comprehensive constitutive model able to capture all relevant nonlinear deformation physics of transient, reverse, and steady-state creep. The determination of the single set of representative material parameters is achieved by framing the calibration process as an optimization problem, for which the global PSO algorithm is employed. Dynamic data integration is achieved by a multi-step calibration strategy for a situation where experiments are included one at a time, as they become available. Additionally, our calibration strategy is made flexible to account for mild heterogeneity between rock samples, resulting in a single set of parameters that is representative of the deformation datasets. As a rigorous mathematical analysis and the lack of relevant experimental datasets, we consider a wide range of synthetic experimental data, inspired by the existing sparse relevant data in the literature. The results of our performance analyses show that the proposed calibration strategy is robust and accuracy is improved as more experiments are included for calibration., Comment: 27 pages, 23 figures

Published
2024

6. HyenaPixel: Global Image Context with Convolutions

Author

Spravil, Julian, Houben, Sebastian, and Behnke, Sven

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

In computer vision, a larger effective receptive field (ERF) is associated with better performance. While attention natively supports global context, its quadratic complexity limits its applicability to tasks that benefit from high-resolution input. In this work, we extend Hyena, a convolution-based attention replacement, from causal sequences to bidirectional data and two-dimensional image space. We scale Hyena's convolution kernels beyond the feature map size, up to 191$\times$191, to maximize ERF while maintaining sub-quadratic complexity in the number of pixels. We integrate our two-dimensional Hyena, HyenaPixel, and bidirectional Hyena into the MetaFormer framework. For image categorization, HyenaPixel and bidirectional Hyena achieve a competitive ImageNet-1k top-1 accuracy of 84.9% and 85.2%, respectively, with no additional training data, while outperforming other convolutional and large-kernel networks. Combining HyenaPixel with attention further improves accuracy. We attribute the success of bidirectional Hyena to learning the data-dependent geometric arrangement of pixels without a fixed neighborhood definition. Experimental results on downstream tasks suggest that HyenaPixel with large filters and a fixed neighborhood leads to better localization performance.

Published
2024

7. Inferring Structure of Cortical Neuronal Networks from Firing Data: A Statistical Physics Approach

Author

Po, Ho Fai, Houben, Akke Mats, Haeb, Anna-Christina, Jenkins, David Rhys, Hill, Eric J., Parri, H. Rheinallt, Soriano, Jordi, and Saad, David

Subjects
Physics - Physics and Society, Condensed Matter - Disordered Systems and Neural Networks
Abstract

Understanding the relation between cortical neuronal network structure and neuronal activity is a fundamental unresolved question in neuroscience, with implications to our understanding of the mechanism by which neuronal networks evolve over time, spontaneously or under stimulation. It requires a method for inferring the structure and composition of a network from neuronal activities. Tracking the evolution of networks and their changing functionality will provide invaluable insight into the occurrence of plasticity and the underlying learning process. We devise a probabilistic method for inferring the effective network structure by integrating techniques from Bayesian statistics, statistical physics and principled machine learning. The method and resulting algorithm allow one to infer the effective network structure, identify the excitatory and inhibitory nature of its constituents, and predict neuronal spiking activities by employing the inferred structure. We validate the method and algorithm's performance using synthetic data, spontaneous activity of an in silico emulator and realistic in vitro neuronal networks of modular and homogeneous connectivity, demonstrating excellent structure inference and activity prediction. We also show that our method outperforms commonly used existing methods for inferring neuronal network structure. Inferring the evolving effective structure of neuronal networks will provide new insight into the learning process due to stimulation in general and will facilitate the development of neuron-based circuits with computing capabilities.

Published
2024

8. Integrated Information Decomposition Unveils Major Structural Traits of $In$ $Silico$ and $In$ $Vitro$ Neuronal Networks

Author

Menesse, Gustavo, Houben, Akke Mats, Soriano, Jordi, and Torres, Joaquin J.

Subjects
Quantitative Biology - Neurons and Cognition, Condensed Matter - Disordered Systems and Neural Networks
Abstract

The properties of complex networked systems arise from the interplay between the dynamics of their elements and the underlying topology. Thus, to understand their behaviour, it is crucial to convene as much information as possible about their topological organization. However, in a large systems such as neuronal networks, the reconstruction of such topology is usually carried out from the information encoded in the dynamics on the network, such as spike train time series, and by measuring the Transfer Entropy between system elements. The topological information recovered by these methods does not necessarily capture the connectivity layout, but rather the causal flow of information between elements. New theoretical frameworks, such as Integrated Information Decomposition ($\Phi$-ID), allow to explore the modes in which information can flow between parts of a system, opening a rich landscape of interactions between network topology, dynamics and information. Here, we apply $\Phi$-ID on $in$ $silico$ and $in$ $vitro$ data to decompose the usual Transfer Entropy measure into different modes of information transfer, namely synergistic, redundant or unique. We demonstrate that the unique information transfer is the most relevant measure to uncover structural topological details from network activity data, while redundant information only introduces residual information for this application. Although the retrieved network connectivity is still functional, it captures more details of the underlying structural topology by avoiding to take into account emergent high-order interactions and information redundancy between elements, which are important for the functional behavior, but mask the detection of direct simple interactions between elements constituted by the structural network topology., Comment: 13 pages, 5 figures

Published
2024
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12. Microvascular Dysfunction and Whole-Brain White Matter Connectivity: The Maastricht Study.

Author

Beran, Magdalena, van Gennip, April, Stehouwer, Coen, Jansen, Jacobus, Gupta, Monideepa, Houben, Alfons, Berendschot, Tos, Webers, Carroll, Wesselius, Anke, Schalkwijk, Casper, Backes, Walter, de Jong, Joost, van der Kallen, Carla, van Greevenbroek, Marleen, Köhler, Sebastian, Vonk, Jet, Geerlings, Mirjam, Schram, Miranda, and van Sloten, Thomas

Subjects
cerebral microcirculation, cohort, diffusion tensor imaging, microvascular dysfunction, white matter connectivity, Humans, Female, Middle Aged, Aged, Male, White Matter, Cross-Sectional Studies, Brain, Diffusion Magnetic Resonance Imaging, Biomarkers
Abstract

BACKGROUND: Microvascular dysfunction is involved in the development of various cerebral disorders. It may contribute to these disorders by disrupting white matter tracts and altering brain connectivity, but evidence is scarce. We investigated the association between multiple biomarkers of microvascular function and whole-brain white matter connectivity. METHODS AND RESULTS: Cross-sectional data from The Maastricht Study, a Dutch population-based cohort (n=4326; age, 59.4±8.6 years; 49.7% women). Measures of microvascular function included urinary albumin excretion, central retinal arteriolar and venular calibers, composite scores of flicker light-induced retinal arteriolar and venular dilation, and plasma biomarkers of endothelial dysfunction (intercellular adhesion molecule-1, vascular cell adhesion molecule-1, E-selectin, and von Willebrand factor). White matter connectivity was calculated from 3T diffusion magnetic resonance imaging to quantify the number (average node degree) and organization (characteristic path length, global efficiency, clustering coefficient, and local efficiency) of white matter connections. A higher plasma biomarkers of endothelial dysfunction composite score was associated with a longer characteristic path length (β per SD, 0.066 [95% CI, 0.017-0.114]) after adjustment for sociodemographic, lifestyle, and cardiovascular factors but not with any of the other white matter connectivity measures. After multiple comparison correction, this association was nonsignificant. None of the other microvascular function measures were associated with any of the connectivity measures. CONCLUSIONS: These findings suggest that microvascular dysfunction as measured by indirect markers is not associated with whole-brain white matter connectivity.

Published
2024

13. IndustReal: A Dataset for Procedure Step Recognition Handling Execution Errors in Egocentric Videos in an Industrial-Like Setting

Author

Schoonbeek, Tim J., Houben, Tim, Onvlee, Hans, de With, Peter H. N., and van der Sommen, Fons

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Although action recognition for procedural tasks has received notable attention, it has a fundamental flaw in that no measure of success for actions is provided. This limits the applicability of such systems especially within the industrial domain, since the outcome of procedural actions is often significantly more important than the mere execution. To address this limitation, we define the novel task of procedure step recognition (PSR), focusing on recognizing the correct completion and order of procedural steps. Alongside the new task, we also present the multi-modal IndustReal dataset. Unlike currently available datasets, IndustReal contains procedural errors (such as omissions) as well as execution errors. A significant part of these errors are exclusively present in the validation and test sets, making IndustReal suitable to evaluate robustness of algorithms to new, unseen mistakes. Additionally, to encourage reproducibility and allow for scalable approaches trained on synthetic data, the 3D models of all parts are publicly available. Annotations and benchmark performance are provided for action recognition and assembly state detection, as well as the new PSR task. IndustReal, along with the code and model weights, is available at: https://github.com/TimSchoonbeek/IndustReal ., Comment: Accepted for WACV 2024. 15 pages, 9 figures, including supplementary materials

Published
2023

22. Guideline for Trustworthy Artificial Intelligence -- AI Assessment Catalog

Author

Poretschkin, Maximilian, Schmitz, Anna, Akila, Maram, Adilova, Linara, Becker, Daniel, Cremers, Armin B., Hecker, Dirk, Houben, Sebastian, Mock, Michael, Rosenzweig, Julia, Sicking, Joachim, Schulz, Elena, Voss, Angelika, and Wrobel, Stefan

Subjects
Computer Science - Computers and Society, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

Artificial Intelligence (AI) has made impressive progress in recent years and represents a key technology that has a crucial impact on the economy and society. However, it is clear that AI and business models based on it can only reach their full potential if AI applications are developed according to high quality standards and are effectively protected against new AI risks. For instance, AI bears the risk of unfair treatment of individuals when processing personal data e.g., to support credit lending or staff recruitment decisions. The emergence of these new risks is closely linked to the fact that the behavior of AI applications, particularly those based on Machine Learning (ML), is essentially learned from large volumes of data and is not predetermined by fixed programmed rules. Thus, the issue of the trustworthiness of AI applications is crucial and is the subject of numerous major publications by stakeholders in politics, business and society. In addition, there is mutual agreement that the requirements for trustworthy AI, which are often described in an abstract way, must now be made clear and tangible. One challenge to overcome here relates to the fact that the specific quality criteria for an AI application depend heavily on the application context and possible measures to fulfill them in turn depend heavily on the AI technology used. Lastly, practical assessment procedures are needed to evaluate whether specific AI applications have been developed according to adequate quality standards. This AI assessment catalog addresses exactly this point and is intended for two target groups: Firstly, it provides developers with a guideline for systematically making their AI applications trustworthy. Secondly, it guides assessors and auditors on how to examine AI applications for trustworthiness in a structured way.

Published
2023

24. High-precision stereotactic irradiation for focal drug-resistant epilepsy versus standard treatment: a randomized waitlist-controlled trial (the PRECISION trial)

Author

Zegers, C. M. L., Swinnen, A., Roumen, C., Hoffmann, A. L., Troost, E. G. C., van Asch, C. J. J., Brandts, L., Compter, I., Dieleman, E. M. T., Dijkstra, J. B., Granzier, M., Hendriks, M., Hofman, P., Houben, R. M. A., Ramaekers, B., Ronner, H. E., Rouhl, R. P. W., van der Salm, S., Santegoeds, R. G. C., Verhoeff, J. J., Wagner, G. L., Zwemmer, J., Schijns, OEMG, Colon, A. J., and Eekers, D. B. P.

Published
2024
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34. Infection prevention and control in Dutch general practices before and during the COVID-19 pandemic and its implications for pandemic preparedness and seasonal respiratory epidemics: a qualitative study on lessons learned

Author

Famke Houben, Casper D. J. den Heijer, Nicole H. T. M. Dukers-Muijrers, Eefje G. P. M. de Bont, Hanneke T. Volbeda, and Christian J. P. A. Hoebe

Subjects
COVID-19, Infection control, Primary health care, General practice, Family medicine, Qualitative research, Medicine (General), R5-920
Abstract

Abstract Background The COVID-19 pandemic has prompted a re-evaluation of infection prevention and control (IPC) in general practices, highlighting the need for comprehensive IPC implementation. This study aimed to evaluate healthcare workers’ (HCWs) experiences and perspectives regarding IPC in general practices before and during the COVID-19 pandemic, and its implications for post-pandemic IPC implementation. Methods This qualitative study involved semi-structured, in-depth interviews during two time periods: (1) prior to the COVID-19 pandemic (July 2019-February 2020), involving 14 general practitioners (GPs) and medical assistants; and (2) during the COVID-19 pandemic (July 2022-February 2023), including 22 GPs and medical assistants. Data analysis included thematic analysis that addressed multiple system levels. Results Findings indicated a shift towards comprehensive IPC implementation and organisation during the pandemic compared to the pre-pandemic period. Since the Omicron variant, some general practices maintained a broad set of IPC measures, while others released most measures. HCWs’ future expectations on post-pandemic IPC implementation varied: some anticipated reduced implementation due to the desire to return to the pre-pandemic standard, while others expected IPC to be structurally scaled up during seasonal respiratory epidemics. Main contextual challenges included patient cooperation, staff shortages (due to infection), shortages of IPC materials/equipment, and frequently changing and ambiguous guidelines. Key lessons learned were enhanced preparedness (e.g., personal protective equipment supply), and a new perspective on care organisation (e.g., digital care). Main recommendations reported by HCWs were to strengthen regional collaboration within primary care, and between primary care, public health, and secondary care. Conclusion HCWs’ experiences, perspectives and recommendations provide insights to enhance preparedness for future epidemics and pandemics, and sustain IPC in general practices. For IPC improvement strategies, adopting an integrated system-based approach that encompasses actions across multiple levels and engages multiple stakeholders is recommended.

Published
2024
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35. Seroprevalence and placental transfer of SARS-CoV-2 antibodies in unvaccinated pregnant women

Author

An Vercoutere, Mbiton Joel Zina, Meltem Telis, Jean-Christophe Goffard, Michel Boulvain, Loïc de Doncker, Sara Derisbourg, Sylvie Houben, Marie-Luce Delforge, Caroline Daelemans, and Dorottya Kelen

Subjects
SARS-COV-2 antibodies, Pregnancy, Seroprevalence, Placental transfer, COVID-19, Antibody, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Purpose Pregnant women are at risk of severe SARS-CoV-2 infection, potentially leading to obstetric and neonatal complications. Placental transfer of antibodies directed to SARS-CoV-2 may be protective against neonatal COVID-19, but this remains to be studied. We aimed to determine the seroprevalence of SARS-CoV-2 antibodies in a population of unvaccinated pregnant women and to determine the placental transfer of these antibodies. Methodology A total of 1197 unvaccinated women with mostly unknown pre-study SARS-CoV-2 infection status, were tested at delivery for SARS-CoV-2 spike protein IgG antibodies during the first year of the pandemic. Umbilical cord samples were collected and assessed for seropositivity if the mother was seropositive. Maternal characteristics, pregnancy and neonatal outcomes and data on SARS-CoV-2 infection were extracted from medical records. Results Specific IgG were detected in 258 women (21.6%). A significant placental transfer to the newborn was observed in 81.3% of cases. The earlier in the 2nd and 3rd trimesters that the mother had contracted the disease and the more symptomatic she was, the greater the likelihood of transplacental transfer of IgG to her newborn. Conclusion Approximately one in five women had detectable anti-SARS-CoV-2 spike protein IgG antibodies at delivery during the first year of the pandemic, and these antibodies were significantly transferred to their fetuses. This research provides further evidence to better understand the dynamics of the placental transfer of SARS-CoV-2 IgG antibodies from mothers to their newborns, which is necessary to improve vaccination strategies.

Published
2024
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36. High-precision stereotactic irradiation for focal drug-resistant epilepsy versus standard treatment: a randomized waitlist-controlled trial (the PRECISION trial)

Author

C. M. L. Zegers, A. Swinnen, C. Roumen, A. L. Hoffmann, E. G. C. Troost, C. J. J. van Asch, L. Brandts, I. Compter, E. M. T. Dieleman, J. B. Dijkstra, M. Granzier, M. Hendriks, P. Hofman, R. M. A. Houben, B. Ramaekers, H. E. Ronner, R. P. W. Rouhl, S. van der Salm, R. G. C. Santegoeds, J. J. Verhoeff, G. L. Wagner, J. Zwemmer, OEMG Schijns, A. J. Colon, and D. B. P. Eekers

Subjects
Epilepsy, Radiosurgery, Stereotactic radiation therapy (SRT), MRI, Cognition, Medicine (General), R5-920
Abstract

Abstract Introduction The standard treatment for patients with focal drug-resistant epilepsy (DRE) who are not eligible for open brain surgery is the continuation of anti-seizure medication (ASM) and neuromodulation. This treatment does not cure epilepsy but only decreases severity. The PRECISION trial offers a non-invasive, possibly curative intervention for these patients, which consist of a single stereotactic radiotherapy (SRT) treatment. Previous studies have shown promising results of SRT in this patient population. Nevertheless, this intervention is not yet available and reimbursed in the Netherlands. We hypothesize that: SRT is a superior treatment option compared to palliative standard of care, for patients with focal DRE, not eligible for open surgery, resulting in a higher reduction of seizure frequency (with 50% of the patients reaching a 75% seizure frequency reduction at 2 years follow-up). Methods In this waitlist-controlled phase 3 clinical trial, participants are randomly assigned in a 1:1 ratio to either receive SRT as the intervention, while the standard treatments consist of ASM continuation and neuromodulation. After 2-year follow-up, patients randomized for the standard treatment (waitlist-control group) are offered SRT. Patients aged ≥ 18 years with focal DRE and a pretreatment defined epileptogenic zone (EZ) not eligible for open surgery will be included. The intervention is a LINAC-based single fraction (24 Gy) SRT treatment. The target volume is defined as the epileptogenic zone (EZ) on all (non) invasive examinations. The seizure frequency will be monitored on a daily basis using an electronic diary and an automatic seizure detection system during the night. Potential side effects are evaluated using advanced MRI, cognitive evaluation, Common Toxicity Criteria, and patient-reported outcome questionnaires. In addition, the cost-effectiveness of the SRT treatment will be evaluated. Discussion This is the first randomized trial comparing SRT with standard of care in patients with DRE, non-eligible for open surgery. The primary objective is to determine whether SRT significantly reduces the seizure frequency 2 years after treatment. The results of this trial can influence the current clinical practice and medical cost reimbursement in the Netherlands for patients with focal DRE who are not eligible for open surgery, providing a non-invasive curative treatment option. Trial registration Clinicaltrials.gov Identifier: NCT05182437. Registered on September 27, 2021.

Published
2024
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37. Major chromosome rearrangements in intergeneric wheat × rye hybrids in compatible and incompatible crosses detected by GBS read coverage analysis

Author

Natalia Tikhenko, Max Haupt, Jörg Fuchs, Dragan Perovic, Axel Himmelbach, Martin Mascher, Andreas Houben, Twan Rutten, Manuela Nagel, Natalia V. Tsvetkova, Stefanie Sehmisch, and Andreas Börner

Subjects
Wheat-rye amphidiploids, Incompatible crosses, Chromosome rearrangements, Embryo lethality, Hybrid sterility, Genotyping-by-sequencing GBS, Medicine, Science
Abstract

Abstract The presence of incompatibility alleles in primary amphidiploids constitutes a reproductive barrier in newly synthesized wheat-rye hybrids. To overcome this barrier, the genome stabilization process includes large-scale chromosome rearrangements. In incompatible crosses resulting in fertile amphidiploids, the elimination of one of the incompatible alleles Eml-A1 or Eml-R1b can occur already in the somatic tissue of the wheat × rye hybrid embryo. We observed that the interaction of incompatible loci Eml-A1 of wheat and Eml-R1b of rye after overcoming embryo lethality leads to hybrid sterility in primary triticale. During subsequent seed reproductions (R1, R2 or R3) most of the chromosomes of A, B, D and R subgenomes undergo rearrangement or eliminations to increase the fertility of the amphidiploid by natural selection. Genotyping-by-sequencing (GBS) coverage analysis showed that improved fertility is associated with the elimination of entire and partial chromosomes carrying factors that either cause the disruption of plant development in hybrid plants or lead to the restoration of the euploid number of chromosomes (2n = 56) in the absence of one of the incompatible alleles. Highly fertile offspring obtained in compatible and incompatible crosses can be successfully adapted for the production of triticale pre-breeding stocks.

Published
2024
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39. The little skate genome and the evolutionary emergence of wing-like fins

Author

Marlétaz, Ferdinand, de la Calle-Mustienes, Elisa, Acemel, Rafael D, Paliou, Christina, Naranjo, Silvia, Martínez-García, Pedro Manuel, Cases, Ildefonso, Sleight, Victoria A, Hirschberger, Christine, Marcet-Houben, Marina, Navon, Dina, Andrescavage, Ali, Skvortsova, Ksenia, Duckett, Paul Edward, González-Rajal, Álvaro, Bogdanovic, Ozren, Gibcus, Johan H, Yang, Liyan, Gallardo-Fuentes, Lourdes, Sospedra, Ismael, Lopez-Rios, Javier, Darbellay, Fabrice, Visel, Axel, Dekker, Job, Shubin, Neil, Gabaldón, Toni, Nakamura, Tetsuya, Tena, Juan J, Lupiáñez, Darío G, Rokhsar, Daniel S, and Gómez-Skarmeta, José Luis

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Animal Fins, Genomics, Homeodomain Proteins, Skates, Fish, Zebrafish, Biological Evolution, Genome, Genes, Reporter, General Science & Technology
Abstract

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

Published
2023

40. Robustness in Fatigue Strength Estimation

Author

Weichert, Dorina, Kister, Alexander, Houben, Sebastian, Ernis, Gunar, and Wrobel, Stefan

Subjects
Computer Science - Machine Learning
Abstract

Fatigue strength estimation is a costly manual material characterization process in which state-of-the-art approaches follow a standardized experiment and analysis procedure. In this paper, we examine a modular, Machine Learning-based approach for fatigue strength estimation that is likely to reduce the number of experiments and, thus, the overall experimental costs. Despite its high potential, deployment of a new approach in a real-life lab requires more than the theoretical definition and simulation. Therefore, we study the robustness of the approach against misspecification of the prior and discretization of the specified loads. We identify its applicability and its advantageous behavior over the state-of-the-art methods, potentially reducing the number of costly experiments., Comment: 2nd Annual AAAI Workshop on AI to Accelerate Science and Engineering (AI2ASE)

Published
2022

41. On the decisional Diffie-Hellman problem for class group actions on oriented elliptic curves

Author

Castryck, Wouter, Houben, Marc, Vercauteren, Frederik, and Wesolowski, Benjamin

Subjects
Mathematics - Number Theory, Computer Science - Cryptography and Security, 14H52, 11R65, 14L30, 11Y16, 94A60
Abstract

We show how the Weil pairing can be used to evaluate the assigned characters of an imaginary quadratic order $\mathcal{O}$ in an unknown ideal class $[\mathfrak{a}] \in \mathrm{Cl}(\mathcal{O})$ that connects two given $\mathcal{O}$-oriented elliptic curves $(E, \iota)$ and $(E', \iota') = [\mathfrak{a}](E, \iota)$. When specialized to ordinary elliptic curves over finite fields, our method is conceptually simpler and often somewhat faster than a recent approach due to Castryck, Sot\'akov\'a and Vercauteren, who rely on the Tate pairing instead. The main implication of our work is that it breaks the decisional Diffie-Hellman problem for practically all oriented elliptic curves that are acted upon by an even-order class group. It can also be used to better handle the worst cases in Wesolowski's recent reduction from the vectorization problem for oriented elliptic curves to the endomorphism ring problem, leading to a method that always works in sub-exponential time., Comment: 18 pp

Published
2022

42. Pediatric emergence delirium is linked to increased early postoperative negative behavior within two weeks after adenoidectomy: an observational study

Author

Anne Houben, Shahab Ghamari, Andreas Fischer, Claudia Neumann, Torsten Baehner, and Richard K. Ellerkmann

Subjects
Adenoidectomy, Behavior, Emergence delirium, Anesthesia, Child, Preschool, Anesthesiology, RD78.3-87.3
Abstract

Background: The aim of this prospective multicenter observational study was to measure the incidence of postoperative pediatric emergence delirium and to investigate the occurrence of early postoperative negative behavior within two weeks after outpatient adenoidectomy in preschool children. Methods: The study comprised 222 patients (1...7 years of age). All children received a multimodal anesthesia based on total intravenous anesthesia with propofol and remifentanil in combination with piritramid (0.1 mg.kg-1), ibuprofen (10 mg.kg-1), dexamethason (0.15 mg.kg-1), and ketanest S (0.1 mg.kg-1). We evaluated emergence delirium using the Pediatric Anesthesia Emergence Delirium Scale (PAED) at different predefined time points during the recovery period. Emergence delirium was defined as a PAED score ... 9 for the first three criteria. Additionally, we defined early postoperative negative behavior to be present when at least 5 of 27 criteria of the post hospitalization behavior questionnaire were positive. Results: The incidence of emergence delirium following our anesthetic regime was 23%. The incidence of early postoperative negative behavior was significantly higher among patients with emergence delirium (24% vs. 11%, p = 0.04). The two categories, ..úsleep disturbance..Ñ and ..úseparation anxiety..Ñ, tested within the questionnaire for early postoperative negative behavior, were identified as the most common postoperative negative behavioral changes. Conclusion: Emergence delirium not only plays a role immediately after surgery but is also linked to early postoperative negative behavior within two weeks after outpatient adenoidectomy. Parents should be informed that early postoperative negative behavior may occur in 1 out of 4 patients if emergence delirium was present postoperatively. Trial Registration: DRKS ... German Clinical Trial Register ID: DRKS00013121

Published
2024
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43. Improving the contribution of mathematical modelling evidence to guidelines and policy: Experiences from tuberculosis

Author

C. Finn McQuaid, Nicolas A. Menzies, Rein M.G.J. Houben, Gabriella B. Gomez, Anna Vassall, Nimalan Arinaminpathy, Peter J. Dodd, and Richard G. White

Subjects
Infectious disease modelling, Guidance, Quality and transparency, Tuberculosis, Infectious and parasitic diseases, RC109-216
Abstract

We read with great interest the recent paper by Lo et al., who argue that there is an urgent need to ensure the quality of modelling evidence used to support international and national guideline development. Here we outline efforts by the Tuberculosis Modelling and Analysis Consortium, together with the World Health Organization Global Task Force on Tuberculosis Impact Measurement, to develop material to improve the quality and transparency of country-level tuberculosis modelling to inform decision-making.

Published
2024
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44. Symptom burden and its associations with clinical characteristics in patients with COPD: a clustering approach

Author

Sarah Houben-Wilke, Qichen Deng, Daisy J.A. Janssen, Frits M.E. Franssen, and Martijn A. Spruit

Subjects
Medicine
Abstract

Background Symptom burden in patients with COPD is often under-recognised. In this cross-sectional analysis, we aimed to study the severity of a variety of (non-)respiratory symptoms in patients with and without COPD and to explore the associations between clusters based on symptom severity and other clinical characteristics. Methods Characteristics were assessed in 538 patients with COPD from primary, secondary and tertiary care and 116 non-COPD participants. The severity of 20 symptoms was measured using a visual analogue scale (VAS), ranging from 0 mm (no symptom) to 100 mm (maximum severity). K-means cluster analysis was applied to symptom severity in the patient sample only. Results People with COPD were comparable with non-COPD participants in terms of gender (58% versus 55% male, p=0.132) and age (64±9 years versus 63±6 years, p=0.552) and had a reduced forced expiratory volume in 1 s (57±23% predicted versus 111±17% predicted, p

Published
2024
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45. Quantification of biochar in arable land: A new approach based on Rock-Eval® thermal analysis

Author

Marie-Liesse Aubertin, Oscar Pascal Malou, Frédéric Delarue, Priscia Oliva, David Houben, and David Sebag

Subjects
Pyrogenic carbon (PyC), Quantification, Rock-Eval®, biochar, soil, Science
Abstract

Pyrogenic carbon (PyC) constitutes an important pool of soil organic carbon and may remain in soil over millennia. Its accurate quantification in soil is necessary to monitor the evolution of soil carbon stocks and fluxes. This study tested new direct approaches to quantify PyC enrichment in soil, using three protocols based on the Rock-Eval® thermal method. Six industrial biochars and four cultivated soils were mixed at five different biochar/soil ratios from 0.05 % to 1 % (w/w). Biochar-C emissions could be identified in the CO2 signal from the oxidation stage (CO2oxi) between 410 °C and 610 °C, independently from carbon and carbonate contents from the original unamended soil. Based on this signal and using a reference sample, the protocol 3 allowed for a good estimation of the PyC enrichment relatively to the reference sample. This protocol is thus well adapted to monitor biochar addition in agricultural soils. However, the use of a reference sample, chosen as the sample with the lowest value of thermo-resistant organic carbon (CorgTR), may be tricky for heterogeneous surface areas and soil profiles. In the latter context, both protocols 1 and 2 are alternative methods to quantify CorgTR from biochar and soil without the need of a reference sample, although less accurate than protocol 3. Protocol 2, based on a more precise identification of the biochar-derived peak of CO2oxi, resulted in more accurate values than protocol 1. However, the use of protocol 2 is suitable when the biochar-derived peak is easily distinguishable from the peaks derived from both thermo-resistant SOM and PyC present in the original unamended soil. In conclusion, the Rock-Eval® thermal method turns out to be a good tool to quantify biochar-C in cultivated soil and is fully adapted in field experiments – in which, the initial content in biochar is controlled – aiming to decipher the potential benefits of biochar on soil functioning and related ecosystem services.

Published
2024
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46. Cardiac (tele)rehabilitation in routine clinical practice for patients with coronary artery disease: protocol of the REHAB + trial

Author

Rutger F. R. van Mierlo, Vitalis J. G. Houben, Sem A. O. F. Rikken, Juan Jose Gómez-Doblas, Jordi Lozano-Torres, and Arnoud W. J. van ’t Hof

Subjects
cardiac rehabilitation, cardiac telerehabilitation, rehabilitation, quality of life, physical activity, tele health, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

IntroductionCardiac rehabilitation programs face the challenge of suboptimal participation, despite being a level Ia recommendation. Cardiac telerehabilitation, with its potential to engage patients who might otherwise not show interest, necessitates the adaption of existing center-based cardiac rehabilitation programs to facilitate rehabilitation at home. REHAB + is a mobile cardiac telerehabilitation program cocreated with patients and rehabilitation centers, aiming to future-proof cardiac rehabilitation and improve accessibility. The REHAB + application enables users to remotely communicate with their coach, receive on-demand feedback on health goal progression, and reduces the need for frequent in-person meetings at the cardiac rehabilitation center. The REHAB + study seeks to compare patient-related outcomes and characteristics of patients between those offered the option to participate in cardiac telerehabilitation and those attending center-based cardiac rehabilitation over a twelve-month period.MethodsThe REHAB + study is a multicenter, prospective, matched controlled, observational study that includes (N)STEMI patients eligible for cardiac rehabilitation. We aim to enroll 300 participants for cardiac telerehabilitation and 600 for center-based cardiac rehabilitation. Participants opting for cardiac telerehabilitation (REHAB+) will be matched with center-based cardiac rehabilitation participants. Additionally, characteristics of patients unwilling to participate in either center-based rehabilitation or telerehabilitation but are willing to share their demographics will be collected. The primary endpoint is quality of life measured with the SF-36 questionnaire at three and twelve months, with patient-related characteristics driving intervention choice as the most important secondary endpoint. Secondary endpoints include physical activity, modifiable risk factors, and digital health experience. The trial is registered at clinicaltrials.gov with registration number NCT05207072.DiscussionThe REHAB + trial is unique by offering patients freedom to choose between cardiac telerehabilitation and center-based rehabilitation. The integration of digital components into cardiac rehabilitation has the potential to complement behavioral change strategies for specific patient groups. Offering patients the option of cardiac telerehabilitation next to center-based rehabilitation could enhance overall cardiac rehabilitation participation rates.

Published
2024
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47. Dynamics of endomorphisms of algebraic groups

Author

Byszewski, Jakub, Cornelissen, Gunther, and Houben, Marc

Subjects
Mathematics - Number Theory, Mathematics - Algebraic Geometry, Mathematics - Dynamical Systems, Primary 14L10, 20G40, 37P55, 37C25, 37C35 Secondary 11B37, 11N45, 14F20, 30B40, 37C30
Abstract

Let $\sigma$ denote an endomorphism of a smooth algebraic group $G$ over the algebraic closure of a finite field, and assume all iterates of $\sigma$ have finitely many fixed points. Steinberg gave a formula for the number of fixed points of $\sigma$ (and hence of all of its iterates $\sigma^n$) in the semisimple case, leading to a representation of its Artin-Mazur zeta function as a rational function. We generalise this to an arbitrary (smooth) algebraic group $G$, where the number of fixed points $\sigma_n$ of $\sigma^n$ can depend on $p$-adic properties of $n$. We axiomatise the structure of the sequence $(\sigma_n)$ via the concept of a `finite-adelically distorted' (FAD-)sequence. Such sequences also occur in topological dynamics, and our subsequent results about zeta functions and asymptotic counting of orbits apply equally well in that situation; for example, to $S$-integer dynamical systems, additive cellular automata and other compact abelian groups. We prove dichotomies for the associated Artin-Mazur zeta function, and study the analogue of the Prime Number Theorem for the function counting periodic orbits of length $\leq N$. For an algebraic group $G$ we express the error term via the $\ell$-adic cohomological zeta function of $G$., Comment: 176 pages, 6 figures, v2: reorganised, extended some of the basic material

Published
2022

48. Generalized class polynomials

Author

Houben, Marc and Streng, Marco

Subjects
Mathematics - Number Theory, 11Y16, 11Y40, 11R29, 11G15
Abstract

The Hilbert class polynomial has as roots the j-invariants of elliptic curves whose endomorphism ring is a given imaginary quadratic order. It can be used to compute elliptic curves over finite fields with a prescribed number of points. Since its coefficients are typically rather large, there has been continued interest in finding alternative modular functions whose corresponding class polynomials are smaller. Best known are Weber's functions, that reduce the size by a factor of 72 for a positive density subset of imaginary quadratic discriminants. On the other hand, Br\"oker and Stevenhagen showed that no modular function will ever do better than a factor of 100.83. We introduce a generalization of class polynomials, with reduction factors that are not limited by the Br\"oker-Stevenhagen bound. We provide examples matching Weber's reduction factor. For an infinite family of discriminants, their reduction factors surpass those of all previously known modular functions by a factor at least 2., Comment: 28 pp. 5 fig

Published
2022

50. Extracellular vesicles as potential biomarkers for diagnosis and recurrence detection of hepatocellular carcinoma

Author

Mazen A. Juratli, Nicola S. Pollmann, Elsie Oppermann, Annika Mohr, Dhruvajyoti Roy, Andreas Schnitzbauer, Sabine Michalik, Thomas Vogl, Nikolas H. Stoecklein, Philipp Houben, Shadi Katou, Felix Becker, Jens Peter Hoelzen, Andreas Andreou, Andreas Pascher, Wolf O. Bechstein, and Benjamin Struecker

Subjects
Hepatocellular carcinoma, Non-malignant liver disease, Extracellular vesicles, Surgery, Recurrence, Medicine, Science
Abstract

Abstract Hepatocellular carcinoma (HCC) is the most common primary malignant liver tumor and a leading cause of cancer-related deaths worldwide. However, current diagnostic tools are often invasive and technically limited. In the last decade, non-invasive liquid biopsies have transformed the field of clinical oncology, showcasing the potential of various liquid-biopsy derived analytes, including extracellular vesicles (EVs), to diagnose and monitor HCC progression and metastatic spreading, serving as promising novel biomarkers. A prospective single-center cohort study including 37 HCC patients and 20 patients with non-malignant liver disease (NMLD), as a control group, was conducted. Serum EVs of both groups were analyzed before and after liver surgery. The study utilized microbead-based magnetic particle sorting and flow cytometry to detect 37 characteristic surface proteins of EVs. Furthermore, HCC patients who experienced tumor recurrence (R-HCC) within 12 months after surgery were compared to HCC patients without recurrence (NR-HCC). EVs of R-HCC patients (n = 12/20) showed significantly lower levels of CD31 compared to EVs of NR-HCC patients (p = 0.0033). EVs of NMLD-group showed significantly higher expressions of CD41b than EVs of HCC group (p = 0.0286). The study determined significant short-term changes in CD19 dynamics in EVs of the NMLD-group, with preoperative values being significantly higher than postoperative values (p = 0.0065). This finding of our pilot study suggests EVs could play a role as potential targets for the development of diagnostic and therapeutic approaches for the early and non-invasive detection of HCC recurrence. Further, more in-depth analysis of the specific EV markers are needed to corroborate their potential role as diagnostic and therapeutic targets for HCC.

Published
2024
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