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1. UltraCortex: Submillimeter Ultra-High Field 9.4 T1 Brain MR Image Collection and Manual Cortical Segmentations

Author

Mahler, Lucas, Steiglechner, Julius, Bender, Benjamin, Lindig, Tobias, Ramadan, Dana, Bause, Jonas, Birk, Florian, Heule, Rahel, Charyasz, Edyta, Erb, Michael, Kumar, Vinod Jangir, Hagberg, Gisela E, Martin, Pascal, Lohmann, Gabriele, and Scheffler, Klaus

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

The UltraCortex repository (https://www.ultracortex.org) houses magnetic resonance imaging data of the human brain obtained at an ultra-high field strength of 9.4 T. It contains 86 structural MR images with spatial resolutions ranging from 0.6 to 0.8 mm. Additionally, the repository includes segmentations of 12 brains into gray and white matter compartments. These segmentations have been independently validated by two expert neuroradiologists, thus establishing them as a reliable gold standard. This resource provides researchers with access to high-quality brain imaging data and validated segmentations, facilitating neuroimaging studies and advancing our understanding of brain structure and function. Existing repositories do not accommodate field strengths beyond 7 T, nor do they offer validated segmentations, underscoring the significance of this new resource.

Published
2024

3. Event‐based modeling in temporal lobe epilepsy demonstrates progressive atrophy from cross‐sectional data

Author

Lopez, Seymour M, Aksman, Leon M, Oxtoby, Neil P, Vos, Sjoerd B, Rao, Jun, Kaestner, Erik, Alhusaini, Saud, Alvim, Marina, Bender, Benjamin, Bernasconi, Andrea, Bernasconi, Neda, Bernhardt, Boris, Bonilha, Leonardo, Caciagli, Lorenzo, Caldairou, Benoit, Caligiuri, Maria Eugenia, Calvet, Angels, Cendes, Fernando, Concha, Luis, Conde‐Blanco, Estefania, Davoodi‐Bojd, Esmaeil, de Bézenac, Christophe, Delanty, Norman, Desmond, Patricia M, Devinsky, Orrin, Domin, Martin, Duncan, John S, Focke, Niels K, Foley, Sonya, Fortunato, Francesco, Galovic, Marian, Gambardella, Antonio, Gleichgerrcht, Ezequiel, Guerrini, Renzo, Hamandi, Khalid, Ives‐Deliperi, Victoria, Jackson, Graeme D, Jahanshad, Neda, Keller, Simon S, Kochunov, Peter, Kotikalapudi, Raviteja, Kreilkamp, Barbara AK, Labate, Angelo, Larivière, Sara, Lenge, Matteo, Lui, Elaine, Malpas, Charles, Martin, Pascal, Mascalchi, Mario, Medland, Sarah E, Meletti, Stefano, Morita‐Sherman, Marcia E, Owen, Thomas W, Richardson, Mark, Riva, Antonella, Rüber, Theodor, Sinclair, Ben, Soltanian‐Zadeh, Hamid, Stein, Dan J, Striano, Pasquale, Taylor, Peter N, Thomopoulos, Sophia I, Thompson, Paul M, Tondelli, Manuela, Vaudano, Anna Elisabetta, Vivash, Lucy, Wang, Yujiang, Weber, Bernd, Whelan, Christopher D, Wiest, Roland, Winston, Gavin P, Yasuda, Clarissa Lin, McDonald, Carrie R, Alexander, Daniel C, Sisodiya, Sanjay M, Altmann, Andre, Bargalló, Núria, Bartolini, Emanuele, O’Brien, Terence J, and Thomas, Rhys H

Subjects
Brain Disorders, Epilepsy, Neurodegenerative, Neurosciences, Clinical Research, Biomedical Imaging, Aetiology, 2.1 Biological and endogenous factors, Neurological, Good Health and Well Being, Atrophy, Biomarkers, Cross-Sectional Studies, Epilepsy, Temporal Lobe, Hippocampus, Humans, Magnetic Resonance Imaging, Sclerosis, disease progression, duration of illness, event-based model, MTLE, patient staging, ENIGMA-Epilepsy Working Group, Clinical Sciences, Neurology & Neurosurgery
Abstract

ObjectiveRecent work has shown that people with common epilepsies have characteristic patterns of cortical thinning, and that these changes may be progressive over time. Leveraging a large multicenter cross-sectional cohort, we investigated whether regional morphometric changes occur in a sequential manner, and whether these changes in people with mesial temporal lobe epilepsy and hippocampal sclerosis (MTLE-HS) correlate with clinical features.MethodsWe extracted regional measures of cortical thickness, surface area, and subcortical brain volumes from T1-weighted (T1W) magnetic resonance imaging (MRI) scans collected by the ENIGMA-Epilepsy consortium, comprising 804 people with MTLE-HS and 1625 healthy controls from 25 centers. Features with a moderate case-control effect size (Cohen d ≥ .5) were used to train an event-based model (EBM), which estimates a sequence of disease-specific biomarker changes from cross-sectional data and assigns a biomarker-based fine-grained disease stage to individual patients. We tested for associations between EBM disease stage and duration of epilepsy, age at onset, and antiseizure medicine (ASM) resistance.ResultsIn MTLE-HS, decrease in ipsilateral hippocampal volume along with increased asymmetry in hippocampal volume was followed by reduced thickness in neocortical regions, reduction in ipsilateral thalamus volume, and finally, increase in ipsilateral lateral ventricle volume. EBM stage was correlated with duration of illness (Spearman ρ = .293, p = 7.03 × 10-16 ), age at onset (ρ = -.18, p = 9.82 × 10-7 ), and ASM resistance (area under the curve = .59, p = .043, Mann-Whitney U test). However, associations were driven by cases assigned to EBM Stage 0, which represents MTLE-HS with mild or nondetectable abnormality on T1W MRI.SignificanceFrom cross-sectional MRI, we reconstructed a disease progression model that highlights a sequence of MRI changes that aligns with previous longitudinal studies. This model could be used to stage MTLE-HS subjects in other cohorts and help establish connections between imaging-based progression staging and clinical features.

Published
2022

5. Topographic divergence of atypical cortical asymmetry and atrophy patterns in temporal lobe epilepsy

Author

Park, Bo-yong, Larivière, Sara, Rodríguez-Cruces, Raul, Royer, Jessica, Tavakol, Shahin, Wang, Yezhou, Caciagli, Lorenzo, Caligiuri, Maria Eugenia, Gambardella, Antonio, Concha, Luis, Keller, Simon S, Cendes, Fernando, Alvim, Marina KM, Yasuda, Clarissa, Bonilha, Leonardo, Gleichgerrcht, Ezequiel, Focke, Niels K, Kreilkamp, Barbara AK, Domin, Martin, von Podewils, Felix, Langner, Soenke, Rummel, Christian, Rebsamen, Michael, Wiest, Roland, Martin, Pascal, Kotikalapudi, Raviteja, Bender, Benjamin, O’Brien, Terence J, Law, Meng, Sinclair, Benjamin, Vivash, Lucy, Kwan, Patrick, Desmond, Patricia M, Malpas, Charles B, Lui, Elaine, Alhusaini, Saud, Doherty, Colin P, Cavalleri, Gianpiero L, Delanty, Norman, Kälviäinen, Reetta, Jackson, Graeme D, Kowalczyk, Magdalena, Mascalchi, Mario, Semmelroch, Mira, Thomas, Rhys H, Soltanian-Zadeh, Hamid, Davoodi-Bojd, Esmaeil, Zhang, Junsong, Lenge, Matteo, Guerrini, Renzo, Bartolini, Emanuele, Hamandi, Khalid, Foley, Sonya, Weber, Bernd, Depondt, Chantal, Absil, Julie, Carr, Sarah JA, Abela, Eugenio, Richardson, Mark P, Devinsky, Orrin, Severino, Mariasavina, Striano, Pasquale, Parodi, Costanza, Tortora, Domenico, Hatton, Sean N, Vos, Sjoerd B, Duncan, John S, Galovic, Marian, Whelan, Christopher D, Bargalló, Núria, Pariente, Jose, Conde-Blanco, Estefania, Vaudano, Anna Elisabetta, Tondelli, Manuela, Meletti, Stefano, Kong, Xiang‐Zhen, Francks, Clyde, Fisher, Simon E, Caldairou, Benoit, Ryten, Mina, Labate, Angelo, Sisodiya, Sanjay M, Thompson, Paul M, McDonald, Carrie R, Bernasconi, Andrea, Bernasconi, Neda, and Bernhardt, Boris C

Subjects
Epilepsy, Neurodegenerative, Clinical Research, Brain Disorders, Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Neurological, Adult, Atrophy, Connectome, Epilepsy, Temporal Lobe, Hippocampus, Humans, Magnetic Resonance Imaging, temporal lobe epilepsy, asymmetry, cortical thickness, multi-site, gradients, Medical and Health Sciences, Psychology and Cognitive Sciences, Neurology & Neurosurgery
Abstract

Temporal lobe epilepsy, a common drug-resistant epilepsy in adults, is primarily a limbic network disorder associated with predominant unilateral hippocampal pathology. Structural MRI has provided an in vivo window into whole-brain grey matter structural alterations in temporal lobe epilepsy relative to controls, by either mapping (i) atypical inter-hemispheric asymmetry; or (ii) regional atrophy. However, similarities and differences of both atypical asymmetry and regional atrophy measures have not been systematically investigated. Here, we addressed this gap using the multisite ENIGMA-Epilepsy dataset comprising MRI brain morphological measures in 732 temporal lobe epilepsy patients and 1418 healthy controls. We compared spatial distributions of grey matter asymmetry and atrophy in temporal lobe epilepsy, contextualized their topographies relative to spatial gradients in cortical microstructure and functional connectivity calculated using 207 healthy controls obtained from Human Connectome Project and an independent dataset containing 23 temporal lobe epilepsy patients and 53 healthy controls and examined clinical associations using machine learning. We identified a marked divergence in the spatial distribution of atypical inter-hemispheric asymmetry and regional atrophy mapping. The former revealed a temporo-limbic disease signature while the latter showed diffuse and bilateral patterns. Our findings were robust across individual sites and patients. Cortical atrophy was significantly correlated with disease duration and age at seizure onset, while degrees of asymmetry did not show a significant relationship to these clinical variables. Our findings highlight that the mapping of atypical inter-hemispheric asymmetry and regional atrophy tap into two complementary aspects of temporal lobe epilepsy-related pathology, with the former revealing primary substrates in ipsilateral limbic circuits and the latter capturing bilateral disease effects. These findings refine our notion of the neuropathology of temporal lobe epilepsy and may inform future discovery and validation of complementary MRI biomarkers in temporal lobe epilepsy.

Published
2022

6. Fast Fisher-Lee approach for conductance calculations on BTB-based molecular junctions: effects of isomerization and electrode coupling

Author

Pitié, Sylvain, Seydou, Mahamadou, Dappe, Yannick. J., Martin, Pascal, Maurel, François, and Lacroix, Jean Christophe

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

In this work, we have implemented the Fisher-Lee formalism to couple non-equilibrium Green functions with tight-binding Density Functional to tackle large molecular systems. This method is used to determine the decay constant of a set of oligomers based on seven different monomers taken from the literature in the non-resonant tunneling regime. Results show good agreement with experimental measurements. The approach is then applied to explore the conformational pattern effect as well as the asymmetry and the strength of coupling with the electrode of bisthienylbenzene oligomers sandwiched between gold (Au),titanium (Ti)and graphene (G)) electrodes The results indicate that conformational patterns have low impact on the conductance, since the delocalization of {\pi}-electrons exhibits similar behavior for all the conformations explored. The calculated attenuation factor is found to be comparable with the strength of contact coupling (Ti > Au = G). Electronic analysis of metal-molecule interactions reveals the ionic nature of Ti-C bonds, through the emergence of a local dipole contributing to the work function variation of 0.35 eV. In addition, the Ti d-orbitals are found to be strongly coupled with the lowest unoccupied orbital (LUMO) of BTB, thus facilitating charge transfer from Ti to the molecule, at the origin of this strong interfacial dipole. However, the Au-C bond is found to be similar to the C-C bond, with pure covalent character. The results confirm the hole transport mechanism observed experimentally in the cases of Au-(BTB)n-Au and Au-(BTB)n-Ti, and predict possible combined mechanism of both hole and electron transport in the case of Ti(BTB)n-Ti.

Published
2021

7. Long-term efficacy and safety of nusinersen in adults with 5q spinal muscular atrophy: a prospective European multinational observational study

Author

Günther, René, Wurster, Claudia Diana, Brakemeier, Svenja, Osmanovic, Alma, Schreiber-Katz, Olivia, Petri, Susanne, Uzelac, Zeljko, Hiebeler, Miriam, Thiele, Simone, Walter, Maggie C., Weiler, Markus, Kessler, Tobias, Freigang, Maren, Lapp, Hanna Sophie, Cordts, Isabell, Lingor, Paul, Deschauer, Marcus, Hahn, Andreas, Martakis, Kyriakos, Steinbach, Robert, Ilse, Benjamin, Rödiger, Annekathrin, Bellut, Julia, Nentwich, Julia, Zeller, Daniel, Muhandes, Mohamad Tareq, Baum, Tobias, Christoph Koch, Jan, Schrank, Bertold, Fischer, Sophie, Hermann, Andreas, Kamm, Christoph, Naegel, Steffen, Mensch, Alexander, Weber, Markus, Neuwirth, Christoph, Lehmann, Helmar C., Wunderlich, Gilbert, Stadler, Christian, Tomforde, Maike, George, Annette, Groß, Martin, Pechmann, Astrid, Kirschner, Janbernd, Türk, Matthias, Schimmel, Mareike, Bernert, Günther, Martin, Pascal, Rauscher, Christian, Meyer zu Hörste, Gerd, Baum, Petra, Löscher, Wolfgang, Flotats-Bastardas, Marina, Köhler, Cornelia, Probst-Schendzielorz, Kristina, Goldbach, Susanne, Schara-Schmidt, Ulrike, Müller-Felber, Wolfgang, Lochmüller, Hanns, von Velsen, Otgonzul, Kleinschnitz, Christoph, Ludolph, Albert C., and Hagenacker, Tim

Published
2024
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8. The ENIGMA‐Epilepsy working group: Mapping disease from large data sets

Author

Sisodiya, Sanjay M, Whelan, Christopher D, Hatton, Sean N, Huynh, Khoa, Altmann, Andre, Ryten, Mina, Vezzani, Annamaria, Caligiuri, Maria Eugenia, Labate, Angelo, Gambardella, Antonio, Ives‐Deliperi, Victoria, Meletti, Stefano, Munsell, Brent C, Bonilha, Leonardo, Tondelli, Manuela, Rebsamen, Michael, Rummel, Christian, Vaudano, Anna Elisabetta, Wiest, Roland, Balachandra, Akshara R, Bargalló, Núria, Bartolini, Emanuele, Bernasconi, Andrea, Bernasconi, Neda, Bernhardt, Boris, Caldairou, Benoit, Carr, Sarah JA, Cavalleri, Gianpiero L, Cendes, Fernando, Concha, Luis, Desmond, Patricia M, Domin, Martin, Duncan, John S, Focke, Niels K, Guerrini, Renzo, Hamandi, Khalid, Jackson, Graeme D, Jahanshad, Neda, Kälviäinen, Reetta, Keller, Simon S, Kochunov, Peter, Kowalczyk, Magdalena A, Kreilkamp, Barbara AK, Kwan, Patrick, Lariviere, Sara, Lenge, Matteo, Lopez, Seymour M, Martin, Pascal, Mascalchi, Mario, Moreira, José CV, Morita‐Sherman, Marcia E, Pardoe, Heath R, Pariente, Jose C, Raviteja, Kotikalapudi, Rocha, Cristiane S, Rodríguez‐Cruces, Raúl, Seeck, Margitta, Semmelroch, Mira KHG, Sinclair, Benjamin, Soltanian‐Zadeh, Hamid, Stein, Dan J, Striano, Pasquale, Taylor, Peter N, Thomas, Rhys H, Thomopoulos, Sophia I, Velakoulis, Dennis, Vivash, Lucy, Weber, Bernd, Yasuda, Clarissa Lin, Zhang, Junsong, Thompson, Paul M, McDonald, Carrie R, Abela, Eugenio, Absil, Julie, Adams, Sophia, Alhusaini, Saud, Alvim, Marina, Balestrini, Simona, Bender, Benjamin, Bergo, Felipe, Bernardes, Tauana, Calvo, Anna, Carreno, Mar, Cherubini, Andrea, David, Philippe, Davoodi‐Bojd, Esmaeil, Delanty, Norman, Depondt, Chantal, Devinsky, Orrin, Doherty, Colin, França, Wendy Caroline, Franceschet, Leticia, Hibar, Derrek P, Ishikawa, Akari, Kaestner, Erik, Langner, Soenke, Liu, Min, Mirandola, Laura, Naylor, Jillian, and Nazem‐Zadeh, Mohammad‐reza

Subjects
Brain Disorders, Biomedical Imaging, Neurosciences, Epilepsy, Neurodegenerative, 2.1 Biological and endogenous factors, Aetiology, Neurological, covariance, deep learning, DTI, event-based modeling, gene expression, genetics, imaging, MRI, quantitative, rsfMRI, ENIGMA Consortium Epilepsy Working Group, Cognitive Sciences, Experimental Psychology
Abstract

Epilepsy is a common and serious neurological disorder, with many different constituent conditions characterized by their electro clinical, imaging, and genetic features. MRI has been fundamental in advancing our understanding of brain processes in the epilepsies. Smaller-scale studies have identified many interesting imaging phenomena, with implications both for understanding pathophysiology and improving clinical care. Through the infrastructure and concepts now well-established by the ENIGMA Consortium, ENIGMA-Epilepsy was established to strengthen epilepsy neuroscience by greatly increasing sample sizes, leveraging ideas and methods established in other ENIGMA projects, and generating a body of collaborating scientists and clinicians to drive forward robust research. Here we review published, current, and future projects, that include structural MRI, diffusion tensor imaging (DTI), and resting state functional MRI (rsfMRI), and that employ advanced methods including structural covariance, and event-based modeling analysis. We explore age of onset- and duration-related features, as well as phenomena-specific work focusing on particular epilepsy syndromes or phenotypes, multimodal analyses focused on understanding the biology of disease progression, and deep learning approaches. We encourage groups who may be interested in participating to make contact to further grow and develop ENIGMA-Epilepsy.

Published
2022

9. Structural network alterations in focal and generalized epilepsy assessed in a worldwide ENIGMA study follow axes of epilepsy risk gene expression

Author

Larivière, Sara, Royer, Jessica, Rodríguez-Cruces, Raúl, Paquola, Casey, Caligiuri, Maria Eugenia, Gambardella, Antonio, Concha, Luis, Keller, Simon S, Cendes, Fernando, Yasuda, Clarissa L, Bonilha, Leonardo, Gleichgerrcht, Ezequiel, Focke, Niels K, Domin, Martin, von Podewills, Felix, Langner, Soenke, Rummel, Christian, Wiest, Roland, Martin, Pascal, Kotikalapudi, Raviteja, O’Brien, Terence J, Sinclair, Benjamin, Vivash, Lucy, Desmond, Patricia M, Lui, Elaine, Vaudano, Anna Elisabetta, Meletti, Stefano, Tondelli, Manuela, Alhusaini, Saud, Doherty, Colin P, Cavalleri, Gianpiero L, Delanty, Norman, Kälviäinen, Reetta, Jackson, Graeme D, Kowalczyk, Magdalena, Mascalchi, Mario, Semmelroch, Mira, Thomas, Rhys H, Soltanian-Zadeh, Hamid, Davoodi-Bojd, Esmaeil, Zhang, Junsong, Winston, Gavin P, Griffin, Aoife, Singh, Aditi, Tiwari, Vijay K, Kreilkamp, Barbara AK, Lenge, Matteo, Guerrini, Renzo, Hamandi, Khalid, Foley, Sonya, Rüber, Theodor, Weber, Bernd, Depondt, Chantal, Absil, Julie, Carr, Sarah JA, Abela, Eugenio, Richardson, Mark P, Devinsky, Orrin, Severino, Mariasavina, Striano, Pasquale, Tortora, Domenico, Kaestner, Erik, Hatton, Sean N, Vos, Sjoerd B, Caciagli, Lorenzo, Duncan, John S, Whelan, Christopher D, Thompson, Paul M, Sisodiya, Sanjay M, Bernasconi, Andrea, Labate, Angelo, McDonald, Carrie R, Bernasconi, Neda, and Bernhardt, Boris C

Subjects
Neurodegenerative, Genetics, Neurosciences, Brain Disorders, Epilepsy, Aetiology, 2.1 Biological and endogenous factors, Neurological, Adult, Connectome, Epilepsy, Generalized, Epilepsy, Temporal Lobe, Gene Expression, Humans, Immunoglobulin E, Magnetic Resonance Imaging, Nerve Net
Abstract

Epilepsy is associated with genetic risk factors and cortico-subcortical network alterations, but associations between neurobiological mechanisms and macroscale connectomics remain unclear. This multisite ENIGMA-Epilepsy study examined whole-brain structural covariance networks in patients with epilepsy and related findings to postmortem epilepsy risk gene expression patterns. Brain network analysis included 578 adults with temporal lobe epilepsy (TLE), 288 adults with idiopathic generalized epilepsy (IGE), and 1328 healthy controls from 18 centres worldwide. Graph theoretical analysis of structural covariance networks revealed increased clustering and path length in orbitofrontal and temporal regions in TLE, suggesting a shift towards network regularization. Conversely, people with IGE showed decreased clustering and path length in fronto-temporo-parietal cortices, indicating a random network configuration. Syndrome-specific topological alterations reflected expression patterns of risk genes for hippocampal sclerosis in TLE and for generalized epilepsy in IGE. These imaging-transcriptomic signatures could potentially guide diagnosis or tailor therapeutic approaches to specific epilepsy syndromes.

Published
2022

10. The BORDER family of negative transcription elongation factors regulates flowering time in Arabidopsis

Author

Yu, Xuhong, Martin, Pascal GP, Zhang, Yixiang, Trinidad, Jonathan C, Xu, Feifei, Huang, Jie, Thum, Karen E, Li, Ke, Zhao, ShuZhen, Gu, Yangnan, Wang, Xingjun, and Michaels, Scott D

Subjects
Genetics, Animals, Arabidopsis, Arabidopsis Proteins, Flowers, Histones, RNA Polymerase II, Transcription, Genetic, BORDER, FLOWERING LOCUS C, RNA polymerase II, flowering time, pausing, transcription elongation, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Transcription initiation has long been considered a primary regulatory step in gene expression. Recent work, however, shows that downstream events, such as transcription elongation, can also play important roles.1-3 A well-characterized example from animals is promoter-proximal pausing, where transcriptionally engaged Pol II accumulates 30-50 bp downstream of the transcription start site (TSS) and is thought to enable rapid gene activation.2 Plants do not make widespread use of promoter-proximal pausing; however, in a phenomenon known as 3' pausing, a significant increase in Pol II is observed near the transcript end site (TES) of many genes.4-6 Previous work has shown that 3' pausing is promoted by the BORDER (BDR) family of negative transcription elongation factors. Here we show that BDR proteins play key roles in gene repression. Consistent with BDR proteins acting to slow or pause elongating Pol II, BDR-repressed genes are characterized by high levels of Pol II occupancy, yet low levels of mRNA. The BDR proteins physically interact with FPA,7 one of approximately two dozen genes collectively referred to as the autonomous floral-promotion pathway,8 which are necessary for the repression of the flowering time gene FLOWERING LOCUS C (FLC).9-11 In early-flowering strains, FLC expression is repressed by repressive histone modifications, such as histone H3 lysine 27 trimethylation (H3K27me3), thereby allowing the plants to flower early. These results suggest that the repression of transcription elongation by BDR proteins may allow for the temporary pausing of transcription or facilitate the long-term repression of genes by repressive histone modifications.

Published
2021

12. Artificial intelligence for classification of temporal lobe epilepsy with ROI-level MRI data: A worldwide ENIGMA-Epilepsy study

Author

Gleichgerrcht, Ezequiel, Munsell, Brent C, Alhusaini, Saud, Alvim, Marina KM, Bargalló, Núria, Bender, Benjamin, Bernasconi, Andrea, Bernasconi, Neda, Bernhardt, Boris, Blackmon, Karen, Caligiuri, Maria Eugenia, Cendes, Fernando, Concha, Luis, Desmond, Patricia M, Devinsky, Orrin, Doherty, Colin P, Domin, Martin, Duncan, John S, Focke, Niels K, Gambardella, Antonio, Gong, Bo, Guerrini, Renzo, Hatton, Sean N, Kälviäinen, Reetta, Keller, Simon S, Kochunov, Peter, Kotikalapudi, Raviteja, Kreilkamp, Barbara AK, Labate, Angelo, Langner, Soenke, Larivière, Sara, Lenge, Matteo, Lui, Elaine, Martin, Pascal, Mascalchi, Mario, Meletti, Stefano, O'Brien, Terence J, Pardoe, Heath R, Pariente, Jose C, Rao, Jun Xian, Richardson, Mark P, Rodríguez-Cruces, Raúl, Rüber, Theodor, Sinclair, Ben, Soltanian-Zadeh, Hamid, Stein, Dan J, Striano, Pasquale, Taylor, Peter N, Thomas, Rhys H, Vaudano, Anna Elisabetta, Vivash, Lucy, von Podewills, Felix, Vos, Sjoerd B, Weber, Bernd, Yao, Yi, Yasuda, Clarissa Lin, Zhang, Junsong, Thompson, Paul M, Sisodiya, Sanjay M, McDonald, Carrie R, Bonilha, Leonardo, Group, ENIGMA-Epilepsy Working, Altmann, Andre, Depondt, Chantal, Galovic, Marian, Thomopoulos, Sophia I, and Wiest, Roland

Subjects
Biomedical Imaging, Neurodegenerative, Neurosciences, Brain Disorders, Prevention, Epilepsy, 2.1 Biological and endogenous factors, Aetiology, Neurological, Artificial Intelligence, Brain, Epilepsy, Temporal Lobe, Hippocampus, Humans, Magnetic Resonance Imaging, Sclerosis, Support Vector Machine, Temporal lobe epilepsy, Machine learning, Artificial inteligence, ENIGMA-Epilepsy Working Group
Abstract

Artificial intelligence has recently gained popularity across different medical fields to aid in the detection of diseases based on pathology samples or medical imaging findings. Brain magnetic resonance imaging (MRI) is a key assessment tool for patients with temporal lobe epilepsy (TLE). The role of machine learning and artificial intelligence to increase detection of brain abnormalities in TLE remains inconclusive. We used support vector machine (SV) and deep learning (DL) models based on region of interest (ROI-based) structural (n = 336) and diffusion (n = 863) brain MRI data from patients with TLE with ("lesional") and without ("non-lesional") radiographic features suggestive of underlying hippocampal sclerosis from the multinational (multi-center) ENIGMA-Epilepsy consortium. Our data showed that models to identify TLE performed better or similar (68-75%) compared to models to lateralize the side of TLE (56-73%, except structural-based) based on diffusion data with the opposite pattern seen for structural data (67-75% to diagnose vs. 83% to lateralize). In other aspects, structural and diffusion-based models showed similar classification accuracies. Our classification models for patients with hippocampal sclerosis were more accurate (68-76%) than models that stratified non-lesional patients (53-62%). Overall, SV and DL models performed similarly with several instances in which SV mildly outperformed DL. We discuss the relative performance of these models with ROI-level data and the implications for future applications of machine learning and artificial intelligence in epilepsy care.

Published
2021

13. Network-based atrophy modeling in the common epilepsies: A worldwide ENIGMA study

Author

Larivière, Sara, Rodríguez-Cruces, Raúl, Royer, Jessica, Caligiuri, Maria Eugenia, Gambardella, Antonio, Concha, Luis, Keller, Simon S, Cendes, Fernando, Yasuda, Clarissa, Bonilha, Leonardo, Gleichgerrcht, Ezequiel, Focke, Niels K, Domin, Martin, von Podewills, Felix, Langner, Soenke, Rummel, Christian, Wiest, Roland, Martin, Pascal, Kotikalapudi, Raviteja, O’Brien, Terence J, Sinclair, Benjamin, Vivash, Lucy, Desmond, Patricia M, Alhusaini, Saud, Doherty, Colin P, Cavalleri, Gianpiero L, Delanty, Norman, Kälviäinen, Reetta, Jackson, Graeme D, Kowalczyk, Magdalena, Mascalchi, Mario, Semmelroch, Mira, Thomas, Rhys H, Soltanian-Zadeh, Hamid, Davoodi-Bojd, Esmaeil, Zhang, Junsong, Lenge, Matteo, Guerrini, Renzo, Bartolini, Emanuele, Hamandi, Khalid, Foley, Sonya, Weber, Bernd, Depondt, Chantal, Absil, Julie, Carr, Sarah JA, Abela, Eugenio, Richardson, Mark P, Devinsky, Orrin, Severino, Mariasavina, Striano, Pasquale, Tortora, Domenico, Hatton, Sean N, Vos, Sjoerd B, Duncan, John S, Whelan, Christopher D, Thompson, Paul M, Sisodiya, Sanjay M, Bernasconi, Andrea, Labate, Angelo, McDonald, Carrie R, Bernasconi, Neda, and Bernhardt, Boris C

Subjects
Mental Health, Brain Disorders, Epilepsy, Clinical Research, Neurosciences, Neurodegenerative, Aetiology, 2.1 Biological and endogenous factors, Neurological
Abstract

Epilepsy is increasingly conceptualized as a network disorder. In this cross-sectional mega-analysis, we integrated neuroimaging and connectome analysis to identify network associations with atrophy patterns in 1021 adults with epilepsy compared to 1564 healthy controls from 19 international sites. In temporal lobe epilepsy, areas of atrophy colocalized with highly interconnected cortical hub regions, whereas idiopathic generalized epilepsy showed preferential subcortical hub involvement. These morphological abnormalities were anchored to the connectivity profiles of distinct disease epicenters, pointing to temporo-limbic cortices in temporal lobe epilepsy and fronto-central cortices in idiopathic generalized epilepsy. Negative effects of age on atrophy further revealed a strong influence of connectome architecture in temporal lobe, but not idiopathic generalized, epilepsy. Our findings were reproduced across individual sites and single patients and were robust across different analytical methods. Through worldwide collaboration in ENIGMA-Epilepsy, we provided deeper insights into the macroscale features that shape the pathophysiology of common epilepsies.

Published
2020

14. White matter abnormalities across different epilepsy syndromes in adults: an ENIGMA-Epilepsy study

Author

Hatton, Sean N, Huynh, Khoa H, Bonilha, Leonardo, Abela, Eugenio, Alhusaini, Saud, Altmann, Andre, Alvim, Marina KM, Balachandra, Akshara R, Bartolini, Emanuele, Bender, Benjamin, Bernasconi, Neda, Bernasconi, Andrea, Bernhardt, Boris, Bargallo, Núria, Caldairou, Benoit, Caligiuri, Maria E, Carr, Sarah JA, Cavalleri, Gianpiero L, Cendes, Fernando, Concha, Luis, Davoodi-bojd, Esmaeil, Desmond, Patricia M, Devinsky, Orrin, Doherty, Colin P, Domin, Martin, Duncan, John S, Focke, Niels K, Foley, Sonya F, Gambardella, Antonio, Gleichgerrcht, Ezequiel, Guerrini, Renzo, Hamandi, Khalid, Ishikawa, Akari, Keller, Simon S, Kochunov, Peter V, Kotikalapudi, Raviteja, Kreilkamp, Barbara AK, Kwan, Patrick, Labate, Angelo, Langner, Soenke, Lenge, Matteo, Liu, Min, Lui, Elaine, Martin, Pascal, Mascalchi, Mario, Moreira, José CV, Morita-Sherman, Marcia E, O’Brien, Terence J, Pardoe, Heath R, Pariente, José C, Ribeiro, Letícia F, Richardson, Mark P, Rocha, Cristiane S, Rodríguez-Cruces, Raúl, Rosenow, Felix, Severino, Mariasavina, Sinclair, Benjamin, Soltanian-Zadeh, Hamid, Striano, Pasquale, Taylor, Peter N, Thomas, Rhys H, Tortora, Domenico, Velakoulis, Dennis, Vezzani, Annamaria, Vivash, Lucy, von Podewils, Felix, Vos, Sjoerd B, Weber, Bernd, Winston, Gavin P, Yasuda, Clarissa L, Zhu, Alyssa H, Thompson, Paul M, Whelan, Christopher D, Jahanshad, Neda, Sisodiya, Sanjay M, and McDonald, Carrie R

Subjects
Genetics, Neurodegenerative, Epilepsy, Clinical Research, Brain Disorders, Neurosciences, Biomedical Imaging, Aetiology, 2.1 Biological and endogenous factors, Neurological, Adult, Brain, Diffusion Magnetic Resonance Imaging, Epileptic Syndromes, Female, Humans, Image Interpretation, Computer-Assisted, Male, Middle Aged, White Matter, epilepsy, diffusion tensor imaging, multisite analysis, white matter, Medical and Health Sciences, Psychology and Cognitive Sciences, Neurology & Neurosurgery
Abstract

The epilepsies are commonly accompanied by widespread abnormalities in cerebral white matter. ENIGMA-Epilepsy is a large quantitative brain imaging consortium, aggregating data to investigate patterns of neuroimaging abnormalities in common epilepsy syndromes, including temporal lobe epilepsy, extratemporal epilepsy, and genetic generalized epilepsy. Our goal was to rank the most robust white matter microstructural differences across and within syndromes in a multicentre sample of adult epilepsy patients. Diffusion-weighted MRI data were analysed from 1069 healthy controls and 1249 patients: temporal lobe epilepsy with hippocampal sclerosis (n = 599), temporal lobe epilepsy with normal MRI (n = 275), genetic generalized epilepsy (n = 182) and non-lesional extratemporal epilepsy (n = 193). A harmonized protocol using tract-based spatial statistics was used to derive skeletonized maps of fractional anisotropy and mean diffusivity for each participant, and fibre tracts were segmented using a diffusion MRI atlas. Data were harmonized to correct for scanner-specific variations in diffusion measures using a batch-effect correction tool (ComBat). Analyses of covariance, adjusting for age and sex, examined differences between each epilepsy syndrome and controls for each white matter tract (Bonferroni corrected at P

Published
2020

15. Safety and efficacy of zilucoplan in patients with generalised myasthenia gravis (RAISE): a randomised, double-blind, placebo-controlled, phase 3 study

Author

Sembinelli, Dylan, Teitelbaum, Jeanne, Nicolle, Michael, Bernard, Emilien, Svahn, Juliette, Spinazzi, Marco, Stojkovic, Tanya, Demeret, Sophie, Weiss, Nicolas, Le Guennec, Loïc, Messai, Sihame, Tranchant, Christine, Nadaj-Pakleza, Aleksandra, Chanson, Jean-Baptiste, Suliman, Muhtadi, Zaidi, Leila, Tard, Celine, Lecointe, Peggy, Zschüntzsch, Jana, Schmidt, Jens, Glaubitz, Stefanie, Zeng, Rachel, Scholl, Matthias, Kowarik, Markus, Ziemann, Ulf, Krumbholz, Markus, Martin, Pascal, Ruschil, Christoph, Dünschede, Jutta, Kemmner, Roswitha, Rumpel, Natalie, Berger, Benjamin, Totzeck, Andreas, Hagenacker, Tim, Stolte, Benjamin, Iorio, Raffaele, Evoli, Amelia, Falso, Silvia, Antozzi, Carlo, Frangiamore, Rita, Vanoli, Fiammetta, Rinaldi, Elena, Deguchi, Kazushi, Minami, Naoya, Nagane, Yuriko, Suzuki, Yasushi, Ishida, Sayaka, Suzuki, Shigeaki, Nakahara, Jin, Nagaoka, Astushi, Yoshimura, Shunsuke, Konno, Shingo, Tsuya, Youko, Uzawa, Akiyuki, Kubota, Tomoya, Takahashi, Masanori, Okuno, Tatsusada, Murai, Hiroyuki, Gilhus, Nils Erik, Boldingh, Marion, Rønning, Tone Hakvåg, Chyrchel-Paszkiewicz, Urszula, Kumor, Klaudiusz, Zielinski, Tomasz, Banaszkiewicz, Krzysztof, Błaż, Michał, Kłósek, Agata, Świderek-Matysiak, Mariola, Szczudlik, Andrzej, Paśko, Aneta, Szczechowski, Lech, Banach, Marta, Ilkowski, Jan, Kapetanovic Garcia, Solange, Ortiz Bagan, Patricia, Belén Cánovas Segura, Ana, Turon Sans, Joana, Vidal Fernandez, Nuria, Cortes Vicente, Elena, Rodrigo Armenteros, Patricia, Ashraghi, Mohammad, Cavey, Ana, Haslam, Liam, Emery, Anna, Liow, Kore, Yegiaian, Sharon, Barboi, Alexandru, Vazquez, Rosa Maria, Lennon, Joshua, Pascuzzi, Robert M, Bodkin, Cynthia, Guingrich, Sandra, Comer, Adam, Bromberg, Mark, Janecki, Teresa, Saba, Sami, Tellez, Marco, Elsheikh, Bakri, Freimer, Miriam, Heintzman, Sarah, Govindarajan, Raghav, Guptill, Jeffrey, Massey, Janice M, Juel, Vern, Gonzalez, Natalia, Habib, Ali A, Mozaffar, Tahseen, Korb, Manisha, Goyal, Namita, Machemehl, Hannah, Manousakis, Georgios, Allen, Jeffrey, Harper, Emily, Farmakidis, Constantine, Saavedra, Lilli, Dimachkie, Mazen, Pasnoor, Mamatha, Akhter, Salma, Beydoun, Said, McIlduff, Courtney, Nye, Joan, Roy, Bhaskar, Munro Sheldon, Bailey, Nowak, Richard, Barnes, Benjamin, Rivner, Michael, Suresh, Niraja, Shaw, Jessica, Harvey, Brittany, Lam, Lucy, Thomas, Nikki, Chopra, Manisha, Traub, Rebecca E, Jones, Sarah, Wagoner, Mary, Smajic, Sejla, Aly, Radwa, Katz, Jonathan, Chen, Henry, Miller, Robert G, Jenkins, Liberty, Khan, Shaida, Khatri, Bhupendra, Sershon, Lisa, Pavlakis, Pantelis, Holzberg, Shara, Li, Yuebing, Caristo, Irys B, Marquardt, Robert, Hastings, Debbie, Rube, Jacob, Lisak, Robert P, Choudhury, Aparna, Ruzhansky, Katherine, Sachdev, Amit, Shin, Susan, Bratton, Joan, Fetter, Mary, McKinnon, Naya, McKinnon, Jonathan, Sissons-Ross, Laura, Sahu, Amos, Distad, B Jane, Howard, James F, Jr, Bresch, Saskia, Genge, Angela, Hewamadduma, Channa, Hinton, John, Hussain, Yessar, Juntas-Morales, Raul, Kaminski, Henry J, Maniaol, Angelina, Mantegazza, Renato, Masuda, Masayuki, Sivakumar, Kumaraswamy, Śmiłowski, Marek, Utsugisawa, Kimiaki, Vu, Tuan, Weiss, Michael D, Zajda, Małgorzata, Boroojerdi, Babak, Brock, Melissa, de la Borderie, Guillemette, Duda, Petra W, Lowcock, Romana, Vanderkelen, Mark, and Leite, M Isabel

Published
2023
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20. Rectification effect in organic junctions based on aryl thin films covalently attached to a multilayer graphene electrode

Author

Barraud, Clément, Lemaitre, Matthieu, Bonnet, Roméo, Rastikian, Jacko, Salhani, Chloé, Lau, Stéphanie, Van Nguyen, Quyen, Decorse, Philippe, Lacroix, Jean-Christophe, Lafarge, Maria Luisa Della Rocca Philippe, and Martin, Pascal

Subjects
Physics - Applied Physics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

The quantum interaction between molecules and electrode s material at molecules-electrode interfaces is a major ingredient in the electronic transport properties of organic junctions. Driven by the coupling strength between the two materials, it results mainly in a broadening and an energy shift of the interacting molecular orbitals. Using new electrodes materials, such as the recent semi-conducting two-dimensional nanomaterials, has become a recent challenge in the field of molecular-organic electronics that opens new possibilities for controlling the interfacial electronic properties and thus the charge injection properties. In this article, we report the use of atomically thin two-dimensional multilayer graphene films as base electrode in organic junctions with a vertical architecture. The interfacial electronic structure dominated by the covalent bonding between bis-thienyl benzene diazonium-based molecules and the multilayer graphene electrode has been probed by ultraviolet photoelectron spectroscopy and the results compared with those obtained on junctions with standard Au electrodes. Room temperature injection properties of such interfaces have been also explored by electronic transport measurements. We find that, despite strong variations of the density of states, the Fermi energy and the injection barriers, both organic junctions with Au base electrodes and multilayer graphene base electrodes show similar electronic responses. We explain this observation by the strong orbital coupling occurring at the bottom electrode-bis(thienyl) benzene molecules interface and by the pinning of the hybridized molecular orbitals., Comment: 14 pages, 4 figures

Published
2018

21. Quantifying entropy production in active fluctuations of the hair-cell bundle from time irreversibility and uncertainty relations

Author

Roldán, Édgar, Barral, Jérémie, Martin, Pascal, Parrondo, Juan M. R., and Jülicher, Frank

Subjects
Condensed Matter - Statistical Mechanics, Physics - Biological Physics, Physics - Data Analysis, Statistics and Probability
Abstract

We introduce lower bounds for the rate of entropy production of an active stochastic process by quantifying the irreversibility of stochastic traces obtained from mesoscopic degrees of freedom. Our measures of irreversibility reveal signatures of time's arrow and provide bounds for entropy production even in the case of active fluctuations that have no drift. We apply these irreversibility measures to experimental recordings of spontaneous hair-bundle oscillations in mechanosensory hair cells from the ear of the bullfrog. By analysing the fluctuations of only the tip position of hair bundles, we reveal irreversibility in active oscillations and estimate an associated rate of entropy production of at least $\sim 3 k_{\rm B}$/s, on average. Applying thermodynamic uncertainty relations, we predict that measuring both the tip position of the hair bundle and the mechano-electrical transduction current that enters the hair cell leads to tighter lower bounds for the rate of entropy production, up to $\sim 10^3 k_{\rm B}$/s in the oscillatory regime., Comment: 15 pages (including Appendix), 10 figures

Published
2018

27. The Zinc Finger proteinSlZFP2 is essential for tomato fruit locular tissue morphogenesis

Author

Hoang, Gabriel, primary, Joana, Jorly, additional, Constantinescu, Dario, additional, Martin, Pascal G P, additional, Gadin, Stéphanie, additional, Mauxion, Jean-Philippe, additional, Brès, Cécile, additional, Garcia, Virginie, additional, Gonzalez, Nathalie, additional, Rothan, Christophe, additional, Bertin, Nadia, additional, Fernandez-Lochu, Lucie, additional, and Lemaire-Chamley, Martine, additional

Published
2024
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28. A worldwide ENIGMA study on epilepsy-related gray and white matter compromise across the adult lifespan

Author

Chen, Judy, primary, Ngo, Alexander, additional, Rodríguez-Cruces, Raúl, additional, Royer, Jessica, additional, Caligiuri, Maria Eugenia, additional, Gambardella, Antonio, additional, Concha, Luis, additional, Keller, Simon S., additional, Cendes, Fernando, additional, Yasuda, Clarissa L., additional, Alvim, Marina K. M., additional, Bonilha, Leonardo, additional, Gleichgerrcht, Ezequiel, additional, Focke, Niels K., additional, Kreilkamp, Barbara, additional, Domin, Martin, additional, von Podewils, Felix, additional, Langner, Soenke, additional, Rummel, Christian, additional, Wiest, Roland, additional, Martin, Pascal, additional, Kotikalapudi, Raviteja, additional, Bender, Benjamin, additional, O’Brien, Terence J., additional, Sinclair, Benjamin, additional, Vivash, Lucy, additional, Kwan, Patrick, additional, Desmond, Patricia M., additional, Lui, Elaine, additional, Duma, Gian Marco, additional, Bonanni, Paolo, additional, Ballerini, Alice, additional, Vaudano, Anna Elisabetta, additional, Meletti, Stefano, additional, Tondelli, Manuela, additional, Alhusaini, Saud, additional, Doherty, Colin P., additional, Cavalleri, Gianpiero L., additional, Delanty, Norman, additional, Kälviäinen, Reetta, additional, Jackson, Graeme D., additional, Kowalczyk, Magdalena, additional, Mascalchi, Mario, additional, Semmelroch, Mira, additional, Thomas, Rhys H., additional, Soltanian-Zadeh, Hamid, additional, Davoodi-Bojd, Esmaeil, additional, Zhang, Junsong, additional, Lenge, Matteo, additional, Guerrini, Renzo, additional, Bartolini, Emanuele, additional, Hamandi, Khalid, additional, Foley, Sonya, additional, Rüber, Theodor, additional, Bauer, Tobias, additional, Weber, Bernd, additional, Caldairou, Benoit, additional, Depondt, Chantal, additional, Absil, Julie, additional, Carr, Sarah J. A., additional, Abela, Eugenio, additional, Richardson, Mark P., additional, Devinsky, Orrin, additional, Pardoe, Heath, additional, Severino, Mariasavina, additional, Striano, Pasquale, additional, Tortora, Domenico, additional, Kaestner, Erik, additional, Hatton, Sean N., additional, Arienzo, Donatello, additional, Vos, Sjoerd B., additional, Ryten, Mina, additional, Taylor, Peter N., additional, Duncan, John S., additional, Whelan, Christopher D., additional, Galovic, Marian, additional, Winston, Gavin P., additional, Thomopoulos, Sophia I., additional, Thompson, Paul M., additional, Sisodiya, Sanjay M., additional, Labate, Angelo, additional, McDonald, Carrie R., additional, Caciagli, Lorenzo, additional, Bernasconi, Neda, additional, Bernasconi, Andrea, additional, Larivière, Sara, additional, Schrader, Dewi, additional, and Bernhardt, Boris C., additional

Published
2024
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33. Patterns of subregional cerebellar atrophy across epilepsy syndromes: An ENIGMA‐Epilepsy study

Author

Kerestes, Rebecca, primary, Perry, Andrew, additional, Vivash, Lucy, additional, O'Brien, Terence J., additional, Alvim, Marina K. M., additional, Arienzo, Donatello, additional, Aventurato, Ítalo K., additional, Ballerini, Alice, additional, Baltazar, Gabriel F., additional, Bargalló, Núria, additional, Bender, Benjamin, additional, Brioschi, Ricardo, additional, Bürkle, Eva, additional, Caligiuri, Maria Eugenia, additional, Cendes, Fernando, additional, de Tisi, Jane, additional, Duncan, John S., additional, Engel, Jerome P., additional, Foley, Sonya, additional, Fortunato, Francesco, additional, Gambardella, Antonio, additional, Giacomini, Thea, additional, Guerrini, Renzo, additional, Hall, Gerard, additional, Hamandi, Khalid, additional, Ives‐Deliperi, Victoria, additional, João, Rafael B., additional, Keller, Simon S., additional, Kleiser, Benedict, additional, Labate, Angelo, additional, Lenge, Matteo, additional, Marotta, Cassandra, additional, Martin, Pascal, additional, Mascalchi, Mario, additional, Meletti, Stefano, additional, Owens‐Walton, Conor, additional, Parodi, Costanza B., additional, Pascual‐Diaz, Saül, additional, Powell, David, additional, Rao, Jun, additional, Rebsamen, Michael, additional, Reiter, Johannes, additional, Riva, Antonella, additional, Rüber, Theodor, additional, Rummel, Christian, additional, Scheffler, Freda, additional, Severino, Mariasavina, additional, Silva, Lucas S., additional, Staba, Richard J., additional, Stein, Dan J., additional, Striano, Pasquale, additional, Taylor, Peter N., additional, Thomopoulos, Sophia I., additional, Thompson, Paul M., additional, Tortora, Domenico, additional, Vaudano, Anna Elisabetta, additional, Weber, Bernd, additional, Wiest, Roland, additional, Winston, Gavin P., additional, Yasuda, Clarissa L., additional, Zheng, Hong, additional, McDonald, Carrie R., additional, Sisodiya, Sanjay M., additional, and Harding, Ian H., additional

Published
2024
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37. Cerebrospinal fluid findings in patients with psychotic symptoms—a retrospective analysis

Author

Rattay, Tim W., Martin, Pascal, Vittore, Debora, Hengel, Holger, Cebi, Idil, Tünnerhoff, Johannes, Stefanou, Maria-Ioanna, Hoffmann, Jonatan F., von der Ehe, Katrin, Klaus, Johannes, Vonderschmitt, Julia, Herrmann, Matthias L., Bombach, Paula, Al Barazi, Hazar, Zeltner, Lena, Richter, Janina, Hesse, Klaus, Eckstein, Kathrin N., Klingberg, Stefan, and Wildgruber, Dirk

Published
2021
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39. Manager en responsabilité à l’heure du digital : Regards croisés de chercheurs

Author

Raveleau, Benoit, Sous la direction de, Ajzen, Michel, Aquilina, Manuelle, Bahier-Michel, Livia, Boutinet, Jean-Pierre, Chevallier, Elodie, Coallier, Jean-Claude, Delaigue, Didier, Duperray, Paola, Fauvy, Stéphane, Flamme, Kevin, Foutrel, Sylvie, Giacomel, Aurore, Glaisner, Johan, Lejeune, Valérie, Léon, Xavier, Masclef, Olivier, Mammar El Hadj, Sihem, Martin, Pascal, Perez, Yves, Raveleau, Benoît, Tesse, Ernest, Raveleau, Benoit, Ajzen, Michel, Aquilina, Manuelle, Bahier-Michel, Livia, Boutinet, Jean-Pierre, Chevallier, Elodie, Coallier, Jean-Claude, Delaigue, Didier, Duperray, Paola, Fauvy, Stéphane, Flamme, Kevin, Foutrel, Sylvie, Giacomel, Aurore, Glaisner, Johan, Lejeune, Valérie, Léon, Xavier, Masclef, Olivier, Mammar El Hadj, Sihem, Martin, Pascal, Perez, Yves, Raveleau, Benoît, and Tesse, Ernest

Published
2022

40. Ploidy‐specific transcriptomes shed light on the heterogeneous identity and metabolism of developing tomato pericarp cells.

Author

Tourdot, Edouard, Martin, Pascal G. P., Maza, Elie, Mauxion, Jean‐Philippe, Djari, Anis, Gévaudant, Frédéric, Chevalier, Christian, Pirrello, Julien, and Gonzalez, Nathalie

Subjects
*PERICARP, *TOMATOES, *TRANSCRIPTOMES, *GENE expression, *FRUIT development, *PLOIDY
Abstract

SUMMARY: Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programmes that are characteristic of each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types, especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of differentially expressed genes presenting only developmental‐specific, only ploidy‐specific expression patterns or profiles resulting from an additive effect of ploidy and development. When comparing ploidy levels at a specific developmental stage, we found that non‐endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome‐based predictions were validated by quantifying ploidy levels within the pericarp tissue. This in situ ploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation and gene expression patterns in the tomato pericarp. [ABSTRACT FROM AUTHOR]

Published
2024
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41. Patterns of subregional cerebellar atrophy across epilepsy syndromes: An ENIGMA-Epilepsy study

Author

Kerestes, Rebecca, primary, Perry, Andrew, additional, Vivash, Lucy, additional, O'Brien, Terence, additional, Alvim, Marina K.M., additional, Arienzo, Donatello, additional, Aventurato, Ìtalo K., additional, Ballerini, Alice, additional, Baltazar, Gabriel F., additional, Bargalló, Núria, additional, Bender, Benjamin, additional, Brioschi, Ricardo, additional, Bürkle, Eva, additional, Caligiuri, Maria Eugenia, additional, Cendes, Fernando, additional, de Tisi, Jane, additional, Duncan, John S., additional, Engel, Jerome P., additional, Foley, Sonya, additional, Fortunato, Francesco, additional, Gambardella, Antonio, additional, Giacomini, Thea, additional, Guerrini, Renzo, additional, Hall, Gerard, additional, Hamandi, Khalid, additional, Ives-Deliperi, Victoria, additional, João, Rafael B., additional, Keller, Simon S., additional, Kleiser, Benedict, additional, Labate, Angelo, additional, Lenge, Matteo, additional, Marotta, Cassandra, additional, Martin, Pascal, additional, Mascalchi, Mario, additional, Meletti, Stefano, additional, Owens-Walton, Conor, additional, Parodi, Costanza b., additional, Pascual-Diaz, Saül, additional, Powell, David, additional, Rao, Jun, additional, Rebsamen, Michael, additional, Reiter, Johannes, additional, Riva, Antonella, additional, Rüeber, Theodor, additional, Rummel, Christian, additional, Scheffler, Freda, additional, Severino, Mariasavina, additional, Silva, Lucas S., additional, Staba, Richard J., additional, Stein, Dan J., additional, Striano, Pasquale, additional, Taylor, Peter N., additional, Thomopoulos, Sophia I., additional, Thompson, Paul M., additional, Tortora, Domenico, additional, Vaudano, Anna Elisabetta, additional, Weber, Bernd I, additional, Wiest, Roland, additional, Winston, Gavin P., additional, Yasuda, Clarissa L., additional, Zheng, Hong, additional, McDonald, Carrie, additional, Sisodiya, Sanjay, additional, and Harding, Ian H., additional

Published
2023
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