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Research paper thumbnail of CEST 2022 – Fast WASABI post-processing: Access to rapid B0 and B1 correction in clinical routine for CEST MRI

Magnetic Resonance Imaging, Jun 1, 2023

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Research paper thumbnail of Modeling, analysis and reduction of biological systems

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Research paper thumbnail of Model reduction and process analysis of biological models

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Research paper thumbnail of CEST MRI provides amide/amine surrogate biomarkers for treatment-naïve glioma sub-typing

European Journal of Nuclear Medicine and Molecular Imaging, Jan 14, 2022

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Research paper thumbnail of Amide proton transfer MRI can accurately stratify gliomas according to their IDH mutation and 1p/19q co-deletion status

Journal of Clinical Oncology, May 20, 2020

2561 Background: Amide proton transfer (APT) MRI provides sensitive metrics at the amides and ami... more 2561 Background: Amide proton transfer (APT) MRI provides sensitive metrics at the amides and amines offsets from the water resonance and has been shown in small cohorts to differentiate low from high grade gliomas with better diagnostic performance than diffusion- and perfusion-weighted MRI. The purpose of our study was to assess APT-MRI performance to stratify gliomas according to their IDH mutation and 1p/19q status. Methods: Forty-five patients with primary gliomas and diffuse astrocytomas (26 WHO grade II, 11 WHO grade III, 8 WHO grade IV) underwent prospectively multi-parametric MRI with APT imaging at 3T scanner. The molecular classification identified 9 patients with IDH-wildtype, 1p/19q retained and 36 with IDH-mutant (22 had 1p/19q-retained, 14 had 1p/19q-codeleted). Tumour segmentations were manually created and the masks were superimposed on the calculated magnetisation transfer ratio asymmetry (MTRasym) spectra and proton transfer ratio APT maps. Individual and group analysis was conducted to analyse the statistical differences between quantitative imaging parameters for the IDH mutation and 1p/19q codeletion statuses. Results: The MTRasym spectra showed a clear difference between IDH-wildtype and IDH-mutant gliomas, with the IDH-mutant gliomas presenting a stronger contribution in the amines (p < 0.001). In IDH-mutant 1p/19q-retained and IDH-mutant 1p/19q-codeleted, the MTRasym spectra showed similarities in shape with higher intensity (approx. 60%) for the IDH-mutant 1p/19q-retained gliomas over the entire spectrum indicating an increased content in amines and amides in IDH-mutant 1p/19q-retained (p < 0.01). Notably, the latter entities showed higher amides levels than the IDH-wildtype gliomas (p < 0.03). Conclusions: APT-MRI shows a remarkable potential to disentangle the protein metabolism in gliomas, to link metabolic patterns to the IDH and 1p/19q status and hence provide robust surrogate biomarkers for non-invasive histomolecular classification with potential use as treatment monitoring tools.

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Research paper thumbnail of Model simplification and process analysis of biological models

HAL (Le Centre pour la Communication Scientifique Directe), Sep 14, 2016

Understanding the dynamical behavior of biological networks is complicated due to their large num... more Understanding the dynamical behavior of biological networks is complicated due to their large number of components and interactions. We present a simple method to analyse key processes for the system behavior, based on the a priori knowledge of the system trajectory and the simplification of mathematical models of these networks. The method consists of the model decomposition into biologically meaningful processes (positive or negative), whose activity or inactivity is evaluated during the time evolution of the system. The structure of the model is reduced to the core mechanisms involving active processes only. We assess the quality of the reduction by means of global relative errors and apply our method to two models of the circa-dian rhythm in Drosophila and the influence of RKIP on the ERK signaling pathway. We give some recent generalizations for a more robust approach.

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Research paper thumbnail of Prédiction de la radionécrose et de la progression tumorale grâce au contraste apt dans les suites d'une radiothérapie stéréotaxique de métastases cérébrales

Journal of Neuroradiology, Mar 1, 2022

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Research paper thumbnail of Principal process analysis of biological models

BMC Systems Biology, Jun 14, 2018

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Research paper thumbnail of Principal Process Analysis and reduction of biological models with order of magnitude

IFAC-PapersOnLine, Jul 1, 2017

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Research paper thumbnail of Reduction and Stability Analysis of a Transcription–Translation Model of RNA Polymerase

Bulletin of Mathematical Biology, Dec 6, 2017

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Research paper thumbnail of Mathematical modelling of microbes: metabolism, gene expression and growth

Journal of the Royal Society Interface, Nov 1, 2017

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Research paper thumbnail of Correction to: CEST MRI provides amide/amine surrogate biomarkers for treatment‑naïve glioma sub‑typing

European Journal of Nuclear Medicine and Molecular Imaging, Apr 12, 2022

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Research paper thumbnail of CEST MRI Provides Amides/amines Surrogate Biomarkers for Treatment-naïve Glioma Sub-typing

Research Square (Research Square), Oct 18, 2021

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Research paper thumbnail of Principal Process Analysis of dynamic GlucoCEST MRI data

arXiv (Cornell University), Mar 13, 2018

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Research paper thumbnail of Glioma staging with CEST asymmetry curves and amides/amines ratio

HAL (Le Centre pour la Communication Scientifique Directe), Aug 8, 2020

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Research paper thumbnail of Modélisation, analyse et réduction des systèmes biologiques

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Research paper thumbnail of Fast WASAB1 post-processing for simultaneous B0 and B1 mapping for CEST imaging use in clinical routine

ISMRM Annual Meeting

This work provides a new method for fast post-processing of MRI data acquired using the WASAB1 se... more This work provides a new method for fast post-processing of MRI data acquired using the WASAB1 sequence for simultaneous B0 and B1 mapping, used in CEST imaging for field inhomogeneity corrections. We are proposing a new processing method with outstanding acceleration of the parameter estimation procedure, without compromising the stability of the estimation. The stability of the method is demonstrated on phantom data and in vivo 3 Tesla clinical data.

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Research paper thumbnail of Improving clinical 3T Amide Proton Transfer weighted contrast in Brain Tumors by using a novel spatial denoising method

ISMRM Annual Meeting

Amide Proton Transfer weighted (APTw) imaging is a promising MR molecular technique for character... more Amide Proton Transfer weighted (APTw) imaging is a promising MR molecular technique for characterizing brain tumors on clinical 3T scanners. However, improving the APT weighted contrast is crucial to translate this approach to clinical practice. In this work we investigated a novel spatial denoising filter in synthetic and clinical APTw data of brain tumor patients.

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Research paper thumbnail of Principal Component selections and filtering by spatial information criteria for multi-acquisition CEST MRI denoising

ISMRM Annual Meeting

This work provides a new denoising methodology for multi-acquisition magnetic resonance images (M... more This work provides a new denoising methodology for multi-acquisition magnetic resonance images (MRI) based on principal components analysis (PCA). We are proposing a new principal component selection criterion that identifies spatial information in the extracted component coefficients, leading to a better preservation of anatomical structures and pathological information. In addition, our adaptive filtering step allows us to further denoise the MRI data, rejecting persistent spatial noise from the extracted component coefficients. In our investigations the proposed method outperformed the eigenvalue based selection criteria on Amide Proton Transfer weighted CEST data.

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Research paper thumbnail of Predicting radionecrosis and recurrent disease through Amide Proton Transfer weighted imaging in brain metastases

ISMRM Annual Meeting

Distinguishing tumor recurrence from radionecrotic injury of pre-irradiated brain metastases is f... more Distinguishing tumor recurrence from radionecrotic injury of pre-irradiated brain metastases is fundamental to provide optimal patient care. Unfortunately, this distinction is often hard to make even with advanced MRI multimodal protocols. This study aims to evaluate APTw imaging in predicting the differentiation between radio-induced tissue changes from tumor progression at 3T in 20 pre-irradiated metastases. Results show that APTw metrics can significantly separate these two common radiological entities (p<0.0001) and suggest the use of fluid-suppressed APTw to reach higher discriminating values.

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Research paper thumbnail of CEST 2022 – Fast WASABI post-processing: Access to rapid B0 and B1 correction in clinical routine for CEST MRI

Magnetic Resonance Imaging, Jun 1, 2023

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Research paper thumbnail of Modeling, analysis and reduction of biological systems

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Model reduction and process analysis of biological models

Bookmarks Related papers MentionsView impact

Research paper thumbnail of CEST MRI provides amide/amine surrogate biomarkers for treatment-naïve glioma sub-typing

European Journal of Nuclear Medicine and Molecular Imaging, Jan 14, 2022

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Amide proton transfer MRI can accurately stratify gliomas according to their IDH mutation and 1p/19q co-deletion status

Journal of Clinical Oncology, May 20, 2020

2561 Background: Amide proton transfer (APT) MRI provides sensitive metrics at the amides and ami... more 2561 Background: Amide proton transfer (APT) MRI provides sensitive metrics at the amides and amines offsets from the water resonance and has been shown in small cohorts to differentiate low from high grade gliomas with better diagnostic performance than diffusion- and perfusion-weighted MRI. The purpose of our study was to assess APT-MRI performance to stratify gliomas according to their IDH mutation and 1p/19q status. Methods: Forty-five patients with primary gliomas and diffuse astrocytomas (26 WHO grade II, 11 WHO grade III, 8 WHO grade IV) underwent prospectively multi-parametric MRI with APT imaging at 3T scanner. The molecular classification identified 9 patients with IDH-wildtype, 1p/19q retained and 36 with IDH-mutant (22 had 1p/19q-retained, 14 had 1p/19q-codeleted). Tumour segmentations were manually created and the masks were superimposed on the calculated magnetisation transfer ratio asymmetry (MTRasym) spectra and proton transfer ratio APT maps. Individual and group analysis was conducted to analyse the statistical differences between quantitative imaging parameters for the IDH mutation and 1p/19q codeletion statuses. Results: The MTRasym spectra showed a clear difference between IDH-wildtype and IDH-mutant gliomas, with the IDH-mutant gliomas presenting a stronger contribution in the amines (p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001). In IDH-mutant 1p/19q-retained and IDH-mutant 1p/19q-codeleted, the MTRasym spectra showed similarities in shape with higher intensity (approx. 60%) for the IDH-mutant 1p/19q-retained gliomas over the entire spectrum indicating an increased content in amines and amides in IDH-mutant 1p/19q-retained (p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.01). Notably, the latter entities showed higher amides levels than the IDH-wildtype gliomas (p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.03). Conclusions: APT-MRI shows a remarkable potential to disentangle the protein metabolism in gliomas, to link metabolic patterns to the IDH and 1p/19q status and hence provide robust surrogate biomarkers for non-invasive histomolecular classification with potential use as treatment monitoring tools.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Model simplification and process analysis of biological models

HAL (Le Centre pour la Communication Scientifique Directe), Sep 14, 2016

Understanding the dynamical behavior of biological networks is complicated due to their large num... more Understanding the dynamical behavior of biological networks is complicated due to their large number of components and interactions. We present a simple method to analyse key processes for the system behavior, based on the a priori knowledge of the system trajectory and the simplification of mathematical models of these networks. The method consists of the model decomposition into biologically meaningful processes (positive or negative), whose activity or inactivity is evaluated during the time evolution of the system. The structure of the model is reduced to the core mechanisms involving active processes only. We assess the quality of the reduction by means of global relative errors and apply our method to two models of the circa-dian rhythm in Drosophila and the influence of RKIP on the ERK signaling pathway. We give some recent generalizations for a more robust approach.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Prédiction de la radionécrose et de la progression tumorale grâce au contraste apt dans les suites d'une radiothérapie stéréotaxique de métastases cérébrales

Journal of Neuroradiology, Mar 1, 2022

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Principal process analysis of biological models

BMC Systems Biology, Jun 14, 2018

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Principal Process Analysis and reduction of biological models with order of magnitude

IFAC-PapersOnLine, Jul 1, 2017

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Reduction and Stability Analysis of a Transcription–Translation Model of RNA Polymerase

Bulletin of Mathematical Biology, Dec 6, 2017

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Mathematical modelling of microbes: metabolism, gene expression and growth

Journal of the Royal Society Interface, Nov 1, 2017

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Correction to: CEST MRI provides amide/amine surrogate biomarkers for treatment‑naïve glioma sub‑typing

European Journal of Nuclear Medicine and Molecular Imaging, Apr 12, 2022

Bookmarks Related papers MentionsView impact

Research paper thumbnail of CEST MRI Provides Amides/amines Surrogate Biomarkers for Treatment-naïve Glioma Sub-typing

Research Square (Research Square), Oct 18, 2021

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Principal Process Analysis of dynamic GlucoCEST MRI data

arXiv (Cornell University), Mar 13, 2018

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Glioma staging with CEST asymmetry curves and amides/amines ratio

HAL (Le Centre pour la Communication Scientifique Directe), Aug 8, 2020

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Modélisation, analyse et réduction des systèmes biologiques

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Fast WASAB1 post-processing for simultaneous B0 and B1 mapping for CEST imaging use in clinical routine

ISMRM Annual Meeting

This work provides a new method for fast post-processing of MRI data acquired using the WASAB1 se... more This work provides a new method for fast post-processing of MRI data acquired using the WASAB1 sequence for simultaneous B0 and B1 mapping, used in CEST imaging for field inhomogeneity corrections. We are proposing a new processing method with outstanding acceleration of the parameter estimation procedure, without compromising the stability of the estimation. The stability of the method is demonstrated on phantom data and in vivo 3 Tesla clinical data.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Improving clinical 3T Amide Proton Transfer weighted contrast in Brain Tumors by using a novel spatial denoising method

ISMRM Annual Meeting

Amide Proton Transfer weighted (APTw) imaging is a promising MR molecular technique for character... more Amide Proton Transfer weighted (APTw) imaging is a promising MR molecular technique for characterizing brain tumors on clinical 3T scanners. However, improving the APT weighted contrast is crucial to translate this approach to clinical practice. In this work we investigated a novel spatial denoising filter in synthetic and clinical APTw data of brain tumor patients.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Principal Component selections and filtering by spatial information criteria for multi-acquisition CEST MRI denoising

ISMRM Annual Meeting

This work provides a new denoising methodology for multi-acquisition magnetic resonance images (M... more This work provides a new denoising methodology for multi-acquisition magnetic resonance images (MRI) based on principal components analysis (PCA). We are proposing a new principal component selection criterion that identifies spatial information in the extracted component coefficients, leading to a better preservation of anatomical structures and pathological information. In addition, our adaptive filtering step allows us to further denoise the MRI data, rejecting persistent spatial noise from the extracted component coefficients. In our investigations the proposed method outperformed the eigenvalue based selection criteria on Amide Proton Transfer weighted CEST data.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Predicting radionecrosis and recurrent disease through Amide Proton Transfer weighted imaging in brain metastases

ISMRM Annual Meeting

Distinguishing tumor recurrence from radionecrotic injury of pre-irradiated brain metastases is f... more Distinguishing tumor recurrence from radionecrotic injury of pre-irradiated brain metastases is fundamental to provide optimal patient care. Unfortunately, this distinction is often hard to make even with advanced MRI multimodal protocols. This study aims to evaluate APTw imaging in predicting the differentiation between radio-induced tissue changes from tumor progression at 3T in 20 pre-irradiated metastases. Results show that APTw metrics can significantly separate these two common radiological entities (p<0.0001) and suggest the use of fluid-suppressed APTw to reach higher discriminating values.

Bookmarks Related papers MentionsView impact