43 results on '"Cadot S"'
Search Results
2. MoS2-assisted growth of highly-oriented AlN thin films by low-temperature van der Waals epitaxy.
- Author
-
Patouillard, J., Bernard, M., Cadot, S., Gassilloud, R., Bernier, N., Grenier, A., Mantoux, A., Blanquet, E., Martin, F., Raynaud, C., and Gianesello, F.
- Subjects
ALUMINUM nitride ,SUBSTRATES (Materials science) ,TRANSITION metals ,THIN films ,ACOUSTIC devices - Abstract
Aluminum nitride (AlN) is a wide bandgap material used in acoustic devices, piezo- micro-electromechanical system and is promising for other electronic applications. However, for most applications, the AlN crystalline quality obtained by PVD or MOCVD is insufficient, and suitable growth substrates providing an adapted lattice match and coefficient of thermal expansion are limited. Alternatively, monocrystalline AlN wafers are not yet available in 200/300 mm sizes and suffer from high costs and quality issues. Here, we propose a novel approach involving a two-dimensional transition metal dichalcogenide (TMD) material as a seed layer, which displays an excellent lattice matching with AlN (>98%) allowing a strong enhancement in the c axis texture of sputtered AlN layers on Si(100)/SiO
2 thermal oxide (500 nm) substrates. We have successfully demonstrated an eightfold improvement of the AlN (002) rocking curve compared to reference samples grown on thermal SiO2 , thus providing a relevant and cost-effective process for the large-scale deployment of high-quality III-N materials on silicon-based substrates. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
3. A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer
- Author
-
Staiger, C., Cadot, S., Kooter, R., Dittrich, M., Mueller, T., Klau, G. W., and Wessels, L. F. A.
- Subjects
Computer Science - Learning ,Quantitative Biology - Quantitative Methods - Abstract
Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single gene classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single gene classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single gene classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single gene sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single gene classifiers for predicting outcome in breast cancer.
- Published
- 2011
- Full Text
- View/download PDF
4. Chemical conversion of MoS2 thin films deposited by atomic layer deposition (ALD) into molybdenum nitride monitored by in situ reflectance measurements
- Author
-
Patouillard, J., primary, Gassilloud, R., additional, Mercier, F., additional, Mantoux, A., additional, Boichot, R., additional, Crisci, A., additional, Bernard, M., additional, Gauthier, N., additional, Cadot, S., additional, Raynaud, C., additional, Gianesello, F., additional, and Blanquet, E., additional
- Published
- 2023
- Full Text
- View/download PDF
5. Chemical conversion of MoS2 thin films deposited by atomic layer deposition (ALD) into molybdenum nitride monitored by in situ reflectance measurements.
- Author
-
Patouillard, J., Gassilloud, R., Mercier, F., Mantoux, A., Boichot, R., Crisci, A., Bernard, M., Gauthier, N., Cadot, S., Raynaud, C., Gianesello, F., and Blanquet, E.
- Subjects
MOLYBDENUM nitrides ,ATOMIC layer deposition ,THIN films ,REFLECTANCE measurement ,METAL nitrides ,MOLYBDENUM disulfide ,NITRIDES ,SILICON nitride films - Abstract
Two-dimensional (2D) metal nitrides are new emerging materials with potential applications in electronics, energy storage, or conversion efficiency. In this paper, we report the synthesis of molybdenum nitride by nitriding molybdenum disulfide (MoS
2 ) via a 700 °C ammonia (NH3 ) reactive heat treatment. A well-controlled uniform MoS2 thin film was prepared by atomic layer deposition (ALD). The progressive MoS2 nitriding reaction has been demonstrated and monitored by in situ reflectance measurements. These results have been confirmed by Raman and x-ray photoelectron spectrometry. This method paves the way to a new potential route to the synthesis of Mo nitride obtained from a well-controlled uniform 2D-MoS2 thin film deposited by ALD. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
6. Telecom-Band Quantum Interference of Frequency-Converted Photons from Remote Detuned NV Centers
- Author
-
Stolk, A.J., primary, van der Enden, K.L., additional, Roehsner, M.-C., additional, Teepe, A., additional, Faes, S.O.J., additional, Bradley, C.E., additional, Cadot, S., additional, van Rantwijk, J., additional, te Raa, I., additional, Hagen, R.A.J., additional, Verlaan, A.L., additional, Biemond, J.J.B., additional, Khorev, A., additional, Vollmer, R., additional, Markham, M., additional, Edmonds, A.M., additional, Morits, J.P.J., additional, Taminiau, T.H., additional, van Zwet, E.J., additional, and Hanson, R., additional
- Published
- 2022
- Full Text
- View/download PDF
7. Two-photon quantum interference between separate NV centres in the telecom-band
- Author
-
Stolk, A.J., primary, van der Enden, K.L., additional, Roehsner, M.-C., additional, Teepe, A., additional, Faes, S.O.J., additional, Bradley, C.E., additional, Cadot, S., additional, van Rantwijk, J., additional, Raa, I. te, additional, Hagen, R.A.J., additional, Verlaan, A.L., additional, Biemond, F.F.B., additional, Khorev, A., additional, Vollmer, R., additional, Markham, M., additional, Edmonds, A.M., additional, Morits, J.P.J., additional, Taminiau, T.H., additional, van Zwet, E.J., additional, and Hanson, R., additional
- Published
- 2022
- Full Text
- View/download PDF
8. In-line characterization of ultrathin transition metal dichalcogenides using X-ray fluorescence and X-ray photoelectron spectroscopy
- Author
-
Nolot, E., primary, Cadot, S., additional, Martin, F., additional, Hönicke, P., additional, Zech, C., additional, and Beckhoff, B., additional
- Published
- 2020
- Full Text
- View/download PDF
9. TMD film growth studied by quasi-insitu XPS on a 300mm silicon wafer
- Author
-
Fraccaroli, M., Gassilloud, R., CADOT, S., Pellissier, B., Vallee, Christophe, Sylvestre, A., Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire des technologies de la microélectronique (LTM ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Génie Electrique de Grenoble (G2ELab), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
- Subjects
[SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2019
10. Hydroxylation of ultra-thin films of α-Cr 2O 3(0 0 0 1) formed on Cr(1 1 0)
- Author
-
Maurice, V, Cadot, S, and Marcus, P
- Published
- 2001
- Full Text
- View/download PDF
11. XPS, LEED and STM study of thin oxide films formed on Cr(110)
- Author
-
Maurice, V, Cadot, S, and Marcus, P
- Published
- 2000
- Full Text
- View/download PDF
12. Biaryl and stilbene synthesis via catalytic decarboxylative cross-coupling
- Author
-
Rameau, N., CADOT, S., PAQUET, A., Pinel, C., Djakovitch, L., BIOVERT (BIOVERT), Institut de recherches sur la catalyse et l'environnement de Lyon (IRCELYON), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), and IRCELYON, ProductionsScientifiques
- Subjects
[CHIM.CATA] Chemical Sciences/Catalysis ,[SDE.ES] Environmental Sciences/Environmental and Society ,[CHIM.CATA]Chemical Sciences/Catalysis ,[SDE.ES]Environmental Sciences/Environmental and Society - Abstract
International @ BIOVERT+NRA:CPI:LDJ; International audience; Due to their biological activities, the synthesis of biaryls has been strongly studied during the last century. Over the past three decades, transition metal-catalyzed cross-coupling procedures have been developed as a methodology of choice for their synthesis. In spite of a high catalytic activity and high turnover number, many of these traditional cross-coupling present several disadvantages, mainly in terms of atom economy as they generally reacted aryl halides with arylmetal derivatives. To answer partially to this dilemma, Goossen et al., and others reported the decarboxylative cross-couplings starting from benzoic acids (Fig. 1) [1]. In this context, we envisioned to develop a new sustainable and environmentally friendly method for the synthesis of biaryls in which two benzoic acids couple together releasing thus only CO2 as co-product. While we initiated our researches, few catalytic systems made of Pd and Ag salts (used in large excess) were reported [2-4]. We pursued our investigations with the aim of developing an efficient and economically viable catalytic system made of Pd and Cu. Several reaction parameters were evaluated (solvent, temperature, metal sources, bases ) on the cross-coupling of 2.6-dimethoxybenzoic acid with 2-nitrobenzoic acid (Fig. 2). Additionally, we investigated deeply the kinetic of the reaction with the goal of understanding the mechanism. These studies allowed us to propose an efficient and economically viable procedure for the synthesis of asymmetric biaryls from two benzoic acids. To the best, 77% yield to biaryl was achieved. Figure 2: Cross-coupling of 2.6-dimethoxybenzoic acid with 2-nitrobenzoic acid Additionally, we will report as an extension of this work the synthesis of 1,1- and 1,2-diarylethylenes from cinnamic acids and aryl halides for which we develop a new Pd-catalyzed procedure (Fig. 3). Figure 3: Synthesis of 1,1- and 1,2-diarylethylenes from cinnamic acids and aryl halides The results of these investigations, together with the scope and limitations, will be presented in this communication. [1] N. Rodriguez, L. J. Goossen, Chem Soc Rev 40 (2011) 5030-5048. [2] J. Cornella, H. Lahlali, I. Larrosa, Chem Comm 46 (2010) 8276-8278. [3] K. Xie, S. Wang, Z. Yang, J. Liu, A. Wang, X. Li, Z. Tan, C.-C. Guo, W. Deng, Eur. J. Org. Chem. 2011 (2011) 5787-5790. [4] P. Hu, Y. Shang, W. Su, Angew Chem Int Ed 51 (2012), 5945-5949
- Published
- 2014
13. Decarboxylative cross-coupling for synthesis of biaryl and stilbene
- Author
-
Rameau, N., CADOT, S., Pinel, C., Djakovitch, L., IRCELYON, ProductionsScientifiques, BIOVERT (BIOVERT), Institut de recherches sur la catalyse et l'environnement de Lyon (IRCELYON), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
- Subjects
[CHIM.CATA] Chemical Sciences/Catalysis ,[CHIM.CATA]Chemical Sciences/Catalysis ,[SDE.ES] Environmental Sciences/Environmental and Society ,[SDE.ES]Environmental Sciences/Environmental and Society - Abstract
International @ BIOVERT+NRA:CPI:LDJ; International audience; Due to their biological activities, the synthesis of biaryls has been strongly studied during the last century. Over the past three decades, transition-metal-catalyzed cross-coupling procedures have been developed becoming methodologies of choice for their synthesis. In spite of a high catalytic activity and high turnover number many of these traditional cross-coupling present several disadvantages, mainly in terms of atom economy as they generally react aryl halides with arylmetal derivatives. To answer partially to this dilemma, Goossen et al., and others reported the decarboxylative cross-couplings in which arylmetal reagents are replaced by benzoic acids. Nowadays, the challenge is to develop new sustainable and environmentally friendly methods. In this context, inspired by the work of Goossen, we envisioned to develop a new method for the synthesis of biaryls in which two benzoic acids couple together releasing thus only carb on dioxide as by product. Another advantage is the accessibility, non-sensitivity and the rather low cost of benzoic acids that are potentially available from biomass. While we initiated our researches, few catalytic systems made of palladium and silver salts (used in large excess) were reported. However, we pursued our investigations with the aim of developing an efficient and economically viable catalytic system made of palladium and copper. Several reaction parameters were evaluated (i.e.: solvent, temperature, nature and loading of metal sources, bases, ligand ) on the cross-coupling of 2.6-dimethoxybenzoic acid with 2-nitrobenzoic acid. Additionally, we investigated deeply the kinetic of the reaction with the goal of understanding the mechanism. These studies allowed us to propose an efficient and economically viable procedure for the synthesis of asymmetric biaryls from two benzoic acids. The results of these investigations, together with the scope and limitations, will be presented in this communication. Additionally, we will report as an extension of this work the synthesis of 1,1- and 1,2-diarylethylenes from cinnamic acids and aryl halides for which we develop a new Pd/Cu-catalyzed procedure.
- Published
- 2013
14. Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis
- Author
-
Staiger, C. (Christine), Cadot, S., Györffy, B., Wessels, L.F.A. (Lodewyk), Klau, G.W. (Gunnar), Staiger, C. (Christine), Cadot, S., Györffy, B., Wessels, L.F.A. (Lodewyk), and Klau, G.W. (Gunnar)
- Published
- 2013
- Full Text
- View/download PDF
15. A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer
- Author
-
Staiger, C. (Christine), Cadot, S., Kooter, R, Dittrich, M. (Marcus), Müller, T. (Tobias), Klau, G.W. (Gunnar), Wessels, L.F.A. (Lodewyk), Staiger, C. (Christine), Cadot, S., Kooter, R, Dittrich, M. (Marcus), Müller, T. (Tobias), Klau, G.W. (Gunnar), and Wessels, L.F.A. (Lodewyk)
- Abstract
Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single genes classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single genes classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single genes classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single genes sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single genes classifiers for predicting outcome in breast cancer.
- Published
- 2012
16. A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer
- Author
-
Staiger, C., Cadot, S., Kooter, R., Dittrich, M., Müller, T., Klau, G.W., Wessels, L.F.A., Staiger, C., Cadot, S., Kooter, R., Dittrich, M., Müller, T., Klau, G.W., and Wessels, L.F.A.
- Abstract
Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single genes classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single genes classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single genes classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single genes sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single genes classifiers for predicting outcome in breast cancer. © 2012 Staiger et al.
- Published
- 2012
- Full Text
- View/download PDF
17. A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer
- Author
-
Staiger, C. (Christine), Cadot, S., Kooter, R, Dittrich, M. (Marcus), Müller, T. (Tobias), Klau, G.W. (Gunnar), Wessels, L.F.A. (Lodewyk), Staiger, C. (Christine), Cadot, S., Kooter, R, Dittrich, M. (Marcus), Müller, T. (Tobias), Klau, G.W. (Gunnar), and Wessels, L.F.A. (Lodewyk)
- Abstract
Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single gene classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single gene classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single gene classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single gene sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single gene classifiers for predicting outcome in breast cancer.
- Published
- 2011
18. Mitochondrial damage revealed by immunoselection for ALS-linked misfolded SOD1
- Author
-
Pickles, S., primary, Destroismaisons, L., additional, Peyrard, S. L., additional, Cadot, S., additional, Rouleau, G. A., additional, Brown, R. H., additional, Julien, J.-P., additional, Arbour, N., additional, and Vande Velde, C., additional
- Published
- 2013
- Full Text
- View/download PDF
19. Hydroxylation of ultra-thin films of α-Cr2O3(0001) formed on Cr(110)
- Author
-
Maurice, V, primary, Cadot, S, additional, and Marcus, P, additional
- Published
- 2001
- Full Text
- View/download PDF
20. Grain Boundary Segregation in Pure and Boron Doped Cobalt Monosilicide (CoSi)
- Author
-
Larere, A., primary, Haut, C., additional, Nguyen, T.T., additional, Cadot, S., additional, and Gas, Patrick, additional
- Published
- 1996
- Full Text
- View/download PDF
21. Co-expression of CD69, CD49d, CD279 and CD20 in chronic lymphocytic leukemia cells is a new biomarker of active disease before or under therapy.
- Author
-
Cadot S, Ysebaert L, Lamy S, Laurent C, and Quillet-Mary A
- Published
- 2025
- Full Text
- View/download PDF
22. New pharmacodynamic parameters linked with ibrutinib responses in chronic lymphocytic leukemia: Prospective study in real-world patients and mathematical modeling.
- Author
-
Cadot S, Audebert C, Dion C, Ken S, Dupré L, Largeaud L, Laurent C, Ysebaert L, Crauste F, and Quillet-Mary A
- Subjects
- Humans, Male, Female, Aged, Middle Aged, Prospective Studies, Models, Theoretical, Aged, 80 and over, Longitudinal Studies, Pyrimidines therapeutic use, Treatment Outcome, Pyrazoles therapeutic use, Pyrazoles pharmacology, Magnetic Resonance Imaging, Protein Kinase Inhibitors therapeutic use, Leukemia, Lymphocytic, Chronic, B-Cell drug therapy, Leukemia, Lymphocytic, Chronic, B-Cell pathology, Adenine analogs & derivatives, Adenine therapeutic use, Piperidines therapeutic use
- Abstract
Background: One of the first clinical observations of ibrutinib activity in the treatment of chronic lymphocytic leukemia (CLL) is a rapid decline in lymph nodes size. This phenomenon is accompanied by an hyperlymphocytosis, either transient or prolonged, which is associated with distinct clinical responses and thus has an impact on long-term outcomes. Understanding which factors determine distinct disease courses upon ibrutinib treatment remains a scientific challenge., Methods and Findings: From 2016 to 2021, we conducted a longitudinal and observational study in 2 cohorts of patients with chronic lymphocytic leukemia (CLL) (cohort 1, n = 41; cohort 2, n = 81). These cohorts reflect the well-known clinical features of CLL patients, such as Male/Female sex ratio of 2/1, a median age of 70 years at diagnosis, and include patients in first-line therapy (27%) or relapsed/refractory patients (73%). Blood cell counts were followed for each patient during 2 years of ibrutinib treatment. In addition, immunophenotyping and whole-body magnetic resonance imaging (MRI) were assessed in patients from cohort 1. These data were integrated in a newly built mathematical model, inspired by previous mathematical works on CLL treatment and combining dynamical and statistical models, leading to the identification of biological mechanisms associated with the 2 types of clinical responses. This multidisciplinary approach allowed to identify baseline parameters that dictated lymphocytes kinetics upon ibrutinib treatment. Indeed, ibrutinib-induced lymphocytosis defined 2 CLL patient subgroups, transient hyperlymphocytosis (tHL) or prolonged hyperlymphocytosis (pHL), that can be discriminated, before the treatment, by absolute counts of CD4+ T lymphocytes (p = 0.026) and regulatory CD4 T cells (p = 0.007), programmed cell death protein 1 PD1 (p = 0.022) and CD69 (p = 0.03) expression on B leukemic cells, CD19/CD5high/CXCR4low level (p = 0.04), and lymph node cellularity. We also pinpointed that the group of patients identified by the transient hyperlymphocytosis has lower duration response and a poor clinical outcome. The mathematical approach led to the reproduction of patient-specific dynamics and the estimation of associated patient-specific biological parameters, and highlighted that the differences between the 2 groups were mainly due to the production of leukemic B cells in lymph node compartments, and to a lesser extent to T lymphocytes and leukemic B cell egress into bloodstream. Access to additional data, especially longitudinal MRI data, could strengthen the conclusions regarding leukemic B cell dynamics in lymph nodes and the relevance of 2 distinct groups of patients., Conclusions: Altogether, our multidisciplinary study provides a better understanding of ibrutinib response and highlights new pharmacodynamic parameters before and along ibrutinib treatment. Since our results highlight a reduced duration response and outcome in patients with transient hyperlymphocytosis, our approach provides support for managing ibrutinib therapy after 3 months of treatment., Trial Registration: ClinicalTrials.gov NCT02824159., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Cadot et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2024
- Full Text
- View/download PDF
23. Lymphocyte migration and retention properties affected by ibrutinib in chronic lymphocytic leukemia.
- Author
-
Rey-Barroso J, Munaretto A, Rouquié N, Mougel A, Chassan M, Gadat S, Dewingle O, Poincloux R, Cadot S, Ysebaert L, Quillet-Mary A, and Dupré L
- Subjects
- Humans, Cell Movement, Lymphoid Tissue, Lymphocytes, Leukemia, Lymphocytic, Chronic, B-Cell drug therapy, Adenine analogs & derivatives, Piperidines
- Abstract
The Bruton tyrosine kinase (BTK) inhibitor ibrutinib is widely used for treatment of patients with relapsed/refractory or treatment-naïve chronic lymphocytic leukemia (CLL). A prominent effect of ibrutinib is to disrupt the retention of CLL cells from supportive lymphoid tissues, by altering BTK-dependent adhesion and migration. To further explore the mechanism of action of ibrutinib and its potential impact on non-leukemic cells, we quantified multiple motility and adhesion parameters of human primary CLL cells and non-leukemic lymphoid cells. In vitro, ibrutinib affected CCL19-, CXCL12- and CXCL13-evoked migration behavior of CLL cells and non-neoplastic lymphocytes, by reducing both motility speed and directionality. De-phosphorylation of BTK induced by ibrutinib in CLL cells was associated with defective polarization over fibronectin and inability to assemble the immunological synapse upon B-cell receptor engagement. In patients' samples collected during a 6-month monitoring of therapy, chemokine-evoked migration was repressed in CLL cells and marginally reduced in T cells. This was accompanied by profound modulation of the expression of chemokine receptors and adhesion molecules. Remarkably, the relative expression of the receptors governing lymph node entry (CCR7) versus exit (S1PR1) stood out as a reliable predictive marker of the clinically relevant treatment-induced lymphocytosis. Together, our data reveal a multifaceted modulation of motility and adhesive properties of ibrutinib on both CLL leukemic cell and T-cell populations and point to intrinsic differences in CLL recirculation properties as an underlying cause for variability in treatment response.
- Published
- 2024
- Full Text
- View/download PDF
24. Towards large scale integration of MoS 2 /graphene heterostructure with ALD-grown MoS 2 .
- Author
-
Hyot B, Ligaud C, Yoo TJ, David-Vifflantzeff J, Gauthier N, Cadot S, Le VH, Brunet P, and Le Van-Jodin L
- Abstract
In the pursuit of ultrathin and highly sensitive photodetectors, a promising approach involves leveraging the combination of light-sensitive two-dimensional (2D) semiconducting transition-metal dichalcogenides, such as MoS
2 and the high electrical conductivity of graphene. Over the past decade, exfoliated 2D materials and electron-beam lithography have been used extensively to demonstrate feasibility on single devices. But for these devices to be used in the real-world systems, it is necessary to demonstrate good device performance similar to lab-based devices with repeatability of the results from device to device and a path to large scale manufacturing. To work in this way, a fabrication process of MoS2 /graphene vertical heterostructures with a wafer-scale integration in a CMOS compatible foundry environment is evaluated here. Large-scale atomic layer deposition on 8 inch silicon wafers is used for the growth of MoS2 layers which are then transferred on a 4 inch graphene-based wafer. The MoS2 /graphene phototransistors are fabricated collectively, achieving a minimum channel length of 10 μ m. The results measured on dozen of devices demonstrate a photoresponsivity of 50 A W-1 and a remarkable sensitivity as low as 10 nW at 660 nm. These results not only compete with lab-based photodetectors made of chemical vapor deposition grown MoS2 layers transferred on graphene, but also pave the way for the large-scale integration of these emerging 2D heterostructures in optoelectronic devices and sensors., (© 2024 IOP Publishing Ltd.)- Published
- 2024
- Full Text
- View/download PDF
25. Multicolor flow cytometry in clinical samples for platelet signaling assessment.
- Author
-
Garcia C, Dejean S, Savy N, Bordet JC, Series J, Cadot S, Ribes A, Voisin S, Rugeri L, Payrastre B, and Sié P
- Abstract
Background: Availability of multichannel cytometers and specific commercial antibodies makes flow cytometry a new option to simultaneously assess multiple intracellular platelet signaling pathways for clinical purposes, in small volume of blood or low platelet count., Objectives: To describe a multicolor flow cytometry with fluorescent barcoding technique for screening signaling pathways downstream membrane receptors of major platelet agonists (adenosine diphosphate, thrombin, thromboxane, and collagen)., Methods: By comparison with immunoblotting, we first selected the target phosphoproteins, AKT, P38MAPK, LIMK, and SPL76; the times of stimulation; and phosphoflow barcoding conditions. We then performed a clinical study on whole blood of patients without evidence of blood platelet disorder on standard biological screening, consulting for trivial or occasionally provoked bleeds without familial antecedent (bleeding of unknown origin, n = 23) or type-1 von Willebrand disease ( n = 9). In addition, we included a small group of patients with definite platelet disorders (Glanzmann thrombasthenia, δ-storage pool deficiency, and immune glycoprotein VI-related disease with granule secretion defect)., Results: The range, kinetics, and distribution of fluorescence intensity were established for each agonist-target protein combination. Principal component analysis indicates a correlation in response to a target phosphoprotein (AKT and P38MAPK) to different agonists but no correlation in the response of different target phosphoproteins to the same agonist. The heterogeneity of individual responses in the whole population displayed was analyzed using clustering algorithm. Patients with platelet storage pool deficiency were positioned as lowest responders on the heatmap., Conclusion: In complement of functional tests, this study introduces a new approach for rapid platelet signaling profiling in clinical practice., (© 2023 The Authors.)
- Published
- 2023
- Full Text
- View/download PDF
26. Soil composition and plant genotype determine benzoxazinoid-mediated plant-soil feedbacks in cereals.
- Author
-
Cadot S, Gfeller V, Hu L, Singh N, Sánchez-Vallet A, Glauser G, Croll D, Erb M, van der Heijden MGA, and Schlaeppi K
- Subjects
- Animals, Food Chain, Insecta physiology, Triticum genetics, Zea mays genetics, Allelopathy, Benzoxazines metabolism, Genotype, Soil chemistry, Triticum physiology, Zea mays physiology
- Abstract
Plant-soil feedbacks refer to effects on plants that are mediated by soil modifications caused by the previous plant generation. Maize conditions the surrounding soil by secretion of root exudates including benzoxazinoids (BXs), a class of bioactive secondary metabolites. Previous work found that a BX-conditioned soil microbiota enhances insect resistance while reducing biomass in the next generation of maize plants. Whether these BX-mediated and microbially driven feedbacks are conserved across different soils and response species is unknown. We found the BX-feedbacks on maize growth and insect resistance conserved between two arable soils, but absent in a more fertile grassland soil, suggesting a soil-type dependence of BX feedbacks. We demonstrated that wheat also responded to BX-feedbacks. While the negative growth response to BX-conditioning was conserved in both cereals, insect resistance showed opposite patterns, with an increase in maize and a decrease in wheat. Wheat pathogen resistance was not affected. Finally and consistent with maize, we found the BX-feedbacks to be cultivar-specific. Taken together, BX-feedbacks affected cereal growth and resistance in a soil and genotype-dependent manner. Cultivar-specificity of BX-feedbacks is a key finding, as it hides the potential to optimize crops that avoid negative plant-soil feedbacks in rotations., (© 2021 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)
- Published
- 2021
- Full Text
- View/download PDF
27. Stabilizing an ultrathin MoS 2 layer during electrocatalytic hydrogen evolution with a crystalline SnO 2 underlayer.
- Author
-
Englhard J, Cao Y, Bochmann S, Barr MKS, Cadot S, Quadrelli EA, and Bachmann J
- Abstract
Amorphous MoS
2 has been investigated abundantly as a catalyst for hydrogen evolution. Not only its performance but also its chemical stability in acidic conditions have been reported widely. However, its adhesion has not been studied systematically in the electrochemical context. The use of MoS2 as a lubricant is not auspicious for this purpose. In this work, we start with a macroporous anodic alumina template as a model support, add an underlayer of SnO2 to provide electrical conduction and adhesion, then provide the catalytically active, amorphous MoS2 material by atomic layer deposition (ALD). The composition, morphology, and crystalline or amorphous character of all layers are confirmed by spectroscopic ellipsometry, X-ray photoelectron spectroscopy, grazing incidence X-ray diffractometry, scanning electron microscopy and energy dispersive X-ray spectroscopy. The electrocatalytic water reduction performance of the macroporous AAO/SnO2 /MoS2 electrodes, quantified by voltammetry, steady-state chronoamperometry and electrochemical impedance spectroscopy, is improved by annealing the SnO2 layer prior to MoS2 deposition. Varying the geometric parameters of the electrode composite yields an optimized performance of 10 mA cm-2 at 0.22 V overpotential, with a catalyst loading of 0.16 mg cm-2 . The electrode's stability is contingent on SnO2 crystallinity. Amorphous SnO2 allows for a gradual dewetting of the originally continuous MoS2 layer over wide areas. In stark contrast to this, crystalline SnO2 maintains the continuity of MoS2 until at least 0.3 V overpotential., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)- Published
- 2021
- Full Text
- View/download PDF
28. Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field.
- Author
-
Cadot S, Guan H, Bigalke M, Walser JC, Jander G, Erb M, van der Heijden MGA, and Schlaeppi K
- Subjects
- Benzoxazines, Europe, Plant Breeding, Plant Roots, Rhizosphere, Soil Microbiology, Microbiota genetics, Zea mays
- Abstract
Background: Plants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of root-associated microbiotas is not well understood, especially not under realistic field conditions. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the USA. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soils with different properties., Results: Our analysis showed that BX secretion affected the community composition of the rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of BX exudation was at least as strong as the genetic background, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three field experiments. However, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae and enriched various potential plant pathogenic fungi in the roots across the different environments., Conclusions: These findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different conditions. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions. Video Abstract.
- Published
- 2021
- Full Text
- View/download PDF
29. Stress Granules in the Post-transcriptional Regulation of Immune Cells.
- Author
-
Curdy N, Lanvin O, Cadot S, Laurent C, Fournié JJ, and Franchini DM
- Abstract
Immune cell activation triggers transcriptional and translational programs eliciting cellular processes, such as differentiation or proliferation, essential for an efficient immune response. These dynamic processes require an intricate orchestration of regulatory mechanisms to control the precise spatiotemporal expression of proteins. Post-transcriptional regulation ensures the control of messenger RNA metabolism and appropriate translation. Among these post-transcriptional regulatory mechanisms, stress granules participate in the control of protein synthesis. Stress granules are ribonucleoprotein complexes that form upon stress, typically under control of the integrated stress response. Such structures assemble upon stimulation of immune cells where they control selective translational programs ensuring the establishment of accurate effector functions. In this review, we summarize the current knowledge about post-transcriptional regulation in immune cells and highlight the role of stress sensors and stress granules in such regulation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Curdy, Lanvin, Cadot, Laurent, Fournié and Franchini.)
- Published
- 2021
- Full Text
- View/download PDF
30. Longitudinal CITE-Seq profiling of chronic lymphocytic leukemia during ibrutinib treatment: evolution of leukemic and immune cells at relapse.
- Author
-
Cadot S, Valle C, Tosolini M, Pont F, Largeaud L, Laurent C, Fournie JJ, Ysebaert L, and Quillet-Mary A
- Abstract
Background: Ibrutinib, an irreversible Bruton Tyrosine Kinase (BTK) inhibitor, has revolutionized Chronic Lymphocytic Leukemia (CLL) treatment, but resistances to ibrutinib have emerged, whether related or not to BTK mutations. Patterns of CLL evolution under ibrutinib therapy are well characterized for the leukemic cells but not for their microenvironment., Methods: Here, we addressed this question at the single cell level of both transcriptome and immune-phenotype. The PBMCs from a CLL patient were monitored during ibrutinib treatment using Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-Seq) technology., Results: This unveiled that the short clinical relapse of this patient driven by BTK mutation is associated with intraclonal heterogeneity in B leukemic cells and up-regulation of common signaling pathways induced by ibrutinib in both B leukemic cells and immune cells. This approach also pinpointed a subset of leukemic cells present before treatment and highly enriched during progression under ibrutinib. These latter exhibit an original gene signature including up-regulated BCR, MYC-activated, and other targetable pathways. Meanwhile, although ibrutinib differentially affected the exhaustion of T lymphocytes, this treatment enhanced the T cell cytotoxicity even during disease progression., Conclusions: These results could open new alternative of therapeutic strategies for ibrutinib-refractory CLL patients, based on immunotherapy or targeting B leukemic cells themselves.
- Published
- 2020
- Full Text
- View/download PDF
31. Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes.
- Author
-
Pizzolato G, Kaminski H, Tosolini M, Franchini DM, Pont F, Martins F, Valle C, Labourdette D, Cadot S, Quillet-Mary A, Poupot M, Laurent C, Ysebaert L, Meraviglia S, Dieli F, Merville P, Milpied P, Déchanet-Merville J, and Fournié JJ
- Subjects
- Adult, Base Sequence, CD8-Positive T-Lymphocytes immunology, Cell Proliferation physiology, Cells, Cultured, Humans, Immunologic Memory immunology, Killer Cells, Natural immunology, Leukocytes, Mononuclear immunology, Sequence Analysis, RNA methods, Transcriptome immunology, Receptors, Antigen, T-Cell, gamma-delta immunology, T-Lymphocyte Subsets immunology
- Abstract
γδ T lymphocytes represent ∼1% of human peripheral blood mononuclear cells and even more cells in most tissues of vertebrates. Although they have important anticancer functions, most current single-cell RNA sequencing (scRNA-seq) studies do not identify γδ T lymphocytes because their transcriptomes at the single-cell level are unknown. Here we show that high-resolution clustering of large scRNA-seq datasets and a combination of gene signatures allow the specific detection of human γδ T lymphocytes and identification of their T cell receptor (TCR)Vδ1 and TCRVδ2 subsets in large datasets from complex cell mixtures. In t -distributed stochastic neighbor embedding plots from blood and tumor samples, the few γδ T lymphocytes appear collectively embedded between cytotoxic CD8 T and NK cells. Their TCRVδ1 and TCRVδ2 subsets form close yet distinct subclusters, respectively neighboring NK and CD8 T cells because of expression of shared and distinct cytotoxic maturation genes. Similar pseudotime maturation trajectories of TCRVδ1 and TCRVδ2 γδ T lymphocytes were discovered, unveiling in both subsets an unattended pool of terminally differentiated effector memory cells with preserved proliferative capacity, a finding confirmed by in vitro proliferation assays. Overall, the single-cell transcriptomes of thousands of individual γδ T lymphocytes from different CMV
+ and CMV- donors reflect cytotoxic maturation stages driven by the immunological history of donors. This landmark study establishes the rationale for identification, subtyping, and deep characterization of human γδ T lymphocytes in further scRNA-seq studies of complex tissues in physiological and disease conditions., Competing Interests: The authors declare no conflict of interest.- Published
- 2019
- Full Text
- View/download PDF
32. Electrocatalytic Performance of Titania Nanotube Arrays Coated with MoS 2 by ALD toward the Hydrogen Evolution Reaction.
- Author
-
Cao Y, Wu Y, Badie C, Cadot S, Camp C, Quadrelli EA, and Bachmann J
- Abstract
The electrochemical splitting of water provides an elegant way to store renewable energy, but it is limited by the cost of the noble metals used as catalysts. Among the catalysts used for the reduction of water to hydrogen, MoS
2 has been identified as one of the most promising materials as it can be engineered to provide not only a large surface area but also an abundance of unsaturated and reactive coordination sites. Using Mo[NMe2 ]4 and H2 S as precursors, a desired thickness of amorphous MoS2 can be deposited on TiO2 nanotubes by atomic layer deposition. The identity and structure of the MoS2 film are confirmed by spectroscopic ellipsometry, X-ray photoelectron spectroscopy, scanning electron microscopy, and energy dispersive X-ray spectroscopy. The electrocatalytic performance of MoS2 is quantified as it depends on the tube length and the MoS2 layer thickness through voltammetry, steady-state chronoamperometry, and electrochemical impedance spectroscopy. The best sample reaches 10 mA/cm2 current density at 189 mV overpotential in 0.5 M H2 SO4 . All of the various geometries of our nanostructured electrodes reach an electrocatalytic proficiency comparable with the state-of-the-art MoS2 electrodes, and the dependence of performance parameters on geometry suggests that the system can even be improved further., Competing Interests: The authors declare no competing financial interest.- Published
- 2019
- Full Text
- View/download PDF
33. Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota.
- Author
-
Hu L, Robert CAM, Cadot S, Zhang X, Ye M, Li B, Manzo D, Chervet N, Steinger T, van der Heijden MGA, Schlaeppi K, and Erb M
- Subjects
- Animals, Bacteria growth & development, Benzoxazoles metabolism, Cyclic N-Oxides pharmacology, Flavonoids pharmacology, Fungi physiology, Glucosides pharmacology, Herbivory drug effects, Larva drug effects, Larva physiology, Plant Leaves metabolism, Plant Leaves parasitology, Plant Roots microbiology, Pyrroles pharmacology, Rhizosphere, Soil chemistry, Spodoptera drug effects, Spodoptera physiology, Zea mays metabolism, Zea mays microbiology, Zea mays parasitology, Benzoxazoles pharmacology, Plant Leaves immunology, Plant Roots metabolism, Soil Microbiology, Zea mays immunology
- Abstract
By changing soil properties, plants can modify their growth environment. Although the soil microbiota is known to play a key role in the resulting plant-soil feedbacks, the proximal mechanisms underlying this phenomenon remain unknown. We found that benzoxazinoids, a class of defensive secondary metabolites that are released by roots of cereals such as wheat and maize, alter root-associated fungal and bacterial communities, decrease plant growth, increase jasmonate signaling and plant defenses, and suppress herbivore performance in the next plant generation. Complementation experiments demonstrate that the benzoxazinoid breakdown product 6-methoxy-benzoxazolin-2-one (MBOA), which accumulates in the soil during the conditioning phase, is both sufficient and necessary to trigger the observed phenotypic changes. Sterilization, fungal and bacterial profiling and complementation experiments reveal that MBOA acts indirectly by altering root-associated microbiota. Our results reveal a mechanism by which plants determine the composition of rhizosphere microbiota, plant performance and plant-herbivore interactions of the next generation.
- Published
- 2018
- Full Text
- View/download PDF
34. A novel 2-step ALD route to ultra-thin MoS 2 films on SiO 2 through a surface organometallic intermediate.
- Author
-
Cadot S, Renault O, Frégnaux M, Rouchon D, Nolot E, Szeto K, Thieuleux C, Veyre L, Okuno H, Martin F, and Quadrelli EA
- Abstract
The lack of scalable-methods for the growth of 2D MoS
2 crystals, an identified emerging material with applications ranging from electronics to energy storage, is a current bottleneck against its large-scale deployment. We report here a two-step ALD route with new organometallic precursors, Mo(NMe2 )4 and 1,2-ethanedithiol (HS(CH2 )2 SH) which consists in the layer-by-layer deposition of an amorphous surface Mo(iv) thiolate at 50 °C, followed by a subsequent annealing at higher temperature leading to ultra-thin MoS2 nanocrystals (∼20 nm-large) in the 1-2 monolayer range. In contrast to the usual high-temperature growth of 2D dichalcogenides, where nucleation is the key parameter to control both thickness and uniformity, our novel two-step ALD approach enables chemical control over these two parameters, the growth of 2D MoS2 crystals upon annealing being ensured by spatial confinement and facilitated by the formation of a buffer oxysulfide interlayer.- Published
- 2017
- Full Text
- View/download PDF
35. Ibrutinib treatment affects collagen and von Willebrand factor-dependent platelet functions.
- Author
-
Levade M, David E, Garcia C, Laurent PA, Cadot S, Michallet AS, Bordet JC, Tam C, Sié P, Ysebaert L, and Payrastre B
- Subjects
- Adenine analogs & derivatives, Blood Platelets drug effects, Dimethyl Sulfoxide chemistry, Enzyme Inhibitors chemistry, Hemostasis, Heparin chemistry, Humans, Longitudinal Studies, Phospholipase C gamma chemistry, Phosphorylation, Piperidines, Platelet Activation, Platelet Adhesiveness, Shear Strength, Blood Platelets cytology, Collagen chemistry, Pyrazoles chemistry, Pyrimidines chemistry, von Willebrand Factor chemistry
- Abstract
The oral Bruton's tyrosine kinase inhibitor, ibrutinib, has recently demonstrated high efficiency in patients with relapsed B-cell malignancies. Occurrence of bleeding events has been reported in a subgroup of ibrutinib-treated patients. We demonstrate that ibrutinib selectively inhibits platelet signaling and functions downstream of the collagen receptor glycoprotein VI and strongly affects firm platelet adhesion on von Willebrand factor (VWF) under arterial flow. A longitudinal study of 14 patients indicated a correlation between occurrence of bleeding events and decreased platelet aggregation in response to collagen in platelet-rich plasma and firm adhesion on VWF under arterial flow. The addition of 50% untreated platelets was sufficient to efficiently reverse the effects of ibrutinib, and platelet functions recovered after treatment interruption as physiological platelet renewal occurred. These data have important clinical implications and provide a basis for hemostasis management during ibrutinib treatment., (© 2014 by The American Society of Hematology.)
- Published
- 2014
- Full Text
- View/download PDF
36. Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis.
- Author
-
Staiger C, Cadot S, Györffy B, Wessels LF, and Klau GW
- Abstract
Integrating gene expression data with secondary data such as pathway or protein-protein interaction data has been proposed as a promising approach for improved outcome prediction of cancer patients. Methods employing this approach usually aggregate the expression of genes into new composite features, while the secondary data guide this aggregation. Previous studies were limited to few data sets with a small number of patients. Moreover, each study used different data and evaluation procedures. This makes it difficult to objectively assess the gain in classification performance. Here we introduce the Amsterdam Classification Evaluation Suite (ACES). ACES is a Python package to objectively evaluate classification and feature-selection methods and contains methods for pooling and normalizing Affymetrix microarrays from different studies. It is simple to use and therefore facilitates the comparison of new approaches to best-in-class approaches. In addition to the methods described in our earlier study (Staiger et al., 2012), we have included two prominent prognostic gene signatures specific for breast cancer outcome, one more composite feature selection method and two network-based gene ranking methods. Employing the evaluation pipeline we show that current composite-feature classification methods do not outperform simple single-genes classifiers in predicting outcome in breast cancer. Furthermore, we find that also the stability of features across different data sets is not higher for composite features. Most stunningly, we observe that prediction performances are not affected when extracting features from randomized PPI networks.
- Published
- 2013
- Full Text
- View/download PDF
37. Gata3 directly regulates early inner ear expression of Fgf10.
- Author
-
Economou A, Datta P, Georgiadis V, Cadot S, Frenz D, and Maconochie M
- Subjects
- Animals, Binding Sites, Enhancer Elements, Genetic, Fibroblast Growth Factor 10 genetics, GATA3 Transcription Factor metabolism, Ganglia metabolism, Genes, Reporter, Mice, Mice, Transgenic, Models, Biological, Mutagenesis, Site-Directed, Mutation, Protein Binding, Transgenes, Tretinoin metabolism, Ear, Inner embryology, Fibroblast Growth Factor 10 biosynthesis, GATA3 Transcription Factor physiology, Gene Expression Regulation, Developmental
- Abstract
The analysis of Fgf10 mouse mutants has demonstrated a critical role for this ligand in neurosensory development of the vertebrate inner ear, and we have been looking to define the direct upstream regulators of Fgf10 in this sensory organ, as part of constructing the programme of early inner ear development. Through the analysis of reporter constructs in transgenic mouse embryos and neonatal mice, in this report we define a minimal 1400 bp enhancer from the 5' flanking region of Fgf10. This enhancer drives reporter transgene expression in a manner that recapitulates endogenous expression of Fgf10, from its initial onset in the invaginating otic placode and onwards throughout gestation, controlling Fgf10 expression in all developing sensory patches and in the developing VIIIth ganglion. This regulatory region includes three putative Gata3 binding sites that we demonstrate directly interacts with Gata3 protein through the DNA binding domain with differing affinities. Site directed mutagenesis of all three sites and functional testing in transgenic embryos using reporter transgenes reveals an absolute requirement for Gata3 in controlling Fgf10 expression. Transgenic analysis of individual Gata3 binding site mutations illustrates that only one of these binding sites is necessary for reporter expression. Together these data demonstrate that Gata3 directly activates Fgf10 in the early inner ear, and does so through a single binding site., (Copyright © 2012 Elsevier Inc. All rights reserved.)
- Published
- 2013
- Full Text
- View/download PDF
38. A regression model for estimating DNA copy number applied to capture sequencing data.
- Author
-
Rigaill GJ, Cadot S, Kluin RJ, Xue Z, Bernards R, Majewski IJ, and Wessels LF
- Subjects
- Algorithms, Breast Neoplasms genetics, Cell Line, Tumor, Female, Genomics methods, Genotype, Humans, Linear Models, Polymorphism, Single Nucleotide, DNA Copy Number Variations, Sequence Analysis, DNA
- Abstract
Motivation: Target enrichment, also referred to as DNA capture, provides an effective way to focus sequencing efforts on a genomic region of interest. Capture data are typically used to detect single-nucleotide variants. It can also be used to detect copy number alterations, which is particularly useful in the context of cancer, where such changes occur frequently. In copy number analysis, it is a common practice to determine log-ratios between test and control samples, but this approach results in a loss of information as it disregards the total coverage or intensity at a locus., Results: We modeled the coverage or intensity of the test sample as a linear function of the control sample. This regression approach is able to deal with regions that are completely deleted, which are problematic for methods that use log-ratios. To demonstrate the utility of our approach, we used capture data to determine copy number for a set of 600 genes in a panel of nine breast cancer cell lines. We found high concordance between our results and those generated using a single-nucleotide polymorphsim genotyping platform. When we compared our results with other log-ratio-based methods, including ExomeCNV, we found that our approach produced better overall correlation with SNP data., Availability: The algorithm is implemented in C and R and the code can be downloaded from http://bioinformatics.nki.nl/ocs/, Contact: l.wessels@nki.nl, Supplementary Information: Supplementary data are available at Bioinformatics online.
- Published
- 2012
- Full Text
- View/download PDF
39. A novel method for retinoic acid administration reveals differential and dose-dependent downregulation of Fgf3 in the developing inner ear and anterior CNS.
- Author
-
Cadot S, Frenz D, and Maconochie M
- Subjects
- Animals, Cell Differentiation drug effects, Central Nervous System drug effects, Central Nervous System embryology, Central Nervous System physiology, Dose-Response Relationship, Drug, Down-Regulation, Ear, Inner drug effects, Ear, Inner embryology, Mice, Administration, Oral, Ear, Inner physiology, Tretinoin administration & dosage
- Abstract
Endogenous retinoic acid plays critical roles in normal vertebrate development, but can be teratogenic in excess. In mice, additional retinoic acid is administered by oral gavage or intraperitoneal injection. Here we evaluate a novel non-invasive system for administering retinoic acid via chocolate/sugar pellets. We use this delivery system to examine the role of retinoic acid in regulating the expression of the fibroblast growth factor Fgf3, and find that the timing of retinoic acid treatment is critical for its effects on Fgf3 expression. Administration of increasing amounts of retinoic acid at 7.75 dpc leads to dose-dependent downregulation of Fgf3 in the otocyst and changes in spatial expression in the hindbrain. Detailed analysis of the developing inner ear also reveals a lateralisation of Fgf3 expression with increasing retinoic acid dose that is dependent on timing of administration. We discuss how these data impact on current models of retinoic acid patterning of the otocyst., (Copyright © 2012 Wiley Periodicals, Inc.)
- Published
- 2012
- Full Text
- View/download PDF
40. Evaluation of bioabsorbable elastin-fibrin matrix as a barrier in surgical periodontal treatment.
- Author
-
Da Costa-Noble R, Soustre EC, Cadot S, Lauverjat Y, Lefebvre F, and Rabaud M
- Subjects
- Adult, Aged, Biocompatible Materials, Biodegradation, Environmental, Female, Humans, Male, Middle Aged, Alveolar Bone Loss surgery, Elastin chemistry, Fibrin chemistry, Furcation Defects surgery, Guided Tissue Regeneration, Periodontal methods, Membranes, Artificial
- Abstract
The purpose of this investigation was to test clinically the efficiency of a recently described bioabsorbable matrix as a guided tissue regeneration membrane. This matrix was prepared from an original reaction between elastin and fibrin monomers and is now extensively used in several domains of surgery. The study group was composed of 26 patients, with a total of 35 lesions (22 intrabony defects, 8 Class II furcations and 5 Class III furcations) presenting moderate to advanced adult periodontitis. After initial therapy, measurements were made with a calibrated periodontal probe. Probing depth (PD) and gingival margin location (GM) measurements were taken twice: immediately before surgery and after 6 months before re-entry. Clinical attachment level (CAL), vertical osseous level (VOL) and alveolar crest location (AC) measurements were taken during surgery and after 6 months with re-entry procedures for all the patients. Color change of the gingival margin was only observed in 4 defects and device exposure occurred in the proportion of 2 out of the 35 defects. No foreign body reaction was observed in any case. At the intrabony defects mean PD reduction was 5 mm (P < 0.001), and mean gain of CAL was 4 mm (P < 0.001). Mean VOL was 4.3 mm (P < 0.001), mean gingival recession was 0.9 mm (P < 0.05) and mean AC was 0.2 mm (NS). At the Class II furcation defects the mean PD reduction was 4.5 mm (P < 0.001), mean gain CAL vertical was 3.2 mm and CAL horizontal was 4.5 mm (P < 0.001). Gingival recession averaged 1 mm (NS). A complete closure was observed in 2 out of the 8 defects. At the Class III furcation defects the mean PD reduction was 3.6 mm (P < 0.05) and mean CAL-V gain was 1.5 mm (P < 0.02). However the 5 sites showed no horizontal attachment gain and none were unchanged. A very low gingival recession, gingival reaction, crestal bone loss, and device exposure occurred during this study. This preliminary study suggests that the use of a biosynthetic barrier may have beneficial effects in the treatment of intrabony defects and Class II furcation defects. Randomized controlled trials are necessary to evaluate the efficacy and safety of this bioabsorbable membrane in periodontal therapy.
- Published
- 1996
- Full Text
- View/download PDF
41. Removal of fixed prostheses using ultrasounds and reactor.
- Author
-
Linares JM, Miquel JL, Cadot S, and Marteau JM
- Subjects
- Dental Cements, Female, Humans, Male, Metal Ceramic Alloys, Middle Aged, Reoperation instrumentation, Reoperation methods, Ultrasonic Therapy methods, Dental Instruments, Dental Restoration Failure, Denture, Partial, Fixed, Ultrasonic Therapy instrumentation
- Published
- 1994
42. [First gerodontic inquiries: PAQUIDENT after one year].
- Author
-
Cadot S, Canet C, Miquel JL, Dartigues JF, Barberger-Gateau P, and Salamon R
- Subjects
- Aged, Dentures statistics & numerical data, Diet, Female, France epidemiology, Health Services Needs and Demand statistics & numerical data, Humans, Male, Oral Hygiene, Prospective Studies, Tooth Loss epidemiology, Dental Care for Aged, Dental Health Surveys
- Published
- 1991
43. [Descriptive and technical study of dental inlays in pre-Colombian Mexico].
- Author
-
Cadot S and Miquel JL
- Subjects
- Cementation, History, Ancient, Humans, Mexico, Self Mutilation, Dental Cements history, Indians, North American, Inlays history
- Abstract
The authors presents, in this paper, a study on dental inlays among Mexican pre-Colombians. To begin with, from the study sources, systematization, classification and some characteristics were extracted, being the best method for later being able to study the descriptive and technical aspects of these inlays while insisting on the quality of the cement used.
- Published
- 1990
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.