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Lorenzi A, Bauland C, Pin S, Madur D, Combes V, Palaffre C, Guillaume C, Touzy G, Mary-Huard T, Charcosset A, Moreau L. Portability of genomic predictions trained on sparse factorial designs across two maize silage breeding cycles. Theor Appl Genet 2024; 137:75. [PMID: 38453705 DOI: 10.1007/s00122-024-04566-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
KEY MESSAGE We validated the efficiency of genomic predictions calibrated on sparse factorial training sets to predict the next generation of hybrids and tested different strategies for updating predictions along generations. Genomic selection offers new prospects for revisiting hybrid breeding schemes by replacing extensive phenotyping of individuals with genomic predictions. Finding the ideal design for training genomic prediction models is still an open question. Previous studies have shown promising predictive abilities using sparse factorial instead of tester-based training sets to predict single-cross hybrids from the same generation. This study aims to further investigate the use of factorials and their optimization to predict line general combining abilities (GCAs) and hybrid values across breeding cycles. It relies on two breeding cycles of a maize reciprocal genomic selection scheme involving multiparental connected reciprocal populations from flint and dent complementary heterotic groups selected for silage performances. Selection based on genomic predictions trained on a factorial design resulted in a significant genetic gain for dry matter yield in the new generation. Results confirmed the efficiency of sparse factorial training sets to predict candidate line GCAs and hybrid values across breeding cycles. Compared to a previous study based on the first generation, the advantage of factorial over tester training sets appeared lower across generations. Updating factorial training sets by adding single-cross hybrids between selected lines from the previous generation or a random subset of hybrids from the new generation both improved predictive abilities. The CDmean criterion helped determine the set of single-crosses to phenotype to update the training set efficiently. Our results validated the efficiency of sparse factorial designs for calibrating hybrid genomic prediction experimentally and showed the benefit of updating it along generations.
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Affiliation(s)
- Alizarine Lorenzi
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
- RAGT2n, Genetics and Analytics Unit, 12510, Druelle, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Sophie Pin
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Carine Palaffre
- UE 0394 SMH, INRAE, 2297 Route de l'INRA, 40390, Saint-Martin-de-Hinx, France
| | | | - Gaëtan Touzy
- RAGT2n, Genetics and Analytics Unit, 12510, Druelle, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution (GQE) - Le Moulon, 91190, Gif-Sur-Yvette, France.
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Bournot L, Payet T, Marcotorchino J, Awada M, Rouquet T, Breniere T, Couturier C, Astier J, Halimi C, Reboul E, Sicard F, Mounien L, Roux J, Bariohay B, Landrier JF. Vitamin D metabolism is altered during aging alone or combined with obesity in male mice. Biofactors 2024. [PMID: 38401051 DOI: 10.1002/biof.2047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/24/2024] [Indexed: 02/26/2024]
Abstract
Aging and obesity are associated with a decrease in plasma 25-hydroxyvitamin D (25(OH)D) levels. In the context of a growing aging population and the rising incidence of obesity, we hypothesized that aging process, either independently or in combination with obesity, could influence vitamin D (VD) metabolism, consequently resulting in the reduced 25(OH)D plasma concentrations. C57BL/6JRJ young (6 months) and old (23 months) mice fed with control (CD) or high fat diet (HF) were compared. Plasma and adipose concentration of cholecalciferol and 25(OH)D and mRNA expression of genes coding for the main VD actors were analyzed. Aging was associated with a decrease in plasma 25(OH)D levels, whereas combined effect of obesity and aging did not generate a cumulative effect on plasma 25(OH)D levels. The mRNA expression of Cyp27a1, Cyp3a11, and Cyp2j6 were decreased in the liver during aging. Together, these regulations could explain the reduced 25-hydroxylation. Interestingly, the lack of cumulative reduction of 25(OH)D in aged and obese mice could be related to the strong induction of Cyp2j6. In kidneys, a complex modulation of Cyp27b1 and Cyp24a1 could contribute to the reduced 25-hydroxylation in the liver. In white adipose tissue, an induction of Cyp2r1 was observed during aging and obesity, together with an increase of 25(OH)D quantity, suggesting an exacerbated storage that may participated to the reduced plasma 25(OH)D levels. These findings support the notion that aging alone or combined with obesity, induces regulation of VD metabolism in the organs, beyond the classical reduction of epidermal VD precursor, which may contribute to the decrease in 25(OH)D levels.
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Affiliation(s)
- Lorrine Bournot
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
- Biomeostasis, La Penne sur Huveaune, France
| | - Thomas Payet
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
| | | | | | | | - Thomas Breniere
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
| | | | - Julien Astier
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
| | - Charlotte Halimi
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
| | | | - Flavie Sicard
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
- PhenoMARS, CriBiom, Marseille, France
| | - Lourdes Mounien
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
- PhenoMARS, CriBiom, Marseille, France
| | | | | | - Jean François Landrier
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
- PhenoMARS, CriBiom, Marseille, France
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Lubrano M, Bellahsen-Harrar Y, Berlemont S, Atallah S, Vaz E, Walter T, Badoual C. Diagnosis with confidence: deep learning for reliable classification of laryngeal dysplasia. Histopathology 2024; 84:343-355. [PMID: 37872676 DOI: 10.1111/his.15067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/08/2023] [Accepted: 09/24/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Diagnosis of head and neck (HN) squamous dysplasias and carcinomas is critical for patient care, cure, and follow-up. It can be challenging, especially for grading intraepithelial lesions. Despite recent simplification in the last WHO grading system, the inter- and intraobserver variability remains substantial, particularly for nonspecialized pathologists, exhibiting the need for new tools to support pathologists. METHODS In this study we investigated the potential of deep learning to assist the pathologist with automatic and reliable classification of HN lesions following the 2022 WHO classification system. We created, for the first time, a large-scale database of histological samples (>2000 slides) intended for developing an automatic diagnostic tool. We developed and trained a weakly supervised model performing classification from whole-slide images (WSI). We evaluated our model on both internal and external test sets and we defined and validated a new confidence score to assess the predictions that can be used to identify difficult cases. RESULTS Our model demonstrated high classification accuracy across all lesion types on both internal and external test sets (respectively average area under the curve [AUC]: 0.878 (95% confidence interval [CI]: [0.834-0.918]) and 0.886 (95% CI: [0.813-0.947])) and the confidence score allowed for accurate differentiation between reliable and uncertain predictions. CONCLUSION Our results demonstrate that the model, associated with confidence measurements, can help in the difficult task of classifying HN squamous lesions by limiting variability and detecting ambiguous cases, taking us one step closer to a wider adoption of AI-based assistive tools.
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Affiliation(s)
- Mélanie Lubrano
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France
- Keen Eye, Paris, France
- Tribun Health, Paris, France
| | - Yaëlle Bellahsen-Harrar
- Department of Pathology, APHP, Hôpital Européen Georges-Pompidou, Paris, France
- Université Paris Cité, Paris, France
| | | | - Sarah Atallah
- Sorbonne Université, Paris, France
- Head and Neck Surgery Department, Hôpital Tenon, Paris, France
| | | | - Thomas Walter
- Centre for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France
- Institut Curie, PSL Université, Paris, France
- INSERM U900, Paris, France
| | - Cécile Badoual
- Department of Pathology, APHP, Hôpital Européen Georges-Pompidou, Paris, France
- Université Paris Cité, Paris, France
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Thiebaut AM, Louet ER, Ianszen M, Guichard MJ, Hanley DF, Gaudin C, Parcq J. O2L-001, an innovative thrombolytic to evacuate intracerebral haematoma. Brain 2023; 146:4690-4701. [PMID: 37450572 PMCID: PMC10629768 DOI: 10.1093/brain/awad237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/31/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
Intracerebral haemorrhage is an unmet medical need affecting more than 3 million people worldwide every year and leading to the formation of an intracerebral haematoma. Updated guidelines (2022) for the management of intracerebral haemorrhage patients recognize that minimally invasive approaches for the evacuation of supratentorial intracerebral haemorrhage have demonstrated reductions in mortality compared with medical management alone. However, improvement of functional outcome with a procedure involving thrombolytic therapy was neutral in the last large phase 3 clinical trial and requires a more effective and safer thrombolytic agent than those currently available. Here, we demonstrate that O2L-001 allows for the extended release of W253R/R275S recombinant tissue-type plasminogen activator (rtPA). A new rtPA variant, called optimized tPA (OptPA), offers improved efficacy for haematoma evacuation as well as improved safety. OptPA was produced in a Chinese hamster ovary cell line before purification, nanoprecipitation using the NANOp2Lysis® technological platform followed by suspension in a solution of 17% poloxamer 407 to obtain O2L-001. Plasmin generation assays were performed to demonstrate O2L-001 safety. Ex vivo haematoma models using human blood were used to demonstrate O2L-001 thrombolysis properties and efficacy. For the best translational significance, a clinical sized haematoma was used to ensure catheter placement and to allow administration of the thrombolytic agent into the core of the haematoma via a minimally invasive procedure. The capacity of OptPA to convert plasminogen into plasmin is strongly decreased compared to rtPA, thereby reducing potential bleeding events. However, a clot lysis assay showed that OptPA had the same fibrinolytic activity as rtPA. We demonstrated that long-term exposure to a thrombolytic agent was essential to achieve high thrombolysis efficacy. Indeed, 24 h continuous exposure to 0.1 µg/ml rtPA had similar efficacy than repeated short exposure to 30 µg/ml rtPA. This finding led to the development of O2L-001, allowing the extended release of OptPA in the first 6 h following injection. An ex vivo model using human blood was used to demonstrate O2L-001 efficacy. Interestingly, unlike rtPA, O2L-001 was able to induce the complete lysis of the 5 ml haematoma. In clinical sized haematomas (obtained from 30 ml of human blood), a single injection of O2L-001 at 1 mg/ml into the core of the haematoma led to a 44% increase in thrombolysis compared to rtPA. Taken together, these results demonstrate that O2L-001 provides new hope for haematoma evacuation and the treatment of patients with intracerebral haemorrhage.
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Affiliation(s)
| | - Estelle R Louet
- Op2Lysis SAS, GIP Cyceron, 14000 Caen, France
- Normandie Univ, UNICAEN, INSERM UMR-S U1237, Physiopathology and Imaging of Neurological Disorders (PhIND), GIP Cyceron, Institut Blood and Brain @ Caen-Normandie (BB@C), 14000 Caen, France
| | | | | | - Daniel F Hanley
- The Johns Hopkins Medical Institutions, BIOS, Baltimore, MD 21202, USA
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Leharanger M, Rodriguez Martinez EA, Balédent O, Vandromme L. Familiarization with Mixed Reality for Individuals with Autism Spectrum Disorder: An Eye Tracking Study. Sensors (Basel) 2023; 23:6304. [PMID: 37514598 PMCID: PMC10383879 DOI: 10.3390/s23146304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023]
Abstract
Mixed Reality (MR) technology is experiencing significant growth in the industrial and healthcare sectors. The headset HoloLens 2 displays virtual objects (in the form of holograms) in the user's environment in real-time. Individuals with Autism Spectrum Disorder (ASD) exhibit, according to the DSM-5, persistent deficits in communication and social interaction, as well as a different sensitivity compared to neurotypical (NT) individuals. This study aims to propose a method for familiarizing eleven individuals with severe ASD with the HoloLens 2 headset and the use of MR technology through a tutorial. The secondary objective is to obtain quantitative learning indicators in MR, such as execution speed and eye tracking (ET), by comparing individuals with ASD to neurotypical individuals. We observed that 81.81% of individuals with ASD successfully familiarized themselves with MR after several sessions. Furthermore, the visual activity of individuals with ASD did not differ from that of neurotypical individuals when they successfully familiarized themselves. This study thus offers new perspectives on skill acquisition indicators useful for supporting neurodevelopmental disorders. It contributes to a better understanding of the neural mechanisms underlying learning in MR for individuals with ASD.
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Affiliation(s)
- Maxime Leharanger
- UR 7516 Laboratory CHIMERE, University of Picardie Jules Verne, 80000 Amiens, France
- Institut Faire Face, CHU Amiens, 80054 Amiens, France
| | - Eder Alejandro Rodriguez Martinez
- UR 7516 Laboratory CHIMERE, University of Picardie Jules Verne, 80000 Amiens, France
- Institut Faire Face, CHU Amiens, 80054 Amiens, France
| | - Olivier Balédent
- UR 7516 Laboratory CHIMERE, University of Picardie Jules Verne, 80000 Amiens, France
- Institut Faire Face, CHU Amiens, 80054 Amiens, France
| | - Luc Vandromme
- UR 7516 Laboratory CHIMERE, University of Picardie Jules Verne, 80000 Amiens, France
- Institut Faire Face, CHU Amiens, 80054 Amiens, France
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Legrand N, Salameh P, Jullien M, Chevallier P, Ferron E, David G, Devilder MC, Willem C, Gendzekhadze K, Parham P, Retière C, Gagne K. Non-Expressed Donor KIR3DL1 Alleles May Represent a Risk Factor for Relapse after T-Replete Haploidentical Hematopoietic Stem Cell Transplantation. Cancers (Basel) 2023; 15:2754. [PMID: 37345091 DOI: 10.3390/cancers15102754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
KIR3DL1 alleles are expressed at different levels on the natural killer (NK) cell surface. In particular, the non-expressed KIR3DL1*004 allele appears to be common in Caucasian populations. However, the overall distribution of non-expressed KIR3DL1 alleles and their clinical relevance after T-replete haploidentical hematopoietic stem cell transplantation (hHSCT) with post-transplant cyclophosphamide remain poorly documented in European populations. In a cohort of French blood donors (N = 278), we compared the distribution of expressed and non-expressed KIR3DL1 alleles using next-generation sequencing (NGS) technology combined with multi-color flow cytometry. We confirmed the predominance of the non-expressed KIR3DL1*004 allele. Using allele-specific constructs, the phenotype and function of the uncommon KIR3DL1*019 allotype were characterized using the Jurkat T cell line and NKL transfectants. Although poorly expressed on the NK cell surface, KIR3DL1*019 is retained within NK cells, where it induces missing self-recognition of the Bw4 epitope. Transposing our in vitro observations to a cohort of hHSCT patients (N = 186) led us to observe that non-expressed KIR3DL1 HSC grafts increased the incidence of relapse in patients with myeloid diseases. Non-expressed KIR3DL1 alleles could, therefore, influence the outcome of hHSCT.
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Affiliation(s)
- Nolwenn Legrand
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Perla Salameh
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Maxime Jullien
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
- Department of Hematology Clinic, Nantes University Hospital, F-44000 Nantes, France
| | - Patrice Chevallier
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
- Department of Hematology Clinic, Nantes University Hospital, F-44000 Nantes, France
| | - Enora Ferron
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Gaelle David
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Marie-Claire Devilder
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Catherine Willem
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Ketevan Gendzekhadze
- Department of Hematology and HCT, HLA Laboratory, City of Hope, Medical Center, Duarte, CA 91010, USA
| | - Peter Parham
- Department of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christelle Retière
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
| | - Katia Gagne
- Etablissement Français du Sang (EFS), F-44011 Nantes, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1307, CNRS UMR 6075, Centre de Recherche en Cancérologie et Immunologie Integrée Nantes Angers (CRCI2NA), Team 12, F-44000 Nantes, France
- LabEx IGO "Immunotherapy, Graft, Oncology", F-44000 Nantes, France
- LabEx Transplantex, Université de Strasbourg, F-67000 Strasbourg, France
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Mazéas A, Chalabaev A, Blond M, Pereira B, Duclos M. Digital intervention promoting physical activity among obese people (DIPPAO) randomised controlled trial: study protocol. BMJ Open 2022; 12:e058015. [PMID: 35710254 PMCID: PMC9204413 DOI: 10.1136/bmjopen-2021-058015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION Physical inactivity and excessive sedentary behaviours are major preventable causes in both the development and the treatment of obesity and type 2 diabetes mellitus (T2DM). Nevertheless, current programmes struggle to engage and sustain physical activity (PA) of patients over long periods of time. To overcome these limitations, the Digital Intervention Promoting Physical Activity among Obese people randomised controlled trial (RCT) aims to evaluate the effectiveness of a group-based digital intervention grounded on gamification strategies, enhanced by social features and informed by the tenets of the self-determination theory and the social identity approach. METHODS AND ANALYSIS This trial is a two-arm parallel RCT testing the effectiveness of the Kiplin digital intervention on obese and patients with T2DM in comparison to the usual supervised PA programme of the University Hospital of Clermont-Ferrand, France. A total of 50 patients will be randomised to one of the two interventions and will follow a 3-month programme with a 6-month follow-up postintervention. The primary outcome of the study is the daily step count change between the baseline assessment and the end of the intervention. Accelerometer data, self-reported PA, body composition and physical capacities will also be evaluated. To advance our understanding of complex interventions like gamified and group-based ones, we will explore several psychological mediators relative to motivation, enjoyment, in-group identification or perceived weight stigma. Finally, to assess a potential superior economic efficiency compared with the current treatment, we will conduct a cost-utility analysis between the two conditions. A mixed-model approach will be used to analyse the change in outcomes over time. ETHICS AND DISSEMINATION The research protocol has been reviewed and approved by the Local Human Protection Committee (CPP Ile de France XI, No 21 004-65219). Results will inform the Kiplin app development, be published in scientific journals and disseminated in international conferences. TRIAL REGISTRATION NUMBER NCT04887077.
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Affiliation(s)
- Alexandre Mazéas
- SENS, Univ. Grenoble Alpes, 38000 Grenoble, France
- Department of Human Nutrition, INRAE Centre Clermont-Auvergne-Rhône-Alpes, Clermont-Ferrand, France
- Kiplin, Nantes, France
| | | | | | - Bruno Pereira
- Department of Biostatistics Unit (DRCI), University Hospital Centre, Clermont-Ferrand, France
| | - Martine Duclos
- Department of Human Nutrition, INRAE Centre Clermont-Auvergne-Rhône-Alpes, Clermont-Ferrand, France
- Department of Sport Medicine and Functional Exploration, University Hospital Centre, Clermont-Ferrand, France
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Dai M, Georgilis E, Goudounet G, Garbay B, Pille J, van Hest JCM, Schultze X, Garanger E, Lecommandoux S. Refining the Design of Diblock Elastin-Like Polypeptides for Self-Assembly into Nanoparticles. Polymers (Basel) 2021; 13:1470. [PMID: 34062852 PMCID: PMC8125372 DOI: 10.3390/polym13091470] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Diblock copolymers based-on elastin-like polypeptide (ELP) have the potential to undergo specific phase transitions when thermally stimulated. This ability is especially suitable to form carriers, micellar structures for instance, for delivering active cargo molecules. Here, we report the design and study of an ELP diblock library based on ELP-[M1V3-i]-[I-j]. First, ELP-[M1V3-i]-[I-j] (i = 20, 40, 60; j = 20, 90) that showed a similar self-assembly propensity (unimer-to-aggregate transition) as their related monoblocks ELP-[M1V3-i] and ELP-[I-j]. By selectively oxidizing methionines of ELP-[M1V3-i] within the different diblocks structures, we have been able to access a thermal phase transition with three distinct regimes (unimers, micelles, aggregates) characteristic of well-defined ELP diblocks.
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Affiliation(s)
- Michèle Dai
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
- L’Oréal Recherche Avancée, 1 Avenue Eugène Schueller, 93600 Aulnay-sous-Bois, France;
| | - Evangelos Georgilis
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
- Current affiliation E.G. (Evangelos Georgilis): CIC nanoGUNE (BRTA), Tolosa Hiribidea 76, 20018 Donostia-San Sebastián, Spain
| | - Guillaume Goudounet
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
| | - Bertrand Garbay
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
| | - Jan Pille
- Bio-organic Chemistry Lab, Eindhoven University of Technology, P.O. Box 513 (STO 3.31), 5600 MB Eindhoven, The Netherlands; (J.P.); (J.C.M.v.H.)
| | - Jan C. M. van Hest
- Bio-organic Chemistry Lab, Eindhoven University of Technology, P.O. Box 513 (STO 3.31), 5600 MB Eindhoven, The Netherlands; (J.P.); (J.C.M.v.H.)
| | - Xavier Schultze
- L’Oréal Recherche Avancée, 1 Avenue Eugène Schueller, 93600 Aulnay-sous-Bois, France;
| | - Elisabeth Garanger
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
| | - Sébastien Lecommandoux
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600 Pessac, France; (M.D.); (E.G.); (G.G.); (B.G.)
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Postic E, Outreman Y, Derocles S, Granado C, Le Ralec A. Genetics of wild and mass-reared populations of a generalist aphid parasitoid and improvement of biological control. PLoS One 2021; 16:e0249893. [PMID: 33848317 PMCID: PMC8043399 DOI: 10.1371/journal.pone.0249893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/28/2021] [Indexed: 11/19/2022] Open
Abstract
Due to their ability to parasitize various insect species, generalist parasitoids are widely used as biological control agents. They can be mass-reared and released in agroecosystems to control several pest species in various crops. However, the existence of genetic differentiation among populations of generalist parasitoid species is increasingly recognized and this can be associated with an adaptation to local conditions or to a reduced range of host species. Moreover, constraints of mass-rearing conditions can alter genetic variation within parasitoid populations released. These features could be associated with a reduced efficiency of the control of targeted pest species. Here, we focused on strawberry greenhouses where the control of aphids with the generalist parasitoid Aphidius ervi appears to be inefficient. We investigated whether this inefficiency may have both genetic and ecological bases comparing wild and commercial populations of A. ervi. We used two complementary genetic approaches: one based on the mitochondrial marker COI and one based on microsatellite markers. COI analysis showed a genetic differentiation within the A. ervi species, but the structure was neither associated with the commercial/wild status nor with host species factors. On the other hand, using microsatellite markers, we showed a genetic differentiation between commercial and wild A. ervi populations associated with a loss of genetic diversity within the mass-reared populations. Our ecological genetics study may potentially explain the weak efficiency of biological control of aphids in protected strawberry crops and enable to provide some insights to improve biological control.
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Affiliation(s)
- Estelle Postic
- IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- AOPn Fraises de France, Estillac, France
| | | | | | | | - Anne Le Ralec
- IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- * E-mail:
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10
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Marcet-Rius M, Pageat P, Bienboire-Frosini C, Teruel E, Monneret P, Leclercq J, Cozzi A. The provision of toys to pigs can improve the human-animal relationship. Porcine Health Manag 2020; 6:29. [PMID: 33292637 PMCID: PMC7653863 DOI: 10.1186/s40813-020-00167-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/25/2020] [Indexed: 11/26/2022] Open
Abstract
It is now widely recognised that a positive human-animal relationship is beneficial not only for farm animals' welfare but also for productivity and the quality of products. A better understanding of animal emotions is an important goal in disciplines ranging from neuroscience to animal welfare science, but few reliable tools exist for measuring these emotions. In this study, whether the provision of toys to solicit play behaviour in pigs is associated with a change in the human-animal relationship and the emotional state of pigs was investigated. We involved a group of sixteen mini-pigs housed in an experimental setting and the use of a preliminary test called the 'strange person' test. After a Control and a Play session (with medium-sized dog toys, balls with ropes), the strange person test was performed. During the test, a person wearing a colourful overall, a hood, a mask, gloves and boots (unknown person with an odd appearance) entered the pen, where 2 mini-pigs were housed, for a 2-min video recording. The strange person test results after the Play and Control sessions were compared. The results showed that the latency to approach the person (duration in seconds) and the duration for which the pig was distant from the strange person (duration in seconds) were significantly lower after the Play session than after the Control session (Degrees of Freedom =30; Statistic of the F test =39.1; p < 0.0001 and Degrees of Freedom =15; Statistic of the F test =54.3; p < 0.0001, respectively). The duration of direct contact (duration in seconds) (Degrees of Freedom =15; Statistic of the F test =14.8; p = 0.002), the need to separate the pig from the strange person (frequency) (Degrees of Freedom =30; Statistic of the F test =9.3; p = 0.005) and the duration of tail movement (duration in seconds) (Degrees of Freedom =15; Statistic of the F test =12.6; p = 0.003) were all significantly higher after the Play sessions than after the Control sessions. Overall, the results suggest a change in the human-animal relationship after the Play sessions: the pigs seemed to be less fearful and more inclined to interact with the strange person, showing a more positive emotional state. This preliminary study suggests that the provision of toys, and more precisely, the opportunity to perform object play behaviour, and sometimes, spontaneously, social play behaviour, can improve the human-animal relationship. Additional research to explore this topic thoroughly may yield interesting results because a positive emotional state of the animals and a good human-animal relationship are essential to ensure good quality of life of farm animals.
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Affiliation(s)
- Míriam Marcet-Rius
- Physiological and Behavioural Mechanisms of Adaptation Department, IRSEA (Research Institute in Semiochemistry and Applied Ethology), Quartier Salignan, 84400, Apt, France.
| | - Patrick Pageat
- Semiochemicals' Identification and Analogs' Design Department, IRSEA (Research Institute in Semiochemistry and Applied Ethology), Quartier Salignan, 84400, Apt, France
| | - Cécile Bienboire-Frosini
- Physiological and Behavioural Mechanisms of Adaptation Department, IRSEA (Research Institute in Semiochemistry and Applied Ethology), Quartier Salignan, 84400, Apt, France
| | - Eva Teruel
- Statistical Analysis Service, IRSEA (Research Institute in Semiochemistry and Applied Ethology), Quartier Salignan, 84400, Apt, France
| | - Philippe Monneret
- Animal Experimentation Service, IRSEA (Research Institute in Semiochemistry and Applied Ethology), Quartier Salignan, 84400, Apt, France
| | - Julien Leclercq
- Animal Experimentation Service, IRSEA (Research Institute in Semiochemistry and Applied Ethology), Quartier Salignan, 84400, Apt, France
| | - Alessandro Cozzi
- Research and Education Board, IRSEA (Research Institute in Semiochemistry and Applied Ethology), Quartier Salignan, 84400, Apt, France
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11
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Cosson P, Hastoy C, Errazzu LE, Budeguer CJ, Boutié P, Rolin D, Schurdi-Levraud V. Genetic diversity and population structure of the sweet leaf herb, Stevia rebaudiana B., cultivated and landraces germplasm assessed by EST-SSRs genotyping and steviol glycosides phenotyping. BMC Plant Biol 2019; 19:436. [PMID: 31638900 PMCID: PMC6805397 DOI: 10.1186/s12870-019-2061-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Stevia rebaudiana (Asteraceae), native from Paraguay, accumulates steviol glycosides (SGs) into its leaves. These compounds exhibit acaloric intense sweet taste which answers to consumer demands for reducing daily sugar intake. Despite the developpement of S. rebaudiana cultivation all over the world, the development of new cultivars is very recent, in particular due to a colossal lack of (1) germplasm collection and breeding, (2) studies on genetic diversity and its structuring, (3) genomic tools. RESULTS In this study, we developped 18 EST-SSR from 150,258 EST from The Compositae Genome Project of UC Davis ( http://compgenomics.ucdavis.edu/data/ ). We genotyped 145 S. rebaudiana individuals, issued from thirty-one cultivars and thirty-one landraces of various origins worldwide. Markers polymorphic information content (PIC) ranged between 0.60 and 0.84. An average of 12 alleles per locus and a high observed heterozygoty of 0.69 could be observed. The landraces revealed twice as many private alleles as cultivars. The genotypes could be clustered into 3 genetic populations. The landraces were grouped in the same cluster in which the oldest cultivars "Eirete" and "MoritaIII" type are also found. The other two clusters only include cultivated genotypes. One of them revealed an original genetic variability. SG phenotypes could not discriminate the three genetic clusters but phenotyping showed a wide range of composition in terms of bitter to sweet SGs. CONCLUSION This is the first study of genetic diversity in Stevia rebaudiana involving 145 genotypes, including known cultivars as well as landrace populations of different origin. This study pointed out the structuration of S. rebaudiana germplasm and the resource of the landrace populations for genetic improvement, even on the trait of SG's composition.
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Affiliation(s)
- Patrick Cosson
- UMR Biologie du Fruit et Pathologie, 1332, INRA Université de Bordeaux, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
| | - Cécile Hastoy
- UMR Biologie du Fruit et Pathologie, 1332, INRA Université de Bordeaux, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
- Oviatis SA, Le Bourg, 47150, Lacaussade, France
| | | | | | | | - Dominique Rolin
- UMR Biologie du Fruit et Pathologie, 1332, INRA Université de Bordeaux, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France
| | - Valérie Schurdi-Levraud
- UMR Biologie du Fruit et Pathologie, 1332, INRA Université de Bordeaux, 71 avenue Edouard Bourlaux, 33883, Villenave d'Ornon cedex, France.
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12
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Arnal M, Larroque H, Leclerc H, Ducrocq V, Robert-Granié C. Genetic parameters for first lactation dairy traits in the Alpine and Saanen goat breeds using a random regression test-day model. Genet Sel Evol 2019; 51:43. [PMID: 31409294 PMCID: PMC6693143 DOI: 10.1186/s12711-019-0485-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Random regression models (RRM) are widely used to analyze longitudinal data in genetic evaluation systems because they can better account for time-course changes in environmental effects and additive genetic values of animals by fitting the test-day (TD) specific effects. Our objective was to implement a random regression model for the evaluation of dairy production traits in French goats. RESULTS The data consisted of milk TD records from 30,186 and 32,256 first lactations of Saanen and Alpine goats. Milk yield, fat yield, protein yield, fat content and protein content were considered. Splines were used to model the environmental factors. The genetic and permanent environmental effects were modeled by the same Legendre polynomials. The goodness-of-fit and the genetic parameters derived from functions of the polynomials of orders 0 to 4 were tested. Results were also compared to those from a lactation model with total milk yield calculated over 250 days and to those of a multiple-trait model that considers performance in six periods throughout lactation as different traits. Genetic parameters were consistent between models. Models with fourth-order Legendre polynomials led to the best fit of the data. In order to reduce complexity, computing time, and interpretation, a rank reduction of the variance covariance matrix was performed using eigenvalue decomposition. With a reduction to rank 2, the first two principal components correctly summarized the genetic variability of milk yield level and persistency, with a correlation close to 0 between them. CONCLUSIONS A random regression model was implemented in France to evaluate and select goats for yield traits and persistency, which are independent i.e. no genetic correlation between them, in first lactation.
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Affiliation(s)
- Mathieu Arnal
- GenPhySE, Université de Toulouse, INRA, ENVT, Toulouse INP, 31326 Castanet-Tolosan, France
- Institut de l’Elevage, Chemin de Borde Rouge, 31326 Castanet-Tolosan Cedex, France
| | - Hélène Larroque
- GenPhySE, Université de Toulouse, INRA, ENVT, Toulouse INP, 31326 Castanet-Tolosan, France
| | - Hélène Leclerc
- INRA UMR1313 GABI, Institut de l’Elevage, 78350 Jouy-en-Josas, France
| | - Vincent Ducrocq
- UMR1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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13
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Betsch L, Boltz V, Brioudes F, Pontier G, Girard V, Savarin J, Wipperman B, Chambrier P, Tissot N, Benhamed M, Mollereau B, Raynaud C, Bendahmane M, Szécsi J. TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals. PLoS Genet 2019; 15:e1007899. [PMID: 30695029 PMCID: PMC6368322 DOI: 10.1371/journal.pgen.1007899] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 02/08/2019] [Accepted: 12/15/2018] [Indexed: 11/30/2022] Open
Abstract
Translationally Controlled Tumor Protein (TCTP) controls growth by regulating the G1/S transition during cell cycle progression. Our genetic interaction studies show that TCTP fulfills this role by interacting with CSN4, a subunit of the COP9 Signalosome complex, known to influence CULLIN-RING ubiquitin ligases activity by controlling CULLIN (CUL) neddylation status. In agreement with these data, downregulation of CSN4 in Arabidopsis and in tobacco cells leads to delayed G1/S transition comparable to that observed when TCTP is downregulated. Loss-of-function of AtTCTP leads to increased fraction of deneddylated CUL1, suggesting that AtTCTP interferes negatively with COP9 function. Similar defects in cell proliferation and CUL1 neddylation status were observed in Drosophila knockdown for dCSN4 or dTCTP, respectively, demonstrating a conserved mechanism between plants and animals. Together, our data show that CSN4 is the missing factor linking TCTP to the control of cell cycle progression and cell proliferation during organ development and open perspectives towards understanding TCTP's role in organ development and disorders associated with TCTP miss-expression.
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Affiliation(s)
- Léo Betsch
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Véronique Boltz
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Florian Brioudes
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Garance Pontier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Victor Girard
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Univ Lyon, Lyon, France
| | - Julie Savarin
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Barbara Wipperman
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Pierre Chambrier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Nicolas Tissot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Orsay, France
| | - Bertrand Mollereau
- Laboratory of Biology and Modelling of the Cell, UMR5239 CNRS/ENS de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Univ Lyon, Lyon, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Orsay, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
| | - Judit Szécsi
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, UMS 3444 Biosciences Lyon Gerland, Ecole Normale Supérieure, Lyon, France
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Bernard A, Barreneche T, Lheureux F, Dirlewanger E. Analysis of genetic diversity and structure in a worldwide walnut (Juglans regia L.) germplasm using SSR markers. PLoS One 2018; 13:e0208021. [PMID: 30481202 PMCID: PMC6258541 DOI: 10.1371/journal.pone.0208021] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/10/2018] [Indexed: 11/18/2022] Open
Abstract
Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known and is grown worldwide in temperate areas. France is the 7th leading producer as of 2016 with 39 kt. Deciphering walnut genetic diversity and structure is important for efficient management and use of genetic resources. In this work, 253 worldwide accessions from the INRA walnut germplasm collection, containing English walnut and several related species, were genotyped using 13 SSR (Single Sequence Repeat) markers selected from the literature to assess diversity and structure. Genetic diversity parameters showed a deficiency of heterozygotes and, for several SSRs, allele-specificities among the accessions tested. Principal Coordinate Analysis (PCoA) showed the 253 accessions clustered in largely in agreement with the existing botanical classification of the genus. Among the 217 J. regia accessions, two main clusters, accessions from Eastern Europe and Asia, and accessions from Western Europe and America, were identified using STRUCTURE software. This was confirmed by Principal Coordinate Analysis and supported by Neighbor-Joining tree construction using DARwin software. Moreover, a substructure was found within the two clusters, mainly according to geographical origin. A core collection containing 50 accessions was selected using the maximum length sub-tree method and prior knowledge about their phenotype. The present study constitutes a preliminary population genetics overview of INRA walnut genetic resources collection using SSR markers. The resulting estimations of genetic diversity and structure are useful for germplasm management and for future walnut breeding programs.
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Affiliation(s)
- Anthony Bernard
- UMR 1332 BFP, INRA, Université de Bordeaux, Villenave d’Ornon, France
- Ctifl, centre opérationnel de Lanxade, Prigonrieux, France
| | - Teresa Barreneche
- UMR 1332 BFP, INRA, Université de Bordeaux, Villenave d’Ornon, France
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15
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Maroun R, Mitrofan L, Benjamin L, Nachbaur G, Maunoury F, Le Jeunne P, Durand-Zaleski I. Real life patterns of care and progression free survival in metastatic renal cell carcinoma patients: retrospective analysis of cross-sectional data. BMC Cancer 2018; 18:214. [PMID: 29466966 PMCID: PMC5822611 DOI: 10.1186/s12885-018-4117-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 02/09/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Patient characteristics and survival outcomes in randomized trials may be different from those in real-life clinical practice. The objective of this study was to describe treatment pathways, safety, drug costs and survival in patients with metastatic Renal Cell Carcinoma (mRCC) in a real world setting. METHODS A retrospective analysis was performed using IQVIA real world oncology cross-sectional survey data, a retrospective treatment database collecting anonymized patient-level data in Europe. Data on treatment naïve patients with mRCC who received a first-line targeted therapy in France were extracted for the period 2005-2015. Descriptive analyses were performed on treatment patterns, patient characteristics and safety profiles. Progression Free Survival (PFS) was determined using Kaplan-Meier survival analysis. RESULTS One thousand three hundred thirty-one patients with mRCC who received a first-line targeted therapy were included. The male/female sex ratio was 2.5 and 66% of patients were aged > 60 years. 83% of patients had clear cell adenocarcinoma. 83% of patients underwent a surgical procedure, 10% had radiotherapy. In patients who received a first-line targeted therapy, 73% received sunitinib. The mean time from diagnosis to first-line treatment by targeted therapies in patients initially diagnosed with metastatic disease was 3.3 months [95% CI:2.5-4.1]. In patients who received second-line targeted therapy n = 257 (19%), the most frequently observed treatment sequences were sunitinib-everolimus (33%) and sunitinib-sorafenib (27%). Adverse events data were available for 501 patients and adverse events were documented in 70% of patients, most frequently diarrhoea. The overall median PFS was 13 months [95% CI:11.5-16]. CONCLUSION Patient characteristics were consistent with the literature. Treatment patterns appeared to follow current practice guidelines. Despite some variations, PFS in our study seems to be consistent with findings from other real world studies. Nevertheless, PFS results were higher than those observed in clinical trials. Due to the use of cross-sectional data, PFS in our study should be interpreted with caution.
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Affiliation(s)
- Rana Maroun
- GlaxoSmithKline, Health Economics and Outcomes Research, Rueil Malmaison, France
- INSERM, ECEVE, UMR 1123, Paris, France
| | | | - Laure Benjamin
- GlaxoSmithKline, Health Economics and Outcomes Research, Rueil Malmaison, France
| | - Gaelle Nachbaur
- GlaxoSmithKline, Health Economics and Outcomes Research, Rueil Malmaison, France
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Valle B, Simonneau T, Boulord R, Sourd F, Frisson T, Ryckewaert M, Hamard P, Brichet N, Dauzat M, Christophe A. PYM: a new, affordable, image-based method using a Raspberry Pi to phenotype plant leaf area in a wide diversity of environments. Plant Methods 2017; 13:98. [PMID: 29151844 PMCID: PMC5678554 DOI: 10.1186/s13007-017-0248-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 10/26/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Plant science uses increasing amounts of phenotypic data to unravel the complex interactions between biological systems and their variable environments. Originally, phenotyping approaches were limited by manual, often destructive operations, causing large errors. Plant imaging emerged as a viable alternative allowing non-invasive and automated data acquisition. Several procedures based on image analysis were developed to monitor leaf growth as a major phenotyping target. However, in most proposals, a time-consuming parameterization of the analysis pipeline is required to handle variable conditions between images, particularly in the field due to unstable light and interferences with soil surface or weeds. To cope with these difficulties, we developed a low-cost, 2D imaging method, hereafter called PYM. The method is based on plant leaf ability to absorb blue light while reflecting infrared wavelengths. PYM consists of a Raspberry Pi computer equipped with an infrared camera and a blue filter and is associated with scripts that compute projected leaf area. This new method was tested on diverse species placed in contrasting conditions. Application to field conditions was evaluated on lettuces grown under photovoltaic panels. The objective was to look for possible acclimation of leaf expansion under photovoltaic panels to optimise the use of solar radiation per unit soil area. RESULTS The new PYM device proved to be efficient and accurate for screening leaf area of various species in wide ranges of environments. In the most challenging conditions that we tested, error on plant leaf area was reduced to 5% using PYM compared to 100% when using a recently published method. A high-throughput phenotyping cart, holding 6 chained PYM devices, was designed to capture up to 2000 pictures of field-grown lettuce plants in less than 2 h. Automated analysis of image stacks of individual plants over their growth cycles revealed unexpected differences in leaf expansion rate between lettuces rows depending on their position below or between the photovoltaic panels. CONCLUSIONS The imaging device described here has several benefits, such as affordability, low cost, reliability and flexibility for online analysis and storage. It should be easily appropriated and customized to meet the needs of various users.
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Affiliation(s)
- Benoît Valle
- UMR759 Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, 2 Place Pierre Viala, 34060 Montpellier Cedex 2, France
- Sun’R SAS, 7 rue de Clichy, 75009 Paris, France
| | - Thierry Simonneau
- UMR759 Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, 2 Place Pierre Viala, 34060 Montpellier Cedex 2, France
| | - Romain Boulord
- UMR759 Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, 2 Place Pierre Viala, 34060 Montpellier Cedex 2, France
| | | | | | | | - Philippe Hamard
- UMR759 Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, 2 Place Pierre Viala, 34060 Montpellier Cedex 2, France
| | - Nicolas Brichet
- UMR759 Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, 2 Place Pierre Viala, 34060 Montpellier Cedex 2, France
| | - Myriam Dauzat
- UMR759 Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, 2 Place Pierre Viala, 34060 Montpellier Cedex 2, France
| | - Angélique Christophe
- UMR759 Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, 2 Place Pierre Viala, 34060 Montpellier Cedex 2, France
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