5,879 results on '"Vignal A"'
Search Results
2. Phenotypic variability related to dominant UCHL1 mutations: about three families with optic atrophy and ataxia
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Marelli, C., Ramond, F., Vignal, C., Blanchet, C., Frost, S., Hao, Q., Bocquet, B., Nadjar, Y., Leboucq, N., Taieb, G., Benkirane, M., Hersent, C., Koenig, M., and Meunier, I.
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- 2024
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3. The black honey bee genome: insights on specific structural elements and a first step towards pangenomes
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Eynard, Sonia E., Klopp, Christophe, Canale-Tabet, Kamila, Marande, William, Vandecasteele, Céline, Roques, Céline, Donnadieu, Cécile, Boone, Quentin, Servin, Bertrand, and Vignal, Alain
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- 2024
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4. Using a Research-Based Assessment Instrument to Explore Undergraduate Students' Proficiencies around Measurement Uncertainty in Physics Lab Contexts
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Gayle Geschwind, Michael Vignal, Marcos D. Caballero, and H. J. Lewandowski
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Concepts and practices surrounding measurement uncertainty are vital knowledge for physicists and are often emphasized in undergraduate physics laboratory courses. We have previously developed a research-based assessment instrument--the Survey of Physics Reasoning on Uncertainty Concepts in Experiments (SPRUCE)--to examine student proficiency with measurement uncertainty along a variety of axes, including sources of uncertainty, handling of uncertainty, and distributions and repeated measurements. We present here initial results from the assessment representing over 1500 students from 20 institutions. We analyze students' performance pre- and postinstruction in lab courses and examine how instruction impacts students with different majors and gender. We find that students typically excel in certain areas, such as reporting the mean of a distribution as their result, while they struggle in other areas, such as comparing measurements with uncertainty and correctly propagating errors using formulas. Additionally, we find that the importance that an instructor places in certain areas of measurement uncertainty is uncorrelated with student performance in those areas.
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- 2024
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5. Representational differences in how students compare measurements
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Geschwind, Gayle, Vignal, Michael, and Lewandowski, H. J.
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Physics - Physics Education - Abstract
Measurement uncertainty plays a critical role in the process of experimental physics. It is useful to be able to assess student proficiency around the topic to iteratively improve instruction and student learning. For the topic of measurement uncertainty, we developed an assessment tool called the Survey of Physics Reasoning on Uncertainty Concepts in Experiments (SPRUCE), which aims to assess students' knowledge, and use of, a variety of concepts related to measurement uncertainty. This assessment includes two isomorphic questions focused on comparing two measurements with uncertainty. One is presented numerically and the other pictorially. Despite the questions probing identical concepts, students answer them in different ways, indicating that they rely on distinct modes of representation to make sense of measurement uncertainty and comparisons. Specifically, students score much higher on the pictorially represented item, which suggests possible instructional changes to leverage students' use of representations while working with concepts of measurement uncertainty., Comment: 4 pages, 2 figures, to be published in PERC Conference Proceedings 2023
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- 2023
6. Overview of couplet scoring in content-focused physics assessments
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Vignal, Michael, Geschwind, Gayle, Caballero, Marcos D., and Lewandowski, H. J.
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Physics - Physics Education - Abstract
Content-focused research-based assessment instruments typically use items (i.e., questions) as the unit of assessment for scoring, reporting, and validation. Couplet scoring employs an alternative unit of assessment called a couplet, which is essentially an item viewed and scored through the lens of a specific assessment objective. With couplet scoring, a single item may have more than one assessment objective and therefore more than one couplet and thus more than one score. We outline the components of traditional item scoring, discuss couplet scoring and its benefits, and use both a recently developed content research-based assessment instrument and an existing one to ground our discussion., Comment: 14 pages, 4 figures
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- 2023
7. Randomized trial of bilateral gene therapy injection for m.11778G>A MT-ND4 Leber optic neuropathy
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Newman, Nancy J, Yu-Wai-Man, Patrick, Subramanian, Prem S, Moster, Mark L, Wang, An-Guor, Donahue, Sean P, Leroy, Bart P, Carelli, Valerio, Biousse, Valerie, Vignal-Clermont, Catherine, Sergott, Robert C, Sadun, Alfredo A, Rebolleda Fernández, Gema, Chwalisz, Bart K, Banik, Rudrani, Bazin, Fabienne, Roux, Michel, Cox, Eric D, Taiel, Magali, Sahel, José-Alain, Giulia, Amore, Shweta, Anand, Rudrani, Banik, Piero, Barboni, Valérie, Biousse, Hayley, Boston, Asma, Burale, Michele, Carbonelli, Valerio, Carelli, Celia, Chen, Hui-Chen, Cheng, Steve, Cho, Manuela, Contin, Pietro, D’Agati, DeBusk, Adam A, Julie, De Zaeytijd, Jannah, Dobbs, Lindreth, DuBois, Simona, Esposti, Alcides, Fernandes Filho, Elizabeth, Fortin, Sapna, Gangaputra, Deborah, Gibbs, François, Girmens Jean, Rabih, Hage, Haller, Julia A, Gad, Heilweil, George Baker, Hubbard III, Jeong-Min, Hwang, Laia, Jaumendreu Urquijo, Neringa, Jurkute, Rustum, Karanjia, Wahiba, Khemliche, La Chiara, Morgia, Maria, Massini, Marc, Mathias, Memon, Muhammad A, Susan, Mohamed, Muñoz Negrete, Francisco J, Ghazala, O’Keefe, Shriji, Patel, Paula, Pecen, Peragallo, Jason H, Lise, Plaine, Mary, Preston, Gema, Rebolleda Fernández, Martina, Romagnoli, José-Alain, Sahel, Melissa, SantaMaria, Chuanbin, Sun, Katy, Tai, Heather, Tollis, Irena, Tsui, Tucker, William R, Catherine, Vignal-Clermont, An-Guor, Wang, Saige, Wilkins, and Patrick, Yu-Wai-Man
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Biomedical and Clinical Sciences ,Ophthalmology and Optometry ,Clinical Research ,Genetics ,Neurosciences ,Clinical Trials and Supportive Activities ,Eye Disease and Disorders of Vision ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Eye ,Humans ,DNA ,Mitochondrial ,Genetic Therapy ,Inflammation ,Mutation ,Optic Atrophy ,Hereditary ,Leber ,LHON REFLECT Study Group ,NADH dehydrogenase 4 ,leber hereditary optic neuropathy ,lenadogene nolparvovec ,mitochondrial DNA ,recombinant adeno-associated virus vector 2 ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Neurology & Neurosurgery ,Biomedical and clinical sciences ,Health sciences ,Psychology - Abstract
Leber hereditary optic neuropathy (LHON) is an important example of mitochondrial blindness with the m.11778G>A mutation in the MT-ND4 gene being the most common disease-causing mtDNA variant worldwide. The REFLECT phase 3 pivotal study is a randomized, double-masked, placebo-controlled trial investigating the efficacy and safety of bilateral intravitreal injection of lenadogene nolparvovec in patients with a confirmed m.11778G>A mutation, using a recombinant adeno-associated virus vector 2, serotype 2 (rAAV2/2-ND4). The first-affected eye received gene therapy; the fellow (affected/not-yet-affected) eye was randomly injected with gene therapy or placebo. The primary end point was the difference in change from baseline of best-corrected visual acuity (BCVA) in second-affected/not-yet-affected eyes treated with lenadogene nolparvovec versus placebo at 1.5 years post-treatment, expressed in logarithm of the minimal angle of resolution (LogMAR). Forty-eight patients were treated bilaterally and 50 unilaterally. At 1.5 years, the change from baseline in BCVA was not statistically different between second-affected/not-yet-affected eyes receiving lenadogene nolparvovec and placebo (primary end point). A statistically significant improvement in BCVA was reported from baseline to 1.5 years in lenadogene nolparvovec-treated eyes: -0.23 LogMAR for the first-affected eyes of bilaterally treated patients (P < 0.01); and -0.15 LogMAR for second-affected/not-yet-affected eyes of bilaterally treated patients and the first-affected eyes of unilaterally treated patients (P < 0.05). The mean improvement in BCVA from nadir to 1.5 years was -0.38 (0.052) LogMAR and -0.33 (0.052) LogMAR in first-affected and second-affected/not-yet-affected eyes treated with lenadogene nolparvovec, respectively (bilateral treatment group). A mean improvement of -0.33 (0.051) LogMAR and -0.26 (0.051) LogMAR was observed in first-affected lenadogene nolparvovec-treated eyes and second-affected/not-yet-affected placebo-treated eyes, respectively (unilateral treatment group). The proportion of patients with one or both eyes on-chart at 1.5 years was 85.4% and 72.0% for bilaterally and unilaterally treated patients, respectively. The gene therapy was well tolerated, with no systemic issues. Intraocular inflammation, which was mostly mild and well controlled with topical corticosteroids, occurred in 70.7% of lenadogene nolparvovec-treated eyes versus 10.2% of placebo-treated eyes. Among eyes treated with lenadogene nolparvovec, there was no difference in the incidence of intraocular inflammation between bilaterally and unilaterally treated patients. Overall, the REFLECT trial demonstrated an improvement of BCVA in LHON eyes carrying the m.11778G>A mtDNA mutation treated with lenadogene nolparvovec or placebo to a degree not reported in natural history studies and supports an improved benefit/risk profile for bilateral injections of lenadogene nolparvovec relative to unilateral injections.
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- 2023
8. Chronic Exposure to Both Electronic and Conventional Cigarettes Alters Ileum and Colon Turnover, Immune Function, and Barrier Integrity in Mice
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Madjid Djouina, Anaïs Ollivier, Christophe Waxin, Gwenola Kervoaze, Muriel Pichavant, Ségolène Caboche, Djamal Achour, Céline Grare, Delphine Beury, David Hot, Sébastien Anthérieu, Jean-Marc Lo-Guidice, Laurent Dubuquoy, David Launay, Cécile Vignal, Philippe Gosset, and Mathilde Body-Malapel
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e-cigarette ,intestinal ,immune response ,proliferation ,permeability ,microbiota ,Therapeutics. Pharmacology ,RM1-950 ,Toxicology. Poisons ,RA1190-1270 - Abstract
Although the effects of cigarette smoke (CS) on the development of several intestinal diseases is well documented, the impact of e-cigarette aerosol (e-cig) on digestive health is largely unknown. To compare the effects of e-cig and CS on mouse ileum and colon, animals were chronically exposed for 6 months by nose-only inhalation to e-cig at 18 or 30 W power, or to 3R4F CS. Results showed that e-cig exposure decreased colon cell proliferation. Several other proliferative defects were observed in response to both e-cig and CS exposure, including up- and down-regulation of cyclin D1 protein levels in the ileum and colon, respectively. E-cig and CS exposure reduced myeloperoxidase activity in the ileum. In the colon, both exposures disrupted gene expression of cytokines and T cell transcription factors. For tight junction genes, ZO-1- and occludin-protein expression levels were reduced in the ileum and colon, respectively, by e-cig and CS exposure. The 16S sequencing of microbiota showed specific mild dysbiosis, according to the type of exposure. Overall, e-cig exposure led to altered proliferation, inflammation, and barrier function in both the ileum and colon, and therefore may be a gut hazard on par with conventional CS.
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- 2024
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9. Anti–IL-4R versus anti–IL-5/5R after anti–IL-5/5R failure in asthma: An emulated target trial
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Devouassoux, G., Taillé, C., Chanez, P., Bonniaud, P., Bourdin, A., Saint Raymond, C., Maurer, C., Beurnier, A., Roux, P., Margelidon, V., Boudjemaa, A., Mangiapan, G., Freymond, N., Didi, T., Russier, M., Garcia, G., Meyer, E. Popin, Dupin, C., Fouquet, F., Jouveshomme, S., Gaspard, W., Dury, S., Maillard, S. Habib, Izadifar, A., Cuvillon, E., Deslée, G., Barnig, C., Perotin, J.M., Gamez, A.S., Oster, J.P., Khayat, N., Chenivesse, C., Li, X., Appere de Vecchi, C., Gicquello, A., Rami, H., Vignal, G., Just, N., Blanc, X., Leroyer, C., Wemeau, L., Achkar, A., Sattler, C., Catherinot, E., Guilleminault, L., Gaillot-Drevon, M., Rochefort-Morel, C., Couturaud, F., Martin, P., Chabrol, A., Pegliasco, H., Sése, L., Romanet, S., Caverstri, B., Tcherakian, C., Magnan, A., Ahmed, E., Allibe, F., Beltramo, G., Michaux, K., Paleiron, N., Martinez, S., Begne, C., Tummino, C., Givel, C., Mourin, G., Salvator, H., Volpato, M., Drucbert, M., Rossignoli, N., Keddache, S., Justet, A., Andrejak, C., Valcke, J., Perrin, J., Mercy, M., Jouvenot, M., Soumagne, T., Elharrar, X., Douvry, B., Godbert, B., Maitre, B., Goyard, C., Didier, A., Cadet, E., Chabot, F., Gonzalez, J., Mattei, L., Gouitaa, M., Chauveau, S., Raymond, S., Dirou, S., Fry, S., Briault, A., Moui, A., Paris, A., NoelSavina, E., Olivier, C., Caradec, E., Roche, N., Picart, G., Belmont, L., Portel, L., Serra, M. Rocca, Guibert, N., Jean, R., Hadjadj, S., Guillo, S., Gauquelin, L., Estellat, C., Prigent, A., Larrousse, M., Jaffuel, D., Bourayou, Karima, Klising, Eve, Yelles, Nessima, Pochon, Sarra, Gouider, Amal, Medina, Hadj Kaci, Yasmine, Sellali, Djouher, Dahmani, Ndao, Diakhou, Vacher, Yannick, Achkar, Antoine, Ahmed, Engi, Alain, Didier, Allibe, Flora, Andrejak, Claire, De Vecchi, Corinne Appere, Barnig, Cindy, Begne, Camille, Belmont, Laure, Beltramo, Guillaume, Blanc, Xavier, Briault, Amandine, Cadet, Emmanuelle, Caradec, Emmanuela, Catherinot, Émilie, Cavestri, Beatrice, Chabrol, Alexandre, Chanez, Pascal, Chauveau, Simon, Couturaud, Francis, Cuvillon, Édouard, Deslee, Gaëtan, Didi, Toufik, Dirou, Stéphanie, Douvry, benoît, Drucbert, Mélanie, Dupin, Clairelyne, Dury, Sandra, Elharrar, Xavier, Fouquet, Helen, Freymond, Nathalie, Fry, Stéphanie, Gaillot-Drevon, Maud, Gamez, Anne Sophie, Garcia, Gilles, Gaspard, Wanda, Gicquello, Alice, Givel, Claire, Godbert, benoit, Gonzalez, Jésus, Gouitaa, Marion, Goupil, François, Goyard, Céline, Guibert, Nicolas, Guilleminault, Laurent, Habib-Maillard, Stéphanie, Hadjadj, Samra, Izadifar, Armine, Jean, Romain, Jouvenot, marie, Jouveshomme, Stéphane, Just, Nicolas, Justet, Aurélien, Keddache, Sophia, Khayath, Naji, Lemaire, Bertrand, Leroyer, Christophe, Li, Xing, Magnan, Antoine, Maitre, Bernard, Mangiapan, Gilles, Margelidon, Victor, Martin, Pascale, Martinez, Stéphanie, Mattei, Laura, Maurer, Cyril, Mercy, Magalie, Michaux, Karine, Moui, Antoine, Mourin, Gisèle, Noel-Savina, Elisa, Olivier, Cécile, Oster, Jean-Philippe, Paleiron, Nicolas, Paris, Audrey, Pegliasco, Hervé, Perotin Collard, Jeanne-Marie, Perrin, Julie, Picart, Gaël, Pison, Christophe, Popin-Meyer, Élisabeth, Portel, Laurent, Rami, Hassina, Raymond, Stéphane, Serra, Mireille Rocca, Rochefort-Morel, Cécile, Romanet, Stéphanie, Rossignoli, Nadine, Roux, Pauline, Russier, Maud, Saint-Raymond, Christel, Salmeron, Sergio, Salvator, Helene, Sattler, Caroline, Sese, Lucile, Soumagne, Thibaud, Tcherakian, Colas, Tiotiu, Angélica, Tummino, Céline, Valcke-Brossollet, Judith, Vignal, Guillaume, Volpato, Mathilde, Wemeau, Lidwine, Valery, Solène, Simon-Tillaux, Noémie, Devouassoux, Gilles, Bonniaud, Philippe, Beurnier, Antoine, Boudjemaa, Amel, Chenivesse, Cécile, Bourdin, Arnaud, Gauquelin, Lisa, Guillo, Sylvie, Taillé, Camille, and Estellat, Candice
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- 2024
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10. Heritability and correlations for honey yield, handling ease, brood quantity, and traits related to resilience in a French honeybee population
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Kistler, Tristan, Kouchner, Coline, Brascamp, Evert W., Dumas, Charlène, Mondet, Fanny, Vignal, Alain, Basso, Benjamin, Bijma, Piter, and Phocas, Florence
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- 2024
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11. Visual Outcomes Following Plasma Exchange for Optic Neuritis: An International Multicenter Retrospective Analysis of 395 Optic Neuritis Attacks.
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Chen, John, Flanagan, Eoin, Pittock, Sean, Stern, Nicole, Tisavipat, Nanthaya, Bhatti, M, Chodnicki, Kevin, Tajfirouz, Deena, Jamali, Sepideh, Kunchok, Amy, Eggenberger, Eric, Nome, Marie, Sotirchos, Elias, Vasileiou, Eleni, Henderson, Amanda, Arnold, Anthony, Bonelli, Laura, Moss, Heather, Navarro, Sylvia, Padungkiatsagul, Tanyatuth, Stiebel-Kalish, Hadas, Lotan, Itay, Wilf-Yarkoni, Adi, Danesh-Meyer, Helen, Ivanov, Stefan, Huda, Saif, Forcadela, Mirasol, Hodge, David, Poullin, Pascale, Rode, Julie, Papeix, Caroline, Saheb, Samir, Boudot de la Motte, Marine, Vignal, Catherine, Hacohen, Yael, Pique, Julie, Maillart, Elisabeth, Deschamps, Romain, Audoin, Bertrand, and Marignier, Romain
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Humans ,Female ,Male ,Plasma Exchange ,Retrospective Studies ,Myelin-Oligodendrocyte Glycoprotein ,Optic Neuritis ,Neuromyelitis Optica ,Vision Disorders ,Autoantibodies - Abstract
PURPOSE: To evaluate the effectiveness of plasma exchange (PLEX) for optic neuritis (ON). METHODS: We conducted an international multicenter retrospective study evaluating the outcomes of ON following PLEX. Outcomes were compared to raw data from the Optic Neuritis Treatment Trial (ONTT) using a matched subset. RESULTS: A total of 395 ON attack treated with PLEX from 317 patients were evaluated. The median age was 37 years (range 9-75), and 71% were female. Causes of ON included multiple sclerosis (108), myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) (92), aquaporin-4-IgG-positive neuromyelitis optica spectrum disorder (AQP4+NMOSD) (75), seronegative-NMOSD (34), idiopathic (83), and other (3). Median time from onset of vision loss to PLEX was 2.6 weeks (interquartile range [IQR], 1.4-4.0). Median visual acuity (VA) at the time of PLEX was count fingers (IQR, 20/200-hand motion), and median final VA was 20/25 (IQR, 20/20-20/60) with no differences among etiologies except MOGAD-ON, which had better outcomes. In 81 (20.5%) ON attacks, the final VA was 20/200 or worse. Patients with poor outcomes were older (P = .002), had worse VA at the time of PLEX (P < .001), and longer delay to PLEX (P < .001). In comparison with the ONTT subset with severe corticosteroid-unresponsive ON, a final VA of worse than 20/40 occurred in 6 of 50 (12%) PLEX-treated ON vs 7 of 19 (37%) from the ONTT treated with intravenous methylprednisolone without PLEX (P = .04). CONCLUSION: Most ON attacks improved with PLEX, and outcomes were better than attacks with similar severity in the ONTT. The presence of severe vision loss at nadir, older age, and longer delay to PLEX predicted a worse outcome whereas MOGAD-ON had a more favorable prognosis. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.
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- 2023
12. Survey of physics reasoning on uncertainty concepts in experiments: an assessment of measurement uncertainty for introductory physics labs
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Vignal, Michael, Geschwind, Gayle, Pollard, Benjamin, Henderson, Rachel, Caballero, Marcos D., and Lewandowski, H. J.
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Physics - Physics Education - Abstract
Measurement uncertainty is a critical feature of experimental research in the physical sciences, and the concepts and practices surrounding measurement uncertainty are important components of physics lab courses. However, there has not been a broadly applicable, research-based assessment tool that allows physics instructors to easily measure students' knowledge of measurement uncertainty concepts and practices. To address this need, we employed Evidence-Centered Design to create the Survey of Physics Reasoning on Uncertainty Concepts in Experiments (SPRUCE). SPRUCE is a pre-post assessment instrument intended for use in introductory (first- and second-year) physics lab courses to help instructors and researchers identify student strengths and challenges with measurement uncertainty. In this paper, we discuss the development of SPRUCE's assessment items guided by Evidence-Centered Design, focusing on how instructors' and researchers' assessment priorities were incorporated into the assessment items and how students' reasoning from pilot testing informed decisions around item answer options. We also present an example of some of the feedback an instructor would receive after implementing SPRUCE in a pre-post fashion, along with a brief discussion of how that feedback could be interpreted and acted upon., Comment: 19 pages, 5 figures, submitted as part of the Physical Review Physics Education Research Focused Collection on Instructional Labs: Improving Traditions and New Directions
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- 2023
13. Diffuse laser illumination for Maxwellian view Doppler holography of the retina
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Bratasz, Zofia, Martinache, Olivier, Blazy, Yohan, Denis, Angèle, Auffret, Coline, Huignard, Jean-Pierre, Rossi, Ethan, Chhablani, Jay, Sahel, José-Alain, Bonnin, Sophie, Hage, Rabih, Koskas, Patricia, Gatinel, Damien, Vignal, Catherine, Yavchitz, Amelie, Vasseur, Vivien, Tadayoni, Ramin, Ducloux, Claire, Ortoli, Manon, Tordjman, Marvin, Tick, Sarah, Mrejen, Sarah, Paques, Michel, and Atlan, Michael
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Physics - Optics ,Physics - Applied Physics ,Physics - Medical Physics - Abstract
We present the benefits of using diffuse illumination in laser holography for ophthalmic applications. Integrating a diffusing element introduces angular diversity in the optical radiation and reduces spatial coherence, effectively distributing the illumination beam's energy across the focal plane of the eyepiece. This configuration allows for an expanded field of view in digitally computed retinal images, as the eyepiece can be positioned closer to the cornea to achieve a Maxwellian view of the retina without compromising ocular safety. By avoiding the formation of a laser hot spot near the cornea, diffuse illumination facilitates easier compliance with American and European safety standards for ophthalmic devices. Importantly, this approach does not introduce any adverse effects on digitally computed Doppler images., Comment: 10 pages
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- 2022
14. High diagnostic accuracy of T2FLAIR at 3 T in the detection of optic nerve head edema in acute optic neuritis
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Shor, Natalia, Lamirel, Cedric, Rebbah, Sana, Vignal, Catherine, Vasseur, Vivien, Savatovsky, Julien, de la Motte, Marine Boudot, Gout, Olivier, Lecler, Augustin, Hage, Rabih, and Deschamps, Romain
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- 2024
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15. Subthalamic high-frequency deep brain stimulation reduces addiction-like alcohol use and the possible negative influence of a peer presence
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Vignal, Lucie, Vielle, Cassandre, Williams, Maya, Maurice, Nicolas, Degoulet, Mickael, and Baunez, Christelle
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- 2024
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16. The black honey bee genome: insights on specific structural elements and a first step towards pangenomes
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Sonia E. Eynard, Christophe Klopp, Kamila Canale-Tabet, William Marande, Céline Vandecasteele, Céline Roques, Cécile Donnadieu, Quentin Boone, Bertrand Servin, and Alain Vignal
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Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Background The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses. Results Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants. Conclusions Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes.
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- 2024
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17. Fatness QTL on chicken chromosome 5 and interaction with sex
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Vignal Alain, Aggrey Sammy, Cogburn Larry, Simon Jean, Vignoles Florence, Demeure Olivier, Le Roy Pascale, Le Bihan-Duval Elisabeth, Lagarrigue Sandrine, Pitel Frédérique, Abasht Behnam, and Douaire Madeleine
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meat-type chickens ,quantitative trait loci ,fatness QTL ,QTL × sex interaction ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Quantitative trait loci (QTL) affecting fatness in male chickens were previously identified on chromosome 5 (GGA5) in a three-generation design derived from two experimental chicken lines divergently selected for abdominal fat weight. A new design, established from the same pure lines, produced 407 F2 progenies (males and females) from 4 F1-sire families. Body weight and abdominal fat were measured on the F2 at 9 wk of age. In each sire family, selective genotyping was carried out for 48 extreme individuals for abdominal fat using seven microsatellite markers from GGA5. QTL analyses confirmed the presence of QTL for fatness on GGA5 and identified a QTL by sex interaction. By crossing one F1 sire heterozygous at the QTL with lean line dams, three recombinant backcross 1 (BC1) males were produced and their QTL genotypes were assessed in backcross 2 (BC2) progenies. These results confirmed the QTL by sex interaction identified in the F2 generation and they allow mapping of the female QTL to less than 8 Mb at the distal part of the GGA5. They also indicate that fat QTL alleles were segregating in both fat and lean lines.
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- 2006
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18. Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness
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Neau André, Pitel Frédérique, Vignal Alain, Simon Jean, Leclercq Bernard, Carré Wilfrid, Cogburn Larry, Aggrey Sammy, Amigues Yves, Lagarrigue Sandrine, Abasht Behnam, Le Roy Pascale, Sourdioux Michel, and Douaire Madeleine
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quantitative trait locus ,abdominal fat ,breast muscle ,chicken ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Quantitative trait loci (QTL) for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meat-type chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation.
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- 2006
19. A genome scan for quantitative trait loci affecting the Salmonella carrier-state in the chicken
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Bumstead Nat, Baret Philippe V, Velge Philippe, Vignal Alain, Plisson-Petit Florence, Pitel Frédérique, Barrow Paul A, Marly José, Tilquin Pierre, and Beaumont Catherine
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fowl ,genetic resistance ,Salmonella ,carrier-state ,SLC11A1 ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Selection for increased resistance to Salmonella colonisation and excretion could reduce the risk of foodborne Salmonella infection. In order to identify potential loci affecting resistance, differences in resistance were identified between the N and 61 inbred lines and two QTL research performed. In an F2 cross, the animals were inoculated at one week of age with Salmonella enteritidis and cloacal swabs were carried out 4 and 5 wk post inoculation (thereafter called CSW4F2 and CSW4F2) and caecal contamination (CAECF2) was assessed 1 week later. The animals from the (N × 61) × N backcross were inoculated at six weeks of age with Salmonella typhimurium and cloacal swabs were studied from wk 1 to 4 (thereafter called CSW1BC to CSW4BC). A total of 33 F2 and 46 backcross progeny were selectively genotyped for 103 and 135 microsatellite markers respectively. The analysis used least-squares-based and non-parametric interval mapping. Two genome-wise significant QTL were observed on Chromosome 1 for CSW2BC and on Chromosome 2 for CSW4F2, and four suggestive QTL for CSW5F2 on Chromosome 2, for CSW5F2 and CSW2BC on chromosome 5 and for CAECF2 on chromosome 16. These results suggest new regions of interest and the putative role of SAL1.
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- 2005
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20. A gene-based radiation hybrid map of chicken microchromosome 14: Comparison to human and alignment to the assembled chicken sequence
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Milan Denis, Faraut Thomas, Feve Katia, Bardes Suzanne, Lagarrigue Sandrine, Pitel Frédérique, Assaf Sirine, Jiguet-Jiglaire Carine, Leroux Sophie, Morisson Mireille, and Vignal Alain
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chicken ,comparative mapping ,radiation hybrids ,microchromosome 14 ,intrachromosomal rearrangement ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract We present a gene-based RH map of the chicken microchromosome GGA14, known to have synteny conservations with human chromosomal regions HSA16p13.3 and HSA17p11.2. Microsatellite markers from the genetic map were used to check the validity of the RH map and additional markers were developed from chicken EST data to yield comparative mapping data. A high rate of intra-chromosomal rearrangements was detected by comparison to the assembled human sequence. Finally, the alignment of the RH map to the assembled chicken sequence showed a small number of discordances, most of which involved the same region of the chromosome spanning between 40.5 and 75.9 cR6000 on the RH map.
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- 2005
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21. Assignment of CPS1, OTC, CRYD2, ARG2 and ASS genes to the chicken RH map
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Vignal Alain, Maeda Yoshizane, Okamoto Shin, Kawabe Kotaro, Morisson Mireille, Bosak Natalia, Shimogiri Takeshi, and Yasue Hiroshi
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ornithine-urea cycle ,chicken ,radiation hybrid mapping ,chromosomal assignment ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract An attempt was made to assign five genes, CPS1, OTC, ASS, CRYD2, and ARG2, to chicken chromosomes (GGA) by radiation-hybrid mapping. OTC was assigned to GGA1; ARG2 to GGA5; CPS1 to GGA7; and CRYD2 to GGA19. ASS was not, however, assigned to a specific chromosomal position.
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- 2004
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22. Indirect Comparison of Lenadogene Nolparvovec Gene Therapy Versus Natural History in Patients with Leber Hereditary Optic Neuropathy Carrying the m.11778G>A MT-ND4 Mutation.
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Carelli, Valerio, Newman, Nancy, Yu-Wai-Man, Patrick, Biousse, Valerie, Moster, Mark, Subramanian, Prem, Vignal-Clermont, Catherine, Wang, An-Guor, Donahue, Sean, Leroy, Bart, Sergott, Robert, Klopstock, Thomas, Sadun, Alfredo, Rebolleda Fernández, Gema, Chwalisz, Bart, Banik, Rudrani, Girmens, Jean, La Morgia, Chiara, DeBusk, Adam, Jurkute, Neringa, Priglinger, Claudia, Karanjia, Rustum, Josse, Constant, Salzmann, Julie, Montestruc, François, Roux, Michel, Taiel, Magali, and Sahel, José-Alain
- Subjects
Gene therapy ,LHON ,Leber hereditary optic neuropathy ,MT-ND4 ,Natural history ,Visual acuity - Abstract
INTRODUCTION: Lenadogene nolparvovec is a promising novel gene therapy for patients with Leber hereditary optic neuropathy (LHON) carrying the m.11778G>A ND4 mutation (MT-ND4). A previous pooled analysis of phase 3 studies showed an improvement in visual acuity of patients injected with lenadogene nolparvovec compared to natural history. Here, we report updated results by incorporating data from the latest phase 3 trial REFLECT in the pool, increasing the number of treated patients from 76 to 174. METHODS: The visual acuity of 174 MT-ND4-carrying patients with LHON injected in one or both eyes with lenadogene nolparvovec from four pooled phase 3 studies (REVERSE, RESCUE and their long-term extension trial RESTORE; and REFLECT trial) was compared to the spontaneous evolution of an external control group of 208 matched patients from 11 natural history studies. RESULTS: Treated patients showed a clinically relevant and sustained improvement in their visual acuity when compared to natural history. Mean improvement versus natural history was - 0.30 logMAR (+ 15 ETDRS letters equivalent) at last observation (P
- Published
- 2023
23. AFLP linkage map of the Japanese quail Coturnix japonica
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Beaumont Catherine, Faure Jean-Michel, Pitel Frédérique, Plisson-Petit Florence, Feve Katia, Roussot Odile, and Vignal Alain
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Japanese quail ,AFLP ,genetic map ,linkage groups ,chromosomes ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract The quail is a valuable farm and laboratory animal. Yet molecular information about this species remains scarce. We present here the first genetic linkage map of the Japanese quail. This comprehensive map is based solely on amplified fragment length polymorphism (AFLP) markers. These markers were developed and genotyped in an F2 progeny from a cross between two lines of quail differing in stress reactivity. A total of 432 polymorphic AFLP markers were detected with 24 TaqI/EcoRI primer combinations. On average, 18 markers were produced per primer combination. Two hundred and fifty eight of the polymorphic markers were assigned to 39 autosomal linkage groups plus the ZW sex chromosome linkage groups. The linkage groups range from 2 to 28 markers and from 0.0 to 195.5 cM. The AFLP map covers a total length of 1516 cM, with an average genetic distance between two consecutive markers of 7.6 cM. This AFLP map can be enriched with other marker types, especially mapped chicken genes that will enable to link the maps of both species and make use of the powerful comparative mapping approach. This AFLP map of the Japanese quail already provides an efficient tool for quantitative trait loci (QTL) mapping.
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- 2003
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24. Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools
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Thomson Pippa, Oortwijn Marian, Mäki-Tanila Asko, Freidlin Paul J, Feldman Marcus W, Elo Kari, Crooijmans Richard PMA, Barre-Dirie Asili, Burke Terry, Kirzhner Valery M, David Lior, Korol Abraham B, Tixier-Boichard Michèle, Groenen Martien AM, Hillel Jossi, Vignal Alain, Wimmers Klaus, and Weigend Steffen
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genetic distance ,polymorphism ,red jungle fowl ,DNA markers ,domesticated chicken ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.
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- 2003
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25. ChickRH6: a chicken whole-genome radiation hybrid panel
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Yerle Martine, Fillon Valérie, Pitel Frédérique, Fève Katia, Delcros Chantal, Pinton Philippe, Plisson-Petit Florence, Galan Maxime, Bosc Sarah, Lemière Alexandre, Morisson Mireille, and Vignal Alain
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chicken ,radiation hybrid ,mapping ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract As a first step towards the development of radiation hybrid maps, we have produced a radiation hybrid panel in the chicken by fusing female embryonic diploid fibroblasts irradiated at 6 000 rads with HPRT-deficient hamster Wg3hCl2 cells. Due to the low retention frequency of the chicken fragments, a high number of clones was produced from which the best ones were selected. Thus, 452 fusion clones were tested for retention frequencies with a panel of 46 markers. Based on these results, 103 clones with a mean marker retention of 23.8% were selected for large scale culture to produce DNA in sufficient quantities for the genotyping of numerous markers. Retention frequency was tested again with the same 46 markers and the 90 best clones, with a final mean retention frequency of 21.9%, were selected for the final panel. This panel will be a valuable resource for fine mapping of markers and genes in the chicken, and will also help in building BAC contigs.
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- 2002
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26. A review on SNP and other types of molecular markers and their use in animal genetics
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Eggen André, SanCristobal Magali, Milan Denis, and Vignal Alain
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SNP ,microsatellite ,molecular marker ,genome ,polymorphism ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. In this review, we will discuss the reasons for this apparent step backwards, and the pertinence of the use of SNPs in animal genetics, in comparison with other marker types.
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- 2002
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27. Mapping the Naked Neck (NA) and Polydactyly (PO) mutants of the chicken with microsatellite molecular markers
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Vignal Alain, Groenen Martien AM, Crooijmans Richard PMA, Coquerelle Gérard, Bergé Régis, Pitel Frédérique, and Tixier-Boichard Michèle
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chicken ,gene mapping ,naked neck gene ,polydactyly ,molecular marker ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract The bulked segregant analysis methodology has been used to map, with microsatellite markers, two morphological mutations in the chicken: polydactyly (PO) and naked neck (NA). These autosomal mutations show partial dominance for NA, and dominance with incomplete penetrance for PO. They were mapped previously to different linkage groups of the classical map, PO to the linkage group IV and NA being linked to the erythrocyte antigen CPPP. An informative family of 70 offspring was produced by mating a sire, heterozygous for each of the mutations, to 7 dams homozygous recessive for each locus. Three DNA pools were prepared, pool PO included 20 chicks exhibiting at least one extra-toe, pool NA included 20 non-polydactyly chicks showing the typical phenotype associated with heterozygosity for the naked neck mutation, and pool NP included 20 chicks exhibiting neither of the mutant phenotypes. Typings were done on an ABI-373 automatic sequencer with 147 microsatellite markers covering most of the genome. An unbalanced distribution of sire marker alleles were detected between pool PO, and pools NA and NP, for two markers of chromosome 2p, MCW0082 and MCW0247. A linkage analysis taking into account the incomplete penetrance of polydactyly (80%) was performed with additional markers of this region and showed that the closest marker to the PO locus was MCW0071 (5 cM, lod score = 9). MCW0071 lies within the engrailed gene EN2 in the chicken. In the mouse, the homologous gene maps on chromosome 5, close to the hemimelic extra-toes mutation Hx. In the case of the NA locus, markers of chromosome 3 were selected because CPPP was mapped on this chromosome. Analysis of individual typings showed a linkage of 5.7 cM (lod score = 13) between the NA locus and ADL0237 in the distal region of chromosome 3q. These results contribute to connecting the former classical map to the molecular genetic map of the chicken, and open the way to the identification of the molecular nature of two developmental mutations of the chicken that are known to occur in many breeds of chickens.
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- 2000
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28. Comparison between contrast-enhanced fat-suppressed 3D FLAIR brain MR images and T2-weighted orbital MR images at 3 Tesla for the diagnosis of acute optic neuritis
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Manasse, Sharmiladevi, Koskas, Patricia, Savatovsky, Julien, Deschamps, Romain, Vignal-Clermont, Catherine, Boudot de la Motte, Marine, Papeix, Caroline, Trunet, Stéphanie, and Lecler, Augustin
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- 2024
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29. Problèmes ophtalmologiques de l’artérite à cellules géantes
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Clavel, Gaëlle and Vignal, Catherine
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- 2024
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30. Periodic membrane fractionation of freshwater organic matter reveals various reactivity patterns during chlorine/chloramine disinfection
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Dejaeger, Karlien, Vanoppen, Marjolein, Criquet, Justine, Billon, Gabriel, Vignal, Cécile, and Cornelissen, Emile R.
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- 2025
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31. Evidence for validity and reliability of a research-based assessment instrument on measurement uncertainty
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Gayle Geschwind, Michael Vignal, Marcos D. Caballero, and H. J. Lewandowski
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Special aspects of education ,LC8-6691 ,Physics ,QC1-999 - Abstract
The Survey of Physics Reasoning on Uncertainty Concepts in Experiments (SPRUCE) was designed to measure students’ proficiency with measurement uncertainty concepts and practices across ten different assessment objectives to help facilitate the improvement of laboratory instruction focused on this important topic. To ensure the reliability and validity of this assessment, we conducted a comprehensive statistical analysis using classical test theory. This analysis includes an evaluation of the test as a whole, as well as an in-depth examination of individual items and assessment objectives. We make use of a previously reported on scoring scheme involving pairing items with assessment objectives, creating a new unit for statistical analysis referred to as a “couplet.” The findings from our analysis provide evidence for the reliability and validity of SPRUCE as an assessment tool for undergraduate physics labs. This increases both instructors’ and researchers’ confidence in using SPRUCE for measuring students’ proficiency with measurement uncertainty concepts and practices to ultimately improve laboratory instruction. Additionally, our results using couplets and assessment objectives demonstrate how these can be used with traditional classic test theory analysis.
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- 2024
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32. Survey of Physics Reasoning on Uncertainty Concepts in Experiments: An Assessment of Measurement Uncertainty for Introductory Physics Labs
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Michael Vignal, Gayle Geschwind, Benjamin Pollard, Rachel Henderson, Marcos D. Caballero, and H. J. Lewandowski
- Abstract
[This paper is part of the Focused Collection on Instructional labs: Improving traditions and new directions.] Measurement uncertainty is a critical feature of experimental research in the physical sciences, and the concepts and practices surrounding measurement uncertainty are important components of physics lab courses. However, there has not been a broadly applicable, research-based assessment tool that allows physics instructors to easily measure students' knowledge of measurement uncertainty concepts and practices. To address this need, we employed evidence-centered design to create the Survey of Physics Reasoning on Uncertainty Concepts in Experiments (SPRUCE). SPRUCE is a pre-post assessment instrument intended for use in introductory (first and second year) physics lab courses to help instructors and researchers identify student strengths and challenges with measurement uncertainty. In this paper, we discuss the development of SPRUCE's assessment items guided by evidence-centered design, focusing on how instructors' and researchers' assessment priorities were incorporated into the assessment items and how students' reasoning from pilot testing informed decisions around item answer options. We also present an example of some of the feedback an instructor would receive after implementing SPRUCE in a pre-post fashion, along with a brief discussion of how that feedback could be interpreted and acted upon.
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- 2023
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33. Pitting corrosion behaviour in sodium chloride solution of intermetallic centreline stringers in super duplex stainless steels
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Erazmus-Vignal, P., Vignal, V., Huguenin, P., and Krajcarz, F.
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- 2023
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34. Incidence and Outcomes of Eye Trauma Associated With Recreative Use of Nonpowder Toy Guns: A 12-Year Retrospective Study
- Author
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Dentel, Alexandre, Boulanger, Etienne, Chapron, Thibaut, Senicourt, Lucile, Metge, Florence, Dureau, Pascal, Vignal-Clermont, Catherine, Caputo, Georges, and Martin, Gilles C.
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- 2024
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35. Combining a transcriptomic approach and a targeted metabolomics approach for deciphering the molecular bases of compatibility phenotype in the snail Biomphalaria glabrata toward Schistosoma mansoni
- Author
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Simphor, Elodie, Rognon, Anne, Vignal, Emmanuel, Henry, Sylvain, Allienne, Jean-François, Turtoi, Andrei, Chaparro, Cristian, Galinier, Richard, Duval, David, and Gourbal, Benjamin
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- 2024
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36. A produção de design nas indústrias criativas: crítica à lógica capitalista neoliberal
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Camille Vignal Frota and Fabiana Oliveira Heinrich
- Subjects
Campo do design ,Capitalismo ,Criatividade ,Crítica ,Indústria criativa ,Communication. Mass media ,P87-96 ,Social sciences (General) ,H1-99 - Abstract
Neste estudo, o trabalho do designer é considerado uma práxis projetual orientada pela lógicadialética, ou seja, é moldada e, ao mesmo tempo, molda o trabalho criativo capitalista. Por meiode uma análise social crítica, é evidenciada a dimensão mercadológica de noções socioeconômicasimperativas no Campo do Design e como estas o impactam, uma vez que o entendimento do atode criar vigente é tecnocrático. Para desenvolver esta investigação, inicia-se com uma apresen-tação do pensamento econômico-político do modo de produção capitalista e sua determinaçãona instância de produção, além do viés crítico que surge como contestação a essa configuração.Em seguida, traça-se o processo histórico do entendimento de “criatividade” e sua influência noCampo do Design. Por último, contextualiza-se a atualidade hegemônica do capitalismo tardio,as Indústrias Criativas, com uma breve análise da Adobe Inc. e sua influência na digitalização dotrabalho no Campo do Design. Com os resultados obtidos nessa análise crítica, evidencia-se a im-portância de observar implicações de fenômenos sociais na práxis do projetar e como o processocriativo é impactado pela materialidade e historicidade das circunstâncias nas quais está inserido.
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- 2024
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37. Natural clines and human management impact the genetic structure of Algerian honey bee populations
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Giovanna Salvatore, Amira Chibani Bahi Amar, Kamila Canale-Tabet, Riad Fridi, Nacera Tabet Aoul, Soumia Saci, Emmanuelle Labarthe, Valentino Palombo, Mariasilvia D’Andrea, Alain Vignal, and Pierre Faux
- Subjects
Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Background The Algerian honey bee population is composed of two described subspecies A. m. intermissa and A. m. sahariensis, of which little is known regarding population genomics, both in terms of genetic differentiation and of possible contamination by exogenous stock. Moreover, the phenotypic differences between the two subspecies are expected to translate into genetic differences and possible adaptation to heat and drought in A. m. sahariensis. To shed light on the structure of this population and to integrate these two subspecies in the growing dataset of available haploid drone sequences, we performed whole-genome sequencing of 151 haploid drones. Results Integrated analysis of our drone sequences with a similar dataset of European reference populations did not detect any significant admixture in the Algerian honey bees. Interestingly, most of the genetic variation was not found between the A. m. intermissa and A. m. sahariensis subspecies; instead, two main genetic clusters were found along an East–West axis. We found that the correlation between genetic and geographic distances was higher in the Western cluster and that close-family relationships were mostly detected in the Eastern cluster, sometimes at long distances. In addition, we selected a panel of 96 ancestry-informative markers to decide whether a sampled bee is Algerian or not, and tested this panel in simulated cases of admixture. Conclusions The differences between the two main genetic clusters suggest differential breeding management between eastern and western Algeria, with greater exchange of genetic material over long distances in the east. The lack of detected admixture events suggests that, unlike what is seen in many places worldwide, imports of queens from foreign countries do not seem to have occurred on a large scale in Algeria, a finding that is relevant for conservation purposes. In addition, the proposed panel of 96 markers was found effective to distinguish Algerian from European honey bees. Therefore, we conclude that applying this approach to other taxa is promising, in particular when genetic differentiation is difficult to capture.
- Published
- 2023
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38. Are PHOMS a clinical sign of optic neuritis?
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Aziria, Ahmed, Philibert, Manon, Deschamps, Romain, Vignal, Catherine, and Hage, Rabih
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- 2023
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39. Application of a Deep Learning System to Detect Papilledema on Nonmydriatic Ocular Fundus Photographs in an Emergency Department
- Author
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Fraser, Clare L., Micieli, Jonathan A., Costello, Fiona, Bénard-Séguin, Étienne, Yang, Hui, Chan, Carmen Kar Mun, Cheung, Carol Y, Chan, Noel CY, Hamann, Steffen, Gohier, Philippe, Vautier, Anaïs, Rougier, Marie-Bénédicte, Chiquet, Christophe, Vignal-Clermont, Catherine, Hage, Rabih, Khanna, Raoul Kanav, Tran, Thi Ha Chau, Lagrèze, Wolf Alexander, Jonas, Jost B, Ambika, Selvakumar, Fard, Masoud Aghsaei, La Morgia, Chiara, Carbonelli, Michele, Barboni, Piero, Carelli, Valerio, Romagnoli, Martina, Amore, Giulia, Nakamura, Makoto, Fumio, Takano, Petzold, Axel, Wenniger lj, Maillette de Buy, Kho, Richard, Fonseca, Pedro L., Bikbov, Mukharram M., Milea, Dan, Najjar, Raymond P, Ting, Daniel, Tang, Zhiqun, Loo, Jing Liang, Tow, Sharon, Singhal, Shweta, Vasseneix, Caroline, Wong, Tien Yin, Lamoureux, Ecosse, Yu Chen, Ching, Aung, Tin, Schmetterer, Leopold, Sanda, Nicolae, Thuman, Gabriele, Hwang, Jeong-Min, Vanikieti, Kavin, Suwan, Yanin, Padungkiatsagul, Tanyatuth, Yu-Wai-Man, Patrick, Jurkute, Neringa, Hong, Eun Hee, Biousse, Valerie, Newman, Nancy J., Peragallo, Jason H., Datillo, Michael, Kedar, Sachin, Lin, Mung Yan, Patil, Ajay, Aung, Andre, Boyko, Matthew, Alsakran, Wael Abdulraman, Zayani, Amani, Bouthour, Walid, Banc, Ana, Mosley, Rasha, Labella, Fernando, Miller, Neil R., Chen, John J., Mejico, Luis J., Kilangalanga, Janvier Ngoy, Biousse, Valérie, Najjar, Raymond P., Wright, David W., Keadey, Matthew T., Wong, Tien Y., and Bruce, Beau B.
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- 2024
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40. Investigating Unprompted and Prompted Diagrams Generated by Physics MajorsDuring Problem Solving
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Vignal, Michael and Wilcox, Bethany R.
- Subjects
Physics - Physics Education - Abstract
Diagrams are ubiquitous in physics, especially in physics education and physics problem solving. Problem solvers may generate diagrams to orient to a scenario, to organize information, to directly extract an answer, or as a tool of communication. In this study, we interviewed 19 undergraduate and graduate physics majors, asking them to solve 18 multiple-choice physics problems -- with no prompting regarding diagrams -- and then six diagramming tasks of situations similar to six of the multiple-choice problems. By comparing spontaneously generated and prompted diagrams, we identify different diagramming elements and features used by physics majors acting towards different ends (\textit{i.e.,} in different epistemic frames). We found that different physical contexts impact how critical it is to draw an accurate diagram, and that the differences in diagramming between cohorts (\textit{e.g.}, between lower-division undergraduate and graduate students) seem to be smaller than the differences within a cohort. We also explore implications for teaching and research., Comment: 16 pages, 11 figures
- Published
- 2021
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41. Investigating graduate student reasoning on a conceptual entropy questionnaire
- Author
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Crossette, Nathan, Vignal, Michael, and Wilcox, Bethany R.
- Subjects
Physics - Physics Education - Abstract
Student learning in upper division thermal physics has not been studied to the same extent as in other courses like electromagnetism and quantum mechanics. Studies addressing reasoning and learning at the graduate level are even more limited. In this study, we conducted think-aloud interviews with eight graduate students involving questions centered around a set of entropy related conceptual tasks, two of which are similar to tasks presented to undergraduates in other studies. We discuss patterns in student reasoning on each question then discuss themes that appeared across questions. We identify conceptual resources that students frequently used to reason about the interview tasks and compare them to prior work. We observed graduate students commonly thinking about entropy in relationship to a number of states, even in situations where such a connection was not directly relevant. Graduate students also frequently made direct associations between entropy and temperature, despite there being no general, explicit relationship between the two quantities. On the whole, graduate students demonstrated adaptability and metacognitive awareness in their approach to reasoning about entropy., Comment: 17 pages, 6 figures, 6 tables, 1 appendix
- Published
- 2021
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42. New COI-COII mtDNA Region Haplotypes in the Endemic Honey Bees Apis mellifera intermissa and Apis mellifera sahariensis (Hymenoptera: Apidae) in Algeria
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Amira Chibani Bahi Amar, Nacera Tabet Aoul, Riad Fridi, Alain Vignal, and Kamila Canale-Tabet
- Subjects
mitochondrial DNA ,COI-COII intergenic region ,Apis mellifera intermissa ,Apis mellifera sahariensis ,A lineage haplotypes ,sequencing ,Science - Abstract
The practice of beekeeping in Algeria is of great cultural, social, and economic importance. However, the importation of non-local subspecies reported by beekeepers has disrupted the natural geographical distribution area and the genetic diversity of the native honey bees. To assess the genetic diversity of A. m. intermissa and A. m. sahariensis, and their relationships with African and European subspecies, the COI-COII intergenic region was analyzed in 335 individuals, 68 sampled in Algeria, 71 in Europe, Madagascar, and the South West Indian Ocean archipelagos, and 196 sequences recovered from GenBank. The results show the presence of the A lineage exclusively in Algerian samples with the identification of 24 haplotypes of which 16 are described for the first time. These haplotypes were found to be shared by both subspecies, with A74 being the most common haplotype in the population studied. The sequence comparison indicates the existence of three polymorphisms of the COI-COII marker: P0Q, P0QQ, and P0QQQ. One new haplotype was identified in the M lineage in samples from France. No evidence of genetic introgression within the Algerian honey bee population was detected. These data enhance our knowledge of the genetic diversity and emphasize the importance of protecting these local subspecies.
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- 2024
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43. The BONSAI (Brain and Optic Nerve Study with Artificial Intelligence) deep learning system can accurately identify pediatric papilledema on standard ocular fundus photographs
- Author
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Fraser, Clare L., Micieli, Jonathan A., Costello, Fiona, Étienne Bénard-Séguin, Yang, Hui, Mun Chan, Carmen Kar, Cheung, Carol Y., Chan, Noel CY., Hamann, Steffen, Gohier, Philippe, Vautier, Anaïs, Rougier, Marie-Bénédicte, Chiquet, Christophe, Vignal-Clermont, Catherine, Hage, Rabih, Khanna, Raoul Kanav, Chau Tran, Thi Ha, Lagrèze, Wolf Alexander, Jonas, Jost B., Ambika, Selvakumar, Fard, Masoud Aghsaei, La Morgia, Chiara, Carbonelli, Michele, Barboni, Piero, Carelli, Valerio, Romagnoli, Martina, Amore, Giulia, Nakamura, Makoto, Fumio, Takano, Petzold, Axel, de Buy Wenniger L.J., Maillette, Kho, Richard, Fonseca, Pedro L., Bikbov, Mukharram M., Milea, Dan, Najjar, Raymond P., Ting, Daniel, Tang, Zhiqun, Loo, Jing Liang, Tow, Sharon, Singhal, Shweta, Vasseneix, Caroline, Wong, Tien Yin, Lamoureux, Ecosse, Chen, Ching Yu, Aung, Tin, Schmetterer, Leopold, Sanda, Nicolae, Thuman, Gabriele, Hwang, Jeong-Min, Vanikieti, Kavin, Suwan, Yanin, Padungkiatsagul, Tanyatuth, Yu-Wai-Man, Patrick, Jurkute, Neringa, Hong, Eun Hee, Biousse, Valerie, Newman, Nancy J., Peragallo, Jason H., Datillo, Michael, Kedar, Sachin, Lin, Mung Yan, Patil, Ajay, Aung, Andre, Boyko, Matthew, Alsakran, Wael Abdulraman, Zayani, Amani, Bouthour, Walid, Banc, Ana, Mosley, Rasha, Labella, Fernando, Miller, Neil R., Chen, John J., Mejico, Luis J., Kilangalanga, Janvier Ngoy, Cioplean, Daniela, Dragomir, Mihaela, Chia, Audrey, and Biousse, Valérie
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- 2024
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44. Are Peripapillary Hyperreflective Ovoid Mass-like Structures with an Elevated Optic Disc Still a Diagnosis Dilemma?
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Maalej, Rim, Bouassida, Mohamed, Picard, Hervé, Clermont, Catherine Vignal, and Hage, Rabih
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- 2024
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45. Meta-analysis of treatment outcomes for patients with m.11778G>A MT-ND4 Leber hereditary optic neuropathy
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Newman, Nancy J., Biousse, Valérie, Yu-Wai-Man, Patrick, Carelli, Valerio, Vignal-Clermont, Catherine, Montestruc, François, Taiel, Magali, and Sahel, José-Alain
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- 2024
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46. Patrimoine immobilier locatif et mobilité sociale : les économies domestiques de propriétaires de classes populaires et immigrées
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Cécile Vignal
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gender ,family ,working class ,immigrant ,landlord ,rental housing ,Ethnology. Social and cultural anthropology ,GN301-674 ,The family. Marriage. Woman ,HQ1-2044 - Abstract
Research Framework: In a French context of widespread access to home ownership since the 1980s, rental property has long remained neglected in sociological analysis, in favor of owner-occupation analysis. Objectives : This article aims to measure the ways in which working-class families accumulate rental assets across generations and genders, and to assess the effects on social trajectories. Methodology: The article is based on a statistical analysis of Institut National de la Statistiques et des Etudes Economiques (Insee)’s “Histoire de Vie et Patrimoine” survey (2017-2018) and on interview material from 30 upper-, middle- and working-class landlords in Lille conurbation. This article focuses on 10 respondents from working-class backgrounds, one of whom is experiencing a strong upward social mobility towards the middle classes: 5 women and 5 men, aged between 43 and 75, mainly of North African immigrant origin. Results: The analysis shows the importance of hard work on self-rehabilitation and division of dwellings that unabled them to become owners and then landlords. Rental income appears as a means of stabilizing the family group’s economy, as a form of “subsistence work” (Collectif Rosa Bonheur, 2019). Being a landlord is a marker of social success for immigrant families, supporting the social mobility of their children. Equal property rights serve, after separation or death, the autonomy of women who have managed to defend their share of the estate.Conclusions : This article helps to understand the mobilization of kinship group in the context of working-class household savings, and the role of deindustrialized urban space in the creation of real estate wealth and rental income.Contribution : This article contributes to the sociology of working-class and immigrant property ownership and to the renewal of analyses on social strata.
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- 2024
47. Natural clines and human management impact the genetic structure of Algerian honey bee populations
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Salvatore, Giovanna, Chibani Bahi Amar, Amira, Canale-Tabet, Kamila, Fridi, Riad, Tabet Aoul, Nacera, Saci, Soumia, Labarthe, Emmanuelle, Palombo, Valentino, D’Andrea, Mariasilvia, Vignal, Alain, and Faux, Pierre
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- 2023
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48. AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap
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Parejo, M., Talenti, A., Richardson, M., Vignal, A., Barnett, M., and Wragg, D.
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- 2023
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49. Cross-Sectional Analysis of Baseline Visual Parameters in Subjects Recruited Into the RESCUE and REVERSE ND4-LHON Gene Therapy Studies.
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Moster, Mark, Sergott, Robert, Newman, Nancy, Yu-Wai-Man, Patrick, Carelli, Valerio, Bryan, Molly, Smits, Gerard, Biousse, Valérie, Vignal-Clermont, Catherine, Klopstock, Thomas, Sadun, Alfredo, DeBusk, Adam, Carbonelli, Michele, Hage, Rabih, Priglinger, Siegfried, Karanjia, Rustum, Blouin, Laure, Taiel, Magali, Katz, Barrett, and Sahel, José
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Adolescent ,Adult ,Aged ,Cross-Sectional Studies ,DNA ,Mitochondrial ,Double-Blind Method ,Female ,Genetic Therapy ,Humans ,Male ,Middle Aged ,Optic Atrophy ,Hereditary ,Leber ,Retinal Ganglion Cells ,Tomography ,Optical Coherence ,Visual Acuity ,Visual Fields ,Young Adult - Abstract
OBJECTIVE: This report presents a cross-sectional analysis of the baseline characteristics of subjects with Leber hereditary optic neuropathy enrolled in the gene therapy trials RESCUE and REVERSE, to illustrate the evolution of visual parameters over the first year after vision loss. METHODS: RESCUE and REVERSE were 2 phase III clinical trials designed to assess the efficacy of rAAV2/2-ND4 gene therapy in ND4-LHON subjects. At enrollment, subjects had vision loss for ≤6 months in RESCUE, and between 6 and 12 months in REVERSE. Functional visual parameters (best-corrected visual acuity [BCVA], contrast sensitivity [CS], and Humphrey Visual Field [HVF]) and structural parameters assessed by spectral-domain optical coherence tomography were analyzed in both cohorts before treatment. The cross-sectional analysis of functional and anatomic parameters included the baseline values collected in all eyes at 2 different visits (Screening and Inclusion). RESULTS: Seventy-six subjects were included in total, 39 in RESCUE and 37 in REVERSE. Mean BCVA was significantly worse in RESCUE subjects compared with REVERSE subjects (1.29 and 1.61 LogMAR respectively, P = 0.0029). Similarly, mean CS and HVF were significantly more impaired in REVERSE vs RESCUE subjects (P < 0.005). The cross-sectional analysis showed that the monthly decrease in BCVA, ganglion cell layer macular volume, and retinal nerve fiber layer thickness was much more pronounced in the first 6 months after onset (+0.24 LogMAR, -0.06 mm3, and -6.00 μm respectively) than between 6 and 12 months after onset (+0.02 LogMAR, -0.01 mm3, and -0.43 μm respectively). CONCLUSION: LHON progresses rapidly in the first months following onset during the subacute phase, followed by relative stabilization during the dynamic phase.
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- 2021
50. Long-Term Follow-Up After Unilateral Intravitreal Gene Therapy for Leber Hereditary Optic Neuropathy: The RESTORE Study.
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Biousse, Valérie, Newman, Nancy, Yu-Wai-Man, Patrick, Carelli, Valerio, Moster, Mark, Vignal-Clermont, Catherine, Klopstock, Thomas, Sadun, Alfredo, Sergott, Robert, Hage, Rabih, Esposti, Simona, La Morgia, Chiara, Priglinger, Claudia, Karanja, Rustum, Blouin, Laure, Taiel, Magali, and Sahel, José-Alain
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Adolescent ,Adult ,Aged ,DNA ,Mitochondrial ,Double-Blind Method ,Female ,Follow-Up Studies ,Genetic Therapy ,Humans ,Intravitreal Injections ,Male ,Middle Aged ,Mutation ,NADH Dehydrogenase ,Optic Atrophy ,Hereditary ,Leber ,Quality of Life ,Recombinant Proteins ,Time Factors ,Tomography ,Optical Coherence ,Visual Acuity ,Visual Fields ,Young Adult - Abstract
BACKGROUND: RESCUE and REVERSE were 2 Phase 3 clinical trials that assessed the efficacy and safety of intravitreal gene therapy with lenadogene nolparvovec (rAAV2/2-ND4) for the treatment of Leber hereditary optic neuropathy (LHON). RESTORE is the long-term follow-up study of subjects treated in the RESCUE and REVERSE trials. METHODS: In RESCUE and REVERSE, 76 subjects with LHON because of the m.11778 G>A mutation in the mitochondrial gene ND4 received a single unilateral intravitreal injection of lenadogene nolparvovec. After 96 weeks, 61 subjects were enrolled in the long-term follow-up study RESTORE. The best-corrected visual acuity (BCVA) was assessed over a period of up to 52 months after onset of vision loss. A locally estimated scatterplot smoothing regression model was used to analyze changes in BCVA over time. Vision-related quality of life was reported using the visual function questionnaire-25 (VFQ-25). RESULTS: The population of MT-ND4 subjects enrolled in RESTORE was representative of the combined cohorts of RESCUE and REVERSE for mean age (35.1 years) and gender distribution (79% males). There was a progressive and sustained improvement of BCVA up to 52 months after the onset of vision loss. The final mean BCVA was 1.26 logarithm of the minimal angle of resolution 48 months after the onset of vision loss. The mean VFQ-25 composite score increased by 7 points compared with baseline. CONCLUSION: The treatment effect of lenadogene nolparvovec on BCVA and vision-related quality of life observed 96 weeks (2 years) after treatment in RESCUE and REVERSE was sustained at 3 years in RESTORE, with a maximum follow-up of 52 months (4.3 years) after the onset of vision loss.
- Published
- 2021
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