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2. Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine

Author

Dupain, Célia, Gutman, Tom, Girard, Elodie, Kamoun, Choumouss, Marret, Grégoire, Castel-Ajgal, Zahra, Sablin, Marie-Paule, Neuzillet, Cindy, Borcoman, Edith, Hescot, Ségolène, Callens, Céline, Trabelsi-Grati, Olfa, Melaabi, Samia, Vibert, Roseline, Antonio, Samantha, Franck, Coralie, Galut, Michèle, Guillou, Isabelle, Halladjian, Maral, Allory, Yves, Cyrta, Joanna, Romejon, Julien, Frouin, Eleonore, Stoppa-Lyonnet, Dominique, Wong, Jennifer, Le Tourneau, Christophe, Bièche, Ivan, Servant, Nicolas, Kamal, Maud, and Masliah-Planchon, Julien

Published
2024
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3. Next generation phenotyping for diagnosis and phenotype–genotype correlations in Kabuki syndrome

Author

Hennocq, Quentin, Willems, Marjolaine, Amiel, Jeanne, Arpin, Stéphanie, Attie-Bitach, Tania, Bongibault, Thomas, Bouygues, Thomas, Cormier-Daire, Valérie, Corre, Pierre, Dieterich, Klaus, Douillet, Maxime, Feydy, Jean, Galliani, Eva, Giuliano, Fabienne, Lyonnet, Stanislas, Picard, Arnaud, Porntaveetus, Thantrira, Rio, Marlène, Rouxel, Flavien, Shotelersuk, Vorasuk, Toutain, Annick, Yauy, Kevin, Geneviève, David, Khonsari, Roman H., and Garcelon, Nicolas

Published
2024
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4. Episignatures in practice: independent evaluation of published episignatures for the molecular diagnostics of ten neurodevelopmental disorders

Author

Husson, Thomas, Lecoquierre, François, Nicolas, Gaël, Richard, Anne-Claire, Afenjar, Alexandra, Audebert-Bellanger, Séverine, Badens, Catherine, Bilan, Frédéric, Bizaoui, Varoona, Boland, Anne, Bonnet-Dupeyron, Marie-Noëlle, Brischoux-Boucher, Elise, Bonnet, Céline, Bournez, Marie, Boute, Odile, Brunelle, Perrine, Caumes, Roseline, Charles, Perrine, Chassaing, Nicolas, Chatron, Nicolas, Cogné, Benjamin, Colin, Estelle, Cormier-Daire, Valérie, Dard, Rodolphe, Dauriat, Benjamin, Delanne, Julian, Deleuze, Jean-François, Demurger, Florence, Denommé-Pichon, Anne-Sophie, Depienne, Christel, Dieux, Anne, Dubourg, Christèle, Edery, Patrick, El Chehadeh, Salima, Faivre, Laurence, Fergelot, Patricia, Fradin, Mélanie, Garde, Aurore, Geneviève, David, Gilbert-Dussardier, Brigitte, Goizet, Cyril, Goldenberg, Alice, Gouy, Evan, Guerrot, Anne-Marie, Guimier, Anne, Harzalla, Inès, Héron, Delphine, Isidor, Bertrand, Lacombe, Didier, Le Guillou Horn, Xavier, Keren, Boris, Kuechler, Alma, Lacaze, Elodie, Lavillaureix, Alinoë, Lehalle, Daphné, Lesca, Gaëtan, Lespinasse, James, Levy, Jonathan, Lyonnet, Stanislas, Morel, Godeliève, Jean-Marçais, Nolwenn, Marlin, Sandrine, Marsili, Luisa, Mignot, Cyril, Nambot, Sophie, Nizon, Mathilde, Olaso, Robert, Pasquier, Laurent, Perrin, Laurine, Petit, Florence, Pingault, Veronique, Piton, Amélie, Prieur, Fabienne, Putoux, Audrey, Planes, Marc, Odent, Sylvie, Quélin, Chloé, Quemener-Redon, Sylvia, Rama, Mélanie, Rio, Marlène, Rossi, Massimiliano, Schaefer, Elise, Rondeau, Sophie, Saugier-Veber, Pascale, Smol, Thomas, Sigaudy, Sabine, Touraine, Renaud, Mau-Them, Frederic Tran, Trimouille, Aurélien, Van Gils, Julien, Vanlerberghe, Clémence, Vantalon, Valérie, Vera, Gabriella, Vincent, Marie, Ziegler, Alban, Guillin, Olivier, Campion, Dominique, and Charbonnier, Camille

Published
2024
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5. Objectivizing issues in the diagnosis of complex rare diseases: lessons learned from testing existing diagnosis support systems on ciliopathies

Author

Carole Faviez, Xiaoyi Chen, Nicolas Garcelon, Mohamad Zaidan, Katy Billot, Friederike Petzold, Hassan Faour, Maxime Douillet, Jean-Michel Rozet, Valérie Cormier-Daire, Tania Attié-Bitach, Stanislas Lyonnet, Sophie Saunier, and Anita Burgun

Subjects
Ciliopathy, Clinical decision support, Rare diseases, Electronic health record, Artificial intelligence, External evaluation, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract Background There are approximately 8,000 different rare diseases that affect roughly 400 million people worldwide. Many of them suffer from delayed diagnosis. Ciliopathies are rare monogenic disorders characterized by a significant phenotypic and genetic heterogeneity that raises an important challenge for clinical diagnosis. Diagnosis support systems (DSS) applied to electronic health record (EHR) data may help identify undiagnosed patients, which is of paramount importance to improve patients’ care. Our objective was to evaluate three online-accessible rare disease DSSs using phenotypes derived from EHRs for the diagnosis of ciliopathies. Methods Two datasets of ciliopathy cases, either proven or suspected, and two datasets of controls were used to evaluate the DSSs. Patient phenotypes were automatically extracted from their EHRs and converted to Human Phenotype Ontology terms. We tested the ability of the DSSs to diagnose cases in contrast to controls based on Orphanet ontology. Results A total of 79 cases and 38 controls were selected. Performances of the DSSs on ciliopathy real world data (best DSS with area under the ROC curve = 0.72) were not as good as published performances on the test set used in the DSS development phase. None of these systems obtained results which could be described as “expert-level”. Patients with multisystemic symptoms were generally easier to diagnose than patients with isolated symptoms. Diseases easily confused with ciliopathy generally affected multiple organs and had overlapping phenotypes. Four challenges need to be considered to improve the performances: to make the DSSs interoperable with EHR systems, to validate the performances in real-life settings, to deal with data quality, and to leverage methods and resources for rare and complex diseases. Conclusion Our study provides insights into the complexities of diagnosing highly heterogenous rare diseases and offers lessons derived from evaluation existing DSSs in real-world settings. These insights are not only beneficial for ciliopathy diagnosis but also hold relevance for the enhancement of DSS for various complex rare disorders, by guiding the development of more clinically relevant rare disease DSSs, that could support early diagnosis and finally make more patients eligible for treatment.

Published
2024
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7. AI-based diagnosis and phenotype – Genotype correlations in syndromic craniosynostoses

Author

Hennocq, Quentin, Paternoster, Giovanna, Collet, Corinne, Amiel, Jeanne, Bongibault, Thomas, Bouygues, Thomas, Cormier-Daire, Valérie, Douillet, Maxime, Dunaway, David J., Jeelani, Nu Owase, van de Lande, Lara S., Lyonnet, Stanislas, Ong, Juling, Picard, Arnaud, Rickart, Alexander J., Rio, Marlène, Schievano, Silvia, Arnaud, Eric, Garcelon, Nicolas, and Khonsari, Roman H.

Published
2024
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8. ATM germ line pathogenic variants affect outcomes in children with ataxia-telangiectasia and hematological malignancies

Author

Elitzur, Sarah, Shiloh, Ruth, Loeffen, Jan L. C., Pastorczak, Agata, Takagi, Masatoshi, Bomken, Simon, Baruchel, Andre, Lehrnbecher, Thomas, Tasian, Sarah K., Abla, Oussama, Arad-Cohen, Nira, Astigarraga, Itziar, Ben-Harosh, Miriam, Bodmer, Nicole, Brozou, Triantafyllia, Ceppi, Francesco, Chugaeva, Liliia, Dalla Pozza, Luciano, Ducassou, Stephane, Escherich, Gabriele, Farah, Roula, Gibson, Amber, Hasle, Henrik, Hoveyan, Julieta, Jacoby, Elad, Jazbec, Janez, Junk, Stefanie, Kolenova, Alexandra, Lazic, Jelena, Lo Nigro, Luca, Mahlaoui, Nizar, Miller, Lane, Papadakis, Vassilios, Pecheux, Lucie, Pillon, Marta, Sarouk, Ifat, Stary, Jan, Stiakaki, Eftichia, Strullu, Marion, Tran, Thai Hoa, Ussowicz, Marek, Verdu-Amoros, Jaime, Wakulinska, Anna, Zawitkowska, Joanna, Stoppa-Lyonnet, Dominique, Taylor, A. Malcolm, Shiloh, Yosef, Izraeli, Shai, Minard-Colin, Veronique, Schmiegelow, Kjeld, Nirel, Ronit, Attarbaschi, Andishe, and Borkhardt, Arndt

Published
2024
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9. Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine

Author

Célia Dupain, Tom Gutman, Elodie Girard, Choumouss Kamoun, Grégoire Marret, Zahra Castel-Ajgal, Marie-Paule Sablin, Cindy Neuzillet, Edith Borcoman, Ségolène Hescot, Céline Callens, Olfa Trabelsi-Grati, Samia Melaabi, Roseline Vibert, Samantha Antonio, Coralie Franck, Michèle Galut, Isabelle Guillou, Maral Halladjian, Yves Allory, Joanna Cyrta, Julien Romejon, Eleonore Frouin, Dominique Stoppa-Lyonnet, Jennifer Wong, Christophe Le Tourneau, Ivan Bièche, Nicolas Servant, Maud Kamal, and Julien Masliah-Planchon

Subjects
Tumor mutational burden, Calculation, Immunotherapy, Precision medicine, Molecular Tumor Board, Biology (General), QH301-705.5
Abstract

Abstract Background High tumor mutational burden (TMB) was reported to predict the efficacy of immune checkpoint inhibitors (ICIs). Pembrolizumab, an anti-PD-1, received FDA-approval for the treatment of unresectable/metastatic tumors with high TMB as determined by the FoundationOne®CDx test. It remains to be determined how TMB can also be calculated using other tests. Results FFPE/frozen tumor samples from various origins were sequenced in the frame of the Institut Curie (IC) Molecular Tumor Board using an in-house next-generation sequencing (NGS) panel. A TMB calculation method was developed at IC (IC algorithm) and compared to the FoundationOne® (FO) algorithm. Using IC algorithm, an optimal 10% variant allele frequency (VAF) cut-off was established for TMB evaluation on FFPE samples, compared to 5% on frozen samples. The median TMB score for MSS/POLE WT tumors was 8.8 mut/Mb versus 45 mut/Mb for MSI/POLE-mutated tumors. When focusing on MSS/POLE WT tumor samples, the highest median TMB scores were observed in lymphoma, lung, endometrial, and cervical cancers. After biological manual curation of these cases, 21% of them could be reclassified as MSI/POLE tumors and considered as “true TMB high.” Higher TMB values were obtained using FO algorithm on FFPE samples compared to IC algorithm (40 mut/Mb [10–3927] versus 8.2 mut/Mb [2.5–897], p

Published
2024
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10. Next generation phenotyping for diagnosis and phenotype–genotype correlations in Kabuki syndrome

Author

Quentin Hennocq, Marjolaine Willems, Jeanne Amiel, Stéphanie Arpin, Tania Attie-Bitach, Thomas Bongibault, Thomas Bouygues, Valérie Cormier-Daire, Pierre Corre, Klaus Dieterich, Maxime Douillet, Jean Feydy, Eva Galliani, Fabienne Giuliano, Stanislas Lyonnet, Arnaud Picard, Thantrira Porntaveetus, Marlène Rio, Flavien Rouxel, Vorasuk Shotelersuk, Annick Toutain, Kevin Yauy, David Geneviève, Roman H. Khonsari, and Nicolas Garcelon

Subjects
Medicine, Science
Abstract

Abstract The field of dysmorphology has been changed by the use Artificial Intelligence (AI) and the development of Next Generation Phenotyping (NGP). The aim of this study was to propose a new NGP model for predicting KS (Kabuki Syndrome) on 2D facial photographs and distinguish KS1 (KS type 1, KMT2D-related) from KS2 (KS type 2, KDM6A-related). We included retrospectively and prospectively, from 1998 to 2023, all frontal and lateral pictures of patients with a molecular confirmation of KS. After automatic preprocessing, we extracted geometric and textural features. After incorporation of age, gender, and ethnicity, we used XGboost (eXtreme Gradient Boosting), a supervised machine learning classifier. The model was tested on an independent validation set. Finally, we compared the performances of our model with DeepGestalt (Face2Gene). The study included 1448 frontal and lateral facial photographs from 6 centers, corresponding to 634 patients (527 controls, 107 KS); 82 (78%) of KS patients had a variation in the KMT2D gene (KS1) and 23 (22%) in the KDM6A gene (KS2). We were able to distinguish KS from controls in the independent validation group with an accuracy of 95.8% (78.9–99.9%, p

Published
2024
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11. Shallow whole genome sequencing approach to detect Homologous Recombination Deficiency in the PAOLA-1/ENGOT-OV25 phase-III trial

Author

Callens, Celine, Rodrigues, Manuel, Briaux, Adrien, Frouin, Eleonore, Eeckhoutte, Alexandre, Pujade-Lauraine, Eric, Renault, Victor, Stoppa-Lyonnet, Dominique, Bieche, Ivan, Bataillon, Guillaume, Karayan-Tapon, Lucie, Rochelle, Tristan, Heitz, Florian, Cecere, Sabrina Chiara, Pérez, Maria Jesús Rubio, Grimm, Christoph, Nøttrup, Trine Jakobi, Colombo, Nicoletta, Vergote, Ignace, Yonemori, Kan, Ray-Coquard, Isabelle, Stern, Marc-Henri, and Popova, Tatiana

Published
2023
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12. Identification of a DNA methylation episignature for recurrent constellations of embryonic malformations

Author

Haghshenas, Sadegheh, Karimi, Karim, Stevenson, Roger E., Levy, Michael A., Relator, Raissa, Kerkhof, Jennifer, Rzasa, Jessica, McConkey, Haley, Lauzon-Young, Carolyn, Balci, Tugce B., White-Brown, Alexandre M., Carter, Melissa T., Richer, Julie, Armour, Christine M., Sawyer, Sarah L., Bhola, Priya T., Tedder, Matthew L., Skinner, Cindy D., van Rooij, Iris A.L.M., van de Putte, Romy, de Blaauw, Ivo, Koeck, Rebekka M., Hoischen, Alexander, Brunner, Han, Esteki, Masoud Zamani, Pelet, Anna, Lyonnet, Stanislas, Amiel, Jeanne, Boycott, Kym M., and Sadikovic, Bekim

Published
2024
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15. Cancer Risks Associated With BRCA1 and BRCA2 Pathogenic Variants

Author

Li, Shuai, Silvestri, Valentina, Leslie, Goska, Rebbeck, Timothy R, Neuhausen, Susan L, Hopper, John L, Nielsen, Henriette Roed, Lee, Andrew, Yang, Xin, McGuffog, Lesley, Parsons, Michael T, Andrulis, Irene L, Arnold, Norbert, Belotti, Muriel, Borg, Åke, Buecher, Bruno, Buys, Saundra S, Caputo, Sandrine M, Chung, Wendy K, Colas, Chrystelle, Colonna, Sarah V, Cook, Jackie, Daly, Mary B, de la Hoya, Miguel, de Pauw, Antoine, Delhomelle, Hélène, Eason, Jacqueline, Engel, Christoph, Evans, D Gareth, Faust, Ulrike, Fehm, Tanja N, Fostira, Florentia, Fountzilas, George, Frone, Megan, Garcia-Barberan, Vanesa, Garre, Pilar, Gauthier-Villars, Marion, Gehrig, Andrea, Glendon, Gord, Goldgar, David E, Golmard, Lisa, Greene, Mark H, Hahnen, Eric, Hamann, Ute, Hanson, Helen, Hassan, Tiara, Hentschel, Julia, Horvath, Judit, Izatt, Louise, Janavicius, Ramunas, Jiao, Yue, John, Esther M, Karlan, Beth Y, Kim, Sung-Won, Konstantopoulou, Irene, Kwong, Ava, Laugé, Anthony, Lee, Jong Won, Lesueur, Fabienne, Mebirouk, Noura, Meindl, Alfons, Mouret-Fourme, Emmanuelle, Musgrave, Hannah, Yie, Joanne Ngeow Yuen, Niederacher, Dieter, Park, Sue K, Pedersen, Inge Sokilde, Ramser, Juliane, Ramus, Susan J, Rantala, Johanna, Rashid, Muhammad U, Reichl, Florian, Ritter, Julia, Rump, Andreas, Santamariña, Marta, Saule, Claire, Schmidt, Gunnar, Schmutzler, Rita K, Senter, Leigha, Shariff, Saba, Singer, Christian F, Southey, Melissa C, Stoppa-Lyonnet, Dominique, Sutter, Christian, Tan, Yen, Teo, Soo Hwang, Terry, Mary Beth, Thomassen, Mads, Tischkowitz, Marc, Toland, Amanda E, Torres, Diana, Vega, Ana, Wagner, Sebastian A, Wang-Gohrke, Shan, Wappenschmidt, Barbara, Weber, Bernhard HF, Yannoukakos, Drakoulis, Spurdle, Amanda B, Easton, Douglas F, and Chenevix-Trench, Georgia

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Prostate Cancer, Women's Health, Digestive Diseases, Breast Cancer, Ovarian Cancer, Pancreatic Cancer, Prevention, Cancer, Urologic Diseases, Rare Diseases, 2.1 Biological and endogenous factors, BRCA1 Protein, BRCA2 Protein, Breast Neoplasms, Breast Neoplasms, Male, Female, Genetic Predisposition to Disease, Heterozygote, Humans, Infant, Newborn, Male, Mutation, Ovarian Neoplasms, Pancreatic Neoplasms, Risk, Clinical Sciences, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

PurposeTo provide precise age-specific risk estimates of cancers other than female breast and ovarian cancers associated with pathogenic variants (PVs) in BRCA1 and BRCA2 for effective cancer risk management.MethodsWe used data from 3,184 BRCA1 and 2,157 BRCA2 families in the Consortium of Investigators of Modifiers of BRCA1/2 to estimate age-specific relative (RR) and absolute risks for 22 first primary cancer types adjusting for family ascertainment.ResultsBRCA1 PVs were associated with risks of male breast (RR = 4.30; 95% CI, 1.09 to 16.96), pancreatic (RR = 2.36; 95% CI, 1.51 to 3.68), and stomach (RR = 2.17; 95% CI, 1.25 to 3.77) cancers. Associations with colorectal and gallbladder cancers were also suggested. BRCA2 PVs were associated with risks of male breast (RR = 44.0; 95% CI, 21.3 to 90.9), stomach (RR = 3.69; 95% CI, 2.40 to 5.67), pancreatic (RR = 3.34; 95% CI, 2.21 to 5.06), and prostate (RR = 2.22; 95% CI, 1.63 to 3.03) cancers. The stomach cancer RR was higher for females than males (6.89 v 2.76; P = .04). The absolute risks to age 80 years ranged from 0.4% for male breast cancer to approximately 2.5% for pancreatic cancer for BRCA1 carriers and from approximately 2.5% for pancreatic cancer to 27% for prostate cancer for BRCA2 carriers.ConclusionIn addition to female breast and ovarian cancers, BRCA1 and BRCA2 PVs are associated with increased risks of male breast, pancreatic, stomach, and prostate (only BRCA2 PVs) cancers, but not with the risks of other previously suggested cancers. The estimated age-specific risks will refine cancer risk management in men and women with BRCA1/2 PVs.

Published
2022

17. Differential alternative splicing analysis links variation in ZRSR2 to a novel type of oral-facial-digital syndrome

Author

Hannes, Laurens, Atzori, Marta, Goldenberg, Alice, Argente, Jesús, Attie-Bitach, Tania, Amiel, Jeanne, Attanasio, Catia, Braslavsky, Débora G., Bruel, Ange-Line, Castanet, Mireille, Dubourg, Christèle, Jacobs, An, Lyonnet, Stanislas, Martinez-Mayer, Julian, Pérez Millán, María Inés, Pezzella, Nunziana, Pelgrims, Elise, Aerden, Mio, Bauters, Marijke, Rochtus, Anne, Scaglia, Paula, Swillen, Ann, Sifrim, Alejandro, Tammaro, Roberta, Mau-Them, Frederic Tran, Odent, Sylvie, Thauvin-Robinet, Christel, Franco, Brunella, and Breckpot, Jeroen

Published
2024
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18. Heavy-flavour studies with a high-luminosity fixed-target experiment at the LHC

Author

Trzeciak, B., Brodsky, S. J., Cavoto, G., Da Silva, C., Echevarria, M. G., Ferreiro, E. G., Hadjidakis, C., Haque, R., Hrivnacova, I., Kikola, D., Klein, A., Kurepin, A., Kusina, A., Lansberg, J. P., Lorce, C., Lyonnet, F., Makdisi, Y., Massacrier, L., Porteboeuf, S., Quintans, C., Rakotozafindrabe, A., Robbe, P., Scandale, W., Schienbein, I., Seixas, J., Shao, H. S., Signori, A., Topilskaya, N., Uras, A., Van Hulse, C., Wagner, J., Yamanaka, N., Yang, Z., and Zelenski, A.

Subjects
Nuclear Experiment
Abstract

Extraction of the multi-TeV proton and lead LHC beams with a bent crystal or by using an internal gas target allows one to perform the most energetic fixed-target experiment ever. pp, pd and pA collisions at $\sqrt{s}$ = 115 GeV and Pbp and PbA collisions at $\sqrt{s_{\rm{NN}}}$ = 72 GeV can be studied with high precision and modern detection techniques over a broad rapidity range. Using the LHCb or the ALICE detector in a fixed-target mode offers unprecedented possibilities to access heavy-flavour production in a new energy domain, half way between the SPS and the nominal RHIC energy. In this contribution, a review of projection studies for quarkonium and open charm and beauty production with both detector set-ups used with various nuclear targets and the LHC lead beams is presented., Comment: Hard Probes 2020 proceedings

Published
2021

19. The predictive ability of the 313 variant-based polygenic risk score for contralateral breast cancer risk prediction in women of European ancestry with a heterozygous BRCA1 or BRCA2 pathogenic variant.

Author

Lakeman, Inge MM, van den Broek, Alexandra J, Vos, Juliën AM, Barnes, Daniel R, Adlard, Julian, Andrulis, Irene L, Arason, Adalgeir, Arnold, Norbert, Arun, Banu K, Balmaña, Judith, Barrowdale, Daniel, Benitez, Javier, Borg, Ake, Caldés, Trinidad, Caligo, Maria A, Chung, Wendy K, Claes, Kathleen BM, GEMO Study Collaborators, EMBRACE Collaborators, Collée, J Margriet, Couch, Fergus J, Daly, Mary B, Dennis, Joe, Dhawan, Mallika, Domchek, Susan M, Eeles, Ros, Engel, Christoph, Evans, D Gareth, Feliubadaló, Lidia, Foretova, Lenka, Friedman, Eitan, Frost, Debra, Ganz, Patricia A, Garber, Judy, Gayther, Simon A, Gerdes, Anne-Marie, Godwin, Andrew K, Goldgar, David E, Hahnen, Eric, Hake, Christopher R, Hamann, Ute, Hogervorst, Frans BL, Hooning, Maartje J, Hopper, John L, Hulick, Peter J, Imyanitov, Evgeny N, OCGN Investigators, HEBON Investigators, KconFab Investigators, Isaacs, Claudine, Izatt, Louise, Jakubowska, Anna, James, Paul A, Janavicius, Ramunas, Jensen, Uffe Birk, Jiao, Yue, John, Esther M, Joseph, Vijai, Karlan, Beth Y, Kets, Carolien M, Konstantopoulou, Irene, Kwong, Ava, Legrand, Clémentine, Leslie, Goska, Lesueur, Fabienne, Loud, Jennifer T, Lubiński, Jan, Manoukian, Siranoush, McGuffog, Lesley, Miller, Austin, Gomes, Denise Molina, Montagna, Marco, Mouret-Fourme, Emmanuelle, Nathanson, Katherine L, Neuhausen, Susan L, Nevanlinna, Heli, Yie, Joanne Ngeow Yuen, Olah, Edith, Olopade, Olufunmilayo I, Park, Sue K, Parsons, Michael T, Peterlongo, Paolo, Piedmonte, Marion, Radice, Paolo, Rantala, Johanna, Rennert, Gad, Risch, Harvey A, Schmutzler, Rita K, Sharma, Priyanka, Simard, Jacques, Singer, Christian F, Stadler, Zsofia, Stoppa-Lyonnet, Dominique, Sutter, Christian, Tan, Yen Yen, Teixeira, Manuel R, Teo, Soo Hwang, Teulé, Alex, Thomassen, Mads, and Thull, Darcy L

Subjects
GEMO Study Collaborators, EMBRACE Collaborators, OCGN Investigators, HEBON Investigators, KconFab Investigators, Humans, Breast Neoplasms, Genetic Predisposition to Disease, BRCA1 Protein, BRCA2 Protein, Risk Factors, Retrospective Studies, Heterozygote, Mutation, Adult, Female, Prevention, Cancer, Aging, Breast Cancer, 2.1 Biological and endogenous factors, Genetics & Heredity, Genetics, Clinical Sciences
Abstract

PurposeTo evaluate the association between a previously published 313 variant-based breast cancer (BC) polygenic risk score (PRS313) and contralateral breast cancer (CBC) risk, in BRCA1 and BRCA2 pathogenic variant heterozygotes.MethodsWe included women of European ancestry with a prevalent first primary invasive BC (BRCA1 = 6,591 with 1,402 prevalent CBC cases; BRCA2 = 4,208 with 647 prevalent CBC cases) from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), a large international retrospective series. Cox regression analysis was performed to assess the association between overall and ER-specific PRS313 and CBC risk.ResultsFor BRCA1 heterozygotes the estrogen receptor (ER)-negative PRS313 showed the largest association with CBC risk, hazard ratio (HR) per SD = 1.12, 95% confidence interval (CI) (1.06-1.18), C-index = 0.53; for BRCA2 heterozygotes, this was the ER-positive PRS313, HR = 1.15, 95% CI (1.07-1.25), C-index = 0.57. Adjusting for family history, age at diagnosis, treatment, or pathological characteristics for the first BC did not change association effect sizes. For women developing first BC

Published
2021

20. Clinical implications of incorporating genetic and non-genetic risk factors in CanRisk-based breast cancer risk prediction

Author

Tüchler, Anja, De Pauw, Antoine, Ernst, Corinna, Anota, Amélie, Lakeman, Inge M.M., Dick, Julia, van der Stoep, Nienke, van Asperen, Christi J., Maringa, Monika, Herold, Natalie, Blümcke, Britta, Remy, Robert, Westerhoff, Anke, Stommel-Jenner, Denise J., Frouin, Eléonore, Richters, Lisa, Golmard, Lisa, Kütting, Nadine, Colas, Chrystelle, Wappenschmidt, Barbara, Rhiem, Kerstin, Devilee, Peter, Stoppa-Lyonnet, Dominique, Schmutzler, Rita K., and Hahnen, Eric

Published
2024
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22. Clinico-biological refinement of BCL11B-related disorder and identification of an episignature: A series of 20 unreported individuals

Author

Sabbagh, Quentin, Haghshenas, Sadegheh, Piard, Juliette, Trouvé, Chloé, Amiel, Jeanne, Attié-Bitach, Tania, Balci, Tugce, Barat-Houari, Mouna, Belonis, Alyce, Boute, Odile, Brightman, Diana S., Bruel, Ange-Line, Caraffi, Stefano Giuseppe, Chatron, Nicolas, Collet, Corinne, Dufour, William, Edery, Patrick, Fong, Chin-To, Fusco, Carlo, Gatinois, Vincent, Gouy, Evan, Guerrot, Anne-Marie, Heide, Solveig, Joshi, Aakash, Karp, Natalya, Keren, Boris, Lesieur-Sebellin, Marion, Levy, Jonathan, Levy, Michael A., Lozano, Claire, Lyonnet, Stanislas, Margot, Henri, Marzin, Pauline, McConkey, Haley, Michaud, Vincent, Nicolas, Gaël, Nizard, Mevyn, Paulet, Alix, Peluso, Francesca, Pernin, Vincent, Perrin, Laurence, Philippe, Christophe, Prasad, Chitra, Prasad, Madhavi, Relator, Raissa, Rio, Marlène, Rondeau, Sophie, Ruault, Valentin, Ruiz-Pallares, Nathalie, Sanchez, Elodie, Shears, Debbie, Siu, Victoria Mok, Sorlin, Arthur, Tedder, Matthew, Tharreau, Mylène, Mau-Them, Frédéric Tran, van der Laan, Liselot, Van Gils, Julien, Verloes, Alain, Whalen, Sandra, Willems, Marjolaine, Yauy, Kévin, Zuntini, Roberta, Kerkhof, Jennifer, Sadikovic, Bekim, and Geneviève, David

Published
2024
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24. Determinants of dental care use in patients with rare diseases: a qualitative exploration

Author

Lisa Friedlander, Ariane Berdal, Valérie Cormier-Daire, Stanislas Lyonnet, and Nicolas Garcelon

Subjects
Rare disease, Quality of life, Care course, Disabilities, Orality disorders, Dentistry, RK1-715
Abstract

Abstract Background Oral health is an inherent part of overall health as an important physiological crossroad of functions such as mastication, swallowing or phonation; and plays a central role in the life of relationships facilitating social and emotional expression.Our hypothesis was that in patients with rare diseases, access to dental care could be difficult because of the lack of professionals who know the diseases and accept to treat the patients, but also because some patients with cognitive and intellectual disabilities could not find adequate infrastructure to assist in managing their oral health. Methods This study employed a qualitative descriptive design including semi-structured interviews using guiding themes. The transcripts were reviewed to identify key themes and interviews were performed until the data were saturated and no further themes emerged. Results Twenty-nine patients from 7 to 24 years old were included in the study of which 15 patients had an intellectual delay. The results show that access to care is complicated more by aspects concerning intellectual disability than by the fact that the disease is rare. Oral disorders are also an obstacle to the maintenance of their oral health. Conclusion The oral health of patients with rare diseases, can be greatly enhanced by a pooling of knowledge between health professionals in the various sectors around the patient’s care. It is essential that this becomes a focus of national public health action that promotes transdisciplinary care for the benefit of these patients.

Published
2023
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25. Male breast cancer: No evidence for mosaic BRCA1 promoter methylation involvement

Author

Mathias Schwartz, Sabrina Ibadioune, Sophie Vacher, Marie-Charlotte Villy, Olfa Trabelsi-Grati, Jessica Le Gall, Sandrine M. Caputo, Hélène Delhomelle, Mathilde Warcoin, Virginie Moncoutier, Christine Bourneix, Nadia Boutry-Kryza, Antoine De Pauw, Marc-Henri Stern, Bruno Buecher, Emmanuelle Mouret-Fourme, Chrystelle Colas, Dominique Stoppa-Lyonnet, Julien Masliah-Planchon, Lisa Golmard, and Ivan Bieche

Subjects
HBOC syndrome, Breast neoplasm, Genetic testing, Homologous recombination, DNA methylation, Epigenomics, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Breast cancers (BC) are rare in men and are often caused by constitutional predisposing factors. In women, mosaic BRCA1 promoter methylations (MBPM) are frequent events, detected in 4–8% of healthy subjects. This constitutional epimutation increases risk of early-onset and triple-negative BC. However, the role of MBPM in male BC predisposition has never been assessed. We screened 40 blood samples from men affected by BC, and performed extensive tumour analysis on MBPM-positive patients. We detected two patients carrying MBPM. Surprisingly, tumour analysis revealed that neither of these two male BCs were caused by the constitutional BRCA1 epimutations carried by the patients.

Published
2024
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26. Clinical implications of incorporating genetic and non-genetic risk factors in CanRisk-based breast cancer risk prediction

Author

Anja Tüchler, Antoine De Pauw, Corinna Ernst, Amélie Anota, Inge M.M. Lakeman, Julia Dick, Nienke van der Stoep, Christi J. van Asperen, Monika Maringa, Natalie Herold, Britta Blümcke, Robert Remy, Anke Westerhoff, Denise J. Stommel-Jenner, Eléonore Frouin, Lisa Richters, Lisa Golmard, Nadine Kütting, Chrystelle Colas, Barbara Wappenschmidt, Kerstin Rhiem, Peter Devilee, Dominique Stoppa-Lyonnet, Rita K. Schmutzler, and Eric Hahnen

Subjects
Breast cancer, Genetic testing, Hereditary breast and ovarian cancer syndrome, Cancer prevention, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Background: Breast cancer (BC) risk prediction models consider cancer family history (FH) and germline pathogenic variants (PVs) in risk genes. It remains elusive to what extent complementation with polygenic risk score (PRS) and non-genetic risk factor (NGRFs) data affects individual intensified breast surveillance (IBS) recommendations according to European guidelines. Methods: For 425 cancer-free women with cancer FH (mean age 40·6 years, range 21–74), recruited in France, Germany and the Netherlands, germline PV status, NGRFs, and a 306 variant-based PRS (PRS306) were assessed to calculate estimated lifetime risks (eLTR) and estimated 10-year risks (e10YR) using CanRisk. The proportions of women changing country-specific European risk categories for IBS recommendations, i.e. ≥20 % and ≥30 % eLTR, or ≥5 % e10YR were determined. Findings: Of the women with non-informative PV status, including PRS306 and NGRFs changed clinical recommendations for 31·0 %, (57/184, 20 % eLTR), 15·8 % (29/184, 30 % eLTR) and 22·4 % (41/183, 5 % e10YR), respectively whereas of the women tested negative for a PV observed in their family, clinical recommendations changed for 16·7 % (25/150), 1·3 % (2/150) and 9·5 % (14/147). No change was observed for 82 women with PVs in high-risk genes (BRCA1/2, PALB2). Combined consideration of eLTRs and e10YRs identified BRCA1/2 PV carriers benefitting from IBS

Published
2024
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27. Impact of LHC vector boson production in heavy ion collisions on strange PDFs

Author

Kusina, A., Ježo, T., Clark, D. B., Duwentäster, P., Godat, E., Hobbs, T. J., Kent, J., Klasen, M., Kovařík, K., Lyonnet, F., Muzakka, K. F., Olness, F. I., Schienbein, I., and Yu, J. Y.

Subjects
High Energy Physics - Phenomenology
Abstract

The extraction of the strange quark parton distribution function (PDF) poses a long-standing puzzle. Measurements from neutrino-nucleus deep inelastic scattering (DIS) experiments suggest the strange quark is suppressed compared to the light sea quarks, while recent studies of W/Z boson production at the LHC imply a larger strange component at small x values. As the parton flavor determination in the proton depends on nuclear corrections, e.g. from heavy-target DIS, LHC heavy ion measurements can provide a distinct perspective to help clarify this situation. In this investigation we extend the nCTEQ15 nPDFs to study the impact of the LHC proton-lead W/Z production data on both the flavor differentiation and nuclear corrections. This complementary data set provides new insights on both the LHC W/Z proton analyses and the neutrino-nucleus DIS data. We identify these new nPDFs as nCTEQ15WZ. Our calculations are performed using a new implementation of the nCTEQ code (nCTEQ++) based on C++ which enables us to easily interface to external programs such as HOPPET, APPLgrid and MCFM. Our results indicate that, as suggested by the proton data, the small x nuclear strange sea appears larger than previously expected, even when the normalization of the W/Z data is accommodated in the fit. Extending the nCTEQ15 analysis to include LHC W/Z data represents an important step as we advance toward the next generation of nPDFs., Comment: nCTEQ15WZ nPDF. 21 pages, 14 figures

Published
2020
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28. Genome-wide analysis of a collective grave from Mentesh Tepe provides insight into the population structure of early neolithic population in the South Caucasus

Author

Perle Guarino-Vignon, Maël Lefeuvre, Amélie Chimènes, Aurore Monnereau, Farhad Guliyev, Laure Pecqueur, Elsa Jovenet, Bertille Lyonnet, and Céline Bon

Subjects
Biology (General), QH301-705.5
Abstract

Genomic analysis of three Neolithic individuals from Mentesh Tepe in Azerbaijan belonging to the beginnings of the Shomu-Shulaveri culture provides insight into the origin and population structure of the Shomu-Shulaveri community.

Published
2023
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30. The Deep Genome Project

Author

Lloyd, KC Kent, Adams, David J, Baynam, Gareth, Beaudet, Arthur L, Bosch, Fatima, Boycott, Kym M, Braun, Robert E, Caulfield, Mark, Cohn, Ronald, Dickinson, Mary E, Dobbie, Michael S, Flenniken, Ann M, Flicek, Paul, Galande, Sanjeev, Gao, Xiang, Grobler, Anne, Heaney, Jason D, Herault, Yann, de Angelis, Martin Hrabě, Lupski, James R, Lyonnet, Stanislas, Mallon, Ann-Marie, Mammano, Fabio, MacRae, Calum A, McInnes, Roderick, McKerlie, Colin, Meehan, Terrence F, Murray, Stephen A, Nutter, Lauryl MJ, Obata, Yuichi, Parkinson, Helen, Pepper, Michael S, Sedlacek, Radislav, Seong, Je Kyung, Shiroishi, Toshihiko, Smedley, Damian, Tocchini-Valentini, Glauco, Valle, David, Wang, Chi-Kuang Leo, Wells, Sara, White, Jacqueline, Wurst, Wolfgang, Xu, Ying, and Brown, Steve DM

Subjects
Animals, Genes, Genome, Humans, Mice, Mutation, Phenotype, Proteins, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Published
2020

32. nCTEQ PDFs at the LHC: Vector boson production in heavy ion collisions

Author

The nCTEQ Collaboration, Clark, D. B., Godat, E., Hobbs, T. J., Ježo, T., Kent, J., Keppel, C., Klasen, M., Kovarík, K., Kusina, A., Lyonnet, F., Morfin, J. G., Olness, F. I., Owens, J. F., Schienbein, I., and Yu, J. Y.

Subjects
High Energy Physics - Phenomenology
Abstract

Extraction of the strange quark PDF is a long-standing puzzle. We use the nCTEQ nPDFs with uncertainties to study the impact of the LHC W/Z production data on both the flavor differentiation and nuclear corrections; this complements the information from neutrino-DIS data. As the proton flavor determination is dependent on nuclear corrections (from heavy target DIS, for example), LHC heavy ion measurements can also help improve proton PDFs. We introduce a new implementation of the nCTEQ code (nCTEQ++) based on C++ which has a modular strucure and enables us to easily integrate programs such as HOPPET, APPLgrid, and MCFM. Using ApplGrids generated from MCFM, we use nCTEQ++ to perform a preliminary fit including the pPb LHC W/Z vector boson data., Comment: 6 pages, 4 figures. DIS2019 Workshop, Torino, Italy

Published
2019

33. Spin Physics with a fixed-target experiment at the LHC

Author

Echevarria, M. G., Brodsky, S. J., Cavoto, G., Da Silva, C., Donato, F., Ferreiro, E. G., Hadjidakis, C., Hřivnáčová, I., Kikola, D., Klein, A., Kurepin, A., Kusina, A., Lansberg, J. P., Lorcé, C., Lyonnet, F., Makdisi, Y., Massacrier, L., Porteboeuf, S., Quintans, C., Rakotozafindrabe, A., Robbe, P., Scandale, W., Schienbein, I., Seixas, J., Shao, H. S., Signori, A., Topilskaya, N., Trzeciak, B., Uras, A., Wagner, J., Yamanaka, N., Yang, Z., and Zelenski, A.

Subjects
High Energy Physics - Phenomenology, High Energy Physics - Experiment
Abstract

The multi-TeV proton and ion beams of the LHC would allow for the most energetic fixed-target experiment ever. In particular, $pp$, $p$d and $p$A collisions could be performed at $\sqrt{s_{NN}}$ = 115~GeV, as well as Pb$p$ and PbA collisions at $\sqrt{s_{NN}}$ = 72~GeV, in a parasitic way by making use of the already existing LHCb and ALICE detectors in fixed-target mode. This would offer the possibility to carry out a ground-breaking physics program, to study the nucleon and nuclear structure at high $x$, the spin content of the nucleon and the phases of the nuclear matter from a new rapidity viewpoint. In this talk I focus on the spin physics axis of the full program developed so far by the AFTER@LHC study group., Comment: 6 pages, 4 figures. Proceedings of the 23rd International Spin Physics Symposium (SPIN 2018), Ferrara, Italy, September 10-14, 2018

Published
2019

34. High luminosity fixed-target experiment at the LHC

Author

Hadjidakis, C., Brodsky, S. J., Cavoto, G., Da Silva, C., Donato, F., Echevarria, M. G., Ferreiro, E. G., Hřivnáčová, I., Kikola, D., Klein, A., Kurepin, A., Kusina, A., Lansberg, J. P., Lorcé, C., Lyonnet, F., Makdisi, Y., Massacrier, L., Porteboeuf, S., Quintans, C., Rakotozafindrabe, A., Robbe, P., Scandale, W., Schienbein, I., Seixas, J., Shao, H. S., Signori, A., Topilskaya, N., Trzeciak, B., Uras, A., Wagner, J., Yamanaka, N., Yang, Z., and Zelenski, A.

Subjects
High Energy Physics - Experiment, Nuclear Experiment
Abstract

By extracting the beam with a bent crystal or by using an internal gas target, the multi-TeV proton and lead LHC beams allow one to perform the most energetic fixed-target experiments ever and to study $pp$, $p$d and $p$A collisions at $\sqrt{s_{NN}}=115$ GeV and Pb$p$ and PbA collisions at $\sqrt{s_{NN}}=72$ GeV with high precision and modern detection techniques. Such studies would address open questions in the domain of the nucleon and nucleus partonic structure at high-$x$, quark-gluon plasma and, by using longitudinally or transversally polarised targets, spin physics. In this paper, we will review the technical solutions to obtain a high-luminosity fixed-target experiment at the LHC and will discuss their possible implementations with the ALICE and LHCb detectors., Comment: 5 pages, 2 figures, 9th International Conference on Hard and Electromagnetic Probes of High-Energy Nuclear Collisions : Hard Probes 2018. (HP2018)

Published
2019

35. Ultra-peripheral-collision studies in the fixed-target mode with the proton and lead LHC beams

Author

Yamanaka, N., Hadjidakis, C., Kikola, D., Lansberg, J. P., Massacrier, L., Echevarria, M. G., Kusina, A., Schienbein, I., Seixas, J., Shao, H. S., Signori, A., Trzeciak, B., Brodsky, S. J., Cavoto, G., Da Silva, C., Donato, F., Ferreiro, E. G., Hrivnacova, I., Klein, A., Kurepin, A., Lorce, C., Lyonnet, F., Makdisi, Y., Porteboeuf, S., Quintans, C., Rakotozafindrabe, A., Robbe, P., Scandale, W., Topilskaya, N., Uras, A., Wagner, J., Yang, Z., and Zelenski, A.

Subjects
High Energy Physics - Experiment, High Energy Physics - Phenomenology, Nuclear Experiment, Nuclear Theory
Abstract

We address the physics case related to the studies of ultra-peripheral pH, pPb, PbH, and PbPb collisions in the fixed-target mode at the LHC. In particular, we discuss how one can measure the gluon generalized parton distribution E_g(x,xi,t) in exclusive J/psi photoproduction with a transversely polarized hydrogen target., Comment: 6 pages, 3 figures, Proceedings of the International Conference on Hard & Electromagnetic Probes of High-Energy Nuclear Collisions (Hard Probes 2018), 30 September-5 October 2018, Aix-Les-Bains, France

Published
2019

36. Probing the high-x content of the nuclei in the fixed-target mode at the LHC

Author

Kusina, A., Hadjidakis, C., Kikola, D., Lansberg, J. P., Massacrier, L., Echevarria, M. G., Schienbein, I., Seixas, J., Shao, H. S., Signori, A., Trzeciak, B., Brodsky, S. J., Cavoto, G., Da Silva, C., Donato, F., Ferreiro, E. G., Hrivnacova, I., Klein, A., Kurepin, A., Lorce, C., Lyonnet, F., Makdisi, Y., Porteboeuf, S., Quintans, C., Rakotozafindrabe, A., Robbe, P., Scandale, W., Topilskaya, N., Uras, A., Wagner, J., Yamanaka, N., Yang, Z., and Zelenski, A.

Subjects
High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract

Using the LHCb and ALICE detectors in the fixed-target mode at the LHC offers unprecedented possibilities to study the quark, gluon and heavy-quark content of the proton and nuclei in the poorly known region of the high-momentum fractions. We review our projections for studies of Drell-Yan, charm, beauty and quarkonium production with both detector set-ups used with various nuclear targets and the LHC proton beams. Based on this, we show the expected improvement in the determination of the quark, charm and gluon proton and nuclear PDFs as well as discuss the implication for a better understanding of the cold-nuclear-matter effects in hard-probe production in proton-nucleus collisions., Comment: Proceedings of the Hard Probes 2018 conference

Published
2019

38. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Abbott, Kristin M., Banka, Siddharth, de Boer, Elke, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Denommé-Pichon, Anne-Sophie, Faivre, Laurence, Gilissen, Christian, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jackson, Adam, Kerstjens, Mieke, Kleefstra, Tjitske, Martín, Estrella López, Macek, Milan, Jr., Matalonga, Leslie, Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Pinelli, Michele, Pizzi, Simone, Posada, Manuel, Radio, Francesca C., Renieri, Alessandra, Riess, Olaf, Rooryck, Caroline, Ryba, Lukas, Agathe, Jean-Madeleine de Sainte, Santen, Gijs W.E., Schwarz, Martin, Tartaglia, Marco, Thauvin, Christel, Torella, Annalaura, Trimouille, Aurélien, Verloes, Alain, Vissers, Lisenka, Vitobello, Antonio, Votypka, Pavel, Zguro, Kristina, Boer, Elke de, Cohen, Enzo, Danis, Daniel, Gao, Fei, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, te Paske, Iris B.A.W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, ‘t Hoen, Peter A.C., Vissers, Lisenka E.L.M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Duffourd, Yannis, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Lišková, Petra, Doležalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Başak, Ayşe Nazlı, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A.L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Radio, Francesca Clementina, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Fallerini, Chiara, Benetti, Elisa, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, Alembik, Yves, Jean-Marçais, Nolwenn, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Safraou, Hana, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, de Vries, Bert B.A., Willemsen, Marjolein H., and Philippe, Christophe

Published
2023
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41. Association and performance of polygenic risk scores for breast cancer among French women presenting or not a familial predisposition to the disease

Author

Jiao, Yue, Truong, Thérèse, Eon-Marchais, Séverine, Mebirouk, Noura, Caputo, Sandrine M., Dondon, Marie-Gabrielle, Karimi, Mojgan, Le Gal, Dorothée, Beauvallet, Juana, Le Floch, Édith, Dandine-Roulland, Claire, Bacq-Daian, Delphine, Olaso, Robert, Albuisson, Juliette, Audebert-Bellanger, Séverine, Berthet, Pascaline, Bonadona, Valérie, Buecher, Bruno, Caron, Olivier, Cavaillé, Mathias, Chiesa, Jean, Colas, Chrystelle, Collonge-Rame, Marie-Agnès, Coupier, Isabelle, Delnatte, Capucine, De Pauw, Antoine, Dreyfus, Hélène, Fert-Ferrer, Sandra, Gauthier-Villars, Marion, Gesta, Paul, Giraud, Sophie, Gladieff, Laurence, Golmard, Lisa, Lasset, Christine, Lejeune-Dumoulin, Sophie, Léoné, Mélanie, Limacher, Jean-Marc, Lortholary, Alain, Luporsi, Élisabeth, Mari, Véronique, Maugard, Christine M., Mortemousque, Isabelle, Mouret-Fourme, Emmanuelle, Nambot, Sophie, Noguès, Catherine, Popovici, Cornel, Prieur, Fabienne, Pujol, Pascal, Sevenet, Nicolas, Sobol, Hagay, Toulas, Christine, Uhrhammer, Nancy, Vaur, Dominique, Venat, Laurence, Boland-Augé, Anne, Guénel, Pascal, Deleuze, Jean-François, Stoppa-Lyonnet, Dominique, Andrieu, Nadine, and Lesueur, Fabienne

Published
2023
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42. Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers

Author

Christopher Hakkaart, John F. Pearson, Louise Marquart, Joe Dennis, George A. R. Wiggins, Daniel R. Barnes, Bridget A. Robinson, Peter D. Mace, Kristiina Aittomäki, Irene L. Andrulis, Banu K. Arun, Jacopo Azzollini, Judith Balmaña, Rosa B. Barkardottir, Sami Belhadj, Lieke Berger, Marinus J. Blok, Susanne E. Boonen, Julika Borde, Angela R. Bradbury, Joan Brunet, Saundra S. Buys, Maria A. Caligo, Ian Campbell, Wendy K. Chung, Kathleen B. M. Claes, GEMO Study Collaborators, EMBRACE Collaborators, Marie-Agnès Collonge-Rame, Jackie Cook, Casey Cosgrove, Fergus J. Couch, Mary B. Daly, Sita Dandiker, Rosemarie Davidson, Miguel de la Hoya, Robin de Putter, Capucine Delnatte, Mallika Dhawan, Orland Diez, Yuan Chun Ding, Susan M. Domchek, Alan Donaldson, Jacqueline Eason, Douglas F. Easton, Hans Ehrencrona, Christoph Engel, D. Gareth Evans, Ulrike Faust, Lidia Feliubadaló, Florentia Fostira, Eitan Friedman, Megan Frone, Debra Frost, Judy Garber, Simon A. Gayther, Andrea Gehrig, Paul Gesta, Andrew K. Godwin, David E. Goldgar, Mark H. Greene, Eric Hahnen, Christopher R. Hake, Ute Hamann, Thomas V. O. Hansen, Jan Hauke, Julia Hentschel, Natalie Herold, Ellen Honisch, Peter J. Hulick, Evgeny N. Imyanitov, SWE-BRCA Investigators, kConFab Investigators, HEBON Investigators, Claudine Isaacs, Louise Izatt, Angel Izquierdo, Anna Jakubowska, Paul A. James, Ramunas Janavicius, Esther M. John, Vijai Joseph, Beth Y. Karlan, Zoe Kemp, Judy Kirk, Irene Konstantopoulou, Marco Koudijs, Ava Kwong, Yael Laitman, Fiona Lalloo, Christine Lasset, Charlotte Lautrup, Conxi Lazaro, Clémentine Legrand, Goska Leslie, Fabienne Lesueur, Phuong L. Mai, Siranoush Manoukian, Véronique Mari, John W. M. Martens, Lesley McGuffog, Noura Mebirouk, Alfons Meindl, Austin Miller, Marco Montagna, Lidia Moserle, Emmanuelle Mouret-Fourme, Hannah Musgrave, Sophie Nambot, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Joanne Ngeow Yuen Yie, Tu Nguyen-Dumont, Liene Nikitina-Zake, Kenneth Offit, Edith Olah, Olufunmilayo I. Olopade, Ana Osorio, Claus-Eric Ott, Sue K. Park, Michael T. Parsons, Inge Sokilde Pedersen, Ana Peixoto, Pedro Perez-Segura, Paolo Peterlongo, Timea Pocza, Paolo Radice, Juliane Ramser, Johanna Rantala, Gustavo C. Rodriguez, Karina Rønlund, Efraim H. Rosenberg, Maria Rossing, Rita K. Schmutzler, Payal D. Shah, Saba Sharif, Priyanka Sharma, Lucy E. Side, Jacques Simard, Christian F. Singer, Katie Snape, Doris Steinemann, Dominique Stoppa-Lyonnet, Christian Sutter, Yen Yen Tan, Manuel R. Teixeira, Soo Hwang Teo, Mads Thomassen, Darcy L. Thull, Marc Tischkowitz, Amanda E. Toland, Alison H. Trainer, Vishakha Tripathi, Nadine Tung, Klaartje van Engelen, Elizabeth J. van Rensburg, Ana Vega, Alessandra Viel, Lisa Walker, Jeffrey N. Weitzel, Marike R. Wevers, Georgia Chenevix-Trench, Amanda B. Spurdle, Antonis C. Antoniou, and Logan C. Walker

Subjects
Biology (General), QH301-705.5
Abstract

The risk of germline copy number variants (CNVs) in BRCA1 and BRCA2 pathogenic variant carriers in breast cancer is assessed, with CNVs overlapping SULT1A1 decreasing breast cancer risk in BRCA1 carriers.

Published
2022
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43. AI-based diagnosis in mandibulofacial dysostosis with microcephaly using external ear shapes

Author

Quentin Hennocq, Thomas Bongibault, Sandrine Marlin, Jeanne Amiel, Tania Attie-Bitach, Geneviève Baujat, Lucile Boutaud, Georges Carpentier, Pierre Corre, Françoise Denoyelle, François Djate Delbrah, Maxime Douillet, Eva Galliani, Wuttichart Kamolvisit, Stanislas Lyonnet, Dan Milea, Véronique Pingault, Thantrira Porntaveetus, Sandrine Touzet-Roumazeille, Marjolaine Willems, Arnaud Picard, Marlène Rio, Nicolas Garcelon, and Roman H. Khonsari

Subjects
AI, machine learning, dysmorphology, craniofacial malformation, MFDM, Pediatrics, RJ1-570
Abstract

IntroductionMandibulo-Facial Dysostosis with Microcephaly (MFDM) is a rare disease with a broad spectrum of symptoms, characterized by zygomatic and mandibular hypoplasia, microcephaly, and ear abnormalities. Here, we aimed at describing the external ear phenotype of MFDM patients, and train an Artificial Intelligence (AI)-based model to differentiate MFDM ears from non-syndromic control ears (binary classification), and from ears of the main differential diagnoses of this condition (multi-class classification): Treacher Collins (TC), Nager (NAFD) and CHARGE syndromes.MethodsThe training set contained 1,592 ear photographs, corresponding to 550 patients. We extracted 48 patients completely independent of the training set, with only one photograph per ear per patient. After a CNN-(Convolutional Neural Network) based ear detection, the images were automatically landmarked. Generalized Procrustes Analysis was then performed, along with a dimension reduction using PCA (Principal Component Analysis). The principal components were used as inputs in an eXtreme Gradient Boosting (XGBoost) model, optimized using a 5-fold cross-validation. Finally, the model was tested on an independent validation set.ResultsWe trained the model on 1,592 ear photographs, corresponding to 1,296 control ears, 105 MFDM, 33 NAFD, 70 TC and 88 CHARGE syndrome ears. The model detected MFDM with an accuracy of 0.969 [0.838–0.999] (p

Published
2023
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45. Using deep-neural-network-driven facial recognition to identify distinct Kabuki syndrome 1 and 2 gestalt

Author

Rouxel, Flavien, Yauy, Kevin, Boursier, Guilaine, Gatinois, Vincent, Barat-Houari, Mouna, Sanchez, Elodie, Lacombe, Didier, Arpin, Stéphanie, Giuliano, Fabienne, Haye, Damien, Rio, Marlène, Toutain, Annick, Dieterich, Klaus, Brischoux-Boucher, Elise, Julia, Sophie, Nizon, Mathilde, Afenjar, Alexandra, Keren, Boris, Jacquette, Aurelia, Moutton, Sebastien, Jacquemont, Marie-Line, Duflos, Claire, Capri, Yline, Amiel, Jeanne, Blanchet, Patricia, Lyonnet, Stanislas, Sanlaville, Damien, and Genevieve, David

Published
2022
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46. Emergence and intensification of dairying in the Caucasus and Eurasian steppes

Author

Scott, Ashley, Reinhold, Sabine, Hermes, Taylor, Kalmykov, Alexey A., Belinskiy, Andrey, Buzhilova, Alexandra, Berezina, Natalia, Kantorovich, Anatoliy R., Maslov, Vladimir E., Guliyev, Farhad, Lyonnet, Bertille, Gasimov, Parviz, Jalilov, Bakhtiyar, Eminli, Jeyhun, Iskandarov, Emil, Hammer, Emily, Nugent, Selin E., Hagan, Richard, Majander, Kerttu, Onkamo, Päivi, Nordqvist, Kerkko, Shishlina, Natalia, Kaverzneva, Elena, Korolev, Arkadiy I., Khokhlov, Aleksandr A., Smolyaninov, Roman V., Sharapova, Svetlana V., Krause, Rüdiger, Karapetian, Marina, Stolarczyk, Eliza, Krause, Johannes, Hansen, Svend, Haak, Wolfgang, and Warinner, Christina

Published
2022
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47. A fixed-target programme at the LHC for heavy-ion, hadron, spin and astroparticle physics: AFTER@LHC

Author

Kikoła, D., Brodsky, S. J., Cavoto, G., Da Silva, C., Donato, F., Echevarria, M. G., Ferreiro, E. G., Hadjidakis, C., Hřivnáčová, I., Klein, A., Kurepin, A., Kusina, A., Lansberg, J. P., Lorcé, C., Lyonnet, F., Makdisi, Y., Massacrier, L., Porteboeuf, S., Quintans, C., Rakotozafindrabe, A., Robbe, P., Scandale, W., Schienbein, I., Seixas, J., Shao, H. S., Signori, A., Topilskaya, N., Trzeciak, B., Uras, A., Wagner, J., Yamanaka, N., Yang, Z., and Zelenski, A.

Subjects
Nuclear Experiment
Abstract

Thanks to its multi-TeV LHC proton and lead beams, the LHC complex allows one to perform the most energetic fixed-target experiments ever and to study with high precision pp, pd and pA collisions at sqrt(s_NN) = 115 GeV and Pbp and PbA collisions at sqrt(s_NN) = 72 GeV. We present a selection of feasibility studies for the production of quarkonia, open heavy-flavor mesons as well as light-flavor hadrons in pA and PbA collisions using the LHCb and ALICE detectors in a fixed-target mode., Comment: Proceedings of the Quark Matter 2018 conference

Published
2018
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48. xFitter 2.0.0: Heavy quark matching scales: Unifying the FFNS and VFNS

Author

Team, The xFitter Developers', Bertone, V., Britzger, D., Camarda, S., Cooper-Sarkar, A., Geiser, A., Giuli, F., Glazov, A., Godat, E., Kusina, A., Luszczak, A., Lyonnet, F., Olness, F., Placakyte, R., Radescu, V., Schienbein, I., and Zenaiev, O.

Subjects
High Energy Physics - Phenomenology
Abstract

xFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton for many different kinds of analyses in Quantum Chromodynamics (QCD). It incorporates experimental data from a wide range of experiments including fixed-target, Tevatron, HERA, and LHC. xFitter version 2.0.0 has recently been released, and offers an expanded set of tools and options. The new xFitter 2.0.0 program links to the APFEL code which has implemented generalized matching conditions that enable the switch from $N_F$ to $N_F+1$ active flavors at an arbitrary matching scale $\mu_m$. This enables us to generalize the transition between a FFNS and a VFNS and essentially vary continuously between the two schemes; in this sense the matching scale $\mu_m$ allows us to unify the FFNS and VFNS in a common framework. This paper provides a brief overview of xFitter with emphasis of these new features., Comment: 6 pages, 5 figures. DIS2018 Workshop, Kobe, Japan

Published
2018

49. PDF Flavor Determination and the nCTEQ PDFs

Author

nCTEQ Collaboration, Godat, E., Clark, D. B., Hobbs, T. J., Jezo, T., Kent, J., Keppel, C., Kovarik, K., Kusina, A., Lyonnet, F., Morfin, J. G., Olness, F. I., Owens, J. F., Schienbein, I., and Yu, J. Y.

Subjects
High Energy Physics - Phenomenology
Abstract

Recent LHC W/Z vector boson production data in proton-lead collisions are quite sensitive to the heavier flavors (especially the strange PDF), and this complements the information from neutrino-DIS data. As the proton flavor determination is dependent on nuclear corrections (from heavy target DIS, for example), LHC heavy ion measurements can also help improve proton PDFs. We introduce a new implementation of the nCTEQ code (nCTEQ++) based on C++ which has a modular strucure and enables us to easily integrate programs such as HOPPET, APPLgrid, and MCFM. Using ApplGrids generated from MCFM, we use nCTEQ++ to perform a fit including the $pPb$ LHC W/Z vector boson data., Comment: 6 pages, 5 figures. DIS2018 Workshop, Kobe, Japan

Published
2018

50. A Fixed-Target Programme at the LHC: Physics Case and Projected Performances for Heavy-Ion, Hadron, Spin and Astroparticle Studies

Author

Hadjidakis, C., Kikoła, D., Lansberg, J. P., Massacrier, L., Echevarria, M. G., Kusina, A., Schienbein, I., Seixas, J., Shao, H. S., Signori, A., Trzeciak, B., Brodsky, S. J., Cavoto, G., Da Silva, C., Donato, F., Ferreiro, E. G., Hrivnacova, I., Klein, A., Kurepin, A., Lyonnet, F., Makdisi, Y., Lorcé, C., Porteboeuf, S., Quintans, C., Rakotozafindrabe, A., Robbe, P., Topilskaya, N., Uras, A., Wagner, J., Yamanaka, N., Yang, Z., and Zelenski, A.

Subjects
High Energy Physics - Experiment, High Energy Physics - Phenomenology, Nuclear Experiment, Nuclear Theory
Abstract

We review the context, the motivations and the expected performances of a comprehensive and ambitious fixed-target program using the multi-TeV proton and ion LHC beams. We also provide a detailed account of the different possible technical implementations ranging from an internal wire target to a full dedicated beam line extracted with a bent crystal. The possibilities offered by the use of the ALICE and LHCb detectors in the fixed-target mode are also reviewed., Comment: LaTeX, 115 pages. v2: version submitted to Physics Reports. A few figures added and some text improved. v3: accepted for publication in Physics Reports

Published
2018
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