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1. Correction: The Parkinson’s disease risk gene cathepsin B promotes fibrillar alpha-synuclein clearance, lysosomal function and glucocerebrosidase activity in dopaminergic neurons

Author

Jones-Tabah, Jace, He, Kathy, Karpilovsky, Nathan, Senkevich, Konstantin, Deyab, Ghislaine, Pietrantonio, Isabella, Goiran, Thomas, Cousineau, Yuting, Nikanorova, Daria, Goldsmith, Taylor, del Cid Pellitero, Esther, Chen, Carol X.-Q., Luo, Wen, You, Zhipeng, Abdian, Narges, Ahmad, Jamil, Ruskey, Jennifer A., Asayesh, Farnaz, Spiegelman, Dan, Fahn, Stanley, Waters, Cheryl, Monchi, Oury, Dauvilliers, Yves, Dupré, Nicolas, Miliukhina, Irina, Timofeeva, Alla, Emelyanov, Anton, Pchelina, Sofya, Greenbaum, Lior, Hassin-Baer, Sharon, Alcalay, Roy N., Milnerwood, Austen, Durcan, Thomas M., Gan-Or, Ziv, and Fon, Edward A.

Published
2024
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2. The Parkinson’s disease risk gene cathepsin B promotes fibrillar alpha-synuclein clearance, lysosomal function and glucocerebrosidase activity in dopaminergic neurons

Author

Jones-Tabah, Jace, He, Kathy, Karpilovsky, Nathan, Senkevich, Konstantin, Deyab, Ghislaine, Pietrantonio, Isabella, Goiran, Thomas, Cousineau, Yuting, Nikanorova, Daria, Goldsmith, Taylor, del Cid Pellitero, Esther, Chen, Carol X.-Q., Luo, Wen, You, Zhipeng, Abdian, Narges, Ahmad, Jamil, Ruskey, Jennifer A., Asayesh, Farnaz, Spiegelman, Dan, Fahn, Stanley, Waters, Cheryl, Monchi, Oury, Dauvilliers, Yves, Dupré, Nicolas, Miliukhina, Irina, Timofeeva, Alla, Emelyanov, Anton, Pchelina, Sofya, Greenbaum, Lior, Hassin-Baer, Sharon, Alcalay, Roy N., Milnerwood, Austen, Durcan, Thomas M., Gan-Or, Ziv, and Fon, Edward A.

Published
2024
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3. Are rare heterozygous SYNJ1 variants associated with Parkinson’s disease?

Author

Senkevich, Konstantin, Parlar, Sitki Cem, Chantereault, Cloe, Yu, Eric, Ahmad, Jamil, Ruskey, Jennifer A., Asayesh, Farnaz, Spiegelman, Dan, Waters, Cheryl, Monchi, Oury, Dauvilliers, Yves, Dupré, Nicolas, Miliukhina, Irina, Timofeeva, Alla, Emelyanov, Anton, Pchelina, Sofya, Greenbaum, Lior, Hassin-Baer, Sharon, Alcalay, Roy N., and Gan-Or, Ziv

Published
2024
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5. Goodbye Hartmann trial: a prospective, international, multicenter, observational study on the current use of a surgical procedure developed a century ago

Author

Perrone, Gennaro, Giuffrida, Mario, Abu-Zidan, Fikri, Kruger, Vitor F., Livrini, Marco, Petracca, Gabriele Luciano, Rossi, Giorgio, Tarasconi, Antonio, Tian, Brian W. C. A., Bonati, Elena, Mentz, Ricardo, Mazzini, Federico N., Campana, Juan P., Gasser, Elisabeth, Kafka-Ritsch, Reinhold, Felsenreich, Daniel M., Dawoud, Christopher, Riss, Stefan, Gomes, Carlos Augusto, Gomes, Felipe Couto, Gonzaga, Ricardo Alessandro Teixeira, Canton, Cassio Alfred Brattig, Pereira, Bruno Monteiro, Fraga, Gustavo P., Zem, Leticia Gonçalves, Cordeiro-Fonseca, Vinicius, de Mesquita Tauil, Renato, Atanasov, Boyko, Belev, Nikolay, Kovachev, Nikola, Meléndez, L. Juan José, Dimova, Ana, Dimov, Stefan, Zelić, Zdravko, Augustin, Goran, Bogdanić, Branko, Morić, Trpimir, Chouillard, Elie, Bajul, Melinda, De Simone, Belinda, Panis, Yves, Esposito, Francesco, Notarnicola, Margherita, Lauka, Lelde, Fabbri, Anna, Hentati, Hassen, Fnaiech, Iskander, Aurélien, Venara, Bougard, Marie, Roulet, Maxime, Demetrashvili, Zaza, Pipia, Irakli, Merabishvili, Giorgi, Bouliaris, Konstantinos, Koukoulis, Georgios, Doudakmanis, Christos, Xenaki, Sofia, Chrysos, Emmanuel, Kokkinakis, Stamatios, Vassiliu, Panteleimon, Michalopoulos, Nikolaos, Margaris, Ioannis, Kechagias, Aristotelis, Avgerinos, Konstantinos, Katunin, Jevgeni, Lostoridis, Eftychios, Nagorni, Eleni-Aikaterini, Pujante, Antonio, Mulita, Francesk, Maroulis, Ioannis, Vailas, Michail, Marinis, Athanasios, Siannis, Ioannis, Bourbouteli, Eirini, Manatakis, Dimitrios K., Tasis, Nikolaos, Acheimastos, Vasileios, Maria, Sotiropoulou, Stylianos, Kapiris, Kuzeridis, Harilaos, Korkolis, Dimitrios, Fradelos, Evangelos, Kavalieratos, George, Petropoulou, Thalia, Polydorou, Andreas, Papacostantinou, Ioannis, Triantafyllou, Tania, Kimpizi, Despina, Theodorou, Dimitrios, Toutouzas, Konstantinos, Chamzin, Alexandros, Frountzas, Maximos, Schizas, Dimitrios, Karavokyros, Ioannis, Syllaios, Athanasios, Charalabopoulos, Alexandros, Boura, Maria, Baili, Efstratia, Ioannidis, Orestis, Loutzidou, Lydia, Anestiadou, Elissavet, Tsouknidas, Ioannis, Petrakis, Georgios, Polenta, Eleni, Bains, Lovenish, Gupta, Rahul, Singh, Sudhir K., Khanduri, Archana, Bala, Miklosh, Kedar, Asaf, Pisano, Marcello, Podda, Mauro, Pisanu, Adolfo, Martines, Gennaro, Trigiante, Giuseppe, Lantone, Giuliano, Agrusa, Antonino, Di Buono, Giuseppe, Buscemi, Salvatore, Veroux, Massimiliano, Gioco, Rossella, Veroux, Gastone, Oragano, Luigi, Zonta, Sandro, Lovisetto, Federico, Feo, Carlo V., Pesce, Antonio, Fabbri, Nicolò, Lantone, Giulio, Marino, Fabio, Perrone, Fabrizio, Vincenti, Leonardo, Papagni, Vincenzo, Picciariello, Arcangelo, Rossi, Stefano, Picardi, Biagio, Del Monte, Simone Rossi, Visconti, Diego, Osella, Giulia, Petruzzelli, Luca, Pignata, Giusto, Andreuccetti, Jacopo, D’Alessio, Rossella, Buonfantino, Massimo, Guaitoli, Eleonora, Spinelli, Stefano, Sampietro, Gianluca Matteo, Corbellini, Carlo, Lorusso, Leonardo, Frontali, Alice, Pezzoli, Isabella, Bonomi, Alessandro, Chierici, Andrea, Cotsoglou, Christian, Manca, Giuseppe, Delvecchio, Antonella, Musa, Nicola, Casati, Massimiliano, Letizia, Laface, Abate, Emmanuele, Ercolani, Giorgio, D’Acapito, Fabrizio, Solaini, Leonardo, Guercioni, Gianluca, Cicconi, Simone, Sasia, Diego, Borghi, Felice, Giraudo, Giorgio, Sena, Giuseppe, Castaldo, Pasquale, Cardamone, Eugenia, Portale, Giuseppe, Zuin, Matteo, Spolverato, Ylenia, Esposito, Marialusia, Isernia, Roberta Maria, Di Salvo, Maria, Manunza, Romina, Esposito, Giuseppe, Agus, Marcello, Asti, Emanuele Luigi Giuseppe, Bernardi, Daniele Tiziano, Tonucci, Tommaso Panici, Luppi, Davide, Casadei, Massimiliano, Bonilauri, Stefano, Pezzolla, Angela, Panebianco, Annunziata, Laforgia, Rita, De Luca, Maurizio, Zese, Monica, Parini, Dario, Jovine, Elio, De Sario, Giuseppina, Lombardi, Raffaele, Aprea, Giovanni, Palomba, Giuseppe, Capuano, Marianna, Argenio, Giulio, Orio, Gianluca, Armellino, Mariano Fortunato, Troian, Marina, Guerra, Martina, Nagliati, Carlo, Biloslavo, Alan, Germani, Paola, Aizza, Giada, Monsellato, Igor, Chahrour, Ali Chaouki, Anania, Gabriele, Bombardini, Cristina, Bagolini, Francesco, Sganga, Gabriele, Fransvea, Pietro, Bianchi, Valentina, Boati, Paolo, Ferrara, Francesco, Palmieri, Francesco, Cianci, Pasquale, Gattulli, Domenico, Restini, Enrico, Cillara, Nicola, Cannavera, Alessandro, Nita, Gabriela Elisa, Sarnari, Jlenia, Roscio, Francesco, Clerici, Federico, Scandroglio, Ildo, Berti, Stefano, Cadeo, Alessandro, Filippelli, Alice, Conti, Luigi, Grassi, Carmine, Cattaneo, Gaetano Maria, Pighin, Marina, Papis, Davide, Gambino, Giovanni, Bertino, Vanessa, Schifano, Domenico, Prando, Daniela, Fogato, Luisella, Cavallo, Fabio, Ansaloni, Luca, Picheo, Roberto, Pontarolo, Nicholas, Depalma, Norma, Spampinato, Marcello, D’Ugo, Stefano, Lepre, Luca, Capponi, Michela Giulii, Campa, Rossella Domenica, Sarro, Giuliano, Dinuzzi, Vincenza Paola, Olmi, Stefano, Uccelli, Matteo, Ferrari, Davide, Inama, Marco, Moretto, Gianluigi, Fontana, Michele, Favi, Francesco, Picariello, Erika, Rampini, Alessia, Barberis, Andrea, Azzinnaro, Antonio, Oliva, Alba, Totaro, Luigi, Benzoni, Ilaria, Ranieri, Valerio, Capolupo, Gabriella Teresa, Carannante, Filippo, Caricato, Marco, Ronconi, Maurizio, Casiraghi, Silvia, Casole, Giovanni, Pantalone, Desire, Alemanno, Giovanni, Scheiterle, Maximilian, Ceresoli, Marco, Cereda, Marco, Fumagalli, Chiara, Zanzi, Federico, Bolzon, Stefano, Guerra, Enrico, Lecchi, Francesca, Cellerino, Paola, Ardito, Antonella, Scaramuzzo, Rosa, Balla, Andrea, Lepiane, Pasquale, Tartaglia, Nicola, Ambrosi, Antonio, Pavone, Giovanna, Palini, Gian Marco, Veneroni, Simone, Garulli, Gianluca, Ricci, Claudio, Torre, Beatrice, Russo, Iris Shari, Rottoli, Matteo, Tanzanu, Marta, Belvedere, Angela, Milone, Marco, Manigrasso, Michele, De Palma, Giovanni Domenico, Piccoli, Micaela, Pattacini, Gianmaria Casoni, Magnone, Stefano, Bertoli, Paolo, Pisano, Michele, Massucco, Paolo, Palisi, Marco, Luzzi, Andrea-Pierre, Fleres, Francesco, Clarizia, Guglielmo, Spolini, Alessandro, Kobe, Yoshiro, Toma, Takayuki, Shimamura, Fumihiko, Parker, Robert, Ranketi, Sinkeet, Mitei, Mercy, Svagzdys, Saulius, Pauzas, Henrikas, Zilinskas, Justas, Poskus, Tomas, Kryzauskas, Marius, Jakubauskas, Matas, Zakaria, Andee Dzulkarnaen, Zakaria, Zaidi, Wong, Michael Pak-Kai, Jusoh, Asri Che, Zakaria, Muhammad Nazreen, Cruz, Daniel Rios, Elizalde, Aurea Barbara Rodriguez, Reynaud, Alejandro Bañon, Hernandez, Edgard Efren Lozada, Monroy, Jose maria Victor Palomo, Hinojosa-Ugarte, Diego, Quiodettis, Martha, Du Bois, María Esther, Latorraca, José, Major, Piotr, Pędziwiatr, Michał, Pisarska-Adamczyk, Magdalena, Walędziak, Maciej, Kwiatkowski, Andrzej, Czyżykowski, Łukasz, da Costa, Silvia Dantas, Pereira, Bela, Ferreira, Ana Rita Oliveira, Almeida, Filipe, Rocha, Ricardo, Carneiro, Carla, Perez, Diego Pita, Carvas, João, Rocha, Catarina, Ferreira, Cátia, Marques, Rita, Fernandes, Urânia, Leao, Pedro, Goulart, André, Pereira, Rita Gonçalves, Patrocínio, Sara Daniela Direito, de Mendonça, Nuno Gonçalo Gonçalves, Manso, Maria Isabel Cerqueira, Morais, Henrique Manuel Cardoso, Cardoso, Paulo Sebastião, Calu, Valentin, Miron, Adrian, Toma, Elena Adelina, Gachabayov, Mahir, Abdullaev, Abakar, Litvin, Andrey, Nechay, Taras, Tyagunov, Alexander, Yuldashev, Anvar, Bradley, Alison, Wilson, Michael, Panyko, Arpád, Látečková, Zuzana, Lacko, Vladimír, Lesko, Dusan, Soltes, Marek, Radonak, Jozef, Turrado-Rodriguez, Victor, Termes-Serra, Roser, Morales-Sevillano, Xavier, Lapolla, Pierfrancesco, Mingoli, Andrea, Brachini, Gioia, Degiuli, Maurizio, Sofia, Silvia, Reddavid, Rossella, de Manzoni Garberini, Andrea, Buffone, Angelica, del Pozo, Eduardo Perea, Aparicio-Sánchez, Daniel, Dos Barbeito, Sandra, Estaire-Gómez, Mercedes, Vitón-Herrero, Rebeca, de los Ángeles Gil Olarte-Marquez, Mª, Gil-Martínez, José, Alconchel, Felipe, Nicolás-López, Tatiana, Rahy-Martin, Aida Cristina, Pelloni, María, Bañolas-Suarez, Raquel, Mendoza-Moreno, Fernando, Nisa, Francisca García-Moreno, Díez-Alonso, Manuel, Rodas, María Elisa Valle, Agundez, María Carmona, Andrés, María Inmaculada Pérez, Moreira, Claudia Cristina Lopes, Perez, Aintzane Lizarazu, Ponce, Iñigo Augusto, González-Castillo, Ana María, Membrilla-Fernández, Estela, Salvans, Silvia, Serradilla-Martín, Mario, Pardo, Pablo Sancho, Rivera-Alonso, Daniel, Dziakova, Jana, Huguet, Jose Mugüerza, Valle, Naila Pagès, Ruiz, Enrique Colás, Valcárcel, Cristina Rey, Moreno, Cristina Ruiz, Salazar, Yeniffer Tatiana Moreno, García, Juan Jesús Rubio, Micó, Silvia Sevila, López, Joaquín Ruiz, Farré, Silvia Pérez, Gomez, Maite Santamaria, Petit, Nuria Mestres, Titos-García, Alberto, Aranda-Narváez, Jose Manuel, Romacho-López, Laura, Sánchez-Guillén, Luis, Aranaz-Ostariz, Veronica, Bosch-Ramírez, Marina, Martínez-Pérez, Aleix, Martínez-López, Elías, Sebastián-Tomás, Juan Carlos, Jimenez-Riera, Granada, Jimenez-Vega, Javier, Cuellar, Jose Aurelio Navas, Campos-Serra, Andrea, Muñoz-Campaña, Anna, Gràcia-Roman, Raquel, Alegre, Javier Martínez, Pinto, Francisca Lima, O’Sullivan, Sara Nuñez, Antona, Francisco Blanco, Jiménez, Beatriz Muñoz, López-Sánchez, Jaime, Carmona, Zahira Gómez, Fernández, Rocio Torres, Sierra, Isabel Blesa, de León, Laura Román García, Moreno, Verónica Polaino, Iglesias, Eva, Cumplido, Paola Lora, Bravo, Altea Arango, Simó, Ignacio Rey, Domínguez, Carlota López, Caamaño, Aloia Guerreiro, Lozano, Rafael Calleja, Martínez, Manuel Durán, Torres, Álvaro Naranjo, de Quiros, Javier Tomas Morales Bernaldo, Pellino, Gianluca, Cloquell, Miriam Moratal, Moller, Elsa García, Jalal-Eldin, Sami, Abdoun, Ahmed K., Hamid, Hytham K. S., Lohsiriwat, Varut, Mongkhonsupphawan, Aitsariya, Baraket, Oussama, Ayed, Karim, Abbassi, Imed, Ali, Ali Ben, Ammar, Houssem, Kchaou, Ali, Tlili, Ahmed, Zribi, Imen, Colak, Elif, Polat, Suleyman, Koylu, Zehra Alan, Guner, Ali, Usta, Mehmet Arif, Reis, Murat Emre, Mantoglu, Baris, Gonullu, Emre, Akin, Emrah, Altintoprak, Fatih, Bayhan, Zulfu, Firat, Necattin, Isik, Arda, Memis, Ufuk, Bayrak, Mehmet, Altıntaş, Yasemin, Kara, Yasin, Bozkurt, Mehmet Abdussamet, Kocataş, Ali, Das, Koray, Seker, Ahmet, Ozer, Nazmi, Atici, Semra Demirli, Tuncer, Korhan, Kaya, Tayfun, Ozkan, Zeynep, Ilhan, Onur, Agackiran, Ibrahim, Uzunoglu, Mustafa Yener, Demirbas, Eren, Altinel, Yuksel, Meric, Serhat, Hacım, Nadir Adnan, Uymaz, Derya Salim, Omarov, Nail, Balık, Emre, Tebala, Giovanni D., Khalil, Hany, Rana, Mridul, Khan, Mansoor, Florence, Charlotte, Swaminathan, Christie, Leo, Cosimo Alex, Liasis, Lampros, Watfah, Josef, Trostchansky, Ivan, Delgado, Edward, Pontillo, Marcelo, Latifi, Rifat, Coimbra, Raul, Edwards, Sara, Lopez, Ana, Velmahos, George, Dorken, Ander, Gebran, Anthony, Palmer, Amanda, Oury, Jeffrey, Bardes, James M., Seng, Sirivan Suon, Coffua, Lauren S., Ratnasekera, Asanthi, Egodage, Tanya, Echeverria-Rosario, Karla, Armento, Isabella, Napolitano, Lena M., Sangji, Naveen F., Hemmila, Mark, Quick, Jacob A., Austin, Tyler R., Hyman, Theodore S., Curtiss, William, McClure, Amanda, Cairl, Nicholas, Biffl, Walter L., Truong, Hung P., Schaffer, Kathryn, Reames, Summer, Banchini, Filippo, Capelli, Patrizio, Coccolini, Federico, Sartelli, Massimo, Bravi, Francesca, Vallicelli, Carlo, Agnoletti, Vanni, Baiocchi, Gian Luca, and Catena, Fausto

Published
2024
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12. Aberrant survival of hippocampal Cajal-Retzius cells leads to memory deficits, gamma rhythmopathies and susceptibility to seizures in adult mice

Author

Riva, Martina, Moriceau, Stéphanie, Morabito, Annunziato, Dossi, Elena, Sanchez-Bellot, Candela, Azzam, Patrick, Navas-Olive, Andrea, Gal, Beatriz, Dori, Francesco, Cid, Elena, Ledonne, Fanny, David, Sabrina, Trovero, Fabrice, Bartolomucci, Magali, Coppola, Eva, Rebola, Nelson, Depaulis, Antoine, Rouach, Nathalie, de la Prida, Liset Menendez, Oury, Franck, and Pierani, Alessandra

Published
2023
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13. Predicting Learning and Retention of a Complex Task Using a Cognitive Architecture

Author

Tehranchi, Farnaz, Oury, Jacob David, and E. Ritter, Frank

Subjects
cognitive science
Abstract

We use a model to explore the implications of ACT-R's learning and forgetting mechanisms to understand learning and retention on a complex task. The model performs a spreadsheet task that has 14 non-iterated subtasks. The model predicts a learning curve and knowledge decay for different learning stages. The model's learning curve fits the human data well for the first four trials without decay. When decay is examined, however, we have to make modifications to the retention equation for the model's predictions to match data and the shapes predicted by the other learning theories. To fix this anomaly, we modified the effect of time on decay (adjusting time outside the experiment to less than the effect of time in the experiment) and the strength of newly learned memories (less well known than the previous default value). From these results, we learn that training and testing have been confounded in many studies.

Published
2021

15. Incidence of Thyroid Function Test Abnormalities in Patients Receiving Immune‐Checkpoint Inhibitors for Cancer Treatment

Author

Patel, Nisha Subhash, Oury, Anais, Daniels, Gregory A, Bazhenova, Lyudmila, and Patel, Sandip Pravin

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cancer, Rare Diseases, Clinical Research, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Adolescent, Adult, Aged, Aged, 80 and over, Female, Humans, Incidence, Male, Middle Aged, Neoplasms, Programmed Cell Death 1 Receptor, Quality of Life, Retrospective Studies, Thyroid Function Tests, Young Adult, Anti-PD1, Anti-CTLA 4, Thyroid, Ipilimumab, Nivolumab, Pembrolizumab, Anti‐CTLA 4, Anti‐PD1, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

BACKGROUND:With the advent of immune-checkpoint inhibitor (ICI) therapy (anti-CTLA-4, anti-PD-1), immune-related adverse events such as thyroid function test abnormalities (TFTAs) are common, with a reported incidence range of 2%-15% depending upon the ICI used. The aim of this study is to describe the incidence of TFTAs retrospectively in patients who received ICI therapy. METHODS:A total of 285 patients were reviewed (178 male, 107 female; 16-94 years of age), of whom 218 had no baseline TFTAs, 61 had baseline TFTAs, and 6 had a history of thyroidectomy (excluded). At least one dose of ipilimumab and/or nivolumab or pembrolizumab was administered. Post-ICI therapy TFTAs were classified according to standard definitions of thyroid conditions when possible. RESULTS:A total of 35% (76/218) patients had new-onset TFTAs on ICI therapy. Of note, 70.5% (43/61) had baseline TFTAs that were exacerbated by ICI therapy. The median times to new-onset or exacerbated baseline TFTA were 46 and 33 days, respectively. Of note, 64.5% (20/31) of patients on both ipilimumab and nivolumab had new-onset TFTAs, compared with 31.3% (15/48) on ipilimumab, 31.5% (28/89) on nivolumab, and 26% (13/50) on pembrolizumab. CONCLUSION:The incidence of TFTAs with ICI therapy was higher than previously reported. Patients with baseline TFTAs and/or who were receiving ipilimumab and nivolumab combination therapy had a higher incidence of TFTAs than patients receiving single-agent ICI therapy. We recommend more frequent evaluation of thyroid function in the first 8 weeks, especially in patients with baseline TFTAs. IMPLICATIONS FOR PRACTICE:Increased use of immune-checkpoint inhibitors in cancer treatment has highlighted the importance of monitoring for and treating immune-related adverse events. This study was conducted to assess the incidence of thyroid function test abnormalities retrospectively in patients with cancer on immune-checkpoint inhibitors, which is not known exactly. This study is unique in that it included patients with a variety of histologic subtypes of cancer and also followed the clinical course of patients with baseline thyroid function test abnormalities. This study can help make oncologists aware that the incidence of thyroid function test abnormalities is higher than anticipated. Early identification and timely treatment can help ameliorate symptoms for patients and improve their overall quality of life.

Published
2018

16. IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes.

Author

Momozawa, Yukihide, Dmitrieva, Julia, Théâtre, Emilie, Deffontaine, Valérie, Rahmouni, Souad, Charloteaux, Benoît, Crins, François, Docampo, Elisa, Elansary, Mahmoud, Gori, Ann-Stephan, Lecut, Christelle, Mariman, Rob, Mni, Myriam, Oury, Cécile, Altukhov, Ilya, Alexeev, Dmitry, Aulchenko, Yuri, Amininejad, Leila, Bouma, Gerd, Hoentjen, Frank, Löwenberg, Mark, Oldenburg, Bas, Pierik, Marieke J, Vander Meulen-de Jong, Andrea E, Janneke van der Woude, C, Visschedijk, Marijn C, International IBD Genetics Consortium, Lathrop, Mark, Hugot, Jean-Pierre, Weersma, Rinse K, De Vos, Martine, Franchimont, Denis, Vermeire, Severine, Kubo, Michiaki, Louis, Edouard, and Georges, Michel

Subjects
International IBD Genetics Consortium, Humans, Inflammatory Bowel Diseases, Crohn Disease, Genetic Predisposition to Disease, Cohort Studies, Gene Expression Profiling, Sequence Analysis, DNA, Genotype, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Adult, Aged, Aged, 80 and over, Middle Aged, Female, Male, Genetic Association Studies, and over, Polymorphism, Single Nucleotide, Sequence Analysis, DNA
Abstract

GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach.

Published
2018

17. Systemic bis-phosphinic acid derivative restores chloride transport in Cystic Fibrosis mice

Author

da Cunha, Mélanie Faria, Pranke, Iwona, Sassi, Ali, Schreiweis, Christiane, Moriceau, Stéphanie, Vidovic, Dragana, Hatton, Aurélie, Carlon, Mariane Sylvia, Creste, Geordie, Berhal, Farouk, Prestat, Guillaume, Freund, Romain, Odolczyk, Norbert, Jais, Jean Philippe, Gravier-Pelletier, Christine, Zielenkiewicz, Piotr, Jullien, Vincent, Hinzpeter, Alexandre, Oury, Franck, Edelman, Aleksander, and Sermet-Gaudelus, Isabelle

Published
2022
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23. Classroom Management with RStudio Server Professional

Author

Carter, Nathan C. and Oury, David T.

Subjects
classroom management, R, RStudio Server, RMarkdown
Abstract

We introduce a new RStudio addin that facilitates the exchange, grading, and real-time supervision of student work in RStudio.  We discuss the results of using the addin in a course in Fall 2016, and conclude with future extensions.  Readers who will find the addin of benefit to their own teaching will find installation instructions in the addin's GitHub repository.  The source code is released under the LGPL version 3.

Published
2018

24. The marbling of carcases is determined more by the characteristics of the animals themselves than by farming practices

Author

Albechaalany, John, Insausti, Kizkitza, and Ellies-Oury, Marie-Pierre

Abstract

AbstractImproved marbling could be of great benefit to the beef industry, responding more effectively to consumer preferences and increasing the market value of the product. To identify the management elements that could determine the degree of marbling of carcases, 128 cows were collected on six different farms, each using different breeding and feeding practices. Multiple statistical tests were carried out to determine whether marbling was more influenced by animal characteristics than by management practices. As expected, within the same farm, the practices used to finish the cows were the same from one animal to the next. We confirm that there was indeed a general level of marbling per farm (highly marbled animals coming from farms ‘used’ to producing highly marbled animals), without being able to determine the weight of genetic choices or feeding and management practices in this determinism. However, we were able to establish that very high marbled carcases came from heavier slaughtered animals and were associated with (1) management that maximised finishing times and time spent on grass (during the animal’s life) and (2) finishing diets rich in maize (grain or silage) and containing flax. The practices and performances associated with low and medium marbling carcases were difficult to separate using the indicators available in this study but were opposite to those of high marbling carcases. This ‘overall level of marbling’ on the farm makes it possible to prioritise the practices that favour or do not favour the development of marbling on the carcase, and allows to formulate advice to breeders to increase the marbling of their carcases. However, there are still grey areas to be covered to effectively achieve a maximum success rate, which will require further work and a more detailed characterisation of the practices and genetic orientations of the animals.

Published
2024
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27. Canonical Labelling of Site Graphs

Author

Oury, Nicolas, Pedersen, Michael, and Petersen, Rasmus

Subjects
Computer Science - Discrete Mathematics, Mathematics - Combinatorics
Abstract

We investigate algorithms for canonical labelling of site graphs, i.e. graphs in which edges bind vertices on sites with locally unique names. We first show that the problem of canonical labelling of site graphs reduces to the problem of canonical labelling of graphs with edge colourings. We then present two canonical labelling algorithms based on edge enumeration, and a third based on an extension of Hopcroft's partition refinement algorithm. All run in quadratic worst case time individually. However, one of the edge enumeration algorithms runs in sub-quadratic time for graphs with "many" automorphisms, and the partition refinement algorithm runs in sub-quadratic time for graphs with "few" bisimulation equivalences. This suite of algorithms was chosen based on the expectation that graphs fall in one of those two categories. If that is the case, a combined algorithm runs in sub-quadratic worst case time. Whether this expectation is reasonable remains an interesting open problem., Comment: In Proceedings CompMod 2013, arXiv:1306.2019

Published
2013
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31. Dual-specificity phosphatase 3 deletion promotes obesity, non-alcoholic steatohepatitis and hepatocellular carcinoma

Author

Jacques, Sophie, Arjomand, Arash, Perée, Hélène, Collins, Patrick, Mayer, Alice, Lavergne, Arnaud, Wéry, Marie, Mni, Myriam, Hego, Alexandre, Thuillier, Virginie, Becker, Guillaume, Bahri, Mohamed Ali, Plenevaux, Alain, Di Valentin, Emmanuel, Oury, Cécile, Moutschen, Michel, Delvenne, Philippe, Paquot, Nicolas, and Rahmouni, Souad

Published
2021
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32. Advancing Parkinson’s Disease Research in Canada: The Canadian Open Parkinson Network (C-OPN) Cohort

Author

Cressatti, Marisa, Pinilla-Monsalve, Gabriel D., Blais, Mathieu, Normandeau, Catherine P., Degroot, Clotilde, Kathol, Iris, Bogard, Sarah, Bendas, Anna, Camicioli, Richard, Dupré, Nicolas, Gan-Or, Ziv, Grimes, David A., Kalia, Lorraine V., MacDonald, Penny A., McKeown, Martin J., Martino, Davide, Miyasaki, Janis M., Schlossmacher, Michael G., Stoessl, A. Jon, Strafella, Antonio P., Fon, Edward A., and Monchi, Oury

Abstract

Background: Enhancing the interactions between study participants, clinicians, and investigators is imperative for advancing Parkinson’s disease (PD) research. The Canadian Open Parkinson Network (C-OPN) stands as a nationwide endeavor, connecting the PD community with ten accredited universities and movement disorders research centers spanning, at the time of this analysis, British Columbia, Alberta, Ontario, and Quebec.Objective: Our aim is to showcase C-OPN as a paradigm for bolstering national collaboration to accelerate PD research and to provide an initial overview of already collected data sets.Methods: The C-OPN database comprises de-identified data concerning demographics, symptoms and signs, treatment approaches, and standardized assessments. Additionally, it collects venous blood-derived biomaterials, such as for analyses of DNA, peripheral blood mononuclear cells (PBMC), and serum. Accessible to researchers, C-OPN resources are available through web-based data management systems for multi-center studies, including REDCap.Results: As of November 2023, the C-OPN had enrolled 1,505 PD participants. The male-to-female ratio was 1.77:1, with 83% (n= 1098) residing in urban areas and 82% (n= 1084) having pursued post-secondary education. The average age at diagnosis was 60.2±10.3 years. Herein, our analysis of the C-OPN PD cohort encompasses environmental factors, motor and non-motor symptoms, disease management, and regional differences among provinces. As of April 2024, 32 research projects have utilized C-OPN resources.Conclusions: C-OPN represents a national platform promoting multidisciplinary and multisite research that focuses on PD to promote innovation, exploration of care models, and collaboration among Canadian scientists.

Published
2024
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33. Equilibrium and Termination

Author

Danos, Vincent and Oury, Nicolas

Subjects
Computer Science - Logic in Computer Science
Abstract

We present a reduction of the termination problem for a Turing machine (in the simplified form of the Post correspondence problem) to the problem of determining whether a continuous-time Markov chain presented as a set of Kappa graph-rewriting rules has an equilibrium. It follows that the problem of whether a computable CTMC is dissipative (ie does not have an equilibrium) is undecidable.

Published
2010
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34. On the duality between trees and disks

Author

Oury, David

Subjects
Mathematics - Category Theory, 18D05, 18D20, 18D35
Abstract

A combinatorial category Disks was introduced by Andr\'e Joyal to play a role in his definition of weak omega-category. He defined the category Theta to be dual to Disks. In the ensuing literature, a more concrete description of Theta was provided. In this paper we provide another proof of the dual equivalence and introduce various categories equivalent to Disk or Theta, each providing a helpful viewpoint. In this second version the paper's contents have been reorganized with the goal of a more readable presentation. We define augmented categories and their reduced counterparts (which lack a single trivial object of the augmented category). These augmented categories are more suitable for inductive arguments and their reduced counterparts are equivalent to Disk and Theta. The equivalence between Disk and Theta is demonstrated in Sections 4 and 6 using categories inductively defined (in Section 3) from intervals and ordinals. The last two sections take a more categorical perspective, constructing categories of so-called labeled trees and showing that they are equivalent to their inductively defined counterparts, and so to Disk and Theta. The distinction between augmented and reduced categories corrects an error in the first version where the terminal tree was included in the category Disk., Comment: 37 pages

Published
2010

35. The Absolute Relativity Theory

Author

Oury, Jean-Marc and Heintz, Bruno

Subjects
Mathematical Physics
Abstract

This paper is a first presentation of a new approach of physics that we propose to refer as the Absolute Relativity Theory (ART) since it refutes the idea of a pre-existing space-time. It includes an algebraic definition of particles, interactions and Lagrangians. It proposed also a purely algebraic explanation of the passing of time phenomenon that leads to see usual Euler-Lagrange equations as the continuous version of the Knizhnik-Zamolodchikov monodromy. The identification of this monodromy with the local ones of the Lorentzian manifolds gives the Einstein equation algebraically explained in a quantized context. A fact that could lead to the unification of physics. By giving an algebraic classification of particles and interactions, the ART also proposes a new branch of physics, namely the Mass Quantification Theory, that provides a general method to calculate the characteristics of particles and interactions. Some examples are provided. The MQT also predicts the existence of as of today not yet observed particles that could be part of the dark matter. By giving a new interpretation of the weak interaction, it also suggests an interpretation of the so-called dark energy.

Published
2009

36. Future Directions in Idiopathic Pulmonary Fibrosis Research. An NHLBI Workshop Report

Author

Blackwell, Timothy S, Tager, Andrew M, Borok, Zea, Moore, Bethany B, Schwartz, David A, Anstrom, Kevin J, Bar-Joseph, Ziv, Bitterman, Peter, Blackburn, Michael R, Bradford, William, Brown, Kevin K, Chapman, Harold A, Collard, Harold R, Cosgrove, Gregory P, Deterding, Robin, Doyle, Ramona, Flaherty, Kevin R, Garcia, Christine Kim, Hagood, James S, Henke, Craig A, Herzog, Erica, Hogaboam, Cory M, Horowitz, Jeffrey C, King, Talmadge E, Loyd, James E, Lawson, William E, Marsh, Clay B, Noble, Paul W, Noth, Imre, Sheppard, Dean, Olsson, Julie, Ortiz, Luis A, O’Riordan, Thomas G, Oury, Tim D, Raghu, Ganesh, Roman, Jesse, Sime, Patricia J, Sisson, Thomas H, Tschumperlin, Daniel, Violette, Shelia M, Weaver, Timothy E, Wells, Rebecca G, White, Eric S, Kaminski, Naftali, Martinez, Fernando J, Wynn, Thomas A, Thannickal, Victor J, and Eu, Jerry P

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Orphan Drug, Lung, Autoimmune Disease, Rare Diseases, Respiratory, Good Health and Well Being, Animals, Biomedical Research, Disease Models, Animal, Extracellular Matrix, Genetic Predisposition to Disease, Humans, Idiopathic Pulmonary Fibrosis, Inflammation, Mice, Pulmonary Alveoli, Respiratory Mucosa, idiopathic pulmonary fibrosis, alveolar epithelial cells, extracellular matrix, interstitial lung disease, inflammation, Medical and Health Sciences, Respiratory System, Cardiovascular medicine and haematology, Clinical sciences
Abstract

The median survival of patients with idiopathic pulmonary fibrosis (IPF) continues to be approximately 3 years from the time of diagnosis, underscoring the lack of effective medical therapies for this disease. In the United States alone, approximately 40,000 patients die of this disease annually. In November 2012, the NHLBI held a workshop aimed at coordinating research efforts and accelerating the development of IPF therapies. Basic, translational, and clinical researchers gathered with representatives from the NHLBI, patient advocacy groups, pharmaceutical companies, and the U.S. Food and Drug Administration to review the current state of IPF research and identify priority areas, opportunities for collaborations, and directions for future research. The workshop was organized into groups that were tasked with assessing and making recommendations to promote progress in one of the following six critical areas of research: (1) biology of alveolar epithelial injury and aberrant repair; (2) role of extracellular matrix; (3) preclinical modeling; (4) role of inflammation and immunity; (5) genetic, epigenetic, and environmental determinants; (6) translation of discoveries into diagnostics and therapeutics. The workshop recommendations provide a basis for directing future research and strategic planning by scientific, professional, and patient communities and the NHLBI.

Published
2014

38. Motivating Students To Change: Intensive Short Term Counseling Techniques Enhance Teaching of Composition.

Author

Lefavor, Ann Oury

Abstract

English instructors try to convince students, sometimes in vain, of their need to learn composition. Through the use of counseling techniques, it is in the instructor's hands to build relationships with students that empower them as individuals and make them want to write well. First, an instructor can build trust by fulfilling promises and assuring students that nothing negative or demeaning will be said about them. Second, by reversing roles with students, instructors can empower students as authors; a simple repositioning of body posture can convey to a student that they share authority in a student-teacher conference. Third, since the comfort zone varies from person to person, an instructor can be sensitive to a student's need for space during conferences. Fourth, by mirroring the student's body posture, instructors may become more aware of that student's emotional state than they would be otherwise. Fifth, by responding to questions with apt questions or by waiting longer than usual for answers, an instructor may help students to generate their own thinking. Sixth, instructors can help students to recognize themselves as strong writers through three techniques: validation (offering compliments about a student's writing), use of positive dominant thought (sending students positive messages about their abilities), and grounding (touching the student lightly when making an important point). Finally, it is most important that an instructor assume enough control and set up enough structure to assure students that the environment is safe enough to take risks. (TB)

Published
1995

39. Author Correction: Report from a multidisciplinary meeting on anxiety as a non-motor manifestation of Parkinson’s disease

Author

Pontone, Gregory M., Dissanayaka, Nadeeka, Apostolova, Liana, Brown, Richard G., Dobkin, Roseanne, Dujardin, Kathy, Friedman, Joseph H., Leentjens, Albert F. G., Lenze, Eric J., Marsh, Laura, Mari, Lynda, Monchi, Oury, Richard, Irene H., Schrag, Anette, Strafella, Antonio P., Vernaleo, Beth, Weintraub, Daniel, and Mari, Zoltan

Published
2020
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41. The effect of transcranial ultrasound pulse repetition frequency on sustained inhibition in the human primary motor cortex: A double-blind, sham-controlled study.

Author

Zadeh, Ali K., Raghuram, Hrishikesh, Shrestha, Shirshak, Kibreab, Mekale, Kathol, Iris, Martino, Davide, Pike, G. Bruce, Pichardo, Samuel, and Monchi, Oury

Abstract

Non-invasive brain stimulation techniques such as transcranial magnetic stimulation and transcranial direct current stimulation hold promise for inducing brain plasticity. However, their limited precision may hamper certain applications. In contrast, Transcranial Ultrasound Stimulation (TUS), known for its precision and deep brain targeting capabilities, requires further investigation to establish its efficacy in producing enduring effects for treating neurological and psychiatric disorders. To investigate the enduring effects of different pulse repetition frequencies (PRF) of TUS on motor corticospinal excitability. T1-, T2-weighted, and zero echo time magnetic resonance imaging scans were acquired from 21 neurologically healthy participants for neuronavigation, skull reconstruction, and the performance of transcranial ultrasound and thermal modelling. The effects of three different TUS PRFs (10, 100, and 1000 Hz) with a constant duty cycle of 10 % on corticospinal excitability in the primary motor cortex were assessed using TMS-induced motor evoked potentials (MEPs). Each PRF and sham condition was evaluated on separate days, with measurements taken 5-, 30-, and 60-min post-TUS. A significant decrease in MEP amplitude was observed with a PRF of 10 Hz (p = 0.007), which persisted for at least 30 min, and with a PRF of 100 Hz (p = 0.001), lasting over 60 min. However, no significant changes were found for the PRF of 1000 Hz and the sham conditions. This study highlights the significance of PRF selection in TUS and underscores its potential as a non-invasive approach to reduce corticospinal excitability, offering valuable insights for future clinical applications. • TUS holds potential for LTD-like plasticity induction. • TUS with 10 Hz PRF and 10 % DC induces MEP inhibition for at least 30 min. • TUS with 100 Hz PRF and 10 % DC induces MEP inhibition lasting over 60 min. • TUS with 1000 Hz PRF and 10 % DC does not change corticospinal excitability. [ABSTRACT FROM AUTHOR]

Published
2024
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42. Evidence for clonal propagation in natural isolates of Plasmodium falciparum from Venezuela

Author

Urdaneta, Ludmel, Lal, Altaf, Barnabé, Christian, Oury, Bruno, Goldman, Ira, Ayala, Francisco J, and Tibayrenc, Michel

Subjects
Rare Diseases, Vector-Borne Diseases, Biotechnology, Infectious Diseases, Genetics, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Animals, Genotype, Linkage Disequilibrium, Phylogeny, Plasmodium falciparum, Polymorphism, Genetic, Random Amplified Polymorphic DNA Technique, Seasons, Venezuela
Abstract

We have analyzed 75 isolates of Plasmodium falciparum, collected in Venezuela during both the dry (November) and rainy (May-July) seasons, with a range of genetic markers including antigen genes and 14 random amplified polymorphic DNA (RAPD) primers. Thirteen P. falciparum stocks from Kenya and four other Plasmodium species are included in the analysis for comparison. Cross-hybridization shows that the 14 RAPD primers reveal 14 separate regions of the parasite's genome. The P. falciparum isolates are a monophyletic clade, significantly different from the other Plasmodium species. We identify three RAPD characters that could be useful as "tags" for rapid species identification. The Venezuelan genotypes fall into two discrete genetic subdivisions associated with either the dry or the rainy season; the isolates collected in the rainy season exhibit greater genetic diversity. There is significant linkage disequilibrium in each seasonal subsample and in the full sample. In contrast, no linkage disequilibrium is detected in the African sample. These results support the hypothesis that the population structure of P. falciparum in Venezuela, but not in Africa, is predominantly clonal. However, the impact of genetic recombination on Venezuelan P. falciparum seems higher than in parasitic species with long-term clonal evolution like Trypanosoma cruzi, the agent of Chagas' disease. The genetic structure of the Venezuelan samples is similar to that of Escherichia coli, a bacterium that propagates clonally, with occasional genetic recombination.

Published
2001

43. Plasmodium falciparum: population genetic analysis by multilocus enzyme electrophoresis and other molecular markers.

Author

Abderrazak, SB, Oury, B, Lal, AA, Bosseno, MF, Force-Barge, P, Dujardin, JP, Fandeur, T, Molez, JF, Kjellberg, F, Ayala, FJ, and Tibayrenc, M

Subjects
Animals, Humans, Plasmodium falciparum, Malaria, Falciparum, Isoenzymes, DNA, Protozoan, Genetic Markers, Antigens, Protozoan, Electrophoresis, Random Amplified Polymorphic DNA Technique, Phylogeny, Linkage Disequilibrium, Polymorphism, Restriction Fragment Length, Genes, Protozoan, Genetic Variation, strain typing, epidemiological, tracking, clonal evolution, self-fertilization, population structure, discrete typing unit, Mycology & Parasitology, Microbiology, Veterinary Sciences
Abstract

Abderrazak, S. B., Oury, B, Lal, A. A., Bosseno, M.-F., Force-Barge, P., Dujardin, J.-P., Fandeur, T., Molez, J.-F., Kjellberg, F., Ayala, F. J., and Tibayrenc, M. 1999. Plasmodium falciparum: Population genetic analysis by multilocus enzyme electrophoresis and other molecular markers. Experimental Parasitology 92, 232-238. The population structure of Plasmodium falciparum, the agent of malignant malaria, is uncertain. We have analyzed multilocus enzyme electrophoresis (MLEE) polymorphisms at 7-12 gene loci in each of four populations (two populations in Burkina Faso, one in Sudan, one in Congo), plus one "cosmopolitan" sample consisting of parasite cultures from 15 distant localities in four different continents. We have also performed random amplified polymorphic DNA analysis (RAPD) and restriction fragment length polymorphism (RFLP) and characterized gene varia tion at four antigen genes in the Congo population. All genetic assays show abundant genetic variability in all populations analyzed. With the isoenzyme assays, strong linkage disequilibrium is apparent in at least two local populations, the Congo population and one population from Burkina Faso, as well as in the cosmopolitan sample, and less definitely in the other Burkina Faso population. However, no linkage disequilibrium is detected in the Congo population with the molecular assays. We failed to detect any nonrandom association between the different kinds of genetic markers; that is, MLEE with RAPD or RFLP, RAPD with RFLP, and so on. Although isoenzyme data show statistical departures from panmictic expectations, these results suggest that in the areas under survey, P. falciparum populations do not undergo predominant clonal evolution and show no clear-cut subdivisions, un like Trypanosoma cruzi, Leishmania sp., and other major parasitic species. We discuss the epidemiological and taxonomical significance of these results.

Published
1999

50. Are eukaryotic microorganisms clonal or sexual? A population genetics vantage.

Author

Tibayrenc, M, Kjellberg, F, Arnaud, J, Oury, B, Brenière, SF, Dardé, ML, and Ayala, FJ

Subjects
Malaria, Rare Diseases, Vector-Borne Diseases, HIV/AIDS, Genetics, Infectious Diseases, Infection, Good Health and Well Being, Animals, DNA Probes, DNA, Fungal, DNA, Protozoan, Eukaryota, Eukaryotic Cells, Fungi, Genetics, Population, Genotype, Leishmania, Nucleic Acid Hybridization, Plasmodium falciparum, Polymorphism, Restriction Fragment Length, Reproduction, Asexual, Toxoplasma, Trypanosoma cruzi, PARASITIC PROTOZOA, FUNGI, MALARIA, LEISHMANIASIS, TOXOPLASMA
Abstract

We argue that the mode of reproduction of microorganisms in nature can only be decided by population genetic information. The evidence available indicates that many parasitic protozoa and unicellular fungi have clonal rather than sexual population structures, which has major consequences for medical research and practice. Plasmodium falciparum, the agent of malaria, is a special case: the scarce evidence available is contradictory, some suggesting that uniparental lineages may exist in nature. This is puzzling (because P. falciparum is known to have a sexual stage) and poses a challenge that can be readily settled by ascertaining the frequency distribution of genotypes in natural populations.

Published
1991

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