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1. Temporal order of clinical and biomarker changes in familial frontotemporal dementia

Author: Staffaroni, Adam M, Quintana, Melanie, Heller, Carolin, Boeve, Bradley F, Rosen, Howard J, Rohrer, Jonathan D, Boxer, Adam L, Initiative, Frontotemporal Dementia Prevention, Apostolova, Liana, Barmada, Sami, Boeve, Bradley, Bozoki, Andrea, Clark, Annie L, Clark, David, Coppola, Giovanni, Darby, Ryan, Dickson, Dennis, Faber, Kelley, Fagan, Anne, Galasko, Douglas R, Grant, Ian M, Huang, Eric, Kerwin, Diana, Taylor, Jack Carson, Lapid, Maria, Lee, Suzee, Leger, Gabriel, Masdeux, Joseph C, McGinnis, Scott, Mendez, Mario, Onyike, Chiadi, Pascual, M Belen, Pressman, Peter, Rademakers, Rosa, Wise, Amy, Ramanan, Vijay, Ritter, Aaron, Seeley, William W, Syrjanen, Jeremy, Taylor, Jack C, Weintraub, Sandra, Esteve, Aitana Sogorb, Nelson, Annabel, Greaves, Caroline V, Thomas, David L, Ong, Elise, Benotmane, Hanya, Zetterberg, Henrik, Nicholas, Jennifer, Samra, Kiran, Shafei, Rachelle, Timberlake, Carolyn, Cope, Thomas, Rittman, Timothy, Benussi, Alberto, Premi, Enrico, Forsberg, Leah, Gasparotti, Roberto, Archetti, Silvana, Gazzina, Stefano, Cantoni, Valentina, Arighi, Andrea, Fenoglio, Chiara, Scarpini, Elio, Fumagalli, Giorgio, Borracci, Vittoria, Rossi, Giacomina, Brushaber, Danielle, Giaccone, Giorgio, Di Fede, Giuseppe, Caroppo, Paola, Prioni, Sara, Redaelli, Veronica, Tang-Wai, David, Rogaeva, Ekaterina, Castelo-Branco, Miguel, Freedman, Morris, Keren, Ron, Rojas, Julio C, Black, Sandra, Mitchell, Sara, Shoesmith, Christen, Bartha, Robart, Poos, Jackie, Papma, Janne M, Giannini, Lucia, van Minkelen, Rick, Pijnenburg, Yolande, Nacmias, Benedetta, VandeVrede, Lawren, Ferrari, Camilla, Polito, Cristina, Lombardi, Gemma, Bessi, Valentina, Veldsman, Michele, Andersson, Christin, Thonberg, Hakan, Öijerstedt, Linn, Jelic, Vesna, Thompson, Paul, Ljubenkov, Peter, Lladó, Albert, Antonell, Anna, Olives, Jaume, Balasa, Mircea, Bargalló, Nuria, Borrego-Ecija, Sergi, Verdelho, Ana, Maruta, Carolina, Ferreira, Catarina B, Miltenberger, Gabriel, Wendelberger, Barbara, Kramer, Joel, Simões do Couto, Frederico, Gabilondo, Alazne, Gorostidi, Ana, Villanua, Jorge, Cañada, Marta, Tainta, Mikel, Zulaica, Miren, Barandiaran, Myriam, Alves, Patricia, Bender, Benjamin, Casaletto, Kaitlin B, Wilke, Carlo, Graf, Lisa, Vogels, Annick, Vandenbulcke, Mathieu, Van Damme, Philip, Bruffaerts, Rose, Poesen, Koen, Rosa-Neto, Pedro, Gauthier, Serge, Camuzat, Agnès, Appleby, Brian, Brice, Alexis, Bertrand, Anne, Funkiewiez, Aurélie, Rinaldi, Daisy, Saracino, Dario, Colliot, Olivier, Sayah, Sabrina, Prix, Catharina, Wlasich, Elisabeth, Wagemann, Olivia, Bordelon, Yvette, Loosli, Sandra, Schönecker, Sonja, Hoegen, Tobias, Lombardi, Jolina, Anderl-Straub, Sarah, Rollin, Adeline, Kuchcinski, Gregory, Bertoux, Maxime, Lebouvier, Thibaud, Deramecourt, Vincent, Botha, Hugo, Santiago, Beatriz, Duro, Diana, Leitão, Maria João, Almeida, Maria Rosario, Tábuas-Pereira, Miguel, Afonso, Sónia, Dickerson, Bradford C, Domoto-Reilly, Kimiko, Fields, Julie A, Foroud, Tatiana, Gavrilova, Ralitza, Heuer, Hilary W, Geschwind, Daniel, Ghoshal, Nupur, Goldman, Jill, Graff-Radford, Jonathon, Graff-Radford, Neill, Grossman, Murray, Hall, Matthew G H, Hsiung, Ging-Yuek, Huey, Edward D, Irwin, David, Russell, Lucy L, Jones, David T, Kantarci, Kejal, Kaufer, Daniel, Knopman, David S, Kremers, Walter, Lago, Argentina Lario, Lapid, Maria I, Litvan, Irene, Lucente, Diane, Mackenzie, Ian R, Cobigo, Yann, Mendez, Mario F, Mester, Carly, Miller, Bruce L, Onyike, Chiadi U, Ramanan, Vijay K, Ramos, Eliana Marisa, Rao, Meghana, Rascovsky, Katya, Rankin, Katherine P, Wolf, Amy, Roberson, Erik D, Savica, Rodolfo, Tartaglia, M Carmela, Wong, Bonnie, Cash, David M, Bouzigues, Arabella, Swift, Imogen J, Peakman, Georgia, Bocchetta, Martina, Goh, Sheng-Yang Matt, Todd, Emily G, Convery, Rhian S, Rowe, James B, Borroni, Barbara, Galimberti, Daniela, Tiraboschi, Pietro, Masellis, Mario, Finger, Elizabeth, van Swieten, John C, Seelaar, Harro, Petrucelli, Leonard, Jiskoot, Lize C, Sorbi, Sandro, Butler, Chris R, Graff, Caroline, Gerhard, Alexander, Langheinrich, Tobias, Laforce, Robert, Sanchez-Valle, Raquel, de Mendonça, Alexandre, Moreno, Fermin, Gendron, Tania F, Synofzik, Matthis, Vandenberghe, Rik, Ducharme, Simon, Le Ber, Isabelle, Levin, Johannes, Danek, Adrian, Otto, Markus, Pasquier, Florence, Santana, Isabel, Kornak, John, Frontotemporal Dementia Prevention Initiative (FPI) Investigators, and Neurology
Subjects: Clinical Trials as Topic, C9orf72 Protein, biomarkers, genetics [Mutation], tau Proteins, General Medicine, Article, General Biochemistry, Genetics and Molecular Biology, genetics [tau Proteins], Chemistry, Frontotemporal Dementia, Mutation, Disease Progression, Humans, ddc:610, Human medicine, genetics [C9orf72 Protein], genetics [Frontotemporal Dementia], Biology, Biomarkers, dementia
Abstract: Data availability: The datasets analyzed for the current study reflect collaborative efforts of two research consortia: ALLFTD and GENFI. Each consortium provides clinical data access based on established policies for data use: processes for request are available for review at allftd.org/data for ALLFTD data and by emailing genfi@ucl.ac.uk. Certain data elements from both consortia (for example raw MRI images) may be restricted due to the potential for identifiability in the context of the sensitive nature of the genetic data. The deidentified combined dataset will be available for request through the FTD Prevention Initiative in 2023 (https://www.thefpi.org/). Code availability: Custom R code is available at https://doi.org/10.5281/zenodo.6687486. Copyright © The Author(s). Unlike familial Alzheimer’s disease, we have been unable to accurately predict symptom onset in presymptomatic familial frontotemporal dementia (f-FTD) mutation carriers, which is a major hurdle to designing disease prevention trials. We developed multimodal models for f-FTD disease progression and estimated clinical trial sample sizes in C9orf72, GRN and MAPT mutation carriers. Models included longitudinal clinical and neuropsychological scores, regional brain volumes and plasma neurofilament light chain (NfL) in 796 carriers and 412 noncarrier controls. We found that the temporal ordering of clinical and biomarker progression differed by genotype. In prevention-trial simulations using model-based patient selection, atrophy and NfL were the best endpoints, whereas clinical measures were potential endpoints in early symptomatic trials. f-FTD prevention trials are feasible but will likely require global recruitment efforts. These disease progression models will facilitate the planning of f-FTD clinical trials, including the selection of optimal endpoints and enrollment criteria to maximize power to detect treatment effects. Data collection and dissemination of the data presented in this paper were supported by the ALLFTD Consortium (U19: AG063911, funded by the National Institute on Aging and the National Institute of Neurological Diseases and Stroke) and the former ARTFL and LEFFTDS Consortia (ARTFL: U54 NS092089, funded by the National Institute of Neurological Diseases and Stroke and National Center for Advancing Translational Sciences; LEFFTDS: U01 AG045390, funded by the National Institute on Aging and the National Institute of Neurological Diseases and Stroke). The manuscript was reviewed by the ALLFTD Executive Committee for scientific content. The authors acknowledge the invaluable contributions of the study participants and families as well as the assistance of the support staffs at each of the participating sites. This work is also supported by the Association for Frontotemporal Degeneration (including the FTD Biomarkers Initiative), the Bluefield Project to Cure FTD, Larry L. Hillblom Foundation (2018-A-025-FEL (A.M.S.)), the National Institutes of Health (AG038791 (A.L.B.), AG032306 (H.J.R.), AG016976 (W.K.), AG062677 (Ron C. Peterson), AG019724 (B.L.M.), AG058233 (Suzee E. Lee), AG072122 (Walter Kukull), P30 AG062422 (B.L.M.), K12 HD001459 (N.G.), K23AG061253 (A.M.S.), AG062422 (RCP), K24AG045333 (H.J.R.)) and the Rainwater Charitable Foundation. Samples from the National Centralized Repository for Alzheimer Disease and Related Dementias (NCRAD), which receives government support under a cooperative agreement grant (U24 AG021886 (T.F.)) awarded by the National Institute on Aging (NIA), were used in this study. This work was also supported by Medical Research Council UK GENFI grant MR/M023664/1 (J.D.R.), the Bluefield Project, the National Institute for Health Research including awards to Cambridge and UCL Biomedical Research Centres and a JPND GENFI-PROX grant (2019–02248). Several authors of this publication are members of the European Reference Network for Rare Neurologic Diseases, project 739510. J.D.R. and L.L.R. are also supported by the National Institute for Health and Care Research (NIHR) UCL/H Biomedical Research Centre, the Leonard Wolfson Experimental Neurology Centre Clinical Research Facility and the UK Dementia Research Institute, which receives its funding from UK DRI Ltd, funded by the UK Medical Research Council, Alzheimer’s Society and Alzheimer’s Research UK. J.D.R. is also supported by the Miriam Marks Brain Research UK Senior Fellowship and has received funding from an MRC Clinician Scientist Fellowship (MR/M008525/1) and the NIHR Rare Disease Translational Research Collaboration (BRC149/NS/MH). M.B. is supported by a Fellowship award from the Alzheimer’s Society, UK (AS-JF-19a-004-517). RC and C.G. are supported by a Frontotemporal Dementia Research Studentships in Memory of David Blechner funded through The National Brain Appeal (RCN 290173). J.B.R. is supported by NIHR Cambridge Biomedical Research Centre (BRC-1215-20014; the views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care), the Wellcome Trust (220258), the Cambridge Centre for Parkinson-plus and the Medical Research Council (SUAG/092 G116768); I.L.B. is supported by ANR-PRTS PREV-DemAls, PHRC PREDICT-PGRN, and several authors of this publication are members of the European Reference Network for Rare Neurological Diseases (project 739510). J.L. is funded by the Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy within the framework of the Munich Cluster for Systems Neurology (EXC 2145 SyNergy – ID 390857198). R.S.-V. was funded at the Hospital Clinic de Barcelona by Instituto de Salud Carlos III, Spain (grant code PI20/00448 to RSV) and Fundació Marató TV3, Spain (grant code 20143810 to R.S.-V.). M.M. was, in part, funded by the UK Medical Research Council, the Italian Ministry of Health and the Canadian Institutes of Health Research as part of a Centres of Excellence in Neurodegeneration grant, by Canadian Institutes of Health Research operating grants (MOP- 371851 and PJT-175242) and by funding from the Weston Brain Institute. R.L. is supported by the Canadian Institutes of Health Research and the Chaire de Recherche sur les Aphasies Primaires Progressives Fondation Famille Lemaire. C.G. is supported by the Swedish Frontotemporal Dementia Initiative Schörling Foundation, Swedish Research Council, JPND Prefrontals, 2015–02926,2018–02754, Swedish Alzheimer Foundation, Swedish Brain Foundation, Karolinska Institutet Doctoral Funding, KI Strat-Neuro, Swedish Dementia Foundation, and Stockholm County Council ALF/Region Stockholm. J.L. is supported by Germany’s Excellence Strategy within the framework of the Munich Cluster for Systems Neurology (German Research Foundation, EXC 2145 Synergy 390857198). The Dementia Research Centre is supported by Alzheimer’s Research UK, Alzheimer’s Society, Brain Research UK, and The Wolfson Foundation. This work was supported by the National Institute for Health Research UCL/H Biomedical Research Centre, the Leonard Wolfson Experimental Neurology Centre Clinical Research Facility and the UK Dementia Research Institute, which receives its funding from UK DRI Ltd, funded by the UK Medical Research Council, Alzheimer’s Society, and Alzheimer’s Research UK.
Published: 2022

2. Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals

Author: Winkler, Thomas W., Rasheed, Humaira, Teumer, Alexander, Gorski, Mathias, Rowan, Bryce X., Stanzick, Kira J., Thomas, Laurent F., Tin, Adrienne, Hoppmann, Anselm, Chu, Audrey Y., Tayo, Bamidele, Thio, Chris H. L., Cusi, Daniele, Chai, Jin-Fang, Sieber, Karsten B., Horn, Katrin, Li, Man, Scholz, Markus, Cocca, Massimiliano, Wuttke, Matthias, van der Most, Peter J., Yang, Qiong, Ghasemi, Sahar, Nutile, Teresa, Li, Yong, Pontali, Giulia, Günther, Felix, Dehghan, Abbas, Correa, Adolfo, Parsa, Afshin, Feresin, Agnese, de Vries, Aiko P. J., Zonderman, Alan B., Smith, Albert V., Oldehinkel, Albertine J., De Grandi, Alessandro, Rosenkranz, Alexander R., Franke, Andre, Teren, Andrej, Metspalu, Andres, Hicks, Andrew A., Morris, Andrew P., Tönjes, Anke, Morgan, Anna, Podgornaia, Anna I., Peters, Annette, Körner, Antje, Mahajan, Anubha, Campbell, Archie, Freedman, Barry I., Spedicati, Beatrice, Ponte, Belen, Schöttker, Ben, Brumpton, Ben, Banas, Bernhard, Krämer, Bernhard K., Jung, Bettina, Åsvold, Bjørn Olav, Smith, Blair H., Ning, Boting, Penninx, Brenda W. J. H., Vanderwerff, Brett R., Psaty, Bruce M., Kammerer, Candace M., Langefeld, Carl D., Hayward, Caroline, Spracklen, Cassandra N., Robinson-Cohen, Cassianne, Hartman, Catharina A., Lindgren, Cecilia M., Wang, Chaolong, Sabanayagam, Charumathi, Heng, Chew-Kiat, Lanzani, Chiara, Khor, Chiea-Chuen, Cheng, Ching-Yu, Fuchsberger, Christian, Gieger, Christian, Shaffer, Christian M., Schulz, Christina-Alexandra, Willer, Cristen J., Chasman, Daniel I., Gudbjartsson, Daniel F., Ruggiero, Daniela, Toniolo, Daniela, Czamara, Darina, Porteous, David J., Waterworth, Dawn M., Mascalzoni, Deborah, Mook-Kanamori, Dennis O., Reilly, Dermot F., Daw, E. Warwick, Hofer, Edith, Boerwinkle, Eric, Salvi, Erika, Bottinger, Erwin P., Tai, E-Shyong, Catamo, Eulalia, Rizzi, Federica, Guo, Feng, Rivadeneira, Fernando, Guilianini, Franco, Sveinbjornsson, Gardar, Ehret, Georg, Waeber, Gerard, Biino, Ginevra, Girotto, Giorgia, Pistis, Giorgio, Nadkarni, Girish N., Delgado, Graciela E., Montgomery, Grant W., Snieder, Harold, Campbell, Harry, White, Harvey D., Gao, He, Stringham, Heather M., Schmidt, Helena, Li, Hengtong, Brenner, Hermann, Holm, Hilma, Kirsten, Holger, Kramer, Holly, Rudan, Igor, Nolte, Ilja M., Tzoulaki, Ioanna, Olafsson, Isleifur, Martins, Jade, Cook, James P., Wilson, James F., Halbritter, Jan, Felix, Janine F., Divers, Jasmin, Kooner, Jaspal S., Lee, Jeannette Jen-Mai, O’Connell, Jeffrey, Rotter, Jerome I., Liu, Jianjun, Xu, Jie, Thiery, Joachim, Ärnlöv, Johan, Kuusisto, Johanna, Jakobsdottir, Johanna, Tremblay, Johanne, Chambers, John C., Whitfield, John B., Gaziano, John M., Marten, Jonathan, Coresh, Josef, Jonas, Jost B., Mychaleckyj, Josyf C., Christensen, Kaare, Eckardt, Kai-Uwe, Mohlke, Karen L., Endlich, Karlhans, Dittrich, Katalin, Ryan, Kathleen A., Rice, Kenneth M., Taylor, Kent D., Ho, Kevin, Nikus, Kjell, Matsuda, Koichi, Strauch, Konstantin, Miliku, Kozeta, Hveem, Kristian, Lind, Lars, Wallentin, Lars, Yerges-Armstrong, Laura M., Raffield, Laura M., Phillips, Lawrence S., Launer, Lenore J., Lyytikäinen, Leo-Pekka, Lange, Leslie A., Citterio, Lorena, Klaric, Lucija, Ikram, M. Arfan, Ising, Marcus, Kleber, Marcus E., Francescatto, Margherita, Concas, Maria Pina, Ciullo, Marina, Piratsu, Mario, Orho-Melander, Marju, Laakso, Markku, Loeffler, Markus, Perola, Markus, de Borst, Martin H., Gögele, Martin, Bianca, Martina La, Lukas, Mary Ann, Feitosa, Mary F., Biggs, Mary L., Wojczynski, Mary K., Kavousi, Maryam, Kanai, Masahiro, Akiyama, Masato, Yasuda, Masayuki, Nauck, Matthias, Waldenberger, Melanie, Chee, Miao-Li, Chee, Miao-Ling, Boehnke, Michael, Preuss, Michael H., Stumvoll, Michael, Province, Michael A., Evans, Michele K., O’Donoghue, Michelle L., Kubo, Michiaki, Kähönen, Mika, Kastarinen, Mika, Nalls, Mike A., Kuokkanen, Mikko, Ghanbari, Mohsen, Bochud, Murielle, Josyula, Navya Shilpa, Martin, Nicholas G., Tan, Nicholas Y. Q., Palmer, Nicholette D., Pirastu, Nicola, Schupf, Nicole, Verweij, Niek, Hutri-Kähönen, Nina, Mononen, Nina, Bansal, Nisha, Devuyst, Olivier, Melander, Olle, Raitakari, Olli T., Polasek, Ozren, Manunta, Paolo, Gasparini, Paolo, Mishra, Pashupati P., Sulem, Patrick, Magnusson, Patrik K. E., Elliott, Paul, Ridker, Paul M., Hamet, Pavel, Svensson, Per O., Joshi, Peter K., Kovacs, Peter, Pramstaller, Peter P., Rossing, Peter, Vollenweider, Peter, van der Harst, Pim, Dorajoo, Rajkumar, Sim, Ralene Z. H., Burkhardt, Ralph, Tao, Ran, Noordam, Raymond, Mägi, Reedik, Schmidt, Reinhold, de Mutsert, Renée, Rueedi, Rico, van Dam, Rob M., Carroll, Robert J., Gansevoort, Ron T., Loos, Ruth J. F., Felicita, Sala Cinzia, Sedaghat, Sanaz, Padmanabhan, Sandosh, Freitag-Wolf, Sandra, Pendergrass, Sarah A., Graham, Sarah E., Gordon, Scott D., Hwang, Shih-Jen, Kerr, Shona M., Vaccargiu, Simona, Patil, Snehal B., Hallan, Stein, Bakker, Stephan J. L., Lim, Su-Chi, Lucae, Susanne, Vogelezang, Suzanne, Bergmann, Sven, Corre, Tanguy, Ahluwalia, Tarunveer S., Lehtimäki, Terho, Boutin, Thibaud S., Meitinger, Thomas, Wong, Tien-Yin, Bergler, Tobias, Rabelink, Ton J., Esko, Tõnu, Haller, Toomas, Thorsteinsdottir, Unnur, Völker, Uwe, Foo, Valencia Hui Xian, Salomaa, Veikko, Vitart, Veronique, Giedraitis, Vilmantas, Gudnason, Vilmundur, Jaddoe, Vincent W. V., Huang, Wei, Zhang, Weihua, Wei, Wen Bin, Kiess, Wieland, März, Winfried, Koenig, Wolfgang, Lieb, Wolfgang, Gao, Xin, Sim, Xueling, Wang, Ya Xing, Friedlander, Yechiel, Tham, Yih-Chung, Kamatani, Yoichiro, Okada, Yukinori, Milaneschi, Yuri, Yu, Zhi, Hung, Adriana M., Stark, Klaus J., Stefansson, Kari, Böger, Carsten A., Kronenberg, Florian, Köttgen, Anna, Pattaro, Cristian, Heid, Iris M., Psychiatry, APH - Mental Health, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Digital Health, University of Helsinki, CAMM - Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, Research Programs Unit, Tampere University, Clinical Medicine, TAYS Heart Centre, Department of Clinical Chemistry, Department of Clinical Physiology and Nuclear Medicine, Internal Medicine, Pediatrics, Epidemiology, Radiology & Nuclear Medicine, Erasmus MC other, Home Office, Imperial College Healthcare NHS Trust- BRC Funding, Medical Research Council (MRC), UK DRI Ltd, Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Life Course Epidemiology (LCE), Groningen Institute for Organ Transplantation (GIOT), Groningen Kidney Center (GKC), Cardiovascular Centre (CVC), Winkler, Thomas W, Rasheed, Humaira, Teumer, Alexander, Gorski, Mathia, Rowan, Bryce X, Stanzick, Kira J, Thomas, Laurent F, Tin, Adrienne, Hoppmann, Anselm, Chu, Audrey Y, Tayo, Bamidele, Thio, Chris H L, Cusi, Daniele, Chai, Jin-Fang, Sieber, Karsten B, Horn, Katrin, Li, Man, Scholz, Marku, Cocca, Massimiliano, Wuttke, Matthia, van der Most, Peter J, Yang, Qiong, Ghasemi, Sahar, Nutile, Teresa, Li, Yong, Pontali, Giulia, Günther, Felix, Dehghan, Abba, Correa, Adolfo, Parsa, Afshin, Feresin, Agnese, de Vries, Aiko P J, Zonderman, Alan B, Smith, Albert V, Oldehinkel, Albertine J, De Grandi, Alessandro, Rosenkranz, Alexander R, Franke, Andre, Teren, Andrej, Metspalu, Andre, Hicks, Andrew A, Morris, Andrew P, Tönjes, Anke, Morgan, Anna, Podgornaia, Anna I, Peters, Annette, Körner, Antje, Mahajan, Anubha, Campbell, Archie, Freedman, Barry I, Spedicati, Beatrice, Ponte, Belen, Schöttker, Ben, Brumpton, Ben, Banas, Bernhard, Krämer, Bernhard K, Jung, Bettina, Åsvold, Bjørn Olav, Smith, Blair H, Ning, Boting, Penninx, Brenda W J H, Vanderwerff, Brett R, Psaty, Bruce M, Kammerer, Candace M, Langefeld, Carl D, Hayward, Caroline, Spracklen, Cassandra N, Robinson-Cohen, Cassianne, Hartman, Catharina A, Lindgren, Cecilia M, Wang, Chaolong, Sabanayagam, Charumathi, Heng, Chew-Kiat, Lanzani, Chiara, Khor, Chiea-Chuen, Cheng, Ching-Yu, Fuchsberger, Christian, Gieger, Christian, Shaffer, Christian M, Schulz, Christina-Alexandra, Willer, Cristen J, Chasman, Daniel I, Gudbjartsson, Daniel F, Ruggiero, Daniela, Toniolo, Daniela, Czamara, Darina, Porteous, David J, Waterworth, Dawn M, Mascalzoni, Deborah, Mook-Kanamori, Dennis O, Reilly, Dermot F, Daw, E Warwick, Hofer, Edith, Boerwinkle, Eric, Salvi, Erika, Bottinger, Erwin P, Tai, E-Shyong, Catamo, Eulalia, Rizzi, Federica, Guo, Feng, Rivadeneira, Fernando, Guilianini, Franco, Sveinbjornsson, Gardar, Ehret, Georg, Waeber, Gerard, Biino, Ginevra, Girotto, Giorgia, Pistis, Giorgio, Nadkarni, Girish N, Delgado, Graciela E, Montgomery, Grant W, Snieder, Harold, Campbell, Harry, White, Harvey D, Gao, He, Stringham, Heather M, Schmidt, Helena, Li, Hengtong, Brenner, Hermann, Holm, Hilma, Kirsten, Holgen, Kramer, Holly, Rudan, Igor, Nolte, Ilja M, Tzoulaki, Ioanna, Olafsson, Isleifur, Martins, Jade, Cook, James P, Wilson, James F, Halbritter, Jan, Felix, Janine F, Divers, Jasmin, Kooner, Jaspal S, Lee, Jeannette Jen-Mai, O'Connell, Jeffrey, Rotter, Jerome I, Liu, Jianjun, Xu, Jie, Thiery, Joachim, Ärnlöv, Johan, Kuusisto, Johanna, Jakobsdottir, Johanna, Tremblay, Johanne, Chambers, John C, Whitfield, John B, Gaziano, John M, Marten, Jonathan, Coresh, Josef, Jonas, Jost B, Mychaleckyj, Josyf C, Christensen, Kaare, Eckardt, Kai-Uwe, Mohlke, Karen L, Endlich, Karlhan, Dittrich, Katalin, Ryan, Kathleen A, Rice, Kenneth M, Taylor, Kent D, Ho, Kevin, Nikus, Kjell, Matsuda, Koichi, Strauch, Konstantin, Miliku, Kozeta, Hveem, Kristian, Lind, Lar, Wallentin, Lar, Yerges-Armstrong, Laura M, Raffield, Laura M, Phillips, Lawrence S, Launer, Lenore J, Lyytikäinen, Leo-Pekka, Lange, Leslie A, Citterio, Lorena, Klaric, Lucija, Ikram, M Arfan, Ising, Marcu, Kleber, Marcus E, Francescatto, Margherita, Concas, Maria Pina, Ciullo, Marina, Piratsu, Mario, Orho-Melander, Marju, Laakso, Markku, Loeffler, Marku, Perola, Marku, de Borst, Martin H, Gögele, Martin, Bianca, Martina La, Lukas, Mary Ann, Feitosa, Mary F, Biggs, Mary L, Wojczynski, Mary K, Kavousi, Maryam, Kanai, Masahiro, Akiyama, Masato, Yasuda, Masayuki, Nauck, Matthia, Waldenberger, Melanie, Chee, Miao-Li, Chee, Miao-Ling, Boehnke, Michael, Preuss, Michael H, Stumvoll, Michael, Province, Michael A, Evans, Michele K, O'Donoghue, Michelle L, Kubo, Michiaki, Kähönen, Mika, Kastarinen, Mika, Nalls, Mike A, Kuokkanen, Mikko, Ghanbari, Mohsen, Bochud, Murielle, Josyula, Navya Shilpa, Martin, Nicholas G, Tan, Nicholas Y Q, Palmer, Nicholette D, Pirastu, Nicola, Schupf, Nicole, Verweij, Niek, Hutri-Kähönen, Nina, Mononen, Nina, Bansal, Nisha, Devuyst, Olivier, Melander, Olle, Raitakari, Olli T, Polasek, Ozren, Manunta, Paolo, Gasparini, Paolo, Mishra, Pashupati P, Sulem, Patrick, Magnusson, Patrik K E, Elliott, Paul, Ridker, Paul M, Hamet, Pavel, Svensson, Per O, Joshi, Peter K, Kovacs, Peter, Pramstaller, Peter P, Rossing, Peter, Vollenweider, Peter, van der Harst, Pim, Dorajoo, Rajkumar, Sim, Ralene Z H, Burkhardt, Ralph, Tao, Ran, Noordam, Raymond, Mägi, Reedik, Schmidt, Reinhold, de Mutsert, Renée, Rueedi, Rico, van Dam, Rob M, Carroll, Robert J, Gansevoort, Ron T, Loos, Ruth J F, Felicita, Sala Cinzia, Sedaghat, Sanaz, Padmanabhan, Sandosh, Freitag-Wolf, Sandra, Pendergrass, Sarah A, Graham, Sarah E, Gordon, Scott D, Hwang, Shih-Jen, Kerr, Shona M, Vaccargiu, Simona, Patil, Snehal B, Hallan, Stein, Bakker, Stephan J L, Lim, Su-Chi, Lucae, Susanne, Vogelezang, Suzanne, Bergmann, Sven, Corre, Tanguy, Ahluwalia, Tarunveer S, Lehtimäki, Terho, Boutin, Thibaud S, Meitinger, Thoma, Wong, Tien-Yin, Bergler, Tobia, Rabelink, Ton J, Esko, Tõnu, Haller, Tooma, Thorsteinsdottir, Unnur, Völker, Uwe, Foo, Valencia Hui Xian, Salomaa, Veikko, Vitart, Veronique, Giedraitis, Vilmanta, Gudnason, Vilmundur, Jaddoe, Vincent W V, Huang, Wei, Zhang, Weihua, Wei, Wen Bin, Kiess, Wieland, März, Winfried, Koenig, Wolfgang, Lieb, Wolfgang, Gao, Xin, Sim, Xueling, Wang, Ya Xing, Friedlander, Yechiel, Tham, Yih-Chung, Kamatani, Yoichiro, Okada, Yukinori, Milaneschi, Yuri, Yu, Zhi, Stark, Klaus J, Stefansson, Kari, Böger, Carsten A, Hung, Adriana M, Kronenberg, Florian, Köttgen, Anna, Pattaro, Cristian, Heid, Iris M, and Lee Kong Chian School of Medicine (LKCMedicine)
Subjects: Life Sciences & Biomedicine - Other Topics, EXPRESSION, Diabetic Nephropathies/genetics, 610 Medizin, LOCI, Medicine (miscellaneous), EFFICIENT, Lifelines cohort study, Kidney, General Biochemistry, Genetics and Molecular Biology, DISEASE, QUALITY-CONTROL, SDG 3 - Good Health and Well-being, Diabetic Nephropathy, Diabetes Mellitus, Humans, Medicine [Science], Diabetic Nephropathies, GENOME-WIDE ASSOCIATION, Biology, DiscovEHR/MyCode study, METAANALYSIS, Glomerular Filtration Rate/genetics, Medicinsk genetik, ddc:610, Science & Technology, genetic, effects, kidney, diabetic, JOINT, Klinisk medicin, Diabetes Mellitu, 3126 Surgery, anesthesiology, intensive care, radiology, Multidisciplinary Sciences, ENVIRONMENT INTERACTION, Creatinine, VA Million Veteran Program, Science & Technology - Other Topics, 3111 Biomedicine, Clinical Medicine, SMOKING, General Agricultural and Biological Sciences, Life Sciences & Biomedicine, Medical Genetics, Human, Genome-Wide Association Study, Glomerular Filtration Rate
Abstract: Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (nDM = 178,691, nnoDM = 1,296,113). Our genome-wide searches identified (i) seven eGFR loci with significant DM/noDM-difference, (ii) four additional novel loci with suggestive difference and (iii) 28 further novel loci (including CUBN) by allowing for potential difference. GWAS on eGFR among DM individuals identified 2 known and 27 potentially responsible loci for diabetic kidney disease. Gene prioritization highlighted 18 genes that may inform reno-protective drug development. We highlight the existence of DM-only and noDM-only effects, which can inform about the target group, if respective genes are advanced as drug targets. Largely shared effects suggest that most drug interventions to alter eGFR should be effective in DM and noDM. Published version The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) supported the meta-analysis—Project-ID 387509280—SFB1350 (Subproject C6 to I.M.H.). A.M.H., B.R., and R.T. were supported by VACSR&D MVP grant CX001897. This research is based on data from the Million Veteran Program, Office of Research and Development, Veterans Health Administration, and was supported by VACSR&D MVP grant CX001897 (A.M.H.). This publication does not represent the views of the Department of Veteran Affairs or the United States Government. We conducted this research using the UK Biobank resource under the application number 20272.
Published: 2022

3. Anomia is present pre-symptomatically in frontotemporal dementia due to MAPT mutations

Author: Bouzigues, Arabella, Russell, Lucy L, Tiraboschi, Pietro, Lladó, Albert, Antonell, Anna, Olives, Jaume, Balasa, Mircea, Bargalló, Nuria, Borrego-Ecija, Sergi, Verdelho, Ana, Maruta, Carolina, Ferreira, Catarina B, Miltenberger, Gabriel, Masellis, Mario, do Couto, Frederico Simões, Gabilondo, Alazne, Gorostidi, Ana, Villanua, Jorge, Cañada, Marta, Tainta, Mikel, Zulaica, Miren, Barandiaran, Myriam, Alves, Patricia, Bender, Benjamin, Tartaglia, Maria Carmela, Wilke, Carlo, Graf, Lisa, Vogels, Annick, Vandenbulcke, Mathieu, Van Damme, Philip, Bruffaerts, Rose, Poesen, Koen, Rosa-Neto, Pedro, Gauthier, Serge, Camuzat, Agnès, Finger, Elizabeth, Brice, Alexis, Bertrand, Anne, Funkiewiez, Aurélie, Rinaldi, Daisy, Saracino, Dario, Colliot, Olivier, Sayah, Sabrina, Prix, Catharina, Wlasich, Elisabeth, Wagemann, Olivia, van Swieten, John C, Loosli, Sandra, Schönecker, Sonja, Hoegen, Tobias, Lombardi, Jolina, Anderl-Straub, Sarah, Rollin, Adeline, Kuchcinski, Gregory, Bertoux, Maxime, Lebouvier, Thibaud, Deramecourt, Vincent, Seelaar, Harro, Santiago, Beatriz, Duro, Diana, Leitão, Maria João, Almeida, Maria Rosario, Tábuas-Pereira, Miguel, Afonso, Sónia, Engel, Annerose, Polyakova, Maryna, Jiskoot, Lize, Sorbi, Sandro, Butler, Chris R, Graff, Caroline, Peakman, Georgia, Gerhard, Alexander, Langheinrich, Tobias, Laforce, Robert, Sanchez-Valle, Raquel, de Mendonça, Alexandre, Moreno, Fermin, Synofzik, Matthis, Vandenberghe, Rik, Ducharme, Simon, Le Ber, Isabelle, Bocchetta, Martina, Levin, Johannes, Danek, Adrian, Otto, Markus, Pasquier, Florence, Santana, Isabel, Rohrer, Jonathan D, Genetic FTD Initiative, GENFI, Esteve, Aitana Sogorb, Nelson, Annabel, Greaves, Caroline V, Heller, Carolin, Cash, David, Thomas, David L, Todd, Emily, Benotmane, Hanya, Zetterberg, Henrik, Swift, Imogen J, Nicholas, Jennifer, Samra, Kiran, Convery, Rhian S, Shafei, Rachelle, Timberlake, Carolyn, Cope, Thomas, Rittman, Timothy, Benussi, Alberto, Premi, Enrico, Gasparotti, Roberto, Archetti, Silvana, Gazzina, Stefano, Cantoni, Valentina, Arighi, Andrea, Fenoglio, Chiara, Scarpini, Elio, Fumagalli, Giorgio, Borracci, Vittoria, Rossi, Giacomina, Giaccone, Giorgio, Rowe, James B, Caroppo, Paola, Prioni, Sara, Redaelli, Veronica, Tang-Wai, David, Rogaeva, Ekaterina, Castelo-Branco, Miguel, Keren, Ron, Black, Sandra, Mitchell, Sara, Borroni, Barbara, Shoesmith, Christen, Bartha, Robart, Rademakers, Rosa, Poos, Jackie, Papma, Janne M, Giannini, Lucia, Minkelen, Rick, Pijnenburg, Yolande, Nacmias, Benedetta, Ferrari, Camilla, Galimberti, Daniela, Polito, Cristina, Lombardi, Gemma, Bessi, Valentina, Veldsman, Michele, Andersson, Christin, Thonberg, Hakan, Öijerstedt, Linn, Jelic, Vesna, Thompson, Paul, Bouzigues, Arabella [0000-0002-0267-8590], Russell, Lucy L [0000-0001-5023-5893], Peakman, Georgia [0000-0002-3319-138X], Bocchetta, Martina [0000-0003-1814-5024], Greaves, Caroline V [0000-0002-6446-1960], Convery, Rhian S [0000-0002-9477-1812], Rowe, James B [0000-0001-7216-8679], Finger, Elizabeth [0000-0003-4461-7427], van Swieten, John C [0000-0001-6278-6844], Levin, Johannes [0000-0001-5092-4306], Otto, Markus [0000-0002-6647-5944], Apollo - University of Cambridge Repository, Esteve, Aitana Sogorb (Beitragende*r), Nelson, Annabel (Beitragende*r), Heller, Carolin (Beitragende*r), Cash, David (Beitragende*r), Thomas, David L (Beitragende*r), Benotmane, Hanya (Beitragende*r), Zetterberg, Henrik (Beitragende*r), Swift, Imogen J (Beitragende*r), Nicholas, Jennifer (Beitragende*r), Samra, Kiran (Beitragende*r), Shafei, Rachelle (Beitragende*r), Timberlake, Carolyn (Beitragende*r), Cope, Thomas (Beitragende*r), Rittman, Timothy (Beitragende*r), Benussi, Alberto (Beitragende*r), Premi, Enrico (Beitragende*r), Gasparotti, Roberto (Beitragende*r), Archetti, Silvana (Beitragende*r), Gazzina, Stefano (Beitragende*r), Cantoni, Valentina (Beitragende*r), Arighi, Andrea (Beitragende*r), Fenoglio, Chiara (Beitragende*r), Scarpini, Elio (Beitragende*r), Fumagalli, Giorgio (Beitragende*r), Borracci, Vittoria (Beitragende*r), Rossi, Giacomina (Beitragende*r), Giaccone, Giorgio (Beitragende*r), Caroppo, Paola (Beitragende*r), Prioni, Sara (Beitragende*r), Redaelli, Veronica (Beitragende*r), Tang-Wai, David (Beitragende*r), Rogaeva, Ekaterina (Beitragende*r), Castelo-Branco, Miguel (Beitragende*r), Keren, Ron (Beitragende*r), Black, Sandra (Beitragende*r), Mitchell, Sara (Beitragende*r), Shoesmith, Christen (Beitragende*r), Bartha, Robart (Beitragende*r), Rademakers, Rosa (Beitragende*r), Poos, Jackie (Beitragende*r), Papma, Janne M (Beitragende*r), Giannini, Lucia (Beitragende*r), Minkelen, Rick (Beitragende*r), Pijnenburg, Yolande (Beitragende*r), Nacmias, Benedetta (Beitragende*r), Ferrari, Camilla (Beitragende*r), Polito, Cristina (Beitragende*r), Lombardi, Gemma (Beitragende*r), Bessi, Valentina (Beitragende*r), Veldsman, Michele (Beitragende*r), Andersson, Christin (Beitragende*r), Thonberg, Hakan (Beitragende*r), Öijerstedt, Linn (Beitragende*r), Jelic, Vesna (Beitragende*r), Thompson, Paul (Beitragende*r), Lladó, Albert (Beitragende*r), Antonell, Anna (Beitragende*r), Olives, Jaume (Beitragende*r), Balasa, Mircea (Beitragende*r), Bargalló, Nuria (Beitragende*r), Borrego-Ecija, Sergi (Beitragende*r), Verdelho, Ana (Beitragende*r), Maruta, Carolina (Beitragende*r), Ferreira, Catarina B (Beitragende*r), Miltenberger, Gabriel (Beitragende*r), do Couto, Frederico Simões (Beitragende*r), Gabilondo, Alazne (Beitragende*r), Gorostidi, Ana (Beitragende*r), Villanua, Jorge (Beitragende*r), Cañada, Marta (Beitragende*r), Tainta, Mikel (Beitragende*r), Zulaica, Miren (Beitragende*r), Barandiaran, Myriam (Beitragende*r), Alves, Patricia (Beitragende*r), Bender, Benjamin (Beitragende*r), Wilke, Carlo (Beitragende*r), Graf, Lisa (Beitragende*r), Vogels, Annick (Beitragende*r), Vandenbulcke, Mathieu (Beitragende*r), Van Damme, Philip (Beitragende*r), Bruffaerts, Rose (Beitragende*r), Poesen, Koen (Beitragende*r), Rosa-Neto, Pedro (Beitragende*r), Gauthier, Serge (Beitragende*r), Camuzat, Agnès (Beitragende*r), Brice, Alexis (Beitragende*r), Bertrand, Anne (Beitragende*r), Funkiewiez, Aurélie (Beitragende*r), Rinaldi, Daisy (Beitragende*r), Saracino, Dario (Beitragende*r), Colliot, Olivier (Beitragende*r), Sayah, Sabrina (Beitragende*r), Prix, Catharina (Beitragende*r), Wlasich, Elisabeth (Beitragende*r), Wagemann, Olivia (Beitragende*r), Loosli, Sandra (Beitragende*r), Schönecker, Sonja (Beitragende*r), Hoegen, Tobias (Beitragende*r), Lombardi, Jolina (Beitragende*r), Anderl-Straub, Sarah (Beitragende*r), Rollin, Adeline (Beitragende*r), Kuchcinski, Gregory (Beitragende*r), Bertoux, Maxime (Beitragende*r), Lebouvier, Thibaud (Beitragende*r), Deramecourt, Vincent (Beitragende*r), Santiago, Beatriz (Beitragende*r), Duro, Diana (Beitragende*r), Leitão, Maria João (Beitragende*r), Almeida, Maria Rosario (Beitragende*r), Tábuas-Pereira, Miguel (Beitragende*r), Afonso, Sónia (Beitragende*r), Engel, Annerose (Beitragende*r), Polyakova, Maryna (Beitragende*r), Repositório da Universidade de Lisboa, Genetic FTD Initiative, GENFI, and Neurology
Subjects: Progranulin, Clinical Neurology, Medizin, Anomia, tau Proteins, Naming, IMPAIRMENTS, VARIANTS, diagnostic imaging [Frontotemporal Dementia], genetics [Progranulins], Cognition, Progranulins, Settore BIO/13 - Biologia Applicata, complications [Frontotemporal Dementia], mental disorders, C9orf72, Humans, ddc:610, genetics [C9orf72 Protein], genetics [Frontotemporal Dementia], Biology, Science & Technology, C9orf72 Protein, MORPHOMETRIC ANALYSES, ANATOMY, ALZHEIMERS-DISEASE, genetics [tau Proteins], Neurology, Frontotemporal Dementia, Mutation, PATTERNS, Frontotemporal dementia, Tau, Human medicine, Neurosciences & Neurology, Neurology (clinical), complications [Anomia], Life Sciences & Biomedicine, MRI
Abstract: Funder: Alzheimer’s Research UK; doi: http://dx.doi.org/10.13039/501100002283, Funder: UCLH Biomedical Research Centre; doi: http://dx.doi.org/10.13039/501100012317, Funder: Medical Research Council; doi: http://dx.doi.org/10.13039/501100000265, Funder: Leonard Wolfson Experimental Neurology Centre (LWENC) Clinical Research Facility, Funder: Bluefield Project, INTRODUCTION: A third of frontotemporal dementia (FTD) is caused by an autosomal-dominant genetic mutation in one of three genes: microtubule-associated protein tau (MAPT), chromosome 9 open reading frame 72 (C9orf72) and progranulin (GRN). Prior studies of prodromal FTD have identified impaired executive function and social cognition early in the disease but few have studied naming in detail. METHODS: We investigated performance on the Boston Naming Test (BNT) in the GENetic Frontotemporal dementia Initiative cohort of 499 mutation carriers and 248 mutation-negative controls divided across three genetic groups: C9orf72, MAPT and GRN. Mutation carriers were further divided into 3 groups according to their global CDR plus NACC FTLD score: 0 (asymptomatic), 0.5 (prodromal) and 1 + (fully symptomatic). Groups were compared using a bootstrapped linear regression model, adjusting for age, sex, language and education. Finally, we identified neural correlates of anomia within carriers of each genetic group using a voxel-based morphometry analysis. RESULTS: All symptomatic groups performed worse on the BNT than controls with the MAPT symptomatic group scoring the worst. Furthermore, MAPT asymptomatic and prodromal groups performed significantly worse than controls. Correlates of anomia in MAPT mutation carriers included bilateral anterior temporal lobe regions and the anterior insula. Similar bilateral anterior temporal lobe involvement was seen in C9orf72 mutation carriers as well as more widespread left frontal atrophy. In GRN mutation carriers, neural correlates were limited to the left hemisphere, and involved frontal, temporal, insula and striatal regions. CONCLUSION: This study suggests the development of early anomia in MAPT mutation carriers, likely to be associated with impaired semantic knowledge. Clinical trials focused on the prodromal period within individuals with MAPT mutations should use language tasks, such as the BNT for patient stratification and as outcome measures.
Published: 2022

4. Towards complete and error-free genome assemblies of all vertebrate species

Author: Richard Hall, Tandy Warnow, Tanya M. Lama, Oliver A. Ryder, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Ivo Gut, Paul Flicek, Mark Chaisson, James Torrance, Guojie Zhang, Andrew J. Crawford, Federica Di Palma, Michael Hiller, Jennifer A. Marshall Graves, Sadye Paez, Sarah E. London, Mark Wilkinson, Kateryna D. Makova, Byung June Ko, Jimin George, Farooq O. Al-Ajli, Emma C. Teeling, George F. Turner, Robert H. S. Kraus, Sonja C. Vernes, Zev N. Kronenberg, Michelle Smith, Jonas Korlach, Daryl Eason, Jonathan Wood, Simona Secomandi, Claudio V. Mello, Arkarachai Fungtammasan, Arang Rhie, Tomas Marques-Bonet, Benedict Paten, Ekaterina Osipova, Richard Durbin, M. Thomas P. Gilbert, Beth Shapiro, Ivan Sović, Bruce C. Robertson, Richard E. Green, Eugene W. Myers, Leanne Haggerty, Sergey Koren, Martin Pippel, Bettina Haase, Patrick Masterson, Jay Ghurye, Maria Simbirsky, Samantha R. Friedrich, Chul Hee Lee, Luis R Nassar, Lindsey J. Cantin, Kerstin Howe, Erich D. Jarvis, Marlys L. Houck, Jason T. Howard, Jacquelyn Mountcastle, Mark Mooney, Paolo Franchini, Giulio Formenti, Siddarth Selvaraj, Robel E. Dagnew, Brett T. Hannigan, Brian P. Walenz, Alan Tracey, Heebal Kim, Constantina Theofanopoulou, Nicholas H. Putnam, Karen Clark, Iliana Bista, H. William Detrich, Dengfeng Guan, David Iorns, Andrew Digby, Trevor Pesout, Zemin Ning, Gregory Gedman, Woori Kwak, Maximilian Wagner, Joanna Collins, Harris A. Lewin, Hannes Svardal, Milan Malinsky, Byrappa Venkatesh, Françoise Thibaud-Nissen, Joana Damas, Andreas F. Kautt, Olivier Fedrigo, Christopher Dunn, William Chow, Warren E. Johnson, Yang Zhou, Adam M. Phillippy, Taylor Edwards, Paul Medvedev, Peter V. Lovell, Joyce V. Lee, Sylke Winkler, Stephen J. O'Brien, Wesley C. Warren, Alex Hastie, Marcela Uliano-Silva, Kevin L. Howe, Sarah B. Kingan, Fergal J. Martin, Christopher N. Balakrishnan, David F. Clayton, Ying Sims, Robert W. Murphy, Axel Meyer, Dave W Burt, Shane A. McCarthy, Sarah Pelan, Erik Garrison, Mark Diekhans, Frank Grützner, Gavin J. P. Naylor, Robert S. Harris, Hiram Clawson, Jinna Hoffman, Ann C Misuraca, J. H. Kim, University of St Andrews. School of Biology, University of St Andrews. St Andrews Bioinformatics Unit, Rhie, Arang [0000-0002-9809-8127], Fedrigo, Olivier [0000-0002-6450-7551], Formenti, Giulio [0000-0002-7554-5991], Koren, Sergey [0000-0002-1472-8962], Uliano-Silva, Marcela [0000-0001-6723-4715], Thibaud-Nissen, Francoise [0000-0003-4957-7807], Mountcastle, Jacquelyn [0000-0003-1078-4905], Winkler, Sylke [0000-0002-0915-3316], Vernes, Sonja C. [0000-0003-0305-4584], Grutzner, Frank [0000-0002-3088-7314], Balakrishnan, Christopher N. [0000-0002-0788-0659], Burt, Dave [0000-0002-9991-1028], George, Julia M. [0000-0001-6194-6914], Digby, Andrew [0000-0002-1870-8811], Robertson, Bruce [0000-0002-5348-2731], Edwards, Taylor [0000-0002-7235-6175], Meyer, Axel [0000-0002-0888-8193], Kautt, Andreas F. [0000-0001-7792-0735], Franchini, Paolo [0000-0002-8184-1463], Detrich, H. William, III [0000-0002-0783-4505], Pippel, Martin [0000-0002-8134-5929], Malinsky, Milan [0000-0002-1462-6317], Kingan, Sarah B. [0000-0002-4900-0189], Hall, Richard [0000-0001-6490-8227], Dunn, Christopher [0000-0002-0601-3254], Lee, Joyce [0000-0002-3492-1102], Putnam, Nicholas H. [0000-0002-1315-782X], Gut, Ivo [0000-0001-7219-632X], Tracey, Alan [0000-0002-4805-9058], Guan, Dengfeng [0000-0002-6376-3940], London, Sarah E. [0000-0002-7839-2644], Clayton, David F. [0000-0002-6395-3488], Mello, Claudio V. [0000-0002-9826-8421], Friedrich, Samantha R. [0000-0003-0570-6080], Osipova, Ekaterina [0000-0002-6769-7223], Al-Ajli, Farooq O. [0000-0002-4692-7106], Secomandi, Simona [0000-0001-8597-6034], Kim, Heebal [0000-0003-3064-1303], Theofanopoulou, Constantina [0000-0003-2014-7563], Zhou, Yang [0000-0003-1247-5049], Martin, Fergal [0000-0002-1672-050X], Flicek, Paul [0000-0002-3897-7955], Walenz, Brian P. [0000-0001-8431-1428], Diekhans, Mark [0000-0002-0430-0989], Paten, Benedict [0000-0001-8863-3539], Crawford, Andrew J. [0000-0003-3153-6898], Gilbert, M. Thomas P. [0000-0002-5805-7195], Zhang, Guojie [0000-0001-6860-1521], Venkatesh, Byrappa [0000-0003-3620-0277], Shapiro, Beth [0000-0002-2733-7776], Johnson, Warren E. [0000-0002-5954-186X], Marques-Bonet, Tomas [0000-0002-5597-3075], Teeling, Emma C. [0000-0002-3309-1346], Ryder, Oliver A. [0000-0003-2427-763X], Haussler, David [0000-0003-1533-4575], Korlach, Jonas [0000-0003-3047-4250], Lewin, Harris A. [0000-0002-1043-7287], Howe, Kerstin [0000-0003-2237-513X], Myers, Eugene W. [0000-0002-6580-7839], Durbin, Richard [0000-0002-9130-1006], Phillippy, Adam M. [0000-0003-2983-8934], Jarvis, Erich D. [0000-0001-8931-5049], Apollo - University of Cambridge Repository, National Institutes of Health (US), National Human Genome Research Institute (US), Ministry of Health and Welfare (South Korea), Wellcome Trust, European Molecular Biology Laboratory, Howard Hughes Medical Institute, Rockefeller University, Robert and Rosabel Osborne Endowment, European Commission, National Library of Medicine (US), Korea Institute of Marine Science & Technology, Ministry of Oceans and Fisheries (South Korea), Alfred P. Sloan Foundation, Max Planck Society, Maine Department of Inland Fisheries & Wildlife, National Science Foundation (US), University of Queensland, Science Exchange, Northeastern University (US), Federal Ministry of Education and Research (Germany), EMBO, National Key Research and Development Program (China), Qatar Society of Al-Gannas (Algannas), Katara Cultural Village, Government of Qatar, Monash University Malaysia, Hessen State Ministry of Higher Education, Research and the Arts, Ministry of Science, Research and Art Baden-Württemberg, Agency for Science, Technology and Research A*STAR (Singapore), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Fundación 'la Caixa', Generalitat de Catalunya, Irish Research Council, Danish National Research Foundation, Australian Research Council, Vernes, Sonja C [0000-0003-0305-4584], Balakrishnan, Christopher N [0000-0002-0788-0659], George, Julia M [0000-0001-6194-6914], Kautt, Andreas F [0000-0001-7792-0735], Detrich, H William [0000-0002-0783-4505], Kingan, Sarah B [0000-0002-4900-0189], Putnam, Nicholas H [0000-0002-1315-782X], London, Sarah E [0000-0002-7839-2644], Clayton, David F [0000-0002-6395-3488], Mello, Claudio V [0000-0002-9826-8421], Friedrich, Samantha R [0000-0003-0570-6080], Al-Ajli, Farooq O [0000-0002-4692-7106], Walenz, Brian P [0000-0001-8431-1428], Crawford, Andrew J [0000-0003-3153-6898], Gilbert, M Thomas P [0000-0002-5805-7195], Johnson, Warren E [0000-0002-5954-186X], Teeling, Emma C [0000-0002-3309-1346], Ryder, Oliver A [0000-0003-2427-763X], Lewin, Harris A [0000-0002-1043-7287], Myers, Eugene W [0000-0002-6580-7839], Phillippy, Adam M [0000-0003-2983-8934], and Jarvis, Erich D [0000-0001-8931-5049]
Subjects: QH301 Biology, Genome, 0302 clinical medicine, Genome Size, Vertebrats, Uncategorized, 64, 0303 health sciences, Sex Chromosomes, Multidisciplinary, High-Throughput Nucleotide Sequencing, Genomics, Mitochondrial, Vertebrates, Identification (biology), Engineering sciences. Technology, Sequence Analysis, Neuroinformatics, 45/23, QH426 Genetics, Biology, Article, Evolutionary genetics, 38, Birds, QH301, 03 medical and health sciences, Molecular evolution, ddc:570, Genome assembly algorithms, Animals, 631/181/735, 14. Life underwater, Genomes, QH426, Gene, Gene Library, Genome, Mitochondrial, Haplotypes, Molecular Sequence Annotation, Sequence Alignment, Sequence Analysis, DNA, 030304 developmental biology, 45/91, 631/61/212/2302, 45, Human evolutionary genetics, Haplotype, DAS, DNA, Research data, 706/648/697, 631/181/2474, Evolutionary biology, Genètica, 030217 neurology & neurosurgery, Reference genome
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences., We thank them for their permission to publish. A.R., S.K., B.P.W. and A.M.P. were supported by the Intramural Research Program of the NHGRI, NIH (1ZIAHG200398). A.R. was also supported by the Korea Health Technology R&D Project through KHIDI, funded by the Ministry of Health & Welfare, Republic of Korea (HI17C2098). S.A.M., I.B. and R.D. were supported by Wellcome Trust grant WT207492; W.C., M. Smith, Z.N., Y.S., J.C., S. Pelan, J.T., A.T., J.W. and Kerstin Howe by WT206194; L.H., F.M., Kevin Howe and P. Flicek by WT108749/Z/15/Z, WT218328/B/19/Z and the European Molecular Biology Laboratory. O.F. and E.D.J. were supported by Howard Hughes Medical Institute and Rockefeller University start-up funds for this project. J.D. and H.A.L. were supported by the Robert and Rosabel Osborne Endowment. M.U.-S. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (750747). F.T.-N., J. Hoffman, P. Masterson and K.C. were supported by the Intramural Research Program of the NLM, NIH. C.L., B.J.K., J. Kim and H.K. were supported by the Marine Biotechnology Program of KIMST, funded by the Ministry of Ocean and Fisheries, Republic of Korea (20180430). M.C. was supported by Sloan Research Fellowship (FG-2020-12932). S.C.V. was funded by a Max Planck Research Group award from the Max Planck Society, and a Human Frontiers Science Program (HFSP) Research grant (RGP0058/2016). T.M.L., W.E.J. and the Canada lynx genome were funded by the Maine Department of Inland Fisheries & Wildlife (F11AF01099), including when W.E.J. held a National Research Council Research Associateship Award at the Walter Reed Army Institute of Research (WRAIR). C.B. was supported by the NSF (1457541 and 1456612). D.B. was funded by The University of Queensland (HFSP - RGP0030/2015). D.I. was supported by Science Exchange Inc. (Palo Alto, CA). H.W.D. was supported by NSF grants (OPP-0132032 ICEFISH 2004 Cruise, PLR-1444167 and OPP-1955368) and the Marine Science Center at Northeastern University (416). G.J.P.N. and the thorny skate genome were funded by Lenfest Ocean Program (30884). M.P. was funded by the German Federal Ministry of Education and Research (01IS18026C). M. Malinsky was supported by an EMBO fellowship (ALTF 456-2016). The following authors’ contributions were supported by the NIH: S. Selvaraj (R44HG008118); C.V.M., S.R.F., P.V.L. (R21 DC014432/DC/NIDCD); K.D.M. (R01GM130691); H.C. (5U41HG002371-19); M.D. (U41HG007234); and B.P. (R01HG010485). D.G. was supported by the National Key Research and Development Program of China (2017YFC1201201, 2018YFC0910504 and 2017YFC0907503). F.O.A. was supported by Al-Gannas Qatari Society and The Cultural Village Foundation-Katara, Doha, State of Qatar and Monash University Malaysia. C.T. was supported by The Rockefeller University. M. Hiller was supported by the LOEWE-Centre for Translational Biodiversity Genomics (TBG) funded by the Hessen State Ministry of Higher Education, Research and the Arts (HMWK). H.C. was supported by the NHGRI (5U41HG002371-19). R.H.S.K. was funded by the Max Planck Society with computational resources at the bwUniCluster and BinAC funded by the Ministry of Science, Research and the Arts Baden-Württemberg and the Universities of the State of Baden-Württemberg, Germany (bwHPC-C5). B.V. was supported by the Biomedical Research Council of A*STAR, Singapore. T.M.-B. was funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (864203), MINECO/FEDER, UE (BFU2017-86471-P), Unidad de Excelencia María de Maeztu, AEI (CEX2018-000792-M), a Howard Hughes International Early Career award, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). E.C.T. was supported by the European Research Council (ERC-2012-StG311000) and an Irish Research Council Laureate Award. M.T.P.G. was supported by an ERC Consolidator Award 681396-Extinction Genomics, and a Danish National Research Foundation Center Grant (DNRF143). T.W. was supported by the NSF (1458652). J. M. Graves was supported by the Australian Research Council (CEO561477). E.W.M. was partially supported by the German Federal Ministry of Education and Research (01IS18026C). Complementary sequencing support for the Anna’s hummingbird and several genomes was provided by Pacific Biosciences, Bionano Genomics, Dovetail Genomics, Arima Genomics, Phase Genomics, 10X Genomics, NRGene, Oxford Nanopore Technologies, Illumina, and DNAnexus. All other sequencing and assembly were conducted at the Rockefeller University, Sanger Institute, and Max Planck Institute Dresden genome labs. Part of this work used the computational resources of the NIH HPC Biowulf cluster (https://hpc.nih.gov). We acknowledge funding from the Wellcome Trust (108749/Z/15/Z) and the European Molecular Biology Laboratory., With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2018-000792-M).
Published: 2021

5. Evaluation of the effect of the use of anti-insect nets on vegetable production in southern Benin

Author: F. Assogba-Komlan, Serge Simon, M. Ngouajio, P. Adegbola, Thibaud Martin, and C. Ahouangninou
Subjects: Toxicology, Hellula undalis, biology, fungi, Plutella, Production (economics), Transplanting, PEST analysis, Pesticide, Helicoverpa armigera, General Agricultural and Biological Sciences, biology.organism_classification, Interview guide
Abstract: The objective of this research is to assess the effects of the use of insect nets in vegetable production. To achieve this goal, data were collected in four departments of southern Benin (Mono, Couffo, Oueme and Plateau) using an interview guide and a structured questionnaire. A total of 223 producers chosen at random from these areas where the CRSP Horticulture Project is located were surveyed. The results of the study show that growers using insect nets have not given up using chemical pesticides. However, a significant reduction in treatment frequencies was recorded in the nursery and after transplanting for most of the pesticides identified. Similarly, a significant reduction (more than 60.0%) in pest attacks (Helicoverpa armigera, Hellula undalis, Plutella xylostella, Bemisia tabaci and cochineals) was recorded among producers using anti-insect nets at 5%. These results involve that it is necessary to sensitize farmers to the use of nets to protect plants. This will significantly reduce pest attacks and reduce the use of pesticides in production. Key words: Anti-insect nets, effects, pests, market gardening, Benin.
Published: 2021

6. Differential impairment of cerebrospinal fluid synaptic biomarkers in the genetic forms of frontotemporal dementia

Author: Sogorb-Esteve, Aitana, Nilsson, Johanna, Borroni, Barbara, Balasa, Mircea, Bargalló, Nuria, Borrego-Ecija, Sergi, de Mendonça, Alexandre, Verdelho, Ana, Maruta, Carolina, Ferreira, Catarina B, Miltenberger, Gabriel, do Couto, Frederico Simões, Gabilondo, Alazne, Galimberti, Daniela, Gorostidi, Ana, Villanua, Jorge, Cañada, Marta, Tainta, Mikel, Zulaica, Miren, Barandiaran, Myriam, Alves, Patricia, Bender, Benjamin, Wilke, Carlo, Graf, Lisa, Sanchez-Valle, Raquel, Vogels, Annick, Vandenbulcke, Mathieu, Van Damme, Philip, Bruffaerts, Rose, Poesen, Koen, Rosa-Neto, Pedro, Gauthier, Serge, Camuzat, Agnès, Brice, Alexis, Bertrand, Anne, Laforce, Robert, Funkiewiez, Aurélie, Rinaldi, Daisy, Saracino, Dario, Colliot, Olivier, Sayah, Sabrina, Prix, Catharina, Wlasich, Elisabeth, Wagemann, Olivia, Loosli, Sandra, Schönecker, Sonja, Moreno, Fermin, Hoegen, Tobias, Lombardi, Jolina, Anderl-Straub, Sarah, Rollin, Adeline, Kuchcinski, Gregory, Bertoux, Maxime, Lebouvier, Thibaud, Deramecourt, Vincent, Santiago, Beatriz, Duro, Diana, Synofzik, Matthis, Leitão, Maria João, Almeida, Maria Rosario, Tábuas-Pereira, Miguel, Afonso, Sónia, Graff, Caroline, Masellis, Mario, Tartaglia, Maria Carmela, Rowe, James B, Swift, Imogen J, Vandenberghe, Rik, Finger, Elizabeth, Tagliavini, Fabrizio, Santana, Isabel, Butler, Chris R, Ducharme, Simon, Gerhard, Alexander, Danek, Adrian, Levin, Johannes, Otto, Markus, Heller, Carolin, Sorbi, Sandro, Le Ber, Isabelle, Pasquier, Florence, Gobom, Johan, Brinkmalm, Ann, Blennow, Kaj, Zetterberg, Henrik, Rohrer, Jonathan D, Initiative, GENetic FTD, Nelson, Annabel, Bocchetta, Martina, Bouzigues, Arabella, Greaves, Caroline V, Cash, David, Thomas, David L, Todd, Emily, Benotmane, Hanya, Nicholas, Jennifer, Samra, Kiran, Shafei, Rachelle, Timberlake, Carolyn, Russell, Lucy L, Cope, Thomas, Rittman, Timothy, Benussi, Alberto, Premi, Enrico, Gasparotti, Roberto, Archetti, Silvana, Gazzina, Stefano, Cantoni, Valentina, Arighi, Andrea, Fenoglio, Chiara, Peakman, Georgia, Scarpini, Elio, Fumagalli, Giorgio, Borracci, Vittoria, Rossi, Giacomina, Giaccone, Giorgio, Di Fede, Giuseppe, Caroppo, Paola, Tiraboschi, Pietro, Prioni, Sara, Redaelli, Veronica, Convery, Rhian S, Tang-Wai, David, Rogaeva, Ekaterina, Castelo-Branco, Miguel, Freedman, Morris, Keren, Ron, Black, Sandra, Mitchell, Sara, Shoesmith, Christen, Bartha, Robart, Rademakers, Rosa, van Swieten, John C, Poos, Jackie, Papma, Janne M, Giannini, Lucia, van Minkelen, Rick, Pijnenburg, Yolande, Nacmias, Benedetta, Ferrari, Camilla, Polito, Cristina, Lombardi, Gemma, Bessi, Valentina, Seelaar, Harro, Veldsman, Michele, Andersson, Christin, Thonberg, Hakan, Öijerstedt, Linn, Jelic, Vesna, Thompson, Paul, Langheinrich, Tobias, Lladó, Albert, Antonell, Anna, Olives, Jaume, Neurology, Amsterdam Neuroscience - Neurodegeneration, Clinical Genetics, GENetic FTD Initiative, Poesen, Koen, Van Damme, Philip, Bruffaerts, rose, Vandenbulcke, Mathieu, Vogels, ann, Bocchetta, Martina [0000-0003-1814-5024], and Apollo - University of Cambridge Repository
Subjects: Synaptic dysfunction, Cognitive Neuroscience, cerebrospinal fluid [gamma-Synuclein], Medizin, cerebrospinal fluid [Syntaxin 1], Syntaxin 1, genetics [Mutation], tau Proteins, cerebrospinal fluid [Frontotemporal Dementia], frontotemporal dementia, beta-Synuclein, gamma-Synuclein, Settore BIO/13 - Biologia Applicata, Humans, ddc:610, genetics [C9orf72 Protein], genetics [Frontotemporal Dementia], Biology, genetics [beta-Synuclein], genetics [Syntaxin 1], C9orf72 Protein, synaptic dysfunction, cerebrospinal fluid [C9orf72 Protein], Research, Biomarkers, Frontotemporal dementia, Mutation, Neurogranin, Frontotemporal Dementia, biomarkers, genetics [Neurogranin], genetics [tau Proteins], Neurology, cerebrospinal fluid [Biomarkers], genetics [gamma-Synuclein], Neurology (clinical), Human medicine, cerebrospinal fluid [Neurogranin]
Abstract: Background Approximately a third of frontotemporal dementia (FTD) is genetic with mutations in three genes accounting for most of the inheritance: C9orf72, GRN, and MAPT. Impaired synaptic health is a common mechanism in all three genetic variants, so developing fluid biomarkers of this process could be useful as a readout of cellular dysfunction within therapeutic trials. Methods A total of 193 cerebrospinal fluid (CSF) samples from the GENetic FTD Initiative including 77 presymptomatic (31 C9orf72, 23 GRN, 23 MAPT) and 55 symptomatic (26 C9orf72, 17 GRN, 12 MAPT) mutation carriers as well as 61 mutation-negative controls were measured using a microflow LC PRM-MS set-up targeting 15 synaptic proteins: AP-2 complex subunit beta, complexin-2, beta-synuclein, gamma-synuclein, 14–3-3 proteins (eta, epsilon, zeta/delta), neurogranin, Rab GDP dissociation inhibitor alpha (Rab GDI alpha), syntaxin-1B, syntaxin-7, phosphatidylethanolamine-binding protein 1 (PEBP-1), neuronal pentraxin receptor (NPTXR), neuronal pentraxin 1 (NPTX1), and neuronal pentraxin 2 (NPTX2). Mutation carrier groups were compared to each other and to controls using a bootstrapped linear regression model, adjusting for age and sex. Results CSF levels of eight proteins were increased only in symptomatic MAPT mutation carriers (compared with controls) and not in symptomatic C9orf72 or GRN mutation carriers: beta-synuclein, gamma-synuclein, 14–3-3-eta, neurogranin, Rab GDI alpha, syntaxin-1B, syntaxin-7, and PEBP-1, with three other proteins increased in MAPT mutation carriers compared with the other genetic groups (AP-2 complex subunit beta, complexin-2, and 14–3-3 zeta/delta). In contrast, CSF NPTX1 and NPTX2 levels were affected in all three genetic groups (decreased compared with controls), with NPTXR concentrations being affected in C9orf72 and GRN mutation carriers only (decreased compared with controls). No changes were seen in the CSF levels of these proteins in presymptomatic mutation carriers. Concentrations of the neuronal pentraxins were correlated with brain volumes in the presymptomatic period for the C9orf72 and GRN groups, suggesting that they become abnormal in proximity to symptom onset. Conclusions Differential synaptic impairment is seen in the genetic forms of FTD, with abnormalities in multiple measures in those with MAPT mutations, but only changes in neuronal pentraxins within the GRN and C9orf72 mutation groups. Such markers may be useful in future trials as measures of synaptic dysfunction, but further work is needed to understand how these markers change throughout the course of the disease.
Published: 2022

7. Reducing the Genetic Redundancy of Arabidopsis PHOSPHATE TRANSPORTER1 Transporters to Study Phosphate Uptake and Signaling

Author: Ayadi, Amal, David, Pascale, Arrighi, Jean-François, Chiarenza, Serge, Thibaud, Marie-Christine, Nussaume, Laurent, and Marin, Elena
Published: 2015

8. Integrated pest management of Tuta absoluta: practical implementations across different world regions

Author: Thierry Brévault, Ramzi Mansour, Fernando Cantor, Mateus R. Campos, Marc Kenis, Abid Ali, Lucia Zappalà, Hossein Madadi, Michele Ricupero, Yunus Bayram, Nicolas Desneux, Gerben J. Messelink, César Ramos, Fedai Erler, Samira A. Mohamed, Peng Han, Thibaud Martin, Raul Narciso C. Guedes, Antonio Biondi, Meritxell Pérez-Hedo, Khasan Ismoilov, Alberto Urbaneja, Khaled Abbes, Judit Arnó, Hao-tian Liu, Raf De Vis, M. Jamal Hajjar, María Gabriela Luna, Emmanouil Roditakis, Khalid Haddi, Robert S. Nofemela, Yi-Bo Zhang, François Verheggen, Fang-Hao Wan, Kouassi Arthur J. Konan, Coline C. Jaworski, Anne-Violette Lavoir, Anaïs Chailleux, P. R. Shashank, Abiola Oke, Andrew G. S. Cuthbertson, D. M. Firake, Ahmed Mazih, Su Wang, Ming-hui Wang, Javad Karimi, Producció Vegetal, and Protecció Vegetal Sostenible
Subjects: H01 - Protection des végétaux - Considérations générales, Integrated pest management, GTB Gewasgez. Bodem en Water, Pheromone, Biological pest control, Gestion intégrée des ravageurs, F06 Irrigation, Botanical insecticides, Pheromones, Méthode de lutte, U40 Surveying methods, H20 Plant diseases, F04 Fertilizing, Resistant cultivars, Lutte antiravageur, Parasitoids, biology, Agroforestry, Entomopathogenic nematodes, food and beverages, PE&RC, Tuta absoluta, Mass trapping, Essential oils, Biological control, Soil fertilization, Lutte biologique contre les ravageurs, Irrigation, Microbial pesticides, Invasive alien species, Plant resistance, Crop health, Traps, business.industry, Pest control, P01 Nature conservation and land resources, F07 Soil cultivation, biology.organism_classification, Gelechiidae, H10 - Ravageurs des plantes, Agronomic control-related research, Predatory mirid bugs, Entomopathogenic fungi, Agriculture, Gewasgezondheid, Chemical control, IPM, PEST analysis, business, Agronomy and Crop Science
Abstract: The South American tomato pinworm, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), has invaded most Afro-Eurasian countries and is threatening worldwide tomato production. Various strategies have been developed and implemented to manage this pest. Here, we present a timely review on the up-to-date development and practical implementation of integrated pest management (IPM) programs for tomato crops across different world regions infested by T. absoluta. While insecticide resistance is a growing concern, biological control via releasing or conserving arthropod natural enemies and sex pheromone-based biotechnical control are the most successful management practices. Agronomic control-related research is an emerging area where the soil fertilization and/or irrigation, as well as breeding of resistant cultivars, has the potential to enhance IPM effectiveness. Grower survey responses in the native areas (i.e., South America), early-invaded areas (i.e., first report between 2006 and 2012) and newly invaded areas (i.e., first report after 2012) showed that the control programs evolved along with the areas and time since invasion. Growers in the early-invaded areas shifted more rapidly from chemical control to biological control compared to those from the native area. In all concerned regions, the pest control failure risk following chemical insecticide applications and the high cost associated with either biological or biotechnical control methods have been the greatest concerns for growers. The information gathered from the native and/or early-invaded areas may help achieve a more effective management in newly invaded areas. Lastly, researchers are expected to break the bottlenecks of some key issues that would enable lowering application cost of novel biorational alternative management options.
Published: 2021

9. Significance of Stenotrophomonas maltophilia When Detected in Sputum of Ambulatory Patients with COPD

Author: Krystelle Godbout, Thibaud Soumagne, Florence Levesque, Yves Lacasse, François Maltais, and Julie Milot
Subjects: medicine.medical_specialty, Exacerbation, Stenotrophomonas maltophilia, medicine.medical_treatment, International Journal of Chronic Obstructive Pulmonary Disease, Sputum culture, Pulmonary Disease, Chronic Obstructive, Risk Factors, Internal medicine, polycyclic compounds, medicine, Humans, Original Research, pulmonary disease, Retrospective Studies, Mechanical ventilation, COPD, chronic obstructive, medicine.diagnostic_test, biology, business.industry, Hazard ratio, Sputum, General Medicine, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, biology.organism_classification, medicine.disease, Anti-Bacterial Agents, respiratory tract diseases, Ambulatory, bacteria, prognosis, medicine.symptom, Gram-Negative Bacterial Infections, business
Abstract: Thibaud Soumagne, Florence Levesque, Julie Milot, Krystelle Godbout, Yves Lacasse, FranÃ§ois Maltais Service de pneumologie, Institut Universitaire de Cardiologie et de Pneumologie de QuÃ©bec, UniversitÃ© Laval, QuÃ©bec, QC, CanadaCorrespondence: Thibaud SoumagneService de pneumologie, Institut Universitaire de Cardiologie et de Pneumologie de QuÃ©bec, UniversitÃ© Laval, QuÃ©bec, QC, CanadaEmail thibaud_soumagne@live.frIntroduction: Stenotrophomonas maltophilia is an emerging Gram-negative MDR bacteria. In patients with chronic obstructive pulmonary disease (COPD), it is mostly found in those with severe exacerbation of COPD requiring mechanical ventilation. The significance of S. maltophilia when detected in the sputum of ambulatory patients with COPD is uncertain.Objective: To access the prevalence and the risk factors of the presence of S. maltophilia in the sputum of ambulatory patients with COPD and to determine whether it was associated with prognosis.Methods: All consecutive unselected ambulatory patients with GOLD 2â 4 COPD were recruited between January 2017 and September 2019 from the COPD clinic of a tertiary care hospital. Presence of S. maltophilia was defined by a positive sputum culture for S. maltophilia. Demographics, COPD characteristics, comorbidities and known predisposing risk factors associated with S. maltophilia were collected from medical records.Results: S. maltophilia was detected in the sputum of 41/393 (10%) of study participants. Comorbidities, exacerbation, use of oral steroids and carbapenems in the previous year were risk factors for the presence of S. maltophilia. After adjusting on confounding factors associated with mortality including age, Charlson comorbidity index and FEV1, S. maltophilia was significantly associated with mortality (adjusted hazard ratio 2.3; 95% CI 1.1â 4.9).Conclusion: In the current study, we found that 10% of ambulatory patients with GOLD 2â 4 COPD had S. maltophilia detected in their sputum. In addition, S. maltophilia may represent a marker of overall morbidity in patients with COPD.Keywords: Stenotrophomonas maltophilia, pulmonary disease, chronic obstructive, risk factors, prognosis
Published: 2021

10. History of extracardiac/cardiac events in cardiac amyloidosis: prevalence and time from initial onset to diagnosis

Author: Etienne Audureau, Coraline Chalard, Elsa Poullot, Emilie Bequignon, Anissa Moktefi, Emmanuel Itti, Soulef Guendouz, Mounira Kharoubi, Silvia Oghina, Vincent Audard, Arnault Galat, Jean-Pascal Lefaucheur, Mukedaisi Abulizi, François Lemonnier, Luc Hittinger, Valérie Molinier-Frenkel, Fabien Le Bras, Mélanie Bézard, Thibaud Damy, Pascale Fanen, Jean-François Deux, Amira Zaroui, Benoît Funalot, Emmanuel Teiger, and Diane Bodez
Subjects: Male, medicine.medical_specialty, Delayed Diagnosis, Cardiac amyloidosis, Transthyretin, Internal medicine, medicine, Prevalence, Diseases of the circulatory (Cardiovascular) system, Humans, Immunoglobulin Light-chain Amyloidosis, Survival rate, Integumentary, Retrospective Studies, biology, business.industry, Amyloidosis, Retrospective cohort study, Original Articles, medicine.disease, AL, RC666-701, Heart failure, Cohort, Symptoms, Cardiology, biology.protein, Original Article, Cardiology and Cardiovascular Medicine, business, Body mass index
Abstract: Aims Cardiac amyloidosis (CA) has a poor prognosis which is aggravated by diagnostic delay. Amyloidosis extracardiac and cardiac events (AECE and ACE) may help improve CA diagnosis and typing. The aim of this study was to compare AECE and ACE between different CA types and assess their relationship with survival. Methods and results This retrospective cohort study conducted in France from June 2008 to May 2019, at the Henry Mondor Hospital. This cohort included 983 patients with CA. Mean age at inclusion was 73.1 ± 11.4 years, 726 (75.1%) were male and the mean body mass index was 24.5 ± 4.1 kg/m2. Among them, 321 had immunoglobulin light chain (AL) amyloidosis, 434 had wild‐type transthyretin (ATTRwt), and 212 had hereditary transthyretin (ATTRv). The first AECE and/or ACE occurred at a mean age of 63 ± 11 years for AL and ATTRv, and 70 ± 12 years for ATTRwt (P
Published: 2021

11. Outcomes in patients with acute myocardial infarction and history of illicit drug use: a French nationwide analysis

Author: Nicolas Clementy, Laurent Fauchier, Thibaud Genet, Fabrice Ivanes, Julien Herbert, Denis Angoulvant, Arnaud Bisson, Iris Ma, Carl Semaan, and Jérémie Bouteau
Subjects: Male, medicine.medical_specialty, Myocardial Infarction, Critical Care and Intensive Care Medicine, Risk Factors, Internal medicine, medicine, Humans, Illicit drug, Longitudinal Studies, Myocardial infarction, Risk factor, Stroke, biology, Illicit Drugs, business.industry, Incidence (epidemiology), General Medicine, medicine.disease, biology.organism_classification, Hospitalization, Heart failure, Propensity score matching, Cannabis, Cardiology and Cardiovascular Medicine, business
Abstract: Aims Several reports suggest that illicit drug use may be a major cause of acute myocardial infarction (AMI) independently of smoking habits and associated with a poorer prognosis. The aim of our study was to evaluate the impact of illicit drug use on (i) the risk of AMI and (ii) its prognosis. Methods and results This French longitudinal cohort study was based on the administrative hospital-discharge database from the entire population. First, we collected data for all patients admitted in hospital in 2013 with at least 5 years of follow-up to identify potential predictors of AMI. In a second phase, we collected data for all patients admitted with AMI from January 2010 to December 2018. We identified patients with a history of illicit drug use (cannabis, cocaine, or opioid). These patients were matched with patients without illicit drug use to assess their prognosis. In 2013, 3 381 472 patients were hospitalized with a mean follow-up of 4.7 ± 1.8 years. In multivariable analysis, among all drugs under evaluation, only cannabis use was significantly associated with a higher risk of AMI [HR 1.32 (95% CI 1.09–1.59), P = 0.004]. Between January 2010 and December 2018, we then identified 738 899 AMI patients. Among these patients, 3827 (0.5%) had a known history of illicit drug use. These patients were younger, most often male and had less comorbidities. After 1:1 propensity score matching, during a mean follow-up of 1.9 ± 2.3 years, there was no significant difference between patients without illicit drug use and patients with illicit drug use regarding all-cause death, cardiovascular death, stroke, or heart failure. Conclusion In a large and systematic nationwide analysis, cannabis use was an independent risk factor for the incidence of AMI. However, the prognosis of illicit drug users presenting with AMI was similar to patients without illicit drug use.
Published: 2021

12. Clinical Failure and Emergence of Resistance during Third Generation Cephalosporin Therapy for Enterobacter spp. Infection: Is the Risk Overestimated? A Prospective Multicentric Study

Author: Solen Kernéis, Etienne Canouï, Jean-Ralph Zahar, Etienne Carbonnelle, Benoit Pilmis, A. Mizrahi, Sophie Alviset, Alexandre Bleibtreu, Thibaud Delerue, Matthieu Lafaurie, Pauline Caraux-Paz, and Anna Belkacem
Subjects: medicine.medical_specialty, biology, business.industry, medicine.drug_class, Cefepime, Cephalosporin, Antibiotics, third generation cephalosporin, Enterobacter, biology.organism_classification, Third generation, Internal medicine, Bloodstream infection, cefepime, Medicine, Observational study, AmpC producing Enterobacteriaceae, Clinical failure, business, piperacilline/tazobactam, medicine.drug
Abstract: Background: Clinical and microbiological guidelines recommend treating infections caused by Enterobacter spp. with cefepime or carbapenems. The main objective of this study was to assess the risk of clinical failure with third generation cephalosporin (3GC) therapy compared to other β-lactams for infections caused by Enterobacter spp. Our secondary objective was to evaluate the risk of emergence of resistance during therapy. Methods: We conducted a prospective observational study in seven French hospitals over an 18-month period including all patients with a pulmonary and/or bloodstream infection due to Enterobacter spp. susceptible to 3GC. Results: Seventy-four patients were included in our study. Among them, 26 (35%) received a 3GC as a first-line treatment, and clinical improvements were observed for 13/21 (62%) of them. Four (5%) cases of emergence of 3GC resistance were observed during therapy including one in the 3GC group. 3GC therapy can be safely used as first-line therapy especially for non-severe patients suffering from pulmonary or bloodstream infections due to Enterobacter spp. Conclusions: Emergence of 3GC resistance remains a rare event, and there is a lack of evidence of the benefit of last-line antibiotics therapies.
Published: 2021

13. Analytical comparison of ELISA and mass spectrometry for quantification of serum hepcidin in critically ill patients

Author: Constance Delaby, Jérôme Vialaret, Christophe Hirtz, Thibaud Lefebvre, Matthias Herkert, Hervé Puy, Sigismond Lasocki, Sylvain Lehmann, Pierre Asfar, Alain Mercat, Thomas Gaillard, Soizic Gergaud, Cyrille Sargentini, Claire Geneve, Philippe Montravers, Thibault Lefebvre, Herve Puy, Grégoire Mercier, Nicolas Nagot, Gerald Chanques, Samir Jaber, Karim Asehnoune, Antoine Roquilly, Claire Dahyot-Fizelier, Olivier Mimoz, Sonia Isslame, Philippe Seguin, Mathilde Barbaz, Martine Ferrandiere, Thomas Kerforne, Katell Peoc'h, François Beloncle, Maxime Leger, Emmanuel Rineau, Gregory Marin, Matthieu Boisson, Yoann Launey, Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)
Subjects: 030213 general clinical medicine, medicine.medical_specialty, Anemia, Critical Illness, [SDV]Life Sciences [q-bio], Clinical Biochemistry, Enzyme-Linked Immunosorbent Assay, Mass spectrometry, Gastroenterology, Mass Spectrometry, Analytical Chemistry, 03 medical and health sciences, 0302 clinical medicine, Hepcidins, Hepcidin, Internal medicine, Humans, Protein Isoforms, Medicine, General Pharmacology, Toxicology and Pharmaceutics, Anemia, Iron-Deficiency, biology, business.industry, Critically ill, 030208 emergency & critical care medicine, General Medicine, medicine.disease, 3. Good health, Medical Laboratory Technology, Iron-deficiency anemia, biology.protein, Reagent Kits, Diagnostic, business
Abstract: International audience; Aim: To compare methods of quantifying serum hepcidin (based on MS and ELISA) and their ability to diagnose true iron deficiency anemia in critically ill patients. Materials & methods: Serum hepcidin was measured in 119 critically ill patients included in the HEPCIDANE clinical trial, using either an ultra-sensitive ELISA kit (from DRG) or two different MS methods. Results: The results show a good correlation between the different methods studied. The Bland–Altman analysis and the Kappa test for clinical groups show a good or very good agreement between the different tests. Conclusion: ELISA or MS show a satisfactory commutability to quantify serum hepcidin. This is of great importance for the determination of therapeutic strategies in iron deficiency.
Published: 2021

14. HMGB1 promotes CXCL12‐dependent egress of murine B cells from Peyer's patches in homeostasis

Author: Jérôme Widmer, Marco Bianchi, Christian Hotz, Noémie Boss, Lorenzo Spagnuolo, Viola Puddinu, Carole Bourquin, Thibaud Spinetti, Anne Oberson, Inès Mottas, Mariagrazia Uguccioni, Spagnuolo, L., Puddinu, V., Boss, N., Spinetti, T., Oberson, A., Widmer, J., Mottas, I., Hotz, C., Bianchi, M. E., Uguccioni, M., and Bourquin, C.
Subjects: 0301 basic medicine, Chemokine, Lymphocyte, Immunology, Adaptive immunity, Peyer's patches, chemical and pharmacologic phenomena, Biology, HMGB1, B-cell migration, 03 medical and health sciences, Mice, 0302 clinical medicine, In vivo, medicine, Extracellular, Immunology and Allergy, Animals, Homeostasis, Basic, HMGB1 Protein, Immunity, Mucosal, Research Articles, B‐cell migration, B-Lymphocytes, Gut immune regulation, biological factors, Chemokine CXCL12, Cell biology, Mice, Inbred C57BL, Chemotaxis, Leukocyte, 030104 developmental biology, Lymphatic system, High-mobility group, medicine.anatomical_structure, embryonic structures, biology.protein, Research Article|Basic, biological phenomena, cell phenomena, and immunity, IgA, 030215 immunology
Abstract: High mobility group box‐1 protein (HMGB1) is an alarmin that, once released, promotes inflammatory responses, alone and as a complex with the chemokine CXCL12. Here, we report that the HMGB1–CXCL12 complex plays an essential role also in homeostasis by controlling the migration of B lymphocytes. We show that extracellular HMGB1 is critical for the CXCL12‐dependent egress of B cells from the Peyer's patches (PP). This promigratory function of the complex was restricted to the PPs, since HMGB1 was not required for B‐cell migratory processes in other locations. Accordingly, we detected higher constitutive levels of the HMGB1–CXCL12 complex in PPs than in other lymphoid organs. HMGB1–CXCL12 in vivo inhibition was associated with a reduced basal IgA production in the gut. Collectively, our results demonstrate a role for the HMGB1–CXCL12 complex in orchestrating B‐cell trafficking in homeostasis, and provide a novel target to control lymphocyte migration in mucosal immunity., Through a set of in vitro and in vivo experiments in mice, we show that HMGB1, in complex with the chemokine CXCL12, controls homeostatic B‐cell egress from Peyer's patches, and that inhibition of the HMGB1‐CXCL12 complex by glycyrrhizin decreases intestinal IgA production. These observations uncover an important role in homeostasis for extracellular HMGB1, to date considered only as a pro‐inflammatory molecule.
Published: 2021

15. A high-quality bonobo genome refines the analysis of hominid evolution

Author: Melanie Sorensen, Yafei Mao, Sofie R. Salama, Claudia Rita Catacchio, Andy Wing Chun Pang, Françoise Thibaud-Nissen, Carl Baker, LaDeana W. Hillier, Ruiyang Li, Arvis Sulovari, Philip C. Dishuck, PingHsun Hsieh, Katherine M. Munson, Ludovica Mercuri, Jason D Fernandes, Jessica M. Storer, Joyce V. Lee, Benedict Paten, Mark A. Batzer, Peter A. Audano, David Porubsky, Tzu-Hsueh Huang, Jason G. Underwood, Evan E. Eichler, Jinna Hoffman, William T. Harvey, Kendra Hoekzema, Jerilyn A. Walker, Ian T. Fiddes, David Gordon, Marina Haukness, Alex Hastie, Alexandra P. Lewis, Francesca Antonacci, Mario Ventura, Shwetha C. Murali, Francesco Montinaro, Ilaria Piccolo, and Mark Diekhans
Subjects: Pan troglodytes, Sequence assembly, Genomics, Biology, Genome informatics, Genome, Article, Evolutionary genetics, Coalescent theory, Evolution, Molecular, 03 medical and health sciences, Segmental Duplications, Genomic, 0302 clinical medicine, Animals, Sequencing, Phylogeny, 030304 developmental biology, Segmental duplication, 0303 health sciences, Gorilla gorilla, Multidisciplinary, Bonobo, Pongo, Molecular Sequence Annotation, Sequence Analysis, DNA, Pan paniscus, biology.organism_classification, Genome evolution, Genes, Evolutionary biology, Eukaryotic Initiation Factor-4A, Female, Human genome, Mobile genetic elements, 030217 neurology & neurosurgery
Abstract: The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3–5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome., A high-quality bonobo genome assembly provides insights into incomplete lineage sorting in hominids and its relevance to gene evolution and the genetic relationship among living hominids.
Published: 2021

16. ATTR amyloidosis during the COVID-19 pandemic: insights from a global medical roundtable

Author: Michaela Auer-Grumbach, Esther Gonzalez, Brian M. Drachman, Chiara Briani, Andrew M. Rosen, Morie A. Gertz, Angela Dispenzieri, Frederick L. Ruberg, Márcia Waddington-Cruz, Julian D. Gillmore, David R. Hurwitz, Thomas H. Brannagan, Hanna K. Gaggin, Hartmut Schmidt, Luis F. Quintana, Kemi Olugemo, Thibaud Damy, Teresa Coelho, John L. Berk, Vera Bril, Jacqueline Shehata, Mazen Hanna, Nowell M. Fine, Carol J. Whelan, Jose Nativi-Nicolau, Sami Khella, and Mathew S. Maurer
Subjects: Amyloid, medicine.medical_specialty, Exacerbation, Population, ATTR, 030204 cardiovascular system & hematology, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Prealbumin, Pharmacology (medical), Position Statement, Intensive care medicine, education, Pandemics, Genetics (clinical), Amyloid Neuropathies, Familial, education.field_of_study, biology, business.industry, SARS-CoV-2, Amyloidosis, Organ dysfunction, COVID-19, General Medicine, medicine.disease, Rare disease, Transthyretin, biology.protein, Medicine, medicine.symptom, business, Polyneuropathy, 030217 neurology & neurosurgery
Abstract: BackgroundThe global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causing the ongoing coronavirus disease 2019 (COVID-19) pandemic has raised serious concern for patients with chronic disease. A correlation has been identified between the severity of COVID-19 and a patient’s preexisting comorbidities. Although COVID-19 primarily involves the respiratory system, dysfunction in multiple organ systems is common, particularly in the cardiovascular, gastrointestinal, immune, renal, and nervous systems. Patients with amyloid transthyretin (ATTR) amyloidosis represent a population particularly vulnerable to COVID-19 morbidity due to the multisystem nature of ATTR amyloidosis.Main bodyATTR amyloidosis is a clinically heterogeneous progressive disease, resulting from the accumulation of amyloid fibrils in various organs and tissues. Amyloid deposition causes multisystem clinical manifestations, including cardiomyopathy and polyneuropathy, along with gastrointestinal symptoms and renal dysfunction. Given the potential for exacerbation of organ dysfunction, physicians note possible unique challenges in the management of patients with ATTR amyloidosis who develop multiorgan complications from COVID-19. While the interplay between COVID-19 and ATTR amyloidosis is still being evaluated, physicians should consider that the heightened susceptibility of patients with ATTR amyloidosis to multiorgan complications might increase their risk for poor outcomes with COVID-19.ConclusionPatients with ATTR amyloidosis are suspected to have a higher risk of morbidity and mortality due to age and underlying ATTR amyloidosis-related organ dysfunction. While further research is needed to characterize this risk and management implications, ATTR amyloidosis patients might require specialized management if they develop COVID-19. The risks of delaying diagnosis or interrupting treatment for patients with ATTR amyloidosis should be balanced with the risk of exposure in the health care setting. Both physicians and patients must adapt to a new construct for care during and possibly after the pandemic to ensure optimal health for patients with ATTR amyloidosis, minimizing treatment interruptions.
Published: 2021

17. Sensorial Impact and Distribution of 3-Methyl-2,4-nonanedione in Cognacs and Spirits

Author: Alexandre Pons, Jean-Charles Mathurin, Louise Urruty, Ana L. Peterson, Philippe Darriet, Fannie Thibaud, Unité de Recherche Oenologie [Villenave d'Ornon], Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and E. Rémy Martin & Co
Subjects: 0106 biological sciences, oxidation, Distribution (economics), Wine, Diacetyl, spirit, 01 natural sciences, 4-nonanedione, Chemical marker, Alkanes, 3-methyl-2, Food science, Aroma, biology, Chemistry, business.industry, Alcoholic Beverages, Cognac, aging, 010401 analytical chemistry, food and beverages, General Chemistry, biology.organism_classification, 0104 chemical sciences, aroma, Odorants, [SDE]Environmental Sciences, distillation with lees, General Agricultural and Biological Sciences, business, 010606 plant biology & botany
Abstract: International audience; The aim of this study was to improve our knowledge on the chemical markers of Cognac aromas. We report results concerning the distribution and sensorial impact of 3-methyl-2,4-nonanedione (MND), a well-known compound in aged red wine, reminiscent of anise or "dried fruit", according to its concentration. We assayed first this diketone (solid-phase microextraction (SPME)-gas chromatography (GC)/mass spectrometry (MS), chemical ionization (CI)) in many Cognac samples followed by grappa, brandy, rum, whisky, vodka, and fruit spirits, and concentrations ranged from traces to 11.2 mu g/L. Highest concentrations were obtained in grappa and freshly distilled eaux-de-vie of Cognac samples. Exceeding its detection threshold (100 ng/L, 70 vol %), MND contributes to the anise descriptor of these spirits. Its concentration decreased over aging while being highly correlated with the total amount of fatty acid ethyl ester. In addition, we showed that MND was produced during distillation according to the oxidation state of the white wine as well as the amount of lees used.
Published: 2021

18. C-reactive protein is a predictive factor for complications after incisional hernia repair using a biological mesh

Author: Sylvaine Durand Fontanier, Muriel Mathonnet, Abdelkader Taibi, Niki Christou, Thibaud Rivaille, Denis Valleix, Sophiane Derbal, Fabien Fredon, Anne Fabre, Stephane Bouvier, and Julien Janet
Subjects: Adult, Male, medicine.medical_specialty, Incisional hernia, Science, 030230 surgery, Surgical planning, Article, law.invention, 03 medical and health sciences, Leukocyte Count, 0302 clinical medicine, Postoperative Complications, law, White blood cell, medicine, Humans, Signs and symptoms, Herniorrhaphy, Aged, Aged, 80 and over, Multidisciplinary, biology, business.industry, C-reactive protein, Incisional hernia repair, Retrospective cohort study, Middle Aged, Surgical Mesh, medicine.disease, Intensive care unit, Surgery, Predictive factor, medicine.anatomical_structure, C-Reactive Protein, 030220 oncology & carcinogenesis, biology.protein, Medicine, Female, business, Biomarkers
Abstract: The introduction of biological or absorbable synthetic meshes has provided an alternative to conventional repair for incisional hernia. The ability to predict the development of complications after hernia surgery is important, as it guides surgical planning and patient management. This retrospective study assessed whether the postoperative C-reactive protein (CRP) level can predict complications after incisional hernia repair using biological mesh reinforcement. Patients who underwent incisional hernia repair surgery using biological meshes between February 2009 and February 2015 were screened for study inclusion. Patients included in the study were divided into two groups: those with and without postoperative complications. The two groups were analysed based on sex, surgical operation, length of intensive care unit stay (ICU), complications and mortality. Laboratory values, including white blood cell (WBC) count and CRP levels, were determined preoperatively and up to postoperative day (POD) 10. Postoperative complications requiring further management occurred in 32 of the 60 patients (53.3%). Among 47 patients, the mean CRP and WBC levels were 6.6 mg/L and 9.073 G/L in the group without complications vs. 141.0 mg/L, 16.704 G/L in the group with complications (p 100 mg/L vs. 46% in the group with CRP 100 mg/L) up to POD10 may serve as a predictor of postoperative complications in patients undergoing incisional hernia using biological meshes.
Published: 2021

19. Impact of Tafamidis on Health-Related Quality of Life in Patients With Transthyretin Amyloid Cardiomyopathy (from the Tafamidis in Transthyretin Cardiomyopathy Clinical Trial)

Author: Michelle Stewart, Jeffrey H. Schwartz, Balarama Gundapaneni, Mathew S. Maurer, Martha Grogan, Mazen Hanna, Terrell A. Patterson, Marla B. Sultan, and Thibaud Damy
Subjects: Male, Tafamidis, medicine.medical_specialty, Visual analogue scale, Cardiomyopathy, 030204 cardiovascular system & hematology, Placebo, law.invention, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Cost of Illness, Randomized controlled trial, law, Internal medicine, Activities of Daily Living, Humans, Medicine, Patient Reported Outcome Measures, Aged, Aged, 80 and over, Amyloid Neuropathies, Familial, Benzoxazoles, biology, business.industry, Social Participation, medicine.disease, Self Efficacy, Clinical trial, Transthyretin, chemistry, Quality of Life, Cardiology, biology.protein, Female, Cardiomyopathies, Cardiology and Cardiovascular Medicine, business, Amyloid cardiomyopathy, 030217 neurology & neurosurgery
Abstract: In the Tafamidis in Transthyretin Cardiomyopathy Clinical Trial, tafamidis significantly reduced all-cause mortality and cardiovascular-related hospitalizations in patients with transthyretin amyloid cardiomyopathy (ATTR-CM). ATTR-CM is associated with a significant burden of disease; further analysis of patient-reported quality of life will provide additional data on the efficacy of tafamidis. In the Tafamidis in Transthyretin Cardiomyopathy Clinical Trial, 441 adult patients with ATTR-CM were randomized (2:1:2) to tafamidis 80 mg, tafamidis 20 mg, or placebo for 30 months, with pooled tafamidis (80 mg and 20 mg) compared with placebo. Change in Kansas City Cardiomyopathy Questionnaire Overall Summary (KCCQ-OS) domain scores, EQ-5D-3L scores, and patient global assessment, were prespecified exploratory end points. A greater proportion of patients improved KCCQ-OS score at month 30 with tafamidis (41.8%) versus placebo (21.4%). Tafamidis significantly reduced the decline in all 4 KCCQ-OS domains (p
Published: 2021

20. Efficacy of Tafamidis in Patients With Hereditary and Wild-Type Transthyretin Amyloid Cardiomyopathy

Author: Terrell A. Patterson, Balarama Gundapaneni, Eric J. Velazquez, Perry M. Elliott, Mathew S. Maurer, Thibaud Damy, Marla B. Sultan, Claudio Rapezzi, Kurt Boman, John L. Berk, Jose Nativi-Nicolau, and Jeffrey H. Schwartz
Subjects: Tafamidis, medicine.medical_specialty, biology, business.industry, Amyloidosis, Hazard ratio, Cardiomyopathy, 030204 cardiovascular system & hematology, medicine.disease, Placebo, Gastroenterology, 03 medical and health sciences, Transthyretin, chemistry.chemical_compound, 0302 clinical medicine, chemistry, Heart failure, Internal medicine, medicine, biology.protein, 030212 general & internal medicine, Cardiology and Cardiovascular Medicine, business, Amyloid cardiomyopathy
Abstract: Objectives Tafamidis is an effective treatment for transthyretin amyloid cardiomyopathy (ATTR-CM), this study aimed to determine whether there is a differential effect between variant transthyretin amyloidosis (ATTRv) and wild-type transthyretin (ATTRwt). Background ATTR-CM is a progressive, fatal disorder resulting from mutations in the ATTRv or the deposition of denatured ATTRwt. Methods In pre-specified analyses from ATTR-ACT (Tafamidis in Transthyretin Cardiomyopathy Clinical Trial), baseline characteristics, all-cause mortality, and change from baseline to month 30 in 6-min walk test distance and Kansas City Cardiomyopathy Questionnaire Overall Summary score were compared in patients with ATTRwt and ATTRv. Results There were 335 patients with ATTRwt (201 tafamidis, 134 placebo) and 106 with ATTRv (63 tafamidis, 43 placebo) enrolled in ATTR-ACT. Patients with ATTRwt (vs. ATTRv) had less advanced disease at baseline and a lower rate of disease progression over the study. The reduction in all-cause mortality with tafamidis compared with placebo was not different between ATTRwt (hazard ratio: 0.706 [95% confidence interval (CI): 0.474 to 1.052]; p = 0.0875) and ATTRv (hazard ratio: 0.690 [95% CI: 0.408 to 1.167]; p = 0.1667). Tafamidis was associated with a similar reduction (vs. placebo) in the decline in 6-min walk test distance in ATTRwt (mean ± SE difference from placebo, 77.14 ± 10.78; p Conclusions Pre-specified analyses from ATTR-ACT confirm the poor prognosis of untreated ATTRv-related cardiomyopathy compared with ATTRwt, but show the reduction in mortality and functional decline with tafamidis treatment is similar in both disease subtypes. (Safety and Efficacy of Tafamidis in Patients With Transthyretin Cardiomyopathy [ATTR-ACT]; NCT01994889 )
Published: 2021

21. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

Author: Farideh Chitsaz, Narmada Thanki, A Scott Durkin, Azat Badretdin, Jiyao Wang, Wenjun Li, Marc Gwadz, James S. Song, George Coulouris, Françoise Thibaud-Nissen, Kathleen R O’Neill, Michael DiCuccio, Aron Marchler-Bauer, Christopher J. Lanczycki, Noreen R. Gonzales, Mingzhang Yang, Chanjuan Zheng, Vyacheslav Chetvernin, Daniel H. Haft, Myra K. Derbyshire, and Roxanne A. Yamashita
Subjects: Internet, Protein family, Computational Biology, Proteins, Molecular Sequence Annotation, Enzyme Commission number, Genomics, Genome project, Computational biology, Biology, Genome, Entrez, User-Computer Interface, Annotation, Genome, Archaeal, Databases, Genetic, Genetics, RefSeq, Database Issue, Data Mining, Data Curation, Genome, Bacterial, Reference genome
Abstract: The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP) since 2018 have resulted in a substantial reduction in spurious annotation. The hierarchical collection of protein family models (PFMs) used by PGAP as evidence for structural and functional annotation was expanded to over 35 000 protein profile hidden Markov models (HMMs), 12 300 BlastRules and 36 000 curated CDD architectures. As a result, >122 million or 79% of RefSeq proteins are now named based on a match to a curated PFM. Gene symbols, Enzyme Commission numbers or supporting publication attributes are available on over 40% of the PFMs and are inherited by the proteins and features they name, facilitating multi-genome analyses and connections to the literature. In adherence with the principles of FAIR (findable, accessible, interoperable, reusable), the PFMs are available in the Protein Family Models Entrez database to any user. Finally, the reference and representative genome set, a taxonomically diverse subset of RefSeq prokaryotic genomes, is now recalculated regularly and available for download and homology searches with BLAST. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/.
Published: 2020

22. Changes of Contamination Rate and Microorganism Evaluation in Organ-Cultured Human Corneas: A 14-Year Review From a French Regional Eye Bank

Author: Garcin Thibaud, Laura Fabre, Marc Puyraveau, Fabienne Pouthier, Anne Sophie Gauthier, Bernard Delbosc, Audrey Jeanvoine, and Joëlle Pizzuto
Subjects: Adult, Male, Bacilli, Veterinary medicine, Adolescent, medicine.drug_class, Microorganism, Antibiotics, Eye Banks, Organ culture, medicine.disease_cause, Eye Infections, Bacterial, Cornea, Corneal Transplantation, 03 medical and health sciences, Organ Culture Techniques, 0302 clinical medicine, medicine, Humans, Aged, Retrospective Studies, Aged, 80 and over, Bacteria, biology, Pseudomonas, Organ Preservation, Middle Aged, Contamination, biology.organism_classification, Tissue Donors, Culture Media, Ophthalmology, 030221 ophthalmology & optometry, Female, France, Staphylococcus, 030217 neurology & neurosurgery
Abstract: PURPOSE This study aimed to assess how the contamination rate of organ-cultured corneas has evolved and to analyze the evolution of microorganisms involved. METHODS Data from the Besancon eye bank were reviewed over 14 years (2005-2018). The changes in the contamination rate and the contaminant species found during the organ culture storage were analyzed. Microbiological tests were performed twice on the storage media-at day 5 and before the deswelling phase. RESULTS Among the 17,979 donor corneas collected, 1240 corneas were microbiological-test positive. The average annual contamination rate was 6.8% (range: 5.2%-8.9%). Seventy-five percent of contaminations were bacterial. The most frequently found bacterium was Staphylococcus spp. (31.3%), followed by non-Enterobacteriaceae Gram-negative Bacilli (GNB) (27.3%), with most Sphingomonas spp. and Pseudomonas spp. Fungal contamination (21.9%) was dominated by Candida (82.7%). Seventy-seven types of microorganisms were identified. The Staphylococcus rate tended to decrease, whereas non-Enterobacteriaceae GNB rate has increased in the past few years to reach 46% of bacteria. Most of the contaminations were detected in the early phase of organ culture at day 5 (89.2%). The second microbiological test found 44.8% of fungal contaminations (predominantly Candida spp.). CONCLUSIONS The annual contamination rate was stable and remains low, but the types of contaminating microorganisms varied from year to year. Staphylococcus spp. and non-Enterobacteriaceae GNB accounted for a significant proportion of the contaminations. We found a significant proportion of contamination, especially fungal, at the late phase of storage. Reassessing the antibiotics and antifungals in the storage medium may be useful to limit corneal disposal.
Published: 2020

23. Natural history and impact of treatment with tafamidis on major cardiovascular outcome‐free survival time in a cohort of patients with transthyretin amyloidosis

Author: Jean-François Deux, Khalil El Karoui, Silvia Oghina, Amira Zaroui, Benoît Funalot, Jean-Pascal Lefaucheur, Arnault Galat, Emmanuel Teiger, Soulef Guendouz, Anissa Moktefi, Mounira Kharoubi, Vincent Audard, Pascale Fanen, Elsa Poullot, Violaine Planté-Bordeneuve, Thibaud Damy, Mélanie Bézard, Mukedaisi Abulizi, Emmanuel Itti, Thierry Gendre, and Florence Canoui-Poitrine
Subjects: Tafamidis, medicine.medical_specialty, Population, Cardiomyopathy, 030204 cardiovascular system & hematology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Internal medicine, medicine, Humans, education, Heart Failure, Amyloid Neuropathies, Familial, Benzoxazoles, education.field_of_study, biology, business.industry, Amyloidosis, Hazard ratio, medicine.disease, Transthyretin, chemistry, Cardiac amyloidosis, Heart failure, biology.protein, France, Cardiology and Cardiovascular Medicine, business
Abstract: AIMS Hereditary (ATTRv) and wild-type (ATTRwt) transthyretin amyloidosis are severe and fatal systemic diseases, characterised by amyloid fibrillar accumulation principally in the heart or peripheral nerves (or both). Since 2012, tafamidis has been used in France to treat patients with ATTRv with neuropathy (alone or combined with cardiomyopathy). Recently, the Phase III ATTR-ACT trial showed that tafamidis decreased the relative risk of mortality in ATTR amyloidosis with cardiomyopathy. The aims of this study were to assess the clinical characteristics of ATTR amyloidosis in a real-life population in comparison to the population included in the ATTR-ACT trial and to assess the impact of tafamidis treatment on major cardiovascular outcome (MCO)-free survival time without cardiac decompensation, heart transplant, or death. METHODS AND RESULTS From June 2008 to November 2018, 648 patients with ATTR amyloidosis (423 ATTRwt and 225 ATTRv) consecutively referred to the French Referral Center for cardiac amyloidosis were included. A total of 467 (72%) patients matched the inclusion criteria of the ATTR-ACT trial. For the 631 patients with cardiomyopathy, tafamidis treatment was associated with a longer median MCO-free survival time (n = 98): 1565 (1010-2400) days vs. 771 (686-895) days without treatment (log-rank P
Published: 2020

24. Variants associated with HHIP expression have sex-differential effects on lung function

Author: Carl A. Melbourne, Caroline Hayward, Stefan Karrasch, Dirk Keidel, Katherine A. Fawcett, Susan M. Ring, Yohan Bossé, Carol A. Wang, Ben Michael Brumpton, Claudia Langenberg, Peter K. Joshi, Ke Hao, Igor Rudan, David J. Porteous, Don D. Sin, Raquel Granell, Blair H. Smith, Jian'an Luan, Kristian Hveem, Sarah E. Harris, Sandosh Padmanabhan, Archie Campbell, Sebastian May-Wilson, Veronique Vitart, Nicola Pirastu, Arnulf Langhammer, Craig E. Pennell, John M. Starr, Stefan Weiss, Karina Patasova, Nicholas J. Wareham, James F. Wilson, Deborah Jarvis, Tim D. Spector, Nick Shrine, David P. Strachan, Martin D. Tobin, Beate Stubbe, David M. Evans, Kirsi H. Pietiläinen, Mangino Massimo, Ian P. Hall, Graham L. Hall, Jaakko Kaprio, Ralf Ewert, Rachel E. Foong, Claudia Flexeder, Louise V. Wain, Ma'en Obeidat, Cristen J. Willer, Leo-Pekka Lyytikäinen, Olli T. Raitakari, John Henderson, Konstantin Strauch, Marta R Moksnes, Cosetta Minelli, Nicole Probst-Hensch, Pirro G. Hysi, Anna L. Guyatt, Henry Völzke, Thomas Meitinger, Peter D. Sly, Ozren Polasek, Anne Richmond, Mika Kähönen, Maarten van den Berge, Medea Imboden, Thibaud Boutin, Lucija Klaric, Laura Portas, Terho Lehtimäki, Ian J. Deary, Taina Rantanen, Catherine John, Teemu Palviainen, Fawcett, Katherine A [0000-0002-6675-2112], Obeidat, Ma'en [0000-0002-5443-2752], Shrine, Nick [0000-0003-3641-4371], Weiss, Stefan [0000-0002-3553-4315], May-Wilson, Sebastian [0000-0003-2668-5717], Boutin, Thibaud S [0000-0003-4754-1675], Portas, Laura [0000-0003-1789-1893], Harris, Sarah E [0000-0002-4941-5106], Lyytikäinen, Leo-Pekka [0000-0002-7200-5455], Palviainen, Teemu [0000-0002-7847-8384], Keidel, Dirk [0000-0003-4706-5728], Minelli, Cosetta [0000-0001-9166-3958], Langenberg, Claudia [0000-0002-5017-7344], Bossé, Yohan [0000-0002-3067-3711], Van den Berge, Maarten [0000-0002-9336-7340], Sin, Don D [0000-0002-0756-6643], Campbell, Archie [0000-0003-0198-5078], Porteous, David [0000-0003-1249-6106], Padmanabhan, Sandosh [0000-0003-3869-5808], Smith, Blair H [0000-0002-5362-9430], Ring, Sue [0000-0003-3103-9330], Rantanen, Taina [0000-0002-1604-1945], Pennell, Craig E [0000-0002-0937-6165], Kaprio, Jaakko [0000-0002-3716-2455], Vitart, Veronique [0000-0002-4991-3797], Hayward, Caroline [0000-0002-9405-9550], Hall, Ian P [0000-0001-9933-3216], Wain, Louise V [0000-0003-4951-1867], Apollo - University of Cambridge Repository, Groningen Research Institute for Asthma and COPD (GRIAC), Technology Centre, University of Helsinki, Institute for Molecular Medicine Finland, Genetic Epidemiology, HUS Abdominal Center, Department of Medicine, Clinicum, CAMM - Research Program for Clinical and Molecular Metabolism, Department of Public Health, Research Programs Unit, Tampere University, Clinical Medicine, Department of Clinical Chemistry, TAYS Heart Centre, and Department of Clinical Physiology and Nuclear Medicine
Subjects: 0301 basic medicine, Spirometry, medicine.medical_specialty, HHIP, Medicine (miscellaneous), Expression, Genome-wide Interaction Study, Hhip, Lung Function, Sex, Single-nucleotide polymorphism, Biology, 3121 Internal medicine, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Genome-wide interaction study, Lung function, Internal medicine, expression, medicine, sex, Allele, Enhancer, Gene, Lung, genome-wide interaction study, medicine.diagnostic_test, 1184 Genetics, developmental biology, physiology, lung function, ALSPAC, Differential effects, 030104 developmental biology, Endocrinology, medicine.anatomical_structure, 030228 respiratory system, 3121 General medicine, internal medicine and other clinical medicine, 3111 Biomedicine
Abstract: Background: Lung function is highly heritable and differs between the sexes throughout life. However, little is known about sex-differential genetic effects on lung function. We aimed to conduct the first genome-wide genotype-by-sex interaction study on lung function to identify genetic effects that differ between males and females. Methods: We tested for interactions between 7,745,864 variants and sex on spirometry-based measures of lung function in UK Biobank (N=303,612), and sought replication in 75,696 independent individuals from the SpiroMeta consortium. Results: Five independent single-nucleotide polymorphisms (SNPs) showed genome-wide significant (P-8) interactions with sex on lung function, and 21 showed suggestive interactions (P-6). The strongest signal, from rs7697189 (chr4:145436894) on forced expiratory volume in 1 second (FEV1) (P=3.15x10-15), was replicated (P=0.016) in SpiroMeta. The C allele increased FEV1 more in males (untransformed FEV1 β=0.028 [SE 0.0022] litres) than females (β=0.009 [SE 0.0014] litres), and this effect was not accounted for by differential effects on height, smoking or pubertal age. rs7697189 resides upstream of the hedgehog-interacting protein (HHIP) gene and was previously associated with lung function and HHIP lung expression. We found HHIP expression was significantly different between the sexes (P=6.90x10-6), but we could not detect sex differential effects of rs7697189 on expression. Conclusions: We identified a novel genotype-by-sex interaction at a putative enhancer region upstream of the HHIP gene. Establishing the mechanism by which HHIP SNPs have different effects on lung function in males and females will be important for our understanding of lung health and diseases in both sexes.
Published: 2021

25. Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia

Author: Swarup, Vivek, Hinz, Flora I., Rexach, Jessica E., Noguchi, Ken-ichi, Toyoshiba, Hiroyoshi, Oda, Akira, Hirai, Keisuke, Sarkar, Arjun, Seyfried, Nicholas T., Cheng, Chialin, Haggarty, Stephen J., Ferrari, Raffaele, Rohrer, Jonathan D., Ramasamy, Adaikalavan, Hardy, John, Hernandez, Dena G., Nalls, Michael A., Singleton, Andrew B., Kwok, John B. J., Dobson-Stone, Carol, Brooks, William S., Schofield, Peter R., Halliday, Glenda M., Hodges, John R., Piguet, Olivier, Bartley, Lauren, Thompson, Elizabeth, Haan, Eric, Hernández, Isabel, Ruiz, Agustín, Boada, Mercè, Borroni, Barbara, Padovani, Alessandro, Cairns, Nigel J., Cruchaga, Carlos, Binetti, Giuliano, Ghidoni, Roberta, Benussi, Luisa, Forloni, Gianluigi, Albani, Diego, Galimberti, Daniela, Fenoglio, Chiara, Serpente, Maria, Scarpini, Elio, Clarimón, Jordi, Lleó, Alberto, Blesa, Rafael, Waldö, Maria Landqvist, Nilsson, Karin, Nilsson, Christer, Mackenzie, Ian R. A., Hsiung, Ging-Yuek R., Mann, David M. A., Grafman, Jordan, Morris, Christopher M., Attems, Johannes, Griffiths, Timothy D., McKeith, Ian G., Thomas, Alan J., Jaros, Evelyn, Pietrini, Pietro, Huey, Edward D., Wassermann, Eric M., Tierney, Michael C., Baborie, Atik, Pastor, Pau, Ortega-Cubero, Sara, Razquin, Cristina, Alonso, Elena, Perneczky, Robert, Diehl-Schmid, Janine, Alexopoulos, Panagiotis, Kurz, Alexander, Rainero, Innocenzo, Rubino, Elisa, Pinessi, Lorenzo, Rogaeva, Ekaterina, George-Hyslop, Peter St., Rossi, Giacomina, Tagliavini, Fabrizio, Giaccone, Giorgio, Rowe, James B., Schlachetzki, Johannes C. M., Uphill, James, Collinge, John, Mead, Simon, Danek, Adrian, Van Deerlin, Vivianna M., Grossman, Murray, Trojanowski, John Q., Pickering-Brown, Stuart, Momeni, Parastoo, van der Zee, Julie, Cruts, Marc, Van Broeckhoven, Christine, Cappa, Stefano F., Leber, Isabelle, Brice, Alexis, Hannequin, Didier, Golfier, Véronique, Vercelletto, Martine, Nacmias, Benedetta, Sorbi, Sandro, Bagnoli, Silvia, Piaceri, Irene, Nielsen, Jørgen E., Hjermind, Lena E., Riemenschneider, Matthias, Mayhaus, Manuel, Gasparoni, Gilles, Pichler, Sabrina, Ibach, Bernd, Rossor, Martin N., Fox, Nick C., Warren, Jason D., Spillantini, Maria Grazia, Morris, Huw R., Rizzu, Patrizia, Heutink, Peter, Snowden, Julie S., Rollinson, Sara, Gerhard, Alexander, Richardson, Anna, Bruni, Amalia C., Maletta, Raffaele, Frangipane, Francesca, Cupidi, Chiara, Bernardi, Livia, Anfossi, Maria, Gallo, Maura, Conidi, Maria Elena, Smirne, Nicoletta, Rademakers, Rosa, Baker, Matt, Dickson, Dennis W., Graff-Radford, Neill R., Petersen, Ronald C., Knopman, David, Josephs, Keith A., Boeve, Bradley F., Parisi, Joseph E., Miller, Bruce L., Karydas, Anna M., Rosen, Howard, Seeley, William W., van Swieten, John C., Dopper, Elise G. P., Seelaar, Harro, Pijnenburg, Yolande A. L., Scheltens, Philip, Logroscino, Giancarlo, Capozzo, Rosa, Novelli, Valeria, Puca, Annibale A., Franceschi, Massimo, Postiglione, Alfredo, Milan, Graziella, Sorrentino, Paolo, Kristiansen, Mark, Chiang, Huei-Hsin, Graff, Caroline, Pasquier, Florence, Rollin, Adeline, Deramecourt, Vincent, Lebouvier, Thibaud, Ferrucci, Luigi, Kapogiannis, Dimitrios, Lah, James J., Levey, Allan I., Kondou, Shinichi, Geschwind, Daniel H., Int Frontotemporal Dementia Gen, Swarup, Vivek, Hinz, Flora I., Rexach, Jessica E., Noguchi, Ken-ichi, Toyoshiba, Hiroyoshi, Oda, Akira, Hirai, Keisuke, Sarkar, Arjun, Seyfried, Nicholas T., Cheng, Chialin, Haggarty, Stephen J., Ferrari, Raffaele, Rohrer, Jonathan D., Ramasamy, Adaikalavan, Hardy, John, Hernandez, Dena G., Nalls, Michael A., Singleton, Andrew B., Kwok, John B. J., Dobson-Stone, Carol, Brooks, William S., Schofield, Peter R., Halliday, Glenda M., Hodges, John R., Piguet, Olivier, Bartley, Lauren, Thompson, Elizabeth, Haan, Eric, Hernández, Isabel, Ruiz, Agustín, Boada, Mercè, Borroni, Barbara, Padovani, Alessandro, Cairns, Nigel J., Cruchaga, Carlo, Binetti, Giuliano, Ghidoni, Roberta, Benussi, Luisa, Forloni, Gianluigi, Albani, Diego, Galimberti, Daniela, Fenoglio, Chiara, Serpente, Maria, Scarpini, Elio, Clarimón, Jordi, Lleó, Alberto, Blesa, Rafael, Waldö, Maria Landqvist, Nilsson, Karin, Nilsson, Christer, Mackenzie, Ian R. A., Hsiung, Ging-Yuek R., Mann, David M. A., Grafman, Jordan, Morris, Christopher M., Attems, Johanne, Griffiths, Timothy D., Mckeith, Ian G., Thomas, Alan J., Jaros, Evelyn, Pietrini, Pietro, Huey, Edward D., Wassermann, Eric M., Tierney, Michael C., Baborie, Atik, Pastor, Pau, Ortega-Cubero, Sara, Razquin, Cristina, Alonso, Elena, Perneczky, Robert, Diehl-Schmid, Janine, Alexopoulos, Panagioti, Kurz, Alexander, Rainero, Innocenzo, Rubino, Elisa, Pinessi, Lorenzo, Rogaeva, Ekaterina, George-Hyslop, Peter St., Rossi, Giacomina, Tagliavini, Fabrizio, Giaccone, Giorgio, Rowe, James B., Schlachetzki, Johannes C. M., Uphill, Jame, Collinge, John, Mead, Simon, Danek, Adrian, Van Deerlin, Vivianna M., Grossman, Murray, Trojanowski, John Q., Pickering-Brown, Stuart, Momeni, Parastoo, van der Zee, Julie, Cruts, Marc, Van Broeckhoven, Christine, Cappa, Stefano F., Leber, Isabelle, Brice, Alexi, Hannequin, Didier, Golfier, Véronique, Vercelletto, Martine, Nacmias, Benedetta, Sorbi, Sandro, Bagnoli, Silvia, Piaceri, Irene, Nielsen, Jørgen E., Hjermind, Lena E., Riemenschneider, Matthia, Mayhaus, Manuel, Gasparoni, Gille, Pichler, Sabrina, Ibach, Bernd, Rossor, Martin N., Fox, Nick C., Warren, Jason D., Spillantini, Maria Grazia, Morris, Huw R., Rizzu, Patrizia, Heutink, Peter, Snowden, Julie S., Rollinson, Sara, Gerhard, Alexander, Richardson, Anna, Bruni, Amalia C., Maletta, Raffaele, Frangipane, Francesca, Cupidi, Chiara, Bernardi, Livia, Anfossi, Maria, Gallo, Maura, Conidi, Maria Elena, Smirne, Nicoletta, Rademakers, Rosa, Baker, Matt, Dickson, Dennis W., Graff-Radford, Neill R., Petersen, Ronald C., Knopman, David, Josephs, Keith A., Boeve, Bradley F., Parisi, Joseph E., Miller, Bruce L., Karydas, Anna M., Rosen, Howard, Seeley, William W., van Swieten, John C., Dopper, Elise G. P., Seelaar, Harro, Pijnenburg, Yolande A. L., Scheltens, Philip, Logroscino, Giancarlo, Capozzo, Rosa, Novelli, Valeria, Puca, Annibale A., Franceschi, Massimo, Postiglione, Alfredo, Milan, Graziella, Sorrentino, Paolo, Kristiansen, Mark, Chiang, Huei-Hsin, Graff, Caroline, Pasquier, Florence, Rollin, Adeline, Deramecourt, Vincent, Lebouvier, Thibaud, Ferrucci, Luigi, Kapogiannis, Dimitrio, Lah, James J., Levey, Allan I., Kondou, Shinichi, and Geschwind, Daniel H.
Subjects: Proteomics, Genetics and Molecular Biology (all), 0301 basic medicine, Messenger, Gene regulatory network, Inbred C57BL, Biochemistry, Transgenic, Mice, 0302 clinical medicine, Gene Regulatory Networks, Regulation of gene expression, Cell Death, Drug discovery, Neurodegeneration, Neurodegenerative Diseases, General Medicine, Chemistry, Frontotemporal Dementia, 030220 oncology & carcinogenesis, Frontotemporal dementia, Evolution, Systems biology, Genetic Vectors, Animals, Dementia, Disease Models, Animal, Gene Expression Regulation, Genetic Predisposition to Disease, Humans, Mice, Inbred C57BL, Mice, Transgenic, MicroRNAs, RNA, Messenger, Reproducibility of Results, Transcriptome, tau Proteins, Evolution, Molecular, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, microRNA, medicine, Biochemistry, Genetics and Molecular Biology (all), Animal, Molecular, medicine.disease, 030104 developmental biology, Disease Models, RNA, Human medicine
Abstract: Identifying the mechanisms through which genetic risk causes dementia is an imperative for new therapeutic development. Here, we apply a multistage, systems biology approach to elucidate the disease mechanisms in frontotemporal dementia. We identify two gene coexpression modules that are preserved in mice harboring mutations in MAPT, GRN and other dementia mutations on diverse genetic backgrounds. We bridge the species divide via integration with proteomic and transcriptomic data from the human brain to identify evolutionarily conserved, disease-relevant networks. We find that overexpression of miR-203, a hub of a putative regulatory microRNA (miRNA) module, recapitulates mRNA coexpression patterns associated with disease state and induces neuronal cell death, establishing this miRNA as a regulator of neurodegeneration. Using a database of drug-mediated gene expression changes, we identify small molecules that can normalize the disease-associated modules and validate this experimentally. Our results highlight the utility of an integrative, cross-species network approach to drug discovery.
Published: 2018

26. Une nouvelle espèce du genre Neacratus d’Amérique centrale (Coleoptera, Brentidae, Acratini)

Author: Antoine Mantilleri and Thibaud Glinez
Subjects: Biology
Published: 2020

27. Contribution of a DNA barcode to an assessment of the specificity of ant taxa (Hymenoptera: Formicidae) on Corsica

Author: Cyril Berquier, Thibaud Decaëns, Rumsaïs Blatrix, Christophe Galkowski, Clément Aubert, Marie Cécile Andrei-Ruiz, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Office de l'environnement de la Corse, Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Aphaenogaster, synonymy, Hymenoptera, ants, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, Myrmica scabrinodis, mediterranean islands, corsica, integrative taxonomy, biology, Temnothorax, barcode, biology.organism_classification, language.human_language, formicidae, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 010602 entomology, coi, Taxon, QL1-991, Evolutionary biology, Insect Science, language, Taxonomy (biology), hymenoptera, Corsican, Zoology
Abstract: International audience; We used the COI marker, the most popular DNA barcode for the animal kingdom, to assess the taxonomic status of Corsican populations of eight groups of species of ants that occur both on Corsica and the European mainland. (i) In two groups, we detected no genetic differentiation between Corsica and the continent. Absence of differentiation across varieties of Aphaenogaster spinosa within Corsica confirm current synonymies. (ii) In four groups, we detected strong genetic differentiation between Corsica and the continent, confirming recent taxonomic studies based on morphology for three of these groups. For the fourth group, we propose that the status of Corsican populations be raised from sub-species to species: Temnothorax cordieri stat. rev. (iii) In one group, the genetic differentiation and morphological differences do not support splitting and as a consequence we propose to accept the previous synonymy Temnothorax tuberum = Temnothorax melanocephalus. (iv) In Myrmica scabrinodis and Myrmica spinosior, COI sequence information is largely inconsistent with morphology and geography, not only on Corsica but also on the mainland, and should not be used to support taxonomic decisions. Although the use of COI has drawbacks, it is globally consistent with morphology and can be used to complement morphological ant taxonomy. We provide an updated checklist of ants of Corsica.
Published: 2020

28. Linnaeus's folly – phylogeny, evolution and classification ofSedum(Crassulaceae) and Crassulaceae subfamily Sempervivoideae

Author: Thibaud F.E. Messerschmid, Johannes Klein, Gudrun Kadereit, and Joachim W. Kadereit
Subjects: Subfamily, biology, Molecular dating, Phylogenetics, Botany, Plant Science, biology.organism_classification, Ecology, Evolution, Behavior and Systematics, Sedum, Crassulaceae
Published: 2020

29. Unveiling Cells’ Local Environment during Cryopreservation by Correlative In Situ Spatial and Thermal Analyses

Author: Kankan Qin, Corentin Eschenbrenner, Francisco M. Fernandes, Dmytro Dedovets, Félix Ginot, Thibaud Coradin, Sylvain Deville, Matériaux et Biologie (LCMCP-MATBIO), Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Synthèse et Fonctionnalisation de Céramiques (LSFC), Saint Gobain-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Liquides et interfaces (L&I), Institut Lumière Matière [Villeurbanne] (ILM), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon
Subjects: Correlative, In situ, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], FOS: Physical sciences, 02 engineering and technology, Computational biology, Biology, 010402 general chemistry, Crystals, 01 natural sciences, Cryopreservation, Biopolymers, Physics - Chemical Physics, Freezing, General Materials Science, Physics - Biological Physics, Physical and Theoretical Chemistry, Chemical Physics (physics.chem-ph), Condensed Matter - Materials Science, Ice, Fungi, Materials Science (cond-mat.mtrl-sci), 021001 nanoscience & nanotechnology, 0104 chemical sciences, Clinical Practice, Biological Physics (physics.bio-ph), [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Local environment, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Biological system, 0210 nano-technology
Abstract: Cryopreservation is the only fully established procedure to extend the lifespan of living cells and tissues, a key to activities spanning from fundamental biology to clinical practice. Despite its prevalence and impact, central aspects of cryopreservation, such as the cell's physico-chemical environment during freezing, remain elusive. Here we address that question by coupling in situ microscopic directional freezing to visualize cells and their surroundings during freezing with the freezing medium phase diagram. We extract the freezing medium spatial distribution in cryopreservation, providing a tool to describe the cell vicinity at any point during freezing. We show that two major events define the cells' local environment over time: the interaction with the moving ice front and with the vitreous moving front - a term we introduce here. Our correlative strategy may be applied to cells relevant in clinical research and practice, and help designing new cryoprotective media based on local physico-chemical cues., 31 pages, 4 figures, 7 supplementary figures
Published: 2020

30. Ferritin levels in patients with COVID‐19: A poor predictor of mortality and hemophagocytic lymphohistiocytosis

Author: Jonathan Feld, Leonard Naymagon, Santiago Thibaud, Douglas Tremblay, and Alaina J. Kessler
Subjects: Male, medicine.medical_treatment, Clinical Biochemistry, 030204 cardiovascular system & hematology, Gastroenterology, 0302 clinical medicine, biology, Area under the curve, Hematology, General Medicine, Middle Aged, Prognosis, Combined Modality Therapy, Hospitalization, Area Under Curve, Cohort, Original Article, Female, Coronavirus Infections, Subset Analysis, medicine.medical_specialty, Pneumonia, Viral, Sensitivity and Specificity, Lymphohistiocytosis, Hemophagocytic, Betacoronavirus, 03 medical and health sciences, COVID‐19, Renal Dialysis, Internal medicine, medicine, Humans, Renal replacement therapy, Pandemics, Aged, Retrospective Studies, Biochemistry, medical, Inflammation, Hemophagocytic lymphohistiocytosis, Receiver operating characteristic, SARS-CoV-2, business.industry, ferritin, Biochemistry (medical), COVID-19, Retrospective cohort study, Original Articles, medicine.disease, Respiration, Artificial, cytokines, COVID-19 Drug Treatment, Ferritin, hemophagocytic lymphohistiocytosis, ROC Curve, interleukin‐6, Ferritins, biology.protein, business, 030215 immunology
Abstract: Introduction A hyperinflammatory environment has been a hallmark of COVID‐19 infection and is thought to be a key mediator of morbidity. Elevated ferritin has been observed in many patients with COVID‐19. Several retrospective studies have shown ferritin levels can be correlated and predictive of poor outcomes in COVID‐19, though a rigorous analysis has been lacking. Methods A retrospective analysis of 942 adult COVID‐19 patients admitted in March 2020 at a large New York City health system with available ferritin levels. Results The primary outcome, all‐cause mortality, was observed in 265 (28.1%) patients. Patients who died had a significantly higher median admission and maximum ferritin levels than those who did not. However, death was poorly predicted by admission and maximum ferritin levels on receiver operator curve (ROC) analysis, with AUCs of 0.677 and 0.638, respectively. AUCs increased when the cohort was limited to progressively younger patients. Ferritin levels were minimally better at predicting our secondary outcomes. These included mechanical ventilation, observed in 280 (29.7%) patients with an ROC yielding an area under the curve (AUC) of 0.769, and new renal replacement therapy, observed in 80 (8.5%) of patients with an ROC yielding an AUC of 0.787. We also performed a subset analysis on 22 patients with ferritins >20 000 ng/mL. None of the patients met HLH‐2004 diagnostic criteria. Fifteen (68.2%) of these patients had suspected or confirmed bacterial infections. Conclusions Though many patients with COVID‐19 present with hyperferritinemia, elevated ferritin levels are not accurate predictors of outcomes and do not appear to be indicative of hemophagocytic lymphohistiocytosis.
Published: 2020

31. DISCOVERY: prevalence of transthyretin (TTR) mutations in a US-centric patient population suspected of having cardiac amyloidosis

Author: Jared Gollob, John Vest, Mathew S. Maurer, Christine Powell, Verena Karsten, Thibaud Damy, Ola Akinboboye, Alberta L. Warner, Herman A. Taylor, and Keyur B. Shah
Subjects: medicine.medical_specialty, biology, business.industry, Amyloidosis, Cardiomyopathy, nutritional and metabolic diseases, 030204 cardiovascular system & hematology, medicine.disease, Gastroenterology, Multisystem disease, 03 medical and health sciences, Transthyretin, Patient population, 0302 clinical medicine, Cardiac amyloidosis, Heart failure, Internal medicine, Internal Medicine, medicine, biology.protein, business, Polyneuropathy, 030217 neurology & neurosurgery
Abstract: Hereditary transthyretin-mediated amyloidosis (hATTR amyloidosis) is a multisystem disease that presents with polyneuropathy and/or cardiomyopathy. DISCOVERY, a multicenter screening study, enrolled patients with clinically suspected cardiac amyloidosis to determine the frequency of transthyretin (TTR) mutations and assess disease characteristics. Of 1007 patients, the majority were from the US (84%), Black/African American (56%), male (63%), and with a mean (standard deviation) age of 65 (13) years. Among 1001 patients with genotyping results, 74 (7%) had a pathogenic TTR mutation (71/836 [8%] from the US). Val122Ile was the most common mutation, found in 11% of Black/African American patients overall; Black/African American ethnicity was an independent predictor of having a pathogenic TTR mutation. Additional independent predictors of such mutations in the total population and Black/African American group were interventricular septum thickness, low electrocardiogram voltage, and age. Pathogenic TTR mutations occurred in 8% of US patients with suspected cardiac amyloidosis. Most mutations were Val122Ile, almost exclusively found in Black/African American patients. Disease often remains undetected until advanced and difficult to treat, therefore, clinicians should assess at-risk patients for hATTR amyloidosis as early as possible.
Published: 2020

32. Extracardiac soft tissue uptake, evidenced on early 99mTc-HMDP SPECT/CT, helps typing cardiac amyloidosis and demonstrates high prognostic value

Author: Arnault Galat, Anissa Moktefi, Thibaud Damy, Benoît Funalot, Silvia Oghina, Pascale Fanen, Emmanuel Itti, Paul Blanc-Durand, Jean-François Deux, Soulef Guendouz, Valérie Molinier-Frenkel, Mukedaisi Abulizi, Nathan Malka, Vincent Audard, Diane Bodez, Mounira Kharoubi, Jean-Pascal Lefaucheur, and Fabien Le Bras
Subjects: medicine.medical_specialty, biology, medicine.diagnostic_test, business.industry, Amyloidosis, Soft tissue, General Medicine, medicine.disease, Scintigraphy, Gastroenterology, 030218 nuclear medicine & medical imaging, Clinical Practice, 03 medical and health sciences, Transthyretin, 0302 clinical medicine, Cardiac amyloidosis, 030220 oncology & carcinogenesis, Internal medicine, medicine, biology.protein, Radiology, Nuclear Medicine and imaging, Digestive tract, Typing, business
Abstract: Increased cardiac uptake (CU) on early-phase 99mTc-HMDP scintigraphy has demonstrated diagnostic and prognostic values in amyloid transthyretin (ATTR) cardiac amyloidosis (CA). Extracardiac uptake (ECU) has been poorly studied. We assessed the clinical value of ECU, in combination with CU, on 99mTc-HMDP scintigraphy using a novel Methodological Amyloidosis Diagnostic Index (MADI). We reviewed all patients referred for suspicion of CA, who underwent 99mTc-HMDP scintigraphy over an 8-year period. ECU, CU, and MADI were determined: MADI0 = neither ECU or CU, MADI1 = ECU alone, MADI2 = CU alone, and MADI3 = ECU + CU. Of 308 eligible patients, 247 had CA, including 75 ATTRv, 107 ATTRwt, and 65 light-chain (AL), while 61 had another cardiopathy (controls). ECU was observed in 29% of CA and 3% of controls. Most frequent sites of ECU were pleuropulmonary (16% of CA, 3% of controls) followed by the digestive tract and subcutaneous tissues. The liver and spleen ECU was only observed in AL-CA (n = 8). CU was only observed in CA patients (n = 187), of whom 182 had ATTR-CA vs. 5 AL-CA, P 0 vs. MADI0 in AL and MADI3 vs. MADI2 in ATTR were associated with a worse prognosis (P = 0.03 and P = 0.002, respectively). ECU combined with CU demonstrates high diagnostic and prognostic values in CA patients. MADI seems an easy and reliable score in clinical practice.
Published: 2020

33. Transthyretin cardiac amyloidosis in continental Western Europe: An insight through the Transthyretin Amyloidosis Outcomes Survey (THAOS)

Author: Ching-Ray Yu, Moh-Lim Ong, Claudio Rapezzi, V. Plante-Bordeneuve, Thaos Investigators, Thibaud Damy, Arnt V. Kristen, Teresa Coelho, Mathew S. Maurer, and Ole B. Suhr
Subjects: medicine.medical_specialty, Registry, Cardiomyopathy, Diastole, 030204 cardiovascular system & hematology, NO, 03 medical and health sciences, 0302 clinical medicine, Genotype-phenotype distinction, Internal medicine, Medicine, ATTR amyloidosis, Cardiac and Cardiovascular Systems, Kardiologi, Ejection fraction, biology, business.industry, Amyloidosis, Hypertrophic cardiomyopathy, 030229 sport sciences, medicine.disease, Transthyretin, Cardiac amyloidosis, biology.protein, Cardiology, ATTR amyloidosis, Cardiomyopathy, Registry, Cardiology and Cardiovascular Medicine, business
Abstract: Aims Transthyretin amyloidosis (ATTR amyloidosis) is a heterogeneous disorder with cardiac, neurologic, and mixed phenotypes. We describe the phenotypic and genotypic profiles of this disease in continental Western Europe as it appears from the Transthyretin Amyloidosis Survey (THAOS). Methods and results THAOS is an ongoing, worldwide, longitudinal, observational survey established to study differences in presentation, diagnosis, and natural history in ATTR amyloidosis subjects. At data cut-off, 1411 symptomatic subjects from nine continental Western European countries were enrolled in THAOS [1286 hereditary (ATTRm) amyloidosis; 125 wild-type ATTR (ATTRwt) amyloidosis]. Genotypes and phenotypes varied notably by country. Four mutations (Val122Ile, Leu111Met, Thr60Ala, and Ile68Leu), and ATTRwt, were associated with a mainly cardiac phenotype showing symmetric left ventricular (LV) hypertrophy, normal diastolic LV dimensions and volume, and mildly depressed LV ejection fraction (LVEF). Morphologic and functional abnormalities on echocardiogram were significantly more severe in subjects with cardiac (n‘= 210), compared with a mixed (n = 298), phenotype: higher median (Q1–Q3) interventricular septal thickness [18 (16–21) vs. 16 (13–20) mm; P = 0.0006]; and more frequent incidence of LVEF Conclusion ATTR amyloidosis genotypes and phenotypes are highly heterogeneous in continental Western Europe. A geographic map of the different disease profiles and awareness that a subset of subjects have a dominant cardiac phenotype, mimicking hypertrophic cardiomyopathy, at presentation can facilitate the clinical recognition of this underdiagnosed disease. Trial registration ClinicalTrials.gov: NCT00628745.
Published: 2022

34. How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Author: Markus S. Dillenberger, Jessica A. Los, Philipp Hühn, Michael A. Gerschwitz-Eidt, Benjamin Rieger, Elvira Hörandl, Thibaud F.E. Messerschmid, Claudia Paetzold, and Gudrun Kadereit
Subjects: 0106 biological sciences, clustering threshold selection, Inference, Locus (genetics), Computational biology, Biology, Crassulaceae, data bias, 010603 evolutionary biology, 01 natural sciences, Genome, Coalescent theory, species tree inference, 03 medical and health sciences, locus filtering, Genetics, coalescent-based summary method, Cluster analysis, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Phylogeny, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, High-Throughput Nucleotide Sequencing, Genomics, RADseq, 500 Naturwissenschaften und Mathematik::570 Biowissenschaften, Biologie::570 Biowissenschaften, Biologie, Tree (data structure)
Abstract: Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed.
Published: 2022
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35. Comparison of clinical rating scales in genetic frontotemporal dementia within the GENFI cohort

Author: Peakman, Georgia, Russell, Lucy L., Convery, Rhian S., Nicholas, Jennifer M., van Swieten, John C., Jiskoot, Lize C., Moreno, Fermin, Sanchez-Valle, Raquel, Laforce, Robert, Graff, Caroline, Masellis, Mario, Tartaglia, Maria Carmela, Rowe, James B., Borroni, Barbara, Finger, Elizabeth, Synofzik, Matthis, Galimberti, Daniela, Vandenberghe, Rik, de Mendonça, Alexandre, Butler, Chris R., Gerhard, Alex, Ducharme, Simon, Le Ber, Isabelle, Tagliavini, Fabrizio, Santana, Isabel, Pasquier, Florence, Levin, Johannes, Danek, Adrian, Otto, Markus, Sorbi, Sandro, Rohrer, Jonathan D., Afonso, Sónia, Almeida, Maria Rosario, Anderl-Straub, Sarah, Andersson, Christin, Antonell, Anna, Archetti, Silvana, Arighi, Andrea, Balasa, Mircea, Barandiaran, Myriam, Bargalló, Nuria, Bartha, Robart, Bender, Benjamin, Benussi, Alberto, Bertoux, Maxime, Bertrand, Anne, Bessi, Valentina, Black, Sandra, Bocchetta, Martina, Borrego-Ecija, Sergi, Bras, Jose, Brice, Alexis, Bruffaerts, Rose, Camuzat, Agnès, Cañada, Marta, Cantoni, Valentina, Caroppo, Paola, Cash, David, Castelo-Branco, Miguel, Colliot, Olivier, Cope, Thomas, Deramecourt, Vincent, de Arriba, María, Di Fede, Giuseppe, Díez, Alina, Duro, Diana, Fenoglio, Chiara, Ferrari, Camilla, Ferreira, Catarina B., Fox, Nick, Freedman, Morris, Fumagalli, Giorgio, Funkiewiez, Aurélie, Gabilondo, Alazne, Gasparotti, Roberto, Gauthier, Serge, Gazzina, Stefano, Giaccone, Giorgio, Gorostidi, Ana, Greaves, Caroline, Guerreiro, Rita, Heller, Carolin, Hoegen, Tobias, Indakoetxea, Begoña, Jelic, Vesna, Karnath, Hans-Otto, Keren, Ron, Kuchcinski, Gregory, Langheinrich, Tobias, Lebouvier, Thibaud, Leitão, Maria João, Lladó, Albert, Lombardi, Gemma, Loosli, Sandra, Maruta, Carolina, Mead, Simon, Meeter, Lieke, Miltenberger, Gabriel, van Minkelen, Rick, Mitchell, Sara, Moore, Katrina, Nacmias, Benedetta, Nelson, Annabel, Öijerstedt, Linn, Olives, Jaume, Ourselin, Sebastien, Padovani, Alessandro, Panman, Jessica, Papma, Janne M., Pijnenburg, Yolande, Polito, Cristina, Premi, Enrico, Prioni, Sara, Prix, Catharina, Rademakers, Rosa, Redaelli, Veronica, Rinaldi, Daisy, Rittman, Tim, Rogaeva, Ekaterina, Rollin, Adeline, Rosa-Neto, Pedro, Rossi, Giacomina, Rossor, Martin, Santiago, Beatriz, Saracino, Dario, Sayah, Sabrina, Scarpini, Elio, Schönecker, Sonja, Seelaar, Harro, Semler, Elisa, Shafei, Rachelle, Shoesmith, Christen, Swift, Imogen, Tábuas-Pereira, Miguel, Tainta, Mikel, Taipa, Ricardo, Tang-Wai, David, Thomas, David L., Thompson, Paul, Thonberg, Hakan, Timberlake, Carolyn, Tiraboschi, Pietro, Todd, Emily, van Damme, Philip, Vandenbulcke, Mathieu, Veldsman, Michele, Verdelho, Ana, Villanua, Jorge, Warren, Jason, Wilke, Carlo, Woollacott, Ione, Wlasich, Elisabeth, Zetterberg, Henrik, Zulaica, Miren, Neurology, Amsterdam Neuroscience - Neurodegeneration, University College of London [London] (UCL), London School of Hygiene and Tropical Medicine (LSHTM), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Donostia International Physics Center - DIPC (SPAIN), Donostia International Physics Center (DIPC), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU)-University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Centre Hospitalier Université Laval [Quebec] (CHUL), CHU de Québec–Université Laval, Université Laval [Québec] (ULaval)-Université Laval [Québec] (ULaval), Karolinska Institutet [Stockholm], University of Toronto, University of Cambridge [UK] (CAM), University of Brescia, University of Western Ontario (UWO), Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Lusófona University [Lisbon], University of Oxford, University of Manchester [Manchester], McGill University = Université McGill [Montréal, Canada], Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de la Mémoire et de la Maladie d'Alzheimer [CHU Pitié-Salpétriêre] (IM2A), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Neurologie [CHU Pitié-Salpêtrière], IFR70-CHU Pitié-Salpêtrière [AP-HP], Fondazione IRCCS Istituto Neurologico 'Carlo Besta', University of Coimbra [Portugal] (UC), Lille Neurosciences & Cognition - U 1172 (LilNCog), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Ludwig-Maximilians-Universität München (LMU), University of Ulm (UUlm), Università degli Studi di Firenze = University of Florence (UniFI), HAL-SU, Gestionnaire, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University of Oxford [Oxford], Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de la Mémoire et de la Maladie d'Alzheimer [Paris] (IM2A), Sorbonne Université (SU), Lille Neurosciences & Cognition - U 1172 (LilNCog (ex-JPARC)), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Peakman, Georgia [0000-0002-3319-138X], Convery, Rhian S [0000-0002-9477-1812], Van Swieten, John C [0000-0001-6278-6844], Jiskoot, Lize C [0000-0002-1120-1858], Rowe, James B [0000-0001-7216-8679], Borroni, Barbara [0000-0001-9340-9814], Finger, Elizabeth [0000-0003-4461-7427], Galimberti, Daniela [0000-0002-9284-5953], Gerhard, Alex [0000-0002-8071-6062], Ducharme, Simon [0000-0002-7309-1113], Le Ber, Isabelle [0000-0002-2508-5181], Danek, Adrian [0000-0001-8857-5383], Otto, Markus [0000-0002-6647-5944], Sorbi, Sandro [0000-0002-0380-6670], Rohrer, Jonathan D [0000-0002-6155-8417], Apollo - University of Cambridge Repository, and Genetic FTD Initiative (GENFI)
Subjects: Oncology, Medizin, LANGUAGE, Disease, Genetic FTD Initiative (GENFI), Cohort Studies, 0302 clinical medicine, diagnosis [Frontotemporal Dementia], ddc:150, C9orf72, CRITERIA, 030212 general & internal medicine, frontotemporal dementia, C9orf72 Protein, Cross-Sectional Studies, Disease Progression, Frontotemporal Dementia, Humans, Mutation, tau Proteins, Mental Status and Dementia Tests, VERSION, 11 Medical and Health Sciences, Psychiatry, UTILITY, DDC 150 / Psychology, biology, FTD, 17 Psychology and Cognitive Sciences, Psychiatry and Mental health, Mutation (genetic algorithm), Cohort, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], medicine.symptom, FTLD, Life Sciences & Biomedicine, Alzheimer’s disease, Frontotemporal dementia, medicine.medical_specialty, Clinical Dementia Rating, Tau protein, Clinical Neurology, Alzheimerkrankheit, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, DIAGNOSIS, Asymptomatic, VALIDATION, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Internal medicine, mental disorders, medicine, ddc:610, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Neurodegeneration, Science & Technology, Neurology & Neurosurgery, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], business.industry, MUTATIONS, medicine.disease, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, biology.protein, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Surgery, Neurology (clinical), Neurosciences & Neurology, business, 030217 neurology & neurosurgery
Abstract: BackgroundTherapeutic trials are now underway in genetic forms of frontotemporal dementia (FTD) but clinical outcome measures are limited. The two most commonly used measures, the Clinical Dementia Rating (CDR)+National Alzheimer’s Disease Coordinating Center (NACC) Frontotemporal Lobar Degeneration (FTLD) and the FTD Rating Scale (FRS), have yet to be compared in detail in the genetic forms of FTD.MethodsThe CDR+NACC FTLD and FRS were assessed cross-sectionally in 725 consecutively recruited participants from the Genetic FTD Initiative: 457 mutation carriers (77 microtubule-associated protein tau (MAPT), 187 GRN, 193 C9orf72) and 268 family members without mutations (non-carrier control group). 231 mutation carriers (51 MAPT, 92 GRN, 88 C9orf72) and 145 non-carriers had available longitudinal data at a follow-up time point.ResultsCross-sectionally, the mean FRS score was lower in all genetic groups compared with controls: GRN mutation carriers mean 83.4 (SD 27.0), MAPT mutation carriers 78.2 (28.8), C9orf72 mutation carriers 71.0 (34.0), controls 96.2 (7.7), p, publishedVersion
Published: 2022

36. Geographical distribution and host range status of Tuta absoluta Meyrick (Lepidoptera: Gelechiidae) in Côte d'Ivoire

Author: S. W. M. Ouali-Ngoran, K. A. J. Konan, G. O. Ochou, Thibaud Martin, Nicolas Desneux, L. Fondio, and D. Koné
Subjects: 0106 biological sciences, Plante hôte, Melongena, Distribution géographique, Infestation, Solanum nigrum, Distribution des populations, 010603 evolutionary biology, 01 natural sciences, Solanum lycopersicum, Ecology, Evolution, Behavior and Systematics, biology, Enquête, Phenology, biology.organism_classification, Gelechiidae, Pheromone trap, H10 - Ravageurs des plantes, Tuta absoluta, 010602 entomology, Horticulture, Insect Science, PEST analysis, Solanum
Abstract: The South American tomato pinworm, Tuta absoluta (Meyrick), is one of the major threats to tomato production. Larvae can cause losses of more than 80% of production. It was officially detected for the first time in West Africa in 2012, in Senegal, and was subsequently reported in most countries in this part of the continent. To identify infested vegetable production areas and determine reservoir plants in Cote d'Ivoire, surveys were carried out and pheromone traps set in the North, South, East, West and Center in the main tomato production areas of the country. The pest was detected in all surveyed areas, with the highest number of males (623 ± 19.5 insects/week) caught by pheromone traps in Bouake in the Center of Cote d'Ivoire and a highest percentage of infested leaves, 96 ± 2.5%, was obtained in the locality of Agnibilekro in the East of the country. Tuta absoluta attacked all phenological stages of tomato plant in field. Larval mines were observed on the eggplant, Solanum melongena, the black nightshade, Solanum nigrum and the peppers, Capsicum annuum. Apart from tomato, T. absoluta seems to prefer S. melongena (41.64 ± 2.95% of infested leaves/plant; 4.88 ± 0.4 mine/plant) and S. nigrum (36.27 ± 3.42% of infested leaves/plant; 4.26 ± 0.6 mine/plant) more than C. annuum (13.48 ± 2.42% of infested leaves/plant and 1.38 ± 0.18 mine/plant). This study led to understanding that T. absoluta is well established in the main tomato production areas of Cote d’Ivoire, causing damage regardless of plant development stages and is present on other plant species.
Published: 2022

37. A Nonsense Variant in Hephaestin Like 1 (HEPHL1) Is Responsible for Congenital Hypotrichosis in Belted Galloway Cattle

Author: Kuca, Thibaud, Marron, Brandy M, Jacinto, Joana G P, Paris, Julia M., Gerspach, Christian, Beever, Jonathan E, Drögemüller, Cord, Kuca, Thibaud, Marron, Brandy M., Jacinto, Joana G. P., Paris, Julia M., Gerspach, Christian, Beever, Jonathan E., and Drögemüller, Cord
Subjects: 630 Agriculture, Bos taurus, hair, 610 Medicine & health, QH426-470, dermatology, monogenic, Genetics, hypotrichosis simplex, 590 Animals (Zoology), 570 Life sciences, biology, Bos tauru, development, genodermatosis
Abstract: Genodermatosis such as hair disorders mostly follow a monogenic mode of inheritance. Congenital hypotrichosis (HY) belong to this group of disorders and is characterized by abnormally reduced hair since birth. The purpose of this study was to characterize the clinical phenotype of a breed-specific non-syndromic form of HY in Belted Galloway cattle and to identify the causative genetic variant for this recessive disorder. An affected calf born in Switzerland presented with multiple small to large areas of alopecia on the limbs and on the dorsal part of the head, neck, and back. A genome-wide association study using Swiss and US Belted Galloway cattle encompassing 12 cases and 61 controls revealed an association signal on chromosome 29. Homozygosity mapping in a subset of cases refined the HY locus to a 1.5 Mb critical interval and subsequent Sanger sequencing of protein-coding exons of positional candidate genes revealed a stop gain variant in the HEPHL1 gene that encodes a multi-copper ferroxidase protein so-called hephaestin like 1 (c.1684A&gt, T, p.Lys562*). A perfect concordance between the homozygous presence of this most likely pathogenic loss-of-function variant and the HY phenotype was found. Genotyping of more than 700 purebred Swiss and US Belted Galloway cattle showed the global spread of the mutation. This study provides a molecular test that will permit the avoidance of risk matings by systematic genotyping of relevant breeding animals. This rare recessive HEPHL1-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002230-9913).
Published: 2021

38. Insights into the genetic basis of retinal detachment

Author: Caroline Hayward, David G. Charteris, Danny Mitry, Thibaud Boutin, David A. Hinds, Archie Campbell, Susan Campbell, Aman Chandra, Priyanka Nandakumar, and Veronique Vitart
Subjects: Genetic Markers, medicine.medical_specialty, Locus (genetics), Genome-wide association study, Biology, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Meta-Analysis as Topic, Epidemiology, Genetics, medicine, Humans, genetics, myopia, Association Studies Article, genome, Molecular Biology, Genetics (clinical), 030304 developmental biology, Genetic association, Sweden, 0303 health sciences, genome-wide association study, datasets, radiation recall dermatitis, Retinal Detachment, direct-to-consumer genetic testing, Case-control study, General Medicine, self-report, Biobank, United Kingdom, cataract, Genetic marker, Case-Control Studies, biobanks, 030221 ophthalmology & optometry, Etiology, Genome-Wide Association Study, retinal detachment
Abstract: Retinal detachment is a serious and common condition, but genetic studies to date have been hampered by the small size of the assembled cohorts. In the UK Biobank dataset, where retinal detachment was ascertained by self-report or hospital records, genetic correlations between retinal detachment and high myopia or cataract operation were respectively 0.46 (SE=0.08) and 0.44 (SE=0.07). These correlations are consistent with known epidemiological associations. Through meta-analysis of genome-wide association studies using UK Biobank retinal detachment cases (N=3977) and two cohorts, each comprising ~1000 clinically-ascertained rhegmatogenous retinal detachment patients, we uncovered 11 genome-wide significant association signals. These are near or within ZC3H11B, BMP3, COL22A1, DLG5, PLCE1, EFEMP2, TYR, FAT3, TRIM29, COL2A1 and LOXL1. Replication in the 23andMe dataset, where retinal detachment is self-reported by participants, firmly establishes six retinal detachment risk loci: FAT3, COL22A1, TYR, BMP3, ZC3H11B and PLCE1. Based on the genetic associations with eye traits described to date, the first two specifically impact risk of a retinal detachment, while the last four point to shared aetiologies with macular condition, myopia and glaucoma. Fine-mapping prioritised the lead common missense variant (TYR S192Y) as causal variant at the TYR locus and a small set of credible causal variants at the FAT3 locus. The larger study size presented here, enabled by resources linked to health records or self-report, provides novel insights into retinal detachment aetiology and underlying pathological pathways.
Published: 2019

39. Endemic foot and mouth disease: pastoral in-herd disease dynamics in sub-Saharan Africa

Author: I McLachlan, Iain J. McKendrick, Glenn Marion, Thibaud Porphyre, Ian Handel, and B.M. deC. Bronsvoort
Subjects: 0301 basic medicine, Sub saharan, Endemic Diseases, 040301 veterinary sciences, Mathematics and computing, animal diseases, Cattle Diseases, lcsh:Medicine, Disease, Biology, Article, Persistence (computer science), Disease Outbreaks, 0403 veterinary science, 03 medical and health sciences, Environmental health, medicine, Animals, General, lcsh:Science, Disease burden, Africa South of the Sahara, 2. Zero hunger, Stochastic Processes, Multidisciplinary, Foot-and-mouth disease, business.industry, lcsh:R, Outbreak, 04 agricultural and veterinary sciences, Models, Theoretical, medicine.disease, 030104 developmental biology, Foot-and-Mouth Disease, Herd, Infectious diseases, Livestock, Cattle, lcsh:Q, business
Abstract: Foot and mouth disease (FMD) burden disproportionally affects Africa where it is considered endemic. Smallholder livestock keepers experience significant losses due to disease, but the dynamics and mechanisms underlying persistence at the herd-level and beyond remain poorly understood. We address this knowledge gap using stochastic, compartmental modelling to explore FMD virus (FMDV) persistence, outbreak dynamics and disease burden in individual cattle herds within an endemic setting. Our analysis suggests repeated introduction of virus from outside the herd is required for long-term viral persistence, irrespective of carrier presence. Risk of new disease exposures resulting in significant secondary outbreaks is reduced by the presence of immune individuals giving rise to a period of reduced risk, the predicted duration of which suggests that multiple strains of FMDV are responsible for observed yearly herd-level outbreaks. Our analysis suggests management of population turnover could potentially reduce disease burden and deliberate infection of cattle, practiced by local livestock keepers in parts of Africa, has little effect on the duration of the reduced risk period but increases disease burden. This work suggests that FMD control should be implemented beyond individual herds but, in the interim, herd management may be used to reduced FMD impact to livestock keepers.
Published: 2019

40. Variant recurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense variants

Author: Sebastien Moutton, Antonio Vitobello, Laurence Faivre, Christophe Philippe, Christel Thauvin-Robinet, Philippine Garret, Thibaud Jouan, Martin Chevarin, Benoit Urteaga, Yannis Duffourd, Sophie Nambot, Frédéric Tran-Mau-Them, Arthur Sorlin, François Lecoquierre, Ange-Line Bruel, and Christine Coubes
Subjects: Male, 0301 basic medicine, Candidate gene, Developmental Disabilities, Mutation, Missense, 030105 genetics & heredity, Biology, 03 medical and health sciences, Neurodevelopmental disorder, Intellectual Disability, Databases, Genetic, Intellectual disability, medicine, Humans, Missense mutation, Exome, Genetic Predisposition to Disease, Genetic Testing, Autistic Disorder, Gene, Genetics (clinical), Exome sequencing, Genetics, Computational Biology, High-Throughput Nucleotide Sequencing, Genomics, Sequence Analysis, DNA, medicine.disease, Phenotype, 030104 developmental biology, Neurodevelopmental Disorders, Autism, Female, Transcription Factors
Abstract: Next-generation sequencing has revealed the major impact of de novo variants (DNVs) in developmental disorders (DD) such as intellectual disability, autism, and epilepsy. However, a substantial fraction of these predicted pathogenic DNVs remains challenging to distinguish from background DNVs, notably the missense variants acting via nonhaploinsufficient mechanisms on specific amino acid residues. We hypothesized that the detection of the same missense variation in at least two unrelated individuals presenting with a similar phenotype could be a powerful approach to reveal novel pathogenic variants. We looked for variations independently present in both our database of >1200 solo exomes and in denovo-db, a large, publicly available collection of de novo variants identified in patients with DD. This approach identified 30 variants with strong evidence of pathogenicity, including variants already classified as pathogenic or probably pathogenic by our team, and also several new variants of interest in known OMIM genes or in novel genes. We identified FEM1B and GNAI2 as good candidate genes for syndromic intellectual disability and confirmed the implication of ACTL6B in a neurodevelopmental disorder. Annotation of local variants with denovo-db can highlight missense variants with high potential for pathogenicity, both facilitating the time-consuming reanalysis process and allowing novel DD gene discoveries.
Published: 2019

41. Aortic Stenosis and Cardiac Amyloidosis

Author: Dania Mohty, Marie-Annick Clavel, Philippe Pibarot, Romain Gallet, Francois Tournoux, Annabelle Nguyen, Julien Magne, Emmanuel Teiger, Nancy Côté, Thibaud Damy, Julien Ternacle, Laura Krapf, and Arnault Galat
Subjects: Tafamidis, medicine.medical_specialty, biology, medicine.diagnostic_test, business.industry, 030204 cardiovascular system & hematology, Doppler echocardiography, medicine.disease, Pharmacological treatment, 03 medical and health sciences, Stenosis, Transthyretin, chemistry.chemical_compound, 0302 clinical medicine, Cardiac amyloidosis, chemistry, Heart failure, Internal medicine, medicine, biology.protein, Cardiology, In patient, 030212 general & internal medicine, Cardiology and Cardiovascular Medicine, business
Abstract: Highlights •CA may be present in ≤15% of patients with AS. •Clinical and imaging “red flags” for CA should be systematically searched in patients with AS. •Transcatheter rather than surgical AVR may be preferred in patients with CA. •Recently developed pharmacological treatment for transthyretin CA should be instituted as soon as diagnosis is confirmed.
Published: 2019

42. Tafamidis and quality of life in people with transthyretin amyloid cardiomyopathy in the study ATTR-ACT: A plain language summary

Author: Mathew S. Maurer, Thibaud Damy, Martha Grogan, Mazen Hanna, Marla B. Sultan, Balarama Gundapaneni, and Michelle Stewart
Subjects: Gerontology, Tafamidis, Adult, Disease, Placebo, chemistry.chemical_compound, Quality of life (healthcare), Medicine, Humans, Prealbumin, Plain language, Language, Heart Failure, Amyloid Neuropathies, Familial, Benzoxazoles, biology, business.industry, Clinical trial, Transthyretin, chemistry, biology.protein, Quality of Life, Molecular Medicine, Cardiology and Cardiovascular Medicine, Amyloid cardiomyopathy, business, Cardiomyopathies
Abstract: This plain language summary describes the results of a study called ATTR-ACT, which was published in the American Journal of Cardiology. In ATTR-ACT, researchers looked at the effects of tafamidis treatment in people with transthyretin amyloid cardiomyopathy (called ATTR-CM for short). Tafamidis is currently available in the USA and other countries as an oral treatment for adults with ATTR-CM. In ATTR-ACT, 441 people with ATTR-CM from 13 different countries took either tafamidis or placebo by mouth for 30 months. First, researchers looked at the effects of tafamidis on the risk of death and hospitalization due to heart problems between the start and the end of the study; they found that these risks were about one-third lower with tafamidis compared with placebo. As described in this summary, researchers also looked at the effects of tafamidis on people's heart failure symptoms, quality of life, and general health over the 30-month study. People who took part in ATTR-ACT rated these effects using questionnaires filled out before, during, and after the study. More people who took tafamidis saw improvement or no change in their heart failure symptoms and quality of life than people who took placebo. In addition, compared with people taking placebo, people taking tafamidis had less worsening of their general health during the study. These results show the benefits of tafamidis in reducing the declines in quality of life and health that often occur with this debilitating disease. To read the full Plain Language Summary of this article, click on the View Article button above and download the PDF. Clinical Trial Registration: NCT01994889 (ClinicalTrials.gov).
Published: 2021

43. Early and rapid identification of COVID-19 patients with neutralizing type I-interferon auto-antibodies by an easily implementable algorithm

Author: Ralf-Harto Huebner, Christoph Tabeling, Nils Schallner, Christian Drosten, Terry Jones, Siegbert Rieg, Horst von Bernuth, Uta Merle, Leif E. Sander, Daniel Duerschmied, Barbara Muehlemann, Christine Goffinet, Dietrich August, Victor M. Corman, Norbert Suttorp, JM Doehn, Uwe Koelsch, Olga Staudacher, Achim Lother, Nadine Unterwalder, Charlotte Thibeault, Bengisu Akbil, Daniela Niemeyer, Cédric Hirzel, Alexandra Nieters, Florian Kurth, Christian Nusshag, Tim Meyer, Thomas Doerner, Paula Stubbemann, David Sanchez, Jenny Jansen, Joerg C. Schefold, Valeria Falcone, Thibaud Spinetti, Klaus Warnatz, Christian Meisel, Jan Nikolaus Lieberum, and Hartmut Hengel
Subjects: biology, Coronavirus disease 2019 (COVID-19), business.industry, Autoantibody, Disease, Neutralization, Interferon, Cohort, biology.protein, Medicine, Biomarker (medicine), Antibody, business, Algorithm, medicine.drug
Abstract: PurposeSix-19% of critically ill COVID-19 patients display circulating auto-antibodies against type I interferons (IFN-AABs). Here, we establish a clinically applicable strategy for early identification of IFN-AAB-positive patients for potential subsequent clinical interventions.MethodsWe analysed sera of 430 COVID-19 patients with severe and critical disease from four hospitals for presence of IFN-AABs by ELISA. Binding specificity and neutralizing activity were evaluated via competition assay and virus-infection-based neutralization assay. We defined clinical parameters associated with IFN-AAB positivity. In a subgroup of critically ill patients, we analyzed effects of therapeutic plasma exchange (TPE) on the levels of IFN-AABs, SARS-CoV-2 antibodies and clinical outcome.ResultsThe prevalence of neutralizing AABs to IFN-α and IFN-ω in COVID-19 patients was 4.2% (18/430), while being undetectable in an uninfected control cohort. Neutralizing IFN-AABs were detectable exclusively in critically affected, predominantly male (83%) patients (7.6% IFN-α and 4.6% IFN-ω in 207 patients with critical COVID-19). IFN-AABs were present early post-symptom onset and at the peak of disease. Fever and oxygen requirement at hospital admission co-presented with neutralizing IFN-AAB positivity. IFN-AABs were associated with higher mortality (92.3% versus 19.1 % in patients without IFN-AABs). TPE reduced levels of IFN-AABs in three of five patients and may increase survival of IFN-AAB-positive patients compared to those not undergoing TPE.ConclusionIFN-AABs may serve as early biomarker for development of severe COVID-19. We propose to implement routine screening of hospitalized COVID-19 patients according to our algorithm for rapid identification of patients with IFN-AABs who most likely benefit from specific therapies.
Published: 2021

44. SARS-CoV-2 infects human GnRH neurons and tanycytes, disrupting hypothalamic-pituitary hormonal axes

Author: Erik Hrabovszky, Marc Baroncini, F. Pasquier, Caio Coelho, Claude-Alain Maurage, Ariane Sharif, Sreekala Nampoothiri, Asis Palazon, Pascal Pigny, Julien Poissy, Julie Dam, Florent Sauve, Ralf Jockers, Laurent Storme, François Trottein, Konstantina Chachlaki, Thibaud Lebouvier, Romain Perbet, Paolo Giacobini, Julie Dewisme, Sophie Catteau-Jonard, Vincent Florent, Daniela Fernandois, Sowmyalakshmi Rasika, Maria Mercado-Gómez, Gaetan Ternier, María L. Martínez-Chantar, Erika Cecon, Markus Schwaninger, Rubén Nogueiras, Virginie Mattot, June Ereño-Orbea, Vincent Prevot, Cristina Iglesias, Helge Müller-Fielitz, and Ludovica Cotellessa
Subjects: medicine.medical_specialty, Fetus, Vomeronasal organ, Biology, medicine.disease, Formyl peptide receptor 2, Pathogenesis, Vomeronasal receptor, Endocrinology, Hypogonadotropic hypogonadism, Internal medicine, medicine, Receptor, Hormone
Abstract: Neuroinvasion by SARS-CoV-2 is now accepted. To investigate whether low testosterone levels observed in men with severe COVID-19 could be of central origin, we retrospectively analyzed blood samples from 60 male intensive-care patients and explored SARS-CoV-2 brain entry using animal and cellular models as well as adult COVID-19 patient and fetal human brains. Most hypotestosteronemic patients displayed hypogonadotropic hypogonadism or abnormal hypothalamic-pituitary-gonadal axis regulation. Neurons producing gonadotropin-releasing hormone (GnRH), the master molecule controlling fertility, expressed angiotensin-converting enzyme 2 and neuropilin-1, two host-cell factors mediating infection, and were infected and dying in all COVID-19 patient brains. Tanycytes - hypothalamic glia that regulate GnRH secretion - were also infected. Additionally, human fetal olfactory and vomeronasal epithelia, from which GnRH neurons arise, richly expressed both the above host-cell susceptibility factors and formyl peptide receptor 2, a putative vomeronasal receptor that also appeared involved in SARS-CoV-2 pathogenesis in humans and mice. Finally, a fetal human GnRH cell line expressing all these receptors could be infected by a SARS-CoV-2-like pseudovirus. Together, our findings suggest that GnRH neurons, which may be implicated in brain development and aging in addition to reproduction, are particularly vulnerable to SARS-CoV-2 in both adults and fetuses/newborns, with potentially devastating long-term consequences.
Published: 2021

45. Autoinhibition and regulation by phosphoinositides of ATP8B1, a human lipid flippase associated with intrahepatic cholestatic disorders

Author: Thibaud Dieudonné, Kahina Slimani, Poul Nissen, Charlott Stock, Michelle Juknaviciute Laursen, Cédric Montigny, Christine Jaxel, Thomas Günther Pomorski, Joseph A. Lyons, Sara Abad Herrera, Guillaume Lenoir, and Maylis Lejeune
Subjects: biology, Chemistry, ATPase, Progressive familial intrahepatic cholestasis, Transporter, Flippase, medicine.disease, Cell biology, Cytosol, ATP hydrolysis, medicine, biology.protein, Endomembrane system, Gene
Abstract: P-type ATPases from the P4 subfamily (P4-ATPases) are primary active transporters that maintain lipid asymmetry in eukaryotic cell membranes by flipping lipids from the exoplasmic to the cytosolic leaflet. Mutations in several human P4-ATPase genes are associated with severe diseases. For instance, mutations in the ATP8B1 gene result in progressive familial intrahepatic cholestasis, a rare inherited disorder that usually progresses toward liver failure. ATP8B1 forms a binary complex with CDC50A and displays a broad specificity to glycerophospholipids, but regulatory mechanisms are unknown. Here, we report the cryo-EM structure of the human lipid flippase ATP8B1-CDC50A at 3.1 angstrom resolution. The lipid flippase complex is autoinhibited by the N- and C-termini of ATP8B1, which in concert form extensive interactions with the catalytic sites and flexible domain interfaces of ATP8B1. Consistently, ATP hydrolysis by the ATP8B1-CDC50A complex requires truncation of its C-terminus as well as the presence of phosphoinositides, with a marked preference for phosphatidylinositol-3,4,5-phosphate (PI(3,4,5)P3), and removal of both N- and C-termini results in full activation. Restored inhibition of ATP8B1 truncation constructs with a synthetic peptide mimicking the C-terminus further suggests molecular communication between N- and C-termini in the autoinhibition process and demonstrates that the regulatory mechanism can be interfered with by exogenous compounds. A conserved (G/A)(Y/F)AFS motif in the C-termini of several P4-ATPase subfamilies suggests that this mechanism is employed widely across P4-ATPase lipid flippases, including both plasma membrane and endomembrane P4-ATPases.
Published: 2021

46. Divergent Expression of SPARC, SPARC-L, and SCPP Genes During Jawed Vertebrate Cartilage Mineralization

Author: David Muñoz, Mélanie Debiais-Thibaud, Nicolas Leurs, Sylvain Marcellini, and Adrian Romero
Subjects: Lineage (genetic), Xenopus, In situ hybridization, QH426-470, Scyliorhinus canicula, biology.animal, medicine, Genetics, Xenopus tropicalis, vertebrate evolution, Gene, Genetics (clinical), Original Research, SCPP, biology, Cartilage, Vertebrate, SPARC, biology.organism_classification, medicine.disease, cartilage mineralization, Cell biology, medicine.anatomical_structure, Phosphoprotein, Molecular Medicine, SPARC-L, Calcification
Abstract: While cartilage is an ancient tissue found both in protostomes and deuterostomes, its mineralization evolved more recently, within the vertebrate lineage. SPARC, SPARC-L, and the SCPP members (Secretory Calcium-binding PhosphoProtein genes which evolved from SPARC-L) are major players of dentine and bone mineralization, but their involvement in the emergence of the vertebrate mineralized cartilage remains unclear. We performed in situ hybridization on mineralizing cartilaginous skeletal elements of the frog Xenopus tropicalis (Xt) and the shark Scyliorhinus canicula (Sc) to examine the expression of SPARC (present in both species), SPARC-L (present in Sc only) and the SCPP members (present in Xt only). We show that while mineralizing cartilage expresses SPARC (but not SPARC-L) in Sc, it expresses the SCPP genes (but not SPARC) in Xt, and propose two possible evolutionary scenarios to explain these opposite expression patterns. In spite of these genetic divergences, our data draw the attention on an overlooked and evolutionarily conserved peripheral cartilage subdomain expressing SPARC or the SCPP genes and exhibiting a high propensity to mineralize.
Published: 2021

47. Patch-seq of mouse DRG neurons reveals candidate genes for specific mechanosensory functions

Author: Thibaud Parpaite, Yasmine Mechioukhi, Nina Séjourné, Patrick Delmas, Bertrand Coste, Lucie Brosse, Amandine Laur, Laboratoire de Neurosciences Cognitives [Marseille] (LNC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Candidate gene, Patch-Clamp Techniques, sensory neuron, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [SDV]Life Sciences [q-bio], Somatosensory system, Mechanotransduction, Cellular, Ion Channels, Membrane Potentials, Transcriptome, Mice, 0302 clinical medicine, Dorsal root ganglion, Ganglia, Spinal, Gene expression, pain, RNA-Seq, nociception, Biology (General), Mechanotransduction, ComputingMilieux_MISCELLANEOUS, Neurons, 0303 health sciences, medicine.anatomical_structure, Mechanosensitive channels, Single-Cell Analysis, somatosensation, dorsal root ganglion, QH301-705.5, In silico, Sensory system, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, Animals, Humans, mechanotransduction, 030304 developmental biology, Gene Expression Profiling, Membrane Proteins, RNA, Sensory neuron, Mice, Inbred C57BL, HEK293 Cells, Gene Expression Regulation, ion channel, NIH 3T3 Cells, Neuron, Neuroscience, 030217 neurology & neurosurgery
Abstract: Summary A variety of mechanosensory neurons are involved in touch, proprioception, and pain. Many molecular components of the mechanotransduction machinery subserving these sensory modalities remain to be discovered. Here, we combine recordings of mechanosensitive (MS) currents in mechanosensory neurons with single-cell RNA sequencing. Transcriptional profiles are mapped onto previously identified sensory neuron types to identify cell-type correlates between datasets. Correlation of current signatures with single-cell transcriptomes provides a one-to-one correspondence between mechanoelectric properties and transcriptomically defined neuronal populations. Moreover, a gene-expression differential comparison provides a set of candidate genes for mechanotransduction complexes. Piezo2 is expectedly found to be enriched in rapidly adapting MS current-expressing neurons, whereas Tmem120a and Tmem150c, thought to mediate slow-type MS currents, are uniformly expressed in all mechanosensory neuron subtypes. Further knockdown experiments disqualify them as mediating MS currents in sensory neurons. This dataset constitutes an open resource to explore further the cell-type-specific determinants of mechanosensory properties., Graphical abstract, Highlights • Patch-seq is performed on mechanically characterized DRG sensory neurons • Transcriptomically defined neuronal classes and current subtypes are correlated • Datasets of specific transcripts of current subtype-expressing neurons are generated • TACAN (Tmem120a) and Tentonin-3 (Tmem150c) do not contribute to DRG mechano-currents, Mechanosensation is the least understood sensory modality at the molecular level. Parpaite et al. combine single-cell RNA sequencing with mechanosensitive current recordings in cultured sensory neurons. One-to-one correspondence between mechanoelectric properties and single-cell transcriptomes provides a valuable resource for the identification of molecular factors involved in mechanosensation.
Published: 2021

48. Iron, Heme Synthesis and Erythropoietic Porphyrias: A Complex Interplay

Author: Hervé Puy, Caroline Schmitt, Arienne Mirmiran, Thibaud Lefebvre, Boualem Moulouel, Antoine Poli, and Laurent Gouya
Subjects: ferrochelatase, erythropoietic protoporphyria, Endocrinology, Diabetes and Metabolism, Congenital erythropoietic porphyria, Iron–sulfur cluster, Review, congenital erythropoietic porphyria, Biochemistry, Microbiology, chemistry.chemical_compound, iron-sulfur cluster, iron, medicine, protoporphyrin IX, Molecular Biology, Heme, Protoporphyrin IX, biology, Chemistry, ALAS2, Ferrochelatase, medicine.disease, hematopoiesis, QR1-502, biology.protein, Erythropoietic protoporphyria, Intracellular
Abstract: Erythropoietic porphyrias are caused by enzymatic dysfunctions in the heme biosynthetic pathway, resulting in porphyrins accumulation in red blood cells. The porphyrins deposition in tissues, including the skin, leads to photosensitivity that is present in all erythropoietic porphyrias. In the bone marrow, heme synthesis is mainly controlled by intracellular labile iron by post-transcriptional regulation: translation of ALAS2 mRNA, the first and rate-limiting enzyme of the pathway, is inhibited when iron availability is low. Moreover, it has been shown that the expression of ferrochelatase (FECH, an iron-sulfur cluster enzyme that inserts iron into protoporphyrin IX to form heme), is regulated by intracellular iron level. Accordingly, there is accumulating evidence that iron status can mitigate disease expression in patients with erythropoietic porphyrias. This article will review the available clinical data on how iron status can modify the symptoms of erythropoietic porphyrias. We will then review the modulation of heme biosynthesis pathway by iron availability in the erythron and its role in erythropoietic porphyrias physiopathology. Finally, we will summarize what is known of FECH interactions with other proteins involved in iron metabolism in the mitochondria.
Published: 2021

49. In memoriam Christian Peeters (1956–2020)

Author: Claudie Doums, Mathieu Molet, and Thibaud Monnin
Subjects: Insect Science, Biology, Theology, Ecology, Evolution, Behavior and Systematics
Published: 2021

50. Global data on earthworm abundance, biomass, diversity and corresponding environmental properties

Author: Phillips, Helen R. P., Bach, Elizabeth M., Bartz, Marie L. C., Bennett, Joanne M., Beugnon, Rémy, Briones, Maria J. I., Brown, George G., Ferlian, Olga, Gongalsky, Konstantin B., Guerra, Carlos A., König-Ries, Birgitta, Krebs, Julia J., Orgiazzi, Alberto, Ramirez, Kelly S., Russell, David J., Schwarz, Benjamin, Wall, Diana H., Brose, Ulrich, Decaëns, Thibaud, Lavelle, Patrick, Loreau, Michel, Mathieu, Jérôme, Mulder, Christian, van der Putten, Wim H., Rillig, Matthias C., Thakur, Madhav P., de Vries, Franciska T., Wardle, David A., Ammer, Christian, Ammer, Sabine, Arai, Miwa, Ayuke, Fredrick O., Baker, Geoff H., Baretta, Dilmar, Barkusky, Dietmar, Beauséjour, Robin, Bedano, Jose C., Birkhofer, Klaus, Blanchart, Eric, Blossey, Bernd, Bolger, Thomas, Bradley, Robert L., Brossard, Michel, Burtis, James C., Capowiez, Yvan, Cavagnaro, Timothy R., Choi, Amy, Clause, Julia, Cluzeau, Daniel, Coors, Anja, Crotty, Felicity V., Crumsey, Jasmine M., Dávalos, Andrea, Cosín, Darío J. Díaz, Dobson, Annise M., Domínguez, Anahí, Duhour, Andrés Esteban, van Eekeren, Nick, Emmerling, Christoph, Falco, Liliana B., Fernández, Rosa, Fonte, Steven J., Fragoso, Carlos, Franco, André L. C., Fusilero, Abegail, Geraskina, Anna P., Gholami, Shaieste, González, Grizelle, Gundale, Michael J., López, Mónica Gutiérrez, Hackenberger, Branimir K., Hackenberger, Davorka K., Hernández, Luis M., Hirth, Jeff R., Hishi, Takuo, Holdsworth, Andrew R., Holmstrup, Martin, Hopfensperger, Kristine N., Lwanga, Esperanza Huerta, Huhta, Veikko, Hurisso, Tunsisa T., Iannone III, Basil V., Iordache, Madalina, Irmler, Ulrich, Ivask, Mari, Jesús, Juan B., Johnson-Maynard, Jodi L., Joschko, Monika, Kaneko, Nobuhiro, Kanianska, Radoslava, Keith, Aidan M., Kernecker, Maria L., Koné, Armand W., Kooch, Yahya, Kukkonen, Sanna T., Lalthanzara, H., Lammel, Daniel R., Lebedev, Iurii M., Le Cadre, Edith, Lincoln, Noa K., López-Hernández, Danilo, Loss, Scott R., Marichal, Raphael, Matula, Radim, Minamiya, Yukio, Moos, Jan Hendrik, Moreno, Gerardo, Morón-Ríos, Alejandro, Motohiro, Hasegawa, Muys, Bart, Neirynck, Johan, Norgrove, Lindsey, Novo, Marta, Nuutinen, Visa, Nuzzo, Victoria, Mujeeb Rahman, P., Pansu, Johan, Paudel, Shishir, Pérès, Guénola, Pérez-Camacho, Lorenzo, Ponge, Jean-François, Prietzel, Jörg, Rapoport, Irina B., Rashid, Muhammad Imtiaz, Rebollo, Salvador, Rodríguez, Miguel Á., Roth, Alexander M., Rousseau, Guillaume X., Rozen, Anna, Sayad, Ehsan, van Schaik, Loes, Scharenbroch, Bryant, Schirrmann, Michael, Schmidt, Olaf, Schröder, Boris, Seeber, Julia, Shashkov, Maxim P., Singh, Jaswinder, Smith, Sandy M., Steinwandter, Michael, Szlavecz, Katalin, Talavera, José Antonio, Trigo, Dolores, Tsukamoto, Jiro, Uribe-López, Sheila, de Valença, Anne W., Virto, Iñigo, Wackett, Adrian A., Warren, Matthew W., Webster, Emily R., Wehr, Nathaniel H., Whalen, Joann K., Wironen, Michael B., Wolters, Volkmar, Wu, Pengfei, Zenkova, Irina V., Zhang, Weixin, Cameron, Erin K., Eisenhauer, Nico, German Centre for Integrative Biodiversity Research (iDiv), Leipzig University, Saint Mary's University [Halifax], Colorado State University [Fort Collins] (CSU), University of Coimbra [Portugal] (UC), Martin-Luther-University Halle-Wittenberg, University of Canberra, Universidade de Vigo, Embrapa Forestry, Brazilian Agricultural Research Corporation (Embrapa), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Lomonosov Moscow State University (MSU), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], European Commission - Joint Research Centre [Ispra] (JRC), Netherlands Institute of Ecology (NIOO-KNAW), University of Freiburg [Freiburg], Department of Biometry and Environmental System Analysis, Albert-Ludwigs-Universität Freiburg, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Catania [Italy], Wageningen University and Research [Wageningen] (WUR), Freie Universität Berlin, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), Asian School of the Environment (ASE), Nanyang Technological University [Singapour], Georg-August-University = Georg-August-Universität Göttingen, National Agriculture and Food Research Organization (NARO), University of Nairobi (UoN), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Santa Catarina State University (UDESC), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Université de Sherbrooke (UdeS), National University of Río Cuarto = Universidad Nacional de Río Cuarto (UNRC), Brandenburg University of Technology [Cottbus – Senftenberg] (BTU), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Cornell University [New York], University College Dublin [Dublin] (UCD), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Adelaide, University of Toronto, Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), ECT Oekotoxikologie GmbH, Institute of Biological, Environmental and Rural Sciences (IBERS), Biotechnology and Biological Sciences Research Council (BBSRC)-Aberystwyth University, Royal Agricultural University (RAU), University of Georgia [USA], State University of New York (SUNY), Department of Biodiversity, Ecology and Evolution [Madrid], Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Yale University [New Haven], Universidad Nacional de Luján [Buenos Aires], Louis Bolk Institute (LBI), Trier University, Animal Biodiversity and Evolution, Institute of Evolutionary Biology (IBE), Department of Soil and Crop Sciences [Fort Collins], Biodiversity and Systematic Network, Instituto de Ecología A.C., Department of Biology [Fort Collins], Department of Biological Science and Environmental Studies, University of the Philippines - Mindanao, Faculty of Bioscience Engineering - Laboratory of Environmental Toxicology and Aquatic Ecology, Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Forest Ecology and Productivity (RAS), Razi University of Kermanshah, USDA Forest Service, Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Josip Juraj Strossmayer University of Osijek, Agriculture engineering, Agroecology Postgraduate Program, Maranhão State University, Agriculture Victoria (AgriBio), Kyushu University [Fukuoka], Minnesota Pollution Control Agency, Department of Bioscience [Aarhus], Northern Kentucky University, Departamento de Agricultura, Sociedad y Ambiente, EI Colegio de la Frontera Sur (ECOSUR), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT)-Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Soil Physics and Land Management Group, University of Jyväskylä (JYU), College of Agriculture, Environmental and Human Sciences, Lincoln University of Missouri, School of Forest Resources and Conservation [Gainesville] (UF|IFAS|FFGS), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Banat University of Agricultural Sciences and Veterinary Medicine (USAMVBT), Christian-Albrechts University of Kiel, Tallinn University of Technology (TTÜ), University of Idaho [Moscow, USA], Faculty of Food and Agricultural Sciences, Fukushima University, Matej Bel University (UMB), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), Université Nangui Abrogoua (UNA), Faculty of Natural Resources and Marine Sciences [Tarbiat], Tarbiat Modares University [Tehran], Natural Resources Institute Finland (LUKE), Department of Zoology, Pachhunga University College, Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Sol Agro et hydrosystème Spatialisation (SAS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, University of Hawai'i [Honolulu] (UH), Universidad Central de Venezuela (UCV), Instituto de Zoología y Ecología Tropical (IZET), Oklahoma State University [Stillwater] (OSU), Agrosystèmes Biodiversifiés (UMR ABSys), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Czech University of Life Sciences Prague (CZU), Tochigi Prefectural Museum, Thuenen-Institute of Biodiversity, Thuenen-Institute of Organic Farming, University of Extremadura, INDEHESA, Forestry School, Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Doshisha University [Kyoto], Department of Earth and Environmental Sciences [Leuven-Heverlee], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Research Institute for Nature and Forest (INBO), School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences (BFH), Natural Area Consultants, Department of Zoology, PSMO College, CSIRO Marine and Atmospheric Research (CSIRO-MAR), Adaptation et diversité en milieu marin (AD2M), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Phipps Conservatory and Botanical Gardens (PHIPPS), Universidad de Alcalá - University of Alcalá (UAH), Forest Ecology and Restoration Group, Department of Life Sciences, Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Department of Ecology and Ecosystem Management, Geobotany, Tembotov Institute of Ecology of Mountain Territories, Russian Academy of Sciences, King Abdulaziz University, Center of Excellence in Environmental Studies, Global Change Ecology and Evolution Research Groupp (GloCEE), Department of Life Sciences, University of Alcalá, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Postgraduate Program in Biodiversity and Conservation, Federal University of Maranhão, Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), College of Natural Resources, University of Wisconsin, The Morton Arboretum, Department Engineering for Crop Production, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), School of Agriculture and Food Science, UCD School of Geography, UCD Earth Institute, University College, Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], Institute of Geoecology, Leopold Franzens Universität Innsbruck - University of Innsbruck, European Academy Bozen/Bolzano (EURAC), Institute for Alpine Environment, European Academy of Bozen-Bolzano (EURAC), Institute of Physicochemical and Biological Problems in Soil Science, RAS, Institute of Mathematical Problems in Biology (IMPB RAS), Post Graduate Department of Zoology, Khalsa College Amritsar, Morton K. Blaustein Department of Earth and Planetary Sciences [Baltimore], Johns Hopkins University (JHU), Universidad de La Laguna [Tenerife - SP] (ULL), Kochi University, Juárez Autonomous University of Tabasco, Nanotechnology Engineering, Multidisciplinary Academic Division of Jalpa de Méndez, Food & Agriculture, WWF-Netherlands, Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), Department of Soil, Water and Climate, University of Minnesota System-University of Minnesota System, Earth Innovation Institute, University of California [Davis] (UC Davis), University of California (UC), Department of Natural Resources and Environmental Management, University of Hawaii, McGill University = Université McGill [Montréal, Canada], Natural resource sciences, The Nature Conservancy, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Southwest Minzu University [Chengdu], Institute of Industrial Ecology Problems of the North of the Kola Science Center of RAS, Henan Agricultural University, Faculty of Biological and Environmental Sciences [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki, H.R.P.P., B.K-R., and the sWorm workshops were supported by the sDiv [Synthesis Centre of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (DFG FZT 118)]. H.R.P.P., O.F. and N.E. acknowledge funding by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 677232 to NE). K.S.R. and W.H.v.d.P. were supported by ERC-ADV grant 323020 to W.H.v.d.P. Also supported by iDiv (DFG FZT118) Flexpool proposal 34600850 (C.A.G. and N.E.), the Academy of Finland (285882) and the Natural Sciences and Engineering Research Council of Canada (postdoctoral fellowship and RGPIN-2019-05758) (E.K.C.), German Federal Ministry of Education and Research (01LO0901A) (D.J.R.), ERC-AdG 694368 (M.R.), the TULIP Laboratory of Excellence (ANR-10-LABX-41) (M.L), and the BBSRC David Phillips Fellowship to F.T.d.V. (BB/L02456X/1). In addition, data collection was funded by the Russian Foundation for Basic Research (12-04-01538-a, 12-04-01734-a, 14-44-03666-r_center_a, 15-29-02724-ofi_m, 16-04-01878-a 19-05-00245, 19-04-00-609-a), Tarbiat Modares University, Aurora Organic Dairy, UGC(NERO) (F. 1-6/Acctt./NERO/2007-08/1485), Natural Sciences and Engineering Research Council (RGPIN-2017-05391), Slovak Research and Development Agency (APVV-0098-12), Science for Global Development through Wageningen University, Norman Borlaug LEAP Programme and International Atomic Energy Agency (IAEA), Sao Paulo Research Foundation - FAPESP (12/22510-8), Oklahoma Agricultural Experiment Station, INIA - Spanish Agency (SUM 2006-00012-00-0), Royal Canadian Geographical Society, Environmental Protection Agency (Ireland) (2005-S-LS-8), University of Hawai'i at Manoa (HAW01127H, HAW01123M), European Union FP7 (FunDivEurope, 265171, ROUTES 265156), U.S. Department of the Navy, Commander Pacific Fleet (W9126G-13-2-0047), Science and Engineering Research Board (SB/SO/AS-030/2013) Department of Science and Technology, New Delhi, India, Strategic Environmental Research and Development Program (SERDP) of the U.S. Department of Defense (RC-1542), Maranhao State Research Foundation (FAPEMA 03135/13, 02471/17), Coordination for the Improvement of Higher Education Personnel (CAPES 3281/2013), Ministry of Education, Youth and Sports of the Czech Republic (LTT17033), Colorado Wheat Research Foundation, Zone Atelier Alpes, French National Research Agency (ANR-11-BSV7-0020, ANR-09-STRA-0002, ANR 06 BIODIV 0009), Austrian Science Fund (P16027, T441), Landwirtschaftliche Rentenbank Frankfurt am Main, Welsh Government and the European Agricultural Fund for Rural Development (Project Ref. A AAB 62 03 qA731606), SEPAQ, Ministry of Agriculture and Forestry of Finland, Science Foundation Ireland (EEB0061), University of Toronto (Faculty of Forestry), National Science and Engineering Research Council of Canada, Haliburton Forest & Wildlife Reserve, NKU College of Arts & Sciences Grant, osterreichische Forschungsforderungsgesellschaft (837393 and 837426), Mountain Agriculture Research Unit of the University of Innsbruck, Higher Education Commission of Pakistan, Kerala Forest Research Institute, Peechi, Kerala, UNEP/GEF/TSBF-CIAT Project on Conservation and Sustainable Management of Belowground Biodiversity, Ministry of Agriculture and Forestry of Finland, Complutense University of Madrid/European Union FP7 project BioBio (FPU UCM 613520), GRDC, AWI, LWRRDC, DRDC, CONICET (National Scientific and Technical Research Council) and FONCyT (National Agency of Scientific and Technological Promotion) (PICT, PAE, PIP), Universidad Nacional de Lujan y FONCyT (PICT 2293 (2006)), Fonds de recherche sur la nature et les technologies du Quebec (131894), Deutsche Forschungsgemeinschaft (SCHR1000/3-1, SCHR1000/6-1, 6-2 (FOR 1598), WO 670/7-1, WO 670/7-2, & SCHA 1719/1-2), CONACYT (FONDOS MIXTOS TABASCO/PROYECTO11316), NSF (DGE-0549245, DGE-0549245, DEB-BE-0909452, NSF1241932, LTER Program DEB-97-14835), Institute for Environmental Science and Policy at the University of Illinois at Chicago, Dean's Scholar Program at UIC, Garden Club of America Zone VI Fellowship in Urban Forestry from the Casey Tree Endowment Fund, J.E. Weaver Competitive Grant from the Nebraska Chapter of The Nature Conservancy, The College of Liberal Arts and Sciences at Depaul University, Elmore Hadley Award for Research in Ecology and Evolution from the UIC Dept. of Biological Sciences, Spanish CICYT (AMB96-1161, REN2000-0783/GLO, REN2003-05553/GLO, REN2003-03989/GLO, CGL2007-60661/BOS), Yokohama National University, MEXT KAKENHI (25220104), Japan Society for the Promotion of Science KAKENHI (25281053, 17KT0074, 25252026), ADEME (0775C0035), Ministry of Science, Innovation and Universities of Spain (CGL2017-86926-P), Syngenta Philippines, UPSTREAM, LTSER (Val Mazia/Matschertal), Marie Sklodowska Curie Postdoctoral Fellowship (747607), National Science & Technology Base Resource Survey Project of China (2018FY100306), McKnight Foundation (14-168), Program of Fundamental Researches of Presidium of Russian Academy of Sciences (AAAA-A18-118021490070-5), Brazilian National Council for Scientific and Technological Development (CNPq 310690/2017-0, 404191/2019-3, 307486/2013-3), French Ministry of Foreign and European Affairs, Bavarian Ministry for Food, Agriculture and Forestry (Project No B62), INRA AIDY project, MIUR PRIN 2008, Idaho Agricultural Experiment Station, Estonian Science Foundation, Ontario Ministry of the Environment, Canada, Russian Science Foundation (16-17-10284), National Natural Science Foundation of China (41371270), Australian Research Council (FT120100463), USDA Forest Service-IITF. Open Access funding enabled and organized by Projekt DEAL., ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-BSV7-0020,METABAR,Metacode-barre ADN pour une nouvelle génération de suivi de la biodiversité(2011), ANR-09-STRA-0002,FORGECO,Du diagnostic à l'action: créer les conditions d'une gestion integrée et viable des écosystèmes forestiers sur les territoires(2009), ANR-06-BDIV-0009,AMAZ_BD,Biodiversité des paysages amazoniens. Déterminants socio-économiques et productio de biens et services écosystèmiques(2006), European Project: 677232,H2020,ERC-2015-STG,ECOWORM(2016), European Project: 323020,EC:FP7:ERC,ERC-2012-ADG_20120314,SPECIALS(2013), European Project: 265171,EC:FP7:ENV,FP7-ENV-2010,FUNDIVEUROPE(2010), European Project: 265156,EC:FP7:ENV,FP7-ENV-2010,ROUTES(2011), European Project: ERC-2015-AdG 694368, European Project: 227161,EC:FP7:KBBE,FP7-KBBE-2008-2B,BIOBIO(2009), Terrestrial Ecology (TE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Department of Natural Resources & The Environment [CALS], College of Agriculture and Life Sciences [Cornell University] (CALS), Cornell University [New York]-Cornell University [New York], Department of Entomology [CALS], Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Kyushu University, Universidad de Extremadura - University of Extremadura (UEX), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa. ISFOOD - Institute for Innovation and Sustainable Development in Food Chain, Universidad Pública de Navarra. Departamento de Ciencias, Nafarroako Unibertsitate Publikoa. Zientziak Saila, Global Soil Biodiversity Initiative and School of Global Environmental Sustainability, Colorado State University, Universidade Positivo, Senckenberg Museum for Natural History Görlitz, Department of Soil Zoology, Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station d'écologie théorique et expérimentale (SETE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), University of Göttingen - Georg-August-Universität Göttingen, Centre of Biodiversity and Sustainable Land Use, Department of Silviculture and Forest Ecology of the Temperate Zones, Georg-August-University [Göttingen], Faculty of Forest Sciences and Forest Ecology, Institute for Agro-Environmental Sciences, Rwanda Institute for Conservation Agriculture (RICA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UCD School of Biology & Environmental Science, UCD Earth Institute, University College Dublin, School of Agriculture, Food and Wine, Waite Research Institute, Faculty of Forestry, University of Toronto, Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Aberystwyth University, Odum School of Ecology, Department of Biological Sciences, SUNY Cortland, Yale School Forestry & Environment Studies, Ciencias Básicas, Instituto de Ecología y Desarrollo Sustentable -INEDES, Universidad Nacional de Lujan, Université Nangui Abrogoua, Tarbiat Modaras University, AGROCAMPUS OUEST, Oklahoma State University [Stillwater], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Animal Biology (Zoology area), Science Faculty, University of La Laguna, University of California, Justus-Liebig-University [Gießen, Germany], University of Helsinki, HELEN R. P. PHILLIPS, German Centre for Integrative Biodiversity Research, ERIN K. CAMERON, Saint Mary’s University, NICO EISENHAUER, German Centre for Integrative Biodiversity Research, Leipzig University., Wageningen University, JOSÉ ANTONIO TALAVERA, University of La Laguna, DOLORES TRIGO, University Complutense of Madrid, JIRO TSUKAMOTO, Kochi University, SHEILA URIBE-LÓPEZ, Juárez Autonomous University of Tabasco, ANNE W. DE VALENÇA, Unit Food & Agriculture, WWF-Netherlands, IÑIGO VIRTO, Universidad Pública de Navarra, ADRIAN A. WACKETT, University of Minnesota, MATTHEW W. WARREN, Earth Innovation Institute, WEIXIN ZHANG, Henan University, DANIEL CLUZEAU, Université de Rennes, ANJA COORS, ECT Oekotoxikologie GmbH, FELICITY V. CROTTY, Aberystwyth Universtiy, Royal Agricultural University, JASMINE M. CRUMSEY, University of Georgia, Saint Marys University, ELIZABETH M. BACH, Colorado State University, MARIE L. C. BARTZ, Universidade Positivo, University of Coimbra, JOANNE M. BENNETT, German Centre for Integrative Biodiversity Research, Martin Luther University Halle-Wittenberg, RÉMY BEUGNON, German Centre for Integrative Biodiversity Research, MARIA J. I. BRIONES, Universidad de Vigo, GEORGE GARDNER BROWN, CNPF, OLGA FERLIAN, German Centre for Integrative Biodiversity Research, KONSTANTIN B. GONGALSKY, Russian Academy of Sciences, Lomonosov Moscow State University, CARLOS A. GUERRA, German Centre for Integrative Biodiversity Research, BIRGITTA KÖNIG-RIES, German Centre for Integrative Biodiversity Research, Friedrich Schiller University, JULIA J. KREBS, German Centre for Integrative Biodiversity Research, ALBERTO ORGIAZZI, European Commission, Joint Research Centre, KELLY S. RAMIREZ, Netherlands Institute of Ecology, DAVID J. RUSSELL, Senckenberg Museum for Natural History Görlitz, BENJAMIN SCHWARZ, University of Freiburg, DIANA H. WALL, Colorado State University, ULRICH BROSE, German Centre for Integrative Biodiversity Research, Friedrich Schiller University Jena, THIBAUD DECAËNS, Univ Paul Valéry Montpellier, PATRICK LAVELLE, Institut d’Ecologie et des Sciences de l’Environnement, MICHEL LOREAU, Theoretical and Experimental Ecology Station, JÉRÔME MATHIEU, Institute of Ecology and Environmental Sciences of Paris, Institut d’Ecologie et des Sciences de l’Environnement de Paris, CHRISTIAN MULDER, University of Catania, WIM H. VAN DER PUTTEN, Netherlands Institute of Ecology, MATTHIAS C. RILLIG, Freie Universität Berlin, MADHAV P. THAKUR, Netherlands Institute of Ecology, FRANCISKA T. DE VRIES, University of Amsterdam, DAVID A. WARDLE, Nanyang Technological University, CHRISTIAN AMMER, University of Göttingen, SABINE AMMER, University of Göttingen, MIWA ARAI, National Agriculture and Food Research Organization, FREDRICK O. AYUKE, University of Nairobi, Rwanda Institute for Conservation Agriculture, GEOFF H. BAKER, Health & Biosecurity, DILMAR BARETTA, Santa Catarina State University, DIETMAR BARKUSKY, Leibniz Centre for Agricultural Landscape Research, ROBIN BEAUSÉJOUR, Université de Sherbrooke, JOSE C. BEDANO, National University of Rio Cuarto, KLAUS BIRKHOFER, Brandenburg University of Technology, ERIC BLANCHART, Institut Agro, BERND BLOSSEY, Cornell University, THOMAS BOLGER, University College Dublin, ROBERT L. BRADLEY, Université de Sherbrooke, MICHEL BROSSARD, Institut Agro, JAMES C. BURTIS, Cornell University, YVAN CAPOWIEZ, Site Agroparc, TIMOTHY R. CAVAGNARO, The University of Adelaide, AMY CHOI, University of Toronto, JULIA CLAUSE, Université de Poitiers, ANDREA DÁVALOS, SUNY Cortland, DARÍO J. DÍAZ COSÍN, University Complutense of Madrid, ANNISE M. DOBSON, Yale University, ANAHÍ DOMÍNGUEZ, National University of Rio Cuarto, ANDRÉS ESTEBAN DUHOUR, Universidad Nacional de Luján, NICK VAN EEKEREN, Louis Bolk Institute, CHRISTOPH EMMERLING, University of Trier, LILIANA B. FALCO, Universidad Nacional de Luján, ROSA FERNÁNDEZ, Institute of Evolutionary Biology, STEVEN J. FONTE, Colorado State University, CARLOS FRAGOSO, Institute of Ecology A.C., ANDRÉ L. C. FRANCO, Colorado State University, ABEGAIL FUSILERO, University of the Philippines Mindanao, Ghent University, ANNA P. GERASKINA, Center for Forest Ecology and Productivity RAS, SHAIESTE GHOLAMI, Razi University, GRIZELLE GONZÁLEZ, International Institute of Tropical Forestry, MICHAEL J. GUNDALE, Swedish University of Agricultural Sciences, MÓNICA GUTIÉRREZ LÓPEZ, University Complutense of Madrid, BRANIMIR K. HACKENBERGER, University of Osijek, DAVORKA K. HACKENBERGER, University of Osijek, LUIS M. HERNÁNDEZ, Maranhão State University, JEFF R. HIRTH, Department of Jobs, Precincts and Regions, Agriculture Victoria, TAKUO HISHI, Kyushu University, ANDREW R. HOLDSWORTH, Minnesota Pollution Control Agency, MARTIN HOLMSTRUP, Aarhus University, KRISTINE N. HOPFENSPERGER, Northern Kentucky University, ESPERANZA HUERTA LWANGA, El Colegio de la Frontera Sur, Wageningen University & Research, VEIKKO HUHTA, University of Jyväskylä, TUNSISA T. HURISSO, Colorado State University, Lincoln University of Missouri, BASIL V. IANNONE III, University of Florida, MADALINA IORDACHE, University of Agricultural Sciences and Veterinary Medicine of Banat 'King Michael the 1st of Romania', ULRICH IRMLER, University of Kiel, MARI IVASK, Tallinn University of Technology, JUAN B. JESÚS, University Complutense of Madrid, JODI L. JOHNSON-MAYNARD, University of Idaho, MONIKA JOSCHKO, Leibniz Centre for Agricultural Landscape Research, NOBUHIRO KANEKO, Fukushima University, RADOSLAVA KANIANSKA, Matej Bel University, AIDAN M. KEITH, Leibniz Centre for Agricultural Landscape Research, MARIA L. KERNECKER, Leibniz Centre for Agricultural Landscape Research, ARMAND W. KONÉ, Université Nangui Abrogoua, YAHYA KOOCH, Tarbiat Modares University, SANNA T. KUKKONEN, Natural Resources Institute Finland, H. LALTHANZARA, Pachhunga University College, DANIEL R. LAMMEL, Freie Universität Berlin, IURII M. LEBEDEV, Russian Academy of Sciences, M.V. Lomonosov Moscow State University, Skolkovo Institute of Science and Technology, EDITH LE CADRE, Institut Agro, NOA K. LINCOLN, University of Hawai’i at Manoa, DANILO LÓPEZ-HERNÁNDEZ, Universidad Central de Venezuela, SCOTT R. LOSS, Oklahoma State University, RAPHAEL MARICHAL, Univ Montpellier, RADIM MATULA, Czech University of Life Sciences Prague, YUKIO MINAMIYA, Tochigi Prefectural Museum, JAN HENDRIK MOOS, Thuenen-Institute of Biodiversity, GERARDO MORENO, University of Extremadura, ALEJANDRO MORÓN-RÍOS, El Colegio de la Frontera Sur, HASEGAWA MOTOHIRO, Doshisha University, BART MUYS, Department of Earth & Environmental Sciences, Division of Forest, Nature and Landscape, JOHAN NEIRYNCK, Research Institute for Nature and Forest, LINDSEY NORGROVE, Bern University of Applied Sciences, MARTA NOVO, University Complutense of Madrid, VISA NUUTINEN, Natural Resources Institute Finland, VICTORIA NUZZO, Natural Area Consultants, P. MUJEEB RAHMAN, PSMO College, JOHAN PANSU, CSIRO Ocean and Atmosphere, Sorbonne Université, SHISHIR PAUDEL, Oklahoma State University, Phipps Conservatory and Botanical Gardens, GUÉNOLA PÉRÈS, CNRS-Université de Rennes, Institut Agro, LORENZO PÉREZ CAMACHO, University of Alcalá, JEAN-FRANÇOIS PONGE, Muséum National d’Histoire Naturelle, JÖRG PRIETZEL, Technical University of Munich, IRINA B. RAPOPORT, Russian Academy of Sciences, MUHAMMAD IMTIAZ RASHID, King Abdulaziz University, SALVADOR REBOLLO, University of Alcalá, MIGUEL Á. RODRÍGUEZ, University of Alcalá, ALEXANDER M. ROTH, University of Minnesot, Friends of the Mississippi River, GUILLAUME X. ROUSSEAU, Maranhão State University, Federal University of Maranhão, ANNA ROZEN, University of Wisconsin, EHSAN SAYAD, Razi University, LOES VAN SCHAIK, Wageningen University & Research, BRYANT SCHARENBROCH, University of Wisconsin, MICHAEL SCHIRRMANN, Leibniz Institute for Agricultural Engineering and Bioeconomy, OLAF SCHMIDT, University College Dublin, Agriculture and Food Science Centre, BORIS SCHRÖDER, Technische Universität Braunschweig, JULIA SEEBER, University of Innsbruck, MAXIM P. SHASHKOV, Russian Academy of Sciences, JASWINDER SINGH, Khalsa College Amritsar, SANDY M. SMITH, University of Toronto, MICHAEL STEINWANDTER, Institute for Alpine Environment, KATALIN SZLAVECZ, Johns Hopkins University, EMILY R. WEBSTER, University of California, NATHANIEL H. WEHR, University of Hawaii, JOANN K. WHALEN, Natural Resource Sciences, McGill University, MICHAEL B. WIRONEN, The Nature Conservancy, VOLKMAR WOLTERS, Animal Ecology, Justus Liebig University, PENGFEI WU, Southwest Minzu University, IRINA V. ZENKOVA, Institute of North Industrial Ecology Problems, Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), and Technical University of Munich (TUM)
Subjects: Data Descriptor, Distribuição Geográfica, Plan_S-Compliant-OA, Soil, Biomass, biodiversity, Diversity, Ecology, Biodiversidade, Biodiversity, eliöyhteisöt, maaperäeliöstö, PE&RC, Computer Science Applications, Multidisciplinary Sciences, Biogeography, international, 1181 Ecology, evolutionary biology, Ecosystem engineers, Science & Technology - Other Topics, Statistics, Probability and Uncertainty, Information Systems, Statistics and Probability, lierot, Science, Invertebrados, Library and Information Sciences, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Ecology and Environment, Education, eliömaantiede, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Minhoca, Serviço ambiental, BIODIVERSITY CHANGE, Life Science, Ecosystem services, Earthworms, Datasets, Animals, Spatial distribution, Community ecology, Oligochaeta, Laboratorium voor Nematologie, Ecosystem, 1172 Environmental sciences, biogeography, Science & Technology, LAND-USE, Biology and Life Sciences, PLATFORM, Bodemfysica en Landbeheer, Ecología, Ecossistema, biodiversiteetti, Soil Physics and Land Management, Solo, Biologia do Solo, maaperäeläimistö, 570 Life sciences, biology, eartworm, abundance, biomass, diversity, Laboratory of Nematology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, COMMUNITIES, community ecology
Abstract: Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change., Measurement(s) earthworm communities • Abundance • organic material • Diversity • environmental properties Technology Type(s) digital curation Factor Type(s) location Sample Characteristic - Organism Lumbricina Sample Characteristic - Environment soil Sample Characteristic - Location global Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13399118
Published: 2021

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