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3,393 results on '"Analysis"'

1. BrainGENIE: The Brain Gene Expression and Network Imputation Engine

Author: Jonathan L. Hess, Thomas P. Quinn, Chunling Zhang, Gentry C. Hearn, Samuel Chen, Neuropsychiatric Consortium for Analysis and Sharing of Transcriptomes, Sek Won Kong, Murray Cairns, Ming T. Tsuang, Stephen V. Faraone, and Stephen J. Glatt
Subjects: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Abstract In vivo experimental analysis of human brain tissue poses substantial challenges and ethical concerns. To address this problem, we developed a computational method called the Brain Gene Expression and Network-Imputation Engine (BrainGENIE) that leverages peripheral-blood transcriptomes to predict brain tissue-specific gene-expression levels. Paired blood–brain transcriptomic data collected by the Genotype-Tissue Expression (GTEx) Project was used to train BrainGENIE models to predict gene-expression levels in ten distinct brain regions using whole-blood gene-expression profiles. The performance of BrainGENIE was compared to PrediXcan, a popular method for imputing gene expression levels from genotypes. BrainGENIE significantly predicted brain tissue-specific expression levels for 2947–11,816 genes (false-discovery rate-adjusted p
Published: 2023
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2. Relationships between species richness and ecosystem services inAmazonian forests strongly infuenced by biogeographical strata and forest types

Author: Steur, Gijs, ter Steege, Hans, Verburg, René W., Sabatier, Daniel, Molino, Jean‑François, Bánki, Olaf S., Castellanos, Hernan, Stropp, Juliana, Fonty, Émile, Ruysschaert, Sofie, Galbraith, David, Kalamandeen, Michelle, van Andel, Tinde R., Brienen, Roel J. W., Phillips, Oliver L., Feeley, Kenneth J., Terborgh, John, Verweij, Pita A., Energy and Resources, Afd Biologie Algemeen, Afd. Botanische tuinen, Energy System Analysis, Sub Algemeen Biologie, Dutch Research Council, Agence Nationale de la Recherche (France), Afd. Botanische tuinen, Energy System Analysis, Energy and Resources, Systems Ecology, Apollo - University of Cambridge Repository, Utrecht University [Utrecht], Naturalis Biodiversity Center [Leiden], Vrije Universiteit Amsterdam [Amsterdam] (VU), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Université de Montpellier (UM), Universidad Nacional Experimental de Guayana, Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universiteit Gent = Ghent University (UGENT), University of Leeds, University of Cambridge [UK] (CAM), Laurentian University, Wageningen University and Research [Wageningen] (WUR), University of Miami, University of Florida [Gainesville] (UF), James Cook University (JCU), G.S. was supported by grant 022.006.011 from the Dutch Research Council (‘NWO’) for the Graduate Programme ‘Nature Conservation, Management and Restoration’. D.S. & J-F.M. benefited from an 'Investissement d’Avenir' grant managed by the Agence Nationale de la Recherche (CEBA: ANR-10-LABX-25-01), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Afd Biologie Algemeen, and Sub Algemeen Biologie
Subjects: Earth Observation and Environmental Informatics, Multidisciplinary, Tropical forests, Aboveground biomass, Biodiversity, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Forests, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Carbon, Biosystematiek, Trees, Carbon stocks, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Plant diversity, Aardobservatie en omgevingsinformatica, Ecosystem services, Life Science, Biosystematics, Tree diversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General, Plant ecology, Ecosystem, Productivity
Abstract: Despite increasing attention for relationships between species richness and ecosystem services, for tropical forests such relationships are still under discussion. Contradicting relationships have been reported concerning carbon stock, while little is known about relationships concerning timber stock and the abundance of non-timber forest product producing plant species (NTFP abundance). Using 151 1-ha plots, we related tree and arborescent palm species richness to carbon stock, timber stock and NTFP abundance across the Guiana Shield, and using 283 1-ha plots, to carbon stock across all of Amazonia. We analysed how environmental heterogeneity influenced these relationships, assessing differences across and within multiple forest types, biogeographic regions and subregions. Species richness showed significant relationships with all three ecosystem services, but relationships differed between forest types and among biogeographical strata. We found that species richness was positively associated to carbon stock in all biogeographical strata. This association became obscured by variation across biogeographical regions at the scale of Amazonia, resembling a Simpson’s paradox. By contrast, species richness was weakly or not significantly related to timber stock and NTFP abundance, suggesting that species richness is not a good predictor for these ecosystem services. Our findings illustrate the importance of environmental stratification in analysing biodiversity-ecosystem services relationships., G.S. was supported by grant 022.006.011 from the Dutch Research Council (‘NWO’) for the Graduate Programme ‘Nature Conservation, Management and Restoration’. D.S. & J-F.M. benefited from an “Investissement d’Avenir” grant managed by the Agence Nationale de la Recherche (CEBA: ANR-10-LABX-25-01).
Published: 2022
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3. A multimodal cell census and atlas of the mammalian primary motor cortex

Author: Callaway, Edward M., Dong, Hong-Wei, Ecker, Joseph R., Hawrylycz, Michael J., Huang, Z. Josh, Lein, Ed S., Ngai, John, Osten, Pavel, Ren, Bing, Tolias, Andreas Savas, White, Owen, Zeng, Hongkui, Zhuang, Xiaowei, Ascoli, Giorgio A., Behrens, M. Margarita, Chun, Jerold, Feng, Guoping, Gee, James C., Ghosh, Satrajit S., Halchenko, Yaroslav O., Hertzano, Ronna, Lim, Byung Kook, Martone, Maryann E., Ng, Lydia, Pachter, Lior, Ropelewski, Alexander J., Tickle, Timothy L., Yang, X. William, Zhang, Kun, Bakken, Trygve E., Berens, Philipp, Daigle, Tanya L., Harris, Julie A., Jorstad, Nikolas L., Kalmbach, Brian E., Kobak, Dmitry, Li, Yang Eric, Liu, Hanqing, Matho, Katherine S., Mukamel, Eran A., Naeemi, Maitham, Scala, Federico, Tan, Pengcheng, Ting, Jonathan T., Xie, Fangming, Zhang, Meng, Zhang, Zhuzhu, Zhou, Jingtian, Zingg, Brian, Armand, Ethan, Yao, Zizhen, Bertagnolli, Darren, Casper, Tamara, Crichton, Kirsten, Dee, Nick, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Dougherty, Elizabeth L., Fong, Olivia, Goldman, Melissa, Goldy, Jeff, Hodge, Rebecca D., Hu, Lijuan, Keene, C. Dirk, Krienen, Fenna M., Kroll, Matthew, Lake, Blue B., Lathia, Kanan, Linnarsson, Sten, Liu, Christine S., Macosko, Evan Z., McCarroll, Steven A., McMillen, Delissa, Nadaf, Naeem M., Nguyen, Thuc Nghi, Palmer, Carter R., Pham, Thanh, Plongthongkum, Nongluk, Reed, Nora M., Regev, Aviv, Rimorin, Christine, Romanow, William J., Savoia, Steven, Siletti, Kimberly, Smith, Kimberly, Sulc, Josef, Tasic, Bosiljka, Tieu, Michael, Torkelson, Amy, Tung, Herman, van Velthoven, Cindy T. J., Vanderburg, Charles R., Yanny, Anna Marie, Fang, Rongxin, Hou, Xiaomeng, Lucero, Jacinta D., Osteen, Julia K., Pinto-Duarte, Antonio, Poirion, Olivier, Preissl, Sebastian, Wang, Xinxin, Aldridge, Andrew I., Bartlett, Anna, Boggeman, Lara, O’Connor, Carolyn, Castanon, Rosa G., Chen, Huaming, Fitzpatrick, Conor, Luo, Chongyuan, Nery, Joseph R., Nunn, Michael, Rivkin, Angeline C., Tian, Wei, Dominguez, Bertha, Ito-Cole, Tony, Jacobs, Matthew, Jin, Xin, Lee, Cheng-Ta, Lee, Kuo-Fen, Miyazaki, Paula Assakura, Pang, Yan, Rashid, Mohammad, Smith, Jared B., Vu, Minh, Williams, Elora, Biancalani, Tommaso, Booeshaghi, A. Sina, Crow, Megan, Dudoit, Sandrine, Fischer, Stephan, Gillis, Jesse, Hu, Qiwen, Kharchenko, Peter V., Niu, Sheng-Yong, Ntranos, Vasilis, Purdom, Elizabeth, Risso, Davide, de Bézieux, Hector Roux, Somasundaram, Saroja, Street, Kelly, Svensson, Valentine, Vaishnav, Eeshit Dhaval, Van den Berge, Koen, Welch, Joshua D., An, Xu, Bateup, Helen S., Bowman, Ian, Chance, Rebecca K., Foster, Nicholas N., Galbavy, William, Gong, Hui, Gou, Lin, Hatfield, Joshua T., Hintiryan, Houri, Hirokawa, Karla E., Kim, Gukhan, Kramer, Daniel J., Li, Anan, Li, Xiangning, Luo, Qingming, Muñoz-Castañeda, Rodrigo, Stafford, David A., Feng, Zhao, Jia, Xueyan, Jiang, Shengdian, Jiang, Tao, Kuang, Xiuli, Larsen, Rachael, Lesnar, Phil, Li, Yaoyao, Li, Yuanyuan, Liu, Lijuan, Peng, Hanchuan, Qu, Lei, Ren, Miao, Ruan, Zongcai, Shen, Elise, Song, Yuanyuan, Wakeman, Wayne, Wang, Peng, Wang, Yimin, Wang, Yun, Yin, Lulu, Yuan, Jing, Zhao, Sujun, Zhao, Xuan, Narasimhan, Arun, Palaniswamy, Ramesh, Banerjee, Samik, Ding, Liya, Huilgol, Dhananjay, Huo, Bingxing, Kuo, Hsien-Chi, Laturnus, Sophie, Li, Xu, Mitra, Partha P., Mizrachi, Judith, Wang, Quanxin, Xie, Peng, Xiong, Feng, Yu, Yang, Eichhorn, Stephen W., Berg, Jim, Bernabucci, Matteo, Bernaerts, Yves, Cadwell, Cathryn René, Castro, Jesus Ramon, Dalley, Rachel, Hartmanis, Leonard, Horwitz, Gregory D., Jiang, Xiaolong, Ko, Andrew L., Miranda, Elanine, Mulherkar, Shalaka, Nicovich, Philip R., Owen, Scott F., Sandberg, Rickard, Sorensen, Staci A., Tan, Zheng Huan, Allen, Shona, Hockemeyer, Dirk, Lee, Angus Y., Veldman, Matthew B., Adkins, Ricky S., Ament, Seth A., Bravo, Héctor Corrada, Carter, Robert, Chatterjee, Apaala, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Felix, Victor, Giglio, Michelle, Herb, Brian R., Kancherla, Jayaram, Mahurkar, Anup, McCracken, Carrie, Nickel, Lance, Olley, Dustin, Orvis, Joshua, Schor, Michael, Hood, Greg, Dichter, Benjamin, Grauer, Michael, Helba, Brian, Bandrowski, Anita, Barkas, Nikolaos, Carlin, Benjamin, D’Orazi, Florence D., Degatano, Kylee, Gillespie, Thomas H., Khajouei, Farzaneh, Konwar, Kishori, Thompson, Carol, Kelly, Kathleen, Mok, Stephanie, Sunkin, Susan, BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, [missing], BICCN contributing principal investigators, [missing], Principal manuscript editors, [missing], Manuscript writing and figure generation, [missing], Analysis coordination, [missing], Integrated data analysis, [missing], scRNA-seq and snRNA-seq data generation and processing, [missing], ATAC-seq data generation and processing, [missing], Methylcytosine data production and analysis, [missing], Epi-retro-seq data generation and processing, [missing], ‘Omics data analysis, [missing], Tracing and connectivity data generation, [missing], Morphology data generation and reconstruction, [missing], OLST/STPT and other data generation, [missing], Morphology, connectivity and imaging analysis, [missing], Spatially resolved single-cell transcriptomics (MERFISH), [missing], Multimodal profiling (Patch-seq), [missing], Transgenic tools, [missing], NeMO archive and analytics, [missing], Brain Image Library (BIL) archive, [missing], DANDI archive, [missing], Brain Cell Data Center (BCDC), [missing], Project management, [missing], and BRAIN Initiative Cell Census Network (BICCN), [missing]
Subjects: Epigenomics, Male, INTERNEURONS, ORGANIZATION, MOUSE, Molecular neuroscience, Neural circuits, CLASSIFICATION, Article, Mice, Atlases as Topic, Glutamates, Species Specificity, Animals, Humans, TRANSCRIPTOMICS, SPECIFICATION, NEURONS, In Situ Hybridization, Fluorescence, Phylogeny, Neurons, Multidisciplinary, Gene Expression Profiling, Biology and Life Sciences, PATHWAYS, Brain, Callithrix, Censuses, Cellular neuroscience, Mathematics and Statistics, SINGLE, Organ Specificity, MORPHOLOGY, Motor cortex, Female, Single-Cell Analysis, Transcriptome
Abstract: Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties., The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.
Published: 2021

4. Strategy games to improve environmental policymaking

Author: Energy System Analysis, Energy and Resources, Garcia, Claude A., Savilaakso, Sini, Verburg, René W., Stoudmann, Natasha, Fernbach, Philip, Sloman, Steven A., Peterson, Garry D., Araújo, Miguel B., Bastin, Jean-François, Blaser, Jürgen, Boutinot, Laurence, Crowther, Thomas W., Dessard, Hélène, Dray, Anne, Francisco, Scott, Ghazoul, Jaboury, Feintrenie, Laurène, Hainzelin, Etienne, Kleinschroth, Fritz, Naimi, Babak, Novotny, Ivan P., Oszwald, Johan, Pietsch, Stephan A., Quétier, Fabien, Robinson, Brian E., Sassen, Marieke, Sist, Plinio, Sunderland, Terry, Vermeulen, Cédric, Wilmé, Lucienne, Wilson, Sarah J., Zorondo-Rodríguez, Francisco, Waeber, Patrick O., Energy System Analysis, Energy and Resources, Garcia, Claude A., Savilaakso, Sini, Verburg, René W., Stoudmann, Natasha, Fernbach, Philip, Sloman, Steven A., Peterson, Garry D., Araújo, Miguel B., Bastin, Jean-François, Blaser, Jürgen, Boutinot, Laurence, Crowther, Thomas W., Dessard, Hélène, Dray, Anne, Francisco, Scott, Ghazoul, Jaboury, Feintrenie, Laurène, Hainzelin, Etienne, Kleinschroth, Fritz, Naimi, Babak, Novotny, Ivan P., Oszwald, Johan, Pietsch, Stephan A., Quétier, Fabien, Robinson, Brian E., Sassen, Marieke, Sist, Plinio, Sunderland, Terry, Vermeulen, Cédric, Wilmé, Lucienne, Wilson, Sarah J., Zorondo-Rodríguez, Francisco, and Waeber, Patrick O.
Published: 2022

5. Initial sequence of the chimpanzee genome and comparison with the human genome

Author: and Analysis Consortium, The Chimpanzee Sequencing
Abstract: Author(s): The Chimpanzee Sequencing and Analysis Consortium [25] More than a century ago Darwin [1] and Huxley [2] posited that humans share recent common ancestors with the African great apes. [...]
Published: 2005
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6. Pan-cancer analysis of whole genomes

Author: IBM, Pharmacyclics, Novartis, Celgene, AstraZeneca, Bayer, Janssen Biotech, University of Chicago, Ipsen, Pfizer, Ono Pharmaceutical, Ariad Pharmaceuticals, Gilead Sciences, Bristol-Myers Squibb, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Heredia-Genestar, José María, Marqués-Bonet, Tomàs, Navarro, Arcadi, IBM, Pharmacyclics, Novartis, Celgene, AstraZeneca, Bayer, Janssen Biotech, University of Chicago, Ipsen, Pfizer, Ono Pharmaceutical, Ariad Pharmaceuticals, Gilead Sciences, Bristol-Myers Squibb, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Heredia-Genestar, José María, Marqués-Bonet, Tomàs, and Navarro, Arcadi
Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation; analyses timings and patterns of tumour evolution; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity; and evaluates a range of more-specialized features of cancer genomes.
Published: 2020

7. Pan-cancer analysis of whole genomes

Author: ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium and ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale$^{1-3}$. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter$^{4}$; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation$^{5,6}$; analyses timings and patterns of tumour evolution$^{7}$; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity$^{8,9}$; and evaluates a range of more-specialized features of cancer genomes$^{8,10-18}$.
Published: 2020

8. Effect of CYP4F2, VKORC1, and CYP2C9 in Influencing Coumarin Dose: A Single-Patient Data Meta-Analysis in More Than 15,000 Individuals

Author: Pharmacoepidemiology and Clinical Pharmacology, Energy System Analysis, Afd Pharmacoepi & Clinical Pharmacology, Danese, Elisa, Raimondi, Sara, Montagnana, Martina, Tagetti, Angela, Langaee, Taimour, Borgiani, Paola, Ciccacci, Cinzia, Carcas, Antonio J, Borobia, Alberto M, Tong, Hoi Y, Dávila-Fajardo, Cristina, Botton, Mariana Rodrigues, Bourgeois, Stephane, Deloukas, Panos, Caldwell, Michael D, Burmester, Jim K, Berg, Richard L, Cavallari, Larisa H, Drozda, Katarzyna, Huang, Min, Zhao, Li-Zi, Cen, Han-Jing, Gonzalez-Conejero, Rocio, Roldan, Vanessa, Nakamura, Yusuke, Mushiroda, Taisei, Gong, Inna Y, Kim, Richard B, Hirai, Keita, Itoh, Kunihiko, Isaza, Carlos, Beltrán, Leonardo, Jiménez-Varo, Enrique, Cañadas-Garre, Marisa, Giontella, Alice, Kringen, Marianne Kristiansen, Bente Foss Haug, Kari, Gwak, Hye Sun, Lee, Kyung Eun, Minuz, Pietro, Lee, Ming Ta Michael, Lubitz, Steven A, Scott, Stuart, Mazzaccara, Cristina, Sacchetti, Lucia, Ramirez, Andrea H, Zhang, Yumao, Maitland-van der Zee, Anke H, Verhoef, Talitha I, de Boer, Anthonius, Pharmacoepidemiology and Clinical Pharmacology, Energy System Analysis, Afd Pharmacoepi & Clinical Pharmacology, Danese, Elisa, Raimondi, Sara, Montagnana, Martina, Tagetti, Angela, Langaee, Taimour, Borgiani, Paola, Ciccacci, Cinzia, Carcas, Antonio J, Borobia, Alberto M, Tong, Hoi Y, Dávila-Fajardo, Cristina, Botton, Mariana Rodrigues, Bourgeois, Stephane, Deloukas, Panos, Caldwell, Michael D, Burmester, Jim K, Berg, Richard L, Cavallari, Larisa H, Drozda, Katarzyna, Huang, Min, Zhao, Li-Zi, Cen, Han-Jing, Gonzalez-Conejero, Rocio, Roldan, Vanessa, Nakamura, Yusuke, Mushiroda, Taisei, Gong, Inna Y, Kim, Richard B, Hirai, Keita, Itoh, Kunihiko, Isaza, Carlos, Beltrán, Leonardo, Jiménez-Varo, Enrique, Cañadas-Garre, Marisa, Giontella, Alice, Kringen, Marianne Kristiansen, Bente Foss Haug, Kari, Gwak, Hye Sun, Lee, Kyung Eun, Minuz, Pietro, Lee, Ming Ta Michael, Lubitz, Steven A, Scott, Stuart, Mazzaccara, Cristina, Sacchetti, Lucia, Ramirez, Andrea H, Zhang, Yumao, Maitland-van der Zee, Anke H, Verhoef, Talitha I, and de Boer, Anthonius
Published: 2019

9. Identification of common variants associated with human hippocampal and intracranial volumes

Author: Stein, Jason L, Medland, Sarah E, Bernard, Manon, Nauck, Matthias, Nöthen, Markus M., Olvera, Rene L, Pandolfo, Massimo, Pike, G Bruce, Puls, Ralf, Reinvang, Ivar, Rentería, Miguel E, Rietschel, Marcella, Roffman, Joshua L, Brown, Andrew A, Royle, Natalie A, Rujescu, Dan, Savitz, Jonathan, Schnack, Hugo G, Schnell, Knut, Seiferth, Nina, Smith, Colin, Steen, Vidar M, Valdés Hernández, Maria C, Van den Heuvel, Martijn, Cannon, Dara M, van der Wee, Nic J, Van Haren, Neeltje E M, Veltman, Joris A, Völzke, Henry, Walker, Robert, Westlye, Lars T, Whelan, Christopher D, Agartz, Ingrid, Boomsma, Dorret I, Cavalleri, Gianpiero L, Chakravarty, M Mallar, Dale, Anders M, Djurovic, Srdjan, Drevets, Wayne C, Hagoort, Peter, Hall, Jeremy, Heinz, Andreas, Jack, Clifford R, Foroud, Tatiana M, Le Hellard, Stephanie, Macciardi, Fabio, Christoforou, Andrea, Montgomery, Grant W, Poline, Jean Baptiste, Porteous, David J, Sisodiya, Sanjay M, Starr, John M, Sussmann, Jessika, Toga, Arthur W, Veltman, Dick J, Walter, Henrik, Weiner, Michael W, Domin, Martin, Initiative, Alzheimer's Disease Neuroimaging, Consortium, EPIGEN, Consortium, IMAGEN, Group, Saguenay Youth Study, Bis, Joshua C, Ikram, M Arfan, Smith, Albert V, Gudnason, Vilmundur, Tzourio, Christophe, Vernooij, Meike W, Grimm, Oliver, Launer, Lenore J, DeCarli, Charles, Seshadri, Sudha, Consortium, Cohorts for Heart and Aging Research in Genomic Epidemiology, Andreassen, Ole A, Apostolova, Liana G, Bastin, Mark E, Blangero, John, Brunner, Han G, Buckner, Randy L, Hollinshead, Marisa, Cichon, Sven, Coppola, Giovanni, de Zubicaray, Greig I, Deary, Ian J, Donohoe, Gary, de Geus, Eco J C, Espeseth, Thomas, Fernández, Guillén, Glahn, David C, Grabe, Hans J, Holmes, Avram J, Hardy, John, Hulshoff Pol, Hilleke E, Jenkinson, Mark, Kahn, René S, McDonald, Colm, McIntosh, Andrew M, McMahon, Francis J, McMahon, Katie L, Meyer-Lindenberg, Andreas, Morris, Derek W, Homuth, Georg, Müller-Myhsok, Bertram, Nichols, Thomas E, Ophoff, Roel A, Paus, Tomas, Pausova, Zdenka, Penninx, Brenda W, Potkin, Steven G, Sämann, Philipp G, Saykin, Andrew J, Schumann, Gunter, Vasquez, Alejandro Arias, Hottenga, Jouke-Jan, Smoller, Jordan W, Wardlaw, Joanna M, Weale, Michael E, Martin, Nicholas G, Franke, Barbara, Wright, Margaret J, Thompson, Paul M, Consortium, Enhancing Neuro Imaging Genetics through Meta-Analysis, Weiner, Michael, Aisen, Paul, Langan, Camilla, Petersen, Ronald, Jagust, William, Trojanowki, John Q, Beckett, Laurel, Green, Robert C, Morris, John, Liu, Enchi, Lopez, Lorna M, Montine, Tom, Gamst, Anthony, Thomas, Ronald G, Donohue, Michael, Walter, Sarah, Gessert, Devon, Sather, Tamie, Hansell, Narelle K, Harvey, Danielle, Kornak, John, Dale, Anders, Bernstein, Matthew, Felmlee, Joel, Fox, Nick, Hwang, Kristy S, Thompson, Paul, Schuff, Norbert, Alexander, Gene, Bandy, Dan, Koeppe, Robert A, Foster, Norm, Reiman, Eric M, Chen, Kewei, Mathis, Chet, Kim, Sungeun, Cairns, Nigel J, Taylor-Reinwald, Lisa, Trojanowki, J. Q., Shaw, Les, Lee, Virginia M Y, Korecka, Magdalena, Crawford, Karen, Neu, Scott, Laje, Gonzalo, Potkin, Steven, Shen, Li, Kachaturian, Zaven, Frank, Richard, Snyder, Peter J, Molchan, Susan, Kaye, Jeffrey, Quinn, Joseph, Lee, Phil H, Lind, Betty, Dolen, Sara, Schneider, Lon S, Pawluczyk, Sonia, Spann, Bryan M, Brewer, James, Vanderswag, Helen, Heidebrink, Judith L, Lord, Joanne L, Liu, Xinmin, Johnson, Kris, Doody, Rachelle S, Villanueva-Meyer, Javier, Chowdhury, Munir, Stern, Yaakov, Honig, Lawrence S, Bell, Karen L, Morris, John C, Ances, Beau, Carroll, Maria, Loth, Eva, Leon, Sue, Mintun, Mark A, Schneider, Stacy, Marson, Daniel, Griffith, Randall, Clark, David, Grossman, Hillel, Mitsis, Effie, Romirowsky, Aliza, deToledo-Morrell, Leyla, Hibar, Derrek P, Lourdusamy, Anbarasu, Shah, Raj C, Duara, Ranjan, Varon, Daniel, Roberts, Peggy, Albert, Marilyn, Onyike, Chiadi, Kielb, Stephanie, Rusinek, Henry, de Leon, Mony J, Glodzik, Lidia, Mattingsdal, Morten, De Santi, Susan, Doraiswamy, P Murali, Petrella, Jeffrey R, Coleman, R Edward, Arnold, Steven E, Karlawish, Jason H, Wolk, David, Smith, Charles D, Jicha, Greg, Hardy, Peter, Mohnke, Sebastian, Lopez, Oscar L, Oakley, MaryAnn, Simpson, Donna M, Porsteinsson, Anton P, Goldstein, Bonnie S, Martin, Kim, Makino, Kelly M, Ismail, M Saleem, Mulnard, Ruth A, Thai, Gaby, Maniega, Susana Muñoz, Mc-Adams-Ortiz, Catherine, Womack, Kyle, Mathews, Dana, Quiceno, Mary, Diaz-Arrastia, Ramon, King, Richard, Weiner, Myron, Martin-Cook, Kristen, DeVous, Michael, Levey, Allan I, Nho, Kwangsik, Lah, James J, Cellar, Janet S, Burns, Jeffrey M, Anderson, Heather S, Swerdlow, Russell H, Apostolova, Liana, Lu, Po H, Bartzokis, George, Silverman, Daniel H S, Graff-Radford, Neill R, Nugent, Allison C, Parfitt, Francine, Johnson, Heather, Farlow, Martin R, Hake, Ann Marie, Matthews, Brandy R, Herring, Scott, van Dyck, Christopher H, Carson, Richard E, MacAvoy, Martha G, Chertkow, Howard, O'Brien, Carol, Bergman, Howard, Hosei, Chris, Black, Sandra, Stefanovic, Bojana, Caldwell, Curtis, Hsiung, Ging-Yuek Robin, Feldman, Howard, Mudge, Benita, Assaly, Michele, Kertesz, Andrew, Papmeyer, Martina, Rogers, John, Trost, Dick, Bernick, Charles, Munic, Donna, Kerwin, Diana, Mesulam, Marek-Marsel, Lipowski, Kristina, Wu, Chuang-Kuo, Johnson, Nancy, Sadowsky, Carl, Pütz, Benno, Martinez, Walter, Villena, Teresa, Turner, Raymond Scott, Johnson, Kathleen, Reynolds, Brigid, Sperling, Reisa A, Johnson, Keith A, Marshall, Gad, Frey, Meghan, Yesavage, Jerome, Ramasamy, Adaikalavan, Taylor, Joy L, Lane, Barton, Rosen, Allyson, Tinklenberg, Jared, Sabbagh, Marwan, Belden, Christine, Jacobson, Sandra, Kowall, Neil, Killiany, Ronald, Budson, Andrew E, Senstad, Rudy E, Rasmussen, Jerod, Norbash, Alexander, Johnson, Patricia Lynn, Obisesan, Thomas O, Wolday, Saba, Bwayo, Salome K, Lerner, Alan, Hudson, Leon, Ogrocki, Paula, Fletcher, Evan, Carmichael, Owen, Rijpkema, Mark, Olichney, John, Kittur, Smita, Borrie, Michael, Lee, T-Y, Bartha, Rob, Johnson, Sterling, Asthana, Sanjay, Carlsson, Cynthia M, Risacher, Shannon L, Preda, Adrian, Nguyen, Dana, Tariot, Pierre, Fleisher, Adam, Reeder, Stephanie, Bates, Vernice, Capote, Horacio, Rainka, Michelle, Scharre, Douglas W, Kataki, Maria, Roddey, J Cooper, Zimmerman, Earl A, Celmins, Dzintra, Brown, Alice D, Pearlson, Godfrey D, Blank, Karen, Anderson, Karen, Santulli, Robert B, Schwartz, Eben S, Sink, Kaycee M, Rose, Emma J, Williamson, Jeff D, Garg, Pradeep, Watkins, Franklin, Ott, Brian R, Querfurth, Henry, Tremont, Geoffrey, Salloway, Stephen, Malloy, Paul, Correia, Stephen, Rosen, Howard J, Ryten, Mina, Miller, Bruce L, Mintzer, Jacobo, Longmire, Crystal Flynn, Spicer, Kenneth, Finger, Elizabeth, Rachinsky, Irina, Drost, Dick, Cavalleri, Gianpiero, Alhusaini, Saud, Delanty, Norman, Whelan, Christopher, Sisodiya, Sanjay, Kasperaviciute, Dalia, Matarin, Mar, Depondt, Chantal, Goldstein, David B, Heinzen, Erin L, Shianna, Kevin, Sprooten, Emma, Radtke, Rodney, Ottmann, Ruth, Sergievsky, G. H., Schumann, G., Conrod, P., Reed, L., Barker, G., Williams, S., Loth, E., Struve, M., Strengman, Eric, Lourdusamy, A., Cattrell, A., Nymberg, C., Topper, L., Smith, L., Havatzias, S., Stueber, K., Mallik, C., Stacey, D., Wong, C Peng, Teumer, Alexander, Werts, H., Andrew, C., Desrivieres, S., Heinz, A., Gallinat, J., Häke, I., Ivanov, N., Klär, A., Reuter, J., Winkler, Anderson M, Trabzuni, Daniah, Palafox, C., Hohmann, C., Schilling, C., Lüdemann, K., Romanowski, A., Ströhle, A., Wolff, E., Rapp, M., Ittermann, B., Brühl, R., Turner, Jessica, Ihlenfeld, A., Walaszek, B., Schubert, F., Garavan, H., Connolly, C., Jones, J., Lalor, E., McCabe, E., Ní Shiothcháin, A., Whelan, R., van Eijk, Kristel, Spanagel, R., Leonardi-Essmann, F., Sommer, W., Flor, H., Vollstaedt-Klein, S., Nees, F., Banaschewski, T., Poustka, L., Steiner, S., Mann, K., van Erp, Theo G M, Buehler, M., Rietschel, M., Stolzenburg, E., Schmal, C., Schirmbeck, F., Paus, T., Gowland, P., Heym, N., Lawrence, C., Newman, C., van Tol, Marie-Jose, Pausova, Z., Smolka, M., Huebner, T., Ripke, S., Mennigen, E., Muller, K., Ziesch, V., Büchel, C., Bromberg, U., Fadai, T., Wittfeld, Katharina, Lueken, L., Yacubian, J., Finsterbusch, J., Martinot, J. L., Artiges, E., Bordas, N., de Bournonville, S., Bricaud, Z., Gollier Briand, F., Lemaitre, H., Wolf, Christiane, Massicotte, J., Miranda, R., Paillère Martinot, M. L., Penttilä, J., Poline, J. B., Barbot, A., Schwartz, Y., Lalanne, C., Frouin, V., Thyreau, B., Woudstra, Saskia, Dalley, J., Mar, A., Robbins, T., Subramaniam, N., Theobald, D., Richmond, N., de Rover, M., Molander, A., Jordan, E., Robinson, E., Aleman, Andre, Hipolata, L., Moreno, M., Arroyo, M., Stephens, D., Ripley, T., Crombag, H., Pena, Y., Lathrop, M., Zelenika, D., Heath, S., Lanzerath, D., Heinrichs, B., Spranger, T., Fuchs, B., Speiser, C., Resch, F., Haffner, J., Parzer, P., Brunner, R., Klaassen, A., Toro, Roberto, Almasy, Laura, Klaassen, I., Constant, P., Mignon, X., Thomsen, T., Zysset, S., Vestboe, A., Ireland, J., Rogers, J., Binder, Elisabeth B, Chakravarty, Mallar, Smith, Albert Vernon, van der Lijn, Fedde, Crivello, Fabrice, Fornage, Myriam, Shulman, Joshua M, Brohawn, David G, Schmidt, Helena, Srikanth, Velandai, Schuur, Maaike, Yu, Lei, Choi, Seung-Hoan, Sigurdsson, Sigurdur, Verhaaren, Benjamin F J, DeStefano, Anita L, Lambert, Jean-Charles, Cantor, Rita M, Struchalin, Maksim, Stankovich, Jim, Ibrahim-Verbaas, Carla A, Fleischman, Debra, Zijdenbos, Alex, den Heijer, Tom, Mazoyer, Bernard, Coker, Laura H, Enzinger, Christian, Danoy, Patrick, Carless, Melanie A, Amin, Najaf, Arfanakis, Konstantinos, van Buchem, Mark A, de Bruijn, Renée F A G, Beiser, Alexa, Dufouil, Carole, Huang, Juebin, Cavalieri, Margherita, Thomson, Russell, Niessen, Wiro J, Corvin, Aiden, Chibnik, Lori B, Gislason, Gauti K, Hofman, Albert, Pikula, Aleksandra, Amouyel, Philippe, Freeman, Kevin B, Phan, Thanh G, Oostra, Ben A, Nalls, Michael A, Uitterlinden, Andre G, Czisch, Michael, Au, Rhoda, Elbaz, Alexis, Beare, Richard J, van Swieten, John C, Lopez, Oscar, Harris, Tamara B, Chouraki, Vincent, Breteler, Monique M B, De Jager, Philip L, Becker, James T, Curran, Joanne E, Knopman, David, Fazekas, Franz, Wolf, Philip A, van der Lugt, Aad, Longstreth, W. T., Brown, Mathew A, Bennett, David A, van Duijn, Cornelia M, Davies, Gail, Mosley, Thomas H, Schmidt, Reinhold, de Almeida, Marcio A A, Appel, Katja, Duggirala, Ravi, Dyer, Thomas D, Erk, Susanne, Fagerness, Jesen, Fox, Peter T, Freimer, Nelson B, Gill, Michael, Göring, Harald H H, Bartecek, Richard, Hagler, Donald J, Hoehn, David, Holsboer, Florian, Hoogman, Martine, Hosten, Norbert, Jahanshad, Neda, Johnson, Matthew P, Kent, Jack W, Kochunov, Peter, Bergmann, Ørjan, Lancaster, Jack L, Lawrie, Stephen M, Liewald, David C, Mandl, René, Mattheisen, Manuel, Meisenzahl, Eva, Melle, Ingrid, Moses, Eric K, Mühleisen, Thomas W, David Geffen School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California-University of California, Queensland Institute of Medical Research, Radboud University Medical Center [Nijmegen], Yale University School of Medicine, Génétique Humaine et Fonctions Cognitives, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Universität Greifswald - University of Greifswald, Universität Heidelberg [Heidelberg], University Medical Center [Utrecht], University of Oslo (UiO), University of Toronto, National University of Ireland [Galway] (NUI Galway), Montreal Neurological Institute and Hospital, McGill University = Université McGill [Montréal, Canada], University of Bergen (UiB), Harvard University [Cambridge], VU University Amsterdam, University of Edinburgh, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], National Institutes of Health [Bethesda] (NIH), Department of Forensic and Neurodevelopmental Sciences, King‘s College London, Institute of Psychiatry, Psychology & Neuroscience, King's College London, Georgia State University, University System of Georgia (USG), Department of Psychiatry and Human Behavior [Irvine], University of California [Irvine] (UCI), Leiden University Medical Center (LUMC), Dundee Technopole, CXR Biosciences Ltd, University of Groningen [Groningen], Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland (RCSI), Department of Genetics, Southwest Foundation for Biomedical Research, Bijvoet Center of Biomolecular Research [Utrecht], Utrecht University [Utrecht], Neurology Division, Beaumont Hospital, Dublin 9, Ireland, Beaumont Hospital, The University of Texas Health Science Center at Houston (UTHealth), Center for Neurobehavioral Genetics, Max Planck Institute of Psychiatry, Max-Planck-Gesellschaft, Department of Computer Science, Durham University, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-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), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], University of California, Institute of Neurology [London], University College of London [London] (UCL), University of California [San Francisco] (UCSF), Department of Medicine, University of Washington [Seattle], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Centre Émile Durkheim (CED), Sciences Po Bordeaux - Institut d'études politiques de Bordeaux (IEP Bordeaux)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Salermo, Università degli Studi di Salerno (UNISA), School of Psychology, University of Queensland, University of Queensland [Brisbane], Hartford Hospital, Lancaster University, Centre for Advanced Imaging, McConnell Brain Imaging Centre (MNI), McGill University = Université McGill [Montréal, Canada]-McGill University = Université McGill [Montréal, Canada], Stanley Center for Psychiatric Research, Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston]-Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Faculteit Medische Wetenschappen/UMCG, Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Perceptual and Cognitive Neuroscience (PCN), Biological Psychology, Neuroscience Campus Amsterdam - Brain Imaging, EMGO+ - Mental Health, EPIGEN Consortium, IMAGENConsortium, Saguenay Youth Study Group, the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Consortium, Psychiatry, NCA - Brain Imaging, EMGO - Mental health, Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Virology, Epidemiology, Clinical Chemistry, Erasmus MC other, Radiology & Nuclear Medicine, University of California (UC)-University of California (UC), Yale School of Medicine [New Haven, Connecticut] (YSM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Universität Heidelberg [Heidelberg] = Heidelberg University, Harvard University, Vrije Universiteit Amsterdam [Amsterdam] (VU), University of California [Irvine] (UC Irvine), Universiteit Leiden, University of California (UC), University of California [San Francisco] (UC San Francisco), Università degli Studi di Salerno = University of Salerno (UNISA), University of Iceland [Reykjavik], McGill University, University of Bergen (UIB), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Bijvoet Center of Biomolecular Research, Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, UMR5116, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), and McGill University-McGill University
Subjects: Netherlands Twin Register (NTR), Pathology, 110 012 Social cognition of verbal communication, [SDV]Life Sciences [q-bio], Hippocampus, Genome-wide association study, DCN PAC - Perception action and control, Hippocampal formation, physiopathology [Brain], Bioinformatics, 0302 clinical medicine, 130 000 Cognitive Neurology & Memory, TEMPORAL-LOBE EPILEPSY, 110 014 Public activities, Renal disorder [IGMD 9], 0303 health sciences, medicine.diagnostic_test, Translational research Immune Regulation [ONCOL 3], Brain, Human brain, Genomic disorders and inherited multi-system disorders [DCN PAC - Perception action and control IGMD 3], ALZHEIMERS-DISEASE, medicine.anatomical_structure, Brain size, genetics [Chromosomes, Human, Pair 12], genetics [Polymorphism, Single Nucleotide], Biomarker (medicine), NA+/H+ EXCHANGER, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Genetic Markers, medicine.medical_specialty, 110 000 Neurocognition of Language, DCN MP - Plasticity and memory, A neurocomputational model for the Processing of Linguistic Utterances based on the Unification-Space architecture [110 007 PLUS], BRAIN VOLUME, UNIFIED APPROACH, 110 013 Binding and the MUC-model, Neuroimaging, Biology, GENOTYPE IMPUTATION, Polymorphism, Single Nucleotide, Article, Genomic disorders and inherited multi-system disorders DCN MP - Plasticity and memory [IGMD 3], 03 medical and health sciences, AUTOMATED SEGMENTATION, Meta-Analysis as Topic, SDG 3 - Good Health and Well-being, ddc:570, FUNCTIONAL IMPLICATIONS, Genetics, medicine, Humans, GENOME-WIDE ASSOCIATION, 030304 developmental biology, Chromosomes, Human, Pair 12, Magnetic resonance imaging, Genetic Loci, physiopathology [Hippocampus], 110 009 The human brain and Chinese prosody, Genetics and epigenetic pathways of disease Genomic disorders and inherited multi-system disorders [NCMLS 6], HUMAN HEIGHT, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Contains fulltext : 108202.pdf (Publisher’s version ) (Closed access) Identifying genetic variants influencing human brain structures may reveal new biological mechanisms underlying cognition and neuropsychiatric illness. The volume of the hippocampus is a biomarker of incipient Alzheimer's disease and is reduced in schizophrenia, major depression and mesial temporal lobe epilepsy. Whereas many brain imaging phenotypes are highly heritable, identifying and replicating genetic influences has been difficult, as small effects and the high costs of magnetic resonance imaging (MRI) have led to underpowered studies. Here we report genome-wide association meta-analyses and replication for mean bilateral hippocampal, total brain and intracranial volumes from a large multinational consortium. The intergenic variant rs7294919 was associated with hippocampal volume (12q24.22; N = 21,151; P = 6.70 x 10(-16)) and the expression levels of the positional candidate gene TESC in brain tissue. Additionally, rs10784502, located within HMGA2, was associated with intracranial volume (12q14.3; N = 15,782; P = 1.12 x 10(-12)). We also identified a suggestive association with total brain volume at rs10494373 within DDR2 (1q23.3; N = 6,500; P = 5.81 x 10(-7)). 01 mei 2012
Published: 2012
Full Text: View/download PDF

10. Alternative pathways to the 1.5 °C target reduce the need for negative emission technologies

Author: Environmental Sciences, Energy and Resources, Energy System Analysis, van Vuuren, Detlef P., Stehfest, Elke, Gernaat, David E. H. J., van den Berg, Maarten, Bijl, David L., de Boer, Harmen Sytze, Daioglou, Vassilis, Doelman, Jonathan C., Edelenbosch, Oreane Y., Harmsen, Mathijs, Hof, Andries F., van Sluisveld, Mariësse A. E., Environmental Sciences, Energy and Resources, Energy System Analysis, van Vuuren, Detlef P., Stehfest, Elke, Gernaat, David E. H. J., van den Berg, Maarten, Bijl, David L., de Boer, Harmen Sytze, Daioglou, Vassilis, Doelman, Jonathan C., Edelenbosch, Oreane Y., Harmsen, Mathijs, Hof, Andries F., and van Sluisveld, Mariësse A. E.
Published: 2018

11. Land-use emissions play a critical role in land-based mitigation for Paris climate Land-use emissions play a critical role in land-based mitigation for Paris climate targetstargets

Author: Energy System Analysis, Environmental Sciences, Energy and Resources, Harper, Anna B, Powell, Tom, Cox, Peter M, House, Joanna, Huntingford, Chris, Lenton, Timothy M, Sitch, Stephen, Burke, Eleanor, Chadburn, Sarah E, Collins, William J, Comyn-Platt, Edward, Daioglou, Vassilis, Doelman, Jonathan C, Hayman, Garry, Robertson, Eddy, van Vuuren, Detlef, Wiltshire, Andy, Webber, Christopher P, Bastos, Ana, Boysen, Lena, Ciais, Philippe, Devaraju, Narayanappa, Jain, Atul K, Krause, Andreas, Poulter, Ben, Shu, Shijie, Energy System Analysis, Environmental Sciences, Energy and Resources, Harper, Anna B, Powell, Tom, Cox, Peter M, House, Joanna, Huntingford, Chris, Lenton, Timothy M, Sitch, Stephen, Burke, Eleanor, Chadburn, Sarah E, Collins, William J, Comyn-Platt, Edward, Daioglou, Vassilis, Doelman, Jonathan C, Hayman, Garry, Robertson, Eddy, van Vuuren, Detlef, Wiltshire, Andy, Webber, Christopher P, Bastos, Ana, Boysen, Lena, Ciais, Philippe, Devaraju, Narayanappa, Jain, Atul K, Krause, Andreas, Poulter, Ben, and Shu, Shijie
Published: 2018

12. Spirometry is not enough to diagnose COPD in epidemiological studies: a follow-up study.

Author: UCL - SSS/IRSS - Institut de recherche santé et société, UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, Andreeva, Elena, Pokhaznikova, Marina, Lebedev, Anatoly, Moiseeva, Irina, Kuznetsova, Olga, Degryse, Jean-Marie, UCL - SSS/IRSS - Institut de recherche santé et société, UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, Andreeva, Elena, Pokhaznikova, Marina, Lebedev, Anatoly, Moiseeva, Irina, Kuznetsova, Olga, and Degryse, Jean-Marie
Abstract: A hallmark of the diagnosis of chronic obstructive pulmonary disease (COPD) is the measurement of post-bronchodilator (post-BD) airflow obstruction (AO) by spirometry, but spirometry is not enough for the provision of a clinical diagnosis. In the majority of previous epidemiological studies, COPD diagnosis has been based on spirometry and a few clinical characteristics. The aim of our study was to identify outcomes in patients newly diagnosed with airflow obstruction (AO) based on a diagnostic work-up conducted as part of a population-based cross-sectional study in North-Western Russia. Spirometry was performed before (pre-BD) and after BD administration, and AO was defined using the FEV1/FVC <0.70 and FEV1/FVC
Published: 2017

13. Greenhouse gas emission curves for advanced biofuel supply chains

Author: Energy System Analysis, Environmental Sciences, Biobased Economy, Energy and Resources, Daioglou, Vassilis, Doelman, Jonathan C., Stehfest, Elke, Müller, Christoph, Wicke, Birka, Faaij, Andre, van Vuuren, Detlef P., Energy System Analysis, Environmental Sciences, Biobased Economy, Energy and Resources, Daioglou, Vassilis, Doelman, Jonathan C., Stehfest, Elke, Müller, Christoph, Wicke, Birka, Faaij, Andre, and van Vuuren, Detlef P.
Published: 2017

14. Rasd2 Modulates Prefronto-Striatal Phenotypes in Humans and 'Schizophrenia-Like Behaviors' in Mice.

Author: UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, Vitucci, Daniela, Di Giorgio, Annabella, Napolitano, Francesco, Pelosi, Barbara, Blasi, Giuseppe, Errico, Francesco, Attrotto, Maria Teresa, Gelao, Barbara, Fazio, Leonardo, Taurisano, Paolo, Di Maio, Anna, Marsili, Valentina, Pasqualetti, Massimo, Bertolino, Alessandro, Usiello, Alessandro, UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, Vitucci, Daniela, Di Giorgio, Annabella, Napolitano, Francesco, Pelosi, Barbara, Blasi, Giuseppe, Errico, Francesco, Attrotto, Maria Teresa, Gelao, Barbara, Fazio, Leonardo, Taurisano, Paolo, Di Maio, Anna, Marsili, Valentina, Pasqualetti, Massimo, Bertolino, Alessandro, and Usiello, Alessandro
Abstract: Rasd2 is a thyroid hormone target gene, which encodes for a GTP-binding protein enriched in the striatum where, among other functions, it modulates dopaminergic neurotransmission. Here we report that human RASD2 mRNA is abundant in putamen, but it also occurs in the cerebral cortex, with a distinctive expression pattern that differs from that present in rodents. Consistent with its localization, we found that a genetic variation in RASD2 (rs6518956) affects postmortem prefrontal mRNA expression in healthy humans and is associated with phenotypes of relevance to schizophrenia, including prefrontal and striatal grey matter volume and physiology during working memory, as measured with magnetic resonance imaging. Interestingly, quantitative real-time PCR analysis indicated that RASD2 mRNA is slightly reduced in postmortem prefrontal cortex of patients with schizophrenia. In the attempt to uncover the neurobiological substrates associated with Rasd2 activity, we used knockout mice to analyze the in vivo influence of this G-protein on the prepulse inhibition of the startle response and psychotomimetic drug-related behavioral response. Data showed that Rasd2 mutants display deficits in basal prepulse inhibition that, in turn, exacerbate gating disruption under psychotomimetic drug challenge. Furthermore, we documented that lack of Rasd2 strikingly enhances the behavioral sensitivity to motor stimulation elicited by amphetamine and phencyclidine. Based on animal model data, along with the finding that RASD2 influences prefronto-striatal phenotypes in healthy humans, we suggest that genetic mutation or reduced levels of this G-protein might have a role in cerebral circuitry dysfunction underpinning exaggerated psychotomimetic drugs responses and development of specific biological phenotypes linked to schizophrenia.
Published: 2016

15. Re-assessment of net energy production and greenhouse gas emissions avoidance after 40 years of photovoltaics development

Author: Energy System Analysis, Sub Algemeen Natuurkunde, Energy and Resources, Louwen, Atse, Van Sark, Wilfried G J H M, Faaij, André P C, Schropp, Ruud E I, Energy System Analysis, Sub Algemeen Natuurkunde, Energy and Resources, Louwen, Atse, Van Sark, Wilfried G J H M, Faaij, André P C, and Schropp, Ruud E I
Published: 2016

16. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

Author: Gaulton, Kyle J, Ferreira, Teresa, Lee, Yeji, Raimondo, Anne, Mägi, Reedik, Reschen, Michael E, Mahajan, Anubha, Locke, Adam, William Rayner, N, Robertson, Neil, Scott, Robert A, Prokopenko, Inga, Scott, Laura J, Green, Todd, Sparso, Thomas, Thuillier, Dorothee, Yengo, Loic, Grallert, Harald, Wahl, Simone, Frånberg, Mattias, Strawbridge, Rona J, Kestler, Hans, Chheda, Himanshu, Eisele, Lewin, Gustafsson, Stefan, Steinthorsdottir, Valgerdur, Thorleifsson, Gudmar, Qi, Lu, Karssen, Lennart C, van Leeuwen, Elisabeth M, Willems, Sara M, Li, Man, Chen, Han, Fuchsberger, Christian, Kwan, Phoenix, Ma, Clement, Linderman, Michael, Lu, Yingchang, Thomsen, Soren K, Rundle, Jana K, Beer, Nicola L, van de Bunt, Martijn, Chalisey, Anil, Kang, Hyun Min, Voight, Benjamin F, Abecasis, Gonçalo R, Almgren, Peter, Baldassarre, Damiano, Balkau, Beverley, van der Schouw, Yvonne T, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Gaulton, Kyle J, Ferreira, Teresa, Lee, Yeji, Raimondo, Anne, Mägi, Reedik, Reschen, Michael E, Mahajan, Anubha, Locke, Adam, William Rayner, N, Robertson, Neil, Scott, Robert A, Prokopenko, Inga, Scott, Laura J, Green, Todd, Sparso, Thomas, Thuillier, Dorothee, Yengo, Loic, Grallert, Harald, Wahl, Simone, Frånberg, Mattias, Strawbridge, Rona J, Kestler, Hans, Chheda, Himanshu, Eisele, Lewin, Gustafsson, Stefan, Steinthorsdottir, Valgerdur, Thorleifsson, Gudmar, Qi, Lu, Karssen, Lennart C, van Leeuwen, Elisabeth M, Willems, Sara M, Li, Man, Chen, Han, Fuchsberger, Christian, Kwan, Phoenix, Ma, Clement, Linderman, Michael, Lu, Yingchang, Thomsen, Soren K, Rundle, Jana K, Beer, Nicola L, van de Bunt, Martijn, Chalisey, Anil, Kang, Hyun Min, Voight, Benjamin F, Abecasis, Gonçalo R, Almgren, Peter, Baldassarre, Damiano, Balkau, Beverley, van der Schouw, Yvonne T, and DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium
Published: 2015

17. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

Author: JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Circulatory Health, Cardiovasculaire Epidemiologie, Gaulton, Kyle J, Ferreira, Teresa, Lee, Yeji, Raimondo, Anne, Mägi, Reedik, Reschen, Michael E, Mahajan, Anubha, Locke, Adam, William Rayner, N, Robertson, Neil, Scott, Robert A, Prokopenko, Inga, Scott, Laura J, Green, Todd, Sparso, Thomas, Thuillier, Dorothee, Yengo, Loic, Grallert, Harald, Wahl, Simone, Frånberg, Mattias, Strawbridge, Rona J, Kestler, Hans, Chheda, Himanshu, Eisele, Lewin, Gustafsson, Stefan, Steinthorsdottir, Valgerdur, Thorleifsson, Gudmar, Qi, Lu, Karssen, Lennart C, van Leeuwen, Elisabeth M, Willems, Sara M, Li, Man, Chen, Han, Fuchsberger, Christian, Kwan, Phoenix, Ma, Clement, Linderman, Michael, Lu, Yingchang, Thomsen, Soren K, Rundle, Jana K, Beer, Nicola L, van de Bunt, Martijn, Chalisey, Anil, Kang, Hyun Min, Voight, Benjamin F, Abecasis, Gonçalo R, Almgren, Peter, Baldassarre, Damiano, Balkau, Beverley, van der Schouw, Yvonne T, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Circulatory Health, Cardiovasculaire Epidemiologie, Gaulton, Kyle J, Ferreira, Teresa, Lee, Yeji, Raimondo, Anne, Mägi, Reedik, Reschen, Michael E, Mahajan, Anubha, Locke, Adam, William Rayner, N, Robertson, Neil, Scott, Robert A, Prokopenko, Inga, Scott, Laura J, Green, Todd, Sparso, Thomas, Thuillier, Dorothee, Yengo, Loic, Grallert, Harald, Wahl, Simone, Frånberg, Mattias, Strawbridge, Rona J, Kestler, Hans, Chheda, Himanshu, Eisele, Lewin, Gustafsson, Stefan, Steinthorsdottir, Valgerdur, Thorleifsson, Gudmar, Qi, Lu, Karssen, Lennart C, van Leeuwen, Elisabeth M, Willems, Sara M, Li, Man, Chen, Han, Fuchsberger, Christian, Kwan, Phoenix, Ma, Clement, Linderman, Michael, Lu, Yingchang, Thomsen, Soren K, Rundle, Jana K, Beer, Nicola L, van de Bunt, Martijn, Chalisey, Anil, Kang, Hyun Min, Voight, Benjamin F, Abecasis, Gonçalo R, Almgren, Peter, Baldassarre, Damiano, Balkau, Beverley, van der Schouw, Yvonne T, and DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium
Published: 2015

18. Coverage and Determinants of Newborn Feeding Practices in Rural Burkina Faso

Author: Johns Hopkins University - Bloomberg School of Public Health - Department of International Health, UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, Institut National de la Statistique et de Démographie - Burkina Faso - Direction, Munos, Melinda K., Mullany, Luke C., Maïga, Abdoulaye, Baya, Banza, Bryce, Jennifer, Johns Hopkins University - Bloomberg School of Public Health - Department of International Health, UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, Institut National de la Statistique et de Démographie - Burkina Faso - Direction, Munos, Melinda K., Mullany, Luke C., Maïga, Abdoulaye, Baya, Banza, and Bryce, Jennifer
Abstract: Objective: Newborn feeding practices are important to neonatal health and survival, but understudied in sub-Saharan Africa. We assessed the prevalence and determinants of newborn feeding practices in Burkina Faso. Study design: An 18 000 household survey was conducted in rural Burkina Faso in 2010 to 2011. Women of reproductive age were asked about antenatal, delivery and newborn care practices for their most recent live birth. Coverage of newborn feeding practices was estimated and multivariate regression was used to assess determinants of these practices. Result: Seventy-six percent of live births were breastfed within 24 h of birth, 84% were given colostrum and 21% received prelacteals. Facility delivery and antenatal care attendance were associated with positive feeding practices. Conclusion: Positive newborn feeding practices were common in rural Burkina Faso, relative to other low-income settings. Interventions are needed to improve feeding practices among home-born babies, and to encourage earlier initiation of breastfeeding among facility-born newborns.
Published: 2014

19. Male longevity in Sardinia, a review of historical sources supporting a causal link with dietary factors

Author: UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, Pes, Gianni, Tolu, F, Dore, M P, Sechi, G P, Errigo, A, Canelada, A, Poulain, Michel, UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, Pes, Gianni, Tolu, F, Dore, M P, Sechi, G P, Errigo, A, Canelada, A, and Poulain, Michel
Abstract: The identification of a hot spot of exceptional longevity, the Longevity Blue Zone (LBZ), in the mountain population of Sardinia has aroused considerable interest toward its traditional food as one of the potential causal factors. This preliminary study on the traditional Sardinian diet has been supported by the literature available, which has been carefully reviewed and compared. Up to a short time ago, the LBZ population depended mostly upon livestock rearing, and consumption of animal-derived foods was relatively higher than in the rest of the island. The nutrition transition (NT) in urbanized and lowland areas began in the mid-1950s, fueled by economic development, whereas in the LBZ it started later owing to prolonged resistance to change by a society organized around a rather efficient pastoral economy. Even nowadays a large proportion of the population in this area still follows the traditional diet based on cereal-derived foods and dairy products. The LBZ cohorts comprising individuals who were of a mature age when NT began may have benefited both from the high-quality, albeit rather monotonous, traditional diet to which they had been exposed most of their life and from the transitional diet, which introduced positive changes such as more variety, increased consumption of fruits and vegetables and moderate meat intake. It could be speculated that these changes may have brought substantial health benefits to this particular aging group, which was in need of nutrient-rich food at this specific time in life, thereby resulting in a decreased mortality risk and, in turn, life-span extension.
Published: 2014

20. Circulating proteomic signature of early death in heart failure patients with reduced ejection fraction

Author: Vincent Vandewalle, Audrey Hulot, Guillemette Marot, Christophe Bauters, Florence Pinet, Pascal de Groote, Maxime Brunin, Olivia Beseme, Marie Cuvelliez, Philippe Amouyel, Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167 (RID-AGE), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Remodeling in Valvulopathy and Heart Failure [CHU Rouen] (FHU REMOD-VHF ), CHU Rouen, Normandie Université (NU)-Normandie Université (NU), MOdel for Data Analysis and Learning (MODAL), Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-École polytechnique universitaire de Lille (Polytech Lille)-Université de Lille, Sciences et Technologies, BILILLE, This work was supported by grants from the French Clinical Research Infrastructure Network INI-CRCT (Investigation Network Initiative-Cardiovascular and Renal Clinical Trialists), the E.U. FP7 HOMAGE (305507), 'Agence Nationale de Recherche' 15-CEA-U16/'Direction Générale de l’Offre de Soins' (5–013) and CHRU de Lille (Bonus H2018). We acknowledge Somalogic Inc. as the provider of the proteomics analysis and EdgeLeap B.V. for the systems biology analysis., Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-École polytechnique universitaire de Lille (Polytech Lille), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Laboratoire Paul Painlevé - UMR 8524 (LPP), Pinet, Florence, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 [METRICS], Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167 [RID-AGE], METRICS : Evaluation des technologies de santé et des pratiques médicales - ULR 2694, and Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement (RID-AGE) - U1167
Subjects: Oncology, Male, Proteomics, medicine.medical_specialty, Proteome, [SDV]Life Sciences [q-bio], lcsh:Medicine, Context (language use), Cardiovascular System, Article, Gene regulatory networks, Prognostic markers, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Risk Factors, Internal medicine, Cause of Death, Medicine, Humans, lcsh:Science, Cathepsin S, Heart Failure, Ejection fraction, business.industry, lcsh:R, Middle Aged, medicine.disease, Blood proteins, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, 3. Good health, Extracellular Matrix, [SDV] Life Sciences [q-bio], Clinical research, Heart failure, Biomarker (medicine), Female, lcsh:Q, business, Extracellular matrix organization
Abstract: Background: Heart failure (HF) remains a main cause of mortality worldwide. Risk stratification of patients with systolic chronic HF is critical to identify those who may benefit from advanced HF therapies. The aim of this study is to identify plasmatic proteins that could predict early death of HF patients. Methods: The subproteome targeted by the aptamer-based assay (SOMAscan) of 1310 proteins was profiled in blood samples from 168 HF patients with reduced ejection fraction hospitalized in CHRU de Lille. Patient's outcome was assessed 3 years after inclusion. Findings: Among the 1310 proteins, 203 were significantly modulated between dead and alive patients (Wilcoxon tests, FDR 5%). The INCA molecular network was built using these 203 proteins and contained 2881 molecules (1639 proteins, 1072 microRNAs, 170 metabolites). To assess mechanistic context of HF, molecules were assigned to 34 clusters annotated to biological pathways from Gene Ontology. Analysis of the INCA network model allowed to highlight extracellular matrix organization as mechanism involved in HF. In parallel, an adaptive LASSO was performed on these 203 proteins and six proteins were selected as candidates to predict early death of HF patients: complement C3, cathepsin S and FAM107B were decreased and MAPKAPK5, MMP1 and MMP7 increased in dead patients compared with patients alive. By conventional assays, complement C3, MMP1 and MMP7 were validated but not cathepsin S due to the low sensitivity and specificity of the assay used. Interpretation: A proteomic signature of 6 plasma proteins allows identifying HF patients with a risk of early death. Funding Statement: This work was supported by grants from French Clinical Research Infrastructure Network INI-CRT (Investigation Network Initiative-Cardiovascular and Renal Clinical Trialists), the E.U. FP7 HOMAGE (305507), “Agence Nationale de Recherche” 15-CEA-U16/”Direction Generale de l'Offre de Soins” (5- 013) and CHRU de Lille (Bonus H2018).We acknowledged Somalogic Inc as the provider of the proteomics analysis and EdgeLeap B.V. for the system biology analysis. Declaration of Interests: MC, VV, MB, OB, AH, PDG, PA, CB, GM, FP have no conflict of interest to disclose for the study performed. Ethics Approval Statement: The INCA study was approved by the ethics committee of the “Centre Hospitalier de Lille” (CP98/94, 5 November 1998) , and written informed consent was obtained for each patient.
Published: 2019
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21. Similar estimates of temperature impacts on global wheat yield by three independent methods

Author: Frank Ewert, Jakarat Anothai, P. V. Vara Prasad, Davide Cammarano, Curtis D. Jones, Elias Fereres, Margarita Garcia-Vila, Soora Naresh Kumar, Eckart Priesack, Phillip D. Alderman, Andrew J. Challinor, Reimund P. Rötter, Alex C. Ruane, Christian Folberth, Gerrit Hoogenboom, Pierre Martre, Roberto C. Izaurralde, Fulu Tao, Pramod K. Aggarwal, Mohamed Jabloun, Jordi Doltra, Joshua Elliott, Christoph Müller, Bing Liu, Iurii Shcherbak, Jeffrey W. White, Bruno Basso, Senthold Asseng, Pierre Stratonovitch, Peter J. Thorburn, Claas Nendel, Taru Palosuo, Joost Wolf, Ann-Kristin Koehler, Thilo Streck, Jørgen E. Olesen, David B. Lobell, Kurt Christian Kersebaum, Delphine Deryng, L. A. Hunt, Garry O'Leary, Katharina Waha, Giacomo De Sanctis, Daniel Wallach, Yan Zhu, James W. Jones, Elke Stehfest, Mikhail A. Semenov, Christian Biernath, Claudio O. Stöckle, Thomas A. M. Pugh, Matthew P. Reynolds, Enli Wang, Bruce A. Kimball, Erwin Schmid, Iwan Supit, Zhigan Zhao, Michael J. Ottman, Sebastian Gayler, Cynthia Rosenzweig, Ehsan Eyshi Rezaei, Gerard W. Wall, National Engineering and Technology Center for Information Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricutural University, Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Potsdam Institute for Climate Impact Research (PIK), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Leibniz-Zentrum für Agrarlandschaftsforschung (ZALF), Leibniz Association, Center for Climate Systems Research [New York] (CCSR), Columbia University [New York], Computation Institute, Loyola University of Chicago, Department of Environmental Earth System Science and Center on Food Security and the Environment, Stanford University, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, CGIAR Research Program on Climate Change, Agriculture and Food Security, Borlaug Institute for South Asia, CIMMYT, Consultative Group on International Agricultural Research (CGIAR), Department of Plant and Soil Sciences, Mississippi State University [Mississippi], Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University (PSU), Department of Geological Sciences, University of Oregon [Eugene], W. K. Kellogg Biological Station (KBS), Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Institute of Soil Ecology [Neuherberg] (IBOE), Helmholtz-Zentrum München (HZM), The James Hutton Institute, Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, CGIAR-ESSP Program on Climate Change, Agriculture and Food Security, International Center for Tropical Agriculture, European Commission - Joint Research Centre [Ispra] (JRC), Cantabrian Agricultural Research and Training Centre, Department of Agronomy, Purdue University [West Lafayette], Department of Geography, University of Liverpool, Ecosystem Services and Management Program, International Institute for Applied Systems Analysis (IIASA), Institute of Soil Science and Land Evaluation, University of Hohenheim, AgWeatherNet Program, Washington State University (WSU), Department of Plant Agriculture, University of Guelph, Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A and M AgriLife Research, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], US Arid-Land Agricultural Research Center, United States Department of Agriculture, Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute (IARI), Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Landscape & Water Sciences, Department of Environment of Victoria, The School of Plant Sciences, University of Arizona, Natural resources institute Finland, Institute of Ecology, German Research Center for Environmental Health, Institut für Meteorologie und Klimaforschung - Atmosphärische Umweltforschung (IMK-IFU), Karlsruher Institut für Technologie (KIT), School of Geography, Earth and Environmental Sciences [Birmingham], University of Birmingham [Birmingham], Birmingham Institute of Forest Research (BIFoR), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Center for Development Research (ZEF), Environmental Impacts Group, Georg-August-University [Göttingen], Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Computational and Systems Biology Department, Rothamsted Research, Biotechnology and Biological Sciences Research Council, Netherlands Environmental Assessment Agency, Department of Biological Systems Engineering, University of Wisconsin-Madison, PPS, WSG and CALM, Wageningen University and Research [Wageningen] (WUR), Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences [Beijing] (CAS), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), USDA-ARS, Arid-Land Agricultural Research Center, China Agricultural University (CAU), National High-Tech Research and Development Program of China (2013AA100404), the National Natural Science Foundation of China (31271616, 31611130182, 41571088 and 31561143003), the National Research Foundation for the Doctoral Program of Higher Education of China (20120097110042), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), China Scholarship Council., IFPRI through the Global Futures and Strategic Foresight project, the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), the CGIAR Research Program on Wheat, the Agricultural Model Intercomparison and Improvement Project (AgMIP), Agricultural & Biological Engineering Department, University of Florida [Gainesville], Institute of Crop Science and Resource Conservation, University of Bonn-Division of Plant Nutrition, Stanford University [Stanford], Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Prince of Songkla University, Texas A&M AgriLife Research and Extension Center, Natural Resources Institute Finland, Georg-August-Universität Göttingen, Wageningen University and Research Center (WUR), China Agricultural University, Division of Plant Nutrition-University of Bonn, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), University of Florida, Potsdam Institute for Climate Impact Research ( PIK ), Leibniz Centre for Agricultural Landscape Research, Institute for Landscape Biogeochemistry, Center for Climate Systems Research [New York] ( CCSR ), Écophysiologie des Plantes sous Stress environnementaux ( LEPSE ), Institut National de la Recherche Agronomique ( INRA ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), NASA Goddard Institute for Space Studies ( GISS ), NASA Goddard Space Flight Center ( GSFC ), Consultative Group on International Agricultural Research ( CGIAR ), W.K. Kellogg Biological Station, Institute of Soil Ecology [Neuherberg] ( IBOE ), Helmholtz-Zentrum München ( HZM ), James Hutton Institute, Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, European Commission - Joint Research Centre [Ispra] ( JRC ), International Institute for Applied Systems Analysis ( IIASA ), Washington State University ( WSU ), Texas A and M University ( TAMU ), Leibniz Centre for Agricultural Landscape Research (ZALF), Centre for Environment Science and Climate Resilient Agriculture ( CESCRA ), Indian Agricultural Research Institute ( IARI ), Institut für Meteorologie und Klimaforschung - Atmosphärische Umweltforschung ( IMK-IFU ), Karlsruher Institut für Technologie ( KIT ), School of Geography, Earth & Environmental Science and Birmingham Institute of Forest Research, University of Birmingham, International Maize and Wheat Improvement Center ( CIMMYT ), Bonn Universität [Bonn], University of Natural Resources and Life Sciences, University of Wisconsin-Madison [Madison], Wageningen University and Research Center ( WUR ), Chinese Academy of Sciences [Beijing] ( CAS ), Commonwealth Scientific and Industrial Research Organisation, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Université de Toulouse (UT)-Université de Toulouse (UT), Helmholtz Zentrum München = German Research Center for Environmental Health, Natural Resources Institute Finland (LUKE), Georg-August-University = Georg-August-Universität Göttingen, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Biotechnology and Biological Sciences Research Council (BBSRC), and Institute of geographical sciences and natural resources research [CAS] (IGSNRR)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, régression statistique, 010504 meteorology & atmospheric sciences, impact sur le rendement, klim, Atmospheric sciences, 01 natural sciences, incertitude, wheat, uncertainty, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, 2. Zero hunger, changement climatique, Regression analysis, statistical regression, simulation, PE&RC, [ SDE.MCG ] Environmental Sciences/Global Changes, sécurité alimentaire, Plant Production Systems, modèle de récolte, Yield (finance), comparaison de modèles, [SDE.MCG]Environmental Sciences/Global Changes, Climate change, Environmental Science (miscellaneous), Earth System Science, blé, température, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, réchauffement climatique, global change, 0105 earth and related environmental sciences, Hydrology, WIMEK, Global temperature, business.industry, Crop yield, Global warming, Climate Resilience, 13. Climate action, Agriculture, Klimaatbestendigheid, Plantaardige Productiesystemen, Environmental science, Leerstoelgroep Aardsysteemkunde, Climate model, business, Social Sciences (miscellaneous), 010606 plant biology & botany
Abstract: The potential impact of global temperature change on global crop yield has recently been assessed with different methods. Here we show that grid-based and point-based simulations and statistical regressions (from historic records), without deliberate adaptation or CO2 fertilization effects, produce similar estimates of temperature impact on wheat yields at global and national scales. With a 1 °C global temperature increase, global wheat yield is projected to decline between 4.1% and 6.4%. Projected relative temperature impacts from different methods were similar for major wheat-producing countries China, India, USA and France, but less so for Russia. Point-based and grid-based simulations, and to some extent the statistical regressions, were consistent in projecting that warmer regions are likely to suffer more yield loss with increasing temperature than cooler regions. By forming a multi-method ensemble, it was possible to quantify ‘method uncertainty’ in addition to model uncertainty. This significantly improves confidence in estimates of climate impacts on global food security. The potential impact of global temperature change on global crop yield has recently been assessed with different methods. Here we show that grid-based and point-based simulations and statistical regressions (from historic records), without deliberate adaptation or CO2 fertilization effects, produce similar estimates of temperature impact on wheat yields at global and national scales. With a 1 °C global temperature increase, global wheat yield is projected to decline between 4.1% and 6.4%. Projected relative temperature impacts from different methods were similar for major wheat-producing countries China, India, USA and France, but less so for Russia. Point-based and grid-based simulations, and to some extent the statistical regressions, were consistent in projecting that warmer regions are likely to suffer more yield loss with increasing temperature than cooler regions. By forming a multi-method ensemble, it was possible to quantify ‘method uncertainty’ in addition to model uncertainty. This significantly improves confidence in estimates of climate impacts on global food security.
Published: 2016
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22. A chaotic self-oscillating sunlight driven polymer actuator

Author: Michael G. Debije, Kamlesh Kumar, Dirk J. Broer, Albertus P. H. J. Schenning, David Bléger, Heiner Friedrich, Mark A. Peletier, Christopher Knie, Stefan Hecht, Stimuli-responsive Funct. Materials & Dev., Center for Analysis, Scientific Computing & Appl., Materials and Interface Chemistry, and Applied Analysis
Subjects: Materials science, Science, Chaotic, General Physics and Astronomy, 02 engineering and technology, Green-light, 010402 general chemistry, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Article, chemistry.chemical_compound, Sunlight, chemistry.chemical_classification, Multidisciplinary, business.industry, Active systems, General Chemistry, Polymer, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Azobenzene, chemistry, Optoelectronics, 0210 nano-technology, Actuator, business, Visible spectrum
Abstract: Nature provides much inspiration for the design of materials capable of motion upon exposure to external stimuli, and many examples of such active systems have been created in the laboratory. However, to achieve continuous motion driven by an unchanging, constant stimulus has proven extremely challenging. Here we describe a liquid crystalline polymer film doped with a visible light responsive fluorinated azobenzene capable of continuous chaotic oscillatory motion when exposed to ambient sunlight in air. The presence of simultaneous illumination by blue and green light is necessary for the oscillating behaviour to occur, suggesting that the dynamics of continuous forward and backward switching are causing the observed effect. Our work constitutes an important step towards the realization of autonomous, persistently self-propelling machines and self-cleaning surfaces powered by sunlight., It is highly desirable, yet challenging to build actuators in a dry environment that can undergo autonomous oscillation. Here, Kumar et al. achieve this goal in a soft actuator based on the use of a nematic liquid crystal film doped by ortho-fluoroazobenzene that is responsive to sunlight.
Published: 2016

23. Effect of combined water drinking test and dark room provocative testing in Caucasian eyes with narrow angles

Author: Henny J. M. Beckers, Hellen C S Römkens, Tos T. J. M. Berendschot, Carroll A.B. Webers, Jan S. A. G. Schouten, Medical Image Analysis, MUMC+: MA AIOS Oogheelkunde (9), Oogheelkunde, MUMC+: MA Oogheelkunde (9), RS: MHeNs - R3 - Neuroscience, RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health, MUMC+: MA Oogheelkunde (3), and MUMC+: Centrum voor Oogheelkunde (3)
Subjects: Intraocular pressure, medicine.medical_specialty, genetic structures, Anterior Chamber, Provocative test, Article, 03 medical and health sciences, Tonometry, Ocular, 0302 clinical medicine, Ophthalmology, medicine, Outpatient clinic, Humans, Clinical significance, In patient, Intraocular Pressure, Dark room, business.industry, Water, Glaucoma, Middle Aged, eye diseases, Water drinking test, 030221 ophthalmology & optometry, sense organs, business, Glaucoma, Angle-Closure, 030217 neurology & neurosurgery, Provocative testing, Tomography, Optical Coherence
Abstract: PURPOSE: To assess the usefulness of water drinking test and dark room provocative testing (WDT + DRPT) in current clinical practice by evaluating input parameters from Swept-source Optical Coherence Tomography (SS-OCT) images, and to determine if clinical factors like axial length, central endothelial cell count (CECC) and retinal nerve fibre layer thickness (RNFL) thickness are associated with a positive WDT + DRPT.METHODS: SS-OCT examination was performed in consecutive subjects presenting as new patients in the outpatient clinic aged > 40 years. If at least one eye met the inclusion criteria (anterior chamber angles RESULTS: A total of 95 subjects with a mean age of 64 years were included. There was an association between IOP increase after WDT + DRPT and anterior chamber angle characteristics, however this was not of clinical significance. No positive results after WDT + DRPT were found in patients with anterior chamber angles ≥ 20°.CONCLUSIONS: The present findings indicate that this combined provocative test has no definite correlative or predictive value in angle closure disease. Further, the test is not useful in predicting early diagnosis or possible CECC or RNFL loss.
Published: 2022
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24. Deep learning-based breast cancer grading and survival analysis on whole-slide histopathology images

Author: Wetstein, Suzanne C., de Jong, Vincent M.T., Stathonikos, Nikolas, Opdam, Mark, Dackus, Gwen M.H.E., Pluim, Josien P.W., van Diest, Paul J., Veta, Mitko, Medical Image Analysis, and EAISI Health
Subjects: Observer Variation, Pathologists, Multidisciplinary, Breast Neoplasms/pathology, Deep Learning, SDG 3 - Good Health and Well-being, Humans, Female, Neoplasm Grading, SDG 3 – Goede gezondheid en welzijn, Survival Analysis
Abstract: Breast cancer tumor grade is strongly associated with patient survival. In current clinical practice, pathologists assign tumor grade after visual analysis of tissue specimens. However, different studies show significant inter-observer variation in breast cancer grading. Computer-based breast cancer grading methods have been proposed but only work on specifically selected tissue areas and/or require labor-intensive annotations to be applied to new datasets. In this study, we trained and evaluated a deep learning-based breast cancer grading model that works on whole-slide histopathology images. The model was developed using whole-slide images from 706 young (n = 327) and high (n = 359) grade groups were used to perform survival analysis. The deep learning system distinguished low/intermediate versus high tumor grade with a Cohen’s Kappa of 0.59 (80% accuracy) compared to expert pathologists. In subsequent survival analysis the two groups predicted by the system were found to have a significantly different overall survival (OS) and disease/recurrence-free survival (DRFS/RFS) (p p
Published: 2022

25. Contributing ocular comorbidity to end-of-life visual acuity in medically treated glaucoma patients, ocular hypertension and glaucoma suspect patients

Author: Jan S. A. G. Schouten, Henny J. M. Beckers, Tos T. J. M. Berendschot, Palwasha Mokhles, Carroll A.B. Webers, Luuk van Gorcom, Oogheelkunde, RS: MHeNs - R3 - Neuroscience, MUMC+: MA AIOS Oogheelkunde (9), MUMC+: MA Oogheelkunde (9), RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health, MUMC+: MA Oogheelkunde (3), MUMC+: Centrum voor Oogheelkunde (3), and Medical Image Analysis
Subjects: medicine.medical_specialty, Intraocular pressure, Visual acuity, PROGNOSIS, genetic structures, Visual impairment, Visual Acuity, Glaucoma, Ocular hypertension, Comorbidity, SDG 3 – Goede gezondheid en welzijn, Article, SDG 3 - Good Health and Well-being, Ophthalmology, Humans, Medicine, VISION LOSS, Macular hole, Intraocular Pressure, RISK, business.industry, Diabetic retinopathy, Macular degeneration, IMPAIRMENT, medicine.disease, eye diseases, PREVALENCE, Death, BLINDNESS, Ocular Hypertension, sense organs, medicine.symptom, OPEN-ANGLE GLAUCOMA, business
Abstract: AIM: To assess the visual acuity at the end of life in glaucoma suspect patients, ocular hypertension, and patients treated for glaucoma and to find factors contributing to a reduced visual acuity in this cohort of deceased patients.METHODS: In a cohort of 3883 medically treated glaucoma patients, glaucoma suspect, or patients with ocular hypertension assembled in 2001-2004, 1639 were deceased. Patient data were collected from electronic and paper patient files. The files of 1378 patients were studied and the last measured visual acuity and ocular comorbidities influencing the visual acuity were extracted.RESULTS: Our results show that only 37.2% of patients had no visual impairment in either eye, 30.5% was visually impaired or blind in both eyes and 4.1% was blind in both eyes, all based on VA. The most common contributing factors for severe visual impairment or blindness (prevalence ≥ 1%) were: glaucoma, retinal vein occlusion, dry and exudative age-related macular degeneration, past retinal detachment, amblyopia, diabetic retinopathy, anterior ischemic optic neuropathy, trauma, decompensated cornea, past keratitis, enucleation, corneal transplantation, and macular hole.CONCLUSIONS: Despite the current advanced treatment modalities for glaucoma, 30.5% of patients had a VA
Published: 2021

26. Spectral photon-counting CT imaging of colorectal peritoneal metastases: initial experience in rats

Author: Vahan Kepenekian, Philippe Douek, Pascal Rousset, Pierre-Emmanuel Bonnot, Loic Boussel, Salim Si-Mohamed, Arnaud Thivolet, Christophe Blanchet, Bodescot, Myriam, In Vivo Spectral Photon Counting CT Molecular Imaging in Cardio- and Neuro-Vascular Diseases - SPCCT - - H20202016-01-01 - 2019-12-31 - 668142 - VALID, Radiology Department [Lyon], Hospices Civils de Lyon (HCL), Ciblage thérapeutique en Oncologie (EA3738), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Université de Lyon, Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Surgical Department [Lyon], Pathology Department [Lyon], Modeling & analysis for medical imaging and Diagnosis (MYRIAD), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), This work was supported by European Union Horizon 2020 grant No 668142, France Life Imaging (FLI)., European Project: 668142,H2020,H2020-PHC-2015-two-stage,SPCCT(2016), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0301 basic medicine, Male, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Gadolinium, chemistry.chemical_element, Contrast Media, lcsh:Medicine, [SDV.CAN]Life Sciences [q-bio]/Cancer, Sensitivity and Specificity, Article, 03 medical and health sciences, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, Cell Line, Tumor, Distribution (pharmacology), Medicine, Animals, Cancer models, lcsh:Science, Peritoneal Neoplasms, Photons, Multidisciplinary, business.industry, Significant difference, Contrast resolution, lcsh:R, Rats, Inbred Strains, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Colorectal cancer, Photon counting, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Disease Models, Animal, 030104 developmental biology, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, chemistry, Preclinical research, Surgical oncology, Immunohistochemistry, Cancer imaging, lcsh:Q, Tomography, Ct imaging, business, Nuclear medicine, Colorectal Neoplasms, Tomography, X-Ray Computed, 030217 neurology & neurosurgery, Neoplasm Transplantation
Abstract: Computed tomography imaging plays a major role in the preoperative assessment of tumor burden by providing an accurate mapping of the distribution of peritoneal metastases (PM). Spectral Photon Counting Computed Tomography (SPCCT) is an innovative imaging modality that could overcome the current limitations of conventional CT, offering not only better spatial resolution but also better contrast resolution by allowing the discrimination of multiple contrast agents. Based on this capability, we tested the feasibility of SPCCT in the detection of PM at different time of tumor growth in 16 rats inoculated with CC531 cells using dual-contrast injection protocols in two compartments (i.e. intravenous iodine and intraperitoneal gadolinium or the reverse protocol), compared to surgery. For all peritoneal regions and for both protocols, sensitivity was 69%, specificity was 100% and accuracy was 80%, and the correlation with surgical exploration was strong (p = 0.97; p = 0.0001). No significant difference was found in terms of diagnostic performance, quality of peritoneal opacification or diagnostic quality between the 2 injection protocols. We also showed poor vascularization of peritoneal metastases by measuring low concentrations of contrast agent in the largest lesions using SPCCT, which was confirmed by immunohistochemical analyses. In conclusion, SPCCT using dual-contrast agent injection protocols in 2 compartments is a promising imaging modality to assess the extent of PM in a rat model.
Published: 2020
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27. Identification of cell surface markers and establishment of monolayer differentiation to retinal pigment epithelial cells

Author: Sofie Westman, Pankaj Kumar, Sandra Petrus-Reurer, Emma Lardner, Fredrik Lanner, Helder André, Anders Kvanta, Iyadh Douagi, Monica Aronsson, Alvaro Plaza Reyes, Sara Padrell Sánchez, Hammurabi Bartuma, Anna Falk, Emeline F. Nandrot, Karolinska Institutet [Stockholm], Karolinska University Hospital [Stockholm], Institut de la Vision, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by grants from the Ming Wai Lau Center for Reparative Medicine, Knut and Alice Wallenberg Foundation, Centre for Innovative Medicine, Swedish Research Council, Ragnar Söderberg Foundation, Wallenberg Academy Fellow, Swedish Foundation for Strategic Research, Stockholm County Council (ALF project), Karolinska Institute, Ögonfonden and Cronqvist Foundation, Strategic Research Area (SRA) Stem Cells and Regenerative Medicine, Crown Princess Margareta’s Foundation for the Visually Impaired, The ARMEC Lindeberg Foundation, The Ulla och Ingemar Dahlberg Foundation, and King Gustav V and Queen Victoria Foundation. This study was performed at the Live Cell Imaging unit/Nikon Center of Excellence, BioNut, KI, supported by Knut and Alice Wallenberg Foundation, Swedish Research Council, Centre for Innovative Medicine and the Jonasson donation. Flow cytometry analysis and cell sorting were performed at the MedH Flow Cytometry core facility, supported by KI/SLL. Sequencing was performed at the ESCG at Science for Life Laboratory (funded by the Knut and Alice Wallenberg Foundation and the Swedish Research Council) with assistance from SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. Open access funding provided by Karolinska Institute., and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Science, General Physics and Astronomy, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, General Biochemistry, Genetics and Molecular Biology, law.invention, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, law, medicine, [SDV.MHEP.OS]Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Induced pluripotent stem cell, lcsh:Science, Multidisciplinary, Cluster of differentiation, Retinal, General Chemistry, Macular degeneration, medicine.disease, Embryonic stem cell, In vitro, eye diseases, Cell biology, 030104 developmental biology, chemistry, Recombinant DNA, lcsh:Q, sense organs, 030217 neurology & neurosurgery, Cell based
Abstract: In vitro differentiation of human pluripotent stem cells into functional retinal pigment epithelial (RPE) cells provides a potentially unlimited source for cell based reparative therapy of age-related macular degeneration. Although the inherent pigmentation of the RPE cells have been useful to grossly evaluate differentiation efficiency and allowed manual isolation of pigmented structures, accurate quantification and automated isolation has been challenging. To address this issue, here we perform a comprehensive antibody screening and identify cell surface markers for RPE cells. We show that these markers can be used to isolate RPE cells during in vitro differentiation and to track, quantify and improve differentiation efficiency. Finally, these surface markers aided to develop a robust, direct and scalable monolayer differentiation protocol on human recombinant laminin-111 and −521 without the need for manual isolation.
Published: 2020
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28. A guide to the organ-on-a-chip

Author: Chak Ming Leung, Pim de Haan, Kacey Ronaldson-Bouchard, Ge-Ah Kim, Jihoon Ko, Hoon Suk Rho, Zhu Chen, Pamela Habibovic, Noo Li Jeon, Shuichi Takayama, Michael L. Shuler, Gordana Vunjak-Novakovic, Olivier Frey, Elisabeth Verpoorte, Yi-Chin Toh, RS: MERLN - Instructive Biomaterials Engineering (IBE), Division Instructive Biomaterials Eng, Pharmaceutical Analysis, and Medicinal Chemistry and Bioanalysis (MCB)
Subjects: FLUORESCENCE OPTICAL-DETECTION, IN-VITRO MODEL, NEURONAL DIFFERENTIATION, CELL-CULTURE ANALOG, SHEAR-STRESS, BLOOD-BRAIN-BARRIER, LIVER-CELLS, General Medicine, ELECTRICAL-RESISTANCE, MICROFLUIDIC SYSTEMS, General Biochemistry, Genetics and Molecular Biology, MICROPHYSIOLOGICAL SYSTEMS MPS
Abstract: Organs-on-chips (OoCs) are systems containing engineered or natural miniature tissues grown inside microfluidic chips. To better mimic human physiology, the chips are designed to control cell microenvironments and maintain tissue-specific functions. Combining advances in tissue engineering and microfabrication, OoCs have gained interest as a next-generation experimental platform to investigate human pathophysiology and the effect of therapeutics in the body. There are as many examples of OoCs as there are applications, making it difficult for new researchers to understand what makes one OoC more suited to an application than another. This Primer is intended to give an introduction to the aspects of OoC that need to be considered when developing an application-specific OoC. The Primer covers guiding principles and considerations to design, fabricate and operate an OoC, as well as subsequent assaying techniques to extract biological information from OoC devices. Alongside this is a discussion of current and future applications of OoC technology, to inform design and operational decisions during the implementation of OoC systems.
Published: 2022
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29. Prostate cancer prognosis after initiation of androgen deprivation therapy among statin users. A population-based cohort study

Author: Teemu J. Murtola, A.I.P. Peltomaa, Anssi Auvinen, Paavo Raittinen, Kirsi Talala, Kimmo Taari, Teuvo L.J. Tammela, Tampere University, Department of Mathematics and Systems Analysis, Finnish Cancer Registry, University of Helsinki, Aalto-yliopisto, Aalto University, Department of Surgery, Clinical Medicine, Health Sciences, HUS Abdominal Center, Clinicum, Urologian yksikkö, and Helsinki University Hospital Area
Subjects: Oncology, Male, Cancer Research, medicine.medical_specialty, Statin, medicine.drug_class, Urology, 3122 Cancers, 030232 urology & nephrology, Article, Androgen deprivation therapy, 03 medical and health sciences, Prostate cancer, 0302 clinical medicine, Cancer epidemiology, Internal medicine, Epidemiology, Epidemiology of cancer, medicine, Humans, Finland, Aged, business.industry, Hazard ratio, Prostatic Neoplasms, Androgen Antagonists, Middle Aged, medicine.disease, Prognosis, 3126 Surgery, anesthesiology, intensive care, radiology, 3. Good health, Survival Rate, 030220 oncology & carcinogenesis, Case-Control Studies, Cohort, Disease Progression, Population study, Drug Therapy, Combination, Hydroxymethylglutaryl-CoA Reductase Inhibitors, business, Follow-Up Studies
Abstract: Purpose Statins’ cholesterol-lowering efficacy is well-known. Recent epidemiological studies have found that inhibition of cholesterol synthesis may have beneficial effects on prostate cancer (PCa) patients, especially patients treated with androgen deprivation therapy (ADT). We evaluated statins’ effect on prostate cancer prognosis among patients treated with ADT. Materials and methods Our study population consisted of 8253 PCa patients detected among the study population of the Finnish randomized study of screening for prostate cancer. These were limited to 4428 men who initiated ADT during the follow-up. Cox proportional regression model adjusted for tumor clinical characteristics and comorbidities was used to estimate hazard ratios for risk of PSA relapse after ADT initiation and prostate cancer death. Results During the median follow-up of 6.3 years after the ADT initiation, there were 834 PCa deaths and 1565 PSA relapses in a study cohort. Statin use after ADT was associated with a decreased risk of PSA relapse (HR 0.73, 95% CI 0.65–0.82) and prostate cancer death (HR 0.82; 95% CI 0.69–0.96). In contrast, statin use defined with a one-year lag (HR 0.89, 95% CI 0.76–1.04), statin use before ADT initiation (HR 1.12, 95% CI 0.96–1.31), and use in the first year on ADT (HR 1.02, 95% CI 0.85–1.24) were not associated with prostate cancer death, without dose dependency. Conclusion Statin use after initiation of ADT, but not before, was associated with improved prostate cancer prognosis.
Published: 2021

30. State-of-the-art global models underestimate impacts from climate extremes

Author: Schewe, J., Gosling, S., Reyer, C., Zhao, F., Ciais, P., Elliott, J., Francois, L., Huber, V., Lotze, H., Seneviratne I, S., van Vliet, M., Vautard, R., Wada, Y., Breuer, L., Buechner, M., Carozza, D., Chang, J., Coll, M., Deryng, D., de Wit, A., Eddy, T., Folberth, C., Frieler, K., Friend, A., Gerten, D., Gudmundsson, L., Hanasaki, N., Ito, A., Khabarov, N., Kim, H., Lawrence, P., Morfopoulos, C., Mueller, C., Schmied, H., Orth, R., Ostberg, S., Pokhrel, Y., Pugh, T., Sakurai, G., Satoh, Y., Schmid, E., Stacke, T., https://orcid.org/0000-0003-4637-5337, Steenbeek, J., Steinkamp, J., Tang, Q., Tian, H., Tittensor, D., Volkholz, J., Wang, X., Warszawski, L., Potsdam-Institut für Klimafolgenforschung (PIK), University of Nottingham, UK (UON), Potsdam Institute for Climate Impact Research (PIK), East China Normal University [Shangaï] (ECNU), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ICOS-ATC (ICOS-ATC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Chicago, Institut d'Astrophysique et de Géophysique [Liège], Université de Liège, Dalhousie University [Halifax], Institute for Atmospheric and Climate Science [Zürich] (IAC), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Wageningen University and Research [Wageningen] (WUR), Extrèmes : Statistiques, Impacts et Régionalisation (ESTIMR), International Institute for Applied Systems Analysis [Laxenburg] (IIASA), Inst Landscape Ecol & Resources Management, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Université du Québec à Montréal = University of Québec in Montréal (UQAM), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Tyndall Centre for Climate Change Research, University of East Anglia [Norwich] (UEA), Wageningen University and Research Centre (WUR), Department of Geography, University of Liverpool, Centre National de la Recherche Scientifique (CNRS), Department of Geosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), National Institute for Environmental Studies (NIES), Institute of Industrial Science (IIS), The University of Tokyo (UTokyo), Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP), Université Jean Monnet - Saint-Étienne (UJM), Goethe-Universität Frankfurt am Main, Department of Civil and Environmental Engineering [Ann Arbor] (CEE), University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Institute for Meteorology and Climate Research (IMK), Karlsruhe Institute of Technology (KIT), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Helmholtz-Zentrum Geesthacht (GKSS), Ecopath International Initiative Research Association, Shandong Agricultural University (SDAU), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Justus-Liebig-Universität Gießen (JLU), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Université Jean Monnet [Saint-Étienne] (UJM), Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Schewe, Jacob [0000-0001-9455-4159], Gosling, Simon N [0000-0001-5973-6862], Ciais, Philippe [0000-0001-8560-4943], Lotze, Heike K [0000-0001-6258-1304], Seneviratne, Sonia I [0000-0001-9528-2917], van Vliet, Michelle TH [0000-0002-2597-8422], Vautard, Robert [0000-0001-5544-9903], Wada, Yoshihide [0000-0003-4770-2539], Breuer, Lutz [0000-0001-9720-1076], Carozza, David A [0000-0001-7343-9442], Chang, Jinfeng [0000-0003-4463-7778], Coll, Marta [0000-0001-6235-5868], de Wit, Allard [0000-0002-5517-6404], Eddy, Tyler D [0000-0002-2833-9407], Folberth, Christian [0000-0002-6738-5238], Gerten, Dieter [0000-0002-6214-6991], Gudmundsson, Lukas [0000-0003-3539-8621], Hanasaki, Naota [0000-0002-5092-7563], Ito, Akihiko [0000-0001-5265-0791], Khabarov, Nikolay [0000-0001-5372-4668], Kim, Hyungjun [0000-0003-1083-8416], Lawrence, Peter [0000-0002-4843-4903], Müller, Christoph [0000-0002-9491-3550], Müller Schmied, Hannes [0000-0001-5330-9923], Ostberg, Sebastian [0000-0002-2368-7015], Pokhrel, Yadu [0000-0002-1367-216X], Steenbeek, Jeroen [0000-0002-7878-8075], Steinkamp, Jörg [0000-0002-7861-8789], Tang, Qiuhong [0000-0002-0886-6699], Tian, Hanqin [0000-0002-1806-4091], Apollo - University of Cambridge Repository, European Commission, and Federal Ministry of Education and Research (Germany)
Subjects: Earth Observation and Environmental Informatics, WIMEK, 0602 Ecology, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Science, Aardobservatie en omgevingsinformatica, Life Science, Water Systems and Global Change, lcsh:Q, PE&RC, lcsh:Science, Article
Abstract: 14 pages, 6 figures, supplementary information .-- Data availability. Simulation data from gridded impact models is available through https://esg.pik-potsdam.de/projects/isimip2a/ and citable using the following DOIs: https://doi.org/10.5880/PIK.2017.002 (terrestrial ecosystems); https://doi.org/10.5880/PIK.2017.006 (agriculture); https://doi.org/10.5880/PIK.2017.010 (hydrology); https://doi.org/10.5880/PIK.2018.004 (marine ecosystems, regional); https://doi.org/10.5880/PIK.2018.005 (marine ecosystems, global). The city-level mortality model data and country-level hydropower model data are available from the authors upon request, Global impact models represent process-level understanding of how natural and human systems may be affected by climate change. Their projections are used in integrated assessments of climate change. Here we test, for the first time, systematically across many important systems, how well such impact models capture the impacts of extreme climate conditions. Using the 2003 European heat wave and drought as a historical analogue for comparable events in the future, we find that a majority of models underestimate the extremeness of impacts in important sectors such as agriculture, terrestrial ecosystems, and heat-related human mortality, while impacts on water resources and hydropower are overestimated in some river basins; and the spread across models is often large. This has important implications for economic assessments of climate change impacts that rely on these models. It also means that societal risks from future extreme events may be greater than previously thought, The work was supported within the framework of the Leibniz Competition (SAW-2013-PIK-5), the EU FP7 project HELIX (grant no. FP7–603864–2), the FP7 project IMPACT2C (grant agreement#282746) and by the German Federal Ministry of Education and Research (BMBF, grant no. 01LS1201A1)
Published: 2019
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31. 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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32. Harmonization of quality metrics and power calculation in multi-omic studies

Author: Ana Conesa, Johan A. Westerhuis, David Gomez-Cabrero, Thomas Hankemeier, Axel Imhof, Jesper Tegnér, Leandro Balzano-Nogueira, Andreas Schmidt, Sonia Tarazona, Biosystems Data Analysis (SILS, FNWI), and 25980629 - Westerhuis, Johannes Arnold
Subjects: 0301 basic medicine, Quality Control, Computer science, media_common.quotation_subject, Science, ESTADISTICA E INVESTIGACION OPERATIVA, General Physics and Astronomy, computer.software_genre, Data type, General Biochemistry, Genetics and Molecular Biology, Field (computer science), Article, Set (abstract data type), Machine Learning, 03 medical and health sciences, 0302 clinical medicine, Quality (business), lcsh:Science, media_common, Multidisciplinary, Design of experiments, Quality control, Computational Biology, General Chemistry, Statistical classification, 030104 developmental biology, Sample size determination, Data integration, lcsh:Q, Data mining, computer, 030217 neurology & neurosurgery, Algorithms
Abstract: [EN] Multi-omic studies combine measurements at different molecular levels to build comprehensive models of cellular systems. The success of a multi-omic data analysis strategy depends largely on the adoption of adequate experimental designs, and on the quality of the measurements provided by the different omic platforms. However, the field lacks a comparative description of performance parameters across omic technologies and a formulation for experimental design in multi-omic data scenarios. Here, we propose a set of harmonized Figures of Merit (FoM) as quality descriptors applicable to different omic data types. Employing this information, we formulate the MultiPower method to estimate and assess the optimal sample size in a multi-omics experiment. MultiPower supports different experimental settings, data types and sample sizes, and includes graphical for experimental design decision-making. MultiPower is complemented with MultiML, an algorithm to estimate sample size for machine learning classification problems based on multi-omic data., This work has been funded by FP7 STATegra project agreement 306000 and Spanish MINECO grant BIO2012-40244. In addition, work in the Imhof lab has been funded by the (DFG; CIPSM and SFB1064). The work of L.B.-N. has been funded by the University of Florida Startup funds.
Published: 2020
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33. A research roadmap for quantifying non-state and subnational climate mitigation action

Author: Thomas Hale, Katharina Lütkehermöller, Sander Chan, Neelam Singh, Jan Corfee-Morlot, Mark Roelfsema, John Moorhead, Nathan E. Hultman, Christopher Weber, Takeshi Kuramochi, Philip Drost, Angel Hsu, David J. Gordon, Pedro Faria, Amy Weinfurter, Ann Gardiner, Yihao Xie, Shirin Reuvers, Oscar Widerberg, Niklas Höhne, Joana Setzer, Environmental Policy Analysis, and Multi-layered governance in EUrope and beyond (MLG)
Subjects: 0303 health sciences, WIMEK, 010504 meteorology & atmospheric sciences, Corporate governance, media_common.quotation_subject, Global warming, Environmental Science (miscellaneous), 01 natural sciences, Terminology, 03 medical and health sciences, Environmental Systems Analysis, Action (philosophy), State (polity), Milieusysteemanalyse, Political science, Credibility, SDG 13 - Climate Action, Life Science, Environmental planning, Social Sciences (miscellaneous), GE Environmental Sciences, 030304 developmental biology, 0105 earth and related environmental sciences, media_common
Abstract: Non-state and subnational climate actors have become central to global climate change governance. Quantitatively assessing climate mitigation undertaken by these entities is critical to understand the credibility of this trend. In this Perspective, we make recommendations regarding five main areas of research and methodological development related to evaluating non-state and subnational climate actions: defining clear boundaries and terminology; use of common methodologies to aggregate and assess non-state and subnational contributions; systematically dealing with issues of overlap; estimating the likelihood of implementation; and addressing data gaps.
Published: 2019
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34. Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs

Author: Wolfram Liebermeister, Matteo Barberis, Hans V. Westerhoff, Thierry D.G.A. Mondeel, Oleksandr Ivanov, Weissing group, Systems, Control and Applied Analysis, Molecular Cell Biology, AIMMS, Molecular Cell Physiology, University of Surrey (UNIS), Swammerdam Institute for Life Sciences, University of Amsterdam [Amsterdam] (UvA)-Center for Neurosciences, Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Bernoulli Institute for Mathematics and Computer Science and Artificial Intelligence, Department of Molecular Cell Physiology [VU Amsterdam], Vrije Universiteit Amsterdam [Amsterdam] (VU), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Systems Biology Grant of the University of Surrey, SILS Starting Grant of the University of Amsterdam, and Synthetic Systems Biology (SILS, FNWI)
Subjects: 0301 basic medicine, Saccharomyces cerevisiae Proteins, BUDDING YEAST, Cell division, B-TYPE CYCLINS, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Saccharomyces cerevisiae, Biology, Cyclin B, Models, Biological, General Biochemistry, Genetics and Molecular Biology, Article, SACCHAROMYCES-CEREVISIAE, 03 medical and health sciences, 0302 clinical medicine, Cyclin-dependent kinase, Biological Clocks, Cyclins, SIC1, Drug Discovery, Dynamical systems, Oscillators, POSITIVE FEEDBACK, PHOSPHORYLATION, lcsh:QH301-705.5, Cyclin, Positive feedback, Kinase, Applied Mathematics, Systems Biology, Cell Cycle, Cell Cycle Checkpoints, Cell cycle, SELF-ORGANIZATION, Phenotype, Cyclin-Dependent Kinases, Computer Science Applications, MODEL, 030104 developmental biology, S-PHASE, lcsh:Biology (General), Modeling and Simulation, biology.protein, Neuroscience, GLYCOLYTIC OSCILLATIONS, 030217 neurology & neurosurgery, Biological network, Cell Division
Abstract: International audience; Some biological networks exhibit oscillations in their components to convert stimuli to time-dependent responses. The eukaryotic cell cycle is such a case, being governed by waves of cyclin-dependent kinase (cyclin/Cdk) activities that rise and fall with specific timing and guarantee its timely occurrence. Disruption of cyclin/Cdk oscillations could result in dysfunction through reduced cell division. Therefore, it is of interest to capture properties of network designs that exhibit robust oscillations. Here we show that a minimal yeast cell cycle network is able to oscillate autonomously, and that cyclin/Cdk-mediated positive feedback loops (PFLs) and Clb3-centered regulations sustain cyclin/Cdk oscillations, in known and hypothetical network designs. We propose that Clb3-mediated coordination of cyclin/Cdk waves reconciles checkpoint and oscillatory cell cycle models. Considering the evolutionary conservation of the cyclin/Cdk network across eukaryotes, we hypothesize that functional ("healthy") phenotypes require the capacity to oscillate autonomously whereas dysfunctional (potentially "diseased") phenotypes may lack this capacity. npj Systems Biology and Applications (2020) 6:8 ; https://doi.
Published: 2020
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35. In-situ, time resolved monitoring of uranium in BFS:OPC grout. Part 2: Corrosion in water

Author: C. A. Stitt, C. Paraskevoulakos, A. Banos, N. J. Harker, K. R. Hallam, H. Pullin, A. Davenport, S. Street, T. B. Scott, Interface Analysis Centre, University of Bristol [Bristol], European Synchrotron Radiation Facility (ESRF), School of Metallurgy and Materials, and University of Birmingham [Birmingham]
Subjects: Multidisciplinary, [SDV]Life Sciences [q-bio], lcsh:R, lcsh:Medicine, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, OXYGEN, Article, 0104 chemical sciences, MECHANISMS, IMMOBILIZATION, CEMENT, TEMPERATURES, VAPOR, lcsh:Q, 0210 nano-technology, lcsh:Science, (null)
Abstract: To reflect potential conditions in a geological disposal facility, uranium was encapsulated in grout and submersed in de-ionised water for time periods between 2–47 weeks. Synchrotron X-ray Powder Diffraction and X-ray Tomography were used to identify the dominant corrosion products and measure their dimensions. Uranium dioxide was observed as the dominant corrosion product and time dependent thickness measurements were used to calculate oxidation rates. The effectiveness of physical and chemical grout properties to uranium corrosion and mobilisation is discussed and Inductively Coupled Plasma Mass Spectrometry was used to measure 238U(aq) content in the residual water of several samples.
Published: 2018
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36. Species-specific host factors rather than virus-intrinsic virulence determine primate lentiviral pathogenicity

Author: James M. Billingsley, Erica H. Parrish, Frank Kirchhoff, Thalia Garcia-Tellez, Nicolas Huot, Guido Silvestri, Ulrike Sauermann, Berit Neumann, Christina M. Stürzel, Gerald H. Learn, Steven E. Bosinger, Christiane Stahl-Hennig, Daniel Sauter, Beatrice H. Hahn, Dietmar Fuchs, Clement W. Gnanadurai, Michaela Müller-Trutwin, Simone Joas, Dominik Hotter, Edina Lump, Cristian Apetrei, Nicholas F. Parrish, Kerstin Mätz Rensing, Universität Ulm - Ulm University [Ulm, Allemagne], University of Pennsylvania, German Primate Centre, Innsbruck Medical University = Medizinische Universität Innsbruck (IMU), Emory University [Atlanta, GA], University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), HIV, Inflammation et persistance - HIV, Inflammation and Persistence, Institut Pasteur [Paris] (IP), Vaccine Research Institute [Créteil, France] (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), This work was supported by NIH grants to B.H.H. (R37 AI50529, R01 AI 120810, R01 AI 114266), G.S. (R37 AI66998), and YYY (R01 AI 120860), and the BEAT-HIV Delaney Consortium (UM1 AI 126620), DFG CRC 1279 and SPP 1923, an Advanced ERC investigator grant to F.K., and a grant from Sidaction to M.M.-T. N.H. was supported by VRI (Créteil, France) and T.G.-T. by the Pasteur-Paris University PhD program. We thank the IDMIT center for access to the stellar Imaging platform and acknowledge the Imagopole France–BioImaging infrastructure, supported by the French ANR (10-INSB-04-01, Investments for the Future), for advice and access to the CV1000 system. S.J. and E.L. were part of IGradU Ulm and S.J. was supported by the DFG RTG CEMMA., We thank K. Regensburger, M. Mayer, R. Linsenmeyer, S. Engelhart, D. Krnavek, S. Heine, and J. Hampe for technical assistance, S. Sopper, K. Töpfer, and T. Schultheiss for support with flow cytometry and Nirav Patel and Greg Tharp of the Yerkes NHP Genomics Core for microarray analysis., University of Pennsylvania [Philadelphia], Innsbruck Medical University [Austria] (IMU), HIV, Inflammation et persistance, Institut Pasteur [Paris], and Vaccine Research Institute (VRI)
Subjects: 0301 basic medicine, MESH: Signal Transduction, MESH: Human Immunodeficiency Virus Proteins, MESH: CD3 Complex, CD3 Complex, Transcription, Genetic, animal diseases, viruses, Human Immunodeficiency Virus Proteins, Wirtsspezifität, General Physics and Astronomy, MESH: NF-kappa B, MESH: Amino Acid Sequence, Simian, MESH: Virulence, Lymphocyte Activation, Virus Replication, MESH: Bone Marrow Stromal Antigen 2, MESH: HIV-1, DDC 570 / Life sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chlorocebus aethiops, MESH: nef Gene Products, Human Immunodeficiency Virus, Viral Regulatory and Accessory Proteins, MESH: Animals, lcsh:Science, Lentiviren, Immunodeficiency, Multidisciplinary, Retrovirus, biology, Virulence, [SDV.BA]Life Sciences [q-bio]/Animal biology, Bone Marrow Stromal Antigen 2, NF-kappa B, virus diseases, Chronic inflammation, Viral Load, MESH: Gene Expression Regulation, 3. Good health, medicine.anatomical_structure, Host specificity, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Simian Immunodeficiency Virus, MESH: Viral Load, MESH: Lentiviruses, Primate, MESH: Viral Regulatory and Accessory Proteins, Signal Transduction, HIV infections, MESH: Host Specificity, T cell, Science, MESH: Simian Immunodeficiency Virus, MESH: Sequence Alignment, Viremia, General Biochemistry, Genetics and Molecular Biology, Virus, Article, 03 medical and health sciences, ddc:570, medicine, Animals, Humans, Amino Acid Sequence, nef Gene Products, Human Immunodeficiency Virus, ddc:610, MESH: Lymphocyte Activation, Species specificity, Lentiviruses, Primate, Pathogenicity, MESH: Humans, MESH: Transcription, Genetic, MESH: Virus Replication, General Chemistry, biology.organism_classification, medicine.disease, Virology, MESH: Cercopithecus aethiops, 030104 developmental biology, Viral replication, Gene Expression Regulation, Tetherin, HIV-1, lcsh:Q, Sequence Alignment, MESH: Female, DDC 610 / Medicine & health, Viral pathogenesis
Abstract: HIV-1 causes chronic inflammation and AIDS in humans, whereas related simian immunodeficiency viruses (SIVs) replicate efficiently in their natural hosts without causing disease. It is currently unknown to what extent virus-specific properties are responsible for these different clinical outcomes. Here, we incorporate two putative HIV-1 virulence determinants, i.e., a Vpu protein that antagonizes tetherin and blocks NF-κB activation and a Nef protein that fails to suppress T cell activation via downmodulation of CD3, into a non-pathogenic SIVagm strain and test their impact on viral replication and pathogenicity in African green monkeys. Despite sustained high-level viremia over more than 4 years, moderately increased immune activation and transcriptional signatures of inflammation, the HIV-1-like SIVagm does not cause immunodeficiency or any other disease. These data indicate that species-specific host factors rather than intrinsic viral virulence factors determine the pathogenicity of primate lentiviruses., In contrast to HIV, simian immunodeficiency viruses (SIV) do not cause disease in their hosts, and the reasons for this are unclear. Here, Joas et al. incorporate two putative HIV virulence factors into SIV and study effects in infected monkeys, suggesting that species-specific host factors are responsible for HIV pathogenesis.
Published: 2018
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37. TUB gene expression in hypothalamus and adipose tissue and its association with obesity in humans

Author: Bruce H. R. Wolffenbuttel, Ghazaleh Hajmousa, Ewa Szalowska, K Fluiter, Marcel G. M. Wolfs, Dicky Struik, J. V. van Vliet-Ostaptchouk, T. P. van der Meer, Johan W. Jonker, Ronit Shiri-Sverdlov, U A Unmehopa, Roel J. Vonk, Vera J. M. Nies, Dick F. Swaab, Farhad Rezaee, W.A. Buurman, Jan Greve, Sander S. Rensen, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Genome Analysis, Other Research, Medical Biology, Amsterdam Gastroenterology Endocrinology Metabolism, Lifestyle Medicine (LM), Center for Liver, Digestive and Metabolic Diseases (CLDM), Netherlands Institute for Neuroscience (NIN), Surgery, RS: NUTRIM - R2 - Liver and digestive health, and Moleculaire Genetica
Subjects: 0301 basic medicine, Gene isoform, CANDIDATE GENE, medicine.medical_specialty, Candidate gene, PROTEINS, Endocrinology, Diabetes and Metabolism, Hypothalamus, Medicine (miscellaneous), Adipose tissue, In situ hybridization, MOUSE, 03 medical and health sciences, Insulin resistance, Gene Frequency, Internal medicine, Gene expression, medicine, Journal Article, otorhinolaryngologic diseases, Humans, Metabolomics, Obesity, MUTATION, Adaptor Proteins, Signal Transducing, 2. Zero hunger, Nutrition and Dietetics, business.industry, ARCUATE NUCLEUS, medicine.disease, Neuropeptide Y receptor, INSULIN, 030104 developmental biology, Endocrinology, TUB/TUB MICE, BODY-WEIGHT, Adipose Tissue, NEUROPEPTIDE-Y, Metabolome, business, MESSENGER-RNA
Abstract: BACKGROUND/OBJECTIVES: Mutations in the Tubby gene (TUB) cause late-onset obesity and insulin resistance in mice and syndromic obesity in humans. Although TUB gene function has not yet been fully elucidated, studies in rodents indicate that TUB is involved in the hypothalamic pathways regulating food intake and adiposity. Aside from the function in central nervous system, TUB has also been implicated in energy metabolism in adipose tissue in rodents. We aimed to determine the expression and distribution patterns of TUB in man as well as its potential association with obesity. SUBJECTS/METHODS: In situ hybridization was used to localize the hypothalamic regions and cells expressing TUB mRNA. Using RT-PCR, we determined the mRNA expression level of the two TUB gene alternative splicing isoforms, the short and the long transcript variants, in the hypothalami of 12 obese and 12 normal-weight subjects, and in biopsies from visceral (VAT) and subcutaneous (SAT) adipose tissues from 53 severely obese and 24 non-obese control subjects, and correlated TUB expression with parameters of obesity and metabolic health. RESULTS: Expression of both TUB transcripts was detected in the hypothalamus, while only the short TUB isoform was found in both VAT and SAT. TUB mRNA was detected in several hypothalamic regions involved in body weight regulation, including the nucleus basalis of Meynert and the paraventricular, supraoptic and tuberomammillary nuclei. We found no difference in the hypothalamic TUB expression between obese and control groups, while the level of TUB mRNA was significantly lower in adipose tissue of obese subjects as compared to controls. Also, TUB expression was negatively correlated with indices of body weight and obesity in a fat-depot-specific manner. CONCLUSIONS: Our results indicate high expression of TUB in the hypothalamus, especially in areas involved in body weight regulation, and the correlation between TUB expression in adipose tissue and obesity. These findings suggest a role for TUB in human obesity.International Journal of Obesity accepted article preview online, 30 August 2017. doi:10.1038/ijo.2017.214.
Published: 2018
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38. Spirometry is not enough to diagnose COPD in epidemiological studies: a follow-up study

Author: Anatoly Lebedev, Olga Kuznetsova, Elena Andreeva, M A Pokhaznikova, Jean-Marie Degryse, Irina E. Moiseeva, UCL - SSS/IRSS - Institut de recherche santé et société, and UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies
Subjects: Male, Pulmonary and Respiratory Medicine, Spirometry, medicine.medical_specialty, medicine.drug_class, Vital Capacity, Population, Physical examination, Article, Russia, law.invention, Pulmonary Disease, Chronic Obstructive, 03 medical and health sciences, FEV1/FVC ratio, 0302 clinical medicine, law, Forced Expiratory Volume, Internal medicine, Bronchodilator, medicine, Humans, 030212 general & internal medicine, education, Asthma, lcsh:RC705-779, education.field_of_study, COPD, medicine.diagnostic_test, business.industry, IRSS, Public Health, Environmental and Occupational Health, lcsh:Diseases of the respiratory system, Middle Aged, respiratory system, medicine.disease, Bronchodilator Agents, respiratory tract diseases, Cross-Sectional Studies, 030228 respiratory system, Female, business, Spirometer, Follow-Up Studies
Abstract: A hallmark of the diagnosis of chronic obstructive pulmonary disease (COPD) is the measurement of post-bronchodilator (post-BD) airflow obstruction (AO) by spirometry, but spirometry is not enough for the provision of a clinical diagnosis. In the majority of previous epidemiological studies, COPD diagnosis has been based on spirometry and a few clinical characteristics. The aim of our study was to identify outcomes in patients newly diagnosed with airflow obstruction (AO) based on a diagnostic work-up conducted as part of a population-based cross-sectional study in North-Western Russia. Spirometry was performed before (pre-BD) and after BD administration, and AO was defined using the FEV1/FVC, COPD: Single lung function test not enough for diagnosis A single lung function test is insufficient to accurately diagnose chronic obstructive pulmonary disease (COPD). A team led by Jean-Marie Degryse from the Université Catholique de Louvain, Belgium, studied patients in Northwestern Russia who showed signs of airflow obstruction, as measured by a spirometer, a medical device that records the amount of air inhaled and exhaled and the speed of breath. Among those who initially showed signs of limited lung function, even after treatment with a bronchodilator, a large proportion did not exhibit airflow obstruction on a second spirometry test months later. Moreover, not everyone who had confirmed airflow obstruction were diagnosed with COPD when examined by a pulmonologist. Some had asthma or asthma-COPD overlap syndrome. The findings point to the need for clinical assessments and follow-up spirometry tests to accurately diagnose and manage COPD.
Published: 2017
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39. Carbon prices across countries

Author: Henri Waisman, Joeri Rogelj, Céline Guivarch, Stephane Hallegatte, Chris Bataille, School of Resource and Environmental Management, Simon Fraser University (SFU.ca), centre international de recherche sur l'environnement et le développement (CIRED), Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-École des hautes études en sciences sociales (EHESS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and International Institute for Applied Systems Analysis [Laxenburg] (IIASA)
Subjects: Science & Technology, 010504 meteorology & atmospheric sciences, Natural resource economics, Environmental Studies, 1. No poverty, chemistry.chemical_element, Environmental Sciences & Ecology, 010501 environmental sciences, Environmental Science (miscellaneous), [SHS.ECO]Humanities and Social Sciences/Economics and Finance, 01 natural sciences, 7. Clean energy, chemistry, 13. Climate action, Physical Sciences, Meteorology & Atmospheric Sciences, Business, Carbon, Life Sciences & Biomedicine, ComputingMilieux_MISCELLANEOUS, Social Sciences (miscellaneous), Environmental Sciences, 0105 earth and related environmental sciences, Market failure
Abstract: With country-specific development objectives and constraints, multiple market failures and limited international transfers, carbon prices do not need to be uniform across countries, but must be part of broader policy packages.
Published: 2018
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40. Tales of future weather

Author: Arthur C. Petersen, B. J. J. M. van den Hurk, G. J. van Oldenborgh, Eleftheria Vasileiadou, David A. Stainforth, Wilco Hazeleger, E. Min, Leonard A. Smith, Water and Climate Risk, Environmental Policy Analysis, Amsterdam Global Change Institute, and Technology, Innovation & Society
Subjects: Meteorologie en Luchtkwaliteit, WIMEK, Meteorology, Meteorology and Air Quality, Computer science, business.industry, SDG 13 – Klimaatactie, Environmental resource management, Climate change, Numerical weather prediction models, Environmental Science (miscellaneous), Environmental studies, Extreme weather, SDG 13 - Climate Action, Life Science, Climate model, Adaptation (computer science), Temporal scales, business, Social Sciences (miscellaneous), Downscaling, GE Environmental Sciences
Abstract: Society is vulnerable to extreme weather events and, by extension, to human impacts on future events. As climate changes weather patterns will change. The search is on for more effective methodologies to aid decision-makers both in mitigation to avoid climate change and in adaptation to changes. The traditional approach uses ensembles of climate model simulations, statistical bias correction, downscaling to the spatial and temporal scales relevant to decision-makers, and then translation into quantities of interest. The veracity of this approach cannot be tested, and it faces in-principle challenges. Alternatively, numerical weather prediction models in a hypothetical climate setting can provide tailored narratives for high-resolution simulations of high-impact weather in a future climate. This 'tales of future weather' approach will aid in the interpretation of lower-resolution simulations. Arguably, it potentially provides complementary, more realistic and more physically consistent pictures of what future weather might look like.
Published: 2015
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41. Blood vessel control of macrophage maturation promotes arteriogenesis in ischemia

Author: Hermann Haller, L. Christian Napp, Christine S. Falk, Christian Weber, Jaba Gamrekelashvili, Tamar Kapanadze, Christine Häger, Florian P. Limbourg, Vladimir J Lozanovski, Christian Beger, Kashyap Krishnasamy, Ralf H. Adams, Johann Bauersachs, Anne Limbourg, Matthias Mack, Biochemie, and RS: CARIM - R3.07 - Structure-function analysis of the chemokine interactome for therapeutic targeting and imaging in atherosclerosis
Subjects: 0301 basic medicine, POLARIZATION, Angiogenesis, General Physics and Astronomy, 030204 cardiovascular system & hematology, ANGIOGENESIS, ACTIVATION, Mice, 0302 clinical medicine, Ischemia, Macrophage, lcsh:Science, GENE-EXPRESSION, Multidisciplinary, Receptors, Notch, POSTNATAL ARTERIOGENESIS, Cell Differentiation, Adoptive Transfer, Cell biology, Hindlimb, NOTCH, medicine.anatomical_structure, MONOCYTES, Immunoglobulin J Recombination Signal Sequence-Binding Protein, Intercellular Signaling Peptides and Proteins, Signal transduction, Blood vessel, Signal Transduction, Science, Notch signaling pathway, Neovascularization, Physiologic, Biology, DENDRITIC CELLS, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, medicine, Animals, RBPJ, RBP-J, Macrophages, Calcium-Binding Proteins, General Chemistry, medicine.disease, ENDOTHELIAL-CELLS, 030104 developmental biology, Immunology, Mutation, Blood Vessels, lcsh:Q, Arteriogenesis, Gene Deletion
Abstract: Ischemia causes an inflammatory response that is intended to restore perfusion and homeostasis yet often aggravates damage. Here we show, using conditional genetic deletion strategies together with adoptive cell transfer experiments in a mouse model of hind limb ischemia, that blood vessels control macrophage differentiation and maturation from recruited monocytes via Notch signaling, which in turn promotes arteriogenesis and tissue repair. Macrophage maturation is controlled by Notch ligand Dll1 expressed in vascular endothelial cells of arteries and requires macrophage canonical Notch signaling via Rbpj, which simultaneously suppresses an inflammatory macrophage fate. Conversely, conditional mutant mice lacking Dll1 or Rbpj show proliferation and transient accumulation of inflammatory macrophages, which antagonizes arteriogenesis and tissue repair. Furthermore, the effects of Notch are sufficient to generate mature macrophages from monocytes ex vivo that display a stable anti-inflammatory phenotype when challenged with pro-inflammatory stimuli. Thus, angiocrine Notch signaling fosters macrophage maturation during ischemia., Molecular mechanisms of macrophage-mediated regulation of artery growth in response to ischemia are poorly understood. Here the authors show that vascular endothelium controls macrophage maturation and differentiation via Notch signaling, which in turn promotes arteriogenesis and ischemic tissue recovery.
Published: 2017

42. In-situ, time resolved monitoring of uranium in BFS:OPC grout. Part 1: Corrosion in water vapour

Author: A. Banos, Steven R. Street, Huw Pullin, Keith R Hallam, N. J. Harker, C.A. Stitt, Alison J. Davenport, C. Paraskevoulakos, Thomas Bligh Scott, Interface Analysis Centre, University of Bristol [Bristol], European Synchrotron Radiation Facility (ESRF), School of Metallurgy and Materials, and University of Birmingham [Birmingham]
Subjects: Materials science, Science, Uranium dioxide, 0211 other engineering and technologies, Oxide, Analytical chemistry, chemistry.chemical_element, Mineralogy, 02 engineering and technology, engineering.material, OXIDATION, Oxygen, Article, OXYGEN, Corrosion, MECHANISMS, Reaction rate, chemistry.chemical_compound, PHASES, TEMPERATURES, CEMENT, 021105 building & construction, KINETICS, [PHYS]Physics [physics], Multidisciplinary, Science & Technology, Grout, MIXTURES, Uranium, 021001 nanoscience & nanotechnology, Multidisciplinary Sciences, chemistry, RAY PHOTOELECTRON-SPECTROSCOPY, engineering, Medicine, Science & Technology - Other Topics, 0210 nano-technology, Water vapor, DIOXIDE
Abstract: Uranium encapsulated in grout was exposed to water vapour for extended periods of time. Through synchrotron x-ray powder diffraction and tomography measurements, uranium dioxide was determined the dominant corrosion product over a 50-week time period. The oxide growth rate initiated rapidly, with rates comparable to the U + H2O reaction. Over time, the reaction rate decreased and eventually plateaued to a rate similar to the U + H2O + O2 reaction. This behaviour was not attributed to oxygen ingress, but instead the decreasing permeability of the grout, limiting oxidising species access to the metal surface.
Published: 2017
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43. The C9ORF72 expansion mutation is a common cause of ALS+/-FTD in Europe and has a single founder

Author: Karen E. Morrison, Franco Taroni, Simon Topp, Janine Kirby, Jacqueline de Belleroche, Robert H. Brown, J. M. B. Vianney de Jong, Wim Robberecht, Markus Weber, Simon Lovestone, Bradley N. Smith, Vincenzo Silani, Michael E. Weale, Michelle K. Lupton, Anneloor ten Asbroek, Claire Troakes, Nicola Ticozzi, John Powell, Peter C. Sapp, Youn-Bok Lee, Kirsten M. Scott, Helenius J. Schelhaas, Jamie Wright, Leonard H. van den Berg, John Landers, Hardev Pall, Safa Al-Sarraj, Christopher Shaw, Alex G. Morris, Pamela J. Shaw, Ammar Al-Chalabi, Jack W. Miller, Ashley R. Jones, Phillip Van Damme, Peter J. Nestor, Cinzia Gellera, Aleksey Shatunov, Jan H. Veldink, Ian Gray, Tibor Hortobágyi, Peter M. Andersen, Lauren Johnson, Caroline Vance, Stephen Newhouse, Boris Rogelj, Frank Baas, ANS - Amsterdam Neuroscience, Human Genetics, Genome Analysis, and Neurology
Subjects: Biology, TARDBP, Polymorphism, Single Nucleotide, Genomic Instability, Article, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, C9orf72, Genetics, medicine, Humans, Amyotrophic lateral sclerosis, Age of Onset, Allele frequency, Genetics (clinical), 030304 developmental biology, Repetitive Sequences, Nucleic Acid, 0303 health sciences, C9orf72 Protein, Haplotype, Amyotrophic Lateral Sclerosis, Proteins, medicine.disease, Founder Effect, 3. Good health, Europe, Haplotypes, Frontotemporal Dementia, Mutation, Age of onset, Trinucleotide repeat expansion, 030217 neurology & neurosurgery, Founder effect
Abstract: A massive hexanucleotide repeat expansion mutation (HREM) in C9ORF72 has recently been linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we describe the frequency, origin and stability of this mutation in ALS+/-FTD from five European cohorts (total n=1347). Single-nucleotide polymorphisms defining the risk haplotype in linked kindreds were genotyped in cases (n=434) and controls (n=856). Haplotypes were analysed using PLINK and aged using DMLE+. In a London clinic cohort, the HREM was the most common mutation in familial ALS+/-FTD: C9ORF72 29/112 (26%), SOD1 27/112 (24%), TARDBP 1/112 (1%) and FUS 4/112 (4%) and detected in 13/216 (6%) of unselected sporadic ALS cases but was rare in controls (3/856, 0.3%). HREM prevalence was high for familial ALS+/-FTD throughout Europe: Belgium 19/22 (86%), Sweden 30/41 (73%), the Netherlands 10/27 (37%) and Italy 4/20 (20%). The HREM did not affect the age at onset or survival of ALS patients. Haplotype analysis identified a common founder in all 137 HREM carriers that arose around 6300 years ago. The haplotype from which the HREM arose is intrinsically unstable with an increased number of repeats (average 8, compared with 2 for controls, P
Published: 2013
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44. NIN-like protein 8 is a master regulator of nitrate-promoted seed germination in Arabidopsis

Author: Vanathy Easwaran, Masanori Okamoto, Ryoichi Yano, Anne Krapp, Yunchen Gong, Steven J. Rothstein, Dawei Yan, Akira Endo, Yong-Mei Bi, David S. Guttman, Vivian Chau, Matthew Ierullo, Nicolas Provart, Eiji Nambara, Mitsuhiro Kimura, Asher Pasha, Department of Cell & Systems Biology, University of Toronto, JST, PRESTO, Tottori University, Shimane University, Université de Tsukuba = University of Tsukuba, Centre for the Analysis of Genome Evolution and Function, Department of Molecular and Cellular Biology, University of Guelph, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, NSERC [RGPIN 355784, RGPIN-2014-03621], JST PRESTO [11105], Labex Saclay Plant Sciences [ANR-10-LABX-0040-SPS], and Nambara, Eiji
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Science, Mutant, Arabidopsis, General Physics and Astronomy, Germination, Biology, 01 natural sciences, Genetic analysis, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chemistry.chemical_compound, Cytochrome P-450 Enzyme System, Plant Growth Regulators, Nitrate, Gene Expression Regulation, Plant, Botany, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Protein Isoforms, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Promoter Regions, Genetic, Abscisic acid, Conserved Sequence, Plant Proteins, chemistry.chemical_classification, Nitrates, Multidisciplinary, Arabidopsis Proteins, Catabolism, fungi, Gene Expression Regulation, Developmental, food and beverages, General Chemistry, biology.organism_classification, Cell biology, 030104 developmental biology, Enzyme, chemistry, Seeds, Abscisic Acid, Transcription Factors, 010606 plant biology & botany
Abstract: Seeds respond to multiple different environmental stimuli that regulate germination. Nitrate stimulates germination in many plants but how it does so remains unclear. Here we show that the Arabidopsis NIN-like protein 8 (NLP8) is essential for nitrate-promoted seed germination. Seed germination in nlp8 loss-of-function mutants does not respond to nitrate. NLP8 functions even in a nitrate reductase-deficient mutant background, and the requirement for NLP8 is conserved among Arabidopsis accessions. NLP8 reduces abscisic acid levels in a nitrate-dependent manner and directly binds to the promoter of CYP707A2, encoding an abscisic acid catabolic enzyme. Genetic analysis shows that NLP8-mediated promotion of seed germination by nitrate requires CYP707A2. Finally, we show that NLP8 localizes to nuclei and unlike NLP7, does not appear to be activated by nitrate-dependent nuclear retention of NLP7, suggesting that seeds have a unique mechanism for nitrate signalling., Nitrate stimulates seed germination in many plant species. Here, Yan et al. show that the Arabidopsis transcription factor NIN-like protein 8 is required to stimulate germination in response to nitrate and induces expression of an enzyme involved in ABA catabolism.
Published: 2016
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45. Importance of mosquito 'quasispecies' in selecting an epidemic arthropod-borne virus

Author: Karima Zouache, Géraldine Piorkowski, Xavier de Lamballerie, Jean-Michel Thiberge, Marie Vazeille, Anna-Bella Failloux, Catherine Dauga, Mosè Manni, Giuliano Gasperi, André Yébakima, Anubis Vega-Rúa, Laurence Mousson, Marie-Christine Vaney, Valérie Caro, Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP), Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Centre de Démoustication, Conseil Général de Martinique, Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), International Group for Data Analysis (IGDA), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Virologie Structurale - Structural Virology, Laboratorio degli insetti di interesse agrario e sanitario, Università degli Studi di Pavia = University of Pavia (UNIPV), This study was funded by the Institut Pasteur and the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant n°. ANR-10-LABX-62-IBEID). KZ was supported by the project 'VECTORIE' and the Foundation Inkermann (Fondation de France)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris], Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Università degli Studi di Pavia, DEMESLAY GOUGAM, MARIE, and Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID
Subjects: 0301 basic medicine, Aedes albopictus, viruses, Population, Viral quasispecies, Alphavirus, Mosquito Vectors, medicine.disease_cause, Article, 03 medical and health sciences, Aedes, Chlorocebus aethiops, medicine, Animals, Humans, Chikungunya, education, Vero Cells, Phylogeny, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, education.field_of_study, Multidisciplinary, biology, fungi, virus diseases, Genetic Variation, Fibroblasts, Viral Load, biology.organism_classification, Virology, 030104 developmental biology, Genetics, Population, Congo, Vector (epidemiology), Togaviridae, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Chikungunya Fever, Female, Chikungunya virus, Reunion
Abstract: Most arthropod-borne viruses (arboviruses), perpetuated by alternation between a vertebrate host and an insect vector, are likely to emerge through minor genetic changes enabling the virus to adapt to new hosts. In the past decade, chikungunya virus (CHIKV; Alphavirus, Togaviridae) has emerged on La Réunion Island following the selection of a unique substitution in the CHIKV E1 envelope glycoprotein (E1-A226V) of an East-Central-South African (ECSA) genotype conferring a higher transmission rate by the mosquito Aedes albopictus. Assumed to have occurred independently on at least four separate occasions, this evolutionary convergence was suspected to be responsible for CHIKV worldwide expansion. However, assumptions on CHIKV emergence were mainly based on viral genetic changes and the role of the mosquito population quasispecies remained unexplored. Here we show that the nature of the vector population is pivotal in selecting the epidemic CHIKV. We demonstrate using microsatellites mosquito genotyping that Ae. albopictus populations are genetically differentiated, contributing to explain their differential ability to select the E1-226V mutation. Aedes albopictus, newly introduced in Congo coinciding with the first CHIKV outbreak, was not able to select the substitution E1-A226V nor to preferentially transmit a CHIKV clone harboring the E1-226V as did Ae. albopictus from La Réunion.
Published: 2016
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46. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance

Author: John R. B. Perry, James B. Meigs, José Dupuis, Luigi Ferrucci, Johan G. Eriksson, Vilmundur Gudnason, Eric J.G. Sijbrands, Jeanette S. Andrews, Jonna L. Grimsby, Lawrence F. Bielak, Peter Kovacs, Panos Deloukas, Marijana Peričić, Johannes H. Smit, Ruth J. F. Loos, Gonneke Willemsen, Eric Boerwinkle, Ben A. Oostra, Manuel Serrano-Ríos, Alena Stančáková, Meena Kumari, Antti Jula, Michael Marmot, Caroline S. Fox, Simon Heath, Guo Li, Ola Hansson, Gerard Waeber, Anne U. Jackson, Nicholas L. Smith, Markku Laakso, George Dedoussis, Aarno Palotie, Sara M. Willems, John F. Peden, Elisabeth Widen, Caroline Hayward, Alan F. Wright, Claes Ladenvall, May E. Montasser, María Teresa Martínez-Larrad, Peter Vollenweider, Louis Pérusse, Tamara B. Harris, Wen Hong L. Kao, Danijela Budimir, Denis Rybin, David B. Savage, Michael A. Province, Alisa K. Manning, Bruna Gigante, Najaf Amin, Lenore J. Launer, Naveed Sattar, Lori L. Bonnycastle, Göran Hallmans, Jeffrey R. O'Connell, Stéphane Lobbens, Jacques S. Beckmann, Gemma Cadby, J. Wouter Jukema, Maria Dimitriou, Michael Stumvoll, Max Vikström, Rona J. Strawbridge, Hugh Watkins, Lyle J. Palmer, Johanna Kuusisto, Aimo Ruokonen, Hanieh Yaghootkar, Yan V. Sun, Inês Barroso, Amy J. Swift, Nancy L. Pedersen, Lars Lind, Mladen Boban, Nita G. Forouhi, Ken K. Ong, Ivana Kolcic, Anke Tönjes, Timothy M. Frayling, Paul W. Franks, Narisu Narisu, Karin Leander, Serge Hercberg, Diana Zelenika, Sharon L.R. Kardia, Min A. Jhun, Marjo-Riitta Järvelin, Stella Trompet, Jaakko Kaprio, Toshiko Tanaka, David S. Siscovick, Toby Johnson, Cornelia M. van Duijn, Veikko Salomaa, Jose C. Florez, James F. Wilson, Leena Peltonen, Pilar Galan, Robert Clarke, Andrew A. Hicks, Claudia Langenberg, Anders Hamsten, David Couper, Albert Hofman, Dawn M. Waterworth, John Blangero, James S. Pankow, Nabila Bouatia-Naji, Sirkka Keinänen-Kiukaanniemi, Mark I. McCarthy, Valeriya Lyssenko, Leif Groop, Brenda W.J.H. Penninx, Ching-Ti Liu, Anuj Goel, Marina Pehlić, Michael Boehnke, Mika Kivimäki, Maria Sabater-Lleal, Emil Rehnberg, Ingrid B. Borecki, Ozren Polasek, Eco J. C. de Geus, Peter P. Pramstaller, Igor Rudan, Richard M. Watanabe, Pierre Meneton, Iva Miljkovic, Vincent Mooser, G. Mark Lathrop, John Beilby, Laura J. Rasmussen-Torvik, Arturo Corbató-Anchuelo, Yvonne Böttcher, Richard N. Bergman, Daniel R. Barnes, Paul C. D. Johnson, Mustafa Atalay, Aroon D. Hingorani, Olga D. Carlson, Perttu Salo, Jacqueline C.M. Witteman, Udo Seedorf, Timo Saaristo, Jian'an Luan, Nicholas J. Wareham, Gudny Eiriksdottir, Matti Uusitupa, Yongmei Liu, Jaakko Tuomilehto, Yurii S. Aulchenko, Peter Schwarz, Robert A. Scott, Lina Zgaga, Joseph Hung, Reedik Mägi, Maria Grazia Franzosi, Eric J. Brunner, Claude Bouchard, Ian Ford, Francis S. Collins, Ulf de Faire, Benjamin F. Voight, Erik Ingelsson, Mario A. Morken, Stefania Bandinelli, Nicole L. Glazer, Dmitry Shungin, Lars Lannfelt, André G. Uitterlinden, Tatijana Zemunik, Markus Perola, Kenneth Rice, Veronique Vitart, Kerrin S. Small, Jouke-Jan Hottenga, Han Chen, Jerome I. Rotter, Philippe Froguel, Karen L. Mohlke, Marie-Claude Vohl, Dorret I. Boomsma, Harry Campbell, Peter S. Chines, Pau Navarro, Vasiliki Lagou, Albert V. Smith, Kathleen Stirrups, Josephine M. Egan, Alan R. Shuldiner, Katri Räikkönen, Inga Prokopenko, Ping An, Rainer Rauramaa, Beverley Balkau, Thor Aspelund, Eleanor Wheeler, Mariza de Andrade, Richa Saxena, Jari Lahti, Cécile Lecoeur, Timo A. Lakka, Jennie Hui, Michael R. Erdos, Stavroula Kanoni, Kirsten Ohm Kyvik, Bengt Sennblad, Sarah H. Wild, Patricia A. Peyser, Patrik K. E. Magnusson, Claire Bellis, Elodie Eury, Jaana Lindström, Boston University [Boston] (BU), Broad Institute of Harvard and MIT, Partenaires INRAE, Massachusetts General Hospital, Massachusetts General Hospital [Boston], Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), Department of Medicine, Université de Sherbrooke (UdeS), Addenbrooke's Hospital, Harvard Medical School [Boston] (HMS)-Beth Israel Deaconess Medical Center [Boston] (BIDMC), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Université Lille Nord de France (COMUE), Department of Epidemiology, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System-Center for Social Epidemiology and Population Health, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford [Oxford], The Wellcome Trust Centre for Human Genetics [Oxford], The Netherlands Cancer Institute, Ontario Institute for Cancer Research, Mount Sinai Hospital [Toronto, Canada] (MSH), VU University Amsterdam, Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], University of Michigan System, Queen Mary University of London (QMUL), The Wellcome Trust Sanger Institute [Cambridge], Lund University [Lund], Diabetes Centre, Lund University, University of Helsinki, Wake Forest School of Medicine, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, University of Maryland School of Medicine, University of Maryland System, University of Edinburgh, University of Exeter, Department of Twin Research and Genetic Epidemiology, King's College London, London, Northwestern University [Evanston], National Institute of Health and Welfare, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Lund University Diabetes Centre, Umeå University, National Institutes of Health, Centre for Medical Systems Biology, Netherlands Genomics Initiative, Washington University in Saint Louis (WUSTL), Department of Health Sciences Research, Mayo Clinic, Wake Forest University, Icelandic Heart Association, Heart Preventive Clinic and Research Institute, University of Iceland, Institute of Biomedicine, Physiology, University of Eastern Finland, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR S 1018, Université Paris-Sud - Paris 11 (UP11), Azienda Sanitaria Firenze, Department of Medical Genetics, Université de Lausanne (UNIL), Centre Hospitalier Universitaire Vaudois (CHUV), Queen Elizabeth II Medical Centre, Research Institute, University of Southern California (USC), University of Split, The University of Texas Health Science Center at Houston (UTHealth), Leipzig University, Pennington Biomedical Research Center, Department of Epidemiology & Public Health, University College of London [London] (UCL), San Carlos Clinical Hospital, University of North Carolina, Harokopio University, National Institute on Aging, Folkhälsan Research Centre, Vaasa Central Hospital, Unité de Recherche en Epidémiologie Nutritionnelle (UREN), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Psychiatry, EMGO - Lifestyle, overweight and diabetes, Epidemiology, Immunology, Erasmus School of Social and Behavioural Sciences, Clinical Genetics, Ophthalmology, Internal Medicine, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Multiple Tissue Human Expression Resource (MUTHER) Consortium, Ahmadi, K.R., Ainali, C., Barrett, A., Bataille, V., Bell, J.T., Buil, A., Deloukas, P., Dermitzakis, E.T., Dimas, A.S., Durbin, R., Glass, D., Grundberg, E., Hassanali, N., Hedman, Å.K., Ingle, C., Knowles, D., Krestyaninova, M., Lindgren, C.M., Lowe, C.E., McCarthy, M.I., Meduri, E., di Meglio, P., Min, J.L., Montgomery, S.B., Nestle, F.O., Nica, A.C., Nisbet, J., O'Rahilly, S., Parts, L., Potter, S., Sekowska, M., Shin, S.Y., Small, K.S., Soranzo, N., Spector, T.D., Surdulescu, G., Travers, M.E., Tsaprouni, L., Tsoka, S., Wilk, A., Yang, T.P., Zondervan, K.T., Voight, B.F., Scott, L.J., Steinthorsdottir, V., Morris, A.P., Dina, C., Welch, R.P., Zeggini, E., Huth, C., Aulchenko, Y.S., Thorleifsson, G., McCulloch, L.J., Ferreira, T., Grallert, H., Amin, N., Wu, G., Willer, C.J., Raychaudhuri, S., McCarroll, S.A., Langenberg, C., Hofmann, O.M., Dupuis, J., Qi, L., Segrè, A.V., van Hoek, M., Navarro, P., Ardlie, K., Balkau, B., Benediktsson, R., Bennett, A.J., Blagieva, R., Boerwinkle, E., Bonnycastle, L.L., Boström, K.B., Bravenboer, B., Bumpstead, S., Burtt, N.P., Charpentier, G., Chines, P.S., Cornelis, M., Couper, D.J., Crawford, G., Doney, A.S., Elliott, K.S., Elliott, A.L., Erdos, M.R., Fox, C.S., Franklin, C.S., Ganser, M., Gieger, C., Grarup, N., Green, T., Griffin, S., Groves, C.J., Guiducci, C., Hadjadj, S., Herder, C., Isomaa, B., Jackson, A.U., Johnson, P.R., Jørgensen, T., Kao, W.H., Klopp, N., Kong, A., Kraft, P., Kuusisto, J., Lauritzen, T., Li, M., Lieverse, A., Lyssenko, V., Marre, M., Meitinger, T., Midthjell, K., Morken, M.A., Narisu, N., Nilsson, P., Owen, K.R., Payne, F., Perry, J.R., Petersen, A.K., Platou, C., Proença, C., Prokopenko, I., Rathmann, W., Rayner, N.W., Robertson, N.R., Rocheleau, G., Roden, M., Sampson, M.J., Saxena, R., Shields, B.M., Shrader, P., Sigurdsson, G., Sparsø, T., Strassburger, K., Stringham, H.M., Sun, Q., Swift, A.J., Thorand, B., Tichet, J., Tuomi, T., van Dam, R.M., van Haeften, T.W., van Herpt, T., van Vliet-Ostaptchouk, J.V., Walters, G.B., Weedon, M.N., Wijmenga, C., Witteman, J., Bergman, R.N., Cauchi, S., Collins, F.S., Gloyn, A.L., Gyllensten, U., Hansen, T., Hide, W.A., Hitman, G.A., Hofman, A., Hunter, D.J., Hveem, K., Laakso, M., Mohlke, K.L., Morris, A.D., Palmer, C.N., Pramstaller, P.P., Rudan, I., Sijbrands, E., Stein, L.D., Tuomilehto, J., Uitterlinden, A., Walker, M., Wareham, N.J., Watanabe, R.M., Abecasis, G.R., Boehm, B.O., Campbell, H., Daly, M.J., Hattersley, A.T., Hu, F.B., Meigs, J.B., Pankow, J.S., Pedersen, O., Wichmann, H.E., Barroso, I., Florez, J.C., Frayling, T.M., Groop, L., Sladek, R., Thorsteinsdottir, U., Wilson, J.F., Illig, T., Froguel, P., van Duijn, C.M., Stefansson, K., Altshuler, D., Boehnke, M., Biological Psychology, EMGO+ - Lifestyle, Overweight and Diabetes, Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut National de la Recherche Agronomique (INRA)
Subjects: Blood Glucose, Netherlands Twin Register (NTR), medicine.medical_treatment, [SDV]Life Sciences [q-bio], LOCI, Genome-wide association study, Type 2 diabetes, SUSCEPTIBILITY, Body Mass Index, GLUCOSE, Blood Glucose/metabolism, Cholesterol, HDL/metabolism, Diabetes Mellitus, Type 2/genetics, Genome-Wide Association Study, Humans, Insulin/metabolism, Insulin Resistance/genetics, Polymorphism, Single Nucleotide, 0302 clinical medicine, Insulin, 2. Zero hunger, Genetics, 0303 health sciences, COMMON VARIANTS, 3. Good health, ENVIRONMENT INTERACTION, OBESITY, CORONARY-ARTERY-DISEASE, medicine.medical_specialty, 030209 endocrinology & metabolism, Accounting, Biology, Article, 03 medical and health sciences, Insulin resistance, SDG 3 - Good Health and Well-being, Internal medicine, Diabetes mellitus, medicine, 030304 developmental biology, Genetic association, Glycemic, loci, SNP, insulin, business.industry, Cholesterol, HDL, medicine.disease, Obesity, POLYMORPHISM, ASSOCIATION ANALYSIS, Endocrinology, Diabetes Mellitus, Type 2, TYPE-2 DIABETES RISK, Insulin Resistance, business
Abstract: Group Authors : DIAGRAM Consortium MUTHER Consortium variants influencing fasting glycemic traits and insulin resistance Seuls les 100 premiers auteurs ont été conservés dans la publication. La liste complète des auteurs et des des affiliations est disponible sur la publication https://www.nature.com/articles/ng.2274.pdf p. 667-669.; International audience; Recent genome-wide association studies have described many loci implicated in type 2 diabetes (T2D) pathophysiology and beta-cell dysfunction but have contributed little to the understanding of the genetic basis of insulin resistance. We hypothesized that genes implicated in insulin resistance pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci associated with fasting insulin at P < 5 x 10(-8) in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals. Risk variants were associated with higher triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci in insulin resistance pathways. The discovery of these loci will aid further characterization of the role of insulin resistance in T2D pathophysiology.
Published: 2012
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47. Genome-wide association study identifies five new schizophrenia loci

Author: Ripke, S., Sanders, A. R., Kendler, K. S., Levinson, D. F., Sklar, P., Holmans, P. A., Lin, D., Duan, J., Ophoff, R. A., Andreassen, O. A., Scolnick, E., Cichon, S., Clair, D. S., Corvin, A., Gurling, H., Werge, T., Rujescu, D., D. H. R., Pato, C. N., Malhotra, A. K., Purcell, S., Dudbridge, F., Neale, B. M., Rossin, L., Visscher, P. M., Posthuma, D., Ruderfer, D. M., Fanous, A., Stefansson, H., Steinberg, S., Mowry, B. J., Golimbet, V., Hert, M. D., Jönsson, E. G., Bitter, I., O. P. H., Collier, D. A., Tosato, Sarah, Agartz, I., Albus, M., Alexander, M., Amdur, R. L., Amin, F., Bass, N., Bergen, S. E., Black, D. W., Børglum, A. D., Brown, M. A., Bruggeman, R., Buccola, N. G., Byerley, W. F., Cahn, W., Cantor, R. M., Carr, V. J., Catts, S. V., Choudhury, K., Cloninger, C. R., Cormican, P., Craddock, N., Danoy, P. A., Datta, S., Haan, L. d., Demontis, D., Dikeos, D., Djurovic, S., Donnelly, P., Donohoe, G., Duong, L., Dwyer, S., Fink Jensen, A., Freedman, R., Freimer, N. B., Friedl, M., Georgieva, L., Giegling, I., Gill, M., Glenthøj, B., Godard, S., Hamshere, M., Hansen, M., Hansen, T., Hartmann, A. M., Henskens, F. A., Hougaard, D. M., Hultman, C. M., Ingason, A., Jablensky, A. V., Jakobsen, K. D., Jay, M., Jürgens, G., Kahn, R. S., Keller, M. C., Kenis, G., Kenny, E., Kim, Y., Kirov, G. K., Konnerth, H., Konte, B., Krabbendam, L., Krasucki, R., Lasseter, V. K., Laurent, C., Lawrence, J., Lencz, T., Lerer, F. B., Liang, K., Lichtenstein, P., Lieberman, J. A., Linszen, D. H., Lönnqvist, J., Loughland, C. M., Maclean, A. W., Maher, B. S., Maier, W., Mallet, J., Malloy, P., Mattheisen, M., Mattingsdal, M., Mcghee, K. A., Mcgrath, J. J., Mcintosh, A., Mclean, D. E., Mcquillin, A., Melle, I., Michie, P. T., Milanova, V., Morris, D. W., Mors, O., Mortensen, P. B., Moskvina, V., Muglia, P., Myin Germeys, I., Nertney, D. A., Nestadt, G., Nielsen, J., Nikolov, I., Nordentoft, M., Norton, N., Nöthen, M. M., O'Dushlaine, C. T., Olincy, A., Olsen, L., O'Neill, F. A., Orntoft, T. F., Owen, M. J., Pantelis, C., Papadimitriou, G., Pato, M. T., Peltonen, L., Petursson, H., Pickard, B., Pimm, J., Pulver, A. E., Puri, V., Quested, D., Quinn, E. M., Rasmussen, H. B., Réthelyi, J. M., Ribble, R., Rietschel, M., Riley, B. P., Ruggeri, Mirella, Schall, U., Schulze, T. G., Schwab, S. G., Scott, R. J., Shi, J., Sigurdsson, E., Silverman, J. M., C. C. A., Stefansson, K., Strange, A., Strengman, E., Stroup, T. S., Suvisaari, J., Terenius, L., Thirumalai, S., Thygesen, J. H., Timm, S., Toncheva, D., Den, E. v., J. v., Os, Winkel, R. v., Veldink, J., Walsh, D., Wang, A. G., Wiersma, D., Wildenauer, D. B., Williams, H. J., Williams, N. M., Wormley, B., Zammit, S., Sullivan, P. F., O'Donovan, M. C., Daly, M. J., Gejman, P. V., Genome Wide, S. P., ANS - Amsterdam Neuroscience, Adult Psychiatry, Functional Genomics, Educational Neuroscience, Clinical Child and Family Studies, Neuroscience Campus Amsterdam - integrative Analysis & Modeling, Neuroscience Campus Amsterdam - Attention & Cognition, LEARN! - Brain, learning and development, Psychiatrie & Neuropsychologie, and RS: MHeNs School for Mental Health and Neuroscience
Subjects: Male, Gene Dosage, Biology, VARIANTS, SUSCEPTIBILITY, ANCESTRY, Polymorphism, Single Nucleotide, Article, Linkage Disequilibrium, White People, 03 medical and health sciences, 0302 clinical medicine, microRNA, Genetics, Humans, Genetic Predisposition to Disease, Alleles, 030304 developmental biology, 0303 health sciences, Genome, Genome, Human, HERITABILITY, MICRORNA, BIPOLAR DISORDER, 3. Good health, schizophrenia, COMMON SNPS EXPLAIN, MicroRNAs, INDIVIDUALS, Logistic Models, Gene Expression Regulation, Haplotypes, LARGE PROPORTION, Genetic Loci, Case-Control Studies, Mutation, Female, HUMAN HEIGHT, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 × 10 -11) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 × 10 -9), ANK3 (rs10994359, P = 2.5 × 10 -8) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 × 10 -9). © 2011 Nature America, Inc. All rights reserved.
Published: 2011
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48. Genetic variation in DPP6 is associated with susceptibility to amyotrophic lateral sclerosis

Author: John H. J. Wokke, Cisca Wijmenga, Anna Birve, Jan H. Veldink, Vianney de Jong, Michael A. van Es, Robin Lemmens, Paul W.J. van Vught, Leonard H. van den Berg, Christine Van Broeckhoven, Peter M. Andersen, Bryan J. Traynor, Kristel Sleegers, Ruben van 't Slot, Ludo Van Den Bosch, Frank Baas, Wim Robberecht, Lude Franke, Jennifer C. Schymick, Roel A. Ophoff, Christiaan G J Saris, Helenius J. Schelhaas, Sonja W. de Jong, Hylke M. Blauw, ANS - Amsterdam Neuroscience, Neurology, Genome Analysis, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), and Stem Cell Aging Leukemia and Lymphoma (SALL)
Subjects: Oncology, medicine.medical_specialty, Potassium Channels, Nerve Tissue Proteins, Biology, Polymorphism, Single Nucleotide, White People, Polymorphism (computer science), Internal medicine, Genetic variation, Genetics, medicine, SNP, Humans, Genetic Predisposition to Disease, Genetic variability, Amyotrophic lateral sclerosis, Dipeptidyl-Peptidases and Tripeptidyl-Peptidases, MUTATIONS, Amyotrophic Lateral Sclerosis, Case-control study, Odds ratio, medicine.disease, Neuromuscular development and genetic disorders [UMCN 3.1], Confidence interval, SPORADIC ALS, Case-Control Studies, Functional Neurogenomics [DCN 2], Chromosomes, Human, Pair 7, Peptide Hydrolases
Abstract: Contains fulltext : 70185.pdf (Publisher’s version ) (Closed access) We identified a SNP in the DPP6 gene that is consistently strongly associated with susceptibility to amyotrophic lateral sclerosis (ALS) in different populations of European ancestry, with an overall P value of 5.04 x 10(-8) in 1,767 cases and 1,916 healthy controls and with an odds ratio of 1.30 (95% confidence interval (CI) of 1.18-1.43). Our finding is the first report of a genome-wide significant association with sporadic ALS and may be a target for future functional studies.
Published: 2008

49. Dysfunctional astrocytic regulation of glutamate transmission in a rat model of depression

Author: A. Van Eeckhaut, Dimitri De Bundel, Marta Gómez-Galán, Maria Lindskog, Ilse Julia Smolders, Pharmaceutical Chemistry, Drug Analysis and Drug Information, and Experimental Pharmacology
Subjects: Male, Patch-Clamp Techniques, Hippocampus, Glutamic Acid, Nerve Tissue Proteins, Tetrodotoxin, D-serine, FSL, GLAST, memory, Neurotransmission, In Vitro Techniques, Synaptic Transmission, Statistics, Nonparametric, Rats, Sprague-Dawley, Cellular and Molecular Neuroscience, Glutamatergic, Glutamate Plasma Membrane Transport Proteins, Serine, Glutamate reuptake, Animals, Humans, Excitatory Amino Acid Agents, Molecular Biology, Swimming, Depression, Pyramidal Cells, Glutamate receptor, Excitatory Postsynaptic Potentials, Long-term potentiation, Recognition, Psychology, Rats, Psychiatry and Mental health, Disease Models, Animal, Receptors, Glutamate, Astrocytes, Synaptic plasticity, NMDA receptor, Psychology, Neuroscience, Sodium Channel Blockers
Abstract: Depression is usually associated with alterations in the monoaminergic system. However, new evidences suggest the involvement of the glutamatergic system in the aetiology of depression. Here we explored the glutamatergic system in a rat model of depression (i.e., the flinders sensitive line (FSL)) to reveal the mechanism underlying the emotional and cognitive aspects associated with the disease. We showed a dramatically elevated level of baseline glutamatergic synaptic transmission by whole-cell recordings as well as impairment in long-term potentiation induced by high-frequency stimulation in hippocampal slices from FSL rats compared with Sprague–Dawley rats. At behavioural level, FSL rats displayed recognition memory impairment in the novel object recognition test. Enantioselective chromatography analysis revealed lower levels of D-serine in the hippocampus of FSL rats and both synaptic plasticity and memory impairments were restored by administration of D-serine. We also observed dysfunctional astrocytic glutamate regulation including downregulation of the glia glutamate transporter GLAST as shown by western blot. One possibility is that the dysfunctional astrocytic glutamate reuptake triggers a succession of events, including the reduction of D-serine production as a safety mechanism to avoid NMDA receptor overactivation, which in turn causes the synaptic plasticity and memory impairments observed. These findings open up new brain targets for the development of more potent and efficient antidepressant drugs.
Published: 2013

50. Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis

Author: Stahl, E. A., Wegmann, D., Trynka, G., Gutierrez Achury, J., Do, R., Voight, B. F., Kraft, P., Chen, R., Kallberg, H. J., F. A. S., Replication, D. G., Consortium, M. a., Genetics, M. I., Kathiresan, S., Wijmenga, C., Gregersen, P. K., Alfredsson, L., Siminovitch, K. A., Worthington, J., P. I. W., Raychaudhuri, S., Plenge, R. M., Voight, Bf, Scott, Lj, Steinthorsdottir, V, Morris, Ap, Dina, C, Welch, Rp, Zeggini, E, Huth, C, Aulchenko, Ys, Thorleifsson, G, Mcculloch, Lj, Ferreira, T, Grallert, H, Amin, N, Wu, G, Willer, Cj, Raychaudhuri, S, Mccarroll, Sa, Langenberg, C, Hofmann, Om, Dupuis, J, Qi, L, Segrè, Av, van Hoek, M, Navarro, P, Ardlie, K, Balkau, B, Benediktsson, R, Bennett, Aj, Blagieva, R, Boerwinkle, E, Bonnycastle, Ll, Boström, Kb, Bravenboer, B, Bumpstead, S, Burtt, Np, Charpentier, G, Chines, Ps, Cornelis, M, Couper, Dj, Crawford, G, Doney, As, Elliott, Ks, Elliott, Al, Erdos, Mr, Fox, Cs, Franklin, Cs, Ganser, M, Gieger, C, Grarup, N, Green, T, Griffin, S, Groves, Cj, Guiducci, C, Hadjadj, S, Hassanali, N, Herder, C, Isomaa, B, Jackson, Au, Johnson, Pr, Jørgensen, T, Kao, Wh, Klopp, N, Kong, A, Kraft, P, Kuusisto, J, Lauritzen, T, Li, M, Lieverse, A, Lindgren, Cm, Lyssenko, V, Marre, M, Meitinger, T, Midthjell, K, Morken, Ma, Narisu, N, Nilsson, P, Owen, Kr, Payne, F, Perry, Jr, Petersen, Ak, Platou, C, Proença, C, Prokopenko, I, Rathmann, W, Rayner, Nw, Robertson, Nr, Rocheleau, G, Roden, M, Sampson, Mj, Saxena, R, Shields, Bm, Shrader, P, Sigurdsson, G, Sparsø, T, Strassburger, K, Stringham, Hm, Sun, Q, Swift, Aj, Thorand, B, Tichet, J, Tuomi, T, van Dam RM, van Haeften TW, van Herpt, T, van Vliet Ostaptchouk JV, Walters, Gb, Weedon, Mn, Wijmenga, C, Witteman, J, Bergman, Rn, Cauchi, S, Collins, Fs, Gloyn, Al, Gyllensten, U, Hansen, T, Hide, Wa, Hitman, Ga, Hofman, A, Hunter, Dj, Hveem, K, Laakso, M, Mohlke, Kl, Morris, Ad, Palmer, Cn, Pramstaller, Pp, Rudan, I, Sijbrands, E, Stein, Ld, Tuomilehto, J, Uitterlinden, A, Walker, M, Wareham, Nj, Watanabe, Rm, Abecasis, Gr, Boehm, Bo, Campbell, H, Daly, Mj, Hattersley, At, Hu, Fb, Meigs, Jb, Pankow, Js, Pedersen, O, Wichmann, He, Barroso, I, Florez, Jc, Frayling, Tm, Groop, L, Sladek, R, Thorsteinsdottir, U, Wilson, Jf, Illig, T, Froguel, P, van Duijn CM, Stefansson, K, Altshuler, D, Boehnke, M, Mccarthy, Mi, Kathiresan, S, Williams, G, Nathan, Dm, Macrae, Ca, O'Donnell, Cj, Ardissino, D, Merlini, Pa, Berzuini, C, Bernardinelli, L, Peyvandi, F, Tubaro, M, Celli, P, Ferrario, M, Fetiveau, R, Marziliano, N, Casari, G, Galli, M, Ribichini, Flavio Luciano, Rossi, M, Bernardi, F, Zonzin, P, Piazza, A, Mannucci, Pm, Schwartz, Sm, Siscovick, Ds, Yee, J, Friedlander, Y, Elosua, R, Marrugat, J, Lucas, G, Subirana, I, Sala, J, Ramos, R, Salomaa, V, Havulinna, As, Peltonen, L, Melander, O, Berglund, G, Hirschhorn, Jn, Asselta, R, Duga, S, Spreafico, M, Musunuru, K, Purcell, S, Surti, A, Gianniny, L, Mirel, D, Parkin, M, Burtt, N, Gabriel, Sb, Stahl, Ea, Wegmann, D, Trynka, G, Gutierrez achury, J, Do, R, Voight, Bf, Kraft, P, Che, R, Kallberg, H, Kurreeman, F, Diabetes Genetics Replication And Meta analysis Consortium: Myocardial Infarction Genetics, Consortium, Casari, GIORGIO NEVIO, Kathiresan, S, Wijmenga, C, Gregersen, Pk, Alfredsson, L, Siminovitch, Ka, Worthington, J, De Bakker, Pi, Raychaudhuri, S, Plenge, Rm, and Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Subjects: Multifactorial Inheritance, SUSCEPTIBILITY LOCI, GENETIC SUSCEPTIBILITY, Genome-wide association study, Single-nucleotide polymorphism, Disease, HEART-DISEASE, Biology, VARIANTS, Polymorphism, Single Nucleotide, Article, Arthritis, Rheumatoid, COMMON SNPS, Missing heritability problem, MISSING HERITABILITY, Rheumatoid, Genetic model, Genetic predisposition, Diabetes Mellitus, Humans, genetics, Genetic Predisposition to Disease, Human height, Polymorphism, GENOME-WIDE ASSOCIATION, Arthritis, genetics, Bayes Theorem, Cardiovascular Diseases, genetics, Case-Control Studies, Celiac Disease, genetics, Diabetes Mellitus, Type 2, genetics, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Genetics, CELIAC-DISEASE, Bayes Theorem, RISK LOCI, Genetic architecture, Celiac Disease, Diabetes Mellitus, Type 2, Cardiovascular Diseases, Genetic Loci, Case-Control Studies, HUMAN HEIGHT, Genome-Wide Association Study
Abstract: The genetic architectures of common, complex diseases are largely uncharacterized. We modeled the genetic architecture underlying genome-wide association study (GWAS) data for rheumatoid arthritis and developed a new method using polygenic risk-score analyses to infer the total liability-scale variance explained by associated GWAS SNPs. Using this method, we estimated that, together, thousands of SNPs from rheumatoid arthritis GWAS explain an additional 20% of disease risk (excluding known associated loci). We further tested this method on datasets for three additional diseases and obtained comparable estimates for celiac disease (43% excluding the major histocompatibility complex), myocardial infarction and coronary artery disease (48%) and type 2 diabetes (49%). Our results are consistent with simulated genetic models in which hundreds of associated loci harbor common causal variants and a smaller number of loci harbor multiple rare causal variants. These analyses suggest that GWAS will continue to be highly productive for the discovery of additional susceptibility loci for common diseases.
Published: 2012

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