TY - JOUR A1 - Hudson, Lawrence N. A1 - Newbold, Tim A1 - Contu, Sara A1 - Hill, Samantha L. L. A1 - Lysenko, Igor A1 - De Palma, Adriana A1 - Phillips, Helen R. P. A1 - Senior, Rebecca A. A1 - Bennett, Dominic J. A1 - Booth, Hollie A1 - Choimes, Argyrios A1 - Correia, David L. P. A1 - Day, Julie A1 - Echeverria-Londono, Susy A1 - Garon, Morgan A1 - Harrison, Michelle L. K. A1 - Ingram, Daniel J. A1 - Jung, Martin A1 - Kemp, Victoria A1 - Kirkpatrick, Lucinda A1 - Martin, Callum D. A1 - Pan, Yuan A1 - White, Hannah J. A1 - Aben, Job A1 - Abrahamczyk, Stefan A1 - Adum, Gilbert B. A1 - Aguilar-Barquero, Virginia A1 - Aizen, Marcelo A1 - Ancrenaz, Marc A1 - Arbelaez-Cortes, Enrique A1 - Armbrecht, Inge A1 - Azhar, Badrul A1 - Azpiroz, Adrian B. A1 - Baeten, Lander A1 - Báldi, András A1 - Banks, John E. A1 - Barlow, Jos A1 - Batáry, Péter A1 - Bates, Adam J. A1 - Bayne, Erin M. A1 - Beja, Pedro A1 - Berg, Ake A1 - Berry, Nicholas J. A1 - Bicknell, Jake E. A1 - Bihn, Jochen H. A1 - Böhning-Gaese, Katrin A1 - Boekhout, Teun A1 - Boutin, Celine A1 - Bouyer, Jeremy A1 - Brearley, Francis Q. A1 - Brito, Isabel A1 - Brunet, Jörg A1 - Buczkowski, Grzegorz A1 - Buscardo, Erika A1 - Cabra-Garcia, Jimmy A1 - Calvino-Cancela, Maria A1 - Cameron, Sydney A. A1 - Cancello, Eliana M. A1 - Carrijo, Tiago F. A1 - Carvalho, Anelena L. A1 - Castro, Helena A1 - Castro-Luna, Alejandro A. A1 - Cerda, Rolando A1 - Cerezo, Alexis A1 - Chauvat, Matthieu A1 - Clarke, Frank M. A1 - Cleary, Daniel F. R. A1 - Connop, Stuart P. A1 - D'Aniello, Biagio A1 - da Silva, Pedro Giovani A1 - Darvill, Ben A1 - Dauber, Jens A1 - Dejean, Alain A1 - Diekötter, Tim A1 - Dominguez-Haydar, Yamileth A1 - Dormann, Carsten F. A1 - Dumont, Bertrand A1 - Dures, Simon G. A1 - Dynesius, Mats A1 - Edenius, Lars A1 - Elek, Zoltán A1 - Entling, Martin H. A1 - Farwig, Nina A1 - Fayle, Tom M. A1 - Felicioli, Antonio A1 - Felton, Annika M. A1 - Ficetola, Gentile F. A1 - Filgueiras, Bruno K. C. A1 - Fonte, Steve J. A1 - Fraser, Lauchlan H. A1 - Fukuda, Daisuke A1 - Furlani, Dario A1 - Ganzhorn, Jörg U. A1 - Garden, Jenni G. A1 - Gheler-Costa, Carla A1 - Giordani, Paolo A1 - Giordano, Simonetta A1 - Gottschalk, Marco S. A1 - Goulson, Dave A1 - Gove, Aaron D. A1 - Grogan, James A1 - Hanley, Mick E. A1 - Hanson, Thor A1 - Hashim, Nor R. A1 - Hawes, Joseph E. A1 - Hébert, Christian A1 - Helden, Alvin J. A1 - Henden, John-André A1 - Hernández, Lionel A1 - Herzog, Felix A1 - Higuera-Diaz, Diego A1 - Hilje, Branko A1 - Horgan, Finbarr G. A1 - Horváth, Roland A1 - Hylander, Kristoffer A1 - Horváth, Roland A1 - Isaacs-Cubides, Paola A1 - Ishitani, Mashiro A1 - Jacobs, Carmen T. A1 - Jaramillo, Victor J. A1 - Jauker, Birgit A1 - Jonsell, Matts A1 - Jung, Thomas S. A1 - Kapoor, Vena A1 - Kati, Vassiliki A1 - Katovai, Eric A1 - Kessler, Michael A1 - Knop, Eva A1 - Kolb, Annette A1 - Körösi, Àdám A1 - Lachat, Thibault A1 - Lantschner, Victoria A1 - Le Féon, Violette A1 - LeBuhn, Gretchen A1 - Légaré, Jean-Philippe A1 - Letcher, Susan G. A1 - Littlewood, Nick A. A1 - López-Quintero, Carlos A. A1 - Louhaichi, Mounir A1 - Lövei, Gabor L. A1 - Lucas-Borja, Manuel Esteban A1 - Luja, Victor H. A1 - Maeto, Kaoru A1 - Magura, Tibor A1 - Mallari, Neil Aldrin A1 - Marin-Spiotta, Erika A1 - Marhall, E. J. P. A1 - Martínez, Eliana A1 - Mayfield, Margaret M. A1 - Mikusinski, Gregorz A1 - Milder, Jeffery C. A1 - Miller, James R. A1 - Morales, Carolina L. A1 - Muchane, Mary N. A1 - Muchane, Muchai A1 - Naidoo, Robin A1 - Nakamura, Akihiro A1 - Naoe, Shoji A1 - Nates-Parra, Guiomar A1 - Navarerete Gutierrez, Dario A. A1 - Neuschulz, Eike L. A1 - Noreika, Norbertas A1 - Norfolk, Olivia A1 - Noriega, Jorge Ari A1 - Nöske, Nicole M. A1 - O'Dea, Niall A1 - Oduro, William A1 - Ofori-Boateng, Caleb A1 - Oke, Chris O. A1 - Osgathorpe, Lynne M. A1 - Paritsis, Juan A1 - Parrah, Alejandro A1 - Pelegrin, Nicolás A1 - Peres, Carlos A. A1 - Persson, Anna S. A1 - Petanidou, Theodora A1 - Phalan, Ben A1 - Philips, T. Keith A1 - Poveda, Katja A1 - Power, Eileen F. A1 - Presley, Steven J. A1 - Proença, Vânia A1 - Quaranta, Marino A1 - Quintero, Carolina A1 - Redpath-Downing, Nicola A. A1 - Reid, J. Leighton A1 - Reis, Yana T. A1 - Ribeiro, Danilo B. A1 - Richardson, Barbara A. A1 - Richardson, Michael J. A1 - Robles, Carolina A. A1 - Römbke, Jörg A1 - Romero-Duque, Luz Piedad A1 - Rosselli, Loreta A1 - Rossiter, Stephen J. A1 - Roulston, T'ai H. A1 - Rousseau, Laurent A1 - Sadler, Jonathan P. A1 - Sáfián, Szbolcs A1 - Saldaña-Vásquez, Romeo A. A1 - Samnegård, Ulrika A1 - Schüepp, Christof A1 - Schweiger, Oliver A1 - Sedlock, Jodi L. A1 - Shahabuddin, Ghazala A1 - Sheil, Douglas A1 - Silva, Fernando A. B. A1 - Slade, Eleanor A1 - Smith-Pardo, Allan H. A1 - Sodhi, Navjot S. A1 - Somarriba, Eduardo J. A1 - Sosa, Ramón A. A1 - Stout, Jane C. A1 - Struebig, Matthew J. A1 - Sung, Yik-Hei A1 - Threlfall, Caragh G. A1 - Tonietto, Rebecca A1 - Tóthmérész, Béla A1 - Tscharntke, Teja A1 - Turner, Edgar C. A1 - Tylianakis, Jason M. A1 - Vanbergen, Adam J. A1 - Vassilev, Kiril A1 - Verboven, Hans A. F. A1 - Vergara, Carlos H. A1 - Vergara, Pablo M. A1 - Verhulst, Jort A1 - Walker, Tony R. A1 - Wang, Yanping A1 - Watling, James I. A1 - Wells, Konstans A1 - Williams, Christopher D. A1 - Willig, Michael R. A1 - Woinarski, John C. Z. A1 - Wolf, Jan H. D. A1 - Woodcock, Ben A. A1 - Yu, Douglas W. A1 - Zailsev, Andreys A1 - Collen, Ben A1 - Ewers, Rob M. A1 - Mace, Georgina M. A1 - Purves, Drew W. A1 - Scharlemann, Jörn P. W. A1 - Pervis, Andy T1 - The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts JF - Ecology and Evolution N2 - Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015. KW - urban-rural gradient KW - instensively managed farmland KW - Mexican coffee plantations KW - Bombus Spp. Hymenoptera KW - bumblebee nest density KW - data sharing KW - land use KW - habitat destruction KW - global change KW - land-use change KW - plant community composition KW - Northeastern Costa Rica KW - dung beetle coleoptera KW - bird species richness Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114425 VL - 4 IS - 24 ER - TY - JOUR A1 - Farmer, Adam D. A1 - Strzelczyk, Adam A1 - Finisguerra, Alessandra A1 - Gourine, Alexander V. A1 - Gharabaghi, Alireza A1 - Hasan, Alkomiet A1 - Burger, Andreas M. A1 - Jaramillo, Andrés M. A1 - Mertens, Ann A1 - Majid, Arshad A1 - Verkuil, Bart A1 - Badran, Bashar W. A1 - Ventura-Bort, Carlos A1 - Gaul, Charly A1 - Beste, Christian A1 - Warren, Christopher M. A1 - Quintana, Daniel S. A1 - Hämmerer, Dorothea A1 - Freri, Elena A1 - Frangos, Eleni A1 - Tobaldini, Eleonora A1 - Kaniusas, Eugenijus A1 - Rosenow, Felix A1 - Capone, Fioravante A1 - Panetsos, Fivos A1 - Ackland, Gareth L. A1 - Kaithwas, Gaurav A1 - O'Leary, Georgia H. A1 - Genheimer, Hannah A1 - Jacobs, Heidi I. L. A1 - Van Diest, Ilse A1 - Schoenen, Jean A1 - Redgrave, Jessica A1 - Fang, Jiliang A1 - Deuchars, Jim A1 - Széles, Jozsef C. A1 - Thayer, Julian F. A1 - More, Kaushik A1 - Vonck, Kristl A1 - Steenbergen, Laura A1 - Vianna, Lauro C. A1 - McTeague, Lisa M. A1 - Ludwig, Mareike A1 - Veldhuizen, Maria G. A1 - De Couck, Marijke A1 - Casazza, Marina A1 - Keute, Marius A1 - Bikson, Marom A1 - Andreatta, Marta A1 - D'Agostini, Martina A1 - Weymar, Mathias A1 - Betts, Matthew A1 - Prigge, Matthias A1 - Kaess, Michael A1 - Roden, Michael A1 - Thai, Michelle A1 - Schuster, Nathaniel M. A1 - Montano, Nicola A1 - Hansen, Niels A1 - Kroemer, Nils B. A1 - Rong, Peijing A1 - Fischer, Rico A1 - Howland, Robert H. A1 - Sclocco, Roberta A1 - Sellaro, Roberta A1 - Garcia, Ronald G. A1 - Bauer, Sebastian A1 - Gancheva, Sofiya A1 - Stavrakis, Stavros A1 - Kampusch, Stefan A1 - Deuchars, Susan A. A1 - Wehner, Sven A1 - Laborde, Sylvain A1 - Usichenko, Taras A1 - Polak, Thomas A1 - Zaehle, Tino A1 - Borges, Uirassu A1 - Teckentrup, Vanessa A1 - Jandackova, Vera K. A1 - Napadow, Vitaly A1 - Koenig, Julian T1 - International Consensus Based Review and Recommendations for Minimum Reporting Standards in Research on Transcutaneous Vagus Nerve Stimulation (Version 2020) JF - Frontiers in Human Neuroscience N2 - Given its non-invasive nature, there is increasing interest in the use of transcutaneous vagus nerve stimulation (tVNS) across basic, translational and clinical research. Contemporaneously, tVNS can be achieved by stimulating either the auricular branch or the cervical bundle of the vagus nerve, referred to as transcutaneous auricular vagus nerve stimulation(VNS) and transcutaneous cervical VNS, respectively. In order to advance the field in a systematic manner, studies using these technologies need to adequately report sufficient methodological detail to enable comparison of results between studies, replication of studies, as well as enhancing study participant safety. We systematically reviewed the existing tVNS literature to evaluate current reporting practices. Based on this review, and consensus among participating authors, we propose a set of minimal reporting items to guide future tVNS studies. The suggested items address specific technical aspects of the device and stimulation parameters. We also cover general recommendations including inclusion and exclusion criteria for participants, outcome parameters and the detailed reporting of side effects. Furthermore, we review strategies used to identify the optimal stimulation parameters for a given research setting and summarize ongoing developments in animal research with potential implications for the application of tVNS in humans. Finally, we discuss the potential of tVNS in future research as well as the associated challenges across several disciplines in research and clinical practice. KW - transcutaneous vagus nerve stimulation KW - minimum reporting standards KW - guidelines & recommendations KW - transcutaneous auricular vagus nerve stimulation KW - transcutaneous cervical vagus nerve stimulation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-234346 SN - 1662-5161 VL - 14 ER - TY - JOUR A1 - Galluzzi, L. A1 - Bravo-San Pedro, J. M. A1 - Vitale, I. A1 - Aaronson, S. A. A1 - Abrams, J. M. A1 - Adam, D. A1 - Alnemri, E. S. A1 - Altucci, L. A1 - Andrews, D. A1 - Annicchiarico-Petruzelli, M. A1 - Baehrecke, E. H. A1 - Bazan, N. G. A1 - Bertrand, M. J. A1 - Bianchi, K. A1 - Blagosklonny, M. V. A1 - Blomgren, K. A1 - Borner, C. A1 - Bredesen, D. E. A1 - Brenner, C. A1 - Campanella, M. A1 - Candi, E. A1 - Cecconi, F. A1 - Chan, F. K. A1 - Chandel, N. S. A1 - Cheng, E. H. A1 - Chipuk, J. E. A1 - Cidlowski, J. A. A1 - Ciechanover, A. A1 - Dawson, T. M. A1 - Dawson, V. L. A1 - De Laurenzi, V. A1 - De Maria, R. A1 - Debatin, K. M. A1 - Di Daniele, N. A1 - Dixit, V. M. A1 - Dynlacht, B. D. A1 - El-Deiry, W. S. A1 - Fimia, G. M. A1 - Flavell, R. A. A1 - Fulda, S. A1 - Garrido, C. A1 - Gougeon, M. L. A1 - Green, D. R. A1 - Gronemeyer, H. A1 - Hajnoczky, G. A1 - Hardwick, J. M. A1 - Hengartner, M. O. A1 - Ichijo, H. A1 - Joseph, B. A1 - Jost, P. J. A1 - Kaufmann, T. A1 - Kepp, O. A1 - Klionsky, D. J. A1 - Knight, R. A. A1 - Kumar, S. A1 - Lemasters, J. J. A1 - Levine, B. A1 - Linkermann, A. A1 - Lipton, S. A. A1 - Lockshin, R. A. A1 - López-Otín, C. A1 - Lugli, E. A1 - Madeo, F. A1 - Malorni, W. A1 - Marine, J. C. A1 - Martin, S. J. A1 - Martinou, J. C. A1 - Medema, J. P. A1 - Meier, P. A1 - Melino, S. A1 - Mizushima, N. A1 - Moll, U. A1 - Muñoz-Pinedo, C. A1 - Nuñez, G. A1 - Oberst, A. A1 - Panaretakis, T. A1 - Penninger, J. M. A1 - Peter, M. E. A1 - Piacentini, M. A1 - Pinton, P. A1 - Prehn, J. H. A1 - Puthalakath, H. A1 - Rabinovich, G. A. A1 - Ravichandran, K. S. A1 - Rizzuto, R. A1 - Rodrigues, C. M. A1 - Rubinsztein, D. C. A1 - Rudel, T. A1 - Shi, Y. A1 - Simon, H. U. A1 - Stockwell, B. R. A1 - Szabadkai, G. A1 - Tait, S. W. A1 - Tang, H. L. A1 - Tavernarakis, N. A1 - Tsujimoto, Y. A1 - Vanden Berghe, T. A1 - Vandenabeele, P. A1 - Villunger, A. A1 - Wagner, E. F. A1 - Walczak, H. A1 - White, E. A1 - Wood, W. G. A1 - Yuan, J. A1 - Zakeri, Z. A1 - Zhivotovsky, B. A1 - Melino, G. A1 - Kroemer, G. T1 - Essential versus accessory aspects of cell death: recommendations of the NCCD 2015 JF - Cell Death and Differentiation N2 - Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as 'accidental cell death' (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. 'Regulated cell death' (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-121207 VL - 22 ER - TY - JOUR A1 - Iyengar, Sudha K. A1 - Sedor, John R. A1 - Freedman, Barry I. A1 - Kao, W. H. Linda A1 - Kretzler, Matthias A1 - Keller, Benjamin J. A1 - Abboud, Hanna E. A1 - Adler, Sharon G. A1 - Best, Lyle G. A1 - Bowden, Donald W. A1 - Burlock, Allison A1 - Chen, Yii-Der Ida A1 - Cole, Shelley A. A1 - Comeau, Mary E. A1 - Curtis, Jeffrey M. A1 - Divers, Jasmin A1 - Drechsler, Christiane A1 - Duggirala, Ravi A1 - Elston, Robert C. A1 - Guo, Xiuqing A1 - Huang, Huateng A1 - Hoffmann, Michael Marcus A1 - Howard, Barbara V. A1 - Ipp, Eli A1 - Kimmel, Paul L. A1 - Klag, Michael J. A1 - Knowler, William C. A1 - Kohn, Orly F. A1 - Leak, Tennille S. A1 - Leehey, David J. A1 - Li, Man A1 - Malhotra, Alka A1 - März, Winfried A1 - Nair, Viji A1 - Nelson, Robert G. A1 - Nicholas, Susanne B. A1 - O’Brien, Stephen J. A1 - Pahl, Madeleine V. A1 - Parekh, Rulan S. A1 - Pezzolesi, Marcus G. A1 - Rasooly, Rebekah S. A1 - Rotimi, Charles N. A1 - Rotter, Jerome I. A1 - Schelling, Jeffrey R. A1 - Seldin, Michael F. A1 - Shah, Vallabh O. A1 - Smiles, Adam M. A1 - Smith, Michael W. A1 - Taylor, Kent D. A1 - Thameem, Farook A1 - Thornley-Brown, Denyse P. A1 - Truitt, Barbara J. A1 - Wanner, Christoph A1 - Weil, E. Jennifer A1 - Winkler, Cheryl A. A1 - Zager, Philip G. A1 - Igo, Jr, Robert P. A1 - Hanson, Robert L. A1 - Langefeld, Carl D. T1 - Genome-wide association and trans-ethnic meta-analysis for advanced diabetic kidney disease: Family Investigation of Nephropathy and Diabetes (FIND) JF - PLoS Genetics N2 - Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10\(^{−9}\)). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10\(^{−8}\)), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD. KW - diabetic kidney disease KW - genome-wide association study KW - Family Investigation of Nephropathy and Diabetes Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-180545 VL - 11 IS - 8 ER - TY - JOUR A1 - Zaho, Huaying A1 - Ghirlando, Rodolfo A1 - Alfonso, Carlos A1 - Arisaka, Fumio A1 - Attali, Ilan A1 - Bain, David L. A1 - Bakhtina, Marina M. A1 - Becker, Donald F. A1 - Bedwell, Gregory J. A1 - Bekdemir, Ahmet A1 - Besong, Tabot M. D. A1 - Birck, Catherine A1 - Brautigam, Chad A. A1 - Brennerman, William A1 - Byron, Olwyn A1 - Bzowska, Agnieszka A1 - Chaires, Jonathan B. A1 - Chaton, Catherine T. A1 - Coelfen, Helmbut A1 - Connaghan, Keith D. A1 - Crowley, Kimberly A. A1 - Curth, Ute A1 - Daviter, Tina A1 - Dean, William L. A1 - Diez, Ana I. A1 - Ebel, Christine A1 - Eckert, Debra M. A1 - Eisele, Leslie E. A1 - Eisenstein, Edward A1 - England, Patrick A1 - Escalante, Carlos A1 - Fagan, Jeffrey A. A1 - Fairman, Robert A1 - Finn, Ron M. A1 - Fischle, Wolfgang A1 - Garcia de la Torre, Jose A1 - Gor, Jayesh A1 - Gustafsson, Henning A1 - Hall, Damien A1 - Harding, Stephen E. A1 - Hernandez Cifre, Jose G. A1 - Herr, Andrew B. A1 - Howell, Elizabeth E. A1 - Isaac, Richard S. A1 - Jao, Shu-Chuan A1 - Jose, Davis A1 - Kim, Soon-Jong A1 - Kokona, Bashkim A1 - Kornblatt, Jack A. A1 - Kosek, Dalibor A1 - Krayukhina, Elena A1 - Krzizike, Daniel A1 - Kusznir, Eric A. A1 - Kwon, Hyewon A1 - Larson, Adam A1 - Laue, Thomas M. A1 - Le Roy, Aline A1 - Leech, Andrew P. A1 - Lilie, Hauke A1 - Luger, Karolin A1 - Luque-Ortega, Juan R. A1 - Ma, Jia A1 - May, Carrie A. A1 - Maynard, Ernest L. A1 - Modrak-Wojcik, Anna A1 - Mok, Yee-Foong A1 - Mücke, Norbert A1 - Nagel-Steger, Luitgard A1 - Narlikar, Geeta J. A1 - Noda, Masanori A1 - Nourse, Amanda A1 - Obsil, Thomas A1 - Park, Chad K A1 - Park, Jin-Ku A1 - Pawelek, Peter D. A1 - Perdue, Erby E. A1 - Perkins, Stephen J. A1 - Perugini, Matthew A. A1 - Peterson, Craig L. A1 - Peverelli, Martin G. A1 - Piszczek, Grzegorz A1 - Prag, Gali A1 - Prevelige, Peter E. A1 - Raynal, Bertrand D. E. A1 - Rezabkova, Lenka A1 - Richter, Klaus A1 - Ringel, Alison E. A1 - Rosenberg, Rose A1 - Rowe, Arthur J. A1 - Rufer, Arne C. A1 - Scott, David J. A1 - Seravalli, Javier G. A1 - Solovyova, Alexandra S. A1 - Song, Renjie A1 - Staunton, David A1 - Stoddard, Caitlin A1 - Stott, Katherine A1 - Strauss, Holder M. A1 - Streicher, Werner W. A1 - Sumida, John P. A1 - Swygert, Sarah G. A1 - Szczepanowski, Roman H. A1 - Tessmer, Ingrid A1 - Toth, Ronald T. A1 - Tripathy, Ashutosh A1 - Uchiyama, Susumu A1 - Uebel, Stephan F. W. A1 - Unzai, Satoru A1 - Gruber, Anna Vitlin A1 - von Hippel, Peter H. A1 - Wandrey, Christine A1 - Wang, Szu-Huan A1 - Weitzel, Steven E A1 - Wielgus-Kutrowska, Beata A1 - Wolberger, Cynthia A1 - Wolff, Martin A1 - Wright, Edward A1 - Wu, Yu-Sung A1 - Wubben, Jacinta M. A1 - Schuck, Peter T1 - A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation JF - PLoS ONE N2 - Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304\(\pm\)0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of \(\pm\)0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies. KW - fluorescence-detected sedimentation KW - size exclusion chromatography KW - field flow fractionation KW - spinco ultracentrifuge KW - aggregation KW - bead models KW - velocity KW - hydrodynamics KW - biopharmaceuticals KW - proteins Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-151903 VL - 10 IS - 5 ER - TY - JOUR A1 - Whisnant, Adam W. A1 - Jürges, Christopher S. A1 - Hennig, Thomas A1 - Wyler, Emanuel A1 - Prusty, Bhupesh A1 - Rutkowski, Andrzej J. A1 - L'hernault, Anne A1 - Djakovic, Lara A1 - Göbel, Margarete A1 - Döring, Kristina A1 - Menegatti, Jennifer A1 - Antrobus, Robin A1 - Matheson, Nicholas J. A1 - Künzig, Florian W. H. A1 - Mastrobuoni, Guido A1 - Bielow, Chris A1 - Kempa, Stefan A1 - Liang, Chunguang A1 - Dandekar, Thomas A1 - Zimmer, Ralf A1 - Landthaler, Markus A1 - Grässer, Friedrich A1 - Lehner, Paul J. A1 - Friedel, Caroline C. A1 - Erhard, Florian A1 - Dölken, Lars T1 - Integrative functional genomics decodes herpes simplex virus 1 JF - Nature Communications N2 - The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research. KW - infected-cell protein KW - messenger RNA KW - binding protein KW - type 1 KW - identification KW - ICP27 KW - translation KW - expression KW - sequence KW - domain Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229884 VL - 11 ER - TY - JOUR A1 - Gröbner, Susanne N. A1 - Worst, Barbara C. A1 - Weischenfeldt, Joachim A1 - Buchhalter, Ivo A1 - Kleinheinz, Kortine A1 - Rudneva, Vasilisa A. A1 - Johann, Pascal D. A1 - Balasubramanian, Gnana Prakash A1 - Segura-Wang, Maia A1 - Brabetz, Sebastian A1 - Bender, Sebastian A1 - Hutter, Barbara A1 - Sturm, Dominik A1 - Pfaff, Elke A1 - Hübschmann, Daniel A1 - Zipprich, Gideon A1 - Heinold, Michael A1 - Eils, Jürgen A1 - Lawerenz, Christian A1 - Erkek, Serap A1 - Lambo, Sander A1 - Waszak, Sebastian A1 - Blattmann, Claudia A1 - Borkhardt, Arndt A1 - Kuhlen, Michaela A1 - Eggert, Angelika A1 - Fulda, Simone A1 - Gessler, Manfred A1 - Wegert, Jenny A1 - Kappler, Roland A1 - Baumhoer, Daniel A1 - Stefan, Burdach A1 - Kirschner-Schwabe, Renate A1 - Kontny, Udo A1 - Kulozik, Andreas E. A1 - Lohmann, Dietmar A1 - Hettmer, Simone A1 - Eckert, Cornelia A1 - Bielack, Stefan A1 - Nathrath, Michaela A1 - Niemeyer, Charlotte A1 - Richter, Günther H. A1 - Schulte, Johannes A1 - Siebert, Reiner A1 - Westermann, Frank A1 - Molenaar, Jan J. A1 - Vassal, Gilles A1 - Witt, Hendrik A1 - Burkhardt, Birgit A1 - Kratz, Christian P. A1 - Witt, Olaf A1 - van Tilburg, Cornelis M. A1 - Kramm, Christof M. A1 - Fleischhack, Gudrun A1 - Dirksen, Uta A1 - Rutkowski, Stefan A1 - Frühwald, Michael A1 - Hoff, Katja von A1 - Wolf, Stephan A1 - Klingebeil, Thomas A1 - Koscielniak, Ewa A1 - Landgraf, Pablo A1 - Koster, Jan A1 - Resnick, Adam C. A1 - Zhang, Jinghui A1 - Liu, Yanling A1 - Zhou, Xin A1 - Waanders, Angela J. A1 - Zwijnenburg, Danny A. A1 - Raman, Pichai A1 - Brors, Benedikt A1 - Weber, Ursula D. A1 - Northcott, Paul A. A1 - Pajtler, Kristian W. A1 - Kool, Marcel A1 - Piro, Rosario M. A1 - Korbel, Jan O. A1 - Schlesner, Matthias A1 - Eils, Roland A1 - Jones, David T. W. A1 - Lichter, Peter A1 - Chavez, Lukas A1 - Zapatka, Marc A1 - Pfister, Stefan M. T1 - The landscape of genomic alterations across childhood cancers JF - Nature N2 - Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7–8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials. KW - cancer genomics KW - oncogenesis KW - paediatric cancer KW - predictive markers KW - translational research Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229579 VL - 555 ER - TY - JOUR A1 - Blanco, Ignacio A1 - Kuchenbaecker, Karoline A1 - Cuadras, Daniel A1 - Wang, Xianshu A1 - Barrowdale, Daniel A1 - Ruiz de Garibay, Gorka A1 - Librado, Pablo A1 - Sanchez-Gracia, Alejandro A1 - Rozas, Julio A1 - Bonifaci, Núria A1 - McGuffog, Lesley A1 - Pankratz, Vernon S. A1 - Islam, Abul A1 - Mateo, Francesca A1 - Berenguer, Antoni A1 - Petit, Anna A1 - Català, Isabel A1 - Brunet, Joan A1 - Feliubadaló, Lidia A1 - Tornero, Eva A1 - Benítez, Javier A1 - Osorio, Ana A1 - Ramón y Cajal, Teresa A1 - Nevanlinna, Heli A1 - Aittomäki, Kristina A1 - Arun, Banu K. A1 - Toland, Amanda E. A1 - Karlan, Beth Y. A1 - Walsh, Christine A1 - Lester, Jenny A1 - Greene, Mark H. A1 - Mai, Phuong L. A1 - Nussbaum, Robert L. A1 - Andrulis, Irene L. A1 - Domchek, Susan M. A1 - Nathanson, Katherine L. A1 - Rebbeck, Timothy R. A1 - Barkardottir, Rosa B. A1 - Jakubowska, Anna A1 - Lubinski, Jan A1 - Durda, Katarzyna A1 - Jaworska-Bieniek, Katarzyna A1 - Claes, Kathleen A1 - Van Maerken, Tom A1 - Díez, Orland A1 - Hansen, Thomas V. A1 - Jønson, Lars A1 - Gerdes, Anne-Marie A1 - Ejlertsen, Bent A1 - De la Hoya, Miguel A1 - Caldés, Trinidad A1 - Dunning, Alison M. A1 - Oliver, Clare A1 - Fineberg, Elena A1 - Cook, Margaret A1 - Peock, Susan A1 - McCann, Emma A1 - Murray, Alex A1 - Jacobs, Chris A1 - Pichert, Gabriella A1 - Lalloo, Fiona A1 - Chu, Carol A1 - Dorkins, Huw A1 - Paterson, Joan A1 - Ong, Kai-Ren A1 - Teixeira, Manuel R. A1 - Hogervorst, Frans B. L. A1 - Van der Hout, Annemarie H. A1 - Seynaeve, Caroline A1 - Van der Luijt, Rob B. A1 - Ligtenberg, Marjolijn J. L. A1 - Devilee, Peter A1 - Wijnen, Juul T. A1 - Rookus, Matti A. A1 - Meijers-Heijboer, Hanne E. J. A1 - Blok, Marinus J. A1 - Van den Ouweland, Ans M. W. A1 - Aalfs, Cora M. A1 - Rodriguez, Gustavo C. A1 - Phillips, Kelly-Anne A. A1 - Piedmonte, Marion A1 - Nerenstone, Stacy R. A1 - Bae-Jump, Victoria L. A1 - O'Malley, David M. A1 - Schmutzler, Rita K. A1 - Wappenschmidt, Barbara A1 - Rhiem, Kerstin A1 - Engel, Christoph A1 - Meindl, Alfons A1 - Ditsch, Nina A1 - Arnold, Norbert A1 - Plendl, Hansjoerg J. A1 - Niederacher, Dieter A1 - Sutter, Christian A1 - Wang-Gohrke, Shan A1 - Steinemann, Doris A1 - Preisler-Adams, Sabine A1 - Kast, Karin A1 - Varon-Mateeva, Raymonda A1 - Gehrig, Andrea A1 - Bojesen, Anders A1 - Pedersen, Inge Sokilde A1 - Sunde, Lone A1 - Birk Jensen, Uffe A1 - Thomassen, Mads A1 - Kruse, Torben A. A1 - Foretova, Lenka A1 - Peterlongo, Paolo A1 - Bernard, Loris A1 - Peissel, Bernard A1 - Scuvera, Giulietta A1 - Manoukian, Siranoush A1 - Radice, Paolo A1 - Ottini, Laura A1 - Montagna, Marco A1 - Agata, Simona A1 - Maugard, Christine A1 - Simard, Jacques A1 - Soucy, Penny A1 - Berger, Andreas A1 - Fink-Retter, Anneliese A1 - Singer, Christian F. A1 - Rappaport, Christine A1 - Geschwantler-Kaulich, Daphne A1 - Tea, Muy-Kheng A1 - Pfeiler, Georg A1 - John, Esther M. A1 - Miron, Alex A1 - Neuhausen, Susan L. A1 - Terry, Mary Beth A1 - Chung, Wendy K. A1 - Daly, Mary B. A1 - Goldgar, David E. A1 - Janavicius, Ramunas A1 - Dorfling, Cecilia M. A1 - Van Rensburg, Elisabeth J. A1 - Fostira, Florentia A1 - Konstantopoulou, Irene A1 - Garber, Judy A1 - Godwin, Andrew K. A1 - Olah, Edith A1 - Narod, Steven A. A1 - Rennert, Gad A1 - Paluch, Shani Shimon A1 - Laitman, Yael A1 - Friedman, Eitan A1 - Liljegren, Annelie A1 - Rantala, Johanna A1 - Stenmark-Askmalm, Marie A1 - Loman, Niklas A1 - Imyanitov, Evgeny N. A1 - Hamann, Ute A1 - Spurdle, Amanda B. A1 - Healey, Sue A1 - Weitzel, Jeffrey N. A1 - Herzog, Josef A1 - Margileth, David A1 - Gorrini, Chiara A1 - Esteller, Manel A1 - Gómez, Antonio A1 - Sayols, Sergi A1 - Vidal, Enrique A1 - Heyn, Holger A1 - Stoppa-Lyonnet, Dominique A1 - Léoné, Melanie A1 - Barjhoux, Laure A1 - Fassy-Colcombet, Marion A1 - Pauw, Antoine de A1 - Lasset, Christine A1 - Fert Ferrer, Sandra A1 - Castera, Laurent A1 - Berthet, Pascaline A1 - Cornelis, François A1 - Bignon, Yves-Jean A1 - Damiola, Francesca A1 - Mazoyer, Sylvie A1 - Sinilnikova, Olga M. A1 - Maxwell, Christopher A. A1 - Vijai, Joseph A1 - Robson, Mark A1 - Kauff, Noah A1 - Corines, Marina J. A1 - Villano, Danylko A1 - Cunningham, Julie A1 - Lee, Adam A1 - Lindor, Noralane A1 - Lázaro, Conxi A1 - Easton, Douglas F. A1 - Offit, Kenneth A1 - Chenevix-Trench, Georgia A1 - Couch, Fergus J. A1 - Antoniou, Antonis C. A1 - Pujana, Miguel Angel T1 - Assessing associations between the AURKA-HMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers JF - PLoS ONE N2 - While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood approach. The association of HMMR rs299290 with breast cancer risk in BRCA1 mutation carriers was confirmed: per-allele hazard ratio (HR) = 1.10, 95% confidence interval (CI) 1.04 - 1.15, p = 1.9 x 10\(^{-4}\) (false discovery rate (FDR)-adjusted p = 0.043). Variation in CSTF1, located next to AURKA, was also found to be associated with breast cancer risk in BRCA2 mutation carriers: rs2426618 per-allele HR = 1.10, 95% CI 1.03 - 1.16, p = 0.005 (FDR-adjusted p = 0.045). Assessment of pairwise interactions provided suggestions (FDR-adjusted p\(_{interaction}\) values > 0.05) for deviations from the multiplicative model for rs299290 and CSTF1 rs6064391, and rs299290 and TUBG1 rs11649877 in both BRCA1 and BRCA2 mutation carriers. Following these suggestions, the expression of HMMR and AURKA or TUBG1 in sporadic breast tumors was found to potentially interact, influencing patients' survival. Together, the results of this study support the hypothesis of a causative link between altered function of AURKA-HMMR-TPX2-TUBG1 and breast carcinogenesis in BRCA1/2 mutation carriers. KW - genetic interaction networks KW - genome-wide association KW - expression signature KW - susceptibility loci KW - survival KW - modifiers KW - polymorphism KW - cell KW - chip-seq KW - elements Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143469 VL - 10 IS - 4 ER - TY - JOUR A1 - Hibar, Derrek P. A1 - Adams, Hieab H.H. A1 - Jahanshad, Neda A1 - Chauhan, Ganesh A1 - Stein, Jason L A1 - Hofer, Edith A1 - Renteria, Miguel E. A1 - Bis, Joshua C. A1 - Arias-Vasquez, Alejandro A1 - Ikram, M. Kamran A1 - Desrivières, Sylvane A1 - Vernooij, Meike W. A1 - Abramovic, Lucija A1 - Alhusaini, Saud A1 - Amin, Najaf A1 - Andersson, Micael A1 - Arfanakis, Konstantinos A1 - Aribisala, Benjamin S. A1 - Armstrong, Nicola J. A1 - Athanasiu, Lavinia A1 - Axelsson, Tomas A1 - Beecham, Ashley H. A1 - Beiser, Alexa A1 - Bernard, Manon A1 - Blanton, Susan H. A1 - Bohlken, Marc M. A1 - Boks, Marco P. A1 - Bralten, Janita A1 - Brickman, Adam M. A1 - Carmichael, Owen T1 - Novel genetic loci associated with hippocampal volume JF - Nature Communications N2 - The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer’s disease (r\(_g\)=−0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness. KW - brain KW - hippocampal formation KW - neuropsychiatric disorders KW - Alzheimer’s disease KW - genetic loci KW - hippocampal volume Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-182115 VL - 8 ER - TY - JOUR A1 - Wittbrodt, J. A1 - Adam, D. A1 - Malitschek, B. A1 - Maueler, W. A1 - Raulf, F. A1 - Telling, A. A1 - Robertson, M. A1 - Schartl, Manfred T1 - Novel putative receptor tyrosine kinase encoded by the melanoma-inducing Tu locus in Xiphophorus N2 - No abstract available KW - Physiologische Chemie Y1 - 1989 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-61800 ER -