@article{DornelasAntaoMoyesetal.2018, author = {Dornelas, Maria and Ant{\~a}o, Laura H. and Moyes, Faye and Bates, Amanda E. and Magurran, Anne E. and Adam, Dušan and Akhmetzhanova, Asem A. and Appeltans, Ward and Arcos, Jos{\´e} Manuel and Arnold, Haley and Ayyappan, Narayanan and Badihi, Gal and Baird, Andrew H. and Barbosa, Miguel and Barreto, Tiago Egydio and B{\"a}ssler, Claus and Bellgrove, Alecia and Belmaker, Jonathan and Benedetti-Cecchi, Lisandro and Bett, Brian J. and Bjorkman, Anne D. and Błażewicz, Magdalena and Blowes, Shane A. and Bloch, Christopher P. Bloch and Bonebrake, Timothy C. and Boyd, Susan and Bradford, Matt and Brooks, Andrew J. and Brown, James H. and Bruelheide, Helge and Budy, Phaedra and Carvalho, Fernando and Casta{\~n}eda-Moya, Edward and Chen, Chaolun Allen and Chamblee, John F. and Chase, Tory J. and Siegwart Collier, Laura and Collinge, Sharon K. and Condit, Richard and Cooper, Elisabeth J. and Cornelissen, J. Hans C. and Cotano, Unai and Crow, Shannan Kyle and Damasceno, Gabriella and Davies, Claire H. and Davis, Robert A. and Day, Frank P. and Degraer, Steven and Doherty, Tim S. and Dunn, Timothy E. and Durigan, Giselda and Duffy, J. Emmett and Edelist, Dor and Edgar, Graham J. and Elahi, Robin and Elmendorf, Sarah C. and Enemar, Anders and Ernest, S. K. Morgan and Escribano, Rub{\´e}n and Estiarte, Marc and Evans, Brian S. and Fan, Tung-Yung and Turini Farah, Fabiano and Loureiro Fernandes, Luiz and Farneda, F{\´a}bio Z. and Fidelis, Alessandra and Fitt, Robert and Fosaa, Anna Maria and Franco, Geraldo Antonio Daher Correa and Frank, Grace E. and Fraser, William R. and Garc{\´i}a, Hernando and Cazzolla Gatti, Roberto and Givan, Or and Gorgone-Barbosa, Elizabeth and Gould, William A. and Gries, Corinna and Grossman, Gary D. and Gutierr{\´e}z, Julio R. and Hale, Stephen and Harmon, Mark E. and Harte, John and Haskins, Gary and Henshaw, Donald L. and Hermanutz, Luise and Hidalgo, Pamela and Higuchi, Pedro and Hoey, Andrew and Van Hoey, Gert and Hofgaard, Annika and Holeck, Kristen and Hollister, Robert D. and Holmes, Richard and Hoogenboom, Mia and Hsieh, Chih-hao and Hubbell, Stephen P. and Huettmann, Falk and Huffard, Christine L. and Hurlbert, Allen H. and Ivanauskas, Nat{\´a}lia Macedo and Jan{\´i}k, David and Jandt, Ute and Jażdżewska, Anna and Johannessen, Tore and Johnstone, Jill and Jones, Julia and Jones, Faith A. M. and Kang, Jungwon and Kartawijaya, Tasrif and Keeley, Erin C. and Kelt, Douglas A. and Kinnear, Rebecca and Klanderud, Kari and Knutsen, Halvor and Koenig, Christopher C. and Kortz, Alessandra R. and Kr{\´a}l, Kamil and Kuhnz, Linda A. and Kuo, Chao-Yang and Kushner, David J. and Laguionie-Marchais, Claire and Lancaster, Lesley T. and Lee, Cheol Min and Lefcheck, Jonathan S. and L{\´e}vesque, Esther and Lightfoot, David and Lloret, Francisco and Lloyd, John D. and L{\´o}pez-Baucells, Adri{\`a} and Louzao, Maite and Madin, Joshua S. and Magn{\´u}sson, Borgþ{\´o}r and Malamud, Shahar and Matthews, Iain and McFarland, Kent P. and McGill, Brian and McKnight, Diane and McLarney, William O. and Meador, Jason and Meserve, Peter L. and Metcalfe, Daniel J. and Meyer, Christoph F. J. and Michelsen, Anders and Milchakova, Nataliya and Moens, Tom and Moland, Even and Moore, Jon and Moreira, Carolina Mathias and M{\"u}ller, J{\"o}rg and Murphy, Grace and Myers-Smith, Isla H. and Myster, Randall W. and Naumov, Andrew and Neat, Francis and Nelson, James A. and Nelson, Michael Paul and Newton, Stephen F. and Norden, Natalia and Oliver, Jeffrey C. and Olsen, Esben M. and Onipchenko, Vladimir G. and Pabis, Krzysztof and Pabst, Robert J. and Paquette, Alain and Pardede, Sinta and Paterson, David M. and P{\´e}lissier, Rapha{\"e}l and Pe{\~n}uelas, Josep and P{\´e}rez-Matus, Alejandro and Pizarro, Oscar and Pomati, Francesco and Post, Eric and Prins, Herbert H. T. and Priscu, John C. and Provoost, Pieter and Prudic, Kathleen L. and Pulliainen, Erkki and Ramesh, B. R. and Ramos, Olivia Mendivil and Rassweiler, Andrew and Rebelo, Jose Eduardo and Reed, Daniel C. and Reich, Peter B. and Remillard, Suzanne M. and Richardson, Anthony J. and Richardson, J. Paul and van Rijn, Itai and Rocha, Ricardo and Rivera-Monroy, Victor H. and Rixen, Christian and Robinson, Kevin P. and Rodrigues, Ricardo Ribeiro and de Cerqueira Rossa-Feres, Denise and Rudstam, Lars and Ruhl, Henry and Ruz, Catalina S. and Sampaio, Erica M. and Rybicki, Nancy and Rypel, Andrew and Sal, Sofia and Salgado, Beatriz and Santos, Flavio A. M. and Savassi-Coutinho, Ana Paula and Scanga, Sara and Schmidt, Jochen and Schooley, Robert and Setiawan, Fakhrizal and Shao, Kwang-Tsao and Shaver, Gaius R. and Sherman, Sally and Sherry, Thomas W. and Siciński, Jacek and Sievers, Caya and da Silva, Ana Carolina and da Silva, Fernando Rodrigues and Silveira, Fabio L. and Slingsby, Jasper and Smart, Tracey and Snell, Sara J. and Soudzilovskaia, Nadejda A. and Souza, Gabriel B. G. and Souza, Flaviana Maluf and Souza, Vin{\´i}cius Castro and Stallings, Christopher D. and Stanforth, Rowan and Stanley, Emily H. and Sterza, Jos{\´e} Mauro and Stevens, Maarten and Stuart-Smith, Rick and Suarez, Yzel Rondon and Supp, Sarah and Tamashiro, Jorge Yoshio and Tarigan, Sukmaraharja and Thiede, Gary P. and Thorn, Simon and Tolvanen, Anne and Toniato, Maria Teresa Zugliani and Totland, {\O}rjan and Twilley, Robert R. and Vaitkus, Gediminas and Valdivia, Nelson and Vallejo, Martha Isabel and Valone, Thomas J. and Van Colen, Carl and Vanaverbeke, Jan and Venturoli, Fabio and Verheye, Hans M. and Vianna, Marcelo and Vieira, Rui P. and Vrška, Tom{\´a}š and Vu, Con Quang and Vu, Lien Van and Waide, Robert B. and Waldock, Conor and Watts, Dave and Webb, Sara and Wesołowski, Tomasz and White, Ethan P. and Widdicombe, Claire E. and Wilgers, Dustin and Williams, Richard and Williams, Stefan B. and Williamson, Mark and Willig, Michael R. and Willis, Trevor J. and Wipf, Sonja and Woods, Kerry D. and Woehler, Eric J. and Zawada, Kyle and Zettler, Michael L.}, title = {BioTIME: A database of biodiversity time series for the Anthropocene}, series = {Global Ecology and Biogeography}, volume = {27}, journal = {Global Ecology and Biogeography}, doi = {10.1111/geb.12729}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-222846}, pages = {760-786}, year = {2018}, abstract = {Motivation The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2). Time period and grain BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates. Software format .csv and .SQL.}, language = {en} } @article{WestphaleBackhausKoenig2022, author = {Westphale, Silke and Backhaus, Joy and Koenig, Sarah}, title = {Quantifying teaching quality in medical education: The impact of learning gain calculation}, series = {Medical Education}, volume = {56}, journal = {Medical Education}, number = {3}, doi = {10.1111/medu.14694}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259576}, pages = {312-320}, year = {2022}, abstract = {Background Student performance is a mirror of teaching quality. The pre-/post-test design allows a pragmatic approach to comparing the effects of interventions. However, the calculation of current knowledge gain scores introduces varying degrees of distortion. Here we present a new metric employing a linear weighting coefficient to reduce skewness on outcome interpretation. Methods We compared and contrasted a number of common scores (raw and relative gain scores) with our new method on two datasets, one simulated and the other empirical from a previous intervention study (n = 180) employing a pre-/post-test design. Results The outcomes of the common scores were clearly different, demonstrating a significant dependency on pre-test scores. Only the new metric revealed a linear relationship to the knowledge baseline, was less skewed on the upper or lower extremes, and proved well suited to allow the calculation of negative learning gains. Employing the empirical dataset, the new method also confirmed the interaction effect of teaching formats with specific subgroups of learner characteristics. Conclusion This work introduces a new weighted metric enabling meaningful comparisons between interventions based on a linear transformation. This method will form the basis to intertwine the calculation of test performance closely with the outcome of learning as an important factor reflecting teaching quality and efficacy. Its regular use can improve the transparency of teaching activities and outcomes, contribute to forming rounded judgements of students' acquisition of knowledge and skills and enable valuable feedforward to develop and enhance curricular concepts.}, language = {en} } @article{BocukWolffKrauseetal.2017, author = {Bocuk, Derya and Wolff, Alexander and Krause, Petra and Salinas, Gabriela and Bleckmann, Annalen and Hackl, Christina and Beissbarth, Tim and Koenig, Sarah}, title = {The adaptation of colorectal cancer cells when forming metastases in the liver: expression of associated genes and pathways in a mouse model}, series = {BMC Cancer}, volume = {17}, journal = {BMC Cancer}, number = {342}, doi = {10.1186/s12885-017-3342-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170853}, year = {2017}, abstract = {Background: Colorectal cancer (CRC) is the second leading cause of cancer-related death in men and women. Systemic disease with metastatic spread to distant sites such as the liver reduces the survival rate considerably. The aim of this study was to investigate the changes in gene expression that occur on invasion and expansion of CRC cells when forming metastases in the liver. Methods: The livers of syngeneic C57BL/6NCrl mice were inoculated with 1 million CRC cells (CMT-93) via the portal vein, leading to the stable formation of metastases within 4 weeks. RNA sequencing performed on the Illumina platform was employed to evaluate the expression profiles of more than 14,000 genes, utilizing the RNA of the cell line cells and liver metastases as well as from corresponding tumour-free liver. Results: A total of 3329 differentially expressed genes (DEGs) were identified when cultured CMT-93 cells propagated as metastases in the liver. Hierarchical clustering on heat maps demonstrated the clear changes in gene expression of CMT-93 cells on propagation in the liver. Gene ontology analysis determined inflammation, angiogenesis, and signal transduction as the top three relevant biological processes involved. Using a selection list, matrix metallopeptidases 2, 7, and 9, wnt inhibitory factor, and chemokine receptor 4 were the top five significantly dysregulated genes. Conclusion: Bioinformatics assists in elucidating the factors and processes involved in CRC liver metastasis. Our results support the notion of an invasion-metastasis cascade involving CRC cells forming metastases on successful invasion and expansion within the liver. Furthermore, we identified a gene expression signature correlating strongly with invasiveness and migration. Our findings may guide future research on novel therapeutic targets in the treatment of CRC liver metastasis.}, language = {en} }