@article{ChristopherAshwoodBittremieuxDeutschetal.2020, author = {Christopher Ashwood, Wout Bittremieux and Bittremieux, Wout and Deutsch, Eric W. and Doncheva, Nadezhda T. and Dorfer, Viktoria and Gabriels, Ralf and Gorshkov, Vladimir and Gupta, Surya and Jones, Andrew R. and K{\"a}ll, Lukas and Kopczynski, Dominik and Lane, Lydie and Lautenbacher, Ludwig and Legeay, Marc and Locard-Paulet, Marie and Mesuere, Bart and Sachsenberg, Timo and Salz, Renee and Samaras, Patroklos and Schiebenhoefer, Henning and Schmidt, Tobias and Schw{\"a}mmle, Veit and Soggiu, Alessio and Uszkoreit, Julian and Van Den Bossche, Tim and Van Puyvelde, Bart and Van Strien, Joeri and Verschaffelt, Pieter and Webel, Henry and Willems, Sander and Perez-Riverolab, Yasset and Netz, Eugen and Pfeuffer, Julianus}, title = {Proceedings of the EuBIC-MS 2020 Developers' Meeting}, series = {EuPA Open Proteomics}, volume = {24}, journal = {EuPA Open Proteomics}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2212-9685}, doi = {10.1016/j.euprot.2020.11.001}, pages = {1 -- 6}, year = {2020}, abstract = {The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers' meeting was held from January 13th to January 17th 2020 in Nyborg, Denmark. Among the participants were scientists as well as developers working in the field of computational mass spectrometry (MS) and proteomics. The 4-day program was split between introductory keynote lectures and parallel hackathon sessions. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts, and to actively contribute to highly relevant research projects. We successfully produced several new tools that will be useful to the proteomics community by improving data analysis as well as facilitating future research. All keynote recordings are available on https://doi.org/10.5281/zenodo.3890181.}, language = {en} } @misc{SchmidtWalzJonesetal.2016, author = {Schmidt, Katja and Walz, Ariane and Jones, Isobel and Metzger, Marc J.}, title = {The sociocultural value of upland regions in the vicinity of cities in comparison with urban green spaces}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {920}, issn = {1866-8372}, doi = {10.25932/publishup-44201}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442010}, pages = {465 -- 474}, year = {2016}, abstract = {Mountain and upland regions provide a wide range of ecosystem services to residents and visitors. While ecosystem research in mountain regions is on the rise, the linkages between sociocultural benefits and ecological systems remain little explored. Mountainous regions close to urban areas provide numerous benefits to a large number of individuals, suggesting a high social value, particularly for cultural ecosystem services. We explored and compared visitors' valuation of ecosystem services in the Pentland Hills, an upland range close to the city of Edinburgh, Scotland, and urban green spaces within Edinburgh. Based on 715 responses to user surveys in both study areas, we identified intense use and high social value for both areas. Several ecosystem services were perceived as equally important in both areas, including many cultural ecosystem services. Significant differences were revealed in the value of physically using nature, which Pentland Hills users rated more highly than those in the urban green spaces, and of mitigation of pollutants and carbon sequestration, for which the urban green spaces were valued more highly. Major differences were further identified for preferences in future land management, with nature-oriented management preferred by about 57\% of the interviewees in the Pentland Hills, compared to 31\% in the urban parks. The study highlights the substantial value of upland areas in close vicinity to a city for physically using and experiencing nature, with a strong acceptance of nature conservation.}, language = {en} } @article{SchmidtBehlLendleinetal.2014, author = {Schmidt, Christian and Behl, Marc and Lendlein, Andreas and Beuermann, Sabine}, title = {Synthesis of high molecular weight polyglycolide in supercritical carbon dioxide}, series = {RSC Advances}, volume = {4}, journal = {RSC Advances}, number = {66}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {2046-2069}, doi = {10.1039/c4ra06815g}, pages = {35099 -- 35105}, year = {2014}, abstract = {Polyglycolide (PGA) is a biodegradable polymer with multiple applications in the medical sector. Here the synthesis of high molecular weight polyglycolide by ring-opening polymerization of diglycolide is reported. For the first time stabilizer free supercritical carbon dioxide (scCO(2)) was used as a reaction medium. scCO(2) allowed for a reduction in reaction temperature compared to conventional processes. Together with the lowering of monomer concentration and consequently reduced heat generation compared to bulk reactions thermal decomposition of the product occurring already during polymerization is strongly reduced. The reaction temperatures and pressures were varied between 120 and 150 degrees C and 145 to 1400 bar. Tin(II) ethyl hexanoate and 1-dodecanol were used as catalyst and initiator, respectively. The highest number average molecular weight of 31 200 g mol(-1) was obtained in 5 hours from polymerization at 120 degrees C and 530 bar. In all cases the products were obtained as a dry white powder. Remarkably, independent of molecular weight the melting temperatures were always at (219 +/- 2)degrees C.}, language = {en} } @misc{SchmidtBehlLendleinetal.2014, author = {Schmidt, Christian and Behl, Marc and Lendlein, Andreas and Bauermann, Sabine}, title = {Synthesis of high molecular weight polyglycolide in supercritical carbon dioxide}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-99439}, year = {2014}, abstract = {Polyglycolide (PGA) is a biodegradable polymer with multiple applications in the medical sector. Here the synthesis of high molecular weight polyglycolide by ring-opening polymerization of diglycolide is reported. For the first time stabilizer free supercritical carbon dioxide (scCO2) was used as a reaction medium. scCO2 allowed for a reduction in reaction temperature compared to conventional processes. Together with the lowering of monomer concentration and consequently reduced heat generation compared to bulk reactions thermal decomposition of the product occurring already during polymerization is strongly reduced. The reaction temperatures and pressures were varied between 120 and 150 °C and 145 to 1400 bar. Tin(II) ethyl hexanoate and 1-dodecanol were used as catalyst and initiator, respectively. The highest number average molecular weight of 31 200 g mol-1 was obtained in 5 hours from polymerization at 120 °C and 530 bar. In all cases the products were obtained as a dry white powder. Remarkably, independent of molecular weight the melting temperatures were always at (219 ± 2) °C.}, language = {en} } @article{AartsAndersonAndersonetal.2015, author = {Aarts, Alexander A. and Anderson, Joanna E. and Anderson, Christopher J. and Attridge, Peter R. and Attwood, Angela and Axt, Jordan and Babel, Molly and Bahnik, Stepan and Baranski, Erica and Barnett-Cowan, Michael and Bartmess, Elizabeth and Beer, Jennifer and Bell, Raoul and Bentley, Heather and Beyan, Leah and Binion, Grace and Borsboom, Denny and Bosch, Annick and Bosco, Frank A. and Bowman, Sara D. and Brandt, Mark J. and Braswell, Erin and Brohmer, Hilmar and Brown, Benjamin T. and Brown, Kristina and Bruening, Jovita and Calhoun-Sauls, Ann and Callahan, Shannon P. and Chagnon, Elizabeth and Chandler, Jesse and Chartier, Christopher R. and Cheung, Felix and Christopherson, Cody D. and Cillessen, Linda and Clay, Russ and Cleary, Hayley and Cloud, Mark D. and Cohn, Michael and Cohoon, Johanna and Columbus, Simon and Cordes, Andreas and Costantini, Giulio and Alvarez, Leslie D. Cramblet and Cremata, Ed and Crusius, Jan and DeCoster, Jamie and DeGaetano, Michelle A. and Della Penna, Nicolas and den Bezemer, Bobby and Deserno, Marie K. and Devitt, Olivia and Dewitte, Laura and Dobolyi, David G. and Dodson, Geneva T. and Donnellan, M. Brent and Donohue, Ryan and Dore, Rebecca A. and Dorrough, Angela and Dreber, Anna and Dugas, Michelle and Dunn, Elizabeth W. and Easey, Kayleigh and Eboigbe, Sylvia and Eggleston, Casey and Embley, Jo and Epskamp, Sacha and Errington, Timothy M. and Estel, Vivien and Farach, Frank J. and Feather, Jenelle and Fedor, Anna and Fernandez-Castilla, Belen and Fiedler, Susann and Field, James G. and Fitneva, Stanka A. and Flagan, Taru and Forest, Amanda L. and Forsell, Eskil and Foster, Joshua D. and Frank, Michael C. and Frazier, Rebecca S. and Fuchs, Heather and Gable, Philip and Galak, Jeff and Galliani, Elisa Maria and Gampa, Anup and Garcia, Sara and Gazarian, Douglas and Gilbert, Elizabeth and Giner-Sorolla, Roger and Gl{\"o}ckner, Andreas and G{\"o}llner, Lars and Goh, Jin X. and Goldberg, Rebecca and Goodbourn, Patrick T. and Gordon-McKeon, Shauna and Gorges, Bryan and Gorges, Jessie and Goss, Justin and Graham, Jesse and Grange, James A. and Gray, Jeremy and Hartgerink, Chris and Hartshorne, Joshua and Hasselman, Fred and Hayes, Timothy and Heikensten, Emma and Henninger, Felix and Hodsoll, John and Holubar, Taylor and Hoogendoorn, Gea and Humphries, Denise J. and Hung, Cathy O. -Y. and Immelman, Nathali and Irsik, Vanessa C. and Jahn, Georg and Jaekel, Frank and Jekel, Marc and Johannesson, Magnus and Johnson, Larissa G. and Johnson, David J. and Johnson, Kate M. and Johnston, William J. and Jonas, Kai and Joy-Gaba, Jennifer A. and Kappes, Heather Barry and Kelso, Kim and Kidwell, Mallory C. and Kim, Seung Kyung and Kirkhart, Matthew and Kleinberg, Bennett and Knezevic, Goran and Kolorz, Franziska Maria and Kossakowski, Jolanda J. and Krause, Robert Wilhelm and Krijnen, Job and Kuhlmann, Tim and Kunkels, Yoram K. and Kyc, Megan M. and Lai, Calvin K. and Laique, Aamir and Lakens, Daniel and Lane, Kristin A. and Lassetter, Bethany and Lazarevic, Ljiljana B. and LeBel, Etienne P. and Lee, Key Jung and Lee, Minha and Lemm, Kristi and Levitan, Carmel A. and Lewis, Melissa and Lin, Lin and Lin, Stephanie and Lippold, Matthias and Loureiro, Darren and Luteijn, Ilse and Mackinnon, Sean and Mainard, Heather N. and Marigold, Denise C. and Martin, Daniel P. and Martinez, Tylar and Masicampo, E. J. and Matacotta, Josh and Mathur, Maya and May, Michael and Mechin, Nicole and Mehta, Pranjal and Meixner, Johannes and Melinger, Alissa and Miller, Jeremy K. and Miller, Mallorie and Moore, Katherine and M{\"o}schl, Marcus and Motyl, Matt and M{\"u}ller, Stephanie M. and Munafo, Marcus and Neijenhuijs, Koen I. and Nervi, Taylor and Nicolas, Gandalf and Nilsonne, Gustav and Nosek, Brian A. and Nuijten, Michele B. and Olsson, Catherine and Osborne, Colleen and Ostkamp, Lutz and Pavel, Misha and Penton-Voak, Ian S. and Perna, Olivia and Pernet, Cyril and Perugini, Marco and Pipitone, R. Nathan and Pitts, Michael and Plessow, Franziska and Prenoveau, Jason M. and Rahal, Rima-Maria and Ratliff, Kate A. and Reinhard, David and Renkewitz, Frank and Ricker, Ashley A. and Rigney, Anastasia and Rivers, Andrew M. and Roebke, Mark and Rutchick, Abraham M. and Ryan, Robert S. and Sahin, Onur and Saide, Anondah and Sandstrom, Gillian M. and Santos, David and Saxe, Rebecca and Schlegelmilch, Rene and Schmidt, Kathleen and Scholz, Sabine and Seibel, Larissa and Selterman, Dylan Faulkner and Shaki, Samuel and Simpson, William B. and Sinclair, H. Colleen and Skorinko, Jeanine L. M. and Slowik, Agnieszka and Snyder, Joel S. and Soderberg, Courtney and Sonnleitner, Carina and Spencer, Nick and Spies, Jeffrey R. and Steegen, Sara and Stieger, Stefan and Strohminger, Nina and Sullivan, Gavin B. and Talhelm, Thomas and Tapia, Megan and te Dorsthorst, Anniek and Thomae, Manuela and Thomas, Sarah L. and Tio, Pia and Traets, Frits and Tsang, Steve and Tuerlinckx, Francis and Turchan, Paul and Valasek, Milan and Van Aert, Robbie and van Assen, Marcel and van Bork, Riet and van de Ven, Mathijs and van den Bergh, Don and van der Hulst, Marije and van Dooren, Roel and van Doorn, Johnny and van Renswoude, Daan R. and van Rijn, Hedderik and Vanpaemel, Wolf and Echeverria, Alejandro Vasquez and Vazquez, Melissa and Velez, Natalia and Vermue, Marieke and Verschoor, Mark and Vianello, Michelangelo and Voracek, Martin and Vuu, Gina and Wagenmakers, Eric-Jan and Weerdmeester, Joanneke and Welsh, Ashlee and Westgate, Erin C. and Wissink, Joeri and Wood, Michael and Woods, Andy and Wright, Emily and Wu, Sining and Zeelenberg, Marcel and Zuni, Kellylynn}, title = {Estimating the reproducibility of psychological science}, series = {Science}, volume = {349}, journal = {Science}, number = {6251}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, organization = {Open Sci Collaboration}, issn = {1095-9203}, doi = {10.1126/science.aac4716}, pages = {8}, year = {2015}, abstract = {Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47\% of original effect sizes were in the 95\% confidence interval of the replication effect size; 39\% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68\% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.}, language = {en} } @article{SongBergstrasserRafatetal.2009, author = {Song, Hui and Bergstrasser, Claudia and Rafat, Neysan and Hoeger, Simone and Schmidt, Marc and Endres, N. and Goebeler, Matthias and Hillebrands, Jan-Luuk and Brigelius-Floh{\´e}, Regina and Banning, Antje and Beck, Grietje and Loesel, Ralf and Yard, Benito A.}, title = {The carbon monoxide releasing molecule (CORM-3) inhibits expression of vascular cell adhesion molecule-1 and E- selectin independently of haem oxygenase-1 expression}, issn = {0007-1188}, doi = {10.1111/j.1476-5381.2009.00215.x}, year = {2009}, abstract = {Background and purpose: Although carbon monoxide (CO) can modulate inflammatory processes, the influence of CO on adhesion molecules is less clear. This might be due to the limited amount of CO generated by haem degradation. We therefore tested the ability of a CO releasing molecule (CORM-3), used in supra-physiological concentrations, to modulate the expression of vascular cell adhesion molecule (VCAM)-1 and E-selectin on endothelial cells and the mechanism(s) involved. Experimental approach: Human umbilical vein endothelial cells (HUVECs) were stimulated with tumour necrosis factor (TNF)-alpha in the presence or absence of CORM-3. The influence of CORM-3 on VCAM-1 and E- selectin expression and the nuclear factor (NF)-kappa B pathway was assessed by flow cytometry, Western blotting and electrophoretic mobility shift assay. Key results: CORM-3 inhibited the expression of VCAM-1 and E-selectin on TNF-alpha- stimulated HUVEC. VCAM-1 expression was also inhibited when CORM-3 was added 24 h after TNF-alpha stimulation or when TNF-alpha was removed. This was paralleled by deactivation of NF-kappa B and a reduction in VCAM-1 mRNA. Although TNF- alpha removal was more effective in this regard, VCAM-1 protein was down-regulated more rapidly when CORM-3 was added. CORM-3 induced haem oxygenase-1 (HO-1) in a dose- and time-dependent manner, mediated by the transcription factor, Nrf2. CORM-3 was still able to down-regulate VCAM-1 expression in HUVEC transfected with siRNA for HO-1 or Nrf2. Conclusions and implications: Down-regulation of VCAM and E-selectin expression induced by CORM-3 was independent of HO-1 up- regulation and was predominantly due to inhibition of sustained NF-kappa B activation.}, language = {en} } @article{SchmidtWalzJonesetal.2016, author = {Schmidt, Katja and Walz, Ariane and Jones, Isobel and Metzger, Marc J.}, title = {The Sociocultural Value of Upland Regions in the Vicinity of Cities in Comparison With Urban Green Spaces}, series = {Mountain research and development}, volume = {36}, journal = {Mountain research and development}, publisher = {American Geophysical Union}, address = {Lawrence}, issn = {0276-4741}, doi = {10.1659/MRD-JOURNAL-D-16-00044.1}, pages = {465 -- 474}, year = {2016}, language = {en} } @article{LilliestamMelligerOllieretal.2020, author = {Lilliestam, Johan and Melliger, Marc Andr{\´e} and Ollier, Lana and Schmidt, Tobias S. and Steffen, Bjarne}, title = {Understanding and accounting for the effect of exchange rate fluctuations on global learning rates}, series = {Nature energy}, volume = {5}, journal = {Nature energy}, number = {1}, publisher = {Nature Publishing Group}, address = {Berlin}, issn = {2058-7546}, doi = {10.1038/s41560-019-0531-y}, pages = {71 -- 78}, year = {2020}, abstract = {Learning rates are a central concept in energy system models and integrated assessment models, as they allow researchers to project the future costs of new technologies and to optimize energy system costs. Here we argue that exchange rate fluctuations are an important, but thus far overlooked, determinant of the learning-rate variance observed in the literature. We explore how empirically observed global learning rates depend on where technologies are installed and which currency is used to calculate the learning rate. Using global data of large-scale photovoltaic (>= 5 MW) plants, we show that the currency choice can result in learning-rate differences of up to 16 percentage points. We then introduce an adjustment factor to correct for the effect of exchange rate and market focus fluctuations and discuss the implications of our findings for innovation scholars, energy modellers and decision makers.
Learning rates are a measure of reduction in costs of energy from technologies such as solar photovoltaics. These are often estimated internationally with all monetary figures converted to a single currency, often US dollars. Lilliestam et al. show that such conversions can significantly affect the learning rate estimates.}, language = {en} } @article{RothwellMurphyAleksandrovaetal.2020, author = {Rothwell, Joseph A. and Murphy, Neil and Aleksandrova, Krasimira and Schulze, Matthias Bernd and Bešević, Jelena and Kliemann, Nathalie and Jenab, Mazda and Ferrari, Pietro and Achaintre, David and Gicquiau, Audrey and Vozar, B{\´e}atrice and Scalbert, Augustin and Huybrechts, Inge and Freisling, Heinz and Prehn, Cornelia and Adamski, Jerzy and Cross, Amanda J. and Pala, Valeria Maria and Boutron-Ruault, Marie-Christine and Dahm, Christina C. and Overvad, Kim and Gram, Inger Torhild and Sandanger, Torkjel M. and Skeie, Guri and Jakszyn, Paula and Tsilidis, Kostas K. and Hughes, David J. and van Guelpen, Bethany and Bod{\´e}n, Stina and S{\´a}nchez, Maria-Jos{\´e} and Schmidt, Julie A. and Katzke, Verena and K{\"u}hn, Tilman and Colorado-Yohar, Sandra and Tumino, Rosario and Bueno-de-Mesquita, Bas and Vineis, Paolo and Masala, Giovanna and Panico, Salvatore and Eriksen, Anne Kirstine and Tj{\o}nneland, Anne and Aune, Dagfinn and Weiderpass, Elisabete and Severi, Gianluca and Chaj{\`e}s, V{\´e}ronique and Gunter, Marc J.}, title = {Metabolic signatures of healthy lifestyle patterns and colorectal cancer risk in a European cohort}, series = {Clinical gastroenterology and hepatology}, volume = {20}, journal = {Clinical gastroenterology and hepatology}, publisher = {Elsevier}, address = {New York, NY}, issn = {1542-3565}, doi = {10.1016/j.cgh.2020.11.045}, pages = {E1061 -- E1082}, year = {2020}, abstract = {BACKGROUND \& AIMS: Colorectal cancer risk can be lowered by adherence to the World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) guidelines. We derived metabolic signatures of adherence to these guidelines and tested their associations with colorectal cancer risk in the European Prospective Investigation into Cancer and Nutrition cohort. METHODS: Scores reflecting adherence to the WCRF/AICR recommendations (scale, 1-5) were calculated from participant data on weight maintenance, physical activity, diet, and alcohol among a discovery set of 5738 cancer-free European Prospective Investigation into Cancer and Nutrition participants with metabolomics data. Partial least-squares regression was used to derive fatty acid and endogenous metabolite signatures of the WCRF/AICR score in this group. In an independent set of 1608 colorectal cancer cases and matched controls, odds ratios (ORs) and 95\% CIs were calculated for colorectal cancer risk per unit increase in WCRF/AICR score and per the corresponding change in metabolic signatures using multivariable conditional logistic regression. RESULTS: Higher WCRF/AICR scores were characterized by metabolic signatures of increased odd-chain fatty acids, serine, glycine, and specific phosphatidylcholines. Signatures were inversely associated more strongly with colorectal cancer risk (fatty acids: OR, 0.51 per unit increase; 95\% CI, 0.29-0.90; endogenous metabolites: OR, 0.62 per unit change; 95\% CI, 0.50-0.78) than the WCRF/AICR score (OR, 0.93 per unit change; 95\% CI, 0.86-1.00) overall. Signature associations were stronger in male compared with female participants. CONCLUSIONS: Metabolite profiles reflecting adherence to WCRF/AICR guidelines and additional lifestyle or biological risk factors were associated with colorectal cancer. Measuring a specific panel of metabolites representative of a healthy or unhealthy lifestyle may identify strata of the population at higher risk of colorectal cancer.}, language = {en} }