@book{RanaMohapatraSidorovaetal.2022, author = {Rana, Kaushik and Mohapatra, Durga Prasad and Sidorova, Julia and Lundberg, Lars and Sk{\"o}ld, Lars and Lopes Grim, Lu{\´i}s Fernando and Sampaio Gradvohl, Andr{\´e} Leon and Cremerius, Jonas and Siegert, Simon and Weltzien, Anton von and Baldi, Annika and Klessascheck, Finn and Kalancha, Svitlana and Lichtenstein, Tom and Shaabani, Nuhad and Meinel, Christoph and Friedrich, Tobias and Lenzner, Pascal and Schumann, David and Wiese, Ingmar and Sarna, Nicole and Wiese, Lena and Tashkandi, Araek Sami and van der Walt, Est{\´e}e and Eloff, Jan H. P. and Schmidt, Christopher and H{\"u}gle, Johannes and Horschig, Siegfried and Uflacker, Matthias and Najafi, Pejman and Sapegin, Andrey and Cheng, Feng and Stojanovic, Dragan and Stojnev Ilić, Aleksandra and Djordjevic, Igor and Stojanovic, Natalija and Predic, Bratislav and Gonz{\´a}lez-Jim{\´e}nez, Mario and de Lara, Juan and Mischkewitz, Sven and Kainz, Bernhard and van Hoorn, Andr{\´e} and Ferme, Vincenzo and Schulz, Henning and Knigge, Marlene and Hecht, Sonja and Prifti, Loina and Krcmar, Helmut and Fabian, Benjamin and Ermakova, Tatiana and Kelkel, Stefan and Baumann, Annika and Morgenstern, Laura and Plauth, Max and Eberhard, Felix and Wolff, Felix and Polze, Andreas and Cech, Tim and Danz, Noel and Noack, Nele Sina and Pirl, Lukas and Beilharz, Jossekin Jakob and De Oliveira, Roberto C. L. and Soares, F{\´a}bio Mendes and Juiz, Carlos and Bermejo, Belen and M{\"u}hle, Alexander and Gr{\"u}ner, Andreas and Saxena, Vageesh and Gayvoronskaya, Tatiana and Weyand, Christopher and Krause, Mirko and Frank, Markus and Bischoff, Sebastian and Behrens, Freya and R{\"u}ckin, Julius and Ziegler, Adrian and Vogel, Thomas and Tran, Chinh and Moser, Irene and Grunske, Lars and Sz{\´a}rnyas, G{\´a}bor and Marton, J{\´o}zsef and Maginecz, J{\´a}nos and Varr{\´o}, D{\´a}niel and Antal, J{\´a}nos Benjamin}, title = {HPI Future SOC Lab - Proceedings 2018}, number = {151}, editor = {Meinel, Christoph and Polze, Andreas and Beins, Karsten and Strotmann, Rolf and Seibold, Ulrich and R{\"o}dszus, Kurt and M{\"u}ller, J{\"u}rgen}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-547-7}, issn = {1613-5652}, doi = {10.25932/publishup-56371}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-563712}, publisher = {Universit{\"a}t Potsdam}, pages = {x, 277}, year = {2022}, abstract = {The "HPI Future SOC Lab" is a cooperation of the Hasso Plattner Institute (HPI) and industry partners. Its mission is to enable and promote exchange and interaction between the research community and the industry partners. The HPI Future SOC Lab provides researchers with free of charge access to a complete infrastructure of state of the art hard and software. This infrastructure includes components, which might be too expensive for an ordinary research environment, such as servers with up to 64 cores and 2 TB main memory. The offerings address researchers particularly from but not limited to the areas of computer science and business information systems. Main areas of research include cloud computing, parallelization, and In-Memory technologies. This technical report presents results of research projects executed in 2018. Selected projects have presented their results on April 17th and November 14th 2017 at the Future SOC Lab Day events.}, language = {en} } @article{KappelFriedrichOberkofleretal.2023, author = {Kappel, Christian and Friedrich, Thomas and Oberkofler, Vicky and Jiang, Li and Crawford, Tim and Lenhard, Michael and B{\"a}urle, Isabel}, title = {Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis}, series = {Genome biology : biology for the post-genomic era}, volume = {24}, journal = {Genome biology : biology for the post-genomic era}, number = {1}, publisher = {BioMed Central}, address = {London}, issn = {1474-760X}, doi = {10.1186/s13059-023-02970-5}, pages = {23}, year = {2023}, abstract = {Background Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. Results HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. Conclusions Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior.}, language = {en} } @book{KubanRottaNolteetal.2023, author = {Kuban, Robert and Rotta, Randolf and Nolte, J{\"o}rg and Chromik, Jonas and Beilharz, Jossekin Jakob and Pirl, Lukas and Friedrich, Tobias and Lenzner, Pascal and Weyand, Christopher and Juiz, Carlos and Bermejo, Belen and Sauer, Joao and Coelh, Leandro dos Santos and Najafi, Pejman and P{\"u}nter, Wenzel and Cheng, Feng and Meinel, Christoph and Sidorova, Julia and Lundberg, Lars and Vogel, Thomas and Tran, Chinh and Moser, Irene and Grunske, Lars and Elsaid, Mohamed Esameldin Mohamed and Abbas, Hazem M. and Rula, Anisa and Sejdiu, Gezim and Maurino, Andrea and Schmidt, Christopher and H{\"u}gle, Johannes and Uflacker, Matthias and Nozza, Debora and Messina, Enza and Hoorn, Andr{\´e} van and Frank, Markus and Schulz, Henning and Alhosseini Almodarresi Yasin, Seyed Ali and Nowicki, Marek and Muite, Benson K. and Boysan, Mehmet Can and Bianchi, Federico and Cremaschi, Marco and Moussa, Rim and Abdel-Karim, Benjamin M. and Pfeuffer, Nicolas and Hinz, Oliver and Plauth, Max and Polze, Andreas and Huo, Da and Melo, Gerard de and Mendes Soares, F{\´a}bio and Oliveira, Roberto C{\´e}lio Lim{\~a}o de and Benson, Lawrence and Paul, Fabian and Werling, Christian and Windheuser, Fabian and Stojanovic, Dragan and Djordjevic, Igor and Stojanovic, Natalija and Stojnev Ilic, Aleksandra and Weidmann, Vera and Lowitzki, Leon and Wagner, Markus and Ifa, Abdessatar Ben and Arlos, Patrik and Megia, Ana and Vendrell, Joan and Pfitzner, Bjarne and Redondo, Alberto and R{\´i}os Insua, David and Albert, Justin Amadeus and Zhou, Lin and Arnrich, Bert and Szab{\´o}, Ildik{\´o} and Fodor, Szabina and Ternai, Katalin and Bhowmik, Rajarshi and Campero Durand, Gabriel and Shevchenko, Pavlo and Malysheva, Milena and Prymak, Ivan and Saake, Gunter}, title = {HPI Future SOC Lab - Proceedings 2019}, number = {158}, editor = {Meinel, Christoph and Polze, Andreas and Beins, Karsten and Strotmann, Rolf and Seibold, Ulrich and R{\"o}dszus, Kurt and M{\"u}ller, J{\"u}rgen}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-564-4}, issn = {1613-5652}, doi = {10.25932/publishup-59791}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-597915}, publisher = {Universit{\"a}t Potsdam}, pages = {xi, 301}, year = {2023}, abstract = {The "HPI Future SOC Lab" is a cooperation of the Hasso Plattner Institute (HPI) and industry partners. Its mission is to enable and promote exchange and interaction between the research community and the industry partners. The HPI Future SOC Lab provides researchers with free of charge access to a complete infrastructure of state of the art hard and software. This infrastructure includes components, which might be too expensive for an ordinary research environment, such as servers with up to 64 cores and 2 TB main memory. The offerings address researchers particularly from but not limited to the areas of computer science and business information systems. Main areas of research include cloud computing, parallelization, and In-Memory technologies. This technical report presents results of research projects executed in 2019. Selected projects have presented their results on April 9th and November 12th 2019 at the Future SOC Lab Day events.}, language = {en} } @article{HempelSavenjieStolterfohtetal.2022, author = {Hempel, Hannes and Savenjie, Tom J. and Stolterfoht, Martin and Neu, Jens and Failla, Michele and Paingad, Vaisakh C. and Kužel, Petr and Heilweil, Edwin J. and Spies, Jacob A. and Schleuning, Markus and Zhao, Jiashang and Friedrich, Dennis and Schwarzburg, Klaus and Siebbeles, Laurens D. A. and D{\"o}rflinger, Patrick and Dyakonov, Vladimir and Katoh, Ryuzi and Hong, Min Ji and Labram, John G. and Monti, Maurizio and Butler-Caddle, Edward and Lloyd-Hughes, James and Taheri, Mohammad M. and Baxter, Jason B. and Magnanelli, Timothy J. and Luo, Simon and Cardon, Joseph M. and Ardo, Shane and Unold, Thomas}, title = {Predicting solar cell performance from terahertz and microwave spectroscopy}, series = {Advanced energy materials}, volume = {12}, journal = {Advanced energy materials}, number = {13}, publisher = {Wiley}, address = {Weinheim}, issn = {1614-6832}, doi = {10.1002/aenm.202102776}, pages = {16}, year = {2022}, abstract = {Mobilities and lifetimes of photogenerated charge carriers are core properties of photovoltaic materials and can both be characterized by contactless terahertz or microwave measurements. Here, the expertise from fifteen laboratories is combined to quantitatively model the current-voltage characteristics of a solar cell from such measurements. To this end, the impact of measurement conditions, alternate interpretations, and experimental inter-laboratory variations are discussed using a (Cs,FA,MA)Pb(I,Br)(3) halide perovskite thin-film as a case study. At 1 sun equivalent excitation, neither transport nor recombination is significantly affected by exciton formation or trapping. Terahertz, microwave, and photoluminescence transients for the neat material yield consistent effective lifetimes implying a resistance-free JV-curve with a potential power conversion efficiency of 24.6 \%. For grainsizes above approximate to 20 nm, intra-grain charge transport is characterized by terahertz sum mobilities of approximate to 32 cm(2) V-1 s(-1). Drift-diffusion simulations indicate that these intra-grain mobilities can slightly reduce the fill factor of perovskite solar cells to 0.82, in accordance with the best-realized devices in the literature. Beyond perovskites, this work can guide a highly predictive characterization of any emerging semiconductor for photovoltaic or photoelectrochemical energy conversion. A best practice for the interpretation of terahertz and microwave measurements on photovoltaic materials is presented.}, language = {en} } @misc{FriedrichFaivreBaeurleetal.2018, author = {Friedrich, Thomas and Faivre, Lea and B{\"a}urle, Isabel and Schubert, Daniel}, title = {Chromatin-based mechanisms of temperature memory in plants}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {42}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/pce.13373}, pages = {762 -- 770}, year = {2018}, abstract = {For successful growth and development, plants constantly have to gauge their environment. Plants are capable to monitor their current environmental conditions, and they are also able to integrate environmental conditions over time and store the information induced by the cues. In a developmental context, such an environmental memory is used to align developmental transitions with favourable environmental conditions. One temperature-related example of this is the transition to flowering after experiencing winter conditions, that is, vernalization. In the context of adaptation to stress, such an environmental memory is used to improve stress adaptation even when the stress cues are intermittent. A somatic stress memory has now been described for various stresses, including extreme temperatures, drought, and pathogen infection. At the molecular level, such a memory of the environment is often mediated by epigenetic and chromatin modifications. Histone modifications in particular play an important role. In this review, we will discuss and compare different types of temperature memory and the histone modifications, as well as the reader, writer, and eraser proteins involved.}, language = {en} }