@article{AbdallaAharonianAitBenkhalietal.2018, author = {Abdalla, Hassan E. and Aharonian, Felix A. and Ait Benkhali, Faical and Ang{\"u}ner, Ekrem Oǧuzhan and Arakawa, M. and Arcaro, C. and Armand, C. and Arrieta, M. and Backes, Michael and Barnard, M. and Becherini, Yvonne and Tjus, J. Becker and Berge, D. and Bernhard, S. and Bernl{\"o}hr, Konrad and Blackwell, R. and B{\"o}ttcher, Markus and Boisson, C. and Bolmont, Julien and Bonnefoy, S. and Bordas, Pol and Bregeon, J. and Brun, F. and Brun, P. and Bryan, M. and B{\"u}chele, M. and Bulik, Tomasz and Bylund, Tomas and Capasso, Massimo and Caroff, S. and Carosi, A. and Casanova, Sabrina and Cerruti, Matteo and Chakraborty, Nachiketa and Chandra, S. and Chaves, R. C. G. and Chen, A. and Colafrancesco, Sergio and Condon, B. and Davids, Isak and Deil, Christoph and Devin, J. and deWilt, P. and Dirson, L. and Djannati-Atai, A. and Dmytriiev, A. and Donath, Axel and Doroshenko, Victor and Dyks, J. and Egberts, Kathrin and Emery, G. and Ernenwein, J. -P. and Eschbach, Stefan and Fegan, S. and Fiasson, Armand and Fontaine, G. and Funk, Sebastian and F{\"u}ßling, Matthias and Gabici, S. and Gallant, Y. A. and Gate, F. and Giavitto, Gianluca and Eisenacher Glawion, Dorit and Glicenstein, Jean-Fran{\c{c}}ois and Gottschall, D. and Grondin, Marie-H{\´e}l{\`e}ne and Hahn, J. and Haupt, M. and Heinzelmann, G. and Henri, Gilles and Hermann, G. and Hinton, James Anthony and Hofmann, Werner and Hoischen, Clemens and Holch, Tim Lukas and Holler, M. and Horns, D. and Huber, D. and Iwasaki, H. and Jacholkowska, A. and Jamrozy, M. and Jankowsky, David and Jankowsky, Felix and Jouvin, L. and Jung-Richardt, I. and Kastendieck, M. A. and Katarzyński, Krzysztof and Katsuragawa, M. and Katz, U. and Kerszberg, D. and Khangulyan, D. and Khelifi, B. and King, J. and Klepser, S. and Kluzniak, W. and Komin, Nu. and Kosack, K. and Krakau, S. and Kraus, M. and Kruger, P. P. and Lamanna, G. and Lau, J. and Lefaucheur, J. and Lemiere, A. and Lemoine-Goumard, M. and Lenain, J. -P. and Leser, Eva and Lohse, T. and Lorentz, M. and Lopez-Coto, R. and Lypova, I. and Malyshev, D. and Marandon, V. and Marcowith, Alexandre and Mariaud, C. and Marti-Devesa, G. and Marx, R. and Maurin, G. and Meintjes, P. J. and Mitchell, A. M. W. and Moderski, R. and Mohamed, M. and Mohrmann, L. and Moulin, Emmanuel and Murach, T. and Nakashima, S. and de Naurois, M. and Ndiyavala, H. and Niederwanger, F. and Niemiec, J. and Oakes, L. and Odaka, H. and Ohm, S. and Ostrowski, M. and Oya, I. and Padovani, M. and Panter, M. and Parsons, R. D. and Perennes, C. and Petrucci, P. -O. and Peyaud, B. and Piel, Q. and Pita, S. and Poireau, V. and Noel, A. Priyana and Prokhorov, D. A. and Prokoph, H. and Puehlhofer, G. and Punch, M. and Quirrenbach, A. and Raab, S. and Rauth, R. and Reimer, A. and Reimer, O. and Renaud, M. and Rieger, F. and Rinchiuso, L. and Romoli, C. and Rowell, G. and Rudak, B. and Ruiz-Velasco, E. and Sahakian, V. and Saito, S. and Sanchez, D. A. and Santangelo, Andrea and Sasaki, M. and Schlickeiser, R. and Schussler, F. and Schulz, A. and Schwanke, U. and Schwemmer, S. and Seglar-Arroyo, M. and Senniappan, M. and Seyffert, A. S. and Shafi, N. and Shilon, I. and Shiningayamwe, K. and Simoni, R. and Sinha, A. and Sol, H. and Spanier, F. and Specovius, A. and Spir-Jacob, M. and Stawarz, L. and Steenkamp, R. and Stegmann, Christian and Steppa, Constantin Beverly and Takahashi, T. and Tavernet, J. -P. and Tavernier, T. and Taylor, A. M. and Terrier, R. and Tibaldo, L. and Tiziani, D. and Tluczykont, M. and Trichard, C. and Tsirou, M. and Tsuji, N. and Tuffs, R. and Uchiyama, Y. and van der Walt, D. J. and van Eldik, C. and van Rensburg, C. and van Soelen, B. and Vasileiadis, G. and Veh, J. and Venter, C. and Viana, A. and Vincent, P. and Vink, J. and Voisin, F. and Voelk, H. J. and Vuillaume, T. and Wadiasingh, Z. and Wagner, S. J. and Wagner, R. M. and White, R. and Wierzcholska, A. and Yang, R. and Zaborov, D. and Zacharias, M. and Zanin, R. and Zdziarski, A. and Zech, Alraune and Zefi, F. and Ziegler, A. and Zorn, J. and Zywucka, N. and Cirelli, M. and Panci, P. and Sala, F. and Silk, J. and Taoso, M.}, title = {Searches for gamma-ray lines and 'pure WIMP' spectra from Dark Matter annihilations in dwarf galaxies with H.E.S.S.}, series = {Journal of cosmology and astroparticle physics}, journal = {Journal of cosmology and astroparticle physics}, number = {11}, publisher = {IOP Publishing Ltd. (Bristol)}, address = {Bristol}, organization = {HESS Collaboration}, issn = {1475-7516}, doi = {10.1088/1475-7516/2018/11/037}, pages = {22}, year = {2018}, abstract = {Dwarf spheroidal galaxies are among the most promising targets for detecting signals of Dark Matter (DM) annihilations. The H.E.S.S. experiment has observed five of these systems for a total of about 130 hours. The data are re-analyzed here, and, in the absence of any detected signals, are interpreted in terms of limits on the DM annihilation cross section. Two scenarios are considered: i) DM annihilation into mono-energetic gamma-rays and ii) DM in the form of pure WIMP multiplets that, annihilating into all electroweak bosons, produce a distinctive gamma-ray spectral shape with a high-energy peak at the DM mass and a lower-energy continuum. For case i), upper limits at 95\% confidence level of about less than or similar to 3 x 10(-25) cm(3) s(-1) are obtained in the mass range of 400 GeV to 1TeV. For case ii), the full spectral shape of the models is used and several excluded regions are identified, but the thermal masses of the candidates are not robustly ruled out.}, language = {en} } @article{MartinMartinGomezRivasBoverArnaletal.2013, author = {Martin-Martin, J. D. and Gomez-Rivas, E. and Bover-Arnal, T. and Trave, A. and Salas, R. and Moreno-Bedmar, J. A. and Tomas, S. and Corbella, M. and Teixell, A. and Verges, J. and Stafford, S. L.}, title = {The Upper Aptian to Lower Albian syn-rift carbonate succession of the southern Maestrat Basin (Spain): Facies architecture and fault-controlled stratabound dolostones}, series = {CRETACEOUS RESEARCH}, volume = {41}, journal = {CRETACEOUS RESEARCH}, number = {4}, publisher = {ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD}, address = {LONDON}, issn = {0195-6671}, doi = {10.1016/j.cretres.2012.12.008}, pages = {217 -- 236}, year = {2013}, abstract = {Syn-rift shallow-marine carbonates of Late Aptian to Early Albian age in the southern Maestrat Basin (E Spain) register the thickest Aptian sedimentary record of the basin, and one of the most complete carbonate successions of this age reported in the northern Tethyan margin. The host limestones (Benassal Formation) are partially replaced by dolostones providing a new case study of fault-controlled hydrothermal dolomitization. The syn-rift sediments filled a graben controlled by normal basement faults. The Benassal Fm was deposited in a carbonate ramp with scarce siliciclastic input. The lithofacies are mainly characterized by the presence of orbitolinid foraminifera, corals and rudist bivalves fauna. The succession is stacked in three transgressive-regressive sequences (T-R) bounded by surfaces with sequence stratigraphic significance. The third sequence, which is reported for the first time in the basin, is formed by fully marine lithofacies of Albian age and represents the marine equivalent to the continental deposits of the Escucha Fm in the rest of the basin. The dolomitization of the host rock is spatially associated with the basement faults, and thus is fault-controlled. The dolostone forms seismic-scale stratabound tabular geobodies that extend several kilometres away from the fault zones, mostly in the hanging wall blocks, and host Mississippi Valley Type (MVT) deposits. The dolostones preferentially replaced middle to inner ramp grain-dominated fades from the third T-R sequences consisting of bioclastic packestones and peloidal grainstones. Field and petrology data indicate that the replacement took place after early calcite cementation and compaction, most likely during the Late Cretaceous post-rift stage of the basin. The dolostone registers the typical hydrothermal paragenesis constituted by the host limestone replacement, dolomite cementation and sulfide MVT mineralization. The Aptian succession studied provides a stratigraphic framework that can be used for oil exploration in age-equivalent rocks, especially in the Valencia Trough, offshore Spain. Moreover, this new case study constitutes a world class outcrop analogue for similar partially stratabound, dolomitized limestone reservoirs worldwide. (c) 2013 Elsevier Ltd. All rights reserved.}, language = {en} } @article{SchubertJonssonChangetal.2014, author = {Schubert, Mikkel and Jonsson, Hakon and Chang, Dan and Sarkissian, Clio Der and Ermini, Luca and Ginolhac, Aurelien and Albrechtsen, Anders and Dupanloup, Isabelle and Foucal, Adrien and Petersen, Bent Larsen and Fumagalli, Matteo and Raghavan, Maanasa and Seguin-Orlando, Andaine and Korneliussen, Thorfinn S. and Velazquez, Amhed M. V. and Stenderup, Jesper and Hoover, Cindi A. and Rubin, Carl-Johan and Alfarhan, Ahmed H. and Alquraishi, Saleh A. and Al-Rasheid, Khaled A. S. and MacHugh, David E. and Kalbfleisch, Ted and MacLeod, James N. and Rubin, Edward M. and Sicheritz-Ponten, Thomas and Andersson, Leif and Hofreiter, Michael and Marques-Bonet, Tomas and Gilbert, M. Thomas P. and Nielsen, Rasmus and Excoffier, Laurent and Willerslev, Eske and Shapiro, Beth and Orlando, Ludovic}, title = {Prehistoric genomes reveal the genetic foundation and cost of horse domestication}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {52}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1416991111}, pages = {E5661 -- E5669}, year = {2014}, language = {en} } @article{LibradoGambaGaunitzetal.2017, author = {Librado, Pablo and Gamba, Cristina and Gaunitz, Charleen and Sarkissian, Clio Der and Pruvost, Melanie and Albrechtsen, Anders and Fages, Antoine and Khan, Naveed and Schubert, Mikkel and Jagannathan, Vidhya and Serres-Armero, Aitor and Kuderna, Lukas F. K. and Povolotskaya, Inna S. and Seguin-Orlando, Andaine and Lepetz, Sebastien and Neuditschko, Markus and Theves, Catherine and Alquraishi, Saleh A. and Alfarhan, Ahmed H. and Al-Rasheid, Khaled A. S. and Rieder, Stefan and Samashev, Zainolla and Francfort, Henri-Paul and Benecke, Norbert and Hofreiter, Michael and Ludwig, Arne and Keyser, Christine and Marques-Bonet, Tomas and Ludes, Bertrand and Crubezy, Eric and Leeb, Tosso and Willerslev, Eske and Orlando, Ludovic}, title = {Ancient genomic changes associated with domestication of the horse}, series = {Science}, volume = {356}, journal = {Science}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.aam5298}, pages = {442 -- 445}, year = {2017}, abstract = {The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between similar to 4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.}, language = {en} } @article{NathanMonkArlinghausetal.2022, author = {Nathan, Ran and Monk, Christopher T. and Arlinghaus, Robert and Adam, Timo and Al{\´o}s, Josep and Assaf, Michael and Baktoft, Henrik and Beardsworth, Christine E. and Bertram, Michael G. and Bijleveld, Allert and Brodin, Tomas and Brooks, Jill L. and Campos-Candela, Andrea and Cooke, Steven J. and Gjelland, Karl O. and Gupte, Pratik R. and Harel, Roi and Hellstrom, Gustav and Jeltsch, Florian and Killen, Shaun S. and Klefoth, Thomas and Langrock, Roland and Lennox, Robert J. and Lourie, Emmanuel and Madden, Joah R. and Orchan, Yotam and Pauwels, Ine S. and Riha, Milan and R{\"o}leke, Manuel and Schl{\"a}gel, Ulrike and Shohami, David and Signer, Johannes and Toledo, Sivan and Vilk, Ohad and Westrelin, Samuel and Whiteside, Mark A. and Jaric, Ivan}, title = {Big-data approaches lead to an increased understanding of the ecology of animal movement}, series = {Science}, volume = {375}, journal = {Science}, number = {6582}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.abg1780}, pages = {734 -- +}, year = {2022}, abstract = {Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences.}, language = {en} } @article{GanchevaOuniJeleniketal.2019, author = {Gancheva, Sofiya and Ouni, Meriem and Jelenik, Tomas and Koliaki, Chrysi and Szendroedi, Julia and Toledo, Frederico G. S. and Markgraf, Daniel Frank and Pesta, Dominik H. and Mastrototaro, Lucia and De Filippo, Elisabetta and Herder, Christian and J{\"a}hnert, Markus and Weiss, J{\"u}rgen and Strassburger, Klaus and Schlensak, Matthias and Sch{\"u}rmann, Annette and Roden, Michael}, title = {Dynamic changes of muscle insulin sensitivity after metabolic surgery}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-12081-0}, pages = {13}, year = {2019}, abstract = {The mechanisms underlying improved insulin sensitivity after surgically-induced weight loss are still unclear. We monitored skeletal muscle metabolism in obese individuals before and over 52 weeks after metabolic surgery. Initial weight loss occurs in parallel with a decrease in muscle oxidative capacity and respiratory control ratio. Persistent elevation of intramyocellular lipid intermediates, likely resulting from unrestrained adipose tissue lipolysis, accompanies the lack of rapid changes in insulin sensitivity. Simultaneously, alterations in skeletal muscle expression of genes involved in calcium/lipid metabolism and mitochondrial function associate with subsequent distinct DNA methylation patterns at 52 weeks after surgery. Thus, initial unfavorable metabolic changes including insulin resistance of adipose tissue and skeletal muscle precede epigenetic modifications of genes involved in muscle energy metabolism and the long-term improvement of insulin sensitivity.}, language = {en} } @article{KarolyiTeldeMouraetal.2004, author = {Karolyi, G. and Tel, Tomas and de Moura, A. P. S. and Grebogi, Celso}, title = {Reactive particles in random flows}, issn = {0031-9007}, year = {2004}, abstract = {We study the dynamics of chemically or biologically active particles advected by open flows of chaotic time dependence, which can be modeled by a random time dependence of the parameters on a stroboscopic map. We develop a general theory for reactions in such random flows, and derive the reaction equation for this case. We show that there is a singular enhancement of the reaction in random flows, and this enhancement is increased as compared to the nonrandom case. We verify our theory in a model flow generated by four point vortices moving chaotically}, language = {en} } @article{FagesHanghojKhanetal.2019, author = {Fages, Antoine and Hanghoj, Kristian and Khan, Naveed and Gaunitz, Charleen and Seguin-Orlando, Andaine and Leonardi, Michela and Constantz, Christian McCrory and Gamba, Cristina and Al-Rasheid, Khaled A. S. and Albizuri, Silvia and Alfarhan, Ahmed H. and Allentoft, Morten and Alquraishi, Saleh and Anthony, David and Baimukhanov, Nurbol and Barrett, James H. and Bayarsaikhan, Jamsranjav and Benecke, Norbert and Bernaldez-Sanchez, Eloisa and Berrocal-Rangel, Luis and Biglari, Fereidoun and Boessenkool, Sanne and Boldgiv, Bazartseren and Brem, Gottfried and Brown, Dorcas and Burger, Joachim and Crubezy, Eric and Daugnora, Linas and Davoudi, Hossein and Damgaard, Peter de Barros and de Chorro y de Villa-Ceballos, Maria de los Angeles and Deschler-Erb, Sabine and Detry, Cleia and Dill, Nadine and Oom, Maria do Mar and Dohr, Anna and Ellingvag, Sturla and Erdenebaatar, Diimaajav and Fathi, Homa and Felkel, Sabine and Fernandez-Rodriguez, Carlos and Garcia-Vinas, Esteban and Germonpre, Mietje and Granado, Jose D. and Hallsson, Jon H. and Hemmer, Helmut and Hofreiter, Michael and Kasparov, Aleksei and Khasanov, Mutalib and Khazaeli, Roya and Kosintsev, Pavel and Kristiansen, Kristian and Kubatbek, Tabaldiev and Kuderna, Lukas and Kuznetsov, Pavel and Laleh, Haeedeh and Leonard, Jennifer A. and Lhuillier, Johanna and von Lettow-Vorbeck, Corina Liesau and Logvin, Andrey and Lougas, Lembi and Ludwig, Arne and Luis, Cristina and Arruda, Ana Margarida and Marques-Bonet, Tomas and Silva, Raquel Matoso and Merz, Victor and Mijiddorj, Enkhbayar and Miller, Bryan K. and Monchalov, Oleg and Mohaseb, Fatemeh A. and Morales, Arturo and Nieto-Espinet, Ariadna and Nistelberger, Heidi and Onar, Vedat and Palsdottir, Albina H. and Pitulko, Vladimir and Pitskhelauri, Konstantin and Pruvost, Melanie and Sikanjic, Petra Rajic and Papesa, Anita Rapan and Roslyakova, Natalia and Sardari, Alireza and Sauer, Eberhard and Schafberg, Renate and Scheu, Amelie and Schibler, Jorg and Schlumbaum, Angela and Serrand, Nathalie and Serres-Armero, Aitor and Shapiro, Beth and Seno, Shiva Sheikhi and Shevnina, Irina and Shidrang, Sonia and Southon, John and Star, Bastiaan and Sykes, Naomi and Taheri, Kamal and Taylor, William and Teegen, Wolf-Rudiger and Vukicevic, Tajana Trbojevic and Trixl, Simon and Tumen, Dashzeveg and Undrakhbold, Sainbileg and Usmanova, Emma and Vahdati, Ali and Valenzuela-Lamas, Silvia and Viegas, Catarina and Wallner, Barbara and Weinstock, Jaco and Zaibert, Victor and Clavel, Benoit and Lepetz, Sebastien and Mashkour, Marjan and Helgason, Agnar and Stefansson, Kari and Barrey, Eric and Willerslev, Eske and Outram, Alan K. and Librado, Pablo and Orlando, Ludovic}, title = {Tracking five millennia of horse management with extensive ancient genome time series}, series = {Cell}, volume = {177}, journal = {Cell}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {0092-8674}, doi = {10.1016/j.cell.2019.03.049}, pages = {1419 -- 1435}, year = {2019}, abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (>= 1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modem legacy of past equestrian civilisations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modem breeding impacted genetic diversity more dramatically than the previous millennia of human management.}, language = {en} } @misc{BollAvetisyanNixonLentzetal.2018, author = {Boll-Avetisyan, Natalie and Nixon, Jessie S. and Lentz, Tomas O. and Liu, Liquan and van Ommen, Sandrien and Coeltekin, Cagri and van Rij, Jacolien}, title = {Neural response development during distributional learning}, series = {19 th annual conference of the international speech communicaton association (INTERSPEECH 2018), VOLS 1-6: Speech research for emerging marjets in multilingual societies}, journal = {19 th annual conference of the international speech communicaton association (INTERSPEECH 2018), VOLS 1-6: Speech research for emerging marjets in multilingual societies}, publisher = {ISCA-International Speech Communication Association}, address = {Baixas}, isbn = {978-1-5108-7221-9}, issn = {2308-457X}, doi = {10.21437/Interspeech.2018-2072}, pages = {1432 -- 1436}, year = {2018}, abstract = {We investigated online electrophysiological components of distributional learning, specifically of tones by listeners of a non tonal language. German listeners were presented with a bimodal distribution of syllables with lexical tones from a synthesized continuum based on Cantonese level tones. Tones were presented in sets of four standards (within-category tokens) followed by a deviant (across-category token). Mismatch negativity (MMN) was measured. Earlier behavioral data showed that exposure to this bimodal distribution improved both categorical perception and perceptual acuity for level tones [I]. In the present study we present analyses of the electrophysiological response recorded during this exposure, i.e., the development of the MMN response during distributional learning. This development over time is analyzed using Generalized Additive Mixed Models and results showed that the MMN amplitude increased for both within and across-category tokens, reflecting higher perceptual acuity accompanying category formation. This is evidence that learners zooming in on phonological categories undergo neural changes associated with more accurate phonetic perception.}, language = {en} } @misc{PajoroMadrigalMuinoetal.2014, author = {Pajoro, Alice and Madrigal, Pedro and Mui{\~n}o, Jose M. and Matus, Jos{\´e} Tom{\´a}s and Jin, Jian and Mecchia, Martin A. and Debernardi, Juan M. and Palatnik, Javier F. and Balazadeh, Salma and Arif, Muhammad and {\´O}'Maoil{\´e}idigh, Diarmuid S. and Wellmer, Frank and Krajewski, Pawel and Riechmann, Jos{\´e}-Luis and Angenent, Gerco C. and Kaufmann, Kerstin}, title = {Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, volume = {15}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, issn = {1866-8372}, doi = {10.25932/publishup-43113}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431139}, pages = {19}, year = {2014}, abstract = {Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.}, language = {en} } @article{AmourMuttiChristetal.2012, author = {Amour, Frederic and Mutti, Maria and Christ, Nicolas and Immenhauser, Adrian and Agar, Susan M. and Benson, Gregory S. and Tomas, Sara and Alway, Robert and Kabiri, Lachen}, title = {Capturing and modelling metre-scale spatial facies heterogeneity in a Jurassic ramp setting (Central High Atlas, Morocco)}, series = {Sedimentology : the journal of the International Association of Sedimentologists}, volume = {59}, journal = {Sedimentology : the journal of the International Association of Sedimentologists}, number = {4}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0037-0746}, doi = {10.1111/j.1365-3091.2011.01299.x}, pages = {1158 -- 1189}, year = {2012}, abstract = {Each simulation algorithm, including Truncated Gaussian Simulation, Sequential Indicator Simulation and Indicator Kriging is characterized by different operating modes, which variably influence the facies proportion, distribution and association of digital outcrop models, as shown in clastic sediments. A detailed study of carbonate heterogeneity is then crucial to understanding these differences and providing rules for carbonate modelling. Through a continuous exposure of Bajocian carbonate strata, a study window (320 m long, 190 m wide and 30 m thick) was investigated and metre-scale lithofacies heterogeneity was captured and modelled using closely-spaced sections. Ten lithofacies, deposited in a shallow-water carbonate-dominated ramp, were recognized and their dimensions and associations were documented. Field data, including height sections, were georeferenced and input into the model. Four models were built in the present study. Model A used all sections and Truncated Gaussian Simulation during the stochastic simulation. For the three other models, Model B was generated using Truncated Gaussian Simulation as for Model A, Model C was generated using Sequential Indicator Simulation and Model D was generated using Indicator Kriging. These three additional models were built by removing two out of eight sections from data input. The removal of sections allows direct insights on geological uncertainties at inter-well spacings by comparing modelled and described sections. Other quantitative and qualitative comparisons were carried out between models to understand the advantages/disadvantages of each algorithm. Model A is used as the base case. Indicator Kriging (Model D) simplifies the facies distribution by assigning continuous geological bodies of the most abundant lithofacies to each zone. Sequential Indicator Simulation (Model C) is confident to conserve facies proportion when geological heterogeneity is complex. The use of trend with Truncated Gaussian Simulation is a powerful tool for modelling well-defined spatial facies relationships. However, in shallow-water carbonate, facies can coexist and their association can change through time and space. The present study shows that the scale of modelling (depositional environment or lithofacies) involves specific simulation constraints on shallow-water carbonate modelling methods.}, language = {en} } @article{AmourMuttiChristetal.2013, author = {Amour, Frederic and Mutti, Maria and Christ, Nicolas and Immenhauser, Adrian and Benson, Gregory S. and Agar, Susan M. and Tomas, Sara and Kabiri, Lahcen}, title = {Outcrop analog for an oolitic carbonate ramp reservoir a scale-dependent geologic modeling approach based on stratigraphic hierarchy}, series = {AAPG bulletin}, volume = {97}, journal = {AAPG bulletin}, number = {5}, publisher = {American Association of Petroleum Geologists}, address = {Tulsa}, issn = {0149-1423}, doi = {10.1306/10231212039}, pages = {845 -- 871}, year = {2013}, abstract = {Considerable effort has been devoted to the development of simulation algorithms for facies modeling, whereas a discussion of how to combine those techniques has not existed. The integration of multiple geologic data into a three-dimensional model, which requires the combination of simulation techniques, is yet a current challenge for reservoir modeling. This article presents a thought process that guides the acquisition and modeling of geologic data at various scales. Our work is based on outcrop data collected from a Jurassic carbonate ramp located in the High Atlas mountain range of Morocco. The study window is 1 km (0.6 mi) wide and 100 m (328.1 ft) thick. We describe and model the spatial and hierarchical arrangement of carbonate bodies spanning from largest to smallest: (1) stacking pattern of high-frequency depositional sequences, (2) facies association, and (3) lithofacies. Five sequence boundaries were modeled using differential global position system mapping and light detection and ranging data. The surface-based model shows a low-angle profile with modest paleotopographic relief at the inner-to-middle ramp transition. Facies associations were populated using truncated Gaussian simulation to preserve ordered trends between the inner, middle, and outer ramps. At the lithofacies scale, field observations and statistical analysis show a mosaiclike distribution that was simulated using a fully stochastic approach with sequential indicator simulation. This study observes that the use of one single simulation technique is unlikely to correctly model the natural patterns and variability of carbonate rocks. The selection and implementation of different techniques customized for each level of the stratigraphic hierarchy will provide the essential computing flexibility to model carbonate settings. This study demonstrates that a scale-dependent modeling approach should be a common procedure when building subsurface and outcrop models.}, language = {en} } @article{ShekharSahniBensonetal.2014, author = {Shekhar, R. and Sahni, I. and Benson, Gregory S. and Agar, Susan M. and Amour, Fr{\´e}d{\´e}ric and Tomas, Sara and Christ, Nicolas and Alway, Robert and Mutti, Maria and Immenhauser, A. and Karcz, Z. and Kabiri, L.}, title = {Modelling and simulation of a Jurassic carbonate ramp outcrop, Amellago, High Atlas Mountains, Morocco}, series = {Petroleum geoscience}, volume = {20}, journal = {Petroleum geoscience}, number = {1}, publisher = {Geological Soc. Publ. House}, address = {Bath}, issn = {1354-0793}, doi = {10.1144/petgeo2013-010}, pages = {109 -- 123}, year = {2014}, abstract = {Carbonate reservoirs pose significant challenges for reservoir modelling and flow prediction due to heterogeneities in rock properties, limits to seismic resolution and limited constraints on subsurface data. Hence, a systematic and streamlined approach is needed to construct geological models and to quickly evaluate key sensitivities in the flow models. This paper discusses results from a reservoir analogue study of a Middle Jurassic carbonate ramp in the High Atlas Mountains of Morocco that has stratigraphic and structural similarities to selected Middle East reservoirs. For this purpose, high-resolution geological models were constructed from the integration of sedimentological, diagenetic and structural studies in the area. The models are approximately 1200 x 1250 m in size, and only faults (no fractures) with offsets greater than 1 m are included. Novel methods have been applied to test the response of flow simulations to the presence or absence of specific geological features, including proxies for hardgrounds, stylolites, patch reefs, and mollusc banks, as a way to guide the level of detail that is suitable for modelling objectives. Our general conclusion from the study is that the continuity of any geological feature with extreme permeability (high or low) has the most significant impact on flow.}, language = {en} }