International Max Planck Research
International Max Planck Research
Pockrandt C.,Free University of Berlin |
Pockrandt C.,International Max Planck Research |
Ehrhardt M.,Free University of Berlin |
Reinert K.,Free University of Berlin
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2017
The unidirectional FM index was introduced by Ferragina and Manzini in 2000 and allows to search a pattern in the index in one direction. The bidirectional FM index (2FM) was introduced by Lam et al. in 2009. It allows to search for a pattern by extending an infix of the pattern arbitrarily to the left or right. If σ is the size of the alphabet then the method of Lam et al. can conduct one step in time O(σ) while needing space O(σ · n) using constant time rank queries on bit vectors. Schnattinger and colleagues improved this time to O(log σ) while using O(log σ · n) bits of space for both, the FM and 2FM index. This is achieved by the use of binary wavelet trees. In this paper we introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in O(1) time per step while using O(log σ · n) +o(log σ · σ · n) bitsofspace.Thisisdoneby replacing the binary wavelet tree by a new data structure, the Enhanced Prefixsum Rank dictionary (EPR-dictionary). We implemented this method in the SeqAn C++ library and experimentally validated our theoretical results. In addition we compared our implementation with other freely available implementations of bidirectional indices and show that we are between ≈ 2.2−4.2 times faster. This will have a large impact for many bioinformatics applications that rely on practical implementations of (2)FM indices e.g. for read mapping. To our knowledge this is the first implementation of a constant time method for a search step in 2FM indices. © Springer International Publishing AG 2017.
Kuhlman K.R.,University of Michigan |
Kuhlman K.R.,International Max Planck Research |
Olson S.L.,University of Michigan |
Olson S.L.,International Max Planck Research |
Lopez-Duran N.L.,University of Michigan
Developmental Psychobiology | Year: 2014
In this study, we examined whether parenting and HPA-axis reactivity during middle childhood predicted increases in internalizing symptoms during the transition to adolescence, and whether HPA-axis reactivity mediated the impact of parenting on internalizing symptoms. The study included 65 children (35 boys) who were assessed at age 5, 7, and 11. Parenting behaviors were assessed via parent report at age 5 and 11. The child's HPA-axis reactivity was measured at age 7 via a stress task. Internalizing symptoms were measured via teacher reports at age 5 and 11. High maternal warmth at age 5 predicted lower internalizing symptoms at age 11. Also, high reported maternal warmth and induction predicted lower HPA-axis reactivity. Additionally, greater HPA-axis reactivity at age 7 was associated with greater increases in internalizing symptoms from age 5 to 11. Finally, the association between age 5 maternal warmth and age 11 internalizing symptoms was partially mediated by lower cortisol in response to the stress task. Thus, parenting behaviors in early development may influence the physiological stress response system and therefore buffer the development of internalizing symptoms during preadolescence when risk for disorder onset is high. © 2013 Wiley Periodicals, Inc.
Sardana N.,Martin Luther University of Halle Wittenberg |
Sardana N.,International Max Planck Research |
Heyroth F.,Martin Luther University of Halle Wittenberg |
Schilling J.,Martin Luther University of Halle Wittenberg
Journal of the Optical Society of America B: Optical Physics | Year: 2012
Nanoporous gold films are prepared using a dealloying method and form a sponge type bicontinuous network. As the structure sizes are below 50 nm, the material forms an effective medium with a negative dielectric constant for near infrared light. The dispersion relation of the propagating surface plasmons on the air/nanoporous gold interface is determined from reflection measurements in the Kretschmann configuration. A characteristic red-shift by ca. 0.85 eV compared to surface plasmons on solid gold layers is observed. The results are compared with calculated dispersion relations applying the Bruggeman effective medium theory for the nanoporous gold films. © 2012 Optical Society of America.
Bose P.,Martin Luther University of Halle Wittenberg |
Bose P.,International Max Planck Research |
Zahn P.,Martin Luther University of Halle Wittenberg |
Henk J.,Max Planck Institute of Microstructure Physics |
And 2 more authors.
Physical Review B - Condensed Matter and Materials Physics | Year: 2010
We report on systematic ab initio investigations of Co and Cr interlayers embedded in Fe(001)/MgO/Fe(001) magnetic tunnel junctions, focusing on the changes in the electronic structure and the transport properties with interlayer thickness. The results of spin-dependent ballistic transport calculations reveal options to specifically manipulate the tunnel magnetoresistance ratio. The resistance-area products and the tunnel magnetoresistance ratios show a monotonous trend with distinct oscillations as a function of the Cr thickness. These modulations are directly addressed and interpreted by means of magnetic structures in the Cr films and by complex band-structure effects. The characteristics for embedded Co interlayers are considerably influenced by interface resonances which are analyzed by the local electronic structure. © 2010 The American Physical Society.
Saka S.K.,Sensory Medical |
Saka S.K.,International Max Planck Research |
Honigmann A.,Max Planck Institute for Biophysical Chemistry |
Eggeling C.,Weatherall Institute of Molecular Medicine |
And 3 more authors.
Nature Communications | Year: 2014
Most proteins have uneven distributions in the plasma membrane. Broadly speaking, this may be caused by mechanisms specific to each protein, or may be a consequence of a general pattern that affects the distribution of all membrane proteins. The latter hypothesis has been difficult to test in the past. Here, we introduce several approaches based on click chemistry, through which we study the distribution of membrane proteins in living cells, as well as in membrane sheets. We found that the plasma membrane proteins form multi-protein assemblies that are long lived (minutes), and in which protein diffusion is restricted. The formation of the assemblies is dependent on cholesterol. They are separated and anchored by the actin cytoskeleton. Specific proteins are preferentially located in different regions of the assemblies, from their cores to their edges. We conclude that the assemblies constitute a basic mesoscale feature of the membrane, which affects the patterning of most membrane proteins, and possibly also their activity. © 2014 Macmillan Publishers Limited.
Fischer N.,Max Planck Institute for Meteorology |
Fischer N.,International Max Planck Research |
Jungclaus J.H.,Max Planck Institute for Meteorology
Climate of the Past | Year: 2011
Changes in the Earth's orbit lead to changes in the seasonal and meridional distribution of insolation. We quantify the influence of orbitally induced changes on the seasonal temperature cycle in a transient simulation of the last 6000 years - from the mid-Holocene to today - using a coupled atmosphere-ocean general circulation model (ECHAM5/MPI-OM) including a land surface model (JSBACH). The seasonal temperature cycle responds directly to the insolation changes almost everywhere. In the Northern Hemisphere, its amplitude decreases according to an increase in winter insolation and a decrease in summer insolation. In the Southern Hemisphere, the opposite is true. Over the Arctic Ocean, decreasing summer insolation leads to an increase in sea-ice cover. The insulating effect of sea ice between the ocean and the atmosphere leads to decreasing heat flux and favors more "continental" conditions over the Arctic Ocean in winter, resulting in strongly decreasing temperatures. Consequently, there are two competing effects: the direct response to insolation changes and a sea-ice insulation effect. The sea-ice insulation effect is stronger, and thus an increase in the amplitude of the seasonal temperature cycle over the Arctic Ocean occurs. This increase is strongest over the Barents Shelf and influences the temperature response over northern Europe. We compare our modeled seasonal temperatures over Europe to paleo reconstructions. We find better agreements in winter temperatures than in summer temperatures and better agreements in northern Europe than in southern Europe, since the model does not reproduce the southern European Holocene summer cooling inferred from the paleo reconstructions. The temperature reconstructions for northern Europe support the notion of the influence of the sea-ice insulation effect on the evolution of the seasonal temperature cycle. © 2011 Author(s).
Krapp M.,Max Planck Institute For Meteorologie |
Krapp M.,International Max Planck Research |
Jungclaus J.H.,Max Planck Institute For Meteorologie
Climate of the Past | Year: 2011
We present simulations with a coupled atmosphere-ocean-biosphere model for the Middle Miocene 15 million years ago. The model is insofar more consistent than previous models because it captures the essential interactions between ocean and atmosphere and between atmosphere and vegetation. The Middle Miocene topography, which alters both large-scale ocean and atmospheric circulations, causes a global warming of 0.7 K compared to present day. Higher than present-day CO 2 levels of 480 and 720 ppm cause a global warming of 2.8 and 4.9 K. The associated water vapour feedback enhances the greenhouse effect which leads to a polar amplification of the warming. These results suggest that higher than present-day CO 2 levels are necessary to drive the warm Middle Miocene climate, also because the dynamic vegetation model simulates a denser vegetation which is in line with fossil records. However, we do not find a flatter than present-day equator-to-pole temperature gradient as has been suggested by marine and terrestrial proxies. Instead, a compensation between atmospheric and ocean heat transport counteracts the flattening of the temperature gradient. The acclaimed role of the large-scale ocean circulation in redistributing heat cannot be supported by our results. Including full ocean dynamics, therefore, does not solve the problem of the flat temperature gradient during the Middle Miocene. © 2011 Author(s).
Goessling H.F.,Max Planck Institute for Meteorology |
Goessling H.F.,International Max Planck Research |
Reick C.H.,Max Planck Institute for Meteorology
Hydrology and Earth System Sciences | Year: 2011
Moisture recycling estimates are diagnostic measures that could ideally be used to deduce the response of precipitation to modified land-evaporation. Recycling estimates are based on moisture-budget considerations in which water is treated as a passive tracer. But in reality water is a thermodynamically active component of the atmosphere. Accordingly, recycling estimates are applicable to deduce the response to a perturbation only if other mechanisms by which evaporation affects climate do not dominate the response-a condition that has not received sufficient attention in the literature. In our analysis of what moisture recycling estimates tell us, we discuss two such additional mechanisms that result from water's active role. These are (I) local coupling, by which precipitation is affected locally via the thermal structure of the atmosphere, and (II) the atmospheric circulation, by which precipitation is affected on a large spatial scale. We perform two global climate model experiments: One with and another without continental evaporation. By this extreme perturbation we test the predictive utility of a certain type of recycling measure, the "continental recycling ratio". Moreover, by such a strong perturbation the whole spectrum of possible responses shows up simultaneously, giving us the opportunity to discuss all concurrent mechanisms jointly. The response to this extreme perturbation largely disagrees with the hypothesis that moisture recycling is the dominant mechanism. Instead, most of the response can be attributed to changes in the atmospheric circulation, while the contributions to the response by moisture recycling as well as local coupling, though noticeable, are smaller. By our case study it is not possible to give a general answer to the question posed in the title, but it demonstrates that recycling estimates do not necessarily mirror the consequences of land-use change for precipitation. © 2011 Author(s).
Barkauskaite E.,Paterson Institute for Cancer Research |
Jankevicius G.,Ludwig Maximilians University of Munich |
Ladurner A.G.,Ludwig Maximilians University of Munich |
Ladurner A.G.,International Max Planck Research |
And 3 more authors.
FEBS Journal | Year: 2013
Poly(ADP-ribosyl)ation is involved in the regulation of a variety of cellular pathways, including, but not limited to, transcription, chromatin, DNA damage and other stress signalling. Similar to other tightly regulated post-translational modifications, poly(ADP-ribosyl)ation employs 'writers', 'readers' and 'erasers' to confer regulatory functions. The generation of poly(ADP-ribose) is catalyzed by poly(ADP-ribose) polymerase enzymes, which use NAD+ as a cofactor to sequentially transfer ADP-ribose units generating long polymers, which, in turn, can affect protein function or serve as a recruitment platform for additional factors. Historically, research has focused on poly(ADP-ribose) generation pathways, with knowledge about PAR recognition and degradation lagging behind. Over recent years, several discoveries have significantly furthered our understanding of poly(ADP-ribose) recognition and, even more so, of poly(ADP-ribose) degradation. In this review, we summarize current knowledge about the protein modules recognizing poly(ADP-ribose) and discuss the newest developments on the complete reversibility of poly(ADP-ribosyl)ation. Poly(ADP-ribosyl)ation is an evolutionary conserved dynamic post-translational modification involved in a variety of biological functions. Poly(ADP-ribose) has a short half-life and the cellular levels of poly(ADP-ribose) are tightly regulated by both its production and degradation. In this review, we discuss the current knowledge of the protein modules that recognize poly(ADP-ribose) and summarize the newest developments on the degradation of poly(ADP-ribose). © 2013 FEBS.
Voigt A.,Max Planck Institute for Meteorology |
Voigt A.,International Max Planck Research |
Abbot D.S.,University of Chicago |
Pierrehumbert R.T.,University of Chicago |
Marotzke J.,Max Planck Institute for Meteorology
Climate of the Past | Year: 2011
We study the initiation of a Marinoan Snowball Earth (∼635 million years before present) with the state-of-the-art atmosphere-ocean general circulation model ECHAM5/MPI-OM. This is the most sophisticated model ever applied to Snowball initiation. A comparison with a pre-industrial control climate shows that the change of surface boundary conditions from present-day to Marinoan, including a shift of continents to low latitudes, induces a global-mean cooling of 4.6 K. Two thirds of this cooling can be attributed to increased planetary albedo, the remaining one third to a weaker greenhouse effect. The Marinoan Snowball Earth bifurcation point for pre-industrial atmospheric carbon dioxide is between 95.5 and 96% of the present-day total solar irradiance (TSI), whereas a previous study with the same model found that it was between 91 and 94% for present-day surface boundary conditions. A Snowball Earth for TSI set to its Marinoan value (94% of the present-day TSI) is prevented by doubling carbon dioxide with respect to its pre-industrial level. A zero-dimensional energy balance model is used to predict the Snowball Earth bifurcation point from only the equilibrium global-mean ocean potential temperature for present-day TSI. We do not find stable states with sea-ice cover above 55%, and land conditions are such that glaciers could not grow with sea-ice cover of 55%. Therefore, none of our simulations qualifies as a "slushball" solution. While uncertainties in important processes and parameters such as clouds and sea-ice albedo suggest that the Snowball Earth bifurcation point differs between climate models, our results contradict previous findings that Snowball Earth initiation would require much stronger forcings. © Author(s) 2011.