@article{ZhangChenSiemiatkowskaetal.2020, author = {Zhang, Youjun and Chen, Moxian and Siemiatkowska, Beata and Toleco, Mitchell Rey and Jing, Yue and Strotmann, Vivien and Zhang, Jianghua and Stahl, Yvonne and Fernie, Alisdair R.}, title = {A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species}, series = {Plant Communications}, volume = {1}, journal = {Plant Communications}, number = {5}, publisher = {Science Direct}, address = {New York}, issn = {2590-3462}, pages = {12}, year = {2020}, abstract = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.}, language = {en} } @article{WangHerzschuhLiuetal.2014, author = {Wang, Yongbo and Herzschuh, Ulrike and Liu, Xingqi and Korup, Oliver and Diekmann, Bernhard}, title = {A high-resolution sedimentary archive from landslide-dammed Lake Mengda, north-eastern Tibetan Plateau}, series = {Journal of paleolimnolog}, volume = {51}, journal = {Journal of paleolimnolog}, number = {2}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2728}, doi = {10.1007/s10933-012-9666-6}, pages = {303 -- 312}, year = {2014}, abstract = {Lacustrine sediments have been widely used to investigate past climatic and environmental changes on millennial to seasonal time scales. Sedimentary archives of lakes in mountainous regions may also record non-climatic events such as earthquakes. We argue herein that a set of 64 annual laminae couplets reconciles a stratigraphically inconsistent accelerator mass spectrometry (AMS) C-14 chronology in a similar to 4-m-long sediment core from Lake Mengda, in the north-eastern Tibetan Plateau. The laminations suggest the lake was formed by a large landslide, triggered by the 1927 Gulang earthquake (M = 8.0). The lake sediment sequence can be separated into three units based on lithologic, sedimentary, and isotopic characteristics. Starting from the bottom of the sequence, these are: (1) unweathered, coarse, sandy valley-floor deposits or landslide debris that pre-date the lake, (2) landslide-induced, fine-grained soil or reworked landslide debris with a high organic content, and (3) lacustrine sediments with low organic content and laminations. These annual laminations provide a high-resolution record of anthropogenic and environmental changes during the twentieth century, recording enhanced sediment input associated with two phases of construction activities. The high mean sedimentation rates of up to 4.8 mm year(-1) underscore the potential for reconstructing such distinct sediment pulses in remote, forested, and seemingly undisturbed mountain catchments.}, language = {en} } @article{NordBoudevillainBerneetal.2017, author = {Nord, Guillaume and Boudevillain, Brice and Berne, Alexis and Branger, Flora and Braud, Isabelle and Dramais, Guillaume and Gerard, Simon and Le Coz, Jerome and Legout, Cedric and Molinie, Gilles and Van Baelen, Joel and Vandervaere, Jean-Pierre and Andrieu, Julien and Aubert, Coralie and Calianno, Martin and Delrieu, Guy and Grazioli, Jacopo and Hachani, Sahar and Horner, Ivan and Huza, Jessica and Le Boursicaud, Raphael and Raupach, Timothy H. and Teuling, Adriaan J. and Uber, Magdalena and Vincendon, Beatrice and Wijbrans, Annette}, title = {A high space-time resolution dataset linking meteorological forcing and hydro-sedimentary response in a mesoscale Mediterranean catchment (Auzon) of the Ardeche region, France}, series = {Earth System Science Data}, volume = {9}, journal = {Earth System Science Data}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1866-3508}, doi = {10.5194/essd-9-221-2017}, pages = {29}, year = {2017}, abstract = {A comprehensive hydrometeorological dataset is presented spanning the period 1 January 201131 December 2014 to improve the understanding of the hydrological processes leading to flash floods and the relation between rainfall, runoff, erosion and sediment transport in a mesoscale catchment (Auzon, 116 km(2)) of the Mediterranean region. Badlands are present in the Auzon catchment and well connected to high-gradient channels of bedrock rivers which promotes the transfer of suspended solids downstream. The number of observed variables, the various sensors involved (both in situ and remote) and the space-time resolution (similar to km(2), similar to min) of this comprehensive dataset make it a unique contribution to research communities focused on hydrometeorology, surface hydrology and erosion. Given that rainfall is highly variable in space and time in this region, the observation system enables assessment of the hydrological response to rainfall fields. Indeed, (i) rainfall data are provided by rain gauges (both a research network of 21 rain gauges with a 5 min time step and an operational network of 10 rain gauges with a 5 min or 1 h time step), S-band Doppler dual-polarization radars (1 km(2), 5 min resolution), disdrometers (16 sensors working at 30 s or 1 min time step) and Micro Rain Radars (5 sensors, 100m height resolution). Additionally, during the special observation period (SOP-1) of the HyMeX (Hydrological Cycle in the Mediterranean Experiment) project, two X-band radars provided precipitation measurements at very fine spatial and temporal scales (1 ha, 5 min). (ii) Other meteorological data are taken from the operational surface weather observation stations of Meteo-France (including 2m air temperature, atmospheric pressure, 2 m relative humidity, 10m wind speed and direction, global radiation) at the hourly time resolution (six stations in the region of interest). (iii) The monitoring of surface hydrology and suspended sediment is multi-scale and based on nested catchments. Three hydrometric stations estimate water discharge at a 2-10 min time resolution. Two of these stations also measure additional physico-chemical variables (turbidity, temperature, conductivity) and water samples are collected automatically during floods, allowing further geochemical characterization of water and suspended solids. Two experimental plots monitor overland flow and erosion at 1 min time resolution on a hillslope with vineyard. A network of 11 sensors installed in the intermittent hydrographic network continuously measures water level and water temperature in headwater subcatchments (from 0.17 to 116 km(2)) at a time resolution of 2-5 min. A network of soil moisture sensors enables the continuous measurement of soil volumetric water content at 20 min time resolution at 9 sites. Additionally, concomitant observations (soil moisture measurements and stream gauging) were performed during floods between 2012 and 2014. Finally, this dataset is considered appropriate for understanding the rainfall variability in time and space at fine scales, improving areal rainfall estimations and progressing in distributed hydrological and erosion modelling.}, language = {en} } @article{PenaHamannRuizetal.2004, author = {Pena, M. and Hamann, Wolf-Rainer and Ruiz, M. T. and Peimbert, A. and Peimbert, M.}, title = {A high resolution spectroscopic study of the extraordinary planetary nebula LMC-N66}, year = {2004}, abstract = {The planetary nebula N66 in the Large Magellanic Cloud is an extraordinary object, as it is the only confirmed PN where the central star is a Wolf-Rayet star of the nitrogen sequence, i.e. of type [WN]. Moreover, the star showed a dramatic brightness outburst in 1993-1994. In a previous paper (Hamann et al. 2003) we analyzed the changing stellar spectra and found evidence that the central star is most likely a binary system where a white dwarf presently accretes matter from a non-degenerate companion at a high rate. Thus the object is a candidate for a future type Ia supernova in our cosmic neighborhood. In the present paper we analyze the morphology and kinematics of the nebula, using images and high-resolution spectra obtained with the Hubble Space Telescope (HST) and the Very Large Telescope (ESO-VLT). The object presents a complex multipolar structure, dominated by very bright lobes located at both sides of the central star and separated by a narrow waist. In addition there is a pair of very extended and twisted loops, also pointing in opposite directions; their symmetry axis and collimation angle differs from those of the bright lobes. High resolution spectroscopy reveals two main velocity components, "approaching" material at an average heliocentric radial velocity Of V-rad = 248 30 km s(-1) and similarly bright "receding" material at V-rad = 331 +/- 25 km s(-1). A systemic velocity of about 300 km s(-1) is derived. Opposite lobes and loops possess opposite velocities. Furthermore there are knots and filaments of complex structure and kinematics. Close to the central star, nebular gas is found, receding at very high velocity (125 km s(-1) relative to the system). The morphology and kinematics of LMC-N66 can be explained as the result of episodic bipolar ejections with changing axis. The bipolar structures could have been produced by collimated streams ejected from a precessing central source. We suggest that the precession could have been produced by an external torque, possibly due to a binary companion. Young, fast-moving nebular knots close to the star appear slightly He- and N-richer than the main body of the nebula, but are still hydrogen-rich in contrast to the helium-dominated atmosphere of the [WN]- type central star. In the binary scenario, this nebular matter must have been accreted from the non-degenerate companion and re-ejected before it was fully burnt}, language = {en} } @article{KlingSchneidenbachSchnor2005, author = {Kling, Christoph and Schneidenbach, Lars and Schnor, Bettina}, title = {A high performance gigabit ethernet messaging method for PVFS}, isbn = {0-88986-525-6}, year = {2005}, abstract = {Parallel File Systems like PVFS2 are a necessary compo nent for high-performance computing. The design of ef ;cient communication layers for these systems is still of great research interest. This paper presents a low- latency messaging method for PVFS2 dedicated for Gigabit Ether net networks and discusses relevant design issues. In con trast to other approaches, we argue that zero-copying can be achieved also for big messages without use of a rendez vous protocol. Further, ef;ciency within the communica tion layer like a small call stack plays an important role.}, language = {en} } @article{Fischer2012, author = {Fischer, Martin H.}, title = {A hierarchical view of grounded, embodied, and situated numerical cognition}, series = {Cognitive processing : international quarterly of cognitive science}, volume = {13}, journal = {Cognitive processing : international quarterly of cognitive science}, publisher = {Springer}, address = {Heidelberg}, issn = {1612-4782}, doi = {10.1007/s10339-012-0477-5}, pages = {S161 -- S164}, year = {2012}, abstract = {There is much recent interest in the idea that we represent our knowledge together with the sensory and motor features that were activated during its acquisition. This paper reviews the evidence for such "embodiment" in the domain of numerical cognition, a traditional stronghold of abstract theories of knowledge representation. The focus is on spatial-numerical associations, such as the SNARC effect (small numbers are associated with left space, larger numbers with right space). Using empirical evidence from behavioral research, I first describe sensory and motor biases induced by SNARC, thus identifying numbers as embodied concepts. Next, I propose a hierarchical relationship between grounded, embodied, and situated aspects of number knowledge. This hierarchical conceptualization helps to understand the variety of SNARC-related findings and yields testable predictions about numerical cognition. I report several such tests, ranging from cross-cultural comparisons of horizontal and vertical SNARC effects (Shaki and Fischer in J Exp Psychol Hum Percept Perform 38(3): 804-809, 2012) to motor cortical activation studies in adults with left- and right-hand counting preferences (Tschentscher et al. in NeuroImage 59: 3139-3148, 2012). It is concluded that the diagnostic features for each level of the proposed hierarchical knowledge representation, together with the spatial associations of numbers, make the domain of numerical knowledge an ideal testing ground for embodied cognition research.}, language = {en} } @article{ChengHartmannGuptaetal.2009, author = {Cheng, Fuxia and Hartmann, Stefanie and Gupta, Mayetri and Ibrahim, Joseph G. and Vision, Todd J.}, title = {A hierarchical model for incomplete alignments in phylogenetic inference}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btp015}, year = {2009}, abstract = {Motivation: Full-length DNA and protein sequences that span the entire length of a gene are ideally used for multiple sequence alignments (MSAs) and the subsequent inference of their relationships. Frequently, however, MSAs contain a substantial amount of missing data. For example, expressed sequence tags (ESTs), which are partial sequences of expressed genes, are the predominant source of sequence data for many organisms. The patterns of missing data typical for EST-derived alignments greatly compromise the accuracy of estimated phylogenies. Results: We present a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data. We propose a class of hierarchical models for modeling pairwise distances between the sequences, and develop a fully Bayesian approach for estimation of the model parameters. Once the distance matrix is estimated, the phylogenetic tree may be constructed by applying neighbor-joining (or any other algorithm of choice). We also show that maximizing the marginal likelihood from the Bayesian approach yields similar results to a pro. le likelihood estimation. The proposed methods are illustrated using simulated protein families, for which the true phylogeny is known, and one real protein family.}, language = {en} } @article{FischerWertherBouaklineetal.2020, author = {Fischer, Eric W. and Werther, Michael and Bouakline, Foudhil and Saalfrank, Peter}, title = {A hierarchical effective mode approach to phonon-driven multilevel vibrational relaxation dynamics at surfaces}, series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistry}, volume = {153}, journal = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistry}, number = {6}, publisher = {American Institute of Physics}, address = {Melville}, issn = {0021-9606}, doi = {10.1063/5.0017716}, pages = {15}, year = {2020}, abstract = {We discuss an efficient Hierarchical Effective Mode (HEM) representation of a high-dimensional harmonic oscillator bath, which describes phonon-driven vibrational relaxation of an adsorbate-surface system, namely, deuterium adsorbed on Si(100). Starting from the original Hamiltonian of the adsorbate-surface system, the HEM representation is constructed via iterative orthogonal transformations, which are efficiently implemented with Householder matrices. The detailed description of the HEM representation and its construction are given in the second quantization representation. The hierarchical nature of this representation allows access to the exact quantum dynamics of the adsorbate-surface system over finite time intervals, controllable via the truncation order of the hierarchy. To study the convergence properties of the effective mode representation, we solve the time-dependent Schrodinger equation of the truncated system-bath HEM Hamiltonian, with the help of the multilayer extension of the Multiconfigurational Time-Dependent Hartree (ML-MCTDH) method. The results of the HEM representation are compared with those obtained with a quantum-mechanical tier-model. The convergence of the HEM representation with respect to the truncation order of the hierarchy is discussed for different initial conditions of the adsorbate-surface system. The combination of the HEM representation with the ML-MCTDH method provides information on the time evolution of the system (adsorbate) and multiple effective modes of the bath (surface). This permits insight into mechanisms of vibration-phonon coupling of the adsorbate-surface system, as well as inter-mode couplings of the effective bath.}, language = {en} } @article{Strohe1998, author = {Strohe, Hans Gerhard}, title = {A heuristic partial-least-squares approach to estimating dynamic path models}, series = {Classification, Data Analysis, and Data Highways}, journal = {Classification, Data Analysis, and Data Highways}, publisher = {Springer}, address = {Berlin, Heidelberg}, isbn = {3-540-63909-8}, doi = {10.1007/978-3-642-72087-1}, year = {1998}, language = {en} } @article{KatterleHolzwarthJesorka2006, author = {Katterle, Martin and Holzwarth, Alfred R. and Jesorka, Aldo}, title = {A Heck-type coupling for the synthesis of novel bridged metallochlorin-fullerene C-60 dyads}, issn = {1434-193X}, doi = {10.1002/ejoc.200500494}, year = {2006}, abstract = {A short and convenient synthesis of metallochlorin-C-60 dyads based on a Heck-type hetero coupling at the 3(2) position of a chlorin is described. p-Bromobenzaldehyde was treated with Zn-metalated 13(2)- demethoxycarbonylmethylpheophorbide a, using a palladium acetate/LiCl catalyst mixture under phase-transfer conditions in DMF at 70 degrees C. The resulting asymmetric olefin was obtained in a high trans/cis ratio. The desired trans isomer was separated and subsequently transformed into a donor-acceptor dyad by a 1,3-dipolar cycloaddition to C-60 in the presence of sarcosine in refluxing toluene. The resulting dyads are expected to undergo efficient photoinduced electron transfer and can potentially be utilized in solar energy conversion devices.}, language = {en} }