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We present the Neural-network-based Upper hybrid Resonance Determination (NURD) algorithm for automatic inference of the electron number density from plasma wave measurements made on board NASA's Van Allen Probes mission. A feedforward neural network is developed to determine the upper hybrid resonance frequency, fuhr, from electric field measurements, which is then used to calculate the electron number density. In previous missions, the plasma resonance bands were manually identified, and there have been few attempts to do robust, routine automated detections. We describe the design and implementation of the algorithm and perform an initial analysis of the resulting electron number density distribution obtained by applying NURD to 2.5 years of data collected with the Electric and Magnetic Field Instrument Suite and Integrated Science (EMFISIS) instrumentation suite of the Van Allen Probes mission. Densities obtained by NURD are compared to those obtained by another recently developed automated technique and also to an existing empirical plasmasphere and trough density model.
Investigation of the TCA cycle and glycolytic metabolons and their physiological impacts in plants
(2016)
Pollen influx (number of pollen grains cm−2 year−1) can objectively reflect the dispersal and deposition features of pollen within a certain time and space, and is often used as a basis for the quantitative reconstruction of palaeovegetation; however, little is known about the features and mechanisms of vertical dispersal of pollen. Here we present the results from a 5 year (2006–2010) monitoring program using pollen traps placed at different heights from ground level up to 60 m and surface soil samples in a mixed coniferous and deciduous broad-leaved woodland in the Changbai mountains, northeastern China. The pollen percentages and pollen influx from the traps have very similar characteristics to the highest values for Betula, Fraxinus, Quercus and Pinus, among the tree taxa and Artemisia, Chenopodiaceae and Asteraceae among the herb taxa. Pollen influx values vary significantly with height and show major differences between three distinct layers, above-canopy (≥32 m), within the trunk layer (8 ≤ 32 m) and on the ground (0 m). These differences in pollen influx are explained by differences in (i) the air flows in each of these layers and (ii) the fall speed of pollen of the various taxa. We found that the pollen recorded on the ground surface is a good representation of the major part of the pollen transported in the trunk space of the woodland. Comparison of the pollen influx values with the theoretical, calculated “characteristic pollen source area” (CPSA) of 12 selected taxa indicates that the pollen deposited on the ground surface of the woodland is a fair representation with 85–90 % of the total pollen deposited at a wind speed of 2.4 m s−1 coming from within ca. 1–5 km for Pinus and Quercus, ca. 5–10 km for Ulmus, Tilia, Oleaceae and Betula, ca. 20–40 km for Fraxinus, Poaceae, Chenopodiaceae, Populus and Salix, and ca. 30–60 km for Artemisia; it is also a good representation with 90–98 % of the total pollen deposited coming from within 60 km at a wind speed of 2.4 m s−1, or 100 km at a wind speed: 6 m s−1, for the 12 selected taxa used in the CPSA calculation. Furthermore, comparison with the vegetation map of the area around the sampling site shows that the pollen deposited on the ground represents all plant communities which grow in the study area within 70 km radius of the sampling site. In this study, the pollen percentages obtained from the soil surface samples are significantly biased towards pollen taxa with good preservation due to thick and robust pollen walls. Therefore, if mosses are available instead, soil samples should be avoided for pollen studies, in particular for the study of pollen-vegetation relationships, the estimation of pollen productivities and quantitative reconstruction of past vegetation. The results also indicate that the existing model of pollen dispersal and deposition, Prentice’s model, provides a fair description of the actual pollen dispersal and deposition in this kind of woodland, which suggests that the application of the landscape reconstruction algorithm would be relevant for reconstruction of this type of woodland in the past.
Inspired by the application of ultrasonic cavitation based mechanical force (CMF) to open small channels in natural soft materials (skin or tissue), it is explored whether an artificial polymer network can be created, in which shape-changes can be induced by CMF. This concept comprises an interconnected macroporous rhodium-phosphine (Rh-P) coordination polymer network, in which a CMF can reversibly dissociate the Rh-P microphases. In this way, the ligand exchange of Rh-P coordination bonds in the polymer network is accelerated, resulting in a topological rearrangement of molecular switches. This rearrangement of molecular switches enables the polymer network to release internal tension under ultrasound exposure, resulting in a CMF-induced shape-memory capability. The interconnected macroporous structure with thin pore walls is essential for allowing the CMF to effectively permeate throughout the polymer network. Potential applications of this CMF-induced shape-memory polymer can be mechanosensors or ultrasound controlled switches.
Тезисы
(2016)
Nowadays, working in an office environment is ubiquitous. At the same time, progressively more people suffer from occupational musculoskeletal disorders. Therefore, the aim of this pilot study was to analyse the influence of back pain on sitting behaviour in the office environment. A textile pressure mat (64-sensor-matrix) placed on the seat pan was used to identify the adopted sitting positions of 20 office workers by means of random forest classification. Additionally, two standardised questionnaires (Korff, BPI) were used to assess short and long-term back pain in order to divide the subjects into two groups (with and without back pain). Independent t-test indicated that subjects who registered back pain within the last 24 h showed a clear trend towards a more static sitting behaviour. Therefore, the developed sensor system has successfully been introduced to characterise and compare sitting behaviour of subjects with and without back pain. (C) 2016 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licensesiby-nc-nd/4.0/).
Erneuertes Gestern?
(2016)
In the reconstruction and regeneration of bone tissue, a primary goal is to initiate bone growth and to stabilize the surrounding bone. In this regard, a potentially useful component in biomaterials for bone tissue engineering is strontium, which acts as cationic active agent, triggering certain intracellular pathways and acting as so called dual action bone agent which inhibits bone resorption while stimulating bone regeneration. In this study we established a novel processing for the foaming of a polymer (poly-epsilon-caprolactone) and simultaneous chemical reaction of a mixture of calcium and strontium hydroxides to the respective carbonates using supercritical carbon dioxide. The resultant porous composite scaffold was optimized in composition and strontium content and was characterized via different spectroscopic (infrared and Raman spectroscopy, energy dispersive X-ray spectroscopy), imaging (SEM, mu CT), mechanical testing and in vitro methods (fluorescence vital staining, MTT-assay). As a result, the composite scaffold showed good in vitro biocompatibility with partly open pore structure and the expected chemistry. First mechanical testing results indicate sufficient mechanical stability to support future in vivo applications. (C) 2016 Elsevier B.V. All rights reserved.
Electrophoretic deposition was used to produce zirconia specimen consisting of alternating layers of fully stabilized cubic zirconia and partially stabilized tetragonal zirconia. In this configuration, the tetragonal stabilized zirconia layers can undergo transformation toughening upon mechanical induced stresses, while the cubic stabilized layers can act as confining element. To understand the volumetric changes due to transformation toughening in these layered materials after indentation, we used an advanced synchrotron-based X-ray mu CT setup and compared the results with surface sensitive methods like Raman spectroscopy, AFM and white light interferometry. The high spatial resolution and the adapted beam energy between the absorption edges of zirconia and yttria allowed discriminating between individual layers due to differences in their yttria content. Furthermore we were able to identify single indents and link volume changes to different physical effects in the different stabilized zirconia parts and visualize the three dimensional volume around only few micrometre sized indents. (C) 2015 Elsevier Ltd. All rights reserved.
The electrophoretic deposition process was used to produce multi-layered ceramics consisting of alternating layers of fully stabilized cubic zirconia and partially stabilized tetragonal zirconia to make use of their different mechanical behaviour, investigating the possibility to deflect advancing cracks at the interfaces of the different layers. This crack deflection is apparently impacted by a toughening mechanism only found in the tetragonal stabilized zirconia polymorph and is characterized by the stress induced transformation of the metastable tetragonal phase into the monoclinic one, which is accompanied by a volume increase resulting in a closing mechanism for advancing cracks. While improving the electrophoretic deposition process, we investigated the transformation toughening mechanism at the layer interfaces and their effect on crack propagation. Investigations involved a combination of different imaging methods, including light microscopy, white light interferometry, atomic force microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy and Raman spectroscopy. (C) 2015 Elsevier Ltd. All rights reserved.
Ionogels (IGs) based on poly(methyl methacrylate) (PMMA) and the metal-containing ionic liquids (ILs) bis-1-butyl-3-methlimidazolium tetrachloridocuprate(II), tetrachloride cobaltate(II), and tetrachlorido manganate(II) have been synthesized and their mechanical and electrical properties have been correlated with their microstructure. Unlike many previous examples, the current IGs show a decreasing stability in stress-strain experiments on increasing IL fractions. The conductivities of the current IGs are lower than those observed in similar examples in the literature. Both effects are caused by a two-phase structure with micrometer-sized IL-rich domains homogeneously dispersed an IL-deficient continuous PMMA phase. This study demonstrates that the IL-polymer miscibility and the morphology of the IGs are key parameters to control the (macroscopic) properties of IGs.
Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.
Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.
We consider the effect of global repulsive coupling on an ensemble of identical excitable elements. An increase of the coupling strength destabilizes the synchronous equilibrium and replaces it with many attracting oscillatory states, created in the transcritical heteroclinic bifurcation. The period of oscillations is inversely proportional to the distance from the critical parameter value. If the elements interact with the global field via the first Fourier harmonics of their phases, the stable equilibrium is in one step replaced by the attracting continuum of periodic motions.
Situated at the intersection of the literatures on speculative storage and non-renewable commodity scarcity, this paper considers whether changes in persistence have occurred in long-run U.S. prices of the energy commodities crude oil, natural gas and bituminous coal. We allow for a structural break when testing for a break in persistence to avoid a change in the stochastic properties of prices being confounded by an unaccounted-for deterministic shift in the price series. We find that coal prices are trend stationary throughout their evolution and that oil prices change from stationarity to non-stationarity in the decade between the late 1960s to late 1970s. The result on gas prices is ambiguous. Our results demonstrate the importance of accounting for a possible structural shift when testing for breaks in persistence, while being robust to the exact date of the structural break. Based on our analysis we caution against viewing long-run energy commodity prices as being non-stationary and conclude in favor of modeling commodity market fundamentals as stationary, meaning that speculative storage will tend to have a dampening effect on prices. We also cannot reject that long-run prices of coal and, with some hesitation, gas follow a Hotelling-type rule. In contrast, we reject the Hotelling rule for oil prices since the late 1960s/early 1970s. (C) 2016 Elsevier B.V. All rights reserved.
Aphasia, the language disorder following brain damage, is frequently accompanied by deficits of working memory (WM) and executive functions (EFs). Recent studies suggest that WM, together with certain EFs, can play a role in sentence comprehension in individuals with aphasia (IWA), and that WM can be enhanced with intensive practice. Our aim was to investigate whether a combined WM and EF training improves the understanding of spoken sentences in IWA. We used a pre-post-test case control design. Three individuals with chronic aphasia practised an adaptive training task (a modified n-back task) three to four times a week for a month. Their performance was assessed before and after the training on outcome measures related to WM and spoken sentence comprehension. One participant showed significant improvement on the training task, another showed a tendency for improvement, and both of them improved significantly in spoken sentence comprehension. The third participant did not improve on the training task, however, she showed improvement on one measure of spoken sentence comprehension. Compared to controls, two individuals improved at least in one condition of the WM outcome measures. Thus, our results suggest that a combined WM and EF training can be beneficial for IWA.
Metal-containing ionic liquids (ILs) are of interest for a variety of technical applications, e.g., particle synthesis and materials with magnetic or thermochromic properties. In this paper we report the synthesis of, and two structures for, some new tetrabromidocuprates(II) with several “onium” cations in comparison to the results of electron paramagnetic resonance (EPR) spectroscopic analyses. The sterically demanding cations were used to separate the paramagnetic Cu(II) ions for EPR measurements. The EPR hyperfine structure in the spectra of these new compounds is not resolved, due to the line broadening resulting from magnetic exchange between the still-incomplete separated paramagnetic Cu(II) centres. For the majority of compounds, the principal g values (g|| and gK) of the tensors could be determined and information on the structural changes in the [CuBr4]2- anions can be obtained. The complexes have high potential, e.g., as ionic liquids, as precursors for the synthesis of copper bromide particles, as catalytically active or paramagnetic ionic liquids.
Metal-containing ionic liquids (ILs) are of interest for a variety of technical applications, e.g., particle synthesis and materials with magnetic or thermochromic properties. In this paper we report the synthesis of, and two structures for, some new tetrabromidocuprates(II) with several “onium” cations in comparison to the results of electron paramagnetic resonance (EPR) spectroscopic analyses. The sterically demanding cations were used to separate the paramagnetic Cu(II) ions for EPR measurements. The EPR hyperfine structure in the spectra of these new compounds is not resolved, due to the line broadening resulting from magnetic exchange between the still-incomplete separated paramagnetic Cu(II) centres. For the majority of compounds, the principal g values (g|| and gK) of the tensors could be determined and information on the structural changes in the [CuBr4]2- anions can be obtained. The complexes have high potential, e.g., as ionic liquids, as precursors for the synthesis of copper bromide particles, as catalytically active or paramagnetic ionic liquids.
Metal-containing ionic liquids (ILs) are of interest for a variety of technical applications, e.g., particle synthesis and materials with magnetic or thermochromic properties. In this paper we report the synthesis of, and two structures for, some new tetrabromidocuprates(II) with several "onium" cations in comparison to the results of electron paramagnetic resonance (EPR) spectroscopic analyses. The sterically demanding cations were used to separate the paramagnetic Cu(II) ions for EPR measurements. The EPR hyperfine structure in the spectra of these new compounds is not resolved, due to the line broadening resulting from magnetic exchange between the still-incomplete separated paramagnetic Cu(II) centres. For the majority of compounds, the principal g values (g|| and g(perpendicular to)) of the tensors could be determined and information on the structural changes in the [CuBr4](2-) anions can be obtained. The complexes have high potential, e.g., as ionic liquids, as precursors for the synthesis of copper bromide particles, as catalytically active or paramagnetic ionic liquids.
Der junge Habermas
(2016)
Roman Yos' Untersuchung über die Ursprünge eines der einflussreichsten Werke der jüngeren Geistesgeschichte zeigt auf originelle Weise, wie Jürgen Habermas seine bereits in jungen Jahren ausgeprägten philosophisch-politischen Denkmotive allmählich in die Bahnen eines tragfähigen Systems überführte. Diese Entwicklung lässt sich als ein Lernprozess begreifen, in dessen Verlauf konträre intellektuelle Einflüsse aufeinandertrafen und der aufwändigen Vermittlung bedurften. Yos rekonstruiert die spannungsreiche Entstehung von Habermas‘ Denken aus dem Zusammenhang frühester Schriften und gibt zugleich einen Einblick in deren zeit- und ideengeschichtliche Hintergründe.
A new view of Ecuador's complex geodynamics has been developed in the course of modeling seismic source zones for probabilistic seismic hazard analysis. This study focuses on two aspects of the plates' interaction at a continental scale: (a) age-related differences in rheology between Farallon and Nazca plates—marked by the Grijalva rifted margin and its inland projection—as they subduct underneath central Ecuador, and (b) the rapidly changing convergence obliquity resulting from the convex shape of the South American northwestern continental margin. Both conditions satisfactorily explain several characteristics of the observed seismicity and of the interseismic coupling. Intermediate-depth seismicity reveals a severe flexure in the Farallon slab as it dips and contorts at depth, originating the El Puyo seismic cluster. The two slabs position and geometry below continental Ecuador also correlate with surface expressions observable in the local and regional geology and tectonics. The interseismic coupling is weak and shallow south of the Grijalva rifted margin and increases northward, with a heterogeneous pattern locally associated to the Carnegie ridge subduction. High convergence obliquity is responsible for the North Andean Block northeastward movement along localized fault systems. The Cosanga and Pallatanga fault segments of the North Andean Block-South American boundary concentrate most of the seismic moment release in continental Ecuador. Other inner block faults located along the western border of the inter-Andean Depression also show a high rate of moderate-size earthquake production. Finally, a total of 19 seismic source zones were modeled in accordance with the proposed geodynamic and neotectonic scheme.
A new electrochemical MIP sensor for the most frequently used drug paracetamol (PAR) was prepared by electropolymerization of mixtures containing the template molecule and the functional monomers ophenylenediamine, resorcinol and aniline. The imprinting factor of 12 reflects the effective target binding to the MIP as compared with the non-imprinted electropolymer. Combination of the MIP with a nonspecific esterase allows the measurement of phenacetin - another analgesic drug. In the second approach the PAR containing sample solution was pretreated with tyrosinase in order to prevent electrochemical interferences by ascorbic acid and uric acid. Interference-free indication at a very low electrode potential without fouling of the electrode surface was achieved with the o-phenylenediamine: resorcinol-based MIP.
We present results on ultrafast gas electron diffraction (UGED) experiments with femtosecond resolution using the MeV electron gun at SLAC National Accelerator Laboratory. UGED is a promising method to investigate molecular dynamics in the gas phase because electron pulses can probe the structure with a high spatial resolution. Until recently, however, it was not possible for UGED to reach the relevant timescale for the motion of the nuclei during a molecular reaction. Using MeV electron pulses has allowed us to overcome the main challenges in reaching femtosecond resolution, namely delivering short electron pulses on a gas target, overcoming the effect of velocity mismatch between pump laser pulses and the probe electron pulses, and maintaining a low timing jitter. At electron kinetic energies above 3 MeV, the velocity mismatch between laser and electron pulses becomes negligible. The relativistic electrons are also less susceptible to temporal broadening due to the Coulomb force. One of the challenges of diffraction with relativistic electrons is that the small de Broglie wavelength results in very small diffraction angles. In this paper we describe the new setup and its characterization, including capturing static diffraction patterns of molecules in the gas phase, finding time-zero with sub-picosecond accuracy and first time-resolved diffraction experiments. The new device can achieve a temporal resolution of 100 fs root-mean-square, and sub-angstrom spatial resolution. The collimation of the beam is sufficient to measure the diffraction pattern, and the transverse coherence is on the order of 2 nm. Currently, the temporal resolution is limited both by the pulse duration of the electron pulse on target and by the timing jitter, while the spatial resolution is limited by the average electron beam current and the signal-to-noise ratio of the detection system. We also discuss plans for improving both the temporal resolution and the spatial resolution.
Imaging changes in molecular geometries on their natural femtosecond timescale with sub-Angstrom spatial precision is one of the critical challenges in the chemical sciences, as the nuclear geometry changes determine the molecular reactivity. For photoexcited molecules, the nuclear dynamics determine the photoenergy conversion path and efficiency. Here we report a gas-phase electron diffraction experiment using megaelectronvolt (MeV) electrons, where we captured the rotational wavepacket dynamics of nonadiabatically laser-aligned nitrogen molecules. We achieved a combination of 100 fs root-mean-squared temporal resolution and sub-Angstrom (0.76 angstrom) spatial resolution that makes it possible to resolve the position of the nuclei within the molecule. In addition, the diffraction patterns reveal the angular distribution of the molecules, which changes from prolate (aligned) to oblate (anti-aligned) in 300 fs. Our results demonstrate a significant and promising step towards making atomically resolved movies of molecular reactions.
We present results on ultrafast gas electron diffraction (UGED) experiments with femtosecond resolution using the MeV electron gun at SLAC National Accelerator Laboratory. UGED is a promising method to investigate molecular dynamics in the gas phase because electron pulses can probe the structure with a high spatial resolution. Until recently, however, it was not possible for UGED to reach the relevant timescale for the motion of the nuclei during a molecular reaction. Using MeV electron pulses has allowed us to overcome the main challenges in reaching femtosecond resolution, namely delivering short electron pulses on a gas target, overcoming the effect of velocity mismatch between pump laser pulses and the probe electron pulses, and maintaining a low timing jitter. At electron kinetic energies above 3 MeV, the velocity mismatch between laser and electron pulses becomes negligible. The relativistic electrons are also less susceptible to temporal broadening due to the Coulomb force. One of the challenges of diffraction with relativistic electrons is that the small de Broglie wavelength results in very small diffraction angles. In this paper we describe the new setup and its characterization, including capturing static diffraction patterns of molecules in the gas phase, finding time-zero with sub-picosecond accuracy and first time-resolved diffraction experiments. The new device can achieve a temporal resolution of 100 fs root-mean-square, and sub-angstrom spatial resolution. The collimation of the beam is sufficient to measure the diffraction pattern, and the transverse coherence is on the order of 2 nm. Currently, the temporal resolution is limited both by the pulse duration of the electron pulse on target and by the timing jitter, while the spatial resolution is limited by the average electron beam current and the signal-to-noise ratio of the detection system. We also discuss plans for improving both the temporal resolution and the spatial resolution.
Observing the motion of the nuclear wave packets during a molecular reaction, in both space and time, is crucial for understanding and controlling the outcome of photoinduced chemical reactions. We have imaged the motion of a vibrational wave packet in isolated iodine molecules using ultrafast electron diffraction with relativistic electrons. The time-varying interatomic distance was measured with a precision 0.07 angstrom and temporal resolution of 230 fs full width at half maximum. The method is not only sensitive to the position but also the shape of the nuclear wave packet.
Background
The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. The possibility of introducing large fragment deletions by RNA-guided Cas9 tool provides the potential to study the function of any DNA region of interest in its ‘endogenous’ environment.
Results
Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable large-fragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 % decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression.
Conclusions
Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants.
Results: Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable large-fragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 % decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression. Conclusions: Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants.
Flower development is a model system to understand organ specification in plants. The identities of different types of floral organs are specified by homeotic MADS transcription factors that interact in a combinatorial fashion. Systematic identification of DNA-binding sites and target genes of these key regulators show that they have shared and unique sets of target genes. DNA binding by MADS proteins is not based on ‘simple’ recognition of a specific DNA sequence, but depends on DNA structure and combinatorial interactions. Homeotic MADS proteins regulate gene expression via alternative mechanisms, one of which may be to modulate chromatin structure and accessibility in their target gene promoters.
Background: The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. The possibility of introducing large fragment deletions by RNA-guided Cas9 tool provides the potential to study the function of any DNA region of interest in its
‘endogenous’ environment.
Results: Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana. We demonstrate the flexibility of our system for knockout of multiple genes, and to generate heritable largefragment deletions in the genome. As a proof of concept, the function of part of the second intron of the flower development gene AGAMOUS in Arabidopsis was studied by generating a Cas9-free mutant plant line in which part of this intron was removed from the genome. Further analysis revealed that deletion of this intron fragment results 40 % decrease of AGAMOUS gene expression without changing the splicing of the gene which indicates that this regulatory region functions as an activator of AGAMOUS gene expression.
Conclusions: Our modified RNA-guided Cas9 system offers a versatile tool for the functional dissection of coding and non-coding DNA sequences in plants.
Multiblock copolymers named PCL-PIBMD consisting of crystallizable poly(epsilon-caprolactone) segments and crystallizable poly[oligo(3S-iso-butylmorpholine-2,5-dione)] segments coupled by trimethyl hexamethylene diisocyanate provide a versatile molecular architecture for achieving shape-memory effects (SMEs) in polymers. The mechanical properties as well as the SME performance of PCL-PIBMD can be tailored by the variation of physical parameters during programming such as deformation strain or applied temperature protocols. In this study, we explored the influence of applying different strain rates during programming on the resulting nanostructure of PCL-PIBMD. Programming was conducted at 50 degrees C by elongation to epsilon(m)=50% with strain rates of 1 or 10 or 50 mmmin(-1). The nanostructural changes were visualized by atomic force microscopy (AFM) measurements and investigated by in situ wide and small angle X-ray scattering experiments. With increasing the strain rate, a higher degree of orientation was observed in the amorphous domains. Simultaneously the strain-induced formation of new PIBMD crystals as well as the fragmentation of existing large PIBMD crystals occurred. The observed differences in shape fixity ratio and recovery stress of samples deformed with various strain rates can be attributed to their different nanostructures. The achieved findings can be relevant parameters for programming the shape-memory polymers with designed recovery forces. (c) 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 1935-1943
The eukaryotic-specific Isd11 is a complex- orphan protein with ability to bind the prokaryotic IscS
(2016)
The eukaryotic protein Isd11 is a chaperone that binds and stabilizes the central component of the essential metabolic pathway responsible for formation of iron-sulfur clusters in mitochondria, the desulfurase Nfs1. Little is known about the exact role of Isd11. Here, we show that human Isd11 (ISD11) is a helical protein which exists in solution as an equilibrium between monomer, dimeric and tetrameric species when in the absence of human Nfs1 (NFS1). We also show that, surprisingly, recombinant ISD11 expressed in E. coli co-purifies with the bacterial orthologue of NFS1, IscS. Binding is weak but specific suggesting that, despite the absence of Isd11 sequences in bacteria, there is enough conservation between the two desulfurases to retain a similar mode of interaction. This knowledge may inform us on the conservation of the mode of binding of Isd11 to the desulfurase. We used evolutionary evidence to suggest Isd11 residues involved in the interaction.
The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS
(2016)
The eukaryotic protein Isd11 is a chaperone that binds and stabilizes the central component of the essential metabolic pathway responsible for formation of iron-sulfur clusters in mitochondria, the desulfurase Nfs1. Little is known about the exact role of Isd11. Here, we show that human Isd11 (ISD11) is a helical protein which exists in solution as an equilibrium between monomer, dimeric and tetrameric species when in the absence of human Nfs1 (NFS1). We also show that, surprisingly, recombinant ISD11 expressed in E. coli co-purifies with the bacterial orthologue of NFS1, IscS. Binding is weak but specific suggesting that, despite the absence of Isd11 sequences in bacteria, there is enough conservation between the two desulfurases to retain a similar mode of interaction. This knowledge may inform us on the conservation of the mode of binding of Isd11 to the desulfurase. We used evolutionary evidence to suggest Isd11 residues involved in the interaction.
As a contribution to a theoretical debate about the degree of high-level influences on saccade targeting during sentence reading, we investigated eye movements during the reading of structurally ambiguous Chinese character strings and examined whether parafoveal word segmentation could influence saccade-target selection. As expected, ambiguous strings took longer to process. More critically there were theoretically relevant interactions between ambiguity and launch site when first-fixation location and saccade amplitude served as dependent variables: Ambiguous strings in the parafovea triggered longer saccades and more rightward fixations for close launch sites than unambiguous ones; the reverse result was obtained for far launch sites. These crossover interactions indicate that parafoveal word segmentation influences saccade generation in Chinese and provide support of the hypothesis that high-level information can be involved in the decision about where to fixate next.
In this paper two groups supporting different views on the mechanism of light induced polymer deformation argue about the respective underlying theoretical conceptions, in order to bring this interesting debate to the attention of the scientific community. The group of Prof. Nicolae Hurduc supports the model claiming that the cyclic isomerization of azobenzenes may cause an athermal transition of the glassy azobenzene containing polymer into a fluid state, the so-called photo-fluidization concept. This concept is quite convenient for an intuitive understanding of the deformation process as an anisotropic flow of the polymer material. The group of Prof. Svetlana Santer supports the re-orientational model where the mass-transport of the polymer material accomplished during polymer deformation is stated to be generated by the light-induced re-orientation of the azobenzene side chains and as a consequence of the polymer backbone that in turn results in local mechanical stress, which is enough to irreversibly deform an azobenzene containing material even in the glassy state. For the debate we chose three polymers differing in the glass transition temperature, 32 degrees C, 87 degrees C and 95 degrees C, representing extreme cases of flexible and rigid materials. Polymer film deformation occurring during irradiation with different interference patterns is recorded using a homemade set-up combining an optical part for the generation of interference patterns and an atomic force microscope for acquiring the kinetics of film deformation. We also demonstrated the unique behaviour of azobenzene containing polymeric films to switch the topography in situ and reversibly by changing the irradiation conditions. We discuss the results of reversible deformation of three polymers induced by irradiation with intensity (IIP) and polarization (PIP) interference patterns, and the light of homogeneous intensity in terms of two approaches: the re-orientational and the photo-fluidization concepts. Both agree in that the formation of opto-mechanically induced stresses is a necessary prerequisite for the process of deformation. Using this argument, the deformation process can be characterized either as a flow or mass transport.
Magnetic reconnection is a fundamental process of topology change and energy release, taking place in plasmas on the Sun, in space, in astrophysical objects and in the laboratory. However, observational evidence has been relatively rare and typically only partial. Here we present evidence of fast reconnection in a solar filament eruption using high-resolution H-alpha images from the New Vacuum Solar Telescope, supplemented by extreme ultraviolet observations. The reconnection is seen to occur between a set of ambient chromospheric fibrils and the filament itself. This allows for the relaxation of magnetic tension in the filament by an untwisting motion, demonstrating a flux rope structure. The topology change and untwisting are also found through nonlinear force-free field modelling of the active region in combination with magnetohydrodynamic simulation. These results demonstrate a new role for reconnection in solar eruptions: the release of magnetic twist.
We study the damping processes of both incompressible and compressible magnetohydrodynamic (MHD) turbulence in a partially ionized medium. We start from the linear analysis of MHD waves, applying both single-fluid and two-fluid treatments. The damping rates derived from the linear analysis are then used in determining the damping scales of MHD turbulence. The physical connection between the damping scale of MHD turbulence and the cutoff boundary of linear MHD waves is investigated. We find two branches of slow modes propagating in ions and neutrals, respectively, below the damping scale of slow MHD turbulence, and offer a thorough discussion of their propagation and dissipation behavior. Our analytical results are shown to be applicable in a variety of partially ionized interstellar medium (ISM) phases and the solar chromosphere. The importance of neutral viscosity in damping the Alfvenic turbulence in the interstellar warm neutral medium and the solar chromosphere is demonstrated. As a significant astrophysical utility, we introduce damping effects to the propagation of cosmic rays in partially ionized ISM. The important role of turbulence damping in both transit-time damping and gyroresonance is identified.
In this study, we investigated the scale sizes of equatorial plasma irregularities (EPIs) using measurements from the Swarm satellites during its early mission and final constellation phases. We found that with longitudinal separation between Swarm satellites larger than 0.4°, no significant correlation was found any more. This result suggests that EPI structures include plasma density scale sizes less than 44 km in the zonal direction. During the Swarm earlier mission phase, clearly better EPI correlations are obtained in the northern hemisphere, implying more fragmented irregularities in the southern hemisphere where the ambient magnetic field is low. The previously reported inverted-C shell structure of EPIs is generally confirmed by the Swarm observations in the northern hemisphere, but with various tilt angles. From the Swarm spacecrafts with zonal separations of about 150 km, we conclude that larger zonal scale sizes of irregularities exist during the early evening hours (around 1900 LT).
In this study we investigated conditions for loss of GPS signals observed by the Swarm satellites during a 2 year period, from December 2013 to November 2015. Our result shows that the Swarm satellites encountered most of the total loss of GPS signal at the ionization anomaly crests, between +/- 5 degrees and +/- 20 degrees magnetic latitude, forming two bands along the magnetic equator, and these low-latitude events mainly appear around postsunset hours from 19: 00 to 22: 00 local time. By further checking the in situ electron density measurements of Swarm, we found that practically, all the total loss of GPS signal events at low latitudes are related to equatorial plasma irregularities (EPIs) that show absolute density depletions larger than 10 x 10(11) m(-3); then, the Swarm satellites encountered for up to 95% loss of GPS signal for at least one channel and up to 45% tracked less than four GPS satellites (making precise orbit determination impossible). For those EPIs with density depletions less than 10 x 10(11) m(-3), the chance of tracked GPS signals less than four reduces to only 1.0%. Swarm also observed total loss of all GPS signal at high latitudes, mainly around local noon, and these events are related to large spatial density gradients due to polar patches or increased geomagnetic/auroral activities. We further found that the loss of GPS signals were less frequent after appropriate settings of the Swarm GPS receivers had been updated. However, the more recent period of the mission, e.g., after the GPS receiver settings have been updated, also coincides with less severe electron density depletions due to the declining solar cycle, making GPS loss events less likely. We conclude that both lower electron density gradients and appropriate GPS receiver settings reduce the probability for Swarm satellites loss of GPS signals.
In this study, we investigated the scale sizes of equatorial plasma irregularities (EPIs) using measurements from the Swarm satellites during its early mission and final constellation phases. We found that with longitudinal separation between Swarm satellites larger than 0.4 degrees, no significant correlation was found any more. This result suggests that EPI structures include plasma density scale sizes less than 44 km in the zonal direction. During the Swarm earlier mission phase, clearly better EPI correlations are obtained in the northern hemisphere, implying more fragmented irregularities in the southern hemisphere where the ambient magnetic field is low. The previously reported inverted-C shell structure of EPIs is generally confirmed by the Swarm observations in the northern hemisphere, but with various tilt angles. From the Swarm spacecrafts with zonal separations of about 150 km, we conclude that larger zonal scale sizes of irregularities exist during the early evening hours (around 1900 LT).
Recently, due to an increasing demand on functionality and flexibility, beforehand isolated systems have become interconnected to gain powerful adaptive Systems of Systems (SoS) solutions with an overall robust, flexible and emergent behavior. The adaptive SoS comprises a variety of different system types ranging from small embedded to adaptive cyber-physical systems. On the one hand, each system is independent, follows a local strategy and optimizes its behavior to reach its goals. On the other hand, systems must cooperate with each other to enrich the overall functionality to jointly perform on the SoS level reaching global goals, which cannot be satisfied by one system alone. Due to difficulties of local and global behavior optimizations conflicts may arise between systems that have to be solved by the adaptive SoS.
This thesis proposes a modeling language that facilitates the description of an adaptive SoS by considering the adaptation capabilities in form of feedback loops as first class entities. Moreover, this thesis adopts the Models@runtime approach to integrate the available knowledge in the systems as runtime models into the modeled adaptation logic. Furthermore, the modeling language focuses on the description of system interactions within the adaptive SoS to reason about individual system functionality and how it emerges via collaborations to an overall joint SoS behavior. Therefore, the modeling language approach enables the specification of local adaptive system behavior, the integration of knowledge in form of runtime models and the joint interactions via collaboration to place the available adaptive behavior in an overall layered, adaptive SoS architecture.
Beside the modeling language, this thesis proposes analysis rules to investigate the modeled adaptive SoS, which enables the detection of architectural patterns as well as design flaws and pinpoints to possible system threats. Moreover, a simulation framework is presented, which allows the direct execution of the modeled SoS architecture. Therefore, the analysis rules and the simulation framework can be used to verify the interplay between systems as well as the modeled adaptation effects within the SoS. This thesis realizes the proposed concepts of the modeling language by mapping them to a state of the art standard from the automotive domain and thus, showing their applicability to actual systems. Finally, the modeling language approach is evaluated by remodeling up to date research scenarios from different domains, which demonstrates that the modeling language concepts are powerful enough to cope with a broad range of existing research problems.