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We show that for a subdiffusive continuous time random walk with scale-free waiting time distribution the first-passage dynamics on a finite interval can be optimized by introduction of a piecewise linear potential barrier. Analytical results for the survival probability and first-passage density based on the fractional Fokker-Planck equation are shown to agree well with Monte Carlo simulations results. As an application we discuss an improved design for efficient translocation of gradient copolymers compared to homopolymer translocation in a quasi-equilibrium approximation.
The pre-clinical and clinical development of viral vehicles for gene transfer increased in recent years, and a recombinant adeno-associated virus (rAAV) drug took center stage upon approval in the European Union. However, lack of standardization, inefficient purification methods and complicated retargeting limit general usability. We address these obstacles by fusing rAAV-2 capsids with two modular targeting molecules (DARPin or Affibody) specific for a cancer cell-surface marker (EGFR) while simultaneously including an affinity tag (His-tag) in a surface-exposed loop. Equipping these particles with genes coding for prodrug converting enzymes (thymidine kinase or cytosine deaminase) we demonstrate tumor marker specific transduction and prodrug-dependent apoptosis of cancer cells. Coding terminal and loop modifications in one gene enabled specific and scalable purification. Our genetic parts for viral production adhere to a standardized cloning strategy facilitating rapid prototyping of virus directed enzyme prodrug therapy (VDEPT).
The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events.
Recently, photosensitive surfactants have re-attracted considerable attention. It has been shown that their association with oppositely charged biologically important polyelectrolytes, such as DNA or microgels, can be efficiently manipulated simply by light exposure. In this article, we investigate the self-assembly of photosensitive surfactants as well as their interactions with DNA by calorimetric and spectroscopic methods. Critical micelle concentration (CMC), standard micellization enthalpy, entropy, and Gibbs energy were determined in different conditions (ionic strengths and temperatures) for a series of cationic surfactants with an azobenzene group in their tail. It is shown, that aggregation forces of photosensitive units play an important role in the micellization giving the major contribution to the micellization enthalpy. The onset of the aggregation can be traced from shift of the absorption peak position in the UV-visible spectrum. Titration UV-visible spectroscopy is used as an alternative, simple, and sensitive approach to estimate CMC. The titration UV-visible spectroscopy was also employed to investigate interactions (CAC: critical aggregation concentration, precipitation, and colloidal stabilization) in the DNA-surfactant complex.
Comparing thermal wave function methods for multi-configuration time-dependent Hartree simulations
(2014)
We compare two methods for creating stochastic temperature wave functions that can be used for Multi-Configuration Time-Dependent Hartree (MCTDH) simulations. In the first method, the MCTDH coefficients are chosen randomly, while the other method uses a single Hartree product of random single-particle functions (SPFs). We find that using random SPFs dramatically improves convergence for a model system for surface sticking.
We have investigated the influence that megathrust earthquake slip has on the activation of splay faults using a 2-D finite element method (FEM), taking into account the effects of gravity and variations in the frictional strength properties of splay faults. We simulated both landward-dipping and seaward-dipping splay fault geometries, and imposed depth-variable slip distributions of subduction events. Our results indicate that the two types of splay fault exhibit a similar behavior, with variations in frictional properties along the faults affecting only the seismic magnitude. The triggering process is controlled by a critical depth. Megathrust slip concentrated at depths shallower than the critical depth will favor normal displacement, while megathrust slip concentrated at depths deeper than the critical depth is likely to result in reverse motion. Our results thus provide a useful tool for predicting the activation of secondary faults and may have direct implications for tsunami hazard research.
The perception of time is a fundamental part of human experience. Recent research suggests that the experience of time emerges from emotional and interoceptive (bodily) states as processed in the insular cortex. Whether there is an interaction between the conscious awareness of interoceptive states and time distortions induced by emotions has rarely been investigated so far. We aimed to address this question by the use of a retrospective time estimation task comparing two groups of participants. One group had a focus on interoceptive states and one had a focus on exteroceptive information while watching film clips depicting fear, amusement and neutral content. Main results were that attention to interoceptive processes significantly affected subjective time experience. Fear was accompanied with subjective time dilation that was more pronounced in the group with interoceptive focus, while amusement led to a quicker passage of time which was also increased by interoceptive focus. We conclude that retrospective temporal distortions are directly influenced by attention to bodily responses. These effects might crucially interact with arousal levels. Sympathetic nervous system activation affecting memory build-up might be the decisive factor influencing retrospective time judgments. Our data substantially extend former research findings underscoring the relevance of interoception for the effects of emotional states on subjective time experience.
In hydrology, the storage-discharge relationship is a fundamental catchment property. Understanding what controls this relationship is at the core of catchment science. To date, there are no direct methods to measure water storage at catchment scales (10(1)-10(3)km(2)). In this study, we use direct measurements of terrestrial water storage dynamics by means of superconducting gravimetry in a small headwater catchment of the Regen River, Germany, to derive empirical storage-discharge relationships in nested catchments of increasing scale. Our results show that the local storage measurements are strongly related to streamflow dynamics at larger scales (> 100km(2); correlation coefficient=0.78-0.81), but at small scale, no such relationship exists (similar to 1km(2); correlation coefficients=-0.11). The geologic setting in the region can explain both the disconnection between local water storage and headwater runoff, and the connectivity between headwater storage and streams draining larger catchment areas. More research is required to understand what controls the form of the observed storage-discharge relationships at the catchment scale. This study demonstrates that high-precision gravimetry can provide new insights into the complex relationship between state and response of hydrological systems.
In this paper a linear-time algorithm for the minimization of acyclic deterministic finite-state automata is presented. The algorithm runs significantly faster than previous algorithms for the same task. This is shown by a comparison of the running times of both algorithms. Additionally, a variation of the new algorithm is presented which handles cyclic automata as input. The new cycle-aware algorithm minimizes acyclic automata in the desired way. In case of cyclic input, the algorithm minimizes all acyclic suffixes of the input automaton.
This Letter is focused on the one-pot formation of CdS nanoparticles in aqueous medium in presence of polyethyleneimine (PEI). Quantum dots can be obtained by adding a pre-cooled aqueous Na2S solution to a pre-cooled aqueous CdCl2 solution dropwise in presence of PEI.
Field flow fractionation in combination with TEM experiments show a time dependent agglomeration of individual quantum dots from 1.6 nm up to 3.2 nm in size. The hyperbranched PEI of moderate molar mass (>20000 g/mol) is an excellent polymer to prevent a further increase of the particle size. Therefore, stable fluorescent PEI-capped CdS quantum dots are available.
Micellar multilayer films were prepared from an amphiphilic comb-like polycation ("polysoap") and the polyanion poly(styrene sulfonate) (PSS) using alternate polyelectrolyte layer-by-layer (LbL) self-assembly. Linear growth of the film thickness was evidenced by UV-vis spectroscopy and spectroscopic ellipsometry. Imaging by atomic force microscopy (AFM) indicated that the micellar conformation adopted by the polycation in solutions was preserved in the films. Thus, hydrophobic photoactive molecules, which were solubilized by the hydrophobic nanodomains of the micellar polymer prior to deposition, could be transferred into the films. Photoinduced energy transfer was observed in the nanostructured multilayers between naphthalene (donor) and perylene (acceptor) molecules embedded inside the polymer micelles. The efficiency of the energy transfer process can be controlled to some extent by introducing spacer layers between the layers containing the donor or acceptor, revealing partial stratification of the micellar LbL films. Also, photoinduced electron transfer was evidenced between perylene (donor) and butyl viologen (acceptor) molecules embedded inside the multilayers by steady-state fluorescence spectroscopy. The obtained photoactive nanostructures are promising candidates for solar-to-chemical energy conversion systems.
Method: Following a known-group differences validation strategy, the doping attitudes of 43 athletes from bodybuilding (representative for a highly doping prone sport) and handball (as a contrast group) were compared using the picture-based doping-BIAT. The Performance Enhancement Attitude Scale (PEAS) was employed as a corresponding direct measure in order to additionally validate the results.
Results: As expected, in the group of bodybuilders, indirectly measured doping attitudes as tested with the picture-based doping-BIAT were significantly less negative (eta(2) = .11). The doping-BIAT and PEAS scores correlated significantly at r = .50 for bodybuilders, and not significantly at r = .36 for handball players. There was a low error rate (7%) and a satisfactory internal consistency (r(dagger dagger) = .66) for the picture-based doping-BIAT.
Conclusions: The picture-based doping-BIAT constitutes a psychometrically tested method, ready to be adopted by the international research community. The test can be administered via the internet. All test material is available "open source". The test might be implemented, for example, as a new effect-measure in the evaluation of prevention programs.
Molybdenum and tungsten enzymes require specific chaperones for folding and cofactor insertion. PaoD is the chaperone of the periplasmic aldehyde oxidoreductase PaoABC. It is the last gene in the paoABCD operon in Escherichia coli and its presence is crucial for obtaining mature enzyme. PaoD is an unstable, 35 kDa, protein. Our biochemical studies showed that it is a dimer in solution with a tendency to form large aggregates, especially after freezing/thawing cycles. In order to improve stability, PaoD was thawed in the presence of two ionic liquids [C(4)mim]Cl and [C(2)OHmim]PF6 and no protein precipitation was observed. This allowed protein concentration and crystallization using polyethylene glycol or ammonium sulfate as precipitating agents. Saturation transfer difference - nuclear magnetic resonance (STD-NMR) experiments have also been performed in order to investigate the effect of the ionic liquids in the stabilization process, showing a clear interaction between the acidic ring protons of the cation and, most likely, negatively charged residues at the protein surface. DLS assays also show a reduction of the overall size of the protein aggregates in presence of ionic liquids. Furthermore, cofactor binding studies on PaoD showed that the protein is able to discriminate between molybdenum and tungsten bound to the molybdenum cofactor, since only a Mo-MPT form of the cofactor remained bound to PaoD.
The photosynthetic carbon metabolism, including the Calvin-Benson cycle, is the primary pathway in C-3-plants, producing starch and sucrose from CO2. Understanding the interplay between regulation and efficiency of this pathway requires the development of mathematical models which would explain the observed dynamics of metabolic transformations. Here, we address this question by casting the existing models of Calvin-Benson cycle and the end-product processes into an analysis framework which not only facilitates the comparison of the different models, but also allows for their ranking with respect to chosen criteria, including stability, sensitivity, robustness and/or compliance with experimental data. The importance of the photosynthetic carbon metabolism for the increase of plant biomass has resulted in many models with various levels of detail. We provide the largest compendium of 15 existing, well-investigated models together with a comprehensive classification as well as a ranking framework to determine the best-performing models for metabolic engineering and planning of in silica experiments. The classification can be additionally used, based on the model structure, as a tool to identify the models which match best the experimental design. The provided ranking is just one alternative to score models and, by changing the weighting factor, this framework also could be applied for selection of other criteria of interest.
Advance in geocomputation
(2014)
In situ UV laser spot Ar-40/Ar-39 analyses of distinct phengite types in eclogite-facies rocks from the Sesia-Lanzo Zone (Western Alps, Italy) were combined with SIMS boron isotope analyses as well as boron (B) and lithium (Li) concentration data to link geochronological information with constraints on fluid-rock interaction. In weakly deformed samples, apparent Ar-40/Ar-39 ages of phengite cores span a range of similar to 20 Ma, but inverse isochrons define two distinct main high-pressure (HP) phengite core crystallization periods of 88-82 and 77-74 Ma, respectively. The younger cores have on average lower B contents (similar to 36 mu g/g) than the older ones (similar to 43-48 mu g/g), suggesting that loss of B and resetting of the Ar isotopic system were related. Phengite cores have variable delta B-11 values (-18 parts per thousand to -10 parts per thousand), indicating the lack of km scale B homogenization during HP crystallization.
Overprinted phengite rims in the weakly deformed samples generally yield younger apparent Ar-40/Ar-39 ages than the respective cores. They also show variable effects of heterogeneous excess 40 Ar incorporation and Ar loss. One acceptable inverse isochron age of 77.1 +/- 1.1 Ma for rims surrounding older cores (82.6 +/- 0.6 Ma) overlaps with the second period of core crystallization. Compared to the phengite cores, all rims have lower B and Li abundances but similar delta B-11 values (-15 parts per thousand to -9 parts per thousand), reflecting internal redistribution of B and Li and internal fluid buffering of the B isotopic composition during rim growth. The combined observation of younger Ar-40/Ar-39 ages and boron loss, yielding comparable values of both parameters only in cores and rims of different samples, is best explained by a selective metasomatic overprint. In low permeability samples, this overprint caused recrystallization of phengite rims, whereas higher permeability in other samples led to complete recrystallization of phengite grains.
Strongly deformed samples from a several km long, blueschist-facies shear zone contain mylonitic phengite that forms a tightly clustered group of relatively young apparent Ar-40/Ar-39 ages (64.7-68.8 Ma), yielding an inverse isochron age of 65.0 +/- 3.0 Ma. Almost complete B and Li removal in mylonitic phengite is due to leaching into a fluid. The B isotopic composition is significantly heavier than in phengites from the weakly deformed samples, indicating an external control by a high-delta B-11 fluid (delta B-11 = + 7 +/- 4 parts per thousand). We interpret this result as reflecting phengite recrystallization related to deformation and associated fluid flow in the shear zone. This event also caused partial resetting of the Ar isotope system and further B loss in more permeable rocks of the adjacent unit. We conclude that geochemical evidence for pervasive or limited fluid flow is crucial for the interpretation of Ar-40/Ar-39 data in partially metasomatized rocks.