N,N'-dimethylperylene-3,4,9,10-bis(dicarboximide) on alkali halide(001) surfaces

The growth of N,N'-dimethylperylene-3,4,9,10-bis(dicarboximide) (DiMe-PTCDI) on KBr(001) and NaCl(001) surfaces has been studied. Experimental results have been achieved using frequency modulation atomic force microscopy at room temperature under ultra-high vacuum conditions. On both substrates, DiMe-PTCDI forms molecular wires with a width of 10 nm, typically, and a length of up to 600 nm at low coverages. All wires grow along the [110] direction (or [1$\bar{1}$0] direction, respectively) of the alkali halide (001) substrates. There is no wetting layer of molecules: Atomic resolution of the substrates can be achieved between the wires. The wires are mobile on KBr surface but substantially more stable on NaCl. A p(2 x 2) superstructure in brickwall arrangement on the ionic crystal surfaces is proposed based on electrostatic considerations. Calculations and Monte-Carlo simulations using empirical potentials reveal possible growth mechanisms for molecules within the first layer for both substrates, also showing a significantly higher binding energy for NaCl(001). For KBr, the p(2 x 2) superstructure is confirmed by the simulations, for NaCl, a less dense, incommensurate superstructure is predicted.Comment: 5 pages, 5 figure

Stoichiometry determination of chalcogenide superlattices by means of X-ray diffraction and its limits

In this paper we explore the potential of stoichiometry determination for chalcogenide superlattices, promising candidates for next-generation phase-change memory, via X-ray diffraction. To this end, a set of epitaxial GeTe/Sb2Te3 superlattice samples with varying layer thicknesses is sputter-deposited. Kinematical scattering theory is employed to link the average composition with the diffraction features. The observed lattice constants of the superlattice reference unit cell follow Vegard's law, enabling a straight-forward and non-destructive stoichiometry determination.Comment: physica status solidi (RRL) - Rapid Research Letters (2019

GraphProt: modeling binding preferences of RNA-binding proteins

We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. We benchmark GraphProt, demonstrating that the modeled binding preferences conform to the literature, and showcase the biological relevance and two applications of GraphProt models. First, estimated binding affinities correlate with experimental measurements. Second, predicted Ago2 targets display higher levels of expression upon Ago2 knockdown, whereas control targets do not. Computational binding models, such as those provided by GraphProt, are essential for predicting RBP binding sites and affinities in all tissues. GraphProt is freely available at http://www.bioinf.uni-freiburg.de/Software/GraphProt

Interband characterization and electronic transport control of nanoscaled GeTe/Sb2_2Te3_3 superlattices

The extraordinary electronic and optical properties of the crystal-to-amorphous transition in phase-change materials led to important developments in memory applications. A promising outlook is offered by nanoscaling such phase-change structures. Following this research line, we study the interband optical transmission spectra of nanoscaled GeTe/Sb$_2$Te$_3$ chalcogenide superlattice films. We determine, for films with varying stacking sequence and growth methods, the density and scattering time of the free electrons, and the characteristics of the valence-to-conduction transition. It is found that the free electron density decreases with increasing GeTe content, for sub-layer thickness below $\sim$3 nm. A simple band model analysis suggests that GeTe and Sb$_2$Te$_3$ layers mix, forming a standard GeSbTe alloy buffer layer. We show that it is possible to control the electronic transport properties of the films by properly choosing the deposition layer thickness and we derive a model for arbitrary film stacks

Characterization of a CdZnTe detector for a low-power CubeSat application

We report spectral and imaging performance of a pixelated CdZnTe detector custom designed for the MeVCube project: a small Compton telescope on a CubeSat platform. MeVCube is expected to cover the energy range between 200 keV and 4 MeV, with a sensitivity comparable to the one of the last generation of larger satellites. In order to achieve this goal, an energy resolution of few percent in full width at half maximum (FWHM) and a 3-D spatial resolution of few millimeters for the individual detectors are needed. The severe power constraints present in small satellites require very low power read-out electronics for the detector. Our read-out is based on the VATA450.3 ASIC developed by Ideas, with a power consumption of only 0.25 mW/channel, which exhibits good performance in terms of dynamic range, noise and linearity. A 2.0 cm× 2.0 cm× 1.5 cm CdZnTe detector, with a custom 8 × 8 pixel anode structure read-out by a VATA450.3 ASIC, has been tested. A preliminary read-out system for the cathode, based on a discrete Amptek A250F charge sensitive pre-amplifier and a DRS4 ASIC, has been implemented. An energy resolution around 3% FWHM has been measured at a gamma energy of 662 keV; at 200 keV the average energy resolution is 6.5%, decreasing to ≲ 2% at energies above 1 MeV. A 3-D spatial resolution of ≈ 2 mm is achieved in each dimension.Peer Reviewe

Characterization of a CdZnTe detector for a low-power CubeSat application

We report spectral and imaging performance of a pixelated CdZnTe detector custom designed for the \emph{MeVCube} project: a small Compton telescope on a CubeSat platform. \emph{MeVCube} is expected to cover the energy range between $200\;\mathrm{keV}$ and $4\;\mathrm{MeV}$, with performance comparable to the last generation of larger satellites. In order to achieve this goal, an energy resolution of few percent in full width at half maximum (FWHM) and a $3$-D spatial resolution of few millimeters for the individual detectors are needed. The severe power constraints present in small satellites require very low power read-out electronics for the detector. Our read-out is based on the VATA450.3 ASIC developed by \emph{Ideas}, with a power consumption of only $0.25\;\mathrm{mW/channel}$, which exhibits good performance in terms of dynamic range, noise and linearity. A $2.0\;\mathrm{cm} \times 2.0\;\mathrm{cm} \times 1.5\;\mathrm{cm}$ CdZnTe detector, with a custom $8 \times 8$ pixel anode structure read-out by a VATA450.3 ASIC, has been tested. A preliminary read-out system for the cathode, based on a discrete \emph{Amptek} A250F charge sensitive pre-amplifier and a DRS4 ASIC, has been implemented. An energy resolution around $3\%$ FWHM has been measured at a gamma energy of $662\;\mathrm{keV}$; at $200\;\mathrm{keV}$ the average energy resolution is $6.5\%$, decreasing to $\lesssim 2\%$ at energies above $1\;\mathrm{MeV}$. A $3$-D spatial resolution of $\approx 2\,\mathrm{mm}$ is achieved

Targeted HIV-1 Latency Reversal Using CRISPR/Cas9-Derived Transcriptional Activator Systems

CRISPR/Cas9 technology is currently considered the most advanced tool for targeted genome engineering. Its sequence-dependent specificity has been explored for locus-directed transcriptional modulation. Such modulation, in particular transcriptional activation, has been proposed as key approach to overcome silencing of dormant HIV provirus in latently infected cellular reservoirs. Currently available agents for provirus activation, so-called latency reversing agents (LRAs), act indirectly through cellular pathways to induce viral transcription. However, their clinical performance remains suboptimal, possibly because reservoirs have diverse cellular identities and/or proviral DNA is intractable to the induced pathways. We have explored two CRISPR/Cas9-derived activator systems as targeted approaches to induce dormant HIV-1 proviral DNA. These systems recruit multiple transcriptional activation domains to the HIV 5'long terminal repeat (LTR), for which we have identified an optimal target region within the LTR U3 sequence. Using this target region, we demonstrate transcriptional activation of proviral genomes via the synergistic activation mediator complex in various in culture model systems for HIV latency. Observed levels of induction are comparable or indeed higher than treatment with established LRAs. Importantly, activation is complete, leading to production of infective viral particles. Our data demonstrate that CRISPR/Cas9-derived technologies can be applied to counteract HIV latency and may therefore represent promising novel approaches in the quest for HIV elimination

‘Location, Location, Location’: a spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate

Motivation: For the analysis of rare variants in sequence data, numerous approaches have been suggested. Fixed and flexible threshold approaches collapse the rare variant information of a genomic region into a test statistic with reduced dimensionality. Alternatively, the rare variant information can be combined in statistical frameworks that are based on suitable regression models, machine learning, etc. Although the existing approaches provide powerful tests that can incorporate information on allele frequencies and prior biological knowledge, differences in the spatial clustering of rare variants between cases and controls cannot be incorporated. Based on the assumption that deleterious variants and protective variants cluster or occur in different parts of the genomic region of interest, we propose a testing strategy for rare variants that builds on spatial cluster methodology and that guides the identification of the biological relevant segments of the region. Our approach does not require any assumption about the directions of the genetic effects. Results: In simulation studies, we assess the power of the clustering approach and compare it with existing methodology. Our simulation results suggest that the clustering approach for rare variants is well powered, even in situations that are ideal for standard methods. The efficiency of our spatial clustering approach is not affected by the presence of rare variants that have opposite effect size directions. An application to a sequencing study for non-syndromic cleft lip with or without cleft palate (NSCL/P) demonstrates its practical relevance. The proposed testing strategy is applied to a genomic region on chromosome 15q13.3 that was implicated in NSCL/P etiology in a previous genome-wide association study, and its results are compared with standard approaches. Availability: Source code and documentation for the implementation in R will be provided online. Currently, the R-implementation only supports genotype data. We currently are working on an extension for VCF files. Contact: [email protected]

Emergency hospital admissions and three-year survival of adults with and without cardiovascular surgery for congenital cardiac disease

AbstractObjective:This study determined the quantity and nature of emergencies leading to unscheduled hospital admissions of adults with congenital cardiac disease and their mid-term survival.ResultsDuring 1 year, 429 adults with congenital cardiac diseases were admitted 571 times, and 124 admissions (22%) of 95 patients (22%) were emergency admissions. Fifteen of the 95 patients were seen for the first time in 1 of the participating centers. The underlying anomalies were Fallot's tetralogy and pulmonary atresia (n = 26/7), univentricular heart after Fontan procedure (n = 25), atrial septal defect (n = 18), Eisenmenger syndrome (n = 12), complete transposition (n = 11), and others (n = 25). Indications for admission were cardiovascular complications (n = 103; 83%) (arrhythmia, cardiac failure, syncope, pacemaker problems, pericardial tamponade, and sudden death), infections (n = 8, 6%) (endocarditis, pacemaker infection, pneumonia, and cerebral abscess), acute chest pain (n = 7; 6%), and acute abdominal pain (n = 4; 3%). All patients required immediate emergency care, and 16 patients (17%) required urgent cardiovascular or abdominal surgery. Six patients died during the hospital stay. During a follow-up of 2.9 years (SD 0.8), 16 (18%) of the discharged patients died, and 2 additional patients underwent heart or heart-lung transplantation.ConclusionAdults with congenital cardiac disease often experience serious emergency situations with a high in-hospital and mid-term post-hospital mortality. Care given by physicians with special expertise is important in this specific group of patients