maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

Motivation: The task of reconstructing a genomic sequence from a particular species is gaining more and more importance in the light of the rapid development of high-throughput sequencing technologies and their limitations. Applications include not only compensation for missing data in unsequenced genomic regions and the design of oligonucleotide primers for target genes in species with lacking sequence information but also the preparation of customized queries for homology searches

The biogeochemical cycle of dissolved aluminium in the Atlantic Ocean

The work presented in this thesis focuses on the biogeochemical cycle of dissolved aluminium in surface waters and the water column of the Atlantic Ocean

Scattered Light Imaging: Resolving the substructure of nerve fiber crossings in whole brain sections with micrometer resolution

For developing a detailed network model of the brain based on image reconstructions, it is necessary to spatially resolve crossing nerve fibers. The accuracy hereby depends on many factors, including the spatial resolution of the imaging technique. 3D Polarized Light Imaging (3D-PLI) allows the three-dimensional reconstruction of nerve fiber tracts in whole brain sections with micrometer in-plane resolution, but leaves uncertainties in pixels containing crossing fibers. Here we introduce Scattered Light Imaging (SLI) to resolve the substructure of nerve fiber crossings. The measurement is performed on the same unstained histological brain sections as in 3D-PLI. By illuminating the brain sections from different angles and measuring the transmitted (scattered) light under normal incidence, SLI provides information about the underlying nerve fiber structure. A fully automated evaluation of the resulting light intensity profiles has been developed, allowing the user to extract various characteristics, like the individual directions of in-plane crossing nerve fibers, for each image pixel at once. We validate the reconstructed nerve fiber directions against results from previous simulation studies, scatterometry measurements, and fiber directions obtained from 3D-PLI. We demonstrate in different brain samples (human optic tracts, vervet monkey brain, rat brain) that the 2D fiber directions can be reliably reconstructed for up to three crossing nerve fiber bundles in each image pixel with an in-plane resolution of up to 6.5 $\mu$m. We show that SLI also yields reliable fiber directions in brain regions with low 3D-PLI signals coming from regions with a low density of myelinated nerve fibers or out-of-plane fibers. In combination with 3D-PLI, the technique can be used for a full reconstruction of the three-dimensional nerve fiber architecture in the brain.Comment: 30 pages, 16 figure

Nature Relatedness and Environmental Concern of Young People in Ecuador and Germany

Today’s societies are confronted by a daily biodiversity loss, which will increase in the face of climate change and environmental pollution. Biodiversity loss is a particularly severe problem in so-called biodiversity hotspots. Ecuador is an example of a country that hosts two different biodiversity hotspots. Human behavior – in developing as well as in industrial countries such as Germany – must be considered as one of the most important direct and indirect drivers of this global trend and thus plays a crucial role in environmentalism and biodiversity conservation. Nature relatedness and environmental concern have been identified as important environmental psychological factors related to people’s pro-environmental behavior. However, the human–nature relationship depends on a variety of other factors, such as values, gender, nationality, qualities of environmental concern and time spent in nature. This study compared young people from Ecuador and Germany with regard to their nature relatedness and environmental concern. Furthermore, the role of the aforementioned factors was investigated. In total, we surveyed 2,173 high school students from Germany (Mage = 14.56 years, SD = 1.45; female: 55.1%) and 451 high school students from Ecuador (Mage = 14.63 years, SD = 1.77; female: 55.3%). We found that young Ecuadorians were more related to nature than young people from Germany. Additionally, we found country-specific differences in the structure of environmental concern and in the role of gender in the explanation of biospheric environmental concern and nature relatedness. In both samples, the self-transcendence value cluster was a significant positive predictor for biospheric environmental concern and nature relatedness. Time spent in nature was a significant positive predictor for nature relatedness in both samples. The results are an empirical basis for the assumption of culture-specific differences in human–nature relationships

NeuroHammer: Inducing Bit-Flips in Memristive Crossbar Memories

Emerging non-volatile memory (NVM) technologies offer unique advantages in energy efficiency, latency, and features such as computing-in-memory. Consequently, emerging NVM technologies are considered an ideal substrate for computation and storage in future-generation neuromorphic platforms. These technologies need to be evaluated for fundamental reliability and security issues. In this paper, we present \emph{NeuroHammer}, a security threat in ReRAM crossbars caused by thermal crosstalk between memory cells. We demonstrate that bit-flips can be deliberately induced in ReRAM devices in a crossbar by systematically writing adjacent memory cells. A simulation flow is developed to evaluate NeuroHammer and the impact of physical parameters on the effectiveness of the attack. Finally, we discuss the security implications in the context of possible attack scenarios