Localized Linear Discriminant Analysis

Despite its age, the Linear Discriminant Analysis performs well even in situations where the underlying premises like normally distributed data with constant covariance matrices over all classes are not met. It is, however, a global technique that does not regard the nature of an individual observation to be classified. By weighting each training observation according to its distance to the observation of interest, a global classifier can be transformed into an observation specific approach. So far, this has been done for logistic discrimination. By using LDA instead, the computation of the local classifier is much simpler. Moreover, it is ready for applications in multi-class situations. --classification,local models,LDA

Characterization of Binding Pocket Flexibility of Aldose Reductase

Aldose Reductase (AR) is the first enzyme of the 'sorbitol pathway'. It is an NADPH dependent enzyme and catalyzes the reduction of various aldehydes to the corresponding alcohols. Its binding pocket shows intrinsic flexibility which is mainly mediated by a small loop region. A specificity pocket can be opened or closed via this loop stretch. In the first part of this work the relevance of considering protein flexibility in structure-based drug design was highlighted. Docking experiments were carried out for two inhibitors which were originally designed to mimic a certain binding mode. By carrying out separate docking simulations for each known major binding pocket conformation, it was shown that the intended binding mode was not predicted to be the most favorable. This hypothesis could later be verified by X-ray crystallography. However, the predictions were by no means perfect. One of the compounds induced a new conformation to the binding pocket. Thus, no appropriate crystal structure was available as template for the docking experiments. For the second molecule the importance of considering water during docking was emphasized. In the second part of this thesis a new method to simplify the tedious process of docking to multiple targets was evaluated in the context of protein flexibility: in-situ cross-docking. With this method, instead of performing sequential docking experiments of multiple ligands into multiple protein structures, several protein conformations can be addressed at once. In the next part of this thesis the flexibility of the AR binding pocket was examined in detail. It was shown that with respect to the binding pocket, flexibility is limited to only a handful amino acids close to the specificity pocket. It was elucidated how the enzyme performs its 'induced-fit' binding mechanism. To further explore the conformational space available to the AR binding pocket, multiple MD simulations were carried out. Good overall agreement between the results from the MD simulations and the crystal structure analysis was found. Residues which exhibited elevated levels of flexibilities in the MD simulations showed in most cases also differences between the single crystal structures. However, a few residues showed unexpected behavior in the MD simulations: Phe 122, Trp 219, and Tyr 309. The behavior of these residues were examined in great detail. In a further project, the generated MD trajectories were used to energetically analyze the process of 'induced-fit' adaptation. The method MM-PBSA was chosen for this purpose. Considering the enormous amount of computational power required to perform the necessary calculations and the remarkable time needed to analyze the results, MM-PBSA did not turn out to be a cost-effective method to predict binding free energies for the dataset of AR inhibitors used in this study. In the final section of this thesis a study was presented where in the first part aspects of flexibility of the C-terminal loop of AR were examined. In a combined study using MD simulations and multiple crystal structures, it was shown that there are clear differences between individual crystal structures of the same protein-ligand complex in this region of the enzyme. A nice agreement between the observations made in the MD and multiple crystal structures derived from different experimental crystallization conditions was found. In the second part of this section the unexpected occurrence of multiple ligands in and close to the binding pocket of AR was described. In summary, this study has dealt with many aspects of protein flexibility using AR as a test case. AR has proves to be a valuable test system to investigate protein flexibility with different methods

Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables

Motivation. In biological sequence analysis, alignment-free (also known as k-mer-based) methods are increasingly replacing mapping- and alignment-based methods for various applications. A basic step of such methods consists of building a table of all k-mers of a given set of sequences (a reference genome or a dataset of sequenced reads) and their counts. Over the past years, efficient methods and tools for k-mer counting have been developed. In a different line of work, the use of gapped k-mers has been shown to offer advantages over the use of the standard contiguous k-mers. However, no tool seems to be available that is able to count gapped k-mers with the same efficiency as contiguous k-mers. One reason is that the most efficient k-mer counters use minimizers (of a length m < k) to group k-mers into buckets, such that many consecutive k-mers are classified into the same bucket. This approach leads to cache-friendly (and hence extremely fast) algorithms, but the approach does not transfer easily to gapped k-mers. Consequently, the existing efficient k-mer counters cannot be trivially modified to count gapped k-mers with the same efficiency. Results. We present a different approach that is equally applicable to contiguous k-mers and gapped k-mers. We use multi-way bucketed Cuckoo hash tables to efficiently store (gapped) k-mers and their counts. We also describe a method to parallelize counting over multiple threads without using locks: We subdivide the hash table into independent subtables, and use a producer-consumer model, such that each thread serves one subtable. This requires designing Cuckoo hash functions with the property that all alternative locations for each k-mer are located in the same subtable. Compared to some of the fastest contiguous k-mer counters, our approach is of comparable speed, or even faster, on large datasets, and it is the only one that supports gapped k-mers

Fast Lightweight Accurate Xenograft Sorting

Motivation: With an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need for methods to separate reads originating from the graft (human) tumor and reads originating from the host species\u27 (mouse) surrounding tissue. Two kinds of methods are in use: On the one hand, alignment-based tools require that reads are mapped and aligned (by an external mapper/aligner) to the host and graft genomes separately first; the tool itself then processes the resulting alignments and quality metrics (typically BAM files) to assign each read or read pair. On the other hand, alignment-free tools work directly on the raw read data (typically FASTQ files). Recent studies compare different approaches and tools, with varying results. Results: We show that alignment-free methods for xenograft sorting are superior concerning CPU time usage and equivalent in accuracy. We improve upon the state of the art by presenting a fast lightweight approach based on three-way bucketed quotiented Cuckoo hashing. Our hash table requires memory comparable to an FM index typically used for read alignment and less than other alignment-free approaches. It allows extremely fast lookups and uses less CPU time than other alignment-free methods and alignment-based methods at similar accuracy

Helicity Dependent Directional Surface Plasmon Polariton Excitation Using A Metasurface with Interfacial Phase Discontinuity

Surface plasmon polaritons (SPPs) have been widely exploited in various scientific communities, ranging from physics, chemistry to biology, due to the strong confinement of light to the metal surface. For many applications it is important that the free space photon can be coupled to SPPs in a controllable manner. In this Letter, we apply the concept of interfacial phase discontinuity for circularly polarizations on a metasurface to the design of a novel type of polarization dependent SPP unidirectional excitation at normal incidence. Selective unidirectional excitation of SPPs along opposite directions is experimentally demonstrated at optical frequencies by simply switching the helicity of the incident light. This approach, in conjunction with dynamic polarization modulation techniques, opens gateway towards integrated plasmonic circuits with electrically reconfigurable functionalities.Comment: 17 pages, 5 figures. Published on <Light:Science & Applications

River Rhine – hydraulic and ship dynamic modelling

River engineeringNavigation waterways and dredgin