"Life" shaped by genes that depend on their surrounds

Never was dogmatic reductionism helpful in conceiving the phenomenon of life. The post-genomic era has made it clear that genes alone cannot explain the functioning of whole organisms. Already each cell represents a unique, non-recurring individual. Recent progress in developmental biology has conveyed new perspectives both on the makings of individual organisms (ontogeny), as on evolutionary change (Evo-Devo). The genome (the entirety of all genes) of an animal remains constant from fertilization onwards in each cell. The realization of genes requires molecular environments, in particular pertinent to the cytoplasm of the unfertilized egg. Individuality of an organism therefore is not only determined by its genome, but is shaped through developmental processes (it needs time!). Organisms can only exist through mutual interplays with their respective (molecular and cellular) environments at all levels of organization. Thus, life can be conceived of as endless networks of communication, e.g. as a mutual continuum, connecting all individuals, all species and all generations within their given environments. Evolutionarily, nature does not select fitting genes, but rather viable traits. The presented concepts render it unlikely that it was genes that founded our living world, but rather that distinct environments shaped “genes” (of whatever chemical nature) which proved to be “life-suitable”

Baseline Detection in Historical Documents using Convolutional U-Nets

Baseline detection is still a challenging task for heterogeneous collections of historical documents. We present a novel approach to baseline extraction in such settings, turning out the winning entry to the ICDAR 2017 Competition on Baseline detection (cBAD). It utilizes deep convolutional nets (CNNs) for both, the actual extraction of baselines, as well as for a simple form of layout analysis in a pre-processing step. To the best of our knowledge it is the first CNN-based system for baseline extraction applying a U-net architecture and sliding window detection, profiting from a high local accuracy of the candidate lines extracted. Final baseline post-processing complements our approach, compensating for inaccuracies mainly due to missing context information during sliding window detection. We experimentally evaluate the components of our system individually on the cBAD dataset. Moreover, we investigate how it generalizes to different data by means of the dataset used for the baseline extraction task of the ICDAR 2017 Competition on Layout Analysis for Challenging Medieval Manuscripts (HisDoc). A comparison with the results reported for HisDoc shows that it also outperforms the contestants of the latter.Comment: 6 pages, accepted to DAS 201

Localization Transition in Incommensurate non-Hermitian Systems

A class of one-dimensional lattice models with incommensurate complex potential $V(\theta)=2[\lambda_r cos(\theta)+i \lambda_i sin(\theta)]$ is found to exhibit localization transition at $|\lambda_r|+|\lambda_i|=1$. This transition from extended to localized states manifests in the behavior of the complex eigenspectum. In the extended phase, states with real eigenenergies have finite measure and this measure goes to zero in the localized phase. Furthermore, all extended states exhibit real spectrum provided $|\lambda_r| \ge |\lambda_i|$. Another novel feature of the system is the fact that the imaginary part of the spectrum is sensitive to the boundary conditions {\it only at the onset to localization}

A compact electron matter wave interferometer for sensor technology

Remarkable progress can be observed in recent years in the controlled emission, guiding and detection of coherent, free electrons. Those methods were applied in matter wave interferometers leading to high phase sensitivities and novel sensor technologies for dephasing influences such as mechanical vibrations or electromagnetic frequencies. However, the previous devices have been large laboratory setups. For future sensor applications or tests of the coherence properties of an electron source, small, portable interferometers are required. Here, we demonstrate a compact biprism electron interferometer that can be used for mobile applications. The design was optimized for small dimensions by beam path simulations. The interferometer has a length between the tip and the superposition plane before magnification of only 47 mm and provides electron interference pattern with a contrast up to 42.7 %. The detection of two dephasing frequencies at 50 and 150 Hz was demonstrated applying second order correlation and Fourier analysis of the interference data

Audiovisual speech perception in cochlear implant patients

Hearing with a cochlear implant (CI) is very different compared to a normal-hearing (NH) experience, as the CI can only provide limited auditory input. Nevertheless, the central auditory system is capable of learning how to interpret such limited auditory input such that it can extract meaningful information within a few months after implant switch-on. The capacity of the auditory cortex to adapt to new auditory stimuli is an example of intra-modal plasticity — changes within a sensory cortical region as a result of altered statistics of the respective sensory input. However, hearing deprivation before implantation and restoration of hearing capacities after implantation can also induce cross-modal plasticity — changes within a sensory cortical region as a result of altered statistics of a different sensory input. Thereby, a preserved cortical region can, for example, support a deprived cortical region, as in the case of CI users which have been shown to exhibit cross-modal visual-cortex activation for purely auditory stimuli. Before implantation, during the period of hearing deprivation, CI users typically rely on additional visual cues like lip-movements for understanding speech. Therefore, it has been suggested that CI users show a pronounced binding of the auditory and visual systems, which may allow them to integrate auditory and visual speech information more efficiently. The projects included in this thesis investigate auditory, and particularly audiovisual speech processing in CI users. Four event-related potential (ERP) studies approach the matter from different perspectives, each with a distinct focus. The first project investigates how audiovisually presented syllables are processed by CI users with bilateral hearing loss compared to NH controls. Previous ERP studies employing non-linguistic stimuli and studies using different neuroimaging techniques found distinct audiovisual interactions in CI users. However, the precise timecourse of cross-modal visual-cortex recruitment and enhanced audiovisual interaction for speech related stimuli is unknown. With our ERP study we fill this gap, and we present differences in the timecourse of audiovisual interactions as well as in cortical source configurations between CI users and NH controls. The second study focuses on auditory processing in single-sided deaf (SSD) CI users. SSD CI patients experience a maximally asymmetric hearing condition, as they have a CI on one ear and a contralateral NH ear. Despite the intact ear, several behavioural studies have demonstrated a variety of beneficial effects of restoring binaural hearing, but there are only few ERP studies which investigate auditory processing in SSD CI users. Our study investigates whether the side of implantation affects auditory processing and whether auditory processing via the NH ear of SSD CI users works similarly as in NH controls. Given the distinct hearing conditions of SSD CI users, the question arises whether there are any quantifiable differences between CI user with unilateral hearing loss and bilateral hearing loss. In general, ERP studies on SSD CI users are rather scarce, and there is no study on audiovisual processing in particular. Furthermore, there are no reports on lip-reading abilities of SSD CI users. To this end, in the third project we extend the first study by including SSD CI users as a third experimental group. The study discusses both differences and similarities between CI users with bilateral hearing loss and CI users with unilateral hearing loss as well as NH controls and provides — for the first time — insights into audiovisual interactions in SSD CI users. The fourth project investigates the influence of background noise on audiovisual interactions in CI users and whether a noise-reduction algorithm can modulate these interactions. It is known that in environments with competing background noise listeners generally rely more strongly on visual cues for understanding speech and that such situations are particularly difficult for CI users. As shown in previous auditory behavioural studies, the recently introduced noise-reduction algorithm "ForwardFocus" can be a useful aid in such cases. However, the questions whether employing the algorithm is beneficial in audiovisual conditions as well and whether using the algorithm has a measurable effect on cortical processing have not been investigated yet. In this ERP study, we address these questions with an auditory and audiovisual syllable discrimination task. Taken together, the projects included in this thesis contribute to a better understanding of auditory and especially audiovisual speech processing in CI users, revealing distinct processing strategies employed to overcome the limited input provided by a CI. The results have clinical implications, as they suggest that clinical hearing assessments, which are currently purely auditory, should be extended to audiovisual assessments. Furthermore, they imply that rehabilitation including audiovisual training methods may be beneficial for all CI user groups for quickly achieving the most effective CI implantation outcome

Phylogenetic trees and Euclidean embeddings

Thesis (M.S.) University of Alaska Fairbanks, 2014In this thesis we develop an intuitive process of encoding any phylogenetic tree and its associated tree-distance matrix as a collection of points in Euclidean space. Using this encoding, we find that information about the structure of the tree can easily be recovered by applying the inner product operation to vector combinations of the Euclidean points. By applying Classical Scaling to the tree-distance matrix, we are able to find the Euclidean points even when the phylogenetic tree is not known. We use the insight gained by encoding the tree as a collection of Euclidean points to modify the Neighbor Joining Algorithm, a method to recover an unknown phylogenetic tree from its tree-distance matrix, to be more resistant to tree-distance proportional errors

Inference Aware Neural Optimization for Top Pair Cross-Section Measurements with CMS Open Data

In recent years novel inference techniques have been developed based on the construction of summary statistics with neural networks by minimizing inference-motivated losses via automatic differentiation. The inference-aware summary statistics aim to be optimal with respect to the statistical inference goal of high energy physics analysis by accounting for the effects of nuisance parameters during the model training. One such technique is INFERNO (P. de Castro and T. Dorigo, Comp.\ Phys.\ Comm.\ 244 (2019) 170) which was shown on toy problems to outperform classical summary statistics for the problem of confidence interval estimation in the presence of nuisance parameters. In this thesis the algorithm is extended to common high energy physics problems based on a differentiable interpolation technique. In order to test and benchmark the algorithm in a real-world application, a complete, systematics-dominated analysis of the CMS experiment, "Measurement of the top-quark pair production cross section in the tau+jets channel in pp collisions at sqrt(s) = 7 TeV" (CMS Collaboration, The European Physical Journal C, 2013) is reproduced with CMS Open Data. The application of the INFERNO-powered neural network architecture to this analysis demonstrates the potential to reduce the impact of systematic uncertainties in real LHC analysis

Case-based cost estimation : a building block for product cost management and design-for-x

This thesis proposes a model for cost estimation of discrete mechanical parts in detail design. This model serves as a building block for product cost management and design-for-X

Structured Plasma Waveguides and Deep EUV Generation Enabled by Intense Laser-Cluster Interactions

Using the unique properties of the interaction between intense, short-pulse lasers and nanometer scale van-der-Waals bonded aggregates (or `clusters'), modulated waveguides in hydrogen, argon and nitrogen plasmas were produced and extreme ultraviolet (EUV) light was generated in deeply ionized nitrogen plasmas. A jet of clusters behaves as an array of mass-limited, solid-density targets with the average density of a gas. Two highly versatile experimental techniques are demonstrated for making preformed plasma waveguides with periodic structure within a laser-ionized cluster jet. The propagation of ultra-intense femtosecond laser pulses with intensities up to 2x1017 W/cm2 has been experimentally demonstrated in waveguides generated using both methods, limited by available laser energy. The first uses a `ring grating' to impose radial intensity modulations on the channel-generating laser pulse, which leads to axial intensity modulations at the laser focus within the cluster jet target. This creates a waveguide with axial modulations in diameter with a period between 35 μm and 2 mm, determined by the choice of ring grating. The second method creates modulated waveguides by focusing a uniform laser pulse within a jet of clusters with flow that has been modulated by periodically spaced wire obstructions. These wires make sharp, stable voids as short as 50 μm with a period as small as 200 μm within waveguides of hydrogen, nitrogen, and argon plasma. The gaps persist as the plasma expands for the full lifetime of the waveguide. This technique is useful for quasi-phase matching applications where index-modulated guides are superior to diameter modulated guides. Simulations show that these `slow wave' guiding structures could allow direct laser acceleration of electrons, achieving gradients of 80 MV/cm and 10 MV/cm for laser pulse powers of 1.9 TW and 30 GW, respectively. Results are also presented from experiments in which a nitrogen cluster jet from a cryogenically cooled gas valve was irradiated with relativistically intense (up to 2x1018 W/cm2) femtosecond laser pulses. The original purpose of these experiments was to create a transient recombination-pumped nitrogen soft x-ray laser on the 2p3/2→1s1/2 (λ = 24.779 Å) and 2p1/2→1s1/2 (λ = 24.785 Å) transitions in H-like nitrogen (N6+). Although no amplification was observed, trends in EUV emission from H-like, He-like and Li-like nitrogen ions in the 15 - 150 Å spectral range were measured as a function of laser intensity and cluster size. These results were compared with calculations run in a 1-D fluid laser-cluster interaction code to study the time-dependent ionization, recombination, and evolution of nitrogen cluster plasmas