Publication Server of Constructor University Library
Not a member yet
858 research outputs found
Sort by
Trace Elements in Mussel Shells as potential Tools for Environmental Reconstructions
No full textRising atmospheric CO2 from anthropogenic sources has led to many changes in the earth ecosystem. To better understand this phenomenon, proxies are being developed to simulate past conditions. The models can be used to accurately predict the future based on the understanding of the climate conditions and changes of the past.
Mussels incorporate trace metals into their shells and chemical analysis of the growth bands is then possible due to the fact that shells are composed of sequentially deposited layers of mineralized material, which are laid down according to the growth of the organism.
Intra-species variability in trace elements, specifically the Rare earths and Yttrium (REY) was investigated using Mytilus edulis shells. Findings through a comparison of the partitioning coefficient patterns to the REY speciation in seawater suggests that the free REY3+ are the likely species incorporated into the shells Additionally, absolute REY concentrations in M. edulis shells may have the potential to be used as a pH proxy, whereas REYSN distribution patterns of the shells may rather be used as a temperature proxy.
Furthermore, trace metal concentrations in shells of Mytilus edulis, Arctica islandica and Serripes groenlandicus, were compared. This thesis highlights the fact that REY and other trace metal accumulations in the shells of mussels from different species is not the same and that there are indeed significant differences in the accumulation of most of the elements between the different species.
Lastly, the possibilities of analyzing trace metals along the growth lines of the M. edulis shells that were grown in a culturing experiment with four different pCO2 conditions are explored. The behavior of the different metal/Ca ratios across the different pCO2 conditions revealed some possible trends that could possibly allow the elements to be used as proxies by responding to changes in pCO2 conditions
Identification and optimisation of bacterial caseinolytic protease inhibitors as potential novel antibiotics
No full textAntibiotic resistance has become a world-wide problem as the number of resistant and multi-resistant bacteria has dramatically increased over the last years, especially for Gram-negative bacteria.
The PhD project, part of INTEGRATE, a multidisciplinary Marie Curie Educational Training Network (ETN), concerned the identification and characterization of small molecule modulators of the enzyme Caseinolytic protease proteolytic subunit (ClpP). ClpP is a serine protease and it has been proposed as an antibacterial target because of its central roles in many essential bacterial cellular processes. The main aim of this work is the identification of inhibitors directed against ClpP from Gram-negative bacteria, using E. coli as model organism.
An in vitro target-centric approach was adopted to identify novel hits by screening collections of small molecules, including diverse compounds. Selected compounds were profiled in biochemical assays and confirmed in biophysical readouts. For the most promising compounds, potential cytotoxicity against selected human cell lines was evaluated. The compound efficacy as an anti-bacterial in the presence and absence of selected stress condition and the hypothetical binding mode (using in silico approaches) were determined. In parallel, an ongoing structural biology effort is ongoing to reveal information on the interaction between selected compounds and ClpP and validate the computational models.
With this PhD thesis, further validation of the existence of phenotypic ClpP-related effects in E. coli can be found and new evidence provided for the role of ClpP as a valid target in Escherichia coli and Gram-negative bacteria antibiotic research. This thesis reports several compounds active in vitro in the low micromolar or sub-micromolar range, with an acceptable safety profile and with possible ClpP-related activity in bacteria. This study must be seen as an important starting point for further development inhibitors in follow on studies
Auditory Display for Image-Guided Medical Interventions
No full textImage-guidance systems help the clinician view patient images, see the location of tracked tools, or become aware of important factors such as instrument measurement values. Although this information is essential when completing many modern procedures, current methods for delivering intraoperative information rely primarily on computer screens within the operating room to display information. This is a significant drawback, because clinicians must often change between viewing patient and screen and might not be aware of immediate changes, resulting in increased time, inaccuracy, and frustration. The dissertation investigates auditory display to improve information display in the operating room. Novel techniques for transmitting the position of tracked instruments in image-guided procedures are presented, including medical needle placement, robotic endoscope and manual laparoscope guidance, and dissector guidance during liver resection. These give the operator auditory display to improve guidance of tracked tools within the body either as an augmentation to existing visual display or to allow screen-free navigation guidance. In addition, a method for hearing fluorescence intensities measured during open brain surgery is presented. Finally, two auditory display approaches are investigated as feedback for novel touchless input using eye tracking and freehand gestures to improve usability and performance. The results of clinically oriented evaluations show that auditory display provides significant advantages in the scope of the selected clinical use cases. The benefits of auditory or combined audiovisual display compared to visual-only display include, in most use cases, increases in accuracy, decrease in cognitive workload, and increases in usability. Drawbacks included increases in task completion time and in some cases, increase in cognitive workload. This dissertation clearly shows that auditory display has a promising future in the operating room
Synthesis of Mono-Functionalized Cucurbit[n]urils and Exploration of Their Applications
No full textThe present doctoral thesis describes the synthetic procedure of clickable mono-functionalized cucurbit[n]urils (n = 6, 7) and mainly on the exploration of new applications based on the mono-functionalized CBn. In principle, with the functionalized clickable group, various functionalized CBn derivatives can be achieved. One explored application is based on a chromophore attached to CB7 which makes the host molecule fluorescent and enables it to form a host-guest FRET pair with a corresponding fluorescent guest, which can be applied to DNA sensing. The other one is based on the functionalization of CB7 on the surface of nano-/macro-particles, thus can be applied to quantify the surface coverage densities of particles.
In particular, the first part of the thesis focuses on the synthesis and characterizations of mono-functionalized CB6 and CB7, including mono-hydroxylated CB6 or CB7, propargyl attached CB6 or CB7, and fluorophore attached CB6 or CB7, and related compounds. The second part of the thesis reports a host-guest FRET pair based on the macrocyclic host CB7 labelled with carboxyfluorescein as acceptor and the nucleic stain DAPI as donor and guest. This supramolecular FRET pair is to be used for quantitative sensing of DNA with an excellent linear dependence of the ratiometric fluorescence intensities. Such approach can be applied to quantify DNA accurately and potentially be used in real-time PCR. The third part of the thesis demonstrates a strategic supramolecular application to precisely control the coverage densities on the surface of nano-/macro-particles. The key is to functionalize CB7 on the surface of particles. After that, incubation of CB7-functionalized particles application-relevant guests.
In the last part, I summarize the main projects during my PhD and give the outlook about exploring more applications based on mono-functionalized CB7
Modeling and Simulation of Microwave Ablation of Liver Tumors
No full textThe goal of this research is to study, understand, and robustly model and simulate microwave ablation of liver tumors. This is one of the possible treatments for cancerous tumors that appear in the liver, and there is room for a better understanding and prediction of how such interventions develop, from a mathematical point of view. The areas that could benefit from a more rigorous quantification range from planning of the invasive aspect of the procedure, influence of the vascular system, all the way to predicting the resulting damage in biological tissue. This would ultimately also benefit clinicians, that have much to gain from such results, as it would allow them to plan microwave ablation procedures on a patient-to-patient basis, thus obtaining a better outcome.
This research has been done under the supervision of Prof. Dr. Tobias Preußer, Head of Modeling and Simulation at Fraunhofer MEVIS, and Professor of Mathematics at Jacobs University Bremen, as well as Prof. Dr. Marcel Oliver, Professor of Mathematics at Jacobs University Bremen. I have also been supervised by Dr. Hanne Ballhausen and Dr. Torben Pätz, from Fraunhofer MEVIS, throughout various phases of my research
A computational cognitive process model for multi-alternative multi-attribute preferential choice
No full textThe 2N-ary choice tree model, a computational cognitive process model of multi-alternative multi-attribute preferential choice is proposed, revised, tested for its ability to simulate three benchmark context effects and interactions between them, and compared with earlier and more recent theories. The 2N-ary choice tree model assumes that the decision maker, given a set of N choice alternatives that are described by the same attributes, repeatedly compares pairs of attribute values and counts how often each alternative wins and loses a comparison. The number of favorable and unfavorable comparisons is stored in two separate counters per alternative and the difference of the counter states forms the preference state for the respective alternative. If the preference state for an alternative hits a negative threshold, this alternative is eliminated from the choice set and the comparison process continues without it. On the other hand, if the preference state for an alternative hits a positive threshold, this alternative is chosen and the whole process stops. The simple choice tree model, a revised version of the 2N-ary choice tree model, introduces an additional parameter for regulating the focus on the winning or losing alternative in a comparison, which has an effect on the proportion of choices and eliminations that take place. The 2N-ary choice tree model and the simple choice tree model are both able to explain similarity, attraction, and compromise effects, three context effects that have been observed after adding a third option to a set of two choice alternatives. With its additional parameter, the simple choice tree model beyond that accounts for recently observed correlations between these effects. It is the only model that accounts for the whole range of related findings, including negative similarity, attraction, and compromise effects
The circulation and distribution of heat within Warm Deep Water in the Weddell Gyre: an Argo float perspective
No full textThe Weddell Gyre (WG) supplies heat towards the Antarctic ice shelves and regulates the density of water masses that feed the deepest limb of the global overturning circulation. Our understanding of WG hydrography is limited due to sparse data availability. Long-term trends are masked by significant variability, and previous estimates show a large range in the strength of the WG’s circulation.
In this thesis, Argo float profile and trajectory data spanning the WG from 2002-2016 are utilised to determine the horizontal circulation and heat distribution within Warm Deep Water (WDW): the primary heat source to the WG. Objective mapping is applied, providing maps of temperature and salinity for 50-2000 dbar. The stream function is obtained, from which horizontal circulation is described. Volume transports are calculated and placed into context of historical estimates. The heat budget for a 1000 m thick layer encompassing the core of WDW is presented, to investigate mechanisms of heat distribution throughout the WG.
The circulation describes an elongated, cyclonic, double-cell gyre. The weaker western cell is barotropic and the stronger eastern cell is influenced by baroclinic shear. There is an inflow of 83 ± 22 Sv into the WG (28 ± 7 Sv WDW). Significant recirculation in the gyre interior is observed (71 ± 28 Sv, 15 ± 8 Sv is WDW). The large variation in previous estimates of the WG strength is likely due to zonal variation in the gyre structure. There is a balance between mean horizontal advection and horizontal turbulent diffusion (representative of eddy processes). Heat is turbulently diffused northward from the southern limb into the interior cell (6.5 ± 3 TW), and coastward towards the ice shelves (inferred as 12.5 ± 10 TW). One outstanding question concerns the response of the double-cell circulation to long-term changes in the wind field, and how this might alter the mechanisms by which heat is injected into and subsequently redistributed throughout the WG
Spectral Learning of Sequential Systems
No full textStochastic multiplicity automata (SMA) are weighted nondeterministic au- tomata that generalize probabilistic automata and have been used in the context of probabilistic grammatical inference. Observable operator mod- els (OOMs) are a generalization of hidden Markov models, which in turn are models for discrete-valued stochastic processes used ubiquitously in the context of speech recognition and bio-sequence modeling. Predictive state representations (PSRs) extend OOMs to stochastic input-output systems and are employed in the context of agent modeling and planning.
In this thesis we first unify these statistical models under the framework of sequential systems (SSs), which are abstract linear algebraic models for certain types of functions on words. The required parts of the theory of SS are presented in a self-contained and easily accessible fashion. We proceed to show how many of the available learning algorithms for these models can be understood as instances of a common learning procedure.
Our focus lies on the state-of-the-art spectral learning algorithm. We gen- eralize two recent learning algorithms for OOMs that are based on entirely di↵erent learning principles and show that these are in fact equivalent or closely related to spectral learning. We improve methods for two key steps that are required in all learning algorithms, namely the selection of “charac- teristic” words and of a suitable model dimension. Furthermore, we develop a new weighted spectral learning algorithm that incorporates weights that take the precision of individual estimates into account and show empirically that these modifications indeed improve standard spectral learning.
Finally, we address the previously unresolved problem of learning OOMs from data that contains missing values
An Intelligent and Robust System for Underwater Vision
No full textCameras are one of the most common sensors in robotics. They are used in both research and industrial applications. Underwater images suffer from extremely unfavourable conditions. Light is heavily attenuated and scattered. Furthermore, underwater images are distorted due to refraction through water-glass-air interfaces. All of this makes using cameras underwater exceptionally difficult.
Work presented in this thesis is mainly motivated by the needs of three EU-founded projects: MORPH, CADDY and DexROV. Work in these projects resulted in development at every stage in the design, calibration and image processing of underwater vision systems
The first part introduces investigated research problems, and describes the background and motivation of the thesis. Furthermore, exemplar projects are described to give a good intuition of the state of the art and what advances have been made in this thesis.
The second part of this thesis describes the issue of refraction-based distortions. An extensive analysis of the problem is undertaken using a novel method, dubbed Pinax, that allows for very efficient and accurate modelling of submerged cameras. The Pinax model does not require any underwater calibration: a single in-air procedure is sufficient to handle a variety of underwater environments, including different salinities, temperatures and pressures.
The third part focuses on designing the stereo vision system from the perspective of selecting hardware and setup parameters that would perform best in a given task.
Part IV addresses the problem of image degradation. The image formation process is discussed and an adaptation of the Dark Channel Prior to underwater conditions is proposed. This resulted with an image correction algorithm that allows for a reduction in backscattering in the registered images.
Part V describes of the practical applications of the methods presented earlier. The achieved results are discussed in terms of their real-life applications
Model order reduction of linear and nonlinear systems in the Loewner framework
No full textThe Loewner framework is an interpolatory model order reduction technique that uses measured or computed data, e.g., measurements of the frequency response of
a to-be approximated dynamical system instead of the system matrices, and constructs reduced models based on a rank revealing factorization of appropriately constructed matrices.
In this thesis, we propose extensions of the classical Loewner framework for reduction of linear systems to some specific applications such as reducing classes of mildly nonlinear systems. The later includes bilinear, quadratic-bilinear and linear switched systems.
The motivation behind this endeavor is that some of these aforementioned classes of systems can be viewed as a bridge between linear and nonlinear systems. For example, one can always write an approximation of a nonlinear system by means of a bilinear system. Moreover, for certain types of nonlinear systems, we can always find an equivalent quadratic-bilinear model without performing any approximation. Linear switched systems have been extensively studied in the literature since they offer a valuable addition to the class of linear systems, although reduction of such systems is arguably new. They can also be viewed as an intermediate step towards hybrid systems.
For all the classes of systems that were previously mentioned, the overall strategy for extending the Loewner framework is conceptually similar. After collecting samples of input/output frequency domain mappings, e.g., either by means of measuring or by direct computation, one makes use of a specific arrangement of the data in matrix format. Hence, following some theoretical considerations, one can build reduced order models directly from the given data. The reduced systems have similar response to the large-scale original systems. More exactly, the input/output mappings for both systems have similar characteristics in the frequency range where the samples were considered