Universitätsbibliothek und Universitätsarchiv der Universität für Bodenkultur

Short presentation of the Library of the University of Natural Resources and Life Sciences Vienn

Towards a Testbed for Dynamic Vehicle Routing Algorithms

Since modern transport services are becoming more flexible, demand-responsive, and energy/cost efficient, there is a growing demand for large-scale microscopic simulation platforms in order to test sophisticated routing algorithms. Such platforms have to simulate in detail, not only the dynamically changing demand and supply of the relevant service, but also traffic flow and other relevant transport services. This paper presents the DVRP extension to the open-source MATSim simulator. The extension is designed to be highly general and customizable to simulate a wide range of dynamic rich vehicle routing problems. The extension allows plugging in of various algorithms that are responsible for continuous re-optimisation of routes in response to changes in the system. The DVRP extension has been used in many research and commercial projects dealing with simulation of electric and autonomous taxis, demand-responsive transport, personal rapid transport, free-floating car sharing and parking search

From nanometers to centimeters: Imaging across spatial scales with smart computer-aided microscopy

Microscopes have been an invaluable tool throughout the history of the life sciences, as they allow researchers to observe the miniscule details of living systems in space and time. However, modern biology studies complex and non-obvious phenotypes and their distributions in populations and thus requires that microscopes evolve from visual aids for anecdotal observation into instruments for objective and quantitative measurements. To this end, many cutting-edge developments in microscopy are fuelled by innovations in the computational processing of the generated images. Computational tools can be applied in the early stages of an experiment, where they allow for reconstruction of images with higher resolution and contrast or more colors compared to raw data. In the final analysis stage, state-of-the-art image analysis pipelines seek to extract interpretable and humanly tractable information from the high-dimensional space of images. In the work presented in this thesis, I performed super-resolution microscopy and wrote image analysis pipelines to derive quantitative information about multiple biological processes. I contributed to studies on the regulation of DNMT1 by implementing machine learning-based segmentation of replication sites in images and performed quantitative statistical analysis of the recruitment of multiple DNMT1 mutants. To study the spatiotemporal distribution of DNA damage response I performed STED microscopy and could provide a lower bound on the size of the elementary spatial units of DNA repair. In this project, I also wrote image analysis pipelines and performed statistical analysis to show a decoupling of DNA density and heterochromatin marks during repair. More on the experimental side, I helped in the establishment of a protocol for many-fold color multiplexing by iterative labelling of diverse structures via DNA hybridization. Turning from small scale details to the distribution of phenotypes in a population, I wrote a reusable pipeline for fitting models of cell cycle stage distribution and inhibition curves to high-throughput measurements to quickly quantify the effects of innovative antiproliferative antibody-drug-conjugates. The main focus of the thesis is BigStitcher, a tool for the management and alignment of terabyte-sized image datasets. Such enormous datasets are nowadays generated routinely with light-sheet microscopy and sample preparation techniques such as clearing or expansion. Their sheer size, high dimensionality and unique optical properties poses a serious bottleneck for researchers and requires specialized processing tools, as the images often do not fit into the main memory of most computers. BigStitcher primarily allows for fast registration of such many-dimensional datasets on conventional hardware using optimized multi-resolution alignment algorithms. The software can also correct a variety of aberrations such as fixed-pattern noise, chromatic shifts and even complex sample-induced distortions. A defining feature of BigStitcher, as well as the various image analysis scripts developed in this work is their interactivity. A central goal was to leverage the user's expertise at key moments and bring innovations from the big data world to the lab with its smaller and much more diverse datasets without replacing scientists with automated black-box pipelines. To this end, BigStitcher was implemented as a user-friendly plug-in for the open source image processing platform Fiji and provides the users with a nearly instantaneous preview of the aligned images and opportunities for manual control of all processing steps. With its powerful features and ease-of-use, BigStitcher paves the way to the routine application of light-sheet microscopy and other methods producing equally large datasets

Orient/East-Med Corridor: Challenges and Demands for the Rail Network Policies

As rail represents an efficient and sustainable transport system, the Trans-European railway network has become subject to special attention from European transport policy. The political objectives are to shift 30% of freight to rail by 2030, 50% by 2050, and to reduce passenger trips on road and in the air. These make it necessary to develop the defined TEN-T core network rail corridors as a priority, which means eliminating bottlenecks along the corridors and increasing capacities and operation quality. This concerns the Orient/East-Med (OEM) Core Network Corridor as well. Considerable parts of the infrastructure of the railway network along the OEM Corridor is not compliant with some of the technical thresholds set out by EU-Regulation 1315/2013. In the meanwhile the EU and the affected states have established activities for extending the core network corridors to the Western Balkans states. In 2015, the European Commission adopted a Joint Statement of the Prime Ministers of six Western Balkans states (WB6), which contains a list of specified Core Network links and Priority Projects for the extension of the TEN-T network to the Western Balkans. During additional common summits of the EU and the WB6, an indicative extension network has been more and more concretized. To date the process has led to the establishment of a common EU-Western Balkans Transport Community signed in 2017, which aims to help WB6 countries integrate into the EU by creating closer transport ties or connections. A continuing aspect is the importance of the OEM Corridor for the Chinese Belt and Road Initiative as a hinterland connection between the sea port of Piraeus (GR) and the central and eastern European countries.Als effizienter und nachhaltiger Verkehrsträger hat die Schiene auch in der europäischen Verkehrspolitik und somit auch im transeuropäischen Eisenbahnnetz besondere Aufmerksamkeit bekommen. So sind als verkehrspolitische Ziele die Verlagerung von 30% des Güterverkehrs auf die Schiene bis 2030, von 50% bis 2050 und die Reduzierung des Personentransportes auf der Straße und in der Luft formuliert. Diese Ziele erfordern die vorrangige Entwicklung definierter TEN-V-Kernnetz-Eisenbahnkorridore. Dies umfasst die Beseitigung von Engpässen entlang der Korridore, sowie die Steigerung von Kapazitäten und Betriebsqualitäten. Dies betrifft auch den Orient/ East-Med (OEM) Core Network Corridor. Große Teile der Infrastruktur des Eisenbahnnetzes entlang des OEM Corridors entsprechen nicht den technischen Standards der EU-Verordnung 1315/2013. Mittlerweile haben die EU und die betroffenen Staaten Maßnahmen zur Ausweitung der Kernnetzkorridore auf die Westbalkanstaaten eingeleitet. Im Jahr 2015 verabschiedete die Europäische Kommission eine Gemeinsame Erklärung der Premierminister von sechs Westbalkanstaaten (WB6), die eine Liste spezifischer Kernnetzwerkverbindungen und prioritärer Projekte für die Ausdehnung des TEN-V-Netzes auf den Westbalkan beinhaltet. Bei weiteren gemeinsamen Gipfeltreffen der EU und der WB6 wurde ein indikatives Erweiterungsnetz zunehmend konkreter. Dieser Prozess hat bisher zur Gründung einer gemeinsamen Verkehrsgemeinschaft EU-Westbalkan geführt, die 2017 unterzeichnet wurde und darauf abzielt, die Integration der WB6-Länder in die EU durch engere Verkehrsbeziehungen oder -verbindungen zu unterstützen. Ein weiterer Aspekt ist die Bedeutung des OEM Corridors für die Chinese Belt and Road Initiative als Hinterlandverbindung zwischen dem Seehafen Piräus (GR) und den mittel- und osteuropäischen Ländern

From nanometers to centimeters: Imaging across spatial scales with smart computer-aided microscopy

Microscopes have been an invaluable tool throughout the history of the life sciences, as they allow researchers to observe the miniscule details of living systems in space and time. However, modern biology studies complex and non-obvious phenotypes and their distributions in populations and thus requires that microscopes evolve from visual aids for anecdotal observation into instruments for objective and quantitative measurements. To this end, many cutting-edge developments in microscopy are fuelled by innovations in the computational processing of the generated images. Computational tools can be applied in the early stages of an experiment, where they allow for reconstruction of images with higher resolution and contrast or more colors compared to raw data. In the final analysis stage, state-of-the-art image analysis pipelines seek to extract interpretable and humanly tractable information from the high-dimensional space of images. In the work presented in this thesis, I performed super-resolution microscopy and wrote image analysis pipelines to derive quantitative information about multiple biological processes. I contributed to studies on the regulation of DNMT1 by implementing machine learning-based segmentation of replication sites in images and performed quantitative statistical analysis of the recruitment of multiple DNMT1 mutants. To study the spatiotemporal distribution of DNA damage response I performed STED microscopy and could provide a lower bound on the size of the elementary spatial units of DNA repair. In this project, I also wrote image analysis pipelines and performed statistical analysis to show a decoupling of DNA density and heterochromatin marks during repair. More on the experimental side, I helped in the establishment of a protocol for many-fold color multiplexing by iterative labelling of diverse structures via DNA hybridization. Turning from small scale details to the distribution of phenotypes in a population, I wrote a reusable pipeline for fitting models of cell cycle stage distribution and inhibition curves to high-throughput measurements to quickly quantify the effects of innovative antiproliferative antibody-drug-conjugates. The main focus of the thesis is BigStitcher, a tool for the management and alignment of terabyte-sized image datasets. Such enormous datasets are nowadays generated routinely with light-sheet microscopy and sample preparation techniques such as clearing or expansion. Their sheer size, high dimensionality and unique optical properties poses a serious bottleneck for researchers and requires specialized processing tools, as the images often do not fit into the main memory of most computers. BigStitcher primarily allows for fast registration of such many-dimensional datasets on conventional hardware using optimized multi-resolution alignment algorithms. The software can also correct a variety of aberrations such as fixed-pattern noise, chromatic shifts and even complex sample-induced distortions. A defining feature of BigStitcher, as well as the various image analysis scripts developed in this work is their interactivity. A central goal was to leverage the user's expertise at key moments and bring innovations from the big data world to the lab with its smaller and much more diverse datasets without replacing scientists with automated black-box pipelines. To this end, BigStitcher was implemented as a user-friendly plug-in for the open source image processing platform Fiji and provides the users with a nearly instantaneous preview of the aligned images and opportunities for manual control of all processing steps. With its powerful features and ease-of-use, BigStitcher paves the way to the routine application of light-sheet microscopy and other methods producing equally large datasets