27 research outputs found
Most vital segment barriers
We study continuous analogues of "vitality" for discrete network flows/paths,
and consider problems related to placing segment barriers that have highest
impact on a flow/path in a polygonal domain. This extends the graph-theoretic
notion of "most vital arcs" for flows/paths to geometric environments. We give
hardness results and efficient algorithms for various versions of the problem,
(almost) completely separating hard and polynomially-solvable cases
Establishing super-resolution imaging of biosilica-embedded proteins in diatoms
Kieselalgen – auch Diatomeen genannt – verfügen über die einzigartige Fähigkeit, nanostrukturierte, hierarchisch aufgebaute Zellwände aus Siliziumdioxid – auch als Biosilica bekannt – mit beispielloser Genauigkeit und Reproduzierbarkeit zu bilden. Ein tieferes Verständnis für diesen Prozess, der als “Biomineralisation“ bekannt ist, ist nicht nur auf dem Gebiet der Grundlagenforschung zu Kieselalgen sehr bedeutsam, sondern auch für die Nutzung dieser Nanostrukturierung in den Materialwissenschaften oder der Nanobiotechnologie. Nach dem derzeitigem Stand der Wissenschaft wird diese Strukturierung durch die Selbstorganisation von Proteinmustern, an denen sich das Siliziumdioxid bildet, erreicht. Um die Funktion und das Zusammenspiel einzelner Proteine, die an diesem Biomineralisationsprozess beteiligt sind, entschlüsseln zu können, ist es essentiell ihre strukturelle Organisation aufzuklären und diese mit den morphologischen Zellwandmerkmalen zu korrelieren. Die Größenordnung dieser Merkmale ist im Bereich von Nanometern angesiedelt. Mit Hilfe der Elektronenmikroskopie können diese Biosilicastrukturen aufgelöst werden, jedoch ist keine proteinspezifische Information verfügbar. Ziel dieser Arbeit war es daher, eine Technik zu etablieren, die in der Lage ist, einzelne Biosilica-assozierte Proteine mit Nanometer-Präzision zu lokalisieren.
Um dieses Ziel zu erreichen, wurde Einzelmoleküllokalisationsmikroskopie (single-molecule localization microscopy, kurz: SMLM) beispielhaft in der Kieselalge Thalassiosira pseudonana etabliert. Die Position verschiedener Biosilica-assoziierte Proteine innerhalb des Biosilicas und nach dessen chemischer Auflösung wurde mit einer hohen räumlichen Auflösung bestimmt. Um quantitative Ergebnisse zu erhalten, wurde ein Analyse-Workflow entwickelt, der grafische Benutzeroberflächen und Skripte für die Visualisierung, das Clustering und die Kolokalisation von SMLM Daten beinhaltet.
Um optimale Markierungen für SMLM an Biosilica-eingebetteten Proteinen zu finden, wurde ein umfassendes Screening von photo-schaltbaren fluoreszierenden Proteinen durchgeführt. Diese wurden als Fusionsproteine mit Silaffin3, einem Protein, welches eng mit der Biosilica-Zellwand assoziiert ist, exprimiert. Es konnte gezeigt werden, dass nur drei von sechs Kandidaten funktional sind, wenn sie in Biosilica eingebettet sind. Silaffin3 konnte indirekt mittels SMLM mit einer Lokalisationsgenauigkeit von 25 nm detektiert werden. Dies erlaubte es, seine strukturelle Organisation aufzulösen und Silaffin3 als eine Hauptkomponente in der Basalkammer der Fultoportulae zu identifizieren.:1 INTRODUCTION 1
1.1 Diatoms – a model system for biomineralization 3
1.2 Imaging of biosilica and associated organic components 8
1.3 Single-molecule localization microscopy (SMLM) 10
2 METHODS & METHOD DEVELOPMENT FOR SMLM DATASETS 17
2.1 Super-resolution reconstruction 19
2.2 Tools for SMLM resolution estimates 21
2.3 Voronoi tessellation for noise-removal and cluster estimation 25
2.4 Tools for SMLM cluster analysis 27
2.5 Coordinate-based co-localization 32
2.6 PairRice – A novel algorithm to extract distances between cluster pairs 33
2.7 SiMoNa – A new GUI for exploring SMLM datasets 35
3 RESOLUTION OF THE SMLM SETUP TESTED WITH DNA ORIGAMI NANOSTRUCTURES 41
3.1 DNA origami as a length standard 42
3.2 Global resolution estimates 44
3.3 Local resolution estimates 47
3.4 Conclusion 53
4 EVALUATION OF PHOTO-CONTROLLABLE FLUORESCENT PROTEINS FOR PALM IN DIATOMS 55
4.1 Selecting PCFPs to minimize interference with the diatom autofluorescence 56
4.2 Screening results for cytosolic and biosilica-embedded PCFPs 58
4.3 The underlying conversion mechanism 61
4.4 Conclusion 63
5 IMAGING THE SIL3 MESHWORK 65
5.1 Analyzing protein layer thickness using tpSil3-Dendra2 65
5.2 Imaging the valve region using tpSil3 68
5.3 Resolution and localization parameters of tpSil3 70
5.4 Conclusion 72
6 DECIPHERING CINGULIN PATTERNS WITH CO LOCALIZATION STUDIES 73
6.1 A two-color cingulin construct for PALM-STORM 73
6.2 Steps towards PALM-STORM: screening, alignment, and imaging routine 76
6.3 Co-localization studies: quantification, clustering, and correlations 83
6.4 Conclusion 91
7 OUTLOOK 93
8 MATERIALS & METHODS 97
8.1 Microscope specifications 97
8.2 DNA origami annealing and AFM measurements 99
8.3 Diatom sample preparations 100
8.4 Fluorescence imaging conditions 102
8.5 Buffer systems 103
9 APPENDICES 105
9.1 Tables and Protocols 105
9.2 Satellite projects 112
9.2.1 Quantitative fluorescence intensity analysis of 3D time-lapse confocal microscopy data in diatoms 112
9.2.2 Applying neural networks to filter SMLM localizations 118
9.2.3 In vivo imaging at super-resolution conditions using SOFI 121
9.2.4 Quantifying chromatic aberrations in the microscope using fiducials 123
10 REFERENCES 127Diatoms feature the unique ability to form nanopatterned hierarchical silica cell walls with unprecedented accuracy and reproducibility. Gathering a deeper understanding of this process that is known as “biomineralization” is vitally important not only in the field of diatom research. In fact, the nanopatterning can also be exploited in the fields of material sciences or nanobiotechnology. According to the current understanding, the self-assembly of protein patterns along which biosilica is formed is key to this nanopatterning. Thus, in order to unravel the function of individual proteins that are involved in this biomineralization process, their structural organization has to be deciphered and correlated to morphological cell wall features that are in the order of tens of nanometer. Electron microscopy is able to resolve these features but does not provide protein-specific information. Therefore, a technique has to be established that is able to localize individual biosilica-associated proteins with nanometer precision.
To achieve this objective, single-molecule localization microscopy (SMLM) for the diatom Thalassiosira pseudonana has been pioneered and exploited to localize different biosilica associated proteins inside silica and after silica removal. To obtain quantitative data, an analysis workflow was developed including graphical user interfaces and scripts for SMLM visualization, clustering, and co-localization.
In order to find optimal labels for SMLM to target biosilica-embedded proteins, a comprehensive screening of photo-controllable fluorescent proteins has been carried out. Only three of six candidates were functional when embedded inside biosilica and fused to Silaffin3 – a protein that is tightly associated with the biosilica cell wall. Silaffin3 could be localized using SMLM with a localization precision of 25 nm. This allowed to resolve its structural organization and therefore identified Silaffin3 as a major component in the basal chamber of the fultoportulae.
Additionally, co-localization studies on cingulins – a protein family hypothesized to be involved in silica formation – have been performed to decipher their pattern-function relationship. Towards this end, novel imaging strategies, co-localization calculations and pattern quantifications have been established. With the help of these results, the spatial arrangement of cingulins W2 and Y2 could be compared with unprecedented resolution.
In summary, this work has laid ground for quantitative SMLM studies of proteins in diatoms in general and contributed insights into the spatial organization of proteins involved in biomineralization in the diatom T. pseudonana.:1 INTRODUCTION 1
1.1 Diatoms – a model system for biomineralization 3
1.2 Imaging of biosilica and associated organic components 8
1.3 Single-molecule localization microscopy (SMLM) 10
2 METHODS & METHOD DEVELOPMENT FOR SMLM DATASETS 17
2.1 Super-resolution reconstruction 19
2.2 Tools for SMLM resolution estimates 21
2.3 Voronoi tessellation for noise-removal and cluster estimation 25
2.4 Tools for SMLM cluster analysis 27
2.5 Coordinate-based co-localization 32
2.6 PairRice – A novel algorithm to extract distances between cluster pairs 33
2.7 SiMoNa – A new GUI for exploring SMLM datasets 35
3 RESOLUTION OF THE SMLM SETUP TESTED WITH DNA ORIGAMI NANOSTRUCTURES 41
3.1 DNA origami as a length standard 42
3.2 Global resolution estimates 44
3.3 Local resolution estimates 47
3.4 Conclusion 53
4 EVALUATION OF PHOTO-CONTROLLABLE FLUORESCENT PROTEINS FOR PALM IN DIATOMS 55
4.1 Selecting PCFPs to minimize interference with the diatom autofluorescence 56
4.2 Screening results for cytosolic and biosilica-embedded PCFPs 58
4.3 The underlying conversion mechanism 61
4.4 Conclusion 63
5 IMAGING THE SIL3 MESHWORK 65
5.1 Analyzing protein layer thickness using tpSil3-Dendra2 65
5.2 Imaging the valve region using tpSil3 68
5.3 Resolution and localization parameters of tpSil3 70
5.4 Conclusion 72
6 DECIPHERING CINGULIN PATTERNS WITH CO LOCALIZATION STUDIES 73
6.1 A two-color cingulin construct for PALM-STORM 73
6.2 Steps towards PALM-STORM: screening, alignment, and imaging routine 76
6.3 Co-localization studies: quantification, clustering, and correlations 83
6.4 Conclusion 91
7 OUTLOOK 93
8 MATERIALS & METHODS 97
8.1 Microscope specifications 97
8.2 DNA origami annealing and AFM measurements 99
8.3 Diatom sample preparations 100
8.4 Fluorescence imaging conditions 102
8.5 Buffer systems 103
9 APPENDICES 105
9.1 Tables and Protocols 105
9.2 Satellite projects 112
9.2.1 Quantitative fluorescence intensity analysis of 3D time-lapse confocal microscopy data in diatoms 112
9.2.2 Applying neural networks to filter SMLM localizations 118
9.2.3 In vivo imaging at super-resolution conditions using SOFI 121
9.2.4 Quantifying chromatic aberrations in the microscope using fiducials 123
10 REFERENCES 12
Geospatial Framework for the Use of Natural Resource Extraction in Public Private Partnerships
Resources for the maintenance and expansion of existing highway infrastructure are scarce. Public Private Partnerships (PPP) are feasible solutions to the concern of lagging investment. PPP are increasingly used for the procurement of services and goods, because of their flexibility and ability to channel private resources. This research addresses the possible implementation of a barter approach in Public Private Partnerships (PPP), which includes natural resources for trade model to offset costs.;Federal law permits the extraction of coal when it is a byproduct of the construction process, coal which under normal circumstances would not be economically feasible to extract. West Virginia law allows PPP to extract coal by surface mining when they develop road beads for new highways. There is no exchange of funds between the coal company and the West Virginia Department of Transportation; the benefits are derived entirely from the construction cost savings for roadbed construction.;This dissertation develops a geospatial method to quantify the availability of natural resources along predetermined roadway alignments. The methodology is divided in three phases: Macroscopic (Level I), Mesoscopic (Level II) and Microscopic (Level III), for the King Coal Highway. The process considers laws and industry best practices in the calculation. The research outcome suggests that there are segments of the road with enough, as well as segments of the road without enough coal
Vector Graphics for Real-time 3D Rendering
Algorithms are presented that enable the use of vector graphics representations
of images in texture maps for 3D real time rendering.
Vector graphics images are resolution independent and
can be zoomed arbitrarily without losing detail
or crispness. Many important types of images, including text and
other symbolic information, are best represented in vector form. Vector
graphics textures can also be used as transparency mattes to augment
geometric detail in models via trim curves.
Spline curves are used to represent boundaries around regions
in standard vector graphics representations, such as PDF and SVG.
Antialiased rendering of such content can be obtained by thresholding
implicit representations of these curves.
The distance function is an especially useful implicit representation.
Accurate distance function computations would also allow the implementation
of special effects such as embossing.
Unfortunately, computing the true distance to higher order spline curves
is too expensive for real time rendering.
Therefore, normally either the distance is approximated
by normalizing some other implicit representation
or the spline curves are approximated with simpler primitives.
In this thesis, three methods for
rendering vector graphics textures in real time are introduced,
based on various approximations of the distance computation.
The first and simplest approach to the distance computation
approximates curves with line segments.
Unfortunately, approximation with line segments gives only C0 continuity.
In order to improve smoothness, spline curves can also be approximated
with circular arcs.
This approximation has C1 continuity and computing the distance
to a circular arc is only slightly more expensive than
computing the distance to a line segment.
Finally an iterative algorithm
is discussed that has good performance in practice and can compute the
distance to any parametrically differentiable curve
(including polynomial splines of any order)
robustly. This algorithm is demonstrated in the context of a system
capable of real-time rendering of SVG content in a texture map on a GPU.
Data structures and acceleration algorithms in the context of massively
parallel GPU architectures are also discussed.
These data structures and acceleration structures allow arbitrary vector
content (with space-variant complexity, and overlapping regions) to be
represented in a random-access texture
Multi-Scale Integral Invariants for Robust Character Extraction from Irregular Polygon Mesh Data
Hunderttausende von antiken Dokumenten in Keilschrift befinden sich in Museen, und täglich werden weitere bei archäologischen Grabungen gefunden. Die Auswertung dieser Dokumente ist wesentlich für das Verständnis der Herkunft von Kultur, Gesetzgebung und Religion. Die Keilschrift ist eine Handschrift und wurde in den Jahrtausenden vor Christi Geburt im gesamten alten Orient benutzt. Der Name leitet sich von den keilförmigen Eindrücken eines Schreibgriffels in den weichen Beschreibstoff Ton ab. Das Anfertigen von Handzeichnungen und Transkriptionen dieser Tontafeln ist eine langwierige Aufgabe und verlangt nach Unterstützung mittels automatisierter rechnergestützter Verfahren.
Das Ziel dieser Arbeit ist die präzise Extraktion von Schriftzeichen mit variablen Formen in 3D. Die für die Merkmalsextraktion aus 2D-Mannigfaltigkeiten in 3D entscheidenden Schritte sind Kantenerkennung und Segmentierung. Robuste Techniken in der Signalverarbeitung und dem Shape Matching benutzen hierfür Integralinvarianten in 2D. In aktuellen Arbeiten werden die Integralinvarianten grob geschätzt, um wenige prägnante Merkmale zu finden, mit denen sich zerbrochene 3D-Objekte zusammensetzen lassen.
Mit dem Ziel der exakten Bestimmung der 3D-Formen von Zeichen, wurde die aus der Bildverarbeitung und Mustererkennung bekannte Verarbeitungskette an 3D-Modelle angepasst. Diese Modelle bestehen aus Millionen von Messpunkten, die mit optischen 3D-Scannern aufgenommen werden. Die Punkte approximieren Mannigfaltigkeiten durch ein irreguläres Dreiecksnetz. Verschiedene Typen von integralinvarianten Filtern in mehreren Skalen führen zu verschiedenen hochdimensionalen Merkmalsräumen. Faltungen und kombinierte Metriken werden auf die Merkmalsräume angewandt, um Zusammenhangskomponenten zu bestimmen. Diese Komponenten stellen die Zeichen genauer als die Messauflösung dar. Parallel zum Design der Algorithmen werden die Eigenschaften der verschiedenen Integralinvarianten analysiert. Die Interpretation der Filterergebnisse sind von großem Nutzen zur Bestimmung von robusten Krümmungsmaßen und zur Segmentierung. Die Extraktion von Keilschriftzeichen wird mit einer Voronoi basierten Berechnung von minimalen normalisierbaren Vektordarstellungen vervollständigt. Diese Darstellung ist eine wichtige Grundlage für die Paläographie. Weitere Abstraktion und Normalisierung der Darstellung führt zur Zeichenerkennung. Die Einbettung der Algorithmen in das neu entworfene mehrschichtige GigaMesh Software Framework erlaubt eine Vielzahl von Anwendungen. Die Algorithmen nutzen den Speicher effektiv und die Verarbeitungskette ist parallelisiert. Die konfigurierbare Verarbeitungskette hat nur einen relevanten Parameter, nämlich die maximale Größe der zu erwartenden Merkmale.
Die vorgestellten Verfahren wurden an Hunderten von Keilschrifttafeln, so wie weiteren realen und synthetischen Objekten getestet.Repräsentative Ergebnisse sowie Aufwands- und Genauigkeitsabschätzung der Algorithmen werden gezeigt. Ein Ausblick auf künftige Erweiterungen und Integralinvarianten in höheren Dimensionen gegeben
Multi-Dimensional Joins
We present three novel algorithms for performing multi-dimensional
joins and an in-depth survey and analysis of a low-dimensional
spatial join. The first algorithm, the Iterative Spatial Join,
performs a spatial join on low-dimensional data and is based
on a plane-sweep technique.
As we show analytically and experimentally,
the Iterative Spatial Join performs well when internal memory is
limited, compared to competing methods. This suggests that
the Iterative Spatial Join would be useful for very large data sets
or in situations where internal memory is a shared resource and
is therefore limited, such as with today's database engines which
share internal memory amongst several queries. Furthermore, the
performance of the Iterative Spatial Join is predictable and has
no parameters which need to be tuned, unlike other algorithms.
The second algorithm, the Quickjoin algorithm,
performs a higher-dimensional
similarity join in which pairs of objects that lie within a
certain distance epsilon of each other are reported.
The Quickjoin algorithm overcomes drawbacks of competing methods,
such as requiring embedding methods on the data first or using
multi-dimensional indices, which limit
the ability to discriminate between objects in each
dimension, thereby degrading performance.
A formal analysis is provided of the Quickjoin method, and
experiments show that the Quickjoin method significantly outperforms
competing methods.
The third algorithm adapts
incremental join techniques to improve the
speed of calculating the Hausdorff distance, which
is used in applications such as image matching, image analysis,
and surface approximations.
The nearest neighbor incremental join technique for indices that
are based on hierarchical containment use a priority queue
of index node pairs and bounds on the distance values between
pairs, both of which need to modified in order to calculate the
Hausdorff distance. Results of experiments are described that
confirm the performance improvement.
Finally, a survey is provided which
instead of just summarizing the literature and presenting each
technique in its entirety, describes distinct components of
the different techniques, and each technique is decomposed into
an overall framework for performing a spatial join
Generative Mesh Modeling
Generative Modeling is an alternative approach for the description of three-dimensional shape. The basic idea is to represent a model not as usual by an agglomeration of geometric primitives (triangles, point clouds, NURBS patches), but by functions. The paradigm change from objects to operations allows for a procedural representation of procedural shapes, such as most man-made objects. Instead of storing only the result of a 3D construction, the construction process itself is stored in a model file. The generative approach opens truly new perspectives in many ways, among others also for 3D knowledge management. It permits for instance to resort to a repository of already solved modeling problems, in order to re-use this knowledge also in different, slightly varied situations. The construction knowledge can be collected in digital libraries containing domain-specific parametric modeling tools. A concrete realization of this approach is a new general description language for 3D models, the "Generative Modeling Language" GML. As a Turing-complete "shape programming language" it is a basis of existing, primitv based 3D model formats. Together with its Runtime engine the GML permits - to store highly complex 3D models in a compact form, - to evaluate the description within fractions of a second, - to adaptively tesselate and to interactively display the model, - and even to change the models high-level parameters at runtime.Die generative Modellierung ist ein alternativer Ansatz zur Beschreibung von dreidimensionaler Form. Zugrunde liegt die Idee, ein Modell nicht wie üblich durch eine Ansammlung geometrischer Primitive (Dreiecke, Punkte, NURBS-Patches) zu beschreiben, sondern durch Funktionen. Der Paradigmenwechsel von Objekten zu Geometrie-erzeugenden Operationen ermöglicht es, prozedurale Modelle auch prozedural zu repräsentieren. Statt das Resultat eines 3D-Konstruktionsprozesses zu speichern, kann so der Konstruktionsprozess selber repräsentiert werden. Der generative Ansatz eröffnet unter anderem gänzlich neue Perspektiven für das Wissensmanagement im 3D-Bereich. Er ermöglicht etwa, auf einen Fundus bereits gelöster Konstruktions-Aufgaben zurückzugreifen, um sie in ähnlichen, aber leicht variierten Situationen wiederverwenden zu können. Das Konstruktions-Wissen kann dazu in Form von Bibliotheken parametrisierter, Domänen-spezifischer Modellier-Werkzeuge gesammelt werden. Konkret wird dazu eine neue allgemeine Modell-Beschreibungs-Sprache vorgeschlagen, die "Generative Modeling Language" GML. Als Turing-mächtige "Programmiersprache für Form" stellt sie eine echte Verallgemeinerung existierender Primitiv-basierter 3D-Modellformate dar. Zusammen mit ihrer Runtime-Engine erlaubt die GML, - hochkomplexe 3D-Objekte extrem kompakt zu beschreiben, - die Beschreibung innerhalb von Sekundenbruchteilen auszuwerten, - das Modell adaptiv darzustellen und interaktiv zu betrachten, - und die Modell-Parameter interaktiv zu verändern
Fabricate
Bringing together pioneers in design and making within architecture, construction, engineering, manufacturing, materials technology and computation, Fabricate is a triennial international conference, now in its third year (ICD, University of Stuttgart, April 2017). Each year it produces a supporting publication, to date the only one of its kind specialising in Digital Fabrication. The 2017 edition features 32 illustrated articles on built projects and works in progress from academia and practice, including contributions from leading practices such as Foster + Partners, Zaha Hadid Architects, Arup, and Ron Arad, and from world-renowned institutions including ICD Stuttgart, Harvard, Yale, MIT, Princeton University, The Bartlett School of Architecture (UCL) and the Architectural Association
Quantitative Techniques in Participatory Forest Management
Forest management has evolved from a mercantilist view to a multi-functional one that integrates economic, social, and ecological aspects. However, the issue of sustainability is not yet resolved. Quantitative Techniques in Participatory Forest Management brings together global research in three areas of application: inventory of the forest variables that determine the main environmental indices, description and design of new environmental indices, and the application of sustainability indices for regional implementations. All these quantitative techniques create the basis for the development of scientific methodologies of participatory sustainable forest management