TY - JOUR A1 - Cui, Pin A1 - Löber, Ulrike A1 - Alquezar-Planas, David E. A1 - Ishida, Yasuko A1 - Courtiol, Alexandre A1 - Timms, Peter A1 - Johnson, Rebecca N. A1 - Lenz, Dorina A1 - Helgen, Kristofer M. A1 - Roca, Alfred L. A1 - Hartman, Stefanie A1 - Greenwood, Alex D. T1 - Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome JF - PeerJ N2 - Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. KW - Integration sites KW - Retroviral endogenization KW - KoRV KW - Target enrichment KW - Clustering Y1 - 2016 U6 - https://doi.org/10.7717/peerj.1847 SN - 2167-8359 VL - 4 PB - PeerJ Inc. CY - London ER - TY - JOUR A1 - Vales, Dina A1 - Dias, Nuno A. A1 - Rio, Ines A1 - Matias, Luis A1 - Silveira, Graca A1 - Madeira, Jose A1 - Weber, Michael H. A1 - Carrilho, Fernando A1 - Haberland, Christian T1 - Intraplate seismicity across the Cape Verde swell: A contribution from a temporary seismic network JF - Tectonophysics : international journal of geotectonics and the geology and physics of the interior of the earth N2 - We present an analysis and characterization of the regional seismicity recorded by a temporary broadband seismic network deployed in the Cape Verde archipelago between November 2007 and September 2008. The detection of earthquakes was based on spectrograms, allowing the discrimination from low-frequency volcanic signals, resulting in 358 events of which 265 were located, the magnitudes usually being smaller than 3. For the location, a new 1-D P-velocity model was derived for the region showing a crust consistent with an oceanic crustal structure. The seismicity is located mostly offshore the westernmost and geologically youngest areas of the archipelago, near the islands of Santo Antao and Sao Vicente in the NW and Brava and Fogo in the SW. The SW cluster has a lower occurrence rate and corresponds to seismicity concentrated mainly along an alignment between Brava and the Cadamosto seamount presenting normal faulting mechanisms. The existence of the NW cluster, located offshore SW of Santo Antao, was so far unknown and concentrates around a recently recognized submarine cone field; this cluster presents focal depths extending from the crust to the upper mantle and suggests volcanic unrest No evident temporal behaviour could be perceived, although the events tend to occur in bursts of activity lasting a few days. In this recording period, no significant activity was detected at Fogo volcano, the most active volcanic edifice in Cape Verde. The seismicity characteristics point mainly to a volcanic origin. The correlation of the recorded seismicity with active volcanic structures agrees with the tendency for a westward migration of volcanic activity in the archipelago as indicated by the geologic record. (C) 2014 Elsevier B.V. All rights reserved. KW - Intraplate seismicity KW - Clustering KW - Local magnitude scale KW - Active volcanism KW - Cape Verde KW - Atlantic Ocean Y1 - 2014 U6 - https://doi.org/10.1016/j.tecto.2014.09.014 SN - 0040-1951 SN - 1879-3266 VL - 636 SP - 325 EP - 337 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Amirkhanyan, Aragats T1 - Methods and frameworks for GeoSpatioTemporal data analytics T1 - Methoden und Frameworks für geo-raumzeitliche Datenanalysen N2 - In the era of social networks, internet of things and location-based services, many online services produce a huge amount of data that have valuable objective information, such as geographic coordinates and date time. These characteristics (parameters) in the combination with a textual parameter bring the challenge for the discovery of geospatiotemporal knowledge. This challenge requires efficient methods for clustering and pattern mining in spatial, temporal and textual spaces. In this thesis, we address the challenge of providing methods and frameworks for geospatiotemporal data analytics. As an initial step, we address the challenges of geospatial data processing: data gathering, normalization, geolocation, and storage. That initial step is the basement to tackle the next challenge -- geospatial clustering challenge. The first step of this challenge is to design the method for online clustering of georeferenced data. This algorithm can be used as a server-side clustering algorithm for online maps that visualize massive georeferenced data. As the second step, we develop the extension of this method that considers, additionally, the temporal aspect of data. For that, we propose the density and intensity-based geospatiotemporal clustering algorithm with fixed distance and time radius. Each version of the clustering algorithm has its own use case that we show in the thesis. In the next chapter of the thesis, we look at the spatiotemporal analytics from the perspective of the sequential rule mining challenge. We design and implement the framework that transfers data into textual geospatiotemporal data - data that contain geographic coordinates, time and textual parameters. By this way, we address the challenge of applying pattern/rule mining algorithms in geospatiotemporal space. As the applicable use case study, we propose spatiotemporal crime analytics -- discovery spatiotemporal patterns of crimes in publicly available crime data. The second part of the thesis, we dedicate to the application part and use case studies. We design and implement the application that uses the proposed clustering algorithms to discover knowledge in data. Jointly with the application, we propose the use case studies for analysis of georeferenced data in terms of situational and public safety awareness. N2 - Heute ist die Zeit der sozialen Netzwerke, des Internets der Dinge und der Standortbezogenen Diensten (Location-Based services). Viele Online-Dienste erzeugen eine riesige Datenmenge, die wertvolle Informationen enthält, wie z. B. geographische Koordinaten und Datum sowie Zeit. Diese Informationen (Parameter) in Kombination mit einem Textparameter stellen die Herausforderung für die Entdeckung von geo-raumzeitlichem (geospatiotemporal) Wissen dar. Diese Herausforderung erfordert effiziente Methoden zum Clustering und Pattern-Mining in räumlichen, zeitlichen und textlichen Aspekten. In dieser Dissertation stellen wir uns der Herausforderung, Methoden und Frameworks für geo-raumzeitliche Datenanalysen bereitzustellen. Im ersten Schritt gehen wir auf die Herausforderungen der Geodatenverarbeitung ein: Datenerfassung, -Normalisierung, -Ortung und -Speicherung. Dieser Schritt ist der Grundstein für die nächste Herausforderung – das geographische Clustering. Es erfordert das Entwerfen einer Methode für das Online-Clustering georeferenzierter Daten. Dieser Algorithmus kann als Serverseitiger Clustering-Algorithmus für Online-Karten verwendet werden, die massive georeferenzierte Daten visualisieren. Im zweiten Schritt entwickeln wir die Erweiterung dieser Methode, die zusätzlich den zeitlichen Aspekt der Daten berücksichtigt. Dazu schlagen wir den Dichte und Intensitätsbasierten geo-raumzeitlichen Clustering-Algorithmus mit festem Abstand und Zeitradius vor. Jede Version des Clustering-Algorithmus hat einen eigenen Anwendungsfall, den wir in dieser Doktorarbeit zeigen. Im nächsten Kapitel dieser Arbeit betrachten wir die raumzeitlich Analyse aus der Perspektive der sequentiellen Regel-Mining-Herausforderung. Wir entwerfen und implementieren ein Framework, das Daten in textliche raumzeitliche Daten umwandelt. Solche Daten enthalten geographische Koordinaten, Zeit und Textparameter. Auf diese Weise stellen wir uns der Herausforderung, Muster- / Regel-Mining-Algorithmen auf geo-raumzeitliche Daten anzuwenden. Als Anwendungsfallstudie schlagen wir raumzeitliche Verbrechensanalysen vor – Entdeckung raumzeitlicher Muster von Verbrechen in öffentlich zugänglichen Datenbanken. Im zweiten Teil der Arbeit diskutieren wir über die Anwendung und die Fallstudien. Wir entwerfen und implementieren eine Anwendungssoftware, die die vorgeschlagene Clustering-Algorithmen verwendet, um das Wissen in Daten zu entdecken. Gemeinsam mit der Anwendungssoftware betrachten wir Anwendungsbeispiele für die Analyse georeferenzierter Daten im Hinblick auf das Situationsbewusstsein. KW - geospatial data KW - data analytics KW - clustering KW - situational awareness KW - Geodaten KW - Datenanalyse KW - Clustering KW - Situationsbewusstsein Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441685 ER - TY - THES A1 - Herrero Alonso, Yohana T1 - Properties of high-redshift galaxies in different environments T1 - Eigenschaften von Galaxien mit hoher Rotverschiebung in verschiedenen Umgebungen N2 - The Lyman-𝛼 (Ly𝛼) line commonly assists in the detection of high-redshift galaxies, the so-called Lyman-alpha emitters (LAEs). LAEs are useful tools to study the baryonic matter distribution of the high-redshift universe. Exploring their spatial distribution not only reveals the large-scale structure of the universe at early epochs, but it also provides an insight into the early formation and evolution of the galaxies we observe today. Because dark matter halos (DMHs) serve as sites of galaxy formation, the LAE distribution also traces that of the underlying dark matter. However, the details of this relation and their co-evolution over time remain unclear. Moreover, theoretical studies predict that the spatial distribution of LAEs also impacts their own circumgalactic medium (CGM) by influencing their extended Ly𝛼 gaseous halos (LAHs), whose origin is still under investigation. In this thesis, I make several contributions to improve the knowledge on these fields using samples of LAEs observed with the Multi Unit Spectroscopic Explorer (MUSE) at redshifts of 3 < 𝑧 < 6. N2 - Die Lyman-𝛼 (Ly𝛼)-Linie erleichtert die Detektion von Galaxien bei hoher Rotverschiebung, sogenannten den Lyman-Alpha-Emittern (LAEs). Die Erforschung ihrer Verteilung enthüllt nicht nur die großräumige Struktur des Universums in frühen Epochen, sondern bietet auch einen Einblick in die Entstehung und Entwicklung der Galaxien, die wir heute beobachten. Da Halos aus Dunkler Materie (DMHs) als Orte der Galaxienentstehung dienen, spiegelt die LAE-Verteilung auch die der zugrunde liegenden Dunklen Materie wider. Darüber hinaus sagen theoretische Studien voraus, dass die Verteilung von LAEs auch Auswirkungen auf ihr eigenes zirkumgalaktisches Medium (CGM) hat, indem sie ihre ausgedehnten gasförmigen Ly𝛼-Halos (LAHs) beeinflusst. In dieser Dissertation leiste ich mehrere Beiträge zur Verbesserung des Wissens über diese Felder anhand von Stichproben von LAEs, die mit dem Multi Unit Spectroscopic Explorer (MUSE) bei Rotverschiebungen von 3 < 𝑧 < 6 beobachtet wurden. KW - high-redshift KW - Lyman-alpha emitters KW - clustering KW - large-scale structure KW - Lyman-Alpha-Emitter KW - Clustering KW - hoher Rotverschiebung KW - großräumige Struktur des Universums Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-613288 ER -