Land cover change along the Willamette River, Oregon

The Willamette River and its floodplain in northwest Oregon have changed dramatically since European settlement. At one time, the river was a vast complex system of braided channels with a broad floodplain forest; it has now been simplified by channelization and dams, and the forest has been removed to support agricultural and urban expansion. This thesis presents three research manuscripts, each of which uses remote sensing and Geographical Information System methods to capture the dynamic nature of land along the Willamette River. In the first article, the river and its floodplain were mapped at four time periods, ranging from pre-settlement to modern day. The paper reports that the river system has been greatly simplified, and the floodplain has lost much of its original forest. An overlay technique was used to identify potential floodplain restoration sites. The second paper details the creation of a landcover map for the Willamette Valley, which shows that the largest portion of the floodplain is now in agriculture, with a significant amount in a built condition. The third manuscript outlines a methodology for detecting land cover change along the river during a twenty-year period that coincides with the implementation of the Willamette River Greenway, a land use designation designed to restrict riparian land conversion. It shows that regressive change is still occuring along the river, although not at the same rate as outside the greenway. The three papers lay the foundation for a future study to analyze the socioeconomic conditions which promote change

Few Shot Learning for the Classification of Confocal Laser Endomicroscopy Images of Head and Neck Tumors

The surgical removal of head and neck tumors requires safe margins, which are usually confirmed intraoperatively by means of frozen sections. This method is, in itself, an oversampling procedure, which has a relatively low sensitivity compared to the definitive tissue analysis on paraffin-embedded sections. Confocal laser endomicroscopy (CLE) is an in-vivo imaging technique that has shown its potential in the live optical biopsy of tissue. An automated analysis of this notoriously difficult to interpret modality would help surgeons. However, the images of CLE show a wide variability of patterns, caused both by individual factors but also, and most strongly, by the anatomical structures of the imaged tissue, making it a challenging pattern recognition task. In this work, we evaluate four popular few shot learning (FSL) methods towards their capability of generalizing to unseen anatomical domains in CLE images. We evaluate this on images of sinunasal tumors (SNT) from five patients and on images of the vocal folds (VF) from 11 patients using a cross-validation scheme. The best respective approach reached a median accuracy of 79.6% on the rather homogeneous VF dataset, but only of 61.6% for the highly diverse SNT dataset. Our results indicate that FSL on CLE images is viable, but strongly affected by the number of patients, as well as the diversity of anatomical patterns.Comment: 6 page

Transferability of Deep Learning Algorithms for Malignancy Detection in Confocal Laser Endomicroscopy Images from Different Anatomical Locations of the Upper Gastrointestinal Tract

Squamous Cell Carcinoma (SCC) is the most common cancer type of the epithelium and is often detected at a late stage. Besides invasive diagnosis of SCC by means of biopsy and histo-pathologic assessment, Confocal Laser Endomicroscopy (CLE) has emerged as noninvasive method that was successfully used to diagnose SCC in vivo. For interpretation of CLE images, however, extensive training is required, which limits its applicability and use in clinical practice of the method. To aid diagnosis of SCC in a broader scope, automatic detection methods have been proposed. This work compares two methods with regard to their applicability in a transfer learning sense, i.e. training on one tissue type (from one clinical team) and applying the learnt classification system to another entity (different anatomy, different clinical team). Besides a previously proposed, patch-based method based on convolutional neural networks, a novel classification method on image level (based on a pre-trained Inception V.3 network with dedicated preprocessing and interpretation of class activation maps) is proposed and evaluated. The newly presented approach improves recognition performance, yielding accuracies of 91.63% on the first data set (oral cavity) and 92.63% on a joint data set. The generalization from oral cavity to the second data set (vocal folds) lead to similar area-under-the-ROC curve values than a direct training on the vocal folds data set, indicating good generalization.Comment: Erratum for version 1, correcting the number of CLE image sequences used in one data se

An Estimation of the Extent of Cropland Abandonment in Mountainous Regions of China

With the wages for migrant workers increasing dramatically in China since 2003, the size of the agricultural labour forces has been shrinking rapidly. Intensively substituting agricultural machinery for the shrinking farm labour force is hardly possible for croplands in the mountainous regions of China where mechanization is difficult to achieve due to small field size and rough terrain. This has eventually led to cropland abandonment in these regions. Considering the high pressure for food security in China, cropland abandonment in the mountainous regions should not be ignored. By employing a novel method, this study estimates the extent of recently abandoned croplands (period 2000–2010) and the changes that can be expected in the future in China's mountainous areas. The results show that the total extent of abandoned croplands in Chinese mountainous counties during the period 2000 to 2010 is estimated at 147 million mu (1 mu = 666.67 m2); in total, about 28% of croplands in mountainous counties was abandoned, including croplands converted in the Grain for Green Programme. With 3 scenario assumptions, a sizeable extent, 114 to 203 million mu, of croplands may be abandoned from 2010 to 2030 with the rapid decrease and ageing of projected farm labour forces. This could exacerbate the future challenges of maintaining China's food security. A substantial increase in agricultural project investments, including land consolidation and agricultural productive fixed assets, especially microtillage machines, could help mitigate the risk of cropland abandonment. Additionally, land‐use and environmental policymaking should take into account the expanding cropland abandonment in mountainous regions

Strukturelle Determinanten des pestiviralen Glykoproteins E(RNS) für die Retention, Sekretion und proteolytische Prozessierung

Das Genus Pestivirus gehört zur Familie der Flaviviridae und enthält eine Reihe von tierpathogenen Erregern, welche (fast) ausschließlich Paarhufer befallen. Das bei Pestiviren vorkommende Strukturprotein ERNS ist einzigartig in der Familie Flaviviridae, es finden sich keine homologen Proteine in den anderen Genera dieser Familie. ERNS ist ein sehr ungewöhnliches Protein, da es für ein virales Strukturprotein verschiedene untypische Eigenschaften aufweist. Neben einer intrinsischen RNase-Aktivität findet sich am C Terminus eine sehr ungewöhnliche Signalpeptidase-Spaltstelle. Während die RNase Aktivität einen wichtigen Virulenzfaktor darstellt, sorgt die ungewöhnliche Spaltstelle mutmaßlich für die verlangsamte Prozessierung des ERNS-E1-Vorläuferproteins. Inwieweit die verlangsamte Spaltung des Vorläuferproteins für das Virus wichtig sein könnte, ist bis dato noch ungeklärt. Auch ist die Ausbildung von Dimeren wichtig für die Virulenz von ERNS. Darüber hinaus erfolgt eine partielle Sekretion von ERNS in den extrazellulären Raum, während ein Großteil in der Zelle verbleibt. Zusätzlich verfügt ERNS über eine untypische Membranverankerung, die durch eine lange, C-terminale amphipathische Helix vermittelt wird. Innerhalb dieser amphipathischen Helix findet sich eine Reihe geladener Aminosäuren, deren Lokalisation und Anordnung zu zwei spiegelsymmetrisch komplementären Gruppen bei Pestiviren konserviert ist. Es stellte sich die Frage, welche biologische Relevanz dieses Muster an geladenen Aminosäuren haben könnte. Ausgehend von der vorgeschlagenen Ausbildung eines „Charge Zippers“ – durch Rückfaltung und Ausbildung von Salzbrücken zwischen den komplementären Ladungen –, wurden mittels transienten Expressionsexperimenten die sechs hoch konservierten Ladungen im „Inneren“ des möglichen „Reißverschlusses“ untersucht, und es zeigte sich, dass der postulierte Charge-Zipper-Mechanismus bei ERNS vermutlich keine Rolle spielt. Für einige der betrachteten Aminosäuren konnten Hinweise erhalten werden, dass sie eine Rolle bei der Prozessierung, der Retention und bei der Dimerisierung von ERNS spielen. Vor allem ein Austausch der Ladung an der Position 194 im ERNS zeigte einen signifikanten Einfluss auf die Prozessierung und Retention von ERNS. Auch bei der Dimerisierung stach diese Position hervor, da entgegen anderer Mutationen ein Austausch hier zu einer vermehrten Dimerbildung führte. Weiterführend wurden diese Mutationen in rekombinante Viren eingeführt, und es zeigte sich, dass vor allem die spezifischen Ladungen an den Positionen 184 und 191 im ERNS wichtig für die effiziente Virusvermehrung sind. Ladungsaustausche an diesen Positionen sorgten für nicht lebensfähige Virusmutanten, während Alaninsubstitutionen im Lauf von Passagen zur ursprünglichen Ladung revertierten. Diese Ergebnisse zeigen die elementare Bedeutung der Ladungen für die Generierung von infektiösen Viren. Die molekularen Mechanismen, in denen diese Reste von Bedeutung sind, müssen in weiteren Arbeiten noch aufgeklärt werden.The genus Pestivirus belongs to the family Flaviviridae and contains several pathogens which (almost) exclusively infect cloven-hoofed animals. The pestiviral structural protein ERNS is unique within the Flaviviridae with no homologous protein being found in the other genera of this family. ERNS is a quite uncommon viral structural protein with various atypical properties. In addition to an intrinsic RNase activity, a very unusual signal peptidase cleavage site can be found at the C-terminal end of ERNS. While the RNase activity is an important virulence factor of pestiviruses, it is assumed that the unusual signal peptidase cleavage site might be involved in the slow processing of the ERNS-E1 precursor protein. To what extent the slow cleavage of the precursor protein might be important for the virus has still not been clarified. Furthermore, the formation of dimers is also important for the virulence of ERNS. In addition, ERNS is partially secreted into the extracellular space, while the majority remains inside the cell. It is worth remarking that ERNS possesses a very uncommon membrane anchoring mediated by a long, C-terminal amphipathic helix. Within this amphipathic helix a series of charged amino acids can be found. Their location and arrangement of two mirror-symmetric complementary groups is highly conserved among pestiviruses. The question arose whether this pattern of charged amino acids might be of any biological relevance. Based on the proposed formation of a "charge zipper" – by refolding and formation of salt bridges between the complementary charges – transient expression experiments were performed with a focus on the six “innermost” highly conserved charges of the assumed charge zipper. The respective results suggest that the postulated charge zipper mechanism might probably not be applicable to ERNS. For some of the amino acids examined, evidence was obtained that they might play a part in the processing, retention and dimerization of ERNS. Particularly a charge exchange at position 194 in ERNS showed a significant influence on the processing and retention of the protein. Regarding an influence on the dimerization of ERNS, position 194 stood out again. Contrary to other mutations, a charge exchange at this position lead to an increase in dimer formation. In addition, mutations were introduced in recombinant viruses, and it was shown that the particular charges at position 184 and 191 in ERNS are important for efficient virus proliferation. Charge exchanges at these positions lead to non-viable virus mutants, while alanine substitutions reverted back to the original charge over several virus passages. These results show the elemental relevance of these charges for the generation of infectious viruses. The molecular mechanisms for which these residues are of particular importance have to be solved in further studies