TY - THES A1 - Zimmermann, Ralf T1 - BAYDAT - Die bayerische Dialektdatenbank T1 - BAYDAT - the Bavarian database of dialects N2 - Die vorliegende Dissertation beschreibt Aufbau und Funktionalität der bayerischen Dialektdatenbank BAYDAT. Die Datenbank fasst die Erhebungsdaten der Teilprojekte des Bayerischen Sprachatlas (BSA) zusammen, speichert sie zukunftssicher und macht sie zentral nutzbar. Die Arbeit zeigt die Vorgehensweise bei der Aufbereitung der Quelldateien, beschreibt die einzelnen Datenbanktabellen der BAYDAT-Datenbank und widmet sich der Realisierung und Funktionalität der Onlineoberfläche, über die die BAYDAT-Datenbank einem weltweiten Nutzerkreis aus Dialektologen und interessierten Laien zur Verfügung stehen soll. N2 - The PhD thesis at hand describes the setup and functionality of the Bavarian dialect database BAYDAT. The database integrates the data of the subprojects of the Bayerischer Sprachatlas (BSA, Atlas of the Bavarian language). The database ensures a future-proof storage of the data and makes the data available at one central point. The thesis describes the methods used in formatting the source data. It also describes the structure of the different database tables. It also contains a description of the development and the functionality of BAYDAT's graphical user interface that will allow linguists and laypersons to access the database online. T3 - WespA. Würzburger elektronische sprachwissenschaftliche Arbeiten - 1 KW - Dialekt KW - Datenbank KW - EDV-Philologie KW - dialects KW - database KW - computing in the Humanities Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-22709 SN - 978-3-923959-34-1 ER - TY - JOUR A1 - Wolf, Beat A1 - Kuonen, Pierre A1 - Dandekar, Thomas A1 - Atlan, David T1 - DNAseq workflow in a diagnostic context and an example of a user friendly implementation JF - BioMed Research International N2 - Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing. KW - next generation sequencing KW - genome browser KW - mutation KW - algorithm KW - database KW - format KW - discovery KW - exome KW - variants KW - alignment Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-144527 IS - 403497 ER - TY - JOUR A1 - Wagner, Ines A1 - Volkmer, Michael A1 - Sharan, Malvika A1 - Villaveces, Jose M. A1 - Oswald, Felix A1 - Surendranath, Vineeth A1 - Habermann, Bianca H. T1 - morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring JF - BMC Bioinformatics N2 - Background: Searching the orthologs of a given protein or DNA sequence is one of the most important and most commonly used Bioinformatics methods in Biology. Programs like BLAST or the orthology search engine Inparanoid can be used to find orthologs when the similarity between two sequences is sufficiently high. They however fail when the level of conservation is low. The detection of remotely conserved proteins oftentimes involves sophisticated manual intervention that is difficult to automate. Results: Here, we introduce morFeus, a search program to find remotely conserved orthologs. Based on relaxed sequence similarity searches, morFeus selects sequences based on the similarity of their alignments to the query, tests for orthology by iterative reciprocal BLAST searches and calculates a network score for the resulting network of orthologs that is a measure of orthology independent of the E-value. Detecting remotely conserved orthologs of a protein using morFeus thus requires no manual intervention. We demonstrate the performance of morFeus by comparing it to state-of-the-art orthology resources and methods. We provide an example of remotely conserved orthologs, which were experimentally shown to be functionally equivalent in the respective organisms and therefore meet the criteria of the orthology-function conjecture. Conclusions: Based on our results, we conclude that morFeus is a powerful and specific search method for detecting remotely conserved orthologs. KW - reciprocal best hit KW - finder using symmetrical best hits KW - sequences KW - annotation KW - identification KW - database KW - genomes KW - proteins KW - homologs KW - hidden markov-models KW - phylogenetic trees KW - PSI-blast KW - eigenvector centrality KW - meta-analysis based orthology KW - orthology KW - remote sequence conservation KW - alignment clustering KW - orthology network Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-115590 VL - 15 IS - 263 ER - TY - JOUR A1 - Stereńczak, Krzysztof A1 - Laurin, Gaia Vaglio A1 - Chirici, Gherardo A1 - Coomes, David A. A1 - Dalponte, Michele A1 - Latifi, Hooman A1 - Puletti, Nicola T1 - Global Airborne Laser Scanning Data Providers Database (GlobALS) — a new tool for monitoring ecosystems and biodiversity JF - Remote Sensing N2 - Protection and recovery of natural resource and biodiversity requires accurate monitoring at multiple scales. Airborne Laser Scanning (ALS) provides high-resolution imagery that is valuable for monitoring structural changes to vegetation, providing a reliable reference for ecological analyses and comparison purposes, especially if used in conjunction with other remote-sensing and field products. However, the potential of ALS data has not been fully exploited, due to limits in data availability and validation. To bridge this gap, the global network for airborne laser scanner data (GlobALS) has been established as a worldwide network of ALS data providers that aims at linking those interested in research and applications related to natural resources and biodiversity monitoring. The network does not collect data itself but collects metadata and facilitates networking and collaborative research amongst the end-users and data providers. This letter describes this facility, with the aim of broadening participation in GlobALS. KW - LiDAR KW - forest KW - database KW - networking KW - GlobALS Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-207819 SN - 2072-4292 VL - 12 IS - 11 ER - TY - JOUR A1 - Staiger, Christine A1 - Cadot, Sidney A1 - Kooter, Raul A1 - Dittrich, Marcus A1 - Müller, Tobias A1 - Klau, Gunnar W. A1 - Wessels, Lodewyk F. A. T1 - A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer JF - PLoS One N2 - Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single genes classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single genes classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single genes classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single genes sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single genes classifiers for predicting outcome in breast cancer. KW - modules KW - protein-interaction networks KW - expression signature KW - classification KW - set KW - metastasis KW - stability KW - survival KW - database KW - markers Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131323 VL - 7 IS - 4 ER - TY - JOUR A1 - Ljunggren, Osten A1 - Barrett, Annabel A1 - Stoykov, Ivaylo A1 - Langdahl, Bente L. A1 - Lems, Willem F. A1 - Walsh, J. Bernard A1 - Fahrleitner-Pammer, Astrid A1 - Rajzbaum, Gerald A1 - Jakob, Franz A1 - Karras, Dimitrios A1 - Marin, Fernando T1 - Effective osteoporosis treatment with teriparatide is associated with enhanced quality of life in postmenopausal women with osteoporosis: the European Forsteo Observational Study JF - BMC Musculoskeletal Disorders N2 - Background: To describe changes in health-related quality of life (HRQoL) of postmenopausal women with osteoporosis treated with teriparatide for up to 18 months and followed-up for a further 18 months, and to assess the influence of recent prior and incident fractures. Methods: The European Forsteo Observational Study (EFOS) is an observational, prospective, multinational study measuring HRQoL using the EQ-5D. The primary objective was to assess changes in HRQoL during 36 months in the whole study population. A secondary post-hoc analysis examined fracture impact on HRQoL in four subgroups classified based on recent prior fracture 12 months before baseline and incident clinical fractures during the study. Changes from baseline were analysed using a repeated measures model. Results: Of the 1581 patients, 48.4% had a recent prior fracture and 15.6% of these patients had an incident fracture during follow-up. 10.9% of the 816 patients with no recent prior fracture had an incident fracture. Baseline mean EQ-VAS scores were similar across the subgroups. In the total study cohort (n = 1581), HRQoL (EQ-VAS and EQ-5D index scores) improved significantly from baseline to 18 months and this improvement was maintained over the 18-month post-teriparatide period. Improvements were seen across all five EQ-5D domains during teriparatide treatment that were maintained after teriparatide was discontinued. Subjects with incident clinical fractures had significantly less improvement in EQ-VAS than those without incident fractures. Recent prior fracture did not influence the change in EQ-VAS during treatment. Conclusions: EFOS is the first longitudinal study in women with severe postmenopausal osteoporosis in the real world setting to show a substantial improvement in HRQoL during teriparatide treatment that was sustained during subsequent treatment with other medications. The increase in HRQoL was lower in the subgroups with incident fracture but was not influenced by recent prior fracture. The results should be interpreted in the context of the design of an observational study. KW - fracture KW - osteoporosis KW - quality of life KW - teriparatide KW - EQ-5D KW - database KW - alendronate KW - persistence KW - metaanalysis KW - prevalent fractures KW - bone-mineral density KW - vertebral fractures KW - back pain KW - impact KW - responsiveness Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-122057 SN - 1471-2474 VL - 14 IS - 251 ER - TY - JOUR A1 - Kunz, Meik A1 - Liang, Chunguang A1 - Nilla, Santosh A1 - Cecil, Alexander A1 - Dandekar, Thomas T1 - The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development JF - Database N2 - The drug-minded protein interaction database (DrumPID) has been designed to provide fast, tailored information on drugs and their protein networks including indications, protein targets and side-targets. Starting queries include compound, target and protein interactions and organism-specific protein families. Furthermore, drug name, chemical structures and their SMILES notation, affected proteins (potential drug targets), organisms as well as diseases can be queried including various combinations and refinement of searches. Drugs and protein interactions are analyzed in detail with reference to protein structures and catalytic domains, related compound structures as well as potential targets in other organisms. DrumPID considers drug functionality, compound similarity, target structure, interactome analysis and organismic range for a compound, useful for drug development, predicting drug side-effects and structure–activity relationships. KW - drug-minded protein KW - database Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147369 VL - 2016 ER - TY - THES A1 - Kaußner, Armin T1 - Dynamische Szenerien in der Fahrsimulation T1 - Dynamic scenarios for driving simulation N2 - In der Arbeit wird ein neues Konzept für Fahrsimulator-Datenbasen vorgestellt. Der Anwender entwirft eine auf seine Fragestellung zugeschnittene Datenbasis mithilfe einer einfachen Skriptsprache. Das Straßennetzwerk wird auf einer topologischen Ebene repäsentiert. In jedem Simulationsschritt wird hieraus im Sichtbarkeitsbereich des Fahrers die geometrische Repäsentation berechnet. Die für den Fahrer unsichtbaren Teile des Straßenetzwerks können während der Simulation verändert werden. Diese Veränderungen können von der Route des Fahrers oder von den in der Simulation erhobenen Messerten abhängen. Zudem kann der Anwender das Straßennetzwerk interaktiv verändern. Das vorgestellte Konzept bietet zahlreiche Möglichkeiten zur Erzeugung reproduzierbarer Szenarien für Experimente in Fahrsimulatoren. N2 - This work presents a new concept for driving simulator databases. Using a simple scripting language the user defines a database tailored for his experiment. The road network is represented in a topological way. Through this the geometrical representation is computed during the simulation in a small area surrounding the driver, including all that is visible for the driver. The parts of the road network that are not visible for the driver can be changed during simulation. This modification can depend on the route the driver takes or on measures available in the simulation. Moreover, the user can change the road network interactively. The presented concept offers various advantages for the design of reproducible scenarios in driving simulators. KW - Straßenverkehr KW - Simulation KW - Fahrsimulator KW - Fahrsimulation KW - Datenbasis KW - Straßennetzwerk KW - Szenariogenerierung KW - driving simulation KW - database KW - road network KW - scenario creation Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-8286 ER - TY - JOUR A1 - Jordan, Martin C. A1 - Jovic, Sebastian A1 - Gilbert, Fabian A1 - Kunz, Andreas A1 - Ertl, Maximilian A1 - Strobl, Ute A1 - Jakubietz, Rafael G. A1 - Jakubietz, Michael G. A1 - Meffert, Rainer H. A1 - Fuchs, Konrad F. T1 - Qualitätssteigerung der Abrechnungsprüfung durch Smartphone-basierte Fotodokumentation in der Unfall-, Hand-, und Plastischen Chirurgie JF - Der Unfallchirurg N2 - Hintergrund Die Fotodokumentation von offenen Frakturen, Wunden, Dekubitalulzera, Tumoren oder Infektionen ist ein wichtiger Bestandteil der digitalen Patientenakte. Bisher ist unklar, welchen Stellenwert diese Fotodokumentation bei der Abrechnungsprüfung durch den Medizinischen Dienst der Krankenkassen (MDK) hat. Fragestellung Kann eine Smartphone-basierte Fotodokumentation die Verteidigung von erlösrelevanten Diagnosen und Prozeduren sowie der Verweildauer verbessern? Material und Methoden Ausstattung der Mitarbeiter mit digitalen Endgeräten (Smartphone/Tablet) in den Bereichen Notaufnahme, Schockraum, OP, Sprechstunden sowie auf den Stationen. Retrospektive Auswertung der Abrechnungsprüfung im Jahr 2019 und Identifikation aller Fallbesprechungen, in denen die Fotodokumentation eine Erlösveränderung bewirkt hat. Ergebnisse Von insgesamt 372 Fallbesprechungen half die Fotodokumentation in 27 Fällen (7,2 %) zur Bestätigung eines Operationen- und Prozedurenschlüssels (OPS) (n = 5; 1,3 %), einer Hauptdiagnose (n = 10; 2,7 %), einer Nebendiagnose (n = 3; 0,8 %) oder der Krankenhausverweildauer (n = 9; 2,4 %). Pro oben genanntem Fall mit Fotodokumentation ergab sich eine durchschnittliche Erlössteigerung von 2119 €. Inklusive Aufwandpauschale für die Verhandlungen wurde somit ein Gesamtbetrag von 65.328 € verteidigt. Diskussion Der Einsatz einer Smartphone-basierten Fotodokumentation kann die Qualität der Dokumentation verbessern und Erlöseinbußen bei der Abrechnungsprüfung verhindern. Die Implementierung digitaler Endgeräte mit entsprechender Software ist ein wichtiger Teil des digitalen Strukturwandels in Kliniken. N2 - Background Photographic documentation of wounds, decubitus ulcers, tumors, open fractures and infections is an important part of digital patient files. It is unclear whether the photographic documentation has an effect on medical accounting with health insurance companies. Objective It was hypothesized that Smartphone-based systematic photographic documentation can improve the confirmation of proceeds-relevant diagnoses and procedures as well as the duration. Material and methods Staff in the emergency room, operating theater, outpatient clinic and on the wards were equipped with digital devices (Smartphone, tablet) including a photo-app. Medical accounting with the health insurance companies and identification of all case conferences in which the photographic documentation had effected a change in proceeds were analyzed for 2019 in a retrospective manner. Results Overall, 372 cases were discussed of which 27 cases were affected by the digital photographic documentation. Photographic documentation was used for clarification of the operative procedure (n = 5), primary diagnosis (n = 10), secondary diagnosis (n = 3), and length of hospitalization (n = 9). An average of 2119 € was negotiated and added per case affected by photographic documentation. Hereby, a level 1 trauma center gained an estimated 65,328 € in revenue. Discussion The use of Smartphone based photographic documentation can improve the overall quality of patient files and thus avoid loss of revenue. The implementation of digital devices with corresponding software is an important component of the digital structural change in hospitals. KW - Digitalisierung KW - Gesundheits-App KW - Künstliche Intelligenz KW - Plattform KW - Strukturwandel KW - artificial intelligence KW - database KW - digital transformation KW - photo app KW - surgery Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-232415 SN - 0177-5537 VL - 124 ER - TY - JOUR A1 - Gupta, Shishir K. A1 - Srivastava, Mugdha A1 - Osmanoglu, Oezge A1 - Dandekar, Thomas T1 - Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs JF - Scientific Reports N2 - Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6% of the entire C. floridanus proteome. KW - interaction map KW - drosophila KW - identification KW - evolutionary KW - reliability KW - annotation KW - database KW - target KW - cycle Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229406 VL - 10 IS - 1 ER -