@article{BauerHerwigLienhardetal.2021, author = {Bauer, Chris and Herwig, Ralf and Lienhard, Matthias and Prasse, Paul and Scheffer, Tobias and Schuchhardt, Johannes}, title = {Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types}, series = {Journal of translational medicine}, volume = {19}, journal = {Journal of translational medicine}, number = {1}, publisher = {BioMed Central}, address = {London}, issn = {1479-5876}, doi = {10.1186/s12967-021-02941-z}, pages = {13}, year = {2021}, abstract = {Background: There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. Methods: In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. Results: We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: . Conclusions: Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.}, language = {en} } @article{JiangNaumann2020, author = {Jiang, Lan and Naumann, Felix}, title = {Holistic primary key and foreign key detection}, series = {Journal of intelligent information systems : JIIS}, volume = {54}, journal = {Journal of intelligent information systems : JIIS}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {0925-9902}, doi = {10.1007/s10844-019-00562-z}, pages = {439 -- 461}, year = {2020}, abstract = {Primary keys (PKs) and foreign keys (FKs) are important elements of relational schemata in various applications, such as query optimization and data integration. However, in many cases, these constraints are unknown or not documented. Detecting them manually is time-consuming and even infeasible in large-scale datasets. We study the problem of discovering primary keys and foreign keys automatically and propose an algorithm to detect both, namely Holistic Primary Key and Foreign Key Detection (HoPF). PKs and FKs are subsets of the sets of unique column combinations (UCCs) and inclusion dependencies (INDs), respectively, for which efficient discovery algorithms are known. Using score functions, our approach is able to effectively extract the true PKs and FKs from the vast sets of valid UCCs and INDs. Several pruning rules are employed to speed up the procedure. We evaluate precision and recall on three benchmarks and two real-world datasets. The results show that our method is able to retrieve on average 88\% of all primary keys, and 91\% of all foreign keys. We compare the performance of HoPF with two baseline approaches that both assume the existence of primary keys.}, language = {en} } @article{Miklashevsky2017, author = {Miklashevsky, Alex A.}, title = {Perceptual experience norms for 506 Russian nouns}, series = {Journal of Psycholinguistic Research}, volume = {47}, journal = {Journal of Psycholinguistic Research}, number = {3}, publisher = {Springer}, address = {New York}, issn = {0090-6905}, doi = {10.1007/s10936-017-9548-1}, pages = {641 -- 661}, year = {2017}, abstract = {A number of new psycholinguistic variables has been proposed during the last years within embodied cognition framework: modality experience rating (i.e., relationship between words and images of a particular perceptive modality-visual, auditory, haptic etc.), manipulability (the necessity for an object to interact with human hands in order to perform its function), vertical spatial localization. However, it is not clear how these new variables are related to each other and to such traditional variables as imageability, AoA and word frequency. In this article, normative data on the modality (visual, auditory, haptic, olfactory, and gustatory) ratings, vertical spatial localization of the object, manipulability, imageability, age of acquisition, and subjective frequency for 506 Russian nouns are presented. Strongest correlations were observed between olfactory and gustatory modalities (.81), visual modality and imageability (.78), haptic modality and manipulability (.7). Other modalities also significantly correlate with imageability: olfactory (.35), gustatory (.24), and haptic (.67). Factor analysis divided variables into four groups where visual and haptic modality ratings were combined with imageability, manipulability and AoA (the first factor); word length, frequency and AoA formed the second factor; olfactory modality was united with gustatory (the third factor); spatial localization only is included in the fourth factor. Present norms of imageability and AoA are consistent with previous as correlation analysis has revealed. The complete database can be downloaded from supplementary material.}, language = {en} } @misc{HeidbachRajabiCuietal.2018, author = {Heidbach, Oliver and Rajabi, Mojtaba and Cui, Xiaofeng and Fuchs, Karl and Mueller, Birgit and Reinecker, John and Reiter, Karsten and Tingay, Mark and Wenzel, Friedemann and Xie, Furen and Ziegler, Moritz O. and Zoback, Mary-Lou and Zoback, Mark}, title = {The World Stress Map database release 2016}, series = {Tectonophysics : international journal of geotectonics and the geology and physics of the interior of the earth}, volume = {744}, journal = {Tectonophysics : international journal of geotectonics and the geology and physics of the interior of the earth}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0040-1951}, doi = {10.1016/j.tecto.2018.07.007}, pages = {484 -- 498}, year = {2018}, abstract = {Knowledge of the present-day crustal in-situ stress field is a key for the understanding of geodynamic processes such as global plate tectonics and earthquakes. It is also essential for the management of geo-reservoirs and underground storage sites for energy and waste. Since 1986, the World Stress Map (WSM) project has systematically compiled the orientation of maximum horizontal stress (S-Hmax). For the 30th anniversary of the project, the WSM database has been updated significantly with 42,870 data records which is double the amount of data in comparison to the database release in 2008. The update focuses on areas with previously sparse data coverage to resolve the stress pattern on different spatial scales. In this paper, we present details of the new WSM database release 2016 and an analysis of global and regional stress pattern. With the higher data density, we can now resolve stress pattern heterogeneities from plate-wide to local scales. In particular, we show two examples of 40 degrees-60 degrees S-Hmax rotations within 70 km. These rotations can be used as proxies to better understand the relative importance of plate boundary forces that control the long wave-length pattern in comparison to regional and local controls of the crustal stress state. In the new WSM project phase IV that started in 2017, we will continue to further refine the information on the S-Hmax orientation and the stress regime. However, we will also focus on the compilation of stress magnitude data as this information is essential for the calibration of geomechanical-numerical models. This enables us to derive a 3-D continuous description of the stress tensor from point-wise and incomplete stress tensor information provided with the WSM database. Such forward models are required for safety aspects of anthropogenic activities in the underground and for a better understanding of tectonic processes such as the earthquake cycle.}, language = {en} } @misc{BrownDonadiniNilssonetal.2015, author = {Brown, Maxwell C. and Donadini, Fabio and Nilsson, Andreas and Panovska, Sanja and Frank, Ute and Korhonen, Kimmo and Schuberth, Maximilian and Korte, Monika and Constable, Catherine G.}, title = {GEOMAGIA50.v3}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {875}, issn = {1866-8372}, doi = {10.25932/publishup-43476}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434768}, pages = {21}, year = {2015}, abstract = {Background: GEOMAGIA50.v3 for sediments is a comprehensive online database providing access to published paleomagnetic, rock magnetic, and chronological data obtained from lake and marine sediments deposited over the past 50 ka. Its objective is to catalogue data that will improve our understanding of changes in the geomagnetic field, physical environments, and climate. Findings: GEOMAGIA50.v3 for sediments builds upon the structure of the pre-existing GEOMAGIA50 database for magnetic data from archeological and volcanic materials. A strong emphasis has been placed on the storage of geochronological data, and it is the first magnetic archive that includes comprehensive radiocarbon age data from sediments. The database will be updated as new sediment data become available. Conclusions: The web-based interface for the sediment database is located at http://geomagia.gfz-potsdam.de/geomagiav3/SDquery.php. This paper is a companion to Brown et al. (Earth Planets Space doi:10.1186/s40623-015-0232-0,2015) and describes the data types, structure, and functionality of the sediment database.}, language = {en} } @misc{BreuningerLenhard2017, author = {Breuninger, Holger and Lenhard, Michael}, title = {Expression of the central growth regulator BIG BROTHER is regulated by multiple cis-elements}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400971}, pages = {10}, year = {2017}, abstract = {Background Much of the organismal variation we observe in nature is due to differences in organ size. The observation that even closely related species can show large, stably inherited differences in organ size indicates a strong genetic component to the control of organ size. Despite recent progress in identifying factors controlling organ growth in plants, our overall understanding of this process remains limited, partly because the individual factors have not yet been connected into larger regulatory pathways or networks. To begin addressing this aim, we have studied the upstream regulation of expression of BIG BROTHER (BB), a central growth-control gene in Arabidopsis thaliana that prevents overgrowth of organs. Final organ size and BB expression levels are tightly correlated, implying the need for precise control of its expression. BB expression mirrors proliferative activity, yet the gene functions to limit proliferation, suggesting that it acts in an incoherent feedforward loop downstream of growth activators to prevent over-proliferation. Results To investigate the upstream regulation of BB we combined a promoter deletion analysis with a phylogenetic footprinting approach. We were able to narrow down important, highly conserved, cis-regulatory elements within the BB promoter. Promoter sequences of other Brassicaceae species were able to partially complement the A. thaliana bb-1 mutant, suggesting that at least within the Brassicaceae family the regulatory pathways are conserved. Conclusions This work underlines the complexity involved in precise quantitative control of gene expression and lays the foundation for identifying important upstream regulators that determine BB expression levels and thus final organ size.}, language = {en} } @article{BrownDonadiniNilssonetal.2015, author = {Brown, Maxwell C. and Donadini, Fabio and Nilsson, Andreas and Panovska, Sanja and Frank, Ute and Korhonen, Kimmo and Schuberth, Maximilian and Korte, Monika and Constable, Catherine G.}, title = {GEOMAGIA50.v3: 2. A new paleomagnetic database for lake and marine sediments}, series = {Earth, planets and space}, volume = {67}, journal = {Earth, planets and space}, publisher = {Springer}, address = {Heidelberg}, issn = {1880-5981}, doi = {10.1186/s40623-015-0233-z}, pages = {19}, year = {2015}, abstract = {Background: GEOMAGIA50.v3 for sediments is a comprehensive online database providing access to published paleomagnetic, rock magnetic, and chronological data obtained from lake and marine sediments deposited over the past 50 ka. Its objective is to catalogue data that will improve our understanding of changes in the geomagnetic field, physical environments, and climate. Findings: GEOMAGIA50.v3 for sediments builds upon the structure of the pre-existing GEOMAGIA50 database for magnetic data from archeological and volcanic materials. A strong emphasis has been placed on the storage of geochronological data, and it is the first magnetic archive that includes comprehensive radiocarbon age data from sediments. The database will be updated as new sediment data become available. Conclusions: The web-based interface for the sediment database is located at http://geomagia.gfz-potsdam.de/geomagiav3/SDquery.php. This paper is a companion to Brown et al. (Earth Planets Space doi:10.1186/s40623-015-0232-0,2015) and describes the data types, structure, and functionality of the sediment database.}, language = {en} } @article{ReiterHeidbachSchmittetal.2014, author = {Reiter, Karsten and Heidbach, Oliver and Schmitt, Douglas and Haug, Kristine and Ziegler, Moritz O. and Moeck, Inga}, title = {A revised crustal stress orientation database for Canada}, series = {Tectonophysics : international journal of geotectonics and the geology and physics of the interior of the earth}, volume = {636}, journal = {Tectonophysics : international journal of geotectonics and the geology and physics of the interior of the earth}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0040-1951}, doi = {10.1016/j.tecto.2014.08.006}, pages = {111 -- 124}, year = {2014}, abstract = {The Canadian database on contemporary crustal stress has not been revised systematically in the past two decades. Here we present the results of our new compilation that contains 514 new data records for the orientation data of maximum compressive horizontal stress and 188 data records that were re-assessed. In total the Canadian stress database has now 1667 data records, which is an increase of about 45\%. From these data, a new Canadian Stress map as well as one for the Province of Alberta is presented. To analyse the stress pattern, we use the quasi median on the circle as a smoothing algorithm that generates a smoothed stress map of the maximum compressive horizontal stress orientation on a regular grid. The newly introduced quasi interquartile range on the circle estimates the spreading of the data and is used as a measure for the wave-length of the stress pattern. The result of the hybrid wavelength analysis confirms that long spatial wavelength stress patterns (>= 1000 km) exist in large areas in Canada. The observed stress pattern is transmitted through the intra-plate regions. The results reveal that shorter spatial wave length variation of the maximum compressive horizontal stress orientation of less than 200 km, prevails particularly in south-eastern and western Canada. Regional stress sources such as density contrasts, active fault systems, crustal structures, etc. might have a significant impact in these regions. In contrast to these variations, the observed stress pattern in the Alberta Basin is very homogeneous and mainly controlled by plate boundary forces and body forces. The influence of curvature of the Rocky Mountains salient in southern Alberta is minimal. The present-day horizontal stress orientations determined herein have important implications for the production of hydrocarbons and geothermal energy in the Alberta Basin. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @unpublished{WellsteinSchroederEsselbachReinekingetal.2011, author = {Wellstein, Camilla and Schr{\"o}der-Esselbach, Boris and Reineking, Bjoern and Zimmermann, Niklaus E.}, title = {Understanding species and community response to environmental change - A functional trait perspective}, series = {Agriculture, ecosystems \& environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere}, volume = {145}, journal = {Agriculture, ecosystems \& environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-8809}, doi = {10.1016/j.agee.2011.06.024}, pages = {1 -- 4}, year = {2011}, language = {en} } @misc{Kunde2013, type = {Master Thesis}, author = {Kunde, Felix}, title = {CityGML in PostGIS : Portierung, Anwendung und Performanz-Analyse am Beipiel der 3D City Database von Berlin}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-63656}, school = {Universit{\"a}t Potsdam}, year = {2013}, abstract = {Der internationale Standard CityGML ist zu einer zentralen Schnittstelle f{\"u}r die geometrische wie semantische Beschreibung von 3D-Stadtmodellen geworden. Das Institut f{\"u}r Geod{\"a}sie und Geoinformationstechnik (IGG) der Technischen Universit{\"a}t Berlin leistet mit ihren Entwicklung der 3D City Database und der Importer/Exporter Software einen entscheidenden Beitrag die Komplexit{\"a}t von CityGML-Daten in einer Geodatenbank intuitiv und effizient nutzen zu k{\"o}nnen. Die Software des IGG ist Open Source, unterst{\"u}tzte mit Oracle Spatial (ab Version 10g) aber bisher nur ein propriet{\"a}res Datenbank Management System (DBMS). Im Rahmen dieser Masterarbeit wurde eine Portierung auf die freie Datenbank-Software PostgreSQL/PostGIS vorgenommen und mit der Performanz der Oracle-Version verglichen. PostGIS gilt als eine der ausgereiftesten Geodatenbanken und wurde in diesem Jahr mit dem Release der Version 2.0 nochmals um zahlreiche Funktionen und Features (u.a. auch 3D-Unterst{\"u}tzung) erweitert. Die Ergebnisse des Vergleiches sowie die umfangreiche Gegen{\"u}berstellung aller verwendeten Konzepte (SQL, PL, Java) geben Aufschluss auf die Charakteristika beider r{\"a}umlicher DBMS und erm{\"o}glichen einen Erkenntnisgewinn {\"u}ber die Projektgrenzen hinaus.}, language = {de} }