@article{PaijmansBarlowHennebergeretal.2020, author = {Paijmans, Johanna L. A. and Barlow, Axel and Henneberger, Kirstin and Fickel, J{\"o}rns and Hofreiter, Michael and Foerste, Daniel W. G.}, title = {Ancestral mitogenome capture of the Southeast Asian banded linsang}, series = {PLoS ONE}, volume = {15}, journal = {PLoS ONE}, number = {6}, publisher = {PLOS}, address = {San Francisco, California, US}, issn = {1932-6203}, doi = {10.1371/journal.pone.0234385}, pages = {12}, year = {2020}, abstract = {Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.}, language = {en} } @article{AktasStede2022, author = {Aktas, Berfin and Stede, Manfred}, title = {Anaphoric distance in oral and written language}, series = {Discours : revue de linguistique, psycholinguistique et informatique}, journal = {Discours : revue de linguistique, psycholinguistique et informatique}, number = {31}, publisher = {Universit{\´e} de Paris-Sorbonne, Maion Recherche}, address = {Paris}, issn = {1963-1723}, doi = {10.4000/discours.12383}, pages = {37}, year = {2022}, abstract = {We investigate the variation in oral and written language in terms of anaphoric distance (i.e., the textual distance between anaphors and their antecedents), expanding corpus-based research with experimental evidence. Contrastive corpus studies demonstrate that oral genres include longer average anaphoric distance than written genres, if the distance is measured in terms of clauses (Fox, 1987; Aktas \& Stede, 2020). We designed an experiment in order to examine the contrasts in oral and written mediums, using the same genre. We aim to gain more insight about the impact of the medium, in a situation where both mediums convey a similar level of spontaneity, informality and interactivity. We designed a story continuation study, where the participants are recruited via crowdsourcing. To our knowledge, this is the first study of its kind, where anaphoric distance is manipulated systematically in a language production experiment in order to examine medium distinctions. We observed that participants use more pronouns in oral medium than in written medium if the anaphoric distance is long. This result is in line with the implications of the earlier corpus-based research. In addition, our results indicate that anaphoric distance has a larger effect in referential choice for the written medium.}, language = {en} } @article{PuchkovMuellerLehmannetal.2023, author = {Puchkov, Dmytro and M{\"u}ller, Paul Markus and Lehmann, Martin and Matth{\"a}us, Claudia}, title = {Analyzing the cellular plasma membrane by fast and efficient correlative STED and platinum replica EM}, series = {Frontiers in cell and developmental biology}, volume = {11}, journal = {Frontiers in cell and developmental biology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-634X}, doi = {10.3389/fcell.2023.1305680}, pages = {15}, year = {2023}, abstract = {The plasma membrane of mammalian cells links transmembrane receptors, various structural components, and membrane-binding proteins to subcellular processes, allowing inter- and intracellular communication. Therefore, membrane-binding proteins, together with structural components such as actin filaments, modulate the cell membrane in their flexibility, stiffness, and curvature. Investigating membrane components and curvature in cells remains challenging due to the diffraction limit in light microscopy. Preparation of 5-15-nm-thin plasma membrane sheets and subsequent inspection by metal replica transmission electron microscopy (TEM) reveal detailed information about the cellular membrane topology, including the structure and curvature. However, electron microscopy cannot identify proteins associated with specific plasma membrane domains. Here, we describe a novel adaptation of correlative super-resolution light microscopy and platinum replica TEM (CLEM-PREM), allowing the analysis of plasma membrane sheets with respect to their structural details, curvature, and associated protein composition. We suggest a number of shortcuts and troubleshooting solutions to contemporary PREM protocols. Thus, implementation of super-resolution stimulated emission depletion (STED) microscopy offers significant reduction in sample preparation time and reduced technical challenges for imaging and analysis. Additionally, highly technical challenges associated with replica preparation and transfer on a TEM grid can be overcome by scanning electron microscopy (SEM) imaging. The combination of STED microscopy and platinum replica SEM or TEM provides the highest spatial resolution of plasma membrane proteins and their underlying membrane and is, therefore, a suitable method to study cellular events like endocytosis, membrane trafficking, or membrane tension adaptations.}, language = {en} } @article{MunyaevSmirnovKostinetal.2020, author = {Munyaev, Vyacheslav O. and Smirnov, Lev A. and Kostin, Vasily A. and Osipov, Grigory V. and Pikovskij, Arkadij}, title = {Analytical approach to synchronous states of globally coupled noisy rotators}, series = {New journal of physics : the open-access journal for physics}, volume = {22}, journal = {New journal of physics : the open-access journal for physics}, number = {2}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab6f93}, pages = {14}, year = {2020}, abstract = {We study populations of globally coupled noisy rotators (oscillators with inertia) allowing a nonequilibrium transition from a desynchronized state to a synchronous one (with the nonvanishing order parameter). The newly developed analytical approaches resulted in solutions describing the synchronous state with constant order parameter for weakly inertial rotators, including the case of zero inertia, when the model is reduced to the Kuramoto model of coupled noise oscillators. These approaches provide also analytical criteria distinguishing supercritical and subcritical transitions to the desynchronized state and indicate the universality of such transitions in rotator ensembles. All the obtained analytical results are confirmed by the numerical ones, both by direct simulations of the large ensembles and by solution of the associated Fokker-Planck equation. We also propose generalizations of the developed approaches for setups where different rotators parameters (natural frequencies, masses, noise intensities, strengths and phase shifts in coupling) are dispersed.}, language = {en} } @article{MunyaevSmirnovKostinetal.2020, author = {Munyaev, Vyacheslav and Smirnov, Lev A. and Kostin, Vasily and Osipov, Grigory V. and Pikovskij, Arkadij}, title = {Analytical approach to synchronous states of globally coupled noisy rotators}, series = {New Journal of Physics}, volume = {22}, journal = {New Journal of Physics}, number = {2}, publisher = {Springer Science}, address = {New York}, pages = {15}, year = {2020}, abstract = {We study populations of globally coupled noisy rotators (oscillators with inertia) allowing a nonequilibrium transition from a desynchronized state to a synchronous one (with the nonvanishing order parameter). The newly developed analytical approaches resulted in solutions describing the synchronous state with constant order parameter for weakly inertial rotators, including the case of zero inertia, when the model is reduced to the Kuramoto model of coupled noise oscillators. These approaches provide also analytical criteria distinguishing supercritical and subcritical transitions to the desynchronized state and indicate the universality of such transitions in rotator ensembles. All the obtained analytical results are confirmed by the numerical ones, both by direct simulations of the large ensembles and by solution of the associated Fokker-Planck equation. We also propose generalizations of the developed approaches for setups where different rotators parameters (natural frequencies, masses, noise intensities, strengths and phase shifts in coupling) are dispersed.}, language = {en} } @article{MatternPudellLaskinetal.2021, author = {Mattern, Maximilian and Pudell, Jan-Etienne and Laskin, Gennadii and Reppert, Alexander von and Bargheer, Matias}, title = {Analysis of the temperature- and fluence-dependent magnetic stress in laser-excited SrRuO3}, series = {Structural dynamics}, volume = {8}, journal = {Structural dynamics}, number = {2}, publisher = {AIP Publishing LLC}, address = {Melville, NY}, issn = {2329-7778}, doi = {10.1063/4.0000072}, pages = {9}, year = {2021}, abstract = {We use ultrafast x-ray diffraction to investigate the effect of expansive phononic and contractive magnetic stress driving the picosecond strain response of a metallic perovskite SrRuO3 thin film upon femtosecond laser excitation. We exemplify how the anisotropic bulk equilibrium thermal expansion can be used to predict the response of the thin film to ultrafast deposition of energy. It is key to consider that the laterally homogeneous laser excitation changes the strain response compared to the near-equilibrium thermal expansion because the balanced in-plane stresses suppress the Poisson stress on the picosecond timescale. We find a very large negative Gr{\"u}neisen constant describing the large contractive stress imposed by a small amount of energy in the spin system. The temperature and fluence dependence of the strain response for a double-pulse excitation scheme demonstrates the saturation of the magnetic stress in the high-fluence regime.}, language = {en} } @article{KocPetrowThieken2020, author = {Ko{\c{c}}, Gamze and Petrow, Theresia and Thieken, Annegret}, title = {Analysis of the Most Severe Flood Events in Turkey (1960-2014)}, series = {Water}, volume = {12}, journal = {Water}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2073-4441}, doi = {10.3390/w12061562}, pages = {32}, year = {2020}, abstract = {The most severe flood events in Turkey were determined for the period 1960-2014 by considering the number of fatalities, the number of affected people, and the total economic losses as indicators. The potential triggering mechanisms (i.e., atmospheric circulations and precipitation amounts) and aggravating pathways (i.e., topographic features, catchment size, land use types, and soil properties) of these 25 events were analyzed. On this basis, a new approach was developed to identify the main influencing factor per event and to provide additional information for determining the dominant flood occurrence pathways for severe floods. The events were then classified through hierarchical cluster analysis. As a result, six different clusters were found and characterized. Cluster 1 comprised flood events that were mainly influenced by drainage characteristics (e.g., catchment size and shape); Cluster 2 comprised events aggravated predominantly by urbanization; steep topography was identified to be the dominant factor for Cluster 3; extreme rainfall was determined as the main triggering factor for Cluster 4; saturated soil conditions were found to be the dominant factor for Cluster 5; and orographic effects of mountain ranges characterized Cluster 6. This study determined pathway patterns of the severe floods in Turkey with regard to their main causal or aggravating mechanisms. Accordingly, geomorphological properties are of major importance in large catchments in eastern and northeastern Anatolia. In addition, in small catchments, the share of urbanized area seems to be an important factor for the extent of flood impacts. This paper presents an outcome that could be used for future urban planning and flood risk prevention studies to understand the flood mechanisms in different regions of Turkey.}, language = {en} } @article{KocPetrowThieken2020, author = {Koc, Gamze and Petrow, Theresia and Thieken, Annegret}, title = {Analysis of the most severe flood events in Turkey (1960-2014)}, series = {Water / Molecular Diversity Preservation International (MDPI)}, volume = {12}, journal = {Water / Molecular Diversity Preservation International (MDPI)}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2073-4441}, doi = {10.3390/w12061562}, pages = {32}, year = {2020}, abstract = {The most severe flood events in Turkey were determined for the period 1960-2014 by considering the number of fatalities, the number of affected people, and the total economic losses as indicators. The potential triggering mechanisms (i.e., atmospheric circulations and precipitation amounts) and aggravating pathways (i.e., topographic features, catchment size, land use types, and soil properties) of these 25 events were analyzed. On this basis, a new approach was developed to identify the main influencing factor per event and to provide additional information for determining the dominant flood occurrence pathways for severe floods. The events were then classified through hierarchical cluster analysis. As a result, six different clusters were found and characterized. Cluster 1 comprised flood events that were mainly influenced by drainage characteristics (e.g., catchment size and shape); Cluster 2 comprised events aggravated predominantly by urbanization; steep topography was identified to be the dominant factor for Cluster 3; extreme rainfall was determined as the main triggering factor for Cluster 4; saturated soil conditions were found to be the dominant factor for Cluster 5; and orographic effects of mountain ranges characterized Cluster 6. This study determined pathway patterns of the severe floods in Turkey with regard to their main causal or aggravating mechanisms. Accordingly, geomorphological properties are of major importance in large catchments in eastern and northeastern Anatolia. In addition, in small catchments, the share of urbanized area seems to be an important factor for the extent of flood impacts. This paper presents an outcome that could be used for future urban planning and flood risk prevention studies to understand the flood mechanisms in different regions of Turkey.}, language = {en} } @article{SchindlerMoldenhawerStangeetal.2021, author = {Schindler, Daniel and Moldenhawer, Ted and Stange, Maike and Lepro, Valentino and Beta, Carsten and Holschneider, Matthias and Huisinga, Wilhelm}, title = {Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows}, series = {PLoS Computational Biology : a new community journal}, volume = {17}, journal = {PLoS Computational Biology : a new community journal}, number = {8}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1009268}, pages = {33}, year = {2021}, abstract = {Amoeboid cell motility is essential for a wide range of biological processes including wound healing, embryonic morphogenesis, and cancer metastasis. It relies on complex dynamical patterns of cell shape changes that pose long-standing challenges to mathematical modeling and raise a need for automated and reproducible approaches to extract quantitative morphological features from image sequences. Here, we introduce a theoretical framework and a computational method for obtaining smooth representations of the spatiotemporal contour dynamics from stacks of segmented microscopy images. Based on a Gaussian process regression we propose a one-parameter family of regularized contour flows that allows us to continuously track reference points (virtual markers) between successive cell contours. We use this approach to define a coordinate system on the moving cell boundary and to represent different local geometric quantities in this frame of reference. In particular, we introduce the local marker dispersion as a measure to identify localized membrane expansions and provide a fully automated way to extract the properties of such expansions, including their area and growth time. The methods are available as an open-source software package called AmoePy, a Python-based toolbox for analyzing amoeboid cell motility (based on time-lapse microscopy data), including a graphical user interface and detailed documentation. Due to the mathematical rigor of our framework, we envision it to be of use for the development of novel cell motility models. We mainly use experimental data of the social amoeba Dictyostelium discoideum to illustrate and validate our approach.
Author summary Amoeboid motion is a crawling-like cell migration that plays an important key role in multiple biological processes such as wound healing and cancer metastasis. This type of cell motility results from expanding and simultaneously contracting parts of the cell membrane. From fluorescence images, we obtain a sequence of points, representing the cell membrane, for each time step. By using regression analysis on these sequences, we derive smooth representations, so-called contours, of the membrane. Since the number of measurements is discrete and often limited, the question is raised of how to link consecutive contours with each other. In this work, we present a novel mathematical framework in which these links are described by regularized flows allowing a certain degree of concentration or stretching of neighboring reference points on the same contour. This stretching rate, the so-called local dispersion, is used to identify expansions and contractions of the cell membrane providing a fully automated way of extracting properties of these cell shape changes. We applied our methods to time-lapse microscopy data of the social amoeba Dictyostelium discoideum.}, language = {en} } @article{ArkesAbereggArpin2022, author = {Arkes, Hal R. and Aberegg, Scott K. and Arpin, Kevin A.}, title = {Analysis of physicians' probability estimates of a medical outcome based on a sequence of events}, series = {JAMA network open / American Medical Association}, volume = {5}, journal = {JAMA network open / American Medical Association}, number = {6}, publisher = {American Veterinary Medical Association}, address = {Chicago}, issn = {2574-3805}, doi = {10.1001/jamanetworkopen.2022.18804}, pages = {10}, year = {2022}, abstract = {IMPORTANCE The probability of a conjunction of 2 independent events is the product of the probabilities of the 2 components and therefore cannot exceed the probability of either component; violation of this basic law is called the conjunction fallacy. A common medical decision-making scenario involves estimating the probability of a final outcome resulting from a sequence of independent events; however, little is known about physicians' ability to accurately estimate the overall probability of success in these situations. OBJECTIVE To ascertain whether physicians are able to correctly estimate the overall probability of a medical outcome resulting from 2 independent events. DESIGN, SETTING, AND PARTICIPANTS This survey study consisted of 3 separate substudies, in which 215 physicians were asked via internet-based survey to estimate the probability of success of each of 2 components of a diagnostic or prognostic sequence as well as the overall probability of success of the 2-step sequence. Substudy 1 was performed from April 2 to 4, 2021, substudy 2 from November 2 toll, 2021, and substudy 3 from May 13 to 19, 2021. All physicians were board certified or board eligible in the primary specialty germane to the substudy (ie, obstetrics and gynecology for substudies land 3 and pulmonology for substudy 2), were recruited from a commercial survey service, and volunteered to participate in the study. EXPOSURES Case scenarios presented in an online survey. MAIN OUTCOMES AND MEASURES Respondents were asked to provide their demographic information in addition to 3 probability estimates. The first substudy included a scenario describing a brow presentation discovered during labor; the 2 conjuncts were the probabilities that the brow presentation would resolve and that the delivery would be vaginal. The second substudy involved a diagnostic evaluation of an incidentally discovered pulmonary nodule; the 2 conjuncts were the probabilities that the patient had a malignant condition and that a technically successful transthoracic needle biopsy would reveal a malignant condition. The third substudy included a modification of the first substudy in an attempt to debias the conjunction fallacy prevalent in the first substudy. Respondents' own probability estimates of the individual events were used to calculate the mathematically correct conjunctive probability. RESULTS Among 215 respondents, the mean (SD) age was 54.0 (9.5) years; 142 respondents (66.0\%) were male. Data on race and ethnicity were not collected. A total of 168 physicians (78.1\%) estimated the probability of the 2-step sequence to be greater than the probability of at least 1 of the 2 component events. Compared with the product of their 2 estimated components, respondents overestimated the combined probability by 12.8\% (95\% CI, 9.6\%-16.1\%; P < .001) in substudy 1, 19.8\% (95\% Cl, 16.6\%-23.0\%; P < .001) in substudy 2, and 18.0\% (95\% CI, 13.4\%-22.5\%; P < .001) in substudy 3, results that were mathematically incoherent (ie, formally illogical and mathematically incorrect). CONCLUSIONS AND RELEVANCE In this survey study of 215 physicians, respondents consistently overestimated the combined probability of 2 events compared with the probability calculated from their own estimates of the individual events. This biased estimation, consistent with the conjunction fallacy, may have substantial implications for diagnostic and prognostic decision-making.}, language = {en} } @article{SchenkeSchjeidePuescheletal.2020, author = {Schenke, Maren and Schjeide, Brit-Maren and P{\"u}schel, Gerhard Paul and Seeger, Bettina}, title = {Analysis of motor neurons differentiated from human induced pluripotent stem cells for the use in cell-based Botulinum neurotoxin activity assays}, series = {Toxins}, volume = {12}, journal = {Toxins}, number = {5}, publisher = {MDPI}, address = {Basel}, issn = {2072-6651}, doi = {10.3390/toxins12050276}, pages = {20}, year = {2020}, abstract = {Botulinum neurotoxins (BoNTs) are potent neurotoxins produced by bacteria, which inhibit neurotransmitter release, specifically in their physiological target known as motor neurons (MNs). For the potency assessment of BoNTs produced for treatment in traditional and aesthetic medicine, the mouse lethality assay is still used by the majority of manufacturers, which is ethically questionable in terms of the 3Rs principle. In this study, MNs were differentiated from human induced pluripotent stem cells based on three published protocols. The resulting cell populations were analyzed for their MN yield and their suitability for the potency assessment of BoNTs. MNs produce specific gangliosides and synaptic proteins, which are bound by BoNTs in order to be taken up by receptor-mediated endocytosis, which is followed by cleavage of specific soluble N-ethylmaleimide-sensitive-factor attachment receptor (SNARE) proteins required for neurotransmitter release. The presence of receptors and substrates for all BoNT serotypes was demonstrated in MNs generated in vitro. In particular, the MN differentiation protocol based on Du et al. yielded high numbers of MNs in a short amount of time with high expression of BoNT receptors and targets. The resulting cells are more sensitive to BoNT/A1 than the commonly used neuroblastoma cell line SiMa. MNs are, therefore, an ideal tool for being combined with already established detection methods.}, language = {en} } @article{MilewskiChabrillatBehling2017, author = {Milewski, Robert and Chabrillat, Sabine and Behling, Robert}, title = {Analyses of Recent Sediment Surface Dynamic of a Namibian Kalahari Salt Pan Based on Multitemporal Landsat and Hyperspectral Hyperion Data}, series = {Remote Sensing}, volume = {9}, journal = {Remote Sensing}, number = {2}, publisher = {MDPI}, address = {Basel}, issn = {2072-4292}, doi = {10.3390/rs9020170}, pages = {24}, year = {2017}, abstract = {This study combines spaceborne multitemporal and hyperspectral data to analyze the spatial distribution of surface evaporite minerals and changes in a semi-arid depositional environment associated with episodic flooding events, the Omongwa salt pan (Kalahari, Namibia). The dynamic of the surface crust is evaluated by a change-detection approach using the Iterative-reweighted Multivariate Alteration Detection (IR-MAD) based on the Landsat archive imagery from 1984 to 2015. The results show that the salt pan is a highly dynamic and heterogeneous landform. A change gradient is observed from very stable pan border to a highly dynamic central pan. On the basis of hyperspectral EO-1 Hyperion images, the current distribution of surface evaporite minerals is characterized using Spectral Mixture Analysis (SMA). Assessment of field and image endmembers revealed that the pan surface can be categorized into three major crust types based on diagnostic absorption features and mineralogical ground truth data. The mineralogical crust types are related to different zones of surface change as well as pan morphology that influences brine flow during the pan inundation and desiccation cycles. These combined information are used to spatially map depositional environments where the more dynamic halite crust concentrates in lower areas although stable gypsum and calcite/sepiolite crusts appear in higher elevated areas.}, language = {en} } @article{MilewskiChabrillatBookhagen2020, author = {Milewski, Robert and Chabrillat, Sabine and Bookhagen, Bodo}, title = {Analyses of Namibian Seasonal Salt Pan Crust Dynamics and Climatic Drivers Using Landsat 8 Time-Series and Ground Data}, series = {Remote Sensing}, journal = {Remote Sensing}, number = {3}, publisher = {MDPI}, address = {Basel}, issn = {2072-4292}, doi = {10.3390/rs12030474}, pages = {24}, year = {2020}, abstract = {Salt pans are highly dynamic environments that are difficult to study by in situ methods because of their harsh climatic conditions and large spatial areas. Remote sensing can help to elucidate their environmental dynamics and provide important constraints regarding their sedimentological, mineralogical, and hydrological evolution. This study utilizes spaceborne multitemporal multispectral optical data combined with spectral endmembers to document spatial distribution of surface crust types over time on the Omongwa pan located in the Namibian Kalahari. For this purpose, 49 surface samples were collected for spectral and mineralogical characterization during three field campaigns (2014-2016) reflecting different seasons and surface conditions of the salt pan. An approach was developed to allow the spatiotemporal analysis of the salt pan crust dynamics in a dense time-series consisting of 77 Landsat 8 cloud-free scenes between 2014 and 2017, covering at least three major wet-dry cycles. The established spectral analysis technique Sequential Maximum Angle Convex Cone (SMACC) extraction method was used to derive image endmembers from the Landsat time-series stack. Evaluation of the extracted endmember set revealed that the multispectral data allowed the differentiation of four endmembers associated with mineralogical mixtures of the crust's composition in dry conditions and three endmembers associated with flooded or muddy pan conditions. The dry crust endmember spectra have been identified in relation to visible, near infrared, and short-wave infrared (VNIR-SWIR) spectroscopy and X-ray diffraction (XRD) analyses of the collected surface samples. According these results, the spectral endmembers are interpreted as efflorescent halite crust, mixed halite-gypsum crust, mixed calcite quartz sepiolite crust, and gypsum crust. For each Landsat scene the spatial distribution of these crust types was mapped with the Spectral Angle Mapper (SAM) method and significant spatiotemporal dynamics of the major surface crust types were observed. Further, the surface crust dynamics were analyzed in comparison with the pan's moisture regime and other climatic parameters. The results show that the crust dynamics are mainly driven by flooding events in the wet season, but are also influenced by temperature and aeolian activity in the dry season. The approach utilized in this study combines the advantages of multitemporal satellite data for temporal event characterization with advantages from hyperspectral methods for the image and ground data analyses that allow improved mineralogical differentiation and characterization.}, language = {en} } @misc{Degen2023, author = {Degen, Andreas}, title = {Analyse visueller Wahrnehmungsqualit{\"a}ten von Lyrik}, series = {Textpraxis : digitales Journal f{\"u}r Philologie / Sonderausgabe}, volume = {7}, journal = {Textpraxis : digitales Journal f{\"u}r Philologie / Sonderausgabe}, number = {2}, publisher = {Westf{\"a}lische Wilhelms-Universit{\"a}t}, address = {M{\"u}nster}, issn = {2191-8236}, doi = {10.17879/19958489288}, pages = {4}, year = {2023}, abstract = {Das Projekt besch{\"a}ftigt sich mit der visuellen Wirkungsdimension von Lyrik und der M{\"o}glichkeit ihrer analytischen Beschreibung. Daf{\"u}r werden die Anordnung von Versen und W{\"o}rtern, Auszeichnungen und andere typographische Strukturen von nicht experimentellen Gedichten seit Ende des 18. Jahrhunderts im Rahmen von Modellanalysen untersucht.}, language = {de} } @article{ThomasCarvalhoHaileetal.2017, author = {Thomas, Jessica E. and Carvalho, Gary R. and Haile, James and Martin, Michael D. and Castruita, Jose A. Samaniego and Niemann, Jonas and Sinding, Mikkel-Holger S. and Sandoval-Velasco, Marcela and Rawlence, Nicolas J. and Fuller, Errol and Fjeldsa, Jon and Hofreiter, Michael and Stewart, John R. and Gilbert, M. Thomas P. and Knapp, Michael}, title = {An ‛Aukward' tale}, series = {Genes}, volume = {8}, journal = {Genes}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes8060164}, pages = {164}, year = {2017}, abstract = {One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller's candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars' minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.}, language = {en} } @article{QinFaassNiedermeier2020, author = {Qin, Xia and Faaß, Marcel and Niedermeier, Frank}, title = {An Overview of the 'National Multiplication Trainings' Programme}, series = {Potsdamer Beitr{\"a}ge zur Hochschulforschung}, journal = {Potsdamer Beitr{\"a}ge zur Hochschulforschung}, number = {5}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-496-8}, issn = {2192-1075}, doi = {10.25932/publishup-49334}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-493344}, pages = {17 -- 35}, year = {2020}, abstract = {The article introduces the efforts exerted to initiate multiplication of the DIES training courses to a wider audience of higher education managers and academics in the target regions. The DIES 'National Multiplication Trainings' Programme has supported three cohorts of alumni teams so far to implement national training courses in the area of higher education leadership and management. The article sets the context of this publication and reflects on the main evaluation results of the programme implementation itself.}, language = {en} } @article{HeHoeperDodenhoeftetal.2020, author = {He, Hai and H{\"o}per, Rune and Dodenh{\"o}ft, Moritz and Marli{\`e}re, Philippe and Bar-Even, Arren}, title = {An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli}, series = {Metabolic Engineering}, volume = {60}, journal = {Metabolic Engineering}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, issn = {1096-7176}, doi = {10.1016/j.ymben.2020.03.002}, pages = {1 -- 13}, year = {2020}, abstract = {Engineering biotechnological microorganisms to use methanol as a feedstock for bioproduction is a major goal for the synthetic metabolism community. Here, we aim to redesign the natural serine cycle for implementation in E. coli. We propose the homoserine cycle, relying on two promiscuous formaldehyde aldolase reactions, as a superior pathway design. The homoserine cycle is expected to outperform the serine cycle and its variants with respect to biomass yield, thermodynamic favorability, and integration with host endogenous metabolism. Even as compared to the RuMP cycle, the most efficient naturally occurring methanol assimilation route, the homoserine cycle is expected to support higher yields of a wide array of products. We test the in vivo feasibility of the homoserine cycle by constructing several E. coli gene deletion strains whose growth is coupled to the activity of different pathway segments. Using this approach, we demonstrate that all required promiscuous enzymes are active enough to enable growth of the auxotrophic strains. Our findings thus identify a novel metabolic solution that opens the way to an optimized methylotrophic platform.}, language = {en} } @book{BaltzerHradilakPfennigschmidtetal.2021, author = {Baltzer, Wanda and Hradilak, Theresa and Pfennigschmidt, Lara and Prestin, Luc Maurice and Spranger, Moritz and Stadlinger, Simon and Wendt, Leo and Lincke, Jens and Rein, Patrick and Church, Luke and Hirschfeld, Robert}, title = {An individual-centered approach to visualize people's opinions and demographic information}, number = {136}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-504-0}, issn = {1613-5652}, doi = {10.25932/publishup-49145}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-491457}, publisher = {Universit{\"a}t Potsdam}, pages = {326}, year = {2021}, abstract = {The noble way to substantiate decisions that affect many people is to ask these people for their opinions. For governments that run whole countries, this means asking all citizens for their views to consider their situations and needs. Organizations such as Africa's Voices Foundation, who want to facilitate communication between decision-makers and citizens of a country, have difficulty mediating between these groups. To enable understanding, statements need to be summarized and visualized. Accomplishing these goals in a way that does justice to the citizens' voices and situations proves challenging. Standard charts do not help this cause as they fail to create empathy for the people behind their graphical abstractions. Furthermore, these charts do not create trust in the data they are representing as there is no way to see or navigate back to the underlying code and the original data. To fulfill these functions, visualizations would highly benefit from interactions to explore the displayed data, which standard charts often only limitedly provide. To help improve the understanding of people's voices, we developed and categorized 80 ideas for new visualizations, new interactions, and better connections between different charts, which we present in this report. From those ideas, we implemented 10 prototypes and two systems that integrate different visualizations. We show that this integration allows consistent appearance and behavior of visualizations. The visualizations all share the same main concept: representing each individual with a single dot. To realize this idea, we discuss technologies that efficiently allow the rendering of a large number of these dots. With these visualizations, direct interactions with representations of individuals are achievable by clicking on them or by dragging a selection around them. This direct interaction is only possible with a bidirectional connection from the visualization to the data it displays. We discuss different strategies for bidirectional mappings and the trade-offs involved. Having unified behavior across visualizations enhances exploration. For our prototypes, that includes grouping, filtering, highlighting, and coloring of dots. Our prototyping work was enabled by the development environment Lively4. We explain which parts of Lively4 facilitated our prototyping process. Finally, we evaluate our approach to domain problems and our developed visualization concepts. Our work provides inspiration and a starting point for visualization development in this domain. Our visualizations can improve communication between citizens and their government and motivate empathetic decisions. Our approach, combining low-level entities to create visualizations, provides value to an explorative and empathetic workflow. We show that the design space for visualizing this kind of data has a lot of potential and that it is possible to combine qualitative and quantitative approaches to data analysis.}, language = {en} } @article{HoanRichterBorsigetal.2022, author = {Hoan, Tran Viet and Richter, Karl-Gerd and Borsig, Nicolas and Bauer, Jonas and Ha, Nguyen Thi and Norra, Stefan}, title = {An improved groundwater model framework for aquifer structures of the quaternary-formed sediment body in the southernmost parts of the Mekong Delta, Vietnam}, series = {Hydrology : open access journal}, volume = {9}, journal = {Hydrology : open access journal}, number = {4}, publisher = {MDPI}, address = {Basel}, issn = {2306-5338}, doi = {10.3390/hydrology9040061}, pages = {20}, year = {2022}, abstract = {The Ca Mau peninsula (CMP) is a key economic region in southern Vietnam. In recent decades, the high demand for water has increased the exploitation of groundwater, thus lowering the groundwater level and leading to risks of degradation, depletion, and land subsidence, as well as salinity intrusion in the groundwater of the whole Mekong Delta region. By using a finite element groundwater model with boundary expansion to the sea, we updated the latest data on hydrogeological profiles, groundwater levels, and exploitation. The basic model setup covers seven aquifers and seven aquitards. It is determined that the inflow along the coastline to the mainland is 39\% of the total inflow. The exploitation of the study area in 2019 was 567,364 m(3)/day. The most exploited aquifers are the upper-middle Pleistocene (qp(2-3)) and the middle Pliocene (n(2)(2)), accounting for 63.7\% and 24.6\%, respectively; the least exploited aquifers are the upper Pleistocene and the upper Miocene, accounting for 0.35\% and 0.02\%, respectively. In the deeper aquifers, qp(2-3) and n(2)(2), the change in storage is negative due to the high exploitation rate, leading to a decline in the reserves of these aquifers. These groundwater model results are the calculations of groundwater reserves from the coast to the mainland in the entire system of aquifers in the CMP. This makes groundwater decision managers, stakeholders, and others more efficient in sustainable water resources planning in the CMP and Mekong Delta (MKD).}, language = {en} } @article{NakoudiStachlewskaRitter2021, author = {Nakoudi, Konstantina and Stachlewska, Iwona S. and Ritter, Christoph}, title = {An extended lidar-based cirrus cloud retrieval scheme}, series = {Optics express : the international electronic journal of optics / Optica}, volume = {29}, journal = {Optics express : the international electronic journal of optics / Optica}, number = {6}, publisher = {Optical Society of America}, address = {Washington}, issn = {1094-4087}, doi = {10.1364/OE.414770}, pages = {8553 -- 8580}, year = {2021}, abstract = {Accurate and precise characterization of cirrus cloud geometrical and optical properties is essential for better constraining their radiative footprint. A lidar-based retrieval scheme is proposed here, with its performance assessed on fine spatio-temporal observations over the Arctic site of Ny-Alesund, Svalbard. Two contributions related to cirrus geometrical (dynamic Wavelet Covariance Transform (WCT)) and optical properties (constrained Klett) are reported. The dynamic WCT rendered cirrus detection more robust, especially for thin cirrus layers that frequently remained undetected by the classical WCT method. Regarding optical characterization, we developed an iterative scheme for determining the cirrus lidar ratio (LRci) that is a crucial parameter for aerosol - cloud discrimination. Building upon the Klett-Fernald method, the LRci was constrained by an additional reference value. In established methods, such as the double-ended Klett, an aerosol-free reference value is applied. In the proposed constrained Klett, however, the reference value was approximated from cloud-free or low cloud optical depth (COD up to 0.2) profiles and proved to agree with independent Raman estimates. For optically thin cirrus, the constrained Klett inherent uncertainties reached 50\% (60-74\%) in terms of COD (LRci). However, for opaque cirrus COD (LRci) uncertainties were lower than 10\% (15\%). The detection method discrepancies (dynamic versus static WCT) had a higher impact on the optical properties of low COD layers (up to 90\%) compared to optically thicker ones (less than 10\%). The constrained Klett presented high agreement with two established retrievals. For an exemplary cirrus cloud, the constrained Klett estimated the COD355 (LRci355) at 0.28 +/- 0.17 (29 +/- 4 sr), the double-ended Klett at 0.27 +/- 0.15 (32 +/- 4 sr) and the Raman retrievals at 0.22 +/- 0.12 (26 +/- 11 sr). Our approach to determine the necessary reference value can also be applied in established methods and increase their accuracy. In contrast, the classical aerosol-free assumption led to 44 sr LRci overestimation in optically thin layers and 2-8 sr in thicker ones. The multiple scattering effect was corrected using Eloranta (1998) and accounted for 50-60\% extinction underestimation near the cloud base and 20-30\% within the cirrus layers.}, language = {en} }