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- ItemTemporal Role Annotation for Named Entities(Amsterdam [u.a.] : Elsevier, 2018) Koutraki, Maria; Bakhshandegan-Moghaddam, Farshad; Sack, Harald; Fensel, Anna; de Boer, Victor; Pellegrini, Tassilo; Kiesling, Elmar; Haslhofer, Bernhard; Hollink, Laura; Schindler, AlexanderNatural language understanding tasks are key to extracting structured and semantic information from text. One of the most challenging problems in natural language is ambiguity and resolving such ambiguity based on context including temporal information. This paper, focuses on the task of extracting temporal roles from text, e.g. CEO of an organization or head of a state. A temporal role has a domain, which may resolve to different entities depending on the context and especially on temporal information, e.g. CEO of Microsoft in 2000. We focus on the temporal role extraction, as a precursor for temporal role disambiguation. We propose a structured prediction approach based on Conditional Random Fields (CRF) to annotate temporal roles in text and rely on a rich feature set, which extracts syntactic and semantic information from text. We perform an extensive evaluation of our approach based on two datasets. In the first dataset, we extract nearly 400k instances from Wikipedia through distant supervision, whereas in the second dataset, a manually curated ground-truth consisting of 200 instances is extracted from a sample of The New York Times (NYT) articles. Last, the proposed approach is compared against baselines where significant improvements are shown for both datasets.
- ItemSemSur: A Core Ontology for the Semantic Representation of Research Findings(Amsterdam [u.a.] : Elsevier, 2018) Fathalla, Said; Vahdati, Sahar; Auer, Sören; Lange, Christoph; Fensel, Anna; de Boer, Victor; Pellegrini, Tassilo; Kiesling, Elmar; Haslhofer, Bernhard; Hollink, Laura; Schindler, AlexanderThe way how research is communicated using text publications has not changed much over the past decades. We have the vision that ultimately researchers will work on a common structured knowledge base comprising comprehensive semantic and machine-comprehensible descriptions of their research, thus making research contributions more transparent and comparable. We present the SemSur ontology for semantically capturing the information commonly found in survey and review articles. SemSur is able to represent scientific results and to publish them in a comprehensive knowledge graph, which provides an efficient overview of a research field, and to compare research findings with related works in a structured way, thus saving researchers a significant amount of time and effort. The new release of SemSur covers more domains, defines better alignment with external ontologies and rules for eliciting implicit knowledge. We discuss possible applications and present an evaluation of our approach with the retrospective, exemplary semantification of a survey. We demonstrate the utility of the SemSur ontology to answer queries about the different research contributions covered by the survey. SemSur is currently used and maintained at OpenResearch.org.
- ItemTargeting malignant melanoma with physical plasmas(Amsterdam [u.a.] : Elsevier, 2018) Pasqual-Melo, Gabriella; Gandhirajan, Rajesh Kumar; Stoffels, Ingo; Bekeschus, SanderMelanoma is the deadliest form of cutaneous neoplasia. With a five-year survival rate of only 5–19%, metastatic melanoma presents severe challenges in clinical therapies. In addition, palliation is often problematic due to large numbers of fast growing metastasis. This calls for new therapeutic avenues targeting highly aggressive melanoma in palliative patients. One recently suggested innovative approach for eradication of topical tumor lesions is the application of cold physical plasma. This partially ionized gas emits a cocktail of reactive oxygen and nitrogen species (ROS/RNS). ROS/RNS have been shown to be a double-edged sword in fueling cancer growth at low doses but abrogating it at higher doses. The ROS/RNS output of plasma devices is tunable, and many studies have successfully decreased cancer cell growth in vitro and tumor burden in vivo. In general, increasing numbers of clinical trials suggest combination therapies to outperform monotherapies with regard to prognosis in patients. This review describes current challenges in melanoma treatment and highlights the concept of plasma therapy in experimental studies performed in melanoma research. Future perspectives are given that combine the usage of physical plasma with e.g. chemotherapy, immunotherapy, and ionizing radiation in melanoma medical oncology.
- ItemPotentiating anti-tumor immunity with physical plasma(Amsterdam [u.a.] : Elsevier, 2018) Bekeschus, Sander; Clemen, Ramona; Metelmann, Hans-RobertThe age of checkpoint blockage emphasizes the importance of adaptive antitumor immune responses. This arm of immune defense is key in recognizing molecules via specific receptors to distinguish between self and foreign or mutated structures. Antigen-specific T-cells identify non-self epitopes, tumor-associated antigens, or neoepitopes on tumors to carry out attacks on malignant cells. Although tumor cells are immunogenic by nature, they have developed strategies to evade an immune response that would otherwise facilitate their clearance. Several steps in antitumor immunity utilize the toxic and signaling properties of reactive oxygen and nitrogen species (ROS/RNS). Cold physical plasmas are potent generators of such ROS/RNS and are demonstrated to have profound antitumor activity in vitro and in vivo. Here we discuss recent evidence and concepts on how plasmas may boost immunity against pathological cells. Specifically, plasma treatment may enhance the immunogenicity of tumor cells by induction of the immunogenic cancer cell death (ICD) and redox regulation of the antigen-presenting machinery. These aspects provide a rationale for localized plasma-based onco-therapies enhancing systemic antitumor immunity, which eventually may target distant tumor metastasis in cancer patients in a T-cell dependent fashion.
- ItemCellulose-carbon nanotube composite aerogels as novel thermoelectric materials(Amsterdam [u.a.] : Elsevier, 2018) Gnanaseelan, Minoj; Chen, Yian; Luo, Jinji; Krause, Beate; Pionteck, Jürgen; Pötschke, Petra; Qu, HaisongThermoelectric materials based on cellulose/carbon nanotube (CNT) nanocomposites have been developed by a facile approach and the effects of amount (2–10 wt%) and types of CNTs (single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs)) on the morphology (films and aerogels) and the thermoelectric properties of the nanocomposites have been investigated. Composite films based on SWCNTs showed significantly higher electrical conductivity (5 S/cm at 10 wt%) and Seebeck coefficient (47.2 μV/K at 10 wt%) compared to those based on MWCNTs (0.9 S/cm and 11 μV/K, respectively). Lyophilization, leading to development of aerogels with sub-micron sized pores, decreased the electrical conductivity for both types by one order of magnitude, but did not affect the Seebeck coefficient of MWCNT based nanocomposites. For SWCNT containing aerogels, higher Seebeck coefficients than for films were measured at 3 and 4 wt% but significantly lower values at higher loadings. CNT addition increased the thermal conductivity from 0.06 to 0.12 W/(m∙K) in the films, whereas the lyophilization significantly reduced it towards values between 0.01 and 0.09 W/(m∙K) for the aerogels. The maximum Seebeck coefficient, power factor, and ZT observed in this study are 49 μV/K for aerogels with 3 wt% SWCNTs, 1.1 μW/(m∙K2) for composite films with 10 wt% SWCNTs, and 7.4 × 10−4 for films with 8 wt% SWCNTs, respectively.
- ItemBiofunctionalized aligned microgels provide 3D cell guidance to mimic complex tissue matrices(Amsterdam [u.a.] : Elsevier, 2018) Rose, Jonas C.; Gehlen, David B.; Haraszti, Tamás; Köhler, Jens; Licht, Christopher J.; De Laporte, LauraNatural healing is based on highly orchestrated processes, in which the extracellular matrix plays a key role. To resemble the native cell environment, we introduce an artificial extracellular matrix (aECM) with the capability to template hierarchical and anisotropic structures in situ, allowing a minimally-invasive application via injection. Synthetic, magnetically responsive, rod-shaped microgels are locally aligned and fixed by a biocompatible surrounding hydrogel, creating a hybrid anisotropic hydrogel (Anisogel), of which the physical, mechanical, and chemical properties can be tailored. The microgels are rendered cell-adhesive with GRGDS and incorporated either inside a cell-adhesive fibrin or bioinert poly(ethylene glycol) hydrogel to strongly interact with fibroblasts. GRGDS-modified microgels inside a fibrin-based Anisogel enhance fibroblast alignment and lead to a reduction in fibronectin production, indicating successful replacement of structural proteins. In addition, YAP-translocation to the nucleus increases with the concentration of microgels, indicating cellular sensing of the overall anisotropic mechanical properties of the Anisogel. For bioinert surrounding PEG hydrogels, GRGDS-microgels are required to support cell proliferation and fibronectin production. In contrast to fibroblasts, primary nerve growth is not significantly affected by the biomodification of the microgels. In conclusion, this approach opens new opportunities towards advanced and complex aECMs for tissue regeneration.
- ItemProteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions(Amsterdam [u.a.] : Elsevier, 2018) Tomazetto, Geizecler; Hahnke, Sarah; Wibberg, Daniel; Pühler, Alfred; Klocke, Michael; Schlüter, AndreasProteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars. © 2018 The Authors
- ItemVisualisation and analysis of shear-deformation bands in unconsolidated Pleistocene sand using ground-penetrating radar: Implications for paleoseismological studies(Amsterdam [u.a.] : Elsevier, 2018) Brandes, Christian; Igel, Jan; Loewer, Markus; Tanner, David C.; Lang, Jörg; Müller, Katharina; Winsemann, JuttaDeformation bands in unconsolidated sediments are of great value for paleoseismological studies in sedimentary archives. Using ground-penetrating radar (GPR), we investigated an array of shear-deformation bands that developed in unconsolidated Pleistocene glacifluvial Gilbert-type delta sediments. A dense grid (spacing 0.6 m) of GPR profiles was measured on top of a 20 m-long outcrop that exposes shear-deformation bands. Features in the radargrams could be directly tied to the exposure. The shear-deformation bands are partly represented by inclined reflectors and partly by the offset of reflections at delta clinoforms. 3-D interpretation of the 2-D radar sections shows that the bands have near-planar geometries that can be traced throughout the entire sediment volume. Thin sections of sediment samples show that the analysed shear-deformation bands have a denser grain packing than the host sediment. Thus they have a lower porosity and smaller pore sizes and therefore, in the vadose zone, the deformation bands have a higher water content due to enhanced capillary forces. This, together with the partially-developed weak calcite cementation and the distinct offset along the bands, are likely the main reasons for the clear and unambiguous expression of the shear-deformation bands in the radar survey. The study shows that deformation-band arrays can clearly be detected using GPR and quickly mapped over larger sediment volumes. With the 3-D analysis, it is further possible to derive the orientation and geometry of the bands. This allows correlation of the bands with the regional fault trend. Studying deformation bands in unconsolidated sediments with GPR is therefore a powerful approach in paleoseismological studies. Based on our data, we postulate that the outcrop is part of a dextral strike-slip zone that was reactivated by glacial isostatic adjustment.
- ItemFrom statistic to deterministic nanostructures in fused silica induced by nanosecond laser radiation(Amsterdam [u.a.] : Elsevier, 2018) Lorenz, Pierre; Klöppel, Michael; Zagoranskiy, Igor; Zimmer, KlausThe production of structures by laser machining below the diffraction limit is still a challenge. However, self-organization processes can be useful. The laser-induced self-organized modification of the shape of photolithographic produced chromium structures on fused silica as well as the structuring of the fused silica surface by nanosecond UV laser radiation was studied, respectively. Low fluence single pulse laser irradiation (□ > 300 mJ/cm2) cause the formation from chromium squares to droplets due to the mass transport in the molten chromium film. This process is governed by the instability of the molten metal due to the surface tension driven liquid phase mass transport. For a chromium pattern size similar to the instability length two specific droplet distributions were found which are single droplets with a determined position near the centre of the original pattern or random distributed smaller droplets arranged circularly. Each of the metal patterns can be transferred into the fused silica by a multi-pulse irradiation. The experimental results can be simulated well for low fluences by sequential solving the heat and Navier-Stokes equation.