The impact of state aid on the survival and financial viability of aided firms

We estimate the causal impact of restructuring aid granted by the European Commission between 2003 and 2012 on the survival and financial viability of aided firms. Using a comprehensive dataset we find that restructuring aid increases a firm’s average survival time by 8 to 15 years and decreases the hazard rate by 58 to 68 percent, depending on the definition of firm survival. Further analysis finds strong support that, in the longer run, aid receiving firms have a significantly higher probability to improve their financial viability than the counterfactual group

Patient-level proteomic network prediction by explainable artificial intelligence

Understanding the pathological properties of dysregulated protein networks in individual patients’ tumors is the basis for precision therapy. Functional experiments are commonly used, but cover only parts of the oncogenic signaling networks, whereas methods that reconstruct networks from omics data usually only predict average network features across tumors. Here, we show that the explainable AI method layer-wise relevance propagation (LRP) can infer protein interaction networks for individual patients from proteomic profiling data. LRP reconstructs average and individual interaction networks with an AUC of 0.99 and 0.93, respectively, and outperforms state-of-the-art network prediction methods for individual tumors. Using data from The Cancer Proteome Atlas, we identify known and potentially novel oncogenic network features, among which some are cancer-type specific and show only minor variation among patients, while others are present across certain tumor types but differ among individual patients. Our approach may therefore support predictive diagnostics in precision oncology by inferring “patient-level” oncogenic mechanisms

Protein sizing with Differential Dynamic Microscopy

Introduced more than fifty years ago, dynamic light scattering is routinely used to determine the size distribution of colloidal suspensions, as well as of macromolecules in solution, such as proteins, nucleic acids, and their complexes. More recently, differential dynamic microscopy has been proposed as a way to perform dynamic light scattering experiments with a microscope, with much less stringent constraints in terms of cleanliness of the optical surfaces, but a potentially lower sensitivity due to the use of camera-based detectors. In this work, we push bright-field differential dynamic microscopy beyond known limits and show it to be sufficiently sensitive to size small macromolecules in diluted solutions. By considering solutions of three different proteins (Bovine Serum Albumin, Lysozyme, and Pepsin), we accurately determine the diffusion coefficient and hydrodynamic radius of both single proteins and small protein aggregates down to concentrations of a few milligrams per milliliter. In addition, we present preliminary results showing unexplored potential for the determination of virial coefficients. Our results are in excellent agreement with the ones obtained in parallel with a state-of-the-art commercial dynamic light scattering setup, showing that differential dynamic microscopy represents a valuable alternative for rapid, label-free protein sizing with an optical microscope

Ontology-based identification of music for places

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-36309-2_37Proceedings of the International Conference on Information and Communication Technologies in Tourism in Innsbruck, Austria, January 22-25, 2013Place is a notion closely linked with the wealth of human experience, and invested by values, attitudes, and cultural influences. In particular, many places are strongly linked to music, which contributes to shaping the perception and the meaning of a place. In this paper we propose a computational approach for identifying musicians and music suited for a place of interest (POI). We present a knowledge-based framework built upon the DBpedia ontology, and a graph-based algorithm that scores musicians with respect to their semantic relatedness to a POI and suggests the top scoring ones. We found that users appreciate and judge as valuable the musician suggestions generated by the proposed approach. Moreover, users perceived compositions of the suggested musicians as suited for the POIs

Multiclass cancer classification in fresh frozen and formalin-fixed paraffin-embedded tissue by DigiWest multiplex protein analysis

Histomorphology and immunohistochemistry are the most common ways of cancer classification in routine cancer diagnostics, but often reach their limits in determining the organ origin in metastasis. These cancers of unknown primary, which are mostly adenocarcinomas or squamous cell carcinomas, therefore require more sophisticated methodologies of classification. Here, we report a multiplex protein profiling-based approach for the classification of fresh frozen and formalin-fixed paraffin-embedded (FFPE) cancer tissue samples using the digital western blot technique DigiWest. A DigiWest-compatible FFPE extraction protocol was developed, and a total of 634 antibodies were tested in an initial set of 16 FFPE samples covering tumors from different origins. Of the 303 detected antibodies, 102 yielded significant correlation of signals in 25 pairs of fresh frozen and FFPE primary tumor samples, including head and neck squamous cell carcinomas (HNSC), lung squamous cell carcinomas (LUSC), lung adenocarcinomas (LUAD), colorectal adenocarcinomas (COAD), and pancreatic adenocarcinomas (PAAD). For this signature of 102 analytes (covering 88 total proteins and 14 phosphoproteins), a support vector machine (SVM) algorithm was developed. This allowed for the classification of the tissue of origin for all five tumor types studied here with high overall accuracies in both fresh frozen (90.4%) and FFPE (77.6%) samples. In addition, the SVM classifier reached an overall accuracy of 88% in an independent validation cohort of 25 FFPE tumor samples. Our results indicate that DigiWest-based protein profiling represents a valuable method for cancer classification, yielding conclusive and decisive data not only from fresh frozen specimens but also FFPE samples, thus making this approach attractive for routine clinical applications

Drawn Stories, Moving Images. Comic Books and their Screen Adaptations

The comic transcends the merely entertaining, and fans of comics become engaged and invested in the field through a range of activities. Major cities host regular comic conventions, attracting hundreds of thousands of attendees each year, who search for special issues of their favourite comic-book series, meet artists, attend workshops and buy merchandise. Many fans do not stop at just attending conventions; they do so dressed as their favourite comic characters or wearing badges, buttons, T-shirts or sweaters with images of those characters on them. In other words: many fans do ot merely consume comic books; rather, they arrange a considerable part of their lives around them and in some cases even embody their heroes, that is, they copy their behaviour and their language. The comic universe, the comic books and the range of activities emerging out of them and around them become a meaningful universe for fans

Mucosal melanomas of different anatomic sites share a common global DNA methylation profile with cutaneous melanoma but show location-dependent patterns of genetic and epigenetic alterations

Cutaneous, ocular, and mucosal melanomas are histologically indistinguishable tumors that are driven by a different spectrum of genetic alterations. With current methods, identification of the site of origin of a melanoma metastasis is challenging. DNA methylation profiling has shown promise for the identification of the site of tumor origin in various settings. Here we explore the DNA methylation landscape of melanomas from different sites and analyze if different melanoma origins can be distinguished by their epigenetic profile. We performed DNA methylation analysis, next generation DNA panel sequencing, and copy number analysis of 82 non-cutaneous and 25 cutaneous melanoma samples. We further analyzed eight normal melanocyte cell culture preparations. DNA methylation analysis separated uveal melanomas from melanomas of other primary sites. Mucosal, conjunctival, and cutaneous melanomas shared a common global DNA methylation profile. Still, we observed location-dependent DNA methylation differences in cancer-related genes, such as low frequencies of RARB (7/63) and CDKN2A promoter methylation (6/63) in mucosal melanomas, or a high frequency of APC promoter methylation in conjunctival melanomas (6/9). Furthermore, all investigated melanomas of the paranasal sinus showed loss of PTEN expression (9/9), mainly caused by promoter methylation. This was less frequently seen in melanomas of other sites (24/98). Copy number analysis revealed recurrent amplifications in mucosal melanomas, including chromosomes 4q, 5p, 11q and 12q. Most melanomas of the oral cavity showed gains of chromosome 5p with TERT amplification (8/10), while 11q amplifications were enriched in melanomas of the nasal cavity (7/16). In summary, mucosal, conjunctival, and cutaneous melanomas show a surprisingly similar global DNA methylation profile and identification of the site of origin by DNA methylation testing is likely not feasible. Still, our study demonstrates tumor location-dependent differences of promoter methylation frequencies in specific cancer-related genes together with tumor site-specific enrichment for specific chromosomal changes and genetic mutations. (c) 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland

The Liver-Selective Thyromimetic T-0681 Influences Reverse Cholesterol Transport and Atherosclerosis Development in Mice

Liver-selective thyromimetics have been reported to efficiently reduce plasma cholesterol through the hepatic induction of both, the low-density lipoprotein receptor (LDLr) and the high-density lipoprotein (HDL) receptor; the scavenger receptor class B type I (SR-BI). Here, we investigated the effect of the thyromimetic T-0681 on reverse cholesterol transport (RCT) and atherosclerosis, and studied the underlying mechanisms using different mouse models, including mice lacking LDLr, SR-BI, and apoE, as well as CETP transgenic mice.T-0681 treatment promoted bile acid production and biliary sterol secretion consistently in the majority of the studied mouse models, which was associated with a marked reduction of plasma cholesterol. Using an assay of macrophage RCT in mice, we found T-0681 to significantly increase fecal excretion of macrophage-derived neutral and acidic sterols. No positive effect on RCT was found in CETP transgenic mice, most likely due to the observed decrease in plasma CETP mass. Studies in SR-BI KO and LDLr KO mice suggested hepatic LDLr to be necessary for the action of T-0681 on lipid metabolism, as the compound did not have any influence on plasma cholesterol levels in mice lacking this receptor. Finally, prolonged treatment with T-0681 reduced the development of atherosclerosis by 60% in apoE KOs on Western type diet. In contrast, at an earlier time-point T-0681 slightly increased small fatty streak lesions, in part due to an impaired macrophage cholesterol efflux capacity, when compared to controls.The present results show that liver-selective thyromimetics can promote RCT and that such compounds may protect from atherosclerosis partly through induction of bile acid metabolism and biliary sterol secretion. On-going clinical trials will show whether selective thyromimetics do prevent atherosclerosis also in humans

Query Extension Suggestions for Visual Query Systems Through Ontology Projection and Indexing

Ontology-based visual query formulation is a viable alternative to textual query editors in the Semantic Web domain for extracting data from structured data sources in terms of the skills and knowledge required. A visual query system is at any moment responsible for providing the user with query extension suggestions; however, suggestions leading to empty results are often not useful. To this end, in this article, we first present an approach for projecting OWL 2 ontologies into navigation graphs to be used for query formulation and then a solution where an efficient finite index is used to calculate non-ranked approximated extension suggestions for ontology-based visual query systems using navigation graphs. The results of our experiments suggest that one can efficiently project an ontology into a navigation graph, query it for running an interactive user interface, and suggest query extensions that do not lead to dead-ends