Information Extraction from Text for Improving Research on Small Molecules and Histone Modifications

The cumulative number of publications, in particular in the life sciences, requires efficient methods for the automated extraction of information and semantic information retrieval. The recognition and identification of information-carrying units in text – concept denominations and named entities – relevant to a certain domain is a fundamental step. The focus of this thesis lies on the recognition of chemical entities and the new biological named entity type histone modifications, which are both important in the field of drug discovery. As the emergence of new research fields as well as the discovery and generation of novel entities goes along with the coinage of new terms, the perpetual adaptation of respective named entity recognition approaches to new domains is an important step for information extraction. Two methodologies have been investigated in this concern: the state-of-the-art machine learning method, Conditional Random Fields (CRF), and an approximate string search method based on dictionaries. Recognition methods that rely on dictionaries are strongly dependent on the availability of entity terminology collections as well as on its quality. In the case of chemical entities the terminology is distributed over more than 7 publicly available data sources. The join of entries and accompanied terminology from selected resources enables the generation of a new dictionary comprising chemical named entities. Combined with the automatic processing of respective terminology – the dictionary curation – the recognition performance reached an F1 measure of 0.54. That is an improvement by 29 % in comparison to the raw dictionary. The highest recall was achieved for the class of TRIVIAL-names with 0.79. The recognition and identification of chemical named entities provides a prerequisite for the extraction of related pharmacological relevant information from literature data. Therefore, lexico-syntactic patterns were defined that support the automated extraction of hypernymic phrases comprising pharmacological function terminology related to chemical compounds. It was shown that 29-50 % of the automatically extracted terms can be proposed for novel functional annotation of chemical entities provided by the reference database DrugBank. Furthermore, they are a basis for building up concept hierarchies and ontologies or for extending existing ones. Successively, the pharmacological function and biological activity concepts obtained from text were included into a novel descriptor for chemical compounds. Its successful application for the prediction of pharmacological function of molecules and the extension of chemical classification schemes, such as the the Anatomical Therapeutic Chemical (ATC), is demonstrated. In contrast to chemical entities, no comprehensive terminology resource has been available for histone modifications. Thus, histone modification concept terminology was primary recognized in text via CRFs with a F1 measure of 0.86. Subsequent, linguistic variants of extracted histone modification terms were mapped to standard representations that were organized into a newly assembled histone modification hierarchy. The mapping was accomplished by a novel developed term mapping approach described in the thesis. The combination of term recognition and term variant resolution builds up a new procedure for the assembly of novel terminology collections. It supports the generation of a term list that is applicable in dictionary-based methods. For the recognition of histone modification in text it could be shown that the named entity recognition method based on dictionaries is superior to the used machine learning approach. In conclusion, the present thesis provides techniques which enable an enhanced utilization of textual data, hence, supporting research in epigenomics and drug discovery

Metabolic changes associated with two endocrine abnormalities in dogs : elevated fructosamine and low thyroxine

Introduction Metabolomics studies in canine endocrine abnormalities are sparse and basic information on these abnormalities must be generated. Objectives To characterize the metabolic changes associated with elevated fructosamine, reflecting poor glycemic control, and low thyroxine, a thyroid hormone controlling metabolism. Methods Leftovers of clinical serum samples; 25 controls, 79 high fructosamine, and 47 low thyroxine, were analyzed using H-1 NMR and differences were evaluated using Firth logistic regression. Results Both high fructosamine and low thyroxine were associated with changes in concentrations of multiple metabolites, including glycoprotein acetyls and lipids. Conclusion These findings suggest promising makers for further research and clinical validation.Peer reviewe

Role of copper efflux in pneumococcal pathogenesis and resistance to macrophage-mediated immune clearance

In bacteria, the intracellular levels of metals are mediated by tightly controlled acquisition and efflux systems. This is particularly true of copper, a trace element that is universally toxic in excess. During infection, the toxic properties of copper are exploited by the mammalian host to facilitate bacterial clearance. To better understand the role of copper during infection, we characterized the contribution of the cop operon to copper homeostasis and virulence in Streptococcus pneumoniae. Deletion of either the exporter, encoded by copA, or the chaperone, encoded by cupA, led to hypersensitivity to copper stress. We further demonstrated that loss of the copper exporter encoded by copA led to decreased virulence in pulmonary, intraperitoneal, and intravenous models of infection. Deletion of copA resulted in enhanced macrophage-mediated bacterial clearance in vitro. The attenuation phenotype of the copA mutant in the lung was found to be dependent on pulmonary macrophages, underscoring the importance of copper efflux in evading immune defenses. Overall, these data provide insight into the role of the cop operon in pneumococcal pathogenesis

Report on the evaluation of the RBRargo|2000 OEM sensor from at sea data analysis

Report of evaluation of the RBRargo|2000 OEM sensor based on at sea experiments on Baltic Sea and North Atlantic, and other national experiment

Towards a standardized method for broth microdilution susceptibility testing of Haemophilus parasuis

Currently, there is no agreed method available for broth microdilution susceptibility testing of Haemophilus parasuis, one of the most important bacterial pathogens in pig production. Therefore, the aim of this study was to develop a method that could be easily performed by diagnostic laboratories and that appears suitable for a harmonized susceptibility testing. Growth determinations using one type strain and three field isolates revealed no visible growth of H. parasuis in media which have proven to be suitable for susceptibility testing of fastidious organisms. Therefore, a new medium, cation-adjusted Mueller-Hinton broth (CAMHB) plus NADH and sterile filtered heat-inactivated chicken serum, was developed. The reproducibility of MICs obtained in this medium was evaluated and statistically analyzed, considering a model with two different variables (precondition of five identical MICs and MIC mode accepting a deviation of ±1 dilution step, respectively). No significant differences for both variables were seen between two time points investigated and between results obtained with the recently proposed test medium broth (TMB). Nearly all MICs of quality control strains were in the acceptable range. Subsequently, 47 H. parasuis isolates representing 13 serovars were tested with the newly developed medium and TMB. Statistical analysis of all isolates and 15 antimicrobial agents and antimicrobial combinations showed no significant difference between MICs obtained in supplemented CAMHB and TMB. Because of a simplified implementation in routine diagnostic and a lower chance of interference between medium components and antimicrobial agents, supplemented CAMHB is recommended with an incubation time of 24 h

Electronic properties of BaCuChF (Ch = S,Se,Te) surfaces and BaCuSeF/ZnPc interfaces

BaCuChF (Ch=S,Se,Te) surfaces and BaCuSeF interfaces with zinc phthalocyanine (ZnPc) were studied by photoelectron spectroscopy. BaCuChF compounds oxidize when exposed to ambient atmosphere. Se capping layers were studied as a means to produce representative surfaces for photoelectron spectroscopic measurements. Decapped BaCuSeF surfaces remain O-free and C-free when the Se layer is evaporated but they become F-deficient. The resulting surfaces have work functions of 4.85 eV and Fermi levels located 0.25 eV above the valence band maximum. In situ stepwise deposition of ZnPc on a BaCuSeF film surface produced a chemically inert interface with a hole-injection barrier of 0.11 eV.This is the publisher’s final pdf. The published article is copyrighted by the American Institute of Physics and can be found at: http://scitation.aip.org/content/aip/journal/jap.Article Copyright (2010) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics

Epigenetic dynamics of monocyte-to-macrophage differentiation

Background Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete transcriptome and epigenome of human monocytes that were differentiated in vitro by addition of colony-stimulating factor 1 in serum-free medium. Results Numerous mRNAs and miRNAs were significantly up- or down-regulated. More than 100 discrete DNA regions, most often far away from transcription start sites, were rapidly demethylated by the ten eleven translocation enzymes, became nucleosome-free and gained histone marks indicative of active enhancers. These regions were unique for macrophages and associated with genes involved in the regulation of the actin cytoskeleton, phagocytosis and innate immune response. Conclusions In summary, we have discovered a phagocytic gene network that is repressed by DNA methylation in monocytes and rapidly de-repressed after the onset of macrophage differentiation

Documenting ---- in Bloomington-Normal: A Community Report on Intolerance, Segregation, Accessibility, Inclusion, and Progress, and Improvement

For the local chapter of Not In Our Town, we document intolerance, discrimination, segregation, disparities of access, and disparities in the criminal justice system in Bloomington-Normal, IL. Using archival material, secondary data, and primary data, we examine these issues from the mid-1990s to the present. We also assess the position of the organization in the community and provide strategies for future success. In sum, Bloomington-Normal was and is intolerant; discrimination did and does take place in this community; there are disparities of access and in the criminal justice system; we are segregated. The community is also less of these things than it used to be and is less of these things than other places. Fifteen undergraduate students in Sociology 300, twelve graduate students in Sociology 477, a teaching assistant, and an instructor conducted this study in spring 2017

Resistance to mesenchymal reprogramming sustains clonal propagation in metastatic breast cancer

The acquisition of mesenchymal traits is considered a hallmark of breast cancer progression. However, the functional relevance of epithelial-to-mesenchymal transition (EMT) remains controversial and context dependent. Here, we isolate epithelial and mesenchymal populations from human breast cancer metastatic biopsies and assess their functional potential in vivo. Strikingly, progressively decreasing epithelial cell adhesion molecule (EPCAM) levels correlate with declining disease propagation. Mechanistically, we find that persistent EPCAM expression marks epithelial clones that resist EMT induction and propagate competitively. In contrast, loss of EPCAM defines clones arrested in a mesenchymal state, with concomitant suppression of tumorigenicity and metastatic potential. This dichotomy results from distinct clonal trajectories impacting global epigenetic programs that are determined by the interplay between human ZEB1 and its target GRHL2. Collectively, our results indicate that susceptibility to irreversible EMT restrains clonal propagation, whereas resistance to mesenchymal reprogramming sustains disease spread in multiple models of human metastatic breast cancer, including patient-derived cells in vivo

Aufbruch ins sozialistische Paradies – Propagandaplakate der frühen Volksrepublik China:

Die 1950er Jahre waren eine Zeit der Kampagnen zur Industrialisierung, Modernisierung und der Verwirklichung der sozialistischen Vision. Was Realität werden sollte, zeigen die Propagandaplakate. Die Studierenden des Seminars Plakatkunst und Propaganda in der frühen Volksrepublik China haben beispielhafte Exemplare der groß angelegten Kampagnen aus der Plakatsammlung des Amsterdamer International Institute of Social History ausgewählt. Diese haben sie im Hinblick auf ihren historischen Kontext untersucht und die Ergebnisse auf zusätzlichen Infoplakaten zusammengefasst. Der Katalog zeigt die Exponate und vermittelt die entsprechenden zeit- und kunsthistorischen Hintergründe