1,721,268 research outputs found
Implementing and advancing Cell Painting-based phenotypic profiling for hazard assessment of substances with endocrine activity
No full textPhenotypic changes in cell morphology and organization can indicate perturbations in cell functions, potentially leading to adverse health effects such as organ dysfunction or cancer. Thus, image-based high-throughput screening (HTS) and high-throughput phenotypic profiling (HTPP) approaches play an important role in basic research, drug discovery, and chemical hazard assessment. The disruption of physiological estrogen function by environmental chemicals is an example of factors contributing to cell function alterations and potentially breast cancer progression. Thus, identification of substances that interfere with hormone pathways and elicit adverse health effects, so-called endocrine disrupting chemicals (EDC), is of high relevance. Additionally, the phasing out of animal-based regulatory testing methods in the EU and beyond necessitates robust in vitro HTS and HTPP approaches utilizing cell-specific, functional readouts for hazard assessment of environmental chemicals, such as EDCs and compounds with specific target organ toxicity (STOT). Cell Painting (CP) is a powerful image-based HTPP method compatible with artificial intelligence (AI)-driven image and data analysis as well as capable of reflecting mode-of-action (MoA)-driven cellular responses caused by compound treatments, genetic perturbations, or disease states in an untargeted manner. However, the CP assay still holds methodical limitations regarding multiplexing capacity, physiological relevance of cell culture conditions, and diversity of cell types, which limits its use for hazard assessments. In this PhD project, the CP assay was implemented in steroid hormone-responsive MCF-7/vBOS cells for identification of environmental chemicals with diverse MoAs, including endocrine activity. Moreover, the CP assay was further developed into the novel Cell Painting PLUS (CPP) assay, which is an efficient, robust, and broadly applicable HTPP approach that overcomes certain methodological limitations of the CP method. A small-scale screen of 15 reference compounds demonstrated that the iterative staining-elution cycle of CPP significantly expands the multiplexing capacity of the CP method. Importantly, it also improves the specificity of phenotypic profiles through completely separate imaging and analysis of single dyes in individual channels. Qualitative and quantitative analysis of screening data confirmed the ability of CPP-based HTPP in MCF-7/vBOS cells to reflect diverse MoA-driven phenotypes, including estrogen receptor (Er) pathway inhibition. In this context, this PhD project also established state-of-the-art requirements for screening large-compound libraries using two targeted HTS approaches, E-Morph assay and E-Morph screening assay, to generate reference data for identifying Erspecific phenotypes in HTPP. To improve the robustness and physiological relevance of image-based HTS and HTPP, serum-free cell culture conditions for MCF-7/vBOS cells were systematically explored. Overall, this PhD project set the ground for future CPP-based large-scale screenings identifying endocrine- or STOT-related compounds and enhancing the exploration of HTPP in the context of hazard assessment. Together with existing data from targeted phenotypic HTS, HTPP data was envisioned to enable an iterative hit prediction and testing cycle supported by AI-based analysis tools.Phänotypische Veränderungen in Zellmorphologie und -aufbau können auf funktionelle Störungen hinweisen, die potenziell mit der Entstehung gesundheitsschädlicher Effekte wie Organdysfunktionen oder Krebs zusammenhängen. Bildbasierte Hochdurchsatzverfahren für Screenings (HTS) und „Phenotypic profiling“ (HTPP) spielen daher eine wichtige Rolle in der Grundlagenforschung, Wirkstoffentwicklung sowie Gefahrenbeurteilung von Chemikalien. Die Störung der physiologischen Östrogenfunktion durch Umweltchemikalien ist ein Beispiel für Faktoren, die zu Veränderungen der Zellfunktionen und potenziell zur Entstehung von Brustkrebs beitragen. Die Identifikation von Substanzen, die Hormonsignalwege stören und gesundheitsschädliche Effekte hervorrufen, sogenannte endokrine Disruptoren (EDC), ist daher hoch relevant. Zudem erfordert die in und außerhalb der EU geplante Abschaffung tierbasierter regulatorischer Testmethoden robuste, auf zellspezifische und funktionale Parameter basierende in vitro HTS- und HTPP-Methoden zur Gefahrenbeurteilung von Umweltchemikalien, wie EDCs und Substanzen mit spezifischer Zielorgan-Toxizität (STOT). Cell Painting (CP) ist eine leistungsstarke, bildbasierte HTPP-Methode, die mit auf künstlicher Intelligenz (AI)-basierten Analysetools kombinierbar ist. Der „untargeted“ CP Assay kann zelluläre, Wirkmechanismus (MoA)-abhängige Reaktionen auf Wirkstoffbehandlungen, genetische Störungen oder Krankheiten abbilden. CP weist jedoch methodische Limitationen bzgl. der Multiplexing-Kapazität, physiologischen Relevanz der Zellkulturbedingungen und Diversität der Zelltypen auf, was seine Nutzung in der Gefahrenbeurteilung einschränkt. In dieser Arbeit wurde der CP Assay in steroid-hormon-responsive MCF-7/vBOS Zellen implementiert, um Umweltchemikalien mit diversen MoAs, einschließlich endokriner Aktivität, zu identifizieren. Zudem wurde der CP Assay zum innovativen Cell Painting PLUS (CPP) Assay weiterentwickelt, einem effizienten, robusten und breit anwendbaren HTPP-Ansatz, der bestimmte methodische Einschränkungen von CP überwindet. Das Screenen von 15 Referenzsubstanzen zeigte, dass der iterative Färbe-Elution-Zyklus von CPP die Multiplexing-Kapazität der CP-Methode erheblich erweitert. Dadurch konnte insbesondere die Spezifität der phänotypischen Profile verbessert werden, da eine vollständig getrennte Bilderfassung und -analyse einzelner Farbstoffe in individuellen Kanälen ermöglicht wird. Qualitative und quantitative Analysen bestätigten, dass CPP-basiertes HTPP in MCF-7/vBOS Zellen diverse MoAabhängige Phänotypen widerspiegeln kann, inklusive eines inhibierten Östrogenrezeptor (Er)-Signalwegs. In diesem Kontext wurde unter Verwendung zweier „targeted“ HTS-Ansätze, dem E-Morph Assay und dem E-Morph Screening Assay, modernste Anforderungen für das Screenen großer Wirkstoffbibliotheken etabliert, um Referenzdaten zur Identifizierung Er-spezifischer Phänotypen in HTPP zu generieren. Um die Robustheit und physiologische Relevanz von bildbasierten HTS und HTPP zu verbessern, wurden zudem serumfreie Zellkulturbedingungen für MCF-7/vBOS Zellen systematisch untersucht. Diese Arbeit legt damit den Grundstein für große CPP-basierte Screenings zur Identifikation von endokrinen oder STOT-relevanten Substanzen sowie der Weitererforschung von HTPP zur Gefahrenbeurteilung. Zusammen mit bestehenden Daten von „targeted“ phänotypischen HTS und AI-basierten Analysetools sollen HTPP-Daten einen iterativen Zyklus aus Aktivitätsprädiktion und -testung ermöglichen
Isolation und Qualifizierung von avinen thermostabilen Proteinen aus hochprozessierten Matrices mittels MS-Verfahren
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Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Induktion oxidativer DNA-Schäden und Beeinflussung der Nukleotidexzisionsreparatur durch Arsen-, Cadmium- und Nickelverbindungen
No full textkoamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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