Macrophage-Derived Biomarkers of Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a severe, rapidly progressive diffuse lung disease. Several pathogenetic mechanisms have been hypothesized on the basis of the fibrotic lung damage occurring in this disease, and a potential profibrotic role of activated alveolar macrophages and their mediators in the pathogenesis of IPF was recently documented. This paper focuses on recent literature on potential biomarkers of IPF derived from activated alveolar macrophages. Biomarker discovery and clinical application are a recent topic of interest in the field of interstitial lung diseases (ILDs). Cytokines, CC-chemokines, and other macrophage-produced mediators are the most promising prognostic biomarkers. Many molecules have been proposed in the literature as potential biomarker of IPF; however, a rigorous validation is needed to confirm their clinical utility

Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types

Background:There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually.Methods:In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data.Results:We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: https://knowledgebase.microdiscovery.de/heatmap.Conclusions:Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the inter-active knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs

Matching anticancer compounds and tumor cell lines by neural networks with ranking loss

Computational drug sensitivity models have the potential to improve therapeutic outcomes by identifying targeted drug components that are likely to achieve the highest efficacy for a cancer cell line at hand at a therapeutic dose. State of the art drug sensitivity models use regression techniques to predict the inhibitory concentration of a drug for a tumor cell line. This regression objective is not directly aligned with either of these principal goals of drug sensitivity models: We argue that drug sensitivity modeling should be seen as a ranking problem with an optimization criterion that quantifies a drug’s inhibitory capacity for the cancer cell line at hand relative to its toxicity for healthy cells. We derive an extension to the well-established drug sensitivity regression model PaccMann that employs a ranking loss and focuses on the ratio of inhibitory concentration and therapeutic dosage range. We find that the ranking extension significantly enhances the model’s capability to identify the most effective anticancer drugs for unseen tumor cell profiles based in on in-vitro data

Evaluating grazing response strategies in winter annuals : A multi-trait approach

Plants minimize fitness losses through grazing by three fundamental strategies: tolerance, avoidance and escape. Annual species have been traditionally assumed to escape grazing through their short life cycle and seed dormancy; however, their grazing response strategies remain almost unexplored. How traits and their coordination affect species' grazing responses, and whether the generalized grazing model, which posits convergent filtering by grazing and drought, is applicable to this ecologically and economically important species group thus remain unclear. We used a trait-based approach to evaluate grazing response strategies of winter annuals from the Middle East. Across 23 species, we examined the coordination of 16 traits hypothesized to be relevant for grazing responses, and linked them to species' fecundity responses, as proxy for fitness responses, to simulated grazing in controlled conditions, to species' abundance responses to grazing in the field and to species' distribution along a large-scale rainfall gradient. Winter annuals exhibited both grazing escape and to a lesser extent tolerance indicated by (a) independent coordination of escape and tolerance traits, and (b) maintenance of higher fecundity in species with more pronounced escape or tolerance traits under simulated grazing. In the natural habitat, species with a more pronounced escape but not tolerance strategy maintained higher abundance under grazing in dry habitats, indicating convergent favouring of escape by both grazing and drought. However, this finding at the local scale was not mirrored by a strategy shift along a large-scale rainfall gradient. Synthesis. The convergent favouring of escape traits by grazing and drought in annuals is consistent with the generalized grazing model. This model, which has been developed for perennials based on the avoidance strategy, can thus be extended to annuals based on escape, a finding that should facilitate projecting consequences of global change in drylands dominated by annuals. © 2021 The Authors. Journal of Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Societ

Teaching, Learning, and Leading with Schools and Communities: One Urban University Re-Envisions Teacher Preparation for the Next Generation

Ultimately, the national goals of improving learning outcomes for all students and reducing, if not eliminating, the achievement gap require a teaching corps that brings knowledge and professional competencies to have positive impacts on diverse learners in diverse settings (Gándara & Maxwell-Jolly, 2006). As central actors in schools, teachers have the greatest impact on student achievement (Cochran-Smith & Fries, 2005). Nevertheless, due to varied challenges of preparing high-quality teachers within the context of traditional schools of education, preparation programs have yet to consistently and comprehensively produce teachers who accomplish these outcomes (Ball & Forzani, 2009; Larabee, 2004, 2010). While substantive reform and evidence of improved teacher education emerges (Ball & Forzani, 2009, 2010; Zumwalt & Craig, 2005), systemic change that contributes to better pre-kindergarten-through-twelfth-grade (PK-12) student outcomes remains elusive (Darling-Hammond, 2010)

Evaluating grazing response strategies in winter annuals : A multi-trait approach

Plants minimize fitness losses through grazing by three fundamental strategies: tolerance, avoidance and escape. Annual species have been traditionally assumed to escape grazing through their short life cycle and seed dormancy; however, their grazing response strategies remain almost unexplored. How traits and their coordination affect species' grazing responses, and whether the generalized grazing model, which posits convergent filtering by grazing and drought, is applicable to this ecologically and economically important species group thus remain unclear. We used a trait-based approach to evaluate grazing response strategies of winter annuals from the Middle East. Across 23 species, we examined the coordination of 16 traits hypothesized to be relevant for grazing responses, and linked them to species' fecundity responses, as proxy for fitness responses, to simulated grazing in controlled conditions, to species' abundance responses to grazing in the field and to species' distribution along a large-scale rainfall gradient. Winter annuals exhibited both grazing escape and to a lesser extent tolerance indicated by (a) independent coordination of escape and tolerance traits, and (b) maintenance of higher fecundity in species with more pronounced escape or tolerance traits under simulated grazing. In the natural habitat, species with a more pronounced escape but not tolerance strategy maintained higher abundance under grazing in dry habitats, indicating convergent favouring of escape by both grazing and drought. However, this finding at the local scale was not mirrored by a strategy shift along a large-scale rainfall gradient. Synthesis. The convergent favouring of escape traits by grazing and drought in annuals is consistent with the generalized grazing model. This model, which has been developed for perennials based on the avoidance strategy, can thus be extended to annuals based on escape, a finding that should facilitate projecting consequences of global change in drylands dominated by annuals. © 2021 The Authors. Journal of Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Societ

Macrophage-derived biomarkers of idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a severe, rapidly progressive diffuse lung disease. Several pathogenetic mechanisms have been hypothesized on the basis of the fibrotic lung damage occurring in this disease, and a potential profibrotic role of activated alveolar macrophages and their mediators in the pathogenesis of IPF was recently documented. This paper focuses on recent literature on potential biomarkers of IPF derived from activated alveolar macrophages. Biomarker discovery and clinical application are a recent topic of interest in the field of interstitial lung diseases (ILDs). Cytokines, CC-chemokines, and other macrophage-produced mediators are the most promising prognostic biomarkers. Many molecules have been proposed in the literature as potential biomarker of IPF; however, a rigorous validation is needed to confirm their clinical utility

Does the exotic equal pollution? Landscape methods for solving the dilemma of using native versus non‐native plant species in drylands

There is a need to resolve methods to determine the merits of native versus nonnative plant use in drylands and indeed in more temperate areas around the world. This is because whilst plant introductions may have positive objectives, they can have significant negative landscape and environmental impacts. A key discussion on this issue focuses on whether the use of non-native plant species can be considered to be pollution and pollutive based on the concept that pollution can be regarded as ‘matter out of place’. The consequences of putting the wrong plant species in the wrong place can be extremely detrimental to the landscape character, quality and value of the land, let alone the effects on ecosystem structure and functioning as well as on biodiversity. These effects can also affect human communities who may rely on the landscape, for example, for tourism. It is thus necessary that the discussion on how decisions are made in determining plant choice evolves so that the right decisions are made when planting is necessary, for the land, for nature and for the people. This discussion has been initiated through COST Action ES1104, which focused on the restoration of degraded dry and arid lands. This article discusses a number of landscape methods based on sustainability principles to determine when and where native and non-native plants could and should be used.info:eu-repo/semantics/publishedVersio

Thematic Working Group 5: Formative assessment supported by technology.

The future of assessment faces major challenges including the use of IT to facilitate formative assessment that is important for improving learners’ development, motivation and engagement in learning. In many countries, in recent years, a renewed focus on assessments to support learning has been pushing against the burgeoning of testing for accountability, which in some countries, renders effective formative assessment practices almost impossible. Moreover, a systematic review by Harlen and Deakin Crick (2002) revealed that a strong focus on summative assessment for accountability can reduce motivation and disengage many learners. At the same time use of IT‐enabled assessments has been increasing rapidly, as they offer promise of cheaper ways of delivering and marking assessments as well as access to vast amounts of assessment data from which a wide range of judgements might be made about students, teachers, schools and education systems (Gibson & Webb, 2015). These opportunities also extend to assessment of complex collaborative work (Webb & Gibson, 2015). Current opportunities for using IT, including for harnessing the data that is being collected automatically, for formative assessment are underexplored and less well understood than those for summative assessments. Opportunities for learning with IT and perhaps with less teacher input are increasing but this depends on students developing as autonomous or independent learners. Research in formative assessment including effective feedback has emphasised the value of peer assessment practices for developing self‐assessment capabilities and hence independent learners (Black, Harrison, Lee, Marshall, & William, 2003). At previous EDUsummITs the possibilities and challenges for IT‐enabled assessments to support simultaneously both formative and summative purposes were analysed (Webb, Gibson, & Forkosh‐Baruch, 2013). While these challenges remain, at EDUsummIT 2017 we focused on the opportunities and challenges of IT supporting formative assessment because effective formative assessment is known to be extremely important for learning.RETHINKING LEARNING IN A DIGITAL AGE, EDUsummIT 2017 Summary Reports 18-20 september, Bulgari

Functions of the Microbiota for the Physiology of Animal Metaorganisms

Animals are usually regarded as independent entities within their respective environments. However, within an organism, eukaryotes and prokaryotes interact dynamically to form the so-called metaorganism or holobiont, where each partner fulfils its versatile and crucial role. This review focuses on the interplay between microorganisms and multicellular eukaryotes in the context of host physiology, in particular aging and mucus-associated crosstalk. In addition to the interactions between bacteria and the host, we highlight the importance of viruses and nonmodel organisms. Moreover, we discuss current culturing and computational methodologies that allow a deeper understanding of underlying mechanisms controlling the physiology of metaorganisms