Search results

DiAgRaMs: selecting biomarkers for gut-permeability

Increased intestinal permeability is linked to both intestinal as well as peripheralinflammatory disease. Contact between intestinal contents and the underlying immune system may account for excessive immune activation and local as well as systemic inflammation. Decreasing intestinal permeability using next-generation food products provides an attractive strategy to improve human health. However, to date, insight in biomarkers which reliably and reproducibly reflect intestinal permeability are lacking. Insight in these biomarkers provides a method to easily assess the effectivity of new healthimproving food products.

DiAgRaMs: Selecting biomarkers for gut-permeability

BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

BACKGROUND: In many genomics projects, numerous lists containing biological identifiers are produced. Often it is useful to see the overlap between different lists, enabling researchers to quickly observe similarities and differences between the data sets they are analyzing. One of the most popular methods to visualize the overlap and differences between data sets is the Venn diagram: a diagram consisting of two or more circles in which each circle corresponds to a data set, and the overlap between the circles corresponds to the overlap between the data sets. Venn diagrams are especially useful when they are 'area-proportional' i.e. the sizes of the circles and the overlaps correspond to the sizes of the data sets. Currently there are no programs available that can create area-proportional Venn diagrams connected to a wide range of biological databases.RESULTS: We designed a web application named BioVenn to summarize the overlap between two or three lists of identifiers, using area-proportional Venn diagrams. The user only needs to input these lists of identifiers in the textboxes and push the submit button. Parameters like colors and text size can be adjusted easily through the web interface. The position of the text can be adjusted by 'drag-and-drop' principle. The output Venn diagram can be shown as an SVG or PNG image embedded in the web application, or as a standalone SVG or PNG image. The latter option is useful for batch queries. Besides the Venn diagram, BioVenn outputs lists of identifiers for each of the resulting subsets. If an identifier is recognized as belonging to one of the supported biological databases, the output is linked to that database. Finally, BioVenn can map Affymetrix and EntrezGene identifiers to Ensembl genes.CONCLUSION: BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used biological databases currently available. Its implementation on the World Wide Web makes it available for use on any computer with internet connection, independent of operating system and without the need to install programs locally. BioVenn is freely accessible at http://www.cmbi.ru.nl/cdd/biovenn/.

Combining hands-on and minds-on learning with interactive diagrams in primary science education

Thinking back and forth between observing physical phenomena and developing scientific ideas, also known as hands-on and minds-on learning, is essential for the development of scientific reasoning in primary science education. In the Netherlands, inquiry-based learning is advocated as the preferred teaching method. However, most teachers lack time and sufficient pedagogical content knowledge to adequately provide the teaching required for this. To address this problem, we designed and evaluated science and technology lessons, consisting of hands-on experiments combined with interactive diagrams, aimed at scaffolding primary school students (9–12 years) in the development of their scientific reasoning. Our proof-of-concept uses an online application, that lets students work through the lessons while alternating hands-on and minds-on activities. A study was carried out (n = 490) showing that most students successfully complete the lessons within a standard lesson timeframe. The approach enables students to effectively apply several types of scientific reasoning and to do so more autonomously than in traditional science classes.

Understanding the complexity of professional development in schools through Causal Loop Diagrams

Changes, challenges and expectations of society call for ongoing professional development of teachers. However, in many schools ongoing professional development cannot be taken for granted. Many governmental, local or institutional policies aim at stimulating teachers’ professional development, but many of these policies have a limited impact. To reach a deeper understanding of this problem casual loop diagrams (Salmon et al, 2022) can be helpful as they visualize how different parts and processes in an organisation are interrelated and either strengthen of weaken one another. Causal loop diagrams originate from the field of system thinking where they are used to understand wicked problems in complex systems (Bore & Wright, 2009; Groff, 2013; Vermaak, 2016). Causal loop diagrams can illustrate how elements like the structure of the profession and of schools, cultures in schools, collegial dynamics, etc are interconnected and can reinforce each other in a positive or negative way. From our observations in schools and from many discussions with teachers and school leaders we developed causal loop diagrams and validated these in literature. Our next step will be to validate the causal loop diagrams in practices in schools through focus group interviews in a variety of schools. In this session we will present some of the causal loop diagrams we developed, the patterns they illustrate and the underlying theory that support these patterns. Additionally, we will discuss to what extend these patterns are unique for the Dutch context in which we developed them, and the extent in which they can also be recognized in other counties and contexts. Finally we will discuss the way in which working with causal loop diagrams can support teachers, schools and teacher educators that collaborate with schools to identify patterns that hinder a systemic approach for ongoing professional development.

Event diagrams

This chapter presents event diagrams as a representational tool that allows students to visualize relativistic phenomena. It puts particular emphasis on thought experiments that can help students obtain a deeper understanding of physical phenomena that are hard to imagine. The chapter is intended for readers who look for instructional models to teach concepts of special relativity at the secondary school level, and also, for those who wish to learn more about thought experiments as instructional tools. Students perform the thought experiment by drawing light propagation in the event diagram. Compared to the traditional presentation of thought experiments, the event diagram stimulates students to reason with light propagation more explicitly. Like all external representations, event diagrams are a simplified and idealized display of reality and are inherently limited. To wrap up, the authors have shown how their tasks stimulate students to perform thought experiments by drawing light propagation in event diagrams.