PlotXpress, a webtool for normalization and visualization of reporter expression data [version 1; peer review: 3 approved]

In molecular cell biology, reporter assays are frequently used to investigate gene expression levels. Reporter assays employ a gene that encodes a light-emitting protein, of which the luminescence is quantified as a proxy of gene expression. Commercial parties provide reporter assay kits that include protocols and specialized detection machinery. However, downstream analysis of the output data and their presentation are not standardized. We have developed plotXpress to fill this gap, providing a free, open-source platform for the semi-automated analysis and standardized visualisation of experimental gene reporter data. Users can upload raw luminescence data acquired from a reporter gene assay with an internal control. In plotXpress, the data is corrected for sample variation with the internal control and the average for each condition is calculated. When a reference condition is selected the fold change is calculated for all other conditions, based on the selected reference. The results are shown as dot plots with a statistical summary, which can be adjusted to create publication-grade plots without requiring coding skills. Altogether, plotXpress is an open-source, low-threshold, web-based tool, that promotes a standardized and reproducible analysis while providing an appealing visualization of reporter data. The webtool can be accessed at: https://huygens.science.uva.nl/PlotXpress

Why and how teachers use nature of science in teaching quantum physics:Research on the use of an ecological teaching intervention in upper secondary schools

Students at upper secondary and college level in many countries are introduced to quantum physics (QP) in a mostly mathless course. Research shows that addressing epistemological and philosophical aspects would be beneficial for novice students’ conceptual understanding. However, physics teachers seldom address these nature of science (NOS) aspects in their lessons. We take the view that teachers only implement these aspects if this serves their goals. This study explores whether experienced Dutch high school teachers, who are not trained for NOS teaching, address NOS in their QP lessons when provided with NOS-infused teaching resources. We based our framework on literature about pedagogic content knowledge and on the principles of the practicality of educational innovations. Teacher interviews (N=10) supported by classroom observations provided insights into how and why teachers use specific elements from the resources. Our research reveals teachers’ perspectives on teaching QP in secondary schools and why they think NOS aspects can be helpful to reach their teaching goals. Our findings support the view that conceptual QP is valuable for all students because an informed NOS view is vital for everybody in today’s society. Additionally, we expect that an ecological intervention that supports teachers and at the same time recognizes their professionality and environment has potential implications for other fields of science education and could have a significant positive impact in classrooms

Secondary school students’ views of nature of science in quantum physics

Epistemological and philosophical issues have always been relevant for the foundations of physics, but usually do not find their way into secondary physics classrooms. As an exception to this, the strangeness of quantum physics (QP) naturally evokes philosophical questions, and learners might have to change their ideas about the nature of science (NOS). In this exploratory mixed-method study, we examined possible connections between upper secondary school students’ QP content knowledge and their ideas about relevant aspects of NOS in the context of QP. We administered a QP concept test to 240 Dutch secondary students (age 17–19) after they attended classes on QP without a focus on NOS. Next, we selected 24 students with a range of test scores for individual semi-structured interviews about their understanding of wave-particle duality and their views on five aspects of NOS. Contrary to NOS studies in other contexts, the interviews showed that all 24 students had well-informed NOS views in the context of QP. We contend that NOS in QP might be more easily accessible than in many other contexts. Our results suggest that QP can have an additional role in the physics curriculum by enhancing students’ understanding of NOS

How high schools teach quantum physics – a cross-national analysis of curricula in secondary education

Quantum physics (QP) changed our worldview, it brought us modern electronic devices, and its almost mythical image fascinates. Although QP is relatively new in secondary education, it is now part of the national curricula of many countries. To understand the current state of QP content in high schools, we scrutinised upper secondary school physics curriculum documents in 15 countries. In these countries, we identified a similar core curriculum of QP which contains the following seven main categories: discrete atomic energy levels, interactions between light and matter, wave-particle duality, de Broglie wavelength, technical applications, Heisenberg's uncertainty principle, and the probabilistic nature of QP. We also found differences in the focus of the listed topics of individual countries, which indicate different views on teaching QP. The thematic focus of QP items is related to the underlying goal of science education and to the way students' knowledge is tested. This overview shows which QP content is generally feasible at a secondary level and which pedagogical perspectives are possible. Therefore this study might lead to reflections on existing QP curricula, and inspire countries that do not have QP in their curriculum yet

Evaluatie Opvangbeleid 2005-2008 overwinterende ganzen en smienten. Deelrapport 10. Hebben overwinterende ganzen invloed op de weidevogelstand?

Dit rapport richt zich op de vraag of de sterk toegenomen dichtheden ganzen in bepaalde gebieden mede verantwoordelijk kunnen zijn voor de achteruitgang van de weidevogels ter plekke. Gebruik makend van data verzameld in de periode 1990-2005 in het kader van het weidevogelmeetnet en de watervogeltellingen in ganzentelgebieden werd onderzocht in hoeverre gebieden met hoge dichtheden ganzen overlappen met gebieden met hoge dichtheden weidevogels. De effecten van hoge dichtheden overwinterende ganzen op in Nederland broedende weidevogels lijken verwaarloosbaar of positief. Resultaten van onderzoek van SOVON en Alterr

Finding Regions of Counterfactual Explanations via Robust Optimization

Counterfactual explanations play an important role in detecting bias and improving the explainability of data-driven classification models. A counterfactual explanation (CE) is a minimal perturbed data point for which the decision of the model changes. Most of the existing methods can only provide one CE, which may not be achievable for the user. In this work we derive an iterative method to calculate robust CEs, i.e. CEs that remain valid even after the features are slightly perturbed. To this end, our method provides a whole region of CEs allowing the user to choose a suitable recourse to obtain a desired outcome. We use algorithmic ideas from robust optimization and prove convergence results for the most common machine learning methods including logistic regression, decision trees, random forests, and neural networks. Our experiments show that our method can efficiently generate globally optimal robust CEs for a variety of common data sets and classification models

Athletes treated for inguinal-related groin pain by endoscopic totally extraperitoneal (TEP) repair:long-term benefits of a prospective cohort

Purpose: Inguinal-related groin pain (IRGP) in athletes is a multifactorial condition, posing a therapeutic challenge. If conservative treatment fails, totally extraperitoneal (TEP) repair is effective in pain relief. Because there are only few long-term follow-up results available, this study was designed to evaluate effectiveness of TEP repair in IRGP-patients years after the initial procedure. Methods: Patients enrolled in the original, prospective cohort study (TEP-ID-study) were subjected to two telephone questionnaires. The TEP-ID-study demonstrated favorable outcomes after TEP repair for IRGP-patients after a median follow-up of 19 months. The questionnaires in the current study assessed different aspects, including, but not limited to pain, recurrence, new groin-related symptoms and physical functioning measured by the Copenhagen Hip and Groin Outcome Score (HAGOS). The primary outcome was pain during exercise on the numeric rating scale (NRS) at very long-term follow-up.Results: Out of 32 male participants in the TEP-ID-study, 28 patients (88%) were available with a median follow-up of 83 months (range: 69–95). Seventy-five percent of athletes were pain free during exercise (p &lt; 0.001). At 83 months follow-up, a median NRS of 0 was observed during exercise (IQR 0–2), which was significantly lower compared to earlier scores (p &lt;0.01). Ten patients (36%) mentioned subjective recurrence of complaints, however, physical functioning improved on all HAGOS subscales (p &lt;0.05).Conclusion:This study demonstrates the safety and effectivity of TEP repair in a prospective cohort of IRGP-athletes, for whom conservative treatment had failed, with a follow-up period of over 80 months.</p