Although systemic immunity is critical to the process of tumor rejection, cancer research has largely focused on immune cells in the tumor microenvironment. To understand molecular changes in the patient systemic response (SR) to the presence of BC, we profiled RNA in blood and matched tumor from 173 patients. We designed a system (MIxT, Matched Interactions Across Tissues) to systematically explore and link molecular processes expressed in each tissue. MIxT confirmed that processes active in the patient SR are especially relevant to BC immunogenicity. The nature of interactions across tissues (i.e. which biological processes are associated and their patterns of expression) varies highly with tumor subtype. For example, aspects of the immune SR are underexpressed proportionally to the level of expression of defined molecular processes specific to basal tumors. The catalog of subtype-specific interactions across tissues from BC patients provides promising new ways to tackle or monitor the disease by exploiting the patient SR.

Scalability is increasingly important for bioinformatics analysis services, since these must handle larger datasets, more jobs, and more users. The pipelines used to implement analyses must therefore scale with respect to the resources on a single compute node, the number of nodes on a cluster, and also to cost-performance. Here, we survey several scalable bioinformatics pipelines and compare their design and their use of underlying frameworks and infrastructures. We also discuss current trends for bioinformatics pipeline development.

Lung cancer is the leading cause of cancer deaths. Novel predictive biomarkers are needed to improve treatment selection and more accurate prognostication. PAX6 is a transcription factor with a proposed tumour suppressor function. Immunohistochemical staining was performed on tissue microarrays from 335 non-small cell lung cancer (NSCLC) patients for PAX6. Multivariate analyses of clinico-pathological variables and disease-specific survival (DSS) was carried out, and phenotypic changes of two NSCLC cell lines with knockdown of PAX6 were characterized. While PAX6 expression was only associated with a trend of better disease-specific survival (DSS) (p = 0.10), the pN+ subgroup (N = 103) showed significant correlation between high PAX6 expression and longer DSS (p = 0.022). Median survival for pN + patients with high PAX6 expression was 127.4 months, versus 22.9 months for patients with low PAX6 expression. In NCI-H661 cells, knockdown of PAX6 strongly activated serum-stimulated migration. In NCI-H460 cells, PAX6 knockdown activated anchorage-independent growth. We did not observe any significant effect of PAX6 on proliferation in either of cell lines. Our findings strongly support the proposition of PAX6 as a valid and positive prognostic marker in NSCLC in node-positive patients. There is a need for further studies, which should provide mechanistical explanation for the role of PAX6 in NSCLC.

We describe our citizen science approach and technologies designed to introduce students in upper secondary schools to computational thinking and engineering. Using an Arduino microcontroller and low-cost sensors we have developed the air:bit, a programmable sensor kit that students build and program to collect air quality data. In our course, students develop their own research questions regarding air quality before using their own air quality sensor kit to answer their respective questions. This project combines electronics and coding with natural sciences providing a truly interdisciplinary course.We have open-sourced the teaching materials including the building and coding instructions. In addition, students can contribute to our webbased platform for storing, visualizing, and exploring the collected air quality data. It also provides an open API for anyone to download air quality data collected by the students. Through the website, available at airbit.uit.no, students are motivated to contribute air quality data open to the public.We describe lessons learned from our pilot project in a Norwegian upper secondary school and how we are deploying it in 10 schools across Northern Norway. In the pilot, students successfully built and coded the air:bits, and after two months of data collection they could correctly describe local patterns in the air quality. We believe that by combining electronics and coding with the natural sciences we motivate students to engage in all scientific disciplines.

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