Designing interactive visualizations for analyzing chronic lung diseases in a user-centered approach.

OBJECTIVES: Medical practitioners analyze numerous types of data, often using archaic representations that do not meet their needs. Pneumologists who analyze lung function exams must often consult multiple exam records manually, making comparisons cumbersome. Such shortcomings can be addressed with interactive visualizations, but these must be designed carefully with practitioners' needs in mind. MATERIALS AND METHODS: A workshop with experts was conducted to gather user requirements and common tasks. Based on the workshop results, we iteratively designed a web-based prototype, continuously consulting experts along the way. The resulting application was evaluated in a formative study via expert interviews with 3 medical practitioners. RESULTS: Participants in our study were able to solve all tasks in accordance with experts' expectations and generally viewed our system positively, though there were some usability and utility issues in the initial prototype. An improved version of our system solves these issues and includes additional customization functionalities. DISCUSSION: The study results showed that participants were able to use our system effectively to solve domain-relevant tasks, even though some shortcomings could be observed. Using a different framework with more fine-grained control over interactions and visual elements, we implemented design changes in an improved version of our prototype that needs to be evaluated in future work. CONCLUSION: Employing a user-centered design approach, we developed a visual analytics system for lung function data that allows medical practitioners to more easily analyze the progression of several key parameters over time.

The oxidative stress response, in particular the katY gene, is temperature-regulated in Yersinia pseudotuberculosis.

Pathogenic bacteria, such as Yersinia pseudotuberculosis encounter reactive oxygen species (ROS) as one of the first lines of defense in the mammalian host. In return, the bacteria react by mounting an oxidative stress response. Previous global RNA structure probing studies provided evidence for temperature-modulated RNA structures in the 5'-untranslated region (5'-UTR) of various oxidative stress response transcripts, suggesting that opening of these RNA thermometer (RNAT) structures at host-body temperature relieves translational repression. Here, we systematically analyzed the transcriptional and translational regulation of ROS defense genes by RNA-sequencing, qRT-PCR, translational reporter gene fusions, enzymatic RNA structure probing and toeprinting assays. Transcription of four ROS defense genes was upregulated at 37°C. The trxA gene is transcribed into two mRNA isoforms, of which the most abundant short one contains a functional RNAT. Biochemical assays validated temperature-responsive RNAT-like structures in the 5'-UTRs of sodB, sodC and katA. However, they barely conferred translational repression in Y. pseudotuberculosis at 25°C suggesting partially open structures available to the ribosome in the living cell. Around the translation initiation region of katY we discovered a novel, highly efficient RNAT that was primarily responsible for massive induction of KatY at 37°C. By phenotypic characterization of catalase mutants and through fluorometric real-time measurements of the redox-sensitive roGFP2-Orp1 reporter in these strains, we revealed KatA as the primary H2O2 scavenger. Consistent with the upregulation of katY, we observed an improved protection of Y. pseudotuberculosis at 37°C. Our findings suggest a multilayered regulation of the oxidative stress response in Yersinia and an important role of RNAT-controlled katY expression at host body temperature.

Impact of essential oils on methane emissions, milk yield, and feed efficiency and resulting influence on the carbon footprint of dairy production systems.

Reducing CO2 emissions is one of the highest priorities in animal production. Regarding methane reduction, feed additives are of growing importance. As shown in a meta-analysis, the use of the essential oil (EO) blend Agolin Ruminant affects methane production per day (- 8.8%), milk yield (+ 4.1%), and feed efficiency (+ 4.4%). Building on these results, the present study investigated the effect of varying individual parameters on the carbon footprint of milk. The environmental and operational management system REPRO was applied to calculate the CO2 emissions. Calculation of CO2 emissions include enteric and storage-related CH4, storage-, and pasture-related N2O as well as direct and indirect energy expenditures. Three feed rations were created, differing in their basic feed components such as grass silage, corn silage, and pasture. Each feed ration was differentiated into three variants: variant 1 CON (no additive), variant 2 EO, and variant 3 (15% reduction of enteric methane compared to CON). Due to the reducing effect of EO on enteric methane production, a reduction potential of up to 6% could be calculated for all rations. Considering other variable parameters, such as the positive effects on ECM yield and feed efficiency, a GHG reduction potential of up to 10% can be achieved for the silage rations and almost 9% for the pasture ration. Modeling showed that indirect methane reduction strategies are important contributors to environmental impacts. Reduction of enteric methane emissions is fundamental, as they account for the largest share of GHG emissions from dairy production.

OmpA, a Common Virulence Factor, Is Under RNA Thermometer Control in Yersinia pseudotuberculosis.

The outer membrane protein OmpA is a virulence factor in many mammalian pathogens. In previous global RNA structure probing studies, we found evidence for a temperature-modulated RNA structure in the 5'-untranslated region (5'-UTR) of the Yersinia pseudotuberculosis ompA transcript suggesting that opening of the structure at host-body temperature might relieve translational repression. Here, we support this hypothesis by quantitative reverse transcription PCR, translational reporter gene fusions, enzymatic RNA structure probing, and toeprinting assays. While ompA transcript levels decreased at 37°C compared to 25°C, translation of the transcript increased with increasing temperature. Biochemical experiments show that this is due to melting of the RNA structure, which permits ribosome binding to the 5'-UTR. A point mutation that locks the RNA structure in a closed conformation prevents translation by impairing ribosome access. Our findings add another common virulence factor to the growing list of pathogen-associated genes that are under RNA thermometer control.