Visualization for epidemiological modelling: challenges, solutions, reflections and recommendations.

We report on an ongoing collaboration between epidemiological modellers and visualization researchers by documenting and reflecting upon knowledge constructs-a series of ideas, approaches and methods taken from existing visualization research and practice-deployed and developed to support modelling of the COVID-19 pandemic. Structured independent commentary on these efforts is synthesized through iterative reflection to develop: evidence of the effectiveness and value of visualization in this context; open problems upon which the research communities may focus; guidance for future activity of this type and recommendations to safeguard the achievements and promote, advance, secure and prepare for future collaborations of this kind. In describing and comparing a series of related projects that were undertaken in unprecedented conditions, our hope is that this unique report, and its rich interactive supplementary materials, will guide the scientific community in embracing visualization in its observation, analysis and modelling of data as well as in disseminating findings. Equally we hope to encourage the visualization community to engage with impactful science in addressing its emerging data challenges. If we are successful, this showcase of activity may stimulate mutually beneficial engagement between communities with complementary expertise to address problems of significance in epidemiology and beyond. See https://ramp-vis.github.io/RAMPVIS-PhilTransA-Supplement/. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

VisLitE: Visualization Literacy and Evaluation.

With the widespread advent of visualization techniques to convey complex data, visualization literacy (VL) is growing in importance. Two noteworthy facets of literacy are user understanding and the discovery of visual patterns with the help of graphical representations. The research literature on VL provides useful guidance and opportunities for further studies in this field. This introduction summarizes and presents research on VL that examines how well users understand basic and advanced data representations. To the best of our knowledge, this is the first tutorial article on interactive VL. We describe evaluation categories of existing relevant research into unique subject groups that facilitate and inform comparisons of literacy literature and provide a starting point for interested readers. In addition, the introduction also provides an overview of the various evaluation techniques used in this field of research and their challenging nature. Our introduction provides researchers with unexplored directions that may lead to future work. This starting point serves as a valuable resource for beginners interested in the topic of VL.

Complex model calibration through emulation, a worked example for a stochastic epidemic model.

Uncertainty quantification is a formal paradigm of statistical estimation that aims to account for all uncertainties inherent in the modelling process of real-world complex systems. The methods are directly applicable to stochastic models in epidemiology, however they have thus far not been widely used in this context. In this paper, we provide a tutorial on uncertainty quantification of stochastic epidemic models, aiming to facilitate the use of the uncertainty quantification paradigm for practitioners with other complex stochastic simulators of applied systems. We provide a formal workflow including the important decisions and considerations that need to be taken, and illustrate the methods over a simple stochastic epidemic model of UK SARS-CoV-2 transmission and patient outcome. We also present new approaches to visualisation of outputs from sensitivity analyses and uncertainty quantification more generally in high input and/or output dimensions.

ADRB3, ROCK2, and GEF Levels in Overactive Bladder Patients.

PURPOSE: The aim of this study was to evaluate changes in levels of adrenergic receptor ß3 (ADRB3), Rho-related kinase 2 (ROCK2), and guanine nucleotide exchange factor (GEF), which play key roles in the adrenergic and cholinergic pathways of contraction-relaxation harmony in voiding physiology, and to explore the relationship between these proteins and overactive bladder (OAB). METHODS: This study included 60 idiopathic OAB patients and a healthy control group. A validated OAB-validated 8 questionnaire was completed by all participants. Serum levels of ADRB3, ROCK2, and GEF were examined with enzyme-linked immunosorbent assays. Patient and control groups were compared in terms of these levels, and receiver operating characteristic (ROC) curves were generated for all parameters. RESULTS: The levels of ROCK2 were significantly elevated, but there were no correlations between the OAB symptom score and the serum levels of ROCK2, ADRB3, and GEF in OAB patients. In the ROC analysis, ROCK2 alone provided the strongest potential relationship (area under the curve=0.651) with 84.9% sensitivity. The ROCK2+GEF combination provided a satisfactory relationship (AUC=0.755). The AUC for the ADRB3+ROCK2+GEF combination was 0.752, with 64.2% sensitivity and 88.2% specificity. CONCLUSION: The study results suggest that alterations in serum ROCK2 levels and the use of this parameter in combination with ADRB3 and GEF levels can shed light on the pathophysiology of idiopathic OAB syndrome and provide a new perspective for treatment.

Relation of ADRB3, GEF, ROCK2 gene polymorphisms to clinical findings in overactive bladder.

PURPOSE: Adrenergic and cholinergic pathways play an important role in contraction-relaxation harmony in human bladder. Functional changes in any proteins in these pathways may result in overactive bladder. We aimed to investigate whether single gene polymorphisms affecting adrenergic and cholinergic pathways are associated with OAB syndrome. METHODS: 60 patients with idiopathic OAB and 60 healthy controls were included in the study. A validated OAB-V8 questionnaire was given to all patients. Polymorphisms of ADRB3, ROCK2, and GEF gene were detected by PCR from whole blood samples. Genotypic structures of patients and controls were compared. The relationship between genotypic structures and OAB symptom scores were investigated. RESULTS: We found no significant difference in the genotype and allele frequencies between the patients and controls for all three SNP. While there was no relationship between ADRB3 and GEF gene polymorphisms and OAB scores in OAB patients, the OAB score in heterozygous polymorphic individuals was significantly higher than in homozygous polymorphic individuals in the ROCK2 gene (p = 0.039). CONCLUSION: The polymorphisms of the ADRB3, ROCK2, and GEF genes were present in both OAB group and healthy controls, but were not associated with OAB syndrome.

Exploring biomarkers in the overactive bladder: Alterations in miRNA levels of a panel of genes in patients with OAB.

AIMS: It has been demonstrated that there are abundant stable microRNAs (miRNAs) in plasma, which is potentially disease-specific. Adrenergic and muscarinic pathways play an important role in voiding physiology. Alterations in the levels of miRNAs are thought to influence the regulation of these pathways at the molecular level. The aim of this study was to investigate the relationship of miRNAs with overactive bladder pathogenesis and to provide a new perspective to treatment approaches. METHODS: This study included patients with an overactive bladder (OAB) diagnosis and a healthy control group. All patients completed a validated OAB-V8 questionnaire. The relative expression levels of 12 miRNAs were examined in plasma by PCR. Receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic qualification of miRNAs. RESULTS: The relative expression levels of let-7b-5p, miR-92a-3p, miR-98-5p, miR-142-3p, and miR-200c-3p were significantly upregulated and miR-139-5p was significantly downregulated in patients with OAB and no correlation was determined between the levels of miRNAs with OAB symptom score. Among the miRNAs, miR-98-5p provided the highest diagnostic accuracy alone (area under curve [AUC] = 0.79) in ROC analysis. The combination of miR-98-5p + miR-139-5p was seen to be a good indicator (AUC = 0.839). CONCLUSIONS: These results suggest that alteration of the miRNA levels can be used as auxiliary parameters to explain the pathophysiology of OAB syndrome and could shed light on new treatment options.