Visual Analytics: A Method to Explore Natural Histories of Oral Epithelial Dysplasia

Risk assessment and follow-up of oral potentially malignant disorders in patients with mild or moderate oral epithelial dysplasia is an ongoing challenge for improved oral cancer prevention. Part of the challenge is a lack of understanding of how observable features of such dysplasia, gathered as data by clinicians during follow-up, relate to underlying biological processes driving progression. Current research is at an exploratory phase where the precise questions to ask are not known. While traditional statistical and the newer machine learning and artificial intelligence methods are effective in well-defined problem spaces with large datasets, these are not the circumstances we face currently. We argue that the field is in need of exploratory methods that can better integrate clinical and scientific knowledge into analysis to iteratively generate viable hypotheses. In this perspective, we propose that visual analytics presents a set of methods well-suited to these needs. We illustrate how visual analytics excels at generating viable research hypotheses by describing our experiences using visual analytics to explore temporal shifts in the clinical presentation of epithelial dysplasia. Visual analytics complements existing methods and fulfills a critical and at-present neglected need in the formative stages of inquiry we are facing.

Design by Immersion: A Transdisciplinary Approach to Problem-Driven Visualizations

While previous work exists on how to conduct and disseminate insights from problem-driven visualization projects and design studies, the literature does not address how to accomplish these goals in transdisciplinary teams in ways that advance all disciplines involved. In this paper we introduce and define a new methodological paradigm we call design by immersion, which provides an alternative perspective on problem-driven visualization work. Design by immersion embeds transdisciplinary experiences at the center of the visualization process by having visualization researchers participate in the work of the target domain (or domain experts participate in visualization research). Based on our own combined experiences of working on cross-disciplinary, problem-driven visualization projects, we present six case studies that expose the opportunities that design by immersion enables, including (1) exploring new domain-inspired visualization design spaces, (2) enriching domain understanding through personal experiences, and (3) building strong transdisciplinary relationships. Furthermore, we illustrate how the process of design by immersion opens up a diverse set of design activities that can be combined in different ways depending on the type of collaboration, project, and goals. Finally, we discuss the challenges and potential pitfalls of design by immersion.

Long-lived and short-lived reactive species produced by a cold atmospheric pressure plasma jet for the inactivation of Pseudomonas aeruginosa and Staphylococcus aureus

Different chemical pathways leading to the inactivation of Pseudomonas aeruginosa and Staphylococcus aureus by a cold atmospheric pressure plasma jet (APPJ) in buffered and non-buffered solutions are reported. As APPJs produce a complex mixture of reactive species in solution, a comprehensive set of diagnostics were used to assess the liquid phase chemistry. This includes absorption and electron paramagnetic resonance spectroscopy in addition to a scavenger study to assess the relative importance of the various plasma produced species involved in the inactivation of bacteria. Different modes of inactivation of bacteria were found for the same plasma source depending on the solution and the plasma feed gas. The inactivation of bacteria in saline is due to the production of short-lived species in the case of argon plasma when the plasma touches the liquid. Long-lived species (ClO^-) formed by the abundant amount of O^. radicals produced by the plasmas played a dominant role in the case of Ar + 1% O₂ and Ar + 1% air plasmas when the plasma is not in direct contact with the liquid. Inactivation of bacteria in distilled water was found to be due to the generation of short-lived species: O^. &O₂^.- for Ar + 1% O₂ plasma and O₂^.- (and ^.OH in absence of saline) for Ar plasma.

Taking the plunge: chemical reaction dynamics in liquids

The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

The fate of plasma-generated oxygen atoms in aqueous solutions: non-equilibrium atmospheric pressure plasmas as an efficient source of atomic O(aq)

It is demonstrated with help of ¹⁸O₂ labeling that O_(aq) is stable in water and can directly react with dissolved molecules.

Alternatives to the 'water oxidation pathway' of biological ozone formation

Recent studies have shown that ozone (O3) is endogenously generated in living tissues, where it makes both positive and negative physiological contributions. A pathway for the formation of both O3 and hydrogen peroxide (H2O2) was previously proposed, beginning with the antibody or amino acid-catalyzed oxidation of water by singlet oxygen ((1)O2) to form hydrogen trioxide (H2O3) as a key intermediate. A key pillar of this hypothesis is that some of the H2O2 molecules incorporate water-derived oxygen atoms. However, H2O3 decomposes extremely readily in water to form (1)O2 and water, rather than O3 and H2O2. This article highlights key literature indicating that the oxidation of organic molecules such as the amino acids methionine, tryptophan, histidine, and cysteine by (1)O2 is involved in ozone formation. Based on this, an alternative hypothesis for ozone formation is developed involving a further reaction of singlet oxygen with various oxidized organic intermediates. H2O2 having water-derived oxygen atoms is subsequently formed during ozone decomposition in water by known reactions.