Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species

The genus Bacillus includes species with diverse natural histories, including free-living nonpathogenic heterotrophs such as B. subtilis and host-dependent pathogens such as B. anthracis (the etiological agent of the disease anthrax) and B. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we developed a pipeline for quantitative total assessment of the use of diverse sources of carbon for general metabolism to better appreciate the “culinary preferences” of three distinct Bacillus species, as well as related Staphylococcus aureus. We show that each species has widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. This approach was applied to the growth and survival of B. anthracis in a blood-like environment and find metabolism shifts from sugar to amino acids as the preferred source of energy. Finally, various nutrients in broth and host-like environments are identified that may promote or interfere with bacterial metabolism during infection.

Multicancer Early Detection: Learning From the Past to Meet the Future

Multicancer early detection (MCED) tests may soon be available to screen for many cancers using a single blood test, yet little is known about these tests beyond their diagnostic performance. Taking lessons from the history of cancer early detection, we highlight 3 factors that influence how performance of early detection tests translates into benefit and benefit-harm trade-offs: the ability to readily confirm a cancer signal, the population testing strategy, and the natural histories of the targeted cancers. We explain why critical gaps in our current knowledge about each factor prevent reliably projecting the expected clinical impact of MCED testing at this point in time. Our goal is to communicate how much uncertainty there is about the possible effects of MCED tests on population health so that patients, providers, regulatory agencies, and the public are well informed about what is reasonable to expect from this potentially important technological advance. We also urge the community to invest in a coordinated effort to collect data on MCED test dissemination and outcomes so that these can be tracked and studied while the tests are rigorously evaluated for benefit, harm, and cost.

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.

Best Paper Selection

Ali SH, Foreman J, Tozan Y, Capasso A, Jones AM, DiClemente RJ. Trends and predictors of COVID-19 information sources and their relationship with knowledge and beliefs related to the pandemic: nationwide cross-sectional study. https://publichealth.jmir.org/2020/4/e21071/ Picone M, Inoue S, DeFelice C, Naujokas MF, Sinrod J, Cruz VA, Stapleton J, Sinrod E, Diebel SE, Wassman J, Robert E. Social listening as a rapid approach to collecting and analyzing COVID-19 symptoms and disease natural histories reported by large numbers of individuals. https://www.liebertpub.com/doi/10.1089/pop.2020.0189?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed Pobiruchin M, Zowalla R, Wiesner M. Temporal and location variations, and link categories for the dissemination of COVID-19-related information on Twitter during the SARS-CoV-2 outbreak in Europe: Infoveillance study. https://www.jmir.org/2020/8/e19629/

Embodiment and the Animal in Guadalupe Nettel’s El matrimonio de los peces rojos

This article explores an interaction between posthumanist and cognitive discourses through the work of award winning Mexican author, Guadalupe Nettel. I focus on her 2014 anthology, Natural Histories, rereading the central motif of the narrative, that animals ‘are like a mirror that reflects submerged emotions or behaviours that we don’t dare to see’ (Nettel, 9). This ‘reflection’ is not simply the image of the human reflected off the opaque surface of the animal, but rather the humans themselves act as a mirror, simulating the behaviour of the animals with which they cohabit. This can be read as a literary representation of a neurophysiological phenomenon — embodied simulation, an internal mimicry, either perceptible or imperceptible, performed when watching others completing certain tasks, movements or expressions (Gazzola et al. 2007; Uithol et al. 2011; Iacoboni 2009). In particular, the first story, ‘El matrimonio de los peces rojos’, depicts a profound human-nonhuman embodied resonance that moves between linguistic, narratological and characterological levels. A cognitive critical approach to the mirroring between animals and humans in the stories reveals the particular intersection between new paradigms in cognitive science, animal studies, and posthumanism that the anthology develops, each of its narratives intertwining mind, body and nonhuman other in a non-hierarchical network.

Root Dilatation Is More Malignant Than Ascending Aortic Dilation

Background Data from the International Registry of Acute Aortic Dissection indicate that the guideline criterion of 5.5 cm for ascending aortic intervention misses many dissections occurring at smaller dimensions. Furthermore, studies of natural behavior have generally treated the aortic root and the ascending aorta as 1 unit despite embryological, anatomical, and functional differences. This study aims to disentangle the natural histories of the aforementioned aortic segments, allowing natural behavior to define specific intervention criteria for root and ascending segments of the aorta. Methods and Results Diameters of the aortic root and mid‐ascending segment were measured separately. Long‐term complications (dissection, rupture, and death) were analyzed retrospectively for 1162 patients with ascending thoracic aortic aneurysm. Cox regression analysis suggested that aortic root dilatation ( P =0.017) is more significant in predicting adverse events than mid‐ascending aortic dilatation ( P =0.087). Short stature posed as a serious risk factor. The dedicated risk curves for the aortic root and the mid‐ascending aorta revealed hinge points at 5.0 and 5.25 cm, respectively. Conclusions The natural histories of the aortic root and mid‐ascending aorta are uniquely different. Dilation of the aortic root imparts a significant higher risk of adverse events. A diameter shift for intervention to 5.0 cm for the aortic root and to 5.25 cm for the mid‐ascending aorta should be considered at expert centers.

The Communication of Hit Quality Using Natural History Visualizations (NHVs)

High-throughput screening (HTS) often yields a list of compounds that requires prioritization before further work is performed. Prioritization criteria typically include activity, selectivity, physicochemical properties, and other absolute or calculated measurements of compound “value.” One critical method of compound prioritization is often not discussed in published accounts of HTS. We have referred to this oft-overlooked metric as “compound natural history.” These natural histories are observational evaluations of how a compound has been reported in the historical literature or compound databases. The purpose of this work was to develop a useful natural history visualization (NHV) that could form a standard, important part of hit reporting and evaluation. In this case report, we propose an efficient and effective NHV that will assist in the prioritization of active compounds and demonstrate its utility using a retrospective analysis of reported hits. We propose that this method of compound natural history evaluation be adopted in HTS triage and become an integral component of published reports of HTS outcomes.

Open access digital tools’ contribution for mapping and monitoring of biodiversity

Biodiversity constitutes a source of natural richness of life on Earth, including all the variety of living organisms. The United Nations Organization proclaimed the period between 2011 and 2020 as the International Decade of Biodiversity. Knowing that the majority of the existing information about species distribution is not promptly reachable, the adoption of Georeferencing tolls as a brace for mapping, managing and handling of the biodiversity stands out. The present essay aims to describe the development and implementation of the Digital Atlas of Herpetofauna from the state of Pernambuco, a new digital tool of open access, which integrates data about species, their natural histories and their spacial distribution. For its development, the Joomla!, version 1.5.26, was adopted as Content Management System and the MySQL as Database System, these were integrated to the Library System PROJ.4 in order to enable graphic projections. The result is the developed tool itself, applying the combination of geographic data stored by mapping based on web browser. This study presented advantages found in the use of open access digital tools for mapping and monitoring species, pointing that its use is a very effective way to aggregate and communicate information about biodiversity.