The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.

Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool's web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.

The stability of Class II correction with functional appliance therapy and orthodontic camouflage: A retrospective cohort study.

OBJECTIVE: The aim of this study was to compare the stability of overjet reduction in adolescents treated with either orthodontic camouflage involving extraction of premolar units or functional appliance therapy. MATERIAL AND METHODS: A retrospective cohort study was undertaken with data collected at pre-treatment (T0), debond (T1) and 12 months post-treatment (T2). The primary outcome measure was stability of overjet reduction, and secondary outcome measures included Angle's molar relationship, and Little's Irregularity Index score. RESULTS: Forty-two Class II participants, 18 treated with a functional appliance and 24 with camouflage, were included with a mean pre-treatment age of 13.07 years (SD 1.72), with 23 (55%) being female. Mean overjet reduction during treatment in the functional appliance group was 6.99mm with relapse of just 0.62mm present at 12 months post-treatment. In the orthodontic camouflage group, there was a mean overjet reduction of 3.54mm with relapse of 0.27mm at 12 months post-treatment. Linear regression analysis confirmed no statistical difference (P=0.501) in overjet relapse between both treatment groups at 12 months post-treatment, adjusting for overjet at baseline. A further regression analysis revealed no significant association between overjet relapse and pre-treatment skeletal discrepancy, labial segment crowding, retention regime or compliance with the retention protocol. CONCLUSIONS: Both functional appliance and orthodontic camouflage therapies appear to have good antero-posterior occlusal stability, with minor degrees of overjet relapse occurring over a 12-month follow-up period. There was no significant difference between the treatments in relation to overjet relapse, buccal segment interdigitation or anterior irregularity.

Metabolic depression and the evolution of hypoxia tolerance in threespine stickleback, Gasterosteus aculeatus.

Anthropogenic increases in global temperature and agricultural runoff are increasing the prevalence of aquatic hypoxia throughout the world. We investigated the potential for a relatively rapid evolution of hypoxia tolerance using two isolated (for less than 11 000 years) populations of threespine stickleback: one from a lake that experiences long-term hypoxia (Alta Lake, British Columbia) and one from a lake that does not (Trout Lake, British Columbia). Loss-of-equilibrium (LOE) experiments revealed that the Alta Lake stickleback were significantly more tolerant of hypoxia than the Trout Lake stickleback, and calorimetry experiments revealed that the enhanced tolerance of Alta Lake stickleback may be associated with their ability to depress metabolic rate (as indicated by metabolic heat production) by 33% in hypoxia. The two populations showed little variation in their capacities for O2 extraction and anaerobic metabolism. These results reveal that intraspecific variation in hypoxia tolerance can develop over relatively short geological timescales, as can metabolic rate depression, a complex biochemical response that may be favoured in long-term hypoxic environments.

Calorespirometry reveals that goldfish prioritize aerobic metabolism over metabolic rate depression in all but near-anoxic environments.

Metabolic rate depression (MRD) has long been proposed as the key metabolic strategy of hypoxic survival, but surprisingly, the effects of changes in hypoxic O2 tensions (PwO2 ) on MRD are largely unexplored. We simultaneously measured the O2 consumption rate (MO2 ) and metabolic heat of goldfish using calorespirometry to test the hypothesis that MRD is employed at hypoxic PwO2  values and initiated just below Pcrit, the PwO2 below which MO2  is forced to progressively decline as the fish oxyconforms to decreasing PwO2 Specifically, we used closed-chamber and flow-through calorespirometry together with terminal sampling experiments to examine the effects of PwO2  and time on MO2 , metabolic heat and anaerobic metabolism (lactate and ethanol production). The closed-chamber and flow-through experiments yielded slightly different results. Under closed-chamber conditions with a continually decreasing PwO2 , goldfish showed a Pcrit of 3.0±0.3 kPa and metabolic heat production was only depressed at PwO2  between 0 and 0.67 kPa. Under flow-through conditions with PwO2  held at a variety of oxygen tensions for 1 and 4 h, goldfish also initiated MRD between 0 and 0.67 kPa but maintained MO2  to 0.67 kPa, indicating that Pcrit is at or below this PwO2 Anaerobic metabolism was strongly activated at PwO2 ≤1.3 kPa, but only used within the first hour at 1.3 and 0.67 kPa, as anaerobic end-products did not accumulate between 1 and 4 h exposure. Taken together, it appears that goldfish reserve MRD for near-anoxia, supporting routine metabolic rate at sub-PcritPwO2  values with the help of anaerobic glycolysis in the closed-chamber experiments, and aerobically after an initial (<1 h) activation of anaerobic metabolism in the flow-through experiments, even at 0.67 kPa PwO2.