Open source software toolchain for automated non‐targeted screening for toxins in alternative foods

Previous published methods for non-targeted screening of toxins in alternative foods such as leaf concentrate, agricultural residues or plastic fed to biological consortia are time consuming and expensive and thus present accessibility, as well as, time-constraint issues for scientists from under resourced settings to identify safe alternative foods. The novel methodology presented here, utilizes a completely free and open source software toolchain for automatically screening unknown alternative foods for toxicity using experimental data from ultra-high-pressure liquid chromatography and mass spectrometry. The process uses three distinct tools (mass spectrometry analysis with MZmine 2, formula assignment with MFAssignR, and data filtering with ToxAssign) enabling it to be modular and easily upgradable in the future. MZmine 2 and MFAssignR have been previously described, while ToxAssign was developed here to match the formulas output by formula assignment to potentially toxic compounds in a local table, then look up toxic data on the Open Food Tox Database for the matched compounds. This process is designed to fill the gap between food safety analysis techniques and developing alternative food production techniques to allow for new methods of food production to be preliminarily tested before animal testing. The methodology was validated against a previous method using proprietary commercial software. The new process identifies all of the toxic elements the previous process identified with more detailed information than the previous process was able to provide automatically. • Efficient analysis to find potentially toxic compounds in alternative foods and resilient foods. • Identification of potentially unsafe products without the use of live animal testing. • Modular free and open source design to allow for upgrading or fitting of user needs

Outcomes and Prognostic Factors of Pulmonary Hypertension Patients Undergoing Emergent Endotracheal Intubation.

Background: Emergent endotracheal intubations (ETI) in pulmonary hypertension (PH) patients are associated with increased mortality. Post-intubation interventions that could increase survivability in this population have not been explored. We evaluate early clinical characteristics and complications following emergent endotracheal intubation and seek predictors of adverse outcomes during this post-intubation period. Methods: Retrospective cohort analysis of adult patients with groups 1 and 3 PH who underwent emergent intubation between 2005-2021 in medical and liver transplant ICUs at a tertiary medical center. PH patients were compared to non-PH patients, matched by Charlson Comorbidity Index. Primary outcomes were 24-h post-intubation and inpatient mortalities. Various 24-h post-intubation secondary outcomes were compared between PH and control cohorts. Results: We identified 48 PH and 110 non-PH patients. Pulmonary hypertension was not associated with increased 24-h mortality (OR 1.32, 95%CI 0.35-4.94, P = .18), but was associated with inpatient mortality (OR 4.03, 95%CI 1.29-12.5, P = .016) after intubation. Within 24 h post-intubation, PH patients experienced more frequent acute kidney injury (43.5% vs. 19.8%, P = .006) and required higher norepinephrine dosing equivalents (6.90 [0.13-10.6] mcg/kg/min, vs. 0.20 [0.10-2.03] mcg/kg/min, P = .037). Additionally, the median P/F ratio (PaO2/FiO2) was lower in PH patients (96.3 [58.9-201] vs. 233 [146-346] in non-PH, P = .001). Finally, a post-intubation increase in PaCO2 was associated with mortality in the PH cohort (post-intubation change in PaCO2 +5.14 ± 16.1 in non-survivors vs. -18.7 ± 28.0 in survivors, P = .007). Conclusions: Pulmonary hypertension was associated with worse outcomes after emergent endotracheal intubation than similar patients without PH. More importantly, our data suggest that the first 24 hours following intubation in the PH group represent a particularly vulnerable period that may determine long-term outcomes. Early post-intubation interventions may be key to improving survival in this population