PathBank 2.0-the pathway database for model organism metabolomics.

PathBank (https://pathbank.org) and its predecessor database, the Small Molecule Pathway Database (SMPDB), have been providing comprehensive metabolite pathway information for the metabolomics community since 2010. Over the past 14 years, these pathway databases have grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in computing technology. This year's update, PathBank 2.0, brings a number of important improvements and upgrades that should make the database more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of primary or canonical pathways (from 1720 to 6951); (ii) a massive increase in the total number of pathways (from 110 234 to 605 359); (iii) significant improvements to the quality of pathway diagrams and pathway descriptions; (iv) a strong emphasis on drug metabolism and drug mechanism pathways; (v) making most pathway images more slide-compatible and manuscript-compatible; (vi) adding tools to support better pathway filtering and selecting through a more complete pathway taxonomy; (vii) adding pathway analysis tools for visualizing and calculating pathway enrichment. Many other minor improvements and updates to the content, the interface and general performance of the PathBank website have also been made. Overall, we believe these upgrades and updates should greatly enhance PathBank's ease of use and its potential applications for interpreting metabolomics data.

An Exploratory Retrospective Study of Factors Affecting Energy Expenditure in Critically Ill Children.

BACKGROUND: Accurate measurement of energy expenditure is not widely available. Patient and clinical factors associated with energy expenditure have been poorly explored, leading to errors in estimation formulae. The objective of this study was to determine clinical factors associated with measured energy expenditure (MEE), expressed in kcal/kg/d, in critically ill children. METHODS: This was a retrospective study at 2 Canadian pediatric intensive care units (ICUs). Patients were mechanically ventilated children who had 1 or more MEE using indirect calorimetry. Associations between MEE and 28 clinical factors were evaluated in univariate regression and 16 factors in a multivariate regression model accounting for repeated measurements. RESULTS: Data from 239 patients (279 measurements) were analyzed. Median (Q1, Q3) MEE was 34.8 (26.8, 46.2) kcal/kg/d. MEE was significantly associated with weight, heart rate, diastolic blood pressure, ICU day of indirect calorimetry (P = 0.004), minute ventilation, vasoactive inotropic score (P = 0.004), opioids, chloral hydrate, dexmedetomidine, inhaled salbutamol (P = 0.02), and propofol dose (all P < 0.0001 unless otherwise specified) in the final multivariate regression model. CONCLUSIONS: This study demonstrated association between MEE (kcal/kg/d) and factors not previously explored in pediatric critical illness. Further evaluation of these factors to confirm associations and more precisely quantify the magnitude of effect is required to support refinement of formulae to estimate energy expenditure.

Parental opinions regarding consent for observational research of no or minimal risk in the pediatric intensive care unit.

BACKGROUND: The aim of the study was to determine opinions and knowledge regarding the process of obtaining informed consent to participate in observational research in pediatric intensive care. METHODS: Survey 1 asked decision makers what model(s) of consent was acceptable for each type of observational research both before and after background information. Survey 2 asked decision makers about the experience of being asked for consent to observational research, and knowledge regarding the consent process both before and after background information. RESULTS: Cooperation rate was 100/117 (85%). The proportion in favor of any of the offered alternatives to signed informed consent for observational research, after receiving all the background information, was 74-80%, lowest for observational prospective research with a minimal risk intervention 37/50 (74%; 95% CI 60-84%). The proportion who agreed they felt overwhelmed by being approached for consent to observational research was 26 (52%; 95% CI 39-65%). Most respondents (from 60 to 74%) felt they understood the concepts regarding observational research; however, after reading background information, most (from 60 to 74%) felt their understanding had improved "a great deal". CONCLUSION: Understanding of risk, practical difficulties, consent bias, and Research Ethics Board safeguards was poor. Future study is needed to confirm our finding that most agreed with alternative methods of consent for observational research.