Connectivity of the Pulley Ridge with remote locations as inferred from satellite- tracked drifter trajectories

Using historical (1994-2017) satellite‐tracked surface drifter trajectory data, we conduct a probabilistic Lagrangian circulation study which sheds light on the connectivity of Pulley Ridge with other locations in the Gulf of Mexico and adjacent areas. The analysis reveals that Pulley Ridge is connected with the North Atlantic, the Caribbean Sea, and most of the Gulf of Mexico. Preferred connecting pathways are identified and arrival times to potential reef sites computed. The study demonstrates the importance of Pulley Ridge as a source for neighboring regions like the Dry Tortugasa, the Florida Keys, Campeche Bank, and the east Florida coast as well as a self‐recruitment area for species with short competence time. The study further suggests that the reefs in the Caribbean Sea, the Dry Tortugas, the western Florida Keys, and the West Florida Shelf can act as sources for Pulley Ridge, indicating the importance of Pulley Ridge as a central refugium for species in the Gulf of Mexico

Comprehensive analyses of circulating cardiometabolic proteins and objective measures of fat mass

Background: The underlying molecular pathways for the effect of excess fat mass on cardiometabolic diseases is not well understood. Since body mass index is a suboptimal measure of body fat content, we investigated the relationship of fat mass measured by dual-energy X-ray absorptiometry with circulating cardiometabolic proteins. Methods: We used data from a population-based cohort of 4950 Swedish women (55–85 years), divided into discovery and replication samples; 276 proteins were assessed with three Olink Proseek Multiplex panels. We used random forest to identify the most relevant biomarker candidates related to fat mass index (FMI), multivariable linear regression to further investigate the associations between FMI characteristics and circulating proteins adjusted for potential confounders, and principal component analysis (PCA) for the detection of common covariance patterns among the proteins. Results: Total FMI was associated with 66 proteins following adjustment for multiple testing in discovery and replication multivariable analyses. Five proteins not previously associated with body size were associated with either lower FMI (calsyntenin-2 (CLSTN2), kallikrein-10 (KLK10)), or higher FMI (scavenger receptor cysteine-rich domain-containing group B protein (SSC4D), trem-like transcript 2 protein (TLT-2), and interleukin-6 receptor subunit alpha (IL-6RA)). PCA provided an efficient summary of the main variation in FMI-related circulating proteins involved in glucose and lipid metabolism, appetite regulation, adipocyte differentiation, immune response and inflammation. Similar patterns were observed for regional fat mass measures. Conclusions: This is the first large study showing associations between fat mass and circulating cardiometabolic proteins. Proteins not previously linked to body size are implicated in modulation of postsynaptic signals, inflammation, and carcinogenesis

A case report of switching from specific vendor-based to R-based pipelines for untargeted LC-MS metabolomics

Data pre-processing of the LC-MS data is a critical step in untargeted metabolomics studies in order to achieve correct biological interpretations. Several tools have been developed for pre-processing, and these can be classified into either commercial or open source software. This case report aims to compare two specific methodologies, Agilent Profinder vs. R pipeline, for a metabolomic study with a large number of samples. Specifically, 369 plasma samples were analyzed by HPLC-ESI-QTOF-MS. The collected data were pre-processed by both methodologies and later evaluated by several parameters (number of peaks, degree of missingness, quality of the peaks, degree of misalignments, and robustness in multivariate models). The vendor software was characterized by ease of use, friendly interface and good quality of the graphs. The open source methodology could more effectively correct the drifts due to between and within batch effects. In addition, the evaluated statistical methods achieved better classification results with higher parsimony for the open source methodology, indicating higher data quality. Although both methodologies have strengths and weaknesses, the open source methodology seems to be more appropriate for studies with a large number of samples mainly due to its higher capacity and versatility that allows combining different packages, functions, and methods in a single environment

Relative Validity and Reproducibility of a Web-Based Semi-Quantitative Food Frequency Questionnaire in the Danish Diet, Cancer, and Health—Next Generations MAX Study

The food frequency questionnaire (FFQ) is designed to capture an individual’s habitual dietary intake and is the most applied method in nutritional epidemiology. Our aim was to assess the relative validity and reproducibility of the FFQ used in the Diet, Cancer, and Health—Next Generations cohort (DCH-NG). We included 415 Danish women and men aged 18–67 years. Spearman’s correlations coefficients, Bland–Altman limits of agreement and cross-classification between dietary intakes estimated from the FFQ administered at baseline (FFQbaseline), and the mean of three 24-h dietary recalls (24-HDRs) and the FFQ administered after 12 months (FFQ12 months) were determined. Nutrient intakes were energy-adjusted by Nutrient Density and Residual methods. Correlation coefficients ranged from 0.18–0.58 for energy and energy-adjusted nutrient intakes, and the percentage of participants classified into the same quartile ranged from 28–47% between the FFQbaseline and the 24-HDRs. For the FFQ12 months compared with FFQbaseline, correlation coefficients ranged from 0.52–0.88 for intakes of energy, energy-adjusted nutrients, and food groups, and the proportion of participants classified into the same quartiles ranged from 43–69%. Overall, the FFQ provided a satisfactory ranking of individuals according to energy, nutrient, and food group intakes, making the FFQ suitable for use in epidemiological studies investigating diet in relation to disease outcomes

Semi-quantitative risk assessment of marine mammal oil exposure: A case study in the western Gulf of Mexico

Marine mammals are highly vulnerable to oil spills, although the effects at both individual and population levels are not fully understood. A first approximation to evaluate the possible consequences of oil spills on marine life is using ecological risk assessments, which are analytical tools used to assess the likelihood of adverse environmental effects due to exposure to stressors derived from human activities. We developed a semi-quantitative framework to evaluate the risk of oil spill exposure on marine mammals that combines the likelihood of exposure based on species-specific biological and ecological traits, and the feasibility of encounter, which considers not only the overlap between the distribution of the species and the total affected area by a spill but also considers the distribution of spilled oil within this area, thus reducing the uncertainty in the estimate. We applied our framework to assess the risk of exposure of eight cetaceans to scenarios of large heavy oil (API gravity<22) spills originating from three hypothetical deep-water wells in the western Gulf of Mexico. High habitat suitability areas obtained using the maximum entropy (MaxEnt) modeling approach were used as a proxy for the geographic regions where each species is likely to be distributed, and oil spill scenarios were generated using numerical models incorporating transport, dispersion, and oil degradation. The analysis allowed identifying those species for which there is a significant risk of exposure in each spill scenario. However, our results suggest that the risk does not appear to be high for any species under any scenario. The information generated by our risk assessment is key to developing management plans in those areas of the Gulf of Mexico where deep-water activities of the hydrocarbon industry are currently being developed or planned

Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies

The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state‐of‐the‐art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative "A Healthy Diet for a Healthy Life" (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful "tips and tricks" along the analytical workflow

LongITools: Dynamic longitudinal exposome trajectories in cardiovascular and metabolic noncommunicable diseases

The current epidemics of cardiovascular and metabolic noncommunicable diseases have emerged alongside dramatic modifications in lifestyle and living environments. These correspond to changes in our “modern” postwar societies globally characterized by rural-to-urban migration, modernization of agricultural practices, and transportation, climate change, and aging. Evidence suggests that these changes are related to each other, although the social and biological mechanisms as well as their interactions have yet to be uncovered. LongITools, as one of the 9 projects included in the European Human Exposome Network, will tackle this environmental health equation linking multidimensional environmental exposures to the occurrence of cardiovascular and metabolic noncommunicable diseases