Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

MotivationMultiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia.ResultsWe performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified.Availability and implementationDatasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/.Supplementary informationSupplementary data are available at Bioinformatics online

Operations of and Future Plans for the Pierre Auger Observatory

Technical reports on operations and features of the Pierre Auger Observatory, including ongoing and planned enhancements and the status of the future northern hemisphere portion of the Observatory. Contributions to the 31st International Cosmic Ray Conference, Lodz, Poland, July 2009.Comment: Contributions to the 31st ICRC, Lodz, Poland, July 200

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy

Motivation Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia. Results We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified. Availability and implementation Datasets and scripts for reproduction of results are available through: Https://nalab.stanford.edu/multiomics-pregnancy/

Oxidative stress and immunologic responses following a dietary exposure to PAHs in Mya arenaria

<p>Abstract</p> <p>Background</p> <p>The aim of this research was to investigate oxidative stress and immune responses following a dietary polycyclic aromatic hydrocarbon (PAH) exposure in a marine bioindicator organism, the soft shell clam, <it>Mya arenaria</it>. Immune parameters in hemolymph (haemocyte number, efficiency of phagocytosis and haemocyte activity) and assessment of oxidative stress using catalase (CAT) activity and levels of malondialdehyde (MDA) performed on the digestive gland were estimated as biomarkers in clams fed in mesocosm with PAH contaminated phytoplankton. MDA levels and CAT activities were also measured <it>in situ </it>in organisms sampled in a control site (Metis Beach, Québec, Canada) as well as organisms sampled in a site receiving domestic effluents (Pointe-au-Père, Québec, Canada), to assess effects of abiotic variables related to seasonal variations and mixed contamination on the selected parameters.</p> <p>Results</p> <p>Results on immune parameters suggest that the PAHs may interfere with the maturation and/or differentiation processes of haemocytes. MDA results showed that lipid peroxidation did not occur following the exposure. The levels of CAT activity corresponded to weak antioxidant activity (no significant differences). Recovery was noted for all the immune endpoints at the end of the experiment.</p> <p>Conclusion</p> <p>Results suggest that immune parameters are early biomarkers that can efficiently detect a physiological change during a short term exposure to low concentrations of PAHs. The <it>in situ </it>survey (in the natural environment) suggested that clams from the Pointe-au-Père site did not show any oxidative stress as well as the clams contaminated in mesocosm, probably due to the low concentrations of PAHs used for this study. MDA levels increased however in organisms from Metis Beach, a response probably related to domestic effluents or parasitism.</p

Summary Report on CO{sub 2} Geologic Sequestration &amp; Water Resources Workshop

The United States Environmental Protection Agency (EPA) and Lawrence Berkeley National Laboratory (LBNL) jointly hosted a workshop on “CO{sub 2} Geologic Sequestration and Water Resources” in Berkeley, June 1–2, 2011. The focus of the workshop was to evaluate R&D needs related to geological storage of CO{sub 2} and potential impacts on water resources. The objectives were to assess the current status of R&amp;D, to identify key knowledge gaps, and to define specific research areas with relevance to EPA’s mission. About 70 experts from EPA, the DOE National Laboratories, industry, and academia came to Berkeley for two days of intensive discussions. Participants were split into four breakout session groups organized around the following themes: Water Quality and Impact Assessment/Risk Prediction; Modeling and Mapping of Area of Potential Impact; Monitoring and Mitigation; Wells as Leakage Pathways. In each breakout group, participants identified and addressed several key science issues. All groups developed lists of specific research needs; some groups prioritized them, others developed short-term vs. long-term recommendations for research directions. Several crosscutting issues came up. Most participants agreed that the risk of CO{sub 2} leakage from sequestration sites that are properly selected and monitored is expected to be low. However, it also became clear that more work needs to be done to be able to predict and detect potential environmental impacts of CO{sub 2} storage in cases where the storage formation may not provide for perfect containment and leakage of CO{sub 2}–brine might occur

Superhydrophilic Functionalization of Microfiltration Ceramic Membranes Enables Separation of Hydrocarbons from Frac and Produced Water

The environmental impact of shale oil and gas production by hydraulic fracturing (fracking) is of increasing concern. The biggest potential source of environmental contamination is flowback and produced water, which is highly contaminated with hydrocarbons, bacteria and particulates, meaning that traditional membranes are readily fouled. We show the chemical functionalisation of alumina ceramic microfiltration membranes (0.22 μm pore size) with cysteic acid creates a superhydrophilic surface, allowing for separation of hydrocarbons from frac and produced waters without fouling. The single pass rejection coefficients was >90% for all samples. The separation of hydrocarbons from water when the former have hydrodynamic diameters smaller than the pore size of the membrane is due to the zwitter ionically charged superhydrophilic pore surface. Membrane fouling is essentially eliminated, while a specific flux is obtained at a lower pressure (<2 bar) than that required achieving the same flux for the untreated membrane (4–8 bar)

Perspectives of Portuguese People with Physical Disabilities Regarding Their Sexual Health: A Focus Group Study

The World Health Organization has considered sexual health as a major dimension of global health and a sexual right. However, the sexual health of people with physical disabilities is still poorly addressed by health and social care professionals, and it is very stigmatized by society. This study aimed to assess the perspectives of Portuguese people living with physical disabilities regarding issues affecting their sexual health. Nine women and 17 men with different physical disabilities participated in the study. Participants were recruited from a professional rehabilitation facility located in the North of Portugal and were assigned to four groups in one-hour sessions. Three main categories emerged from the content analysis: (1) meanings and beliefs regarding sexuality; (2) experiences of sexuality; (3) necessary changes. Despite the positive social changes towards sexuality, participants expressed that their sexual rights are still unfulfilled, as they live in a context that perpetuates their dependency. They pointed out low self-esteem, prejudice and social isolation, poor architectural accessibility and scarcity of financial support as some of the barriers to their lives and their sexual health. Finally, participants identified the main needs regarding their sexual health, such as: access to specialized information; training for health professionals. This study gives voice to people with physical disabilities and sheds light into both individual and contextual factors affecting their sexual health. Of utmost importance, this study draws attention to the need for reinforcing sexuality of people with disabilities in the social agenda and brings implications for future research and practice.This study was supported by a Grant attributed to the first author by the Portuguese Foundation for Science and Technology (SFRH/BD/112168/2015)info:eu-repo/semantics/publishedVersio

Risk factors of one year increment of coronary calcifications and survival in hemodialysis patients

<p>Abstract</p> <p>Background</p> <p>Heart and coronary calcifications in hemodialysis patients are of very common occurrence and linked to cardiovascular events and mortality. Several studies have been published with similar results. Most of them were mainly cross-sectional and some of the prospective protocols were aimed to evaluate the results of the control of altered biochemical parameters of mineral disturbances with special regard to serum calcium, phosphate and CaxP with the use of calcium containing and calcium free phosphate chelating agents. The aim of the present study was to evaluate in hemodialysis patients classic and some non classic risk factors as predictors of calcification changes after one year and to evaluate the impact of progression on survival.</p> <p>Methods</p> <p>81 patients on hemodialysis were studied, with a wide age range and HD vintage. Several classic parameters and some less classic risk factors were studied like fetuin-A, CRP, 25-OHD and leptin. Calcifications, as Agatston scores, were evaluated with Multislice CT basally and after 12-18 months.</p> <p>Results</p> <p>Coronary artery calcifications were observed in 71 of 81 patients. Non parametric correlations between Agatston scores and Age, HD Age, PTH and CRP were significant. Delta increments of Agatston scores correlated also with serum calcium, CaxP, Fetuin-A, triglycerides and serum albumin. Logistic regression analysis showed Age, PTH and serum calcium as important predictors of Delta Agatston scores. LN transformation of the not normally distributed variables restricted the significant correlations to Age, BMI and CRP. Considering the Delta Agatston scores as dependent, significant predictors were Age, PTH and HDL. A strong association was found between basal calcification scores and Delta increment at one year. By logistic analysis, the one year increments in Agatston scores were found to be predictors of mortality. Diabetic and hypertensive patients have significantly higher Delta scores.</p> <p>Conclusions</p> <p>Progression of calcification is of common occurrence, with special regard to elevated basal scores, and is predictive of survival. Higher predictive value of survival is linked to the one year increment of calcification scores. Some classic and non classic risk factors play an important role in progression. Some of them could be controlled with appropriate management with possible improvement of mortality.</p