Petroleum generation kinetics: Single versus multiple heating- ramp open-system pyrolysis

A B S T R A C T Some recent publications promote one-run, open-system pyrolysis experiments using a single heating rate (ramp) and fixed frequency factor to determine the petroleum generation kinetics of source-rock samples because, compared to multiple-ramp experiments, the method is faster, less expensive, and presumably yields similar results. Some one-ramp pyrolysis experiments yield kinetic results similar to those from multiple-ramp experiments. However, our data for 52 worldwide source rocks containing types I, II, IIS, II/III, and III kerogen illustrate that one-ramp kinetics introduce the potential for significant error that can be avoided by using high-quality kinetic measurements and multiple-ramp experiments in which the frequency factor is optimized by the kinetic software rather than fixed at some universal value. The data show that kinetic modeling based on a discrete activation energy distribution and three different pyrolysis temperature ramps closely approximates that determined from additional runs, provided the three ramps span an appropriate range of heating rates. For some source rocks containing well-preserved kerogen and having narrow activation energy distributions, both single-and multiple-ramp discrete models are insufficient, and nucleation-growth models are necessary. Instrument design, thermocouple size or orientation, and sample weight likely influence the acceptable upper limit of pyrolysis heating rate. Caution is needed for ramps of 30-50°C/min, which can cause temperature errors due to impaired heat transfer between the oven, sample, and thermocouple. Compound volatility may inhibit pyrolyzate yield at the lowest heating rates, depending on the effectiveness of the gas sweep. We recommend at least three pyrolysis ramps that span at least a 20-fold variation of comparatively lower rates, such as 1, 5, and 25°C/min. The product of heating rate an

Photoinduced Ullmann C–N Coupling: Demonstrating the Viability of a Radical Pathway

Carbon–nitrogen (C–N) bond-forming reactions of amines with aryl halides to generate arylamines (anilines), mediated by a stoichiometric copper reagent at elevated temperature (>180°C), were first described by Ullmann in 1903. In the intervening century, this and related C–N bond-forming processes have emerged as powerful tools for organic synthesis. Here, we report that Ullmann C–N coupling can be photoinduced by using a stoichiometric or a catalytic amount of copper, which enables the reaction to proceed under unusually mild conditions (room temperature or even –40°C). An array of data are consistent with a single-electron transfer mechanism, representing the most substantial experimental support to date for the viability of this pathway for Ullmann C–N couplings

The future of North American trade policy: lessons from NAFTA

This repository item contains a single issue of the Pardee Center Task Force Reports, a publication series that began publishing in 2009 by the Boston University Frederick S. Pardee Center for the Study of the Longer-Range Future.This Task Force Report written by an international group of trade policy experts calls for significant reforms to address adverse economic, environmental, labor and societal impacts created by the 1994 North American Free Trade Agreement (NAFTA). The report is intended to contribute to the discussion and decisions stemming from ongoing reviews of proposed reforms to NAFTA as well as to help shape future trade agreements. It offers detailed proposals on topics including services, manufacturing, agriculture, investment, intellectual property, labor, environment, and migration. Fifteen years after NAFTA was enacted, there is widespread agreement that the trade treaty among the United States, Canada and Mexico has fallen short of its stated goals. While proponents credit the agreement with stimulating the flow of goods, services, and investment among the North American countries, critics in all three countries argue that this has not brought improvements in the standards of living of most people. Rather than triggering a convergence across the three nations, NAFTA has accentuated the economic and regulatory asymmetries that had existed among the three countries. [TRUNCATED

Long term temperature observations on the lunar surface at Apollo sites 15 and 17

An analysis of the long term temperature histories of the heat flow experiment thermometers is presented.Contract NAS 9-6037by Kenneth Peters, Marcus G. Langseth.Measurements -- Results of thermocouple measurement above the lunar surface -- Factors affecting long- term temperature variations of the lunar surface -- Thermocouple temperatures -- Discuss ion of measurements -- Reference thermometer temperatures -- Conclusion

MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues.

MOTIVATION: Analysing the joint association between a large set of responses and predictors is a fundamental statistical task in integrative genomics, exemplified by numerous expression Quantitative Trait Loci (eQTL) studies. Of particular interest are the so-called ': hotspots ': , important genetic variants that regulate the expression of many genes. Recently, attention has focussed on whether eQTLs are common to several tissues, cell-types or, more generally, conditions or whether they are specific to a particular condition. RESULTS: We have implemented MT-HESS, a Bayesian hierarchical model that analyses the association between a large set of predictors, e.g. SNPs, and many responses, e.g. gene expression, in multiple tissues, cells or conditions. Our Bayesian sparse regression algorithm goes beyond ': one-at-a-time ': association tests between SNPs and responses and uses a fully multivariate model search across all linear combinations of SNPs, coupled with a model of the correlation between condition/tissue-specific responses. In addition, we use a hierarchical structure to leverage shared information across different genes, thus improving the detection of hotspots. We show the increase of power resulting from our new approach in an extensive simulation study. Our analysis of two case studies highlights new hotspots that would remain undetected by standard approaches and shows how greater prediction power can be achieved when several tissues are jointly considered. AVAILABILITY AND IMPLEMENTATION: C[Formula: see text] source code and documentation including compilation instructions are available under GNU licence at http://www.mrc-bsu.cam.ac.uk/software/

Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network.

BACKGROUND: Tumour necrosis factor (TNF) superfamily cytokines and their receptors regulate diverse immune system functions through a common set of signalling pathways. Genetic variants in and expression of individual TNF superfamily cytokines, receptors and signalling proteins have been associated with autoimmune and inflammatory diseases, but their interconnected biology has been largely unexplored. METHODS: We took a hypothesis-driven approach using available genome-wide datasets to identify genetic variants regulating gene expression in the TNF superfamily cytokine signalling network and the association of these variants with autoimmune and autoinflammatory disease. Using paired gene expression and genetic data, we identified genetic variants associated with gene expression, expression quantitative trait loci (eQTLs), in four peripheral blood cell subsets. We then examined whether eQTLs were dependent on gene expression level or the presence of active enhancer chromatin marks. Using these eQTLs as genetic markers of the TNF superfamily signalling network, we performed targeted gene set association analysis in eight autoimmune and autoinflammatory disease genome-wide association studies. RESULTS: Comparison of TNF superfamily network gene expression and regulatory variants across four leucocyte subsets revealed patterns that differed between cell types. eQTLs for genes in this network were not dependent on absolute gene expression levels and were not enriched for chromatin marks of active enhancers. By examining autoimmune disease risk variants among our eQTLs, we found that risk alleles can be associated with either increased or decreased expression of co-stimulatory TNF superfamily cytokines, receptors or downstream signalling molecules. Gene set disease association analysis revealed that eQTLs for genes in the TNF superfamily pathway were associated with six of the eight autoimmune and autoinflammatory diseases examined, demonstrating associations beyond single genome-wide significant hits. CONCLUSIONS: This systematic analysis of the influence of regulatory genetic variants in the TNF superfamily network reveals widespread and diverse roles for these cytokines in susceptibility to a number of immune-mediated diseases.The Intramural Research Program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and the National Library of Medicine of the US National Institutes of Health (Intramural Research Program) , Wellcome Trust (080327/Z/06/Z, 087007/Z/08/Z, 094227/Z/10/Z, Clinical PhD Programme, 079895, 076113 and 085475) , Medical Research Council (G0400929) , National Institute for Health Research , National Institutes of Health (Oxford-Cambridge Scholars Program) , Istanbul University Research Fund and UK Behcet’s Syndrome Society.This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13073-016-0329-

Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease

Genome-wide association studies (GWAS) have transformed our understanding of the genetics of complex traits such as autoimmune diseases, but how risk variants contribute to pathogenesis remains largely unknown. Identifying genetic variants that affect gene expression (expression quantitative trait loci, or eQTLs) is crucial to addressing this. eQTLs vary between tissues and following in vitro cellular activation, but have not been examined in the context of human inflammatory diseases. We performed eQTL mapping in five primary immune cell types from patients with active inflammatory bowel disease (n = 91), anti-neutrophil cytoplasmic antibody-associated vasculitis (n = 46) and healthy controls (n = 43), revealing eQTLs present only in the context of active inflammatory disease. Moreover, we show that following treatment a proportion of these eQTLs disappear. Through joint analysis of expression data from multiple cell types, we reveal that previous estimates of eQTL immune cell-type specificity are likely to have been exaggerated. Finally, by analysing gene expression data from multiple cell types, we find eQTLs not previously identified by database mining at 34 inflammatory bowel disease-associated loci. In summary, this parallel eQTL analysis in multiple leucocyte subsets from patients with active disease provides new insights into the genetic basis of immune-mediated diseases.This research was funded by a Wellcome Trust Clinical PhD Programme Fellowship (JEP), the NIH-Oxford-Cambridge Scholars Program (ACR), Wellcome Trust Grant 083650/Z/07/Z and MRC Grant MR/L19027/1 (KGCS), and the National Institute for Health Research Cambridge Biomedical Research Centre. KGCS is a National Institute for Health Research Senior Investigator. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Reduced monocyte and macrophage TNFSF15/TL1A expression is associated with susceptibility to inflammatory bowel disease.

Chronic inflammation in inflammatory bowel disease (IBD) results from a breakdown of intestinal immune homeostasis and compromise of the intestinal barrier. Genome-wide association studies have identified over 200 genetic loci associated with risk for IBD, but the functional mechanisms of most of these genetic variants remain unknown. Polymorphisms at the TNFSF15 locus, which encodes the TNF superfamily cytokine commonly known as TL1A, are associated with susceptibility to IBD in multiple ethnic groups. In a wide variety of murine models of inflammation including models of IBD, TNFSF15 promotes immunopathology by signaling through its receptor DR3. Such evidence has led to the hypothesis that expression of this lymphocyte costimulatory cytokine increases risk for IBD. In contrast, here we show that the IBD-risk haplotype at TNFSF15 is associated with decreased expression of the gene by peripheral blood monocytes in both healthy volunteers and IBD patients. This association persists under various stimulation conditions at both the RNA and protein levels and is maintained after macrophage differentiation. Utilizing a "recall-by-genotype" bioresource for allele-specific expression measurements in a functional fine-mapping assay, we localize the polymorphism controlling TNFSF15 expression to the regulatory region upstream of the gene. Through a T cell costimulation assay, we demonstrate that genetically regulated TNFSF15 has functional relevance. These findings indicate that genetically enhanced expression of TNFSF15 in specific cell types may confer protection against the development of IBD