Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)
Drilling into and around salt bodies can present different kinds of geohazards, such as shrinkage or stuck and crushed casings, resulting in well abandonment and huge economic losses. These engineering disasters are more likely to happen when ignoring the stress perturbations caused by the geomechanical interactions between the salt and surrounding sediments. For a better understanding of the stress perturbations, we use a commercial finite-element software, Abaqus, to build a 2D plane-strain finite-element model of the salt structure of Kuqa depression (...) in the Tarim Basin and simulate the stress perturbations around the salt body in the environment of tectonic compression. By analyzing the patterns of stress perturbations due to different salt geometries such as concave and convex salt, we have come to the conclusion that the convex salt causes compressional stresses on the horizontal and out-of-plane directions but the extensional stress on the vertical direction. On the contrary, the concave salt induces extensional stresses on the horizontal and out-of-plane directions but compressional stress on the vertical direction. The results of stress perturbations near a salt structure in the environment of compressional tectonic stress are opposite to those in the environment of extensional tectonic stress, such as the Mad Dog, in the deepwater northern Gulf of Mexico. The shear stress near the salt structure is bigger than those far away from the salt structure, but is much smaller when compared with horizontal, vertical, and out-of-plane stresses in the profile, in the salt body, horizontal stress drops and converges to vertical stress and von Mises stress equals to zero due to isotropic stresses. The results provide scientific insights on stress perturbations and wellbore drilling design near salt structures in the Tarim Basin. (shrink)
Hydrate formation poses a risk to deepwater drilling operations. Most current studies on the hydrate formation and its impact on deepwater drilling operations have focused on the risk associated with hydrates inside the wellbore. Few researchers have studied the risk of hydrate formation outside the wellbore, and the risks to deepwater drilling are still unclear. In the South China Sea, there have been several events of hydrate growth on the outer surfaces of the subsea wellhead. The mechanisms of hydrate growth (...) on the outer surface of the subsea wellhead are analyzed, and the gas source is predicted by analyzing the logging data of the adjacent wells. A model for the wellhead stability is developed, and the impacts of hydrate formation on the stability of the subsea wellhead are analyzed. The gas source, temperature, pressure, solid surface roughness, and relative static subsea environment are found to be the key factors in the formation of hydrate in the marine environment. The risk of hydrate formation to wellhead stability is subtle, but to blowout preventer could be significant. Hydrates may cause BOP control failure in which the BOP could not be closed in the event of emergency; hydrate formation between the BOP and the wellhead may cause BOP not to be separated from the bottom of the wellhead. A tool was designed for controlling the formation of hydrates, with particular tilt angle and surface roughness. Because the appropriate tilt angle can divert the gas bubbles to avoid the hydrate formations at the wellhead. The designed hydrate control tool successfully mitigates the risks to drilling operations. (shrink)
The Fuling gas field, the largest commercial discovery of shale gas in China, has been producing from the organic-rich shale in the Upper Ordovician Wufeng Formation and Lower Silurian Longmaxi Formation in the Sichuan Basin, China. A refined shale gas E&P and sweet spots identification require studies to be carried out not only at the sedimentary facies scale but also at the petrographic scale. This paper focuses on the characteristics of organic-rich shales. Based on data from outcrops, drilling cores, X-ray (...) diffraction, thin sections, and scanning electric microscope, a systematic analysis of wells and well-correlation sections indicates that shales in the study area underwent two progressive and regressive cycles. In addition, differences in lithofacies and their organic or inorganic components are significant either in the vertical or in the horizontal direction, which generally controls the material basis of shale gas. The early-stage siliceous shale distributes in the east, whereas the late-stage carbonate-bearing shale extends to the west. In the southeastern Sichuan Basin, the siliceous composition decreases, whereas the clay minerals increase upward. In the central Sichuan uplift, there is a higher carbonate content. And with our new lithofacies maps, distribution of the sweet spots was identified. The northeastern Sichuan Basin has the siliceous shale in the Wufeng Formation and the silicon-bearing shale in the Longmaxi Formation, making it a play area with the greatest gas potential. The southern Sichuan Basin occurs as a favorable lithofacies area with the stacked siliceous shale in the Wufeng Formation and the calcareous shale in the Longmaxi Formation. The relatively favorable lithofacies area covers the regions extending from the periphery of southern Sichuan Basin toward the central Sichuan uplift and the northern Guizhou uplift, featuring stacked carbonate-bearing shale and clay mineral-bearing shale in the Longmaxi Formation. The shallow-marine areas close to the uplifts are dominated by mudstone and silty mudstone, thereby possessing poor material basis. (shrink)
Within the same pathogen-stress framework as proposed by Fincher & Thornhill (F&T), we argue further that pathogen stress promotes matrilocal rather than patrilocal family ties which, in turn, slow down the process of modernity; and that pathogen stress promotes social learning or copying, including the adoption of foreign religions.
Based on their framework, Müller & Schumann (M&S) propose a staged drug policy that matches well the neoliberal governance scheme. To mend the sad loss of the sociocultural dimension in their model, I propose three such considerations: first, sociocultural interactions with the brain; second, sociocultural context and justice of drug use; and third, sociocultural preparedness for implementing their drug policy.
Deliberative democracy is one of the best designs that could facilitate good public policy decision making and bring about epistemic good based on Mercier and Sperber's (M&S's) theory of reasoning. However, three conditions are necessary: (1) an ethic of individual epistemic humility, (2) a pragmatic deflationist definition of truth, and (3) a microscopic framing power analysis during group reasoning.