73 research outputs found
ASSIST: A fast versatile local structural comparison tool
No full textMotivation: Structural genomics initiatives are increasingly leading to the determination of the 3D structure of target proteins whose catalytic function is not known. The aim of this work was that of developing a novel versatile tool for searching structural similarity, which allows to predict the catalytic function, if any, of these proteins.Results: The algorithm implemented by the tool is based on local structural comparison to find the largest subset of similar residues between an input protein and known functional sites. The method uses a geometric hashing approach where information related to residue pairs from the input structures is stored in a hash table and then is quickly retrieved during the comparison step. Tests on proteins belonging to different functional classes, done using the Catalytic Site Atlas entries as targets, indicate that the algorithm is able to identify the correct functional class of the input protein in the vast majority of the cases. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved
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Carbonate factory response and recovery after Ocean Anoxic Event 1a, Pearsall Formation, Central Texas
No full textOcean Anoxic Events (OAEs) are major carbon cycle perturbations that occurred several times in the Mesozoic. OAEs are commonly found to have been caused by a combination of climatic warming and increased surface weathering delivering surface nutrients to the oceans. This feedback loop leads to the expansion of the oxygen minimum zone of the waterbody and increased influx of terrigenous material. The resultant dysoxic to euxinic conditions are thought to have played a prominent role in the suppression of the benthic carbonate factory and deposition of organic-rich mudstones. The establishment of these oceanographic conditions are postulated to have imparted a lasting effect on the deposition of stressed-carbonate facies during the recovery phase of OAEs. Major questions regarding OAE events remain, including the degree of variability in the impact that OAEs have on carbonate factories and the drivers for this variability, on both global and regional scales. This study builds upon previous work and further investigates the regional Early Cretaceous (Aptian) OAE-1a signal that is recorded in the Pearsall Formation in Central Texas, with a particular focus on the record of carbonate factory recovery observed in transects from the San Marcos Arch to the Pearsall Arch. Shoreline-proximal data include outcrops and 8 cores with 1530 ft of coverage. Distal cores include 7 subsurface exploration wells (total 1745 ft core) from the San Marcos Arch to the Pearsall Arch, a strike-parallel distance of 210 km. Physical characterization of stratigraphic data was paired with the multivariate statistical analysis of 10 pXRF datasets, involving Principal Component Analysis (PCA) segmentation, which led to the establishment of five end member chemofacies. These chemofacies allow for high-resolution identification of mineralogic variability across OAE-1a, including the documentation of pulses of terrigenous input as well as cycles of dysoxic to euxinic oceanographic conditions at a sub-lithofacies scale. When paired with the development and application of a deep learning neural network trained by a type-pXRF training dataset, this study outlines a new methodology that allows for the direct comparison of pXRF data across core control through a unified chemofacies schema. The oceanographic conditions identified with this workflow are then used to delineate oceanographic variability and pulses of terrigenous enrichment in association with the recovery from OAE-1a. The characterization of these geochemical processes is particularly relevant in the mudrock component of depositional systems, where biologic productivity, bottom-water redox conditions, and any subsequent diagenesis are critical determinants for the ultimate preservation of TOC in organic-rich shales. TOC rich shale intervals then create potential for an economical petroleum source rock and successive charge of either conventional or unconventional reservoirs. The incidence of OAE-1a is found to be a fundamental driver of facies evolution and faunal composition in the three composite sequences studied: the James (Aptian) composite sequence, the Bexar (Aptian-Albian) composite sequence, and the Glen Rose composite sequence (Albian) (cf. Phelps et al., 2014). OAE-1 is coincident with the drowning of the antecedent Sligo reef margin and deposition of the Pine Island Shale. This drowning event was a result of environmental stressors posed by the OAE and the resultant suppression of sedimentation rates on the platform as the carbonate factory was substantially weakened. Partial recovery of the carbonate factory from OAE-1a is expressed in the deposition of the Cow Creek Member before punctuation of deposition due to the subaerial exposure event at the top-James composite sequence boundary. A second phase of recovery is documented in the Bexar and Glen Rose composite sequences, including reef systems in the platform interior that are coeval with transgression and deposition of the Hensel Formation, as well as the progradation of Lower Glen Rose carbonates and the aggradation of microbial-coral-rudist bioherms in highstand depositional sequences of the Glen Rose Formation. Recovery of the carbonate factory was fundamentally different between the San Marcos Arch and Pearsall Arch areas. Earliest recovery fauna in the Cow Creek Member is comprised of monospecific echinoid-mollusk packstones-grainstones in shoreline proximal settings and oyster-oncoid rudstones distally. Combined observations from pXRF data and the heightened prevalence of pyrite in oncoid cortices on the San Marcos Arch compared to the Pearsall area is interpreted to represent a higher degree of dysoxic and/or euxinic conditions on the San Marcos Arch. During later stages of recovery, the Cow Creek in the Pearsall Arch area is shown to have maintained healthier carbonate deposition in comparison to the San Marcos Arch, including the sustained deposition of reefal assemblages, such as the sequence of stromatoporoid boundstone present in the Tenneco Sirianni well. This combined core-outcrop framework demonstrates the superimposed regional variability inherent even in global carbon cycle perturbations such as OAE-1a, driven by the degree of shelf restriction, oceanographic circulation patterns, basin geometry, and the degree of terrigenous influx. The documented differences in oceanographic conditions and carbonate factory recovery on the regional scale of OAE-1a will aid in better understanding the multi-scaled geochemical and environmental evolution associated with these events, and ultimately pushes towards the development of predictive concepts for future studies.Earth and Planetary Science
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The behavior of dissolved organic carbon (DOC) at geological sequestration sites
No full texttextGeologic carbon sequestration has been proposed as a means of mitigating anthropogenic greenhouse gas emissions. At depth, supercritical CO₂ may rise above the surrounding fluid. Detecting leaks from CO₂ storage reservoirs is important to evaluate the effectiveness of carbon sequestration and address public concern for negative environmental impacts. Other attempts have been made to detect leaks, such as changes in pH, pressure and direct observation of CO₂ in the AZMI (Above Zone Monitoring Interval). Each has limitations and here we investigate dissolved organic carbon (DOC) as a potential indicator for fugitive CO₂. This study uses a series of batch experiments to evaluate the interaction between dissolved CO₂ and DOC. The batches consist of homogenized and sieved 250 micron to 425 micron matrix samples of varying mass and type, 2mL of DI water and a headspace of pure carbon dioxide or air. The three different rock samples analyzed are Buffalo River Sediment, illite and Barnett Shale. A pure CO₂ headspace results in lower amount of DOC in solution than an air headspace. All matrix samples demonstrated this effect. The proposed mechanism to describe the observed results is that a lowered pH shifts speciation of weak organic acids and protonated humic substances causing decreased solubility and increasing the adsorption of these compounds. These results suggest that a decrease in DOC concentrations could be used to detect CO₂ leakage and that CO₂ leakage would not deteriorate water quality by releasing DOC.Earth and Planetary Science
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Experimental analysis and modeling of perfluorocarbon transport in the vadose zone : implications for monitoring CO₂ leakage at CCS sites
No full texttextPerfluorocarbon tracers (PFTs) are commonly proposed tracers for use in carbon capture and sequestration (CCS) leak detection and vadose zone monitoring programs. Tracers are co-injected with supercritical CO₂ and monitored in the vadose zone to identify leakage and calculate leakage rates. These calculations assume PFTs exhibit “ideal” tracer behavior (i.e. do not sorb onto or react with porous media, partition into liquid phases or undergo decay). This assumption has been brought into question by lab and field evaluations showing PFT partitioning into soil contaminants and sorbing onto clay. The objective of this study is to identify substrates in which PFTs behave conservatively and quantify non-conservative behavior. PFT breakthrough curves are compared to those of a second, conservative tracer, sulfur hexafluoride (SF₆). Breakthrough curves are generated in 1D flow-through columns packed with 5 different substrates: silica beads, quartz sand, illite, organic-rich soil, and organic-poor soil. Constant flow rate of carrier gas, N₂, is maintained. A known mass of tracer is injected at the head of the columns and the effluent analyzed at regular intervals for tracers at picogram levels by gas chromatography. PFT is expected to behave conservatively with respect to SF₆ in silica beads or quartz sand and non-conservatively in columns with clay or organics. However, results demonstrate PFT retardation with respect to SF₆ in all media (retardation factor is 1.1 in silica beads and quartz sand, 2.5 in organic-rich soil, >20 in organic-poor soil, and >100 in illite). Retardation is most likely due to sorption onto clays and soil organic matter or condensation to the liquid phase. Sorption onto clays appears to be the most significant factor. Experimental data are consistent with an analytical advection/diffusion model. These results show that PFT retardation in the vadose zone has not been adequately considered for interpretation of PFT data for CCS monitoring. These results are preliminary and do not take into account more realistic vadose zone conditions such as the presence of water, in which PFTs are insoluble. Increased moisture content will likely decrease sorption onto porous media and retardation in the vadose zone may be less than determined in these experiments.Earth and Planetary Science
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Under-pressure in the Bravo Dome natural CO₂ field and its implications for geological CO₂ storage (GCS)
No full textGeological carbon storage (GCS) has the potential to reduce anthropogenic CO₂ emissions, if large volumes can be injected. Storage capacity is limited by regional pressure build-up in the subsurface. However, natural CO₂ reservoirs are commonly under-pressured, suggesting that natural processes counteract the pressure build-up and increase storage security. To identifythese processes, I studied Bravo Dome natural CO₂ reservoir, where the gas pressure are significantly below hydrostatic pressure. Here, I showed that the dissolution of CO₂ into the brine contributes to observed under-pressure conditions because Bravo Dome appears to be isolated from the ambient hydrologic system. This study indicated that the pressure drop in the gas due to CO₂ dissolution slows down convective dissolution dramatically. I present 2D numerical simulations and reproduce the observed reservoir pressures and noble gas compositions. Based on this study, CO₂ at Bravo Dome must at least persist for 300 ka to produce the observed noble gas composition and reservoir pressures. Lastly, I showed that compartmental gas pressure observed at Bravo Dome are controlled by capillary forces.Earth and Planetary Science
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Geological characterization and reservoir analysis of the Eagle Ford Group in DeWitt County, Texas
No full textThe Eagle Ford Group is a significant reservoir for unconventional oil and gas, presenting drilling and production challenges in proximity to the San Marcos Arch and into East Texas. To fully understand the transition from the deep-water carbonate strata in South Texas to the argillaceous and siliciclastic strata of the Woodbine in East Texas, a detailed investigation is required. By conducting a geological characterization of the Devon No. 1 Medina core in northeast DeWitt County, valuable insights into these drilling and production issues have been gained. This study evaluates the complex interplay of sedimentary and diagenetic processes in fine-grained, unconventional reservoir systems, focusing on the Upper Cretaceous Eagle Ford Group. The aim of this investigation is to define chemolithofacies and their influence on reservoir quality by utilizing an integrated approach combining core description, geochemical analyses, and advanced data analytics. The integration of lithofacies with chemofacies into chemolithofacies provides a comprehensive framework that combines physical rock characteristics with their geochemical signatures, thereby enhancing the understanding of sediment input, depositional environment, and diagenetic alterations in the Eagle Ford Group. Results indicate significant variability in carbonate- and clay-mineral content across the Eagle Ford Group, with evidence of redox-sensitive elements that suggest fluctuations in bottom-water oxygenation. The study also highlights the role of diagenesis in altering reservoir properties, specifically impacting brittleness, porosity, permeability, and total organic content (TOC) content. Units such as the Maness Shale and the Clay Wedge, which are characterized by high mineral-clay content, represent potential drilling hazards and emphasize the importance of accurate identification during exploration. The stratigraphic and chemolithofacies model developed in this study contributes to a better understanding of reservoir heterogeneity, assisting in identifying economically significant reservoir facies with favorable brittleness, porosity, permeability, and TOC content for hydrocarbon exploration and development. The detailed stratigraphic framework developed in this study, which identifies five distinct stratigraphic sections within the Eagle Ford Group based on lithologic, geochemical, and depositional characteristics, provides insights into the vertical and lateral variability of the formation and aids in the optimization of exploration and production strategies for unconventional reservoirs in the region.Earth and Planetary Science
Anthropometry and Scan: A Computational Exploration on Measuring and Imaging
No full textNew developments in the field of technology have led to the use of scanners in order to obtain anthropometric measurements. As a matter of fact, anthropometry finds its roots in the seventeenth century, currently its usage has been strengthened by the employment of scanners. 3D whole-body scanners allow to collect reliable data and to visualise the exact human body shape. Thus, this paper aims at exploring the combination of these topics, anthropometry and scan, through an innovative tool, the scientometrics analysis. This technique provides a clear overview of the existing literature in the field investigated. In our study we examined 1’652 papers from the Web of Science Core Collection database. Network analyses have shown an interesting scenario, emphasising the research evolution over time. Specifically, endocrinology and metabolism emerged as the most active publication domains. Accordingly, the two most high-impact journals and the most cited paper regard nutrition issues and metabolic risk factors respectively. However, the predominance of the USA for number of publications has not been confirmed by the institution’s analysis, which has shown the University of Copenhagen as the most influential one. On the other hand, Yumei Zhang currently appears as the main authority in the field and Leslie G. Farkas as the most influential author over the entire time span analysed. The relevant implications of the findings are discussed in terms of future research lines
Commentarii historici duo hactenus inediti, alter de regibus vetustis Norvagicis; alter de profectione Danorum in Terram sanctam circa annum 1185 suscepta, eodem tempore ab inserto autore conscriptus /
No full text"Per errorem typographi, absente editore, factum est, ut praefatio toti operi praemittenda parti posteriori fuerit addita. Quod hic monendum putavimus."--P. [3] (1st group)Author statement for the 1st work in contents from p. [5] (1st group)Includes indexes.Signatures: *⁸(*1+1) A-L⁸.Europeana-GoogleBook
Sprouts of Green/Germogli Verdi
No full textI have written permission by the author for translation and publication of the original poems, which are presently unpublished
A letter to T----- P----, Esq; from the author of Siris: Containing some farther remarks on the virtues of tar-water, and the methods for preparing and using of it. To which is added, an answer to a supposed physician's letter to the ... bishop of Cloyne, occasioned by his Lordship's treatise on the virtues of tar-water.
No full text[4],28p. ; 8⁰.Author of Siris = George Berkeley.T----- P---- = Thomas Prior.- With a half-title.In this issue, the Latin quote 'Non sibi, sed toti' is above the section that begins: 'To which is added, an answer..'. - 'Remarks on a letter to .. the bishop of Cloyne' (pp.17-28), attributed to Thomas Prior, has a divisional titlepage.Reproduction of original from the British Library.English Short Title Catalog, ESTCT92782.Electronic data. Farmington Hills, Mich. : Thomson Gale, 2003. Page image (PNG). Digitized image of the microfilm version produced in Woodbridge, CT by Research Publications, 1982-2002 (later known as Primary Source Microfilm, an imprint of the Gale Group)
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