bluuebunny/crossref_metadata_2025_split huggingface dataset:
A NiTi alloy-based cuff for external banding valvuloplasty: a six-week follow-up study in pigs
Authors: Hiebl B , MÜLler C , GÖRs J , Jung* F , Lendlein* A , Jünger M , Hamm B , Niehues S M 
Published: December 2011

Objective The study aimed to test a Nitinol®-based vein cuff model for external banding valvuloplasty. Method In 12 adult minipigs, the vena jugularis externa was covered for 42 days by a cuff with an inner diameter adapted to the outer vein diameter in supine position. By changing from supine into prone position hypostatically vein dilation was induced to simulate varicose vein dilation. Cuff position and the inner diameter of the vein lumen under the cuff were examined by computer tomography scanning. Also, histological analysis of the vein wall within the cuff was performed. Results The preset tubular shape of the cuff and the cuff position did not change in both prone and supine position, but due to fibrosis the luminal vein diameter within the cuff was decreased ( P < 0.01) already after 21 days. Conclusion A foreign body response resulted in a fibrous capsule covering the cuff which might limit cuff functionality.
Destruction Complex Function in the Wnt Signaling Pathway ofDrosophilaRequires Multiple Interactions Between Adenomatous Polyposis Coli 2 and Armadillo
Authors: Kunttas-Tatli Ezgi , Zhou Meng-Ning , Zimmerman Sandra , Molinar Olivia , Zhouzheng Fangyuan , Carter Krista , Kapur Megha , Cheatle Alys , Decal Richard , McCartney Brooke M 
Published: December 2011

AbstractThe tumor suppressor Adenomatous polyposis coli (APC) negatively regulates Wnt signaling through its activity in the destruction complex. APC binds directly to the main effector of the pathway, β-catenin (βcat, Drosophila Armadillo), and helps to target it for degradation. In vitro studies demonstrated that a nonphosphorylated 20-amino-acid repeat (20R) of APC binds to βcat through the N-terminal extended region of a 20R. When phosphorylated, the phospho-region of an APC 20R also binds βcat and the affinity is significantly increased. These distinct APC–βcat interactions suggest different models for the sequential steps of destruction complex activity. However, the in vivo role of 20R phosphorylation and extended region interactions has not been rigorously tested. Here we investigated the functional role of these molecular interactions by making targeted mutations in Drosophila melanogaster APC2 that disrupt phosphorylation and extended region interactions and deletion mutants missing the Armadillo binding repeats. We tested the ability of these mutants to regulate Wnt signaling in APC2 null and in APC2 APC1 double-null embryos. Overall, our in vivo data support the role of phosphorylation and extended region interactions in APC2’s destruction complex function, but suggest that the extended region plays a more significant functional role. Furthermore, we show that the Drosophila 20Rs with homology to the vertebrate APC repeats that have the highest affinity for βcat are functionally dispensable, contrary to biochemical predictions. Finally, for some mutants, destruction complex function was dependent on APC1, suggesting that APC2 and APC1 may act cooperatively in the destruction complex.
The Coalescent with Selection on Copy Number Variants
Authors: Teshima Kosuke M , Innan Hideki 
Published: December 2011

AbstractWe develop a coalescent-based simulation tool to generate patterns of single nucleotide polymorphisms (SNPs) in a wide region encompassing both the original and duplicated genes. Selection on the new duplicated copy and interlocus gene conversion between the two copies are incorporated. This simulation enables us to explore how selection on duplicated copies affects the pattern of SNPs. The fixation of an advantageous duplicated copy causes a strong reduction in polymorphism not only in the duplicated copy but also in its flanking regions, which is a typical signature of a selective sweep by positive selection. After fixation, polymorphism gradually increases by accumulating neutral mutations and eventually reaches the equilibrium value if there is no gene conversion. When gene conversion is active, the number of SNPs in the duplicated copy quickly increases by transferring SNPs from the original copy; therefore, the time when we can recognize the signature of selection is decreased. Because this effect of gene conversion is restricted only to the duplicated region, more power to detect selection is expected if a flanking region to the duplicated copy is used.
Gene Capture byHelitronTransposons Reshuffles the Transcriptome of Maize
Authors: Barbaglia Allison M , Klusman Katarina M , Higgins John , Shaw Janine R , Hannah L Curtis , Lal Shailesh K 
Published: December 2011

AbstractHelitrons are a family of mobile elements that were discovered in 2001 and are now known to exist in the entire eukaryotic kingdom. Helitrons, particularly those of maize, exhibit an intriguing property of capturing gene fragments and placing them into the mobile element. Helitron-captured genes are sometimes transcribed, giving birth to chimeric transcripts that intertwine coding regions of different captured genes. Here, we perused the B73 maize genome for high-quality, putative Helitrons that exhibit plus/minus polymorphisms and contain pieces of more than one captured gene. Selected Helitrons were monitored for expression via in silico EST analysis. Intriguingly, expression validation of selected elements by RT–PCR analysis revealed multiple transcripts not seen in the EST databases. The differing transcripts were generated by alternative selection of splice sites during pre-mRNA processing. Selection of splice sites was not random since different patterns of splicing were observed in the root and shoot tissues. In one case, an exon residing in close proximity but outside of the Helitron was found conjoined with Helitron-derived exons in the mature transcript. Hence, Helitrons have the ability to synthesize new genes not only by placing unrelated exons into common transcripts, but also by transcription readthrough and capture of nearby exons. Thus, Helitrons have a phenomenal ability to “display” new coding regions for possible selection in nature. A highly conservative, minimum estimate of the number of new transcripts expressed by Helitrons is ∼11,000 or ∼25% of the total number of genes in the maize genome.
Stringent Analysis of Gene Function and Protein–Protein Interactions Using Fluorescently Tagged Genes
Authors: Neumüller Ralph A , Wirtz-Peitz Frederik , Lee Stella , Kwon Young , Buckner Michael , Hoskins Roger A , Venken Koen J T , Bellen Hugo J , Mohr Stephanie E , Perrimon Norbert 
Published: December 2011

AbstractIn Drosophila collections of green fluorescent protein (GFP) trap lines have been used to probe the endogenous expression patterns of trapped genes or the subcellular localization of their protein products. Here, we describe a method, based on nonoverlapping, highly specific, shRNA transgenes directed against GFP, that extends the utility of these collections to loss-of-function studies. Furthermore, we used a MiMIC transposon to generate GFP traps in Drosophila cell lines with distinct subcellular localization patterns, which will permit high-throughput screens using fluorescently tagged proteins. Finally, we show that fluorescent traps, paired with recombinant nanobodies and mass spectrometry, allow the study of endogenous protein complexes in Drosophila.
Review Essay
Authors: Clingerman Forrest 
Published: December 2011

Roger S. Gottlieb, A Greener Faith: Religious Environmentalism and Our Planet’s Future (Oxford and New York: Oxford University Press, 2006), 288 pp., $35.00 (hbk), ISBN: 978-0-1951-7648-3.

Roger Gottlieb’s A Greener Faith: Religious Environmentalism and Our Planet’s Future (2006) and The Oxford Handbook of Religion and Ecology (2006) form an interesting pair. A Greener Faith advocates for a spiritual or ‘religious environmentalism’ grounded in Gottlieb’s own pluralistic ecotheological vision. In contrast, The Oxford Handbook is a multiauthored reference collection that, for the most part, surveys the relationship between longstanding religious traditions and the environmental crisis. Taken together, these books introduce the reader to a wide range of religious environmentalism as well as the current academic study of religion and ecology. Both books are meant to inspire religious
environmentalism among audiences, as they oscillate between descriptive and normative genres. Gottlieb is an excellent guide for this task: As one of the most prolific and provocative contributors in the field, he embodies an eclectic, interdisciplinary spirit, writes with passion and charm, and can also be intensely personal—even brash and unapologetic. In places Gottlieb’s writing even reads like a spiritual manual.
Achieving Brazilian Extended Reach Drilling records on Polvo project with Ultra-High Torque Connection
Authors: Biddle Nathan , Osório Luciana , Arevalo Hector , Velho Marcelo , Flores Vincent , Granger Scott , Carrois Fabien 
Published: December 2011

Abstract
The Polvo project is a platform based drilling rig located ~95km off the Brazilian coast in the Campos Basin. The field consists of two distinct reservoirs, a carbonate reservoir to the southwest, and a sandstone reservoir to the east. The Polvo project began drilling in March 2007 and has since drilled a total of 32 wellbores. The wells range in difficulty from "short reach" to "very extended reach" wellbores. The deviation is from 3–7° DLS at angles of 30–92°. Wellbores are 3-dimensionally designed in order to improve total reservoir exposure.
Extended reach, deep and high deviation wells require the use of a drill string that has both higher torsional yield strength drill pipe body and greater torque capacity tool joints than are afforded by standard API connections. VAM Express double shoulder connection has been designed in order to address the drilling challenges linked to the development of such complex wells. This proprietary high torque connection incorporates four major design features allowing pushing further the drilling envelope limits: quick rig make-up, high torque performance, user friendly and durability.
After beginning the project and platform placement, it was discovered that sandstone reservoir targets further to the east had higher productivity than expected. After drilling 12 wells and numerous lessons learned, the furthest extended reach well in the history of Brazil was attempted and successfully completed.
The Pol-O wellbore was drilled to a total measured depth of 6,489 m (2,429 m TVD) and a vertical section step out of 5,615 m. This wellbore was and continues to hold the record for furthest reach wellbore in the history of Brazil.
In addition to obtaining this extended reach record, Polvo also attained the record of fastest 24 hours drilling in and 8 ½" hole with 1,610 m in 24 hours. To obtain this drilling record, it was not only critical to have high on bottom ROP, but also to optimize connection time. The high torque connection helped to achieve this fast connection time and also prevented any drillstring failure.
Having drilled over 100,000 m of total hole in highly deviated wellbores using the same drillstring, there have not been any twist-offs or back-offs on the Polvo project.
By being able drill these further reach wellbores successfully and more economically, the Polvo Platform has proved up further reserves that can be produced without requiring installation of another platform or subsea tiebacks. The rig is not limited by connection strength and plans are in place to improve the top-drive to deliver more torque, while staying with the same double shoulder connection size.
Horizontal Fractures in Single and Multilayer Reservoirs
Authors: Larsen Leif 
Published: December 2011

Abstract
Type curves for circular uniform-flux fractures in unbounded single-layer reservoirs were presented in the literature several decades ago. Unfortunately, these results have restricted validity since the simple uniform-flux inner-boundary condition will cease to be physically meaningful when significant boundary effects from the top and bottom of the formation start to affect the data. This is especially important for large fractures in formations of limited thickness. For horizontal fractures it is therefore important to include finite conductivity as part of the fracture model. Solutions addressing these issues are presented in this paper along with examples highlighting effects of different modeling options. The solutions include both compressible and incompressible flow inside the fractures.
The solutions have also been extended to multi-layer reservoirs through a decoupling approach, with both unbounded and bounded circular models used in examples. Solutions for layered reservoirs are important because layering is common with obvious effects on productivity and because layering can create unusual pressure-transient characteristics during buildups if there are shale streaks or other low-permeability flow barriers between layers acting as partially sealing boundaries.
Horizontal fractures are becoming more important due to an increasing number of shallow-depth disposal wells, for instance as part of carbon capture and storage developments. Shallow gas developments with fracturing needed to obtain sufficient productivity are also adding to the importance of these fracture models. Both for producers and disposal wells, layering will be an issue and has to be addressed.
Shape Memory Polymer as a Sand Management Alternative to Gravel Packing
Authors: Carrejo Nick , Horner Don N. , Johnson Mike H. 
Published: December 2011

Abstract
Shape memory polymer foam is currently being deployed in down-hole sand control applications. The shape memory polymer is molded in a cylindrical geometry with a desired outer diameter and inner diameter. The geometric profile is altered to specifications with an inner drainage layer, to satisfy the run in requirements of the tool. Once set down hole, the shape memory polymer will start deploying to the original outer diameter of the original geometric profile. The polymer will continue to deploy and conform to the bore wall. This shape memory polymer has a permeability that is 25 times greater than that of the formation permeability to prevent plugging risk, and ensure that there is negligible to no impedance to production.
Gravel packing is a form of sand management used for decades during the production of oil and gas. This paper compares the sand control characteristics of shape memory polymer foam against conventional gravel packs under similar conditions, loads, and formation sands. We will show how the performance of the shape memory polymer can eliminate the need of gravel packing altogether within a given bottom hole temperature range.
Effects of CO2 Sequestration on the Petrophysical Properties of an Aquifer Rock
Authors: Ofori Albert , Engler Thomas 
Published: December 2011

Abstract
Carbon dioxide capture and sequestration (CCS) into deep geological formations is widely considered as a preferred option for reducing green house gases (GHG) in the atmosphere. The preferred storage location is the saline aquifers due to their exceptional sequestration capacity compared to depleted oil and gas reservoirs. Since CO2 is a relatively reactive substance, injecting it into an aquifer could initiate various chemical reactions with aquifer rock and cap rock. This underscores the need to plan the sequestration process carefully and to investigate possible consequences in terms of rock-fluid reactions that may affect Petrophysical properties.
The results presented here are based on a compositional reservoir simulation study of a prototypical CO2 sequestration project in a deep saline aquifer. The purpose of this study was to try to determine the effects of CO2 sequestration on the Petrophysical properties of an aquifer rock. CO2 was injected for a 10 year period, followed by 1,000 years of natural gradient flow. The impact of several parameters including temperature, vertical to horizontal permeability ratio, and salinity were also studied and the results are presented here.
Accurate Porosity Measurement in Gas Bearing Formations
Authors: Desport Olivier , Copping Kim , Johnson Barry L 
Published: December 2011

Abstract
Porosity is a key reservoir parameter and high accuracy is needed to properly estimate reserves. But even though there is a long history of porosity measurements and various tools from which to derive it, this can still remain a difficult task. None of the logging tools directly measure porosity but instead respond to density, lithology and fluid. Combining different measurements can help to solve for porosity but also brings the complexity of invasion as all the tools do not have the same radial response. This problem is even more complex when dealing with gas formations as the fluid effect on the measurements is very high.
This paper looks at various methods to improve porosity computations via the integration of Nuclear Magnetic Resonance (NMR) and other porosity measurements in South China Sea gas reservoirs.
Production Data Analysis: Unraveling Rock Properties and Completion Parameters
Authors: Jochen Valerie , Malpani Raj , Moncada Katharine , Altman Raphael , Luo Fang , Xu Jian 
Published: December 2011

Abstract
The measurements available to estimate reservoir parameters are numerous, yet most wells are completed in various shales without traditional log measurements. Horizontal wells continue to be drilled, and while the number of stimulation stages pumped per lateral length continues to increase, many questions remain: Is there an increase in production commensurate to the added cost, or will it soon become unsustainable? Would better characterization of the effective surface area after hydraulic fracture stimulation help explain the reservoir potential?
Analysis of production data from fractured shale gas wells is difficult. Operators try to estimate fracture and reservoir properties for a horizontal well with multiple hydraulic fractures by using pressure transient testing, even though in reality it could take 10,000 years for the actual reservoir pressure to be measured. Alternatively, others model the production of fractured shale gas reservoirs from a zone-altered permeability area, which may be quite limited in areal extent but is surrounded by a low-matrix-permeability reservoir to account for the well productivity. Ultimately a simplistic reservoir model for production forecasting uses whatever data is available and our basin experience.
How do we validate these models? Traditionally we look at case studies to find an analogous situation to validate and identify the dominate production drivers. Existing approaches to model shales require years of production data, and even then they cannot uncouple reservoir properties from completion parameters to help optimize flow efficiency. When production is measured on a stage-by-stage basis, and laboratory and log analysis data are presented for reservoir and fluid characterization, solving for the created effective surface area should be straightforward. By better characterizing along the wellbore and by discriminating the contributions of RQ and CQ to the reservoir production, we will be able to better predict long-term well production and better understand the reservoir potential.
This paper discusses the current status of production prediction for shale gas reservoirs and provides a vision of possibilities for better interpretation, i.e these production models must go hand-in-hand with hydraulic fracture models to determine the crucial parameters that drive production, thus fully optimize well and field production.
Using a New Intelligent Well Technology Completions Strategy to Increase Thermal EOR Recoveries–SAGD Field Trial
Authors: Shaw Joel , Bedry Mark 
Published: December 2011

Abstract
A completions strategy has been developed for improving both steam injection and production conformance in a thermal enhanced oil recovery (EOR) project by using intelligent well technology incorporating interval control valves (ICV), well segmentation, and instrumentation. The initial field trial is ongoing in the injector of a Northern Alberta steam-assisted gravity drainage (SAGD) well pair. The development of the completion technology suitable for thermal conditions, initial field trial results and the plans for further development are described. The application modeling shows that, depending on the level of heterogeneity present in the reservoir, a 45% reduction in the steam-oil ratio and an almost 70% increase in recovery can be achieved in a SAGD process when both improved injection conformance and producer differential steam trap control can be applied in a segmented horizontal well pair. A cost-effective intelligent well completion solution to achieve this segmentation and control has the potential to add substantial value to field developments through improved steam conformance resulting in increased energy efficiency and oil recovery. The method being developed is also applicable to a wide range of other thermal EOR processes such as cyclic steam stimulation (CSS), steam drive, and variations, including, for example, those involving solvent additives. The initial field deployment in the injector well was primarily to prove the technology, to demonstrate the feasibility of modifying the steam distribution and to learn for future developments. A successful installation and commissioning of the intelligent completion has substantially validated the technology. Lessons learned are highlighted. Early injection test results and data show a significant increase in the understanding of the injection and production behavior in the well pair. A test program to optimize the distribution of the steam injection in the well is underway and the results are discussed. The intelligent completion technology under trial, and proposed further developments, should enable more extensive use of downhole measurement and control in thermal EOR projects than has been possible to date.
Utilization of Non-damaging Drilling Fluid Composed of Potassium Formate Brine and Manganese Tetra Oxide to Drill Sandstone Formation in Tight Gas Reservoir
Authors: Bialy M. El , Mohsen M. , Ezell R. G. , Abdulaziz M. Emad , Kompantsev A. , Khakimov A. , Ganizade F. , Ashoor A. 
Published: December 2011

Abstract
An engineered fluid formulation was designed to provide a 114-pcf non-damaging drill-in fluid for the Unayzah A and B sandstone reservoirs. Employment of potassium formate high density brine and manganese tetra oxide weighting agent provided superior drilling properties that delivered reduced formation damage, improved thermal stability, and lower drilling costs.
The use of acid-soluble manganese tetra oxide allowed engineers to increase the density of potassium formate drilling fluids and extend the density window above that offered by calcium carbonate. The reduced particle size (D50= 1 micron) and the spherical shape of the manganese tetra oxide reduced friction and drag. This improved control of equivalent circulating density (ECD) and plastic viscosity (PV) and significantly lowered rheological profiles. These optimal properties were maintained at temperatures exceeding 155°C.
Laboratory testing confirmed high performance features such as:
Excellent hole cleaning characteristics Thin filter cake with low lift-off pressures Low differential sticking potential Low treatment cost during drilling and re-use capability Superior rheological performance compared to high solids content oil-based fluids Improved drilling performance and hydraulic efficiency with the formate base system.
The vertical well in the Unayzah A and B sandstone reservoirs was completed with zero hole problems. The potassium formate/manganese tetra oxide system provided superior performance and stability even with elevated bottomhole temperatures in the tight gas formation. This paper reviews the laboratory design and development as well as the field application of the high performance, brine-based drill-in fluid.