bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutations affecting interaction of integrase with TNPO3 do not prevent HIV-1 cDNA nuclear import
Authors: Cribier Alexandra , Ségéral Emmanuel , Delelis Olivier , Parissi Vincent , Simon Aurélie , Ruff Marc , Benarous Richard , Emiliani Stéphane 
Published: December 2011

AbstractBackgroundIntegration of human immunodeficiency virus type 1 (HIV-1) into a host cell chromosome is an essential step under the control of the viral integrase (IN). Although this enzyme is necessary and sufficient to catalyze the integration reactionin vitro, cellular cofactors are involved in the processin vivo. The chromatin-associated factor LEDGF/p75 interacts with IN and promotes integration to transcription units of the host genome. HIV-1 IN also binds the karyopherin TNPO3, however the significance of this interaction during viral replication remains to be explored.ResultsHere we present a functional analysis of IN mutants impaired for LEDGF/p75 and TNPO3 interaction. Among them, IN W131A and IN Q168L, that were previously identified to be deficient for LEDGF/p75 interaction, were also partially impaired for TNPO3 binding. We observed that mutations abolishing IN ability to form tetramers resulted in a severe reduction in LEDGF/p75 binding. In sharp contrast, no correlation could be found between the ability of IN to multimerize and TNPO3 interaction. Most of the mutant viruses were essentially impaired for the integration step whereas the amount of 2-LTR circles, reflecting the nuclear import of the viral DNA, was not significantly affected.ConclusionOur functional analysis of HIV-1 IN mutants reveals distinct structural basis for TNPO3 interaction and suggests that the interaction between IN and TNPO3 is not a major determinant of nuclear import but could take place at a nuclear step prior to integration.
The interaction between the PARP10 protein and the NS1 protein of H5N1 AIV and its effect on virus replication
Authors: Yu Mengbin , Zhang Chuanfu , Yang Yutao , Yang Zhixin , Zhao Lixia , Xu Long , Wang Rong , Zhou Xiaowei , Huang Peitang 
Published: December 2011

Abstract

Background
During the process that AIV infect hosts, the NS1 protein can act on hosts, change corresponding signal pathways, promote the translation of virus proteins and result in virus replication.

Results
In our study, we found that PARP domain and Glu-rich region of PARP10 interacted with NS1, and the presence of NS1 could induce PARP10 migrate from cytoplasm to nucleus. NS1 high expression could reduce the endogenous PARP10 expression. Cell cycle analysis showed that with inhibited PARP10 expression, NS1 could induce cell arrest in G2-M stage, and the percentage of cells in G2-M stage rise from the previous 10%-45%, consistent with the cell proliferation result. Plague forming unit measurement showed that inhibited PARP10 expression could help virus replication.

Conclusions
In a word, our results showed that NS1 acts on host cells and PARP10 plays a regulating role in virus replication.
Multi-Country analysis of palm oil consumption and cardiovascular disease mortality for countries at different stages of economic development: 1980-1997
Authors: Chen Brian K , Seligman Benjamin , Farquhar John W , Goldhaber-Fiebert Jeremy D 
Published: December 2011

Abstract

Background
Cardiovascular diseases represent an increasing share of the global disease burden. There is concern that increased consumption of palm oil could exacerbate mortality from ischemic heart disease (IHD) and stroke, particularly in developing countries where it represents a major nutritional source of saturated fat.

Methods
The study analyzed country-level data from 1980-1997 derived from the World Health Organization's Mortality Database, U.S. Department of Agriculture international estimates, and the World Bank (234 annual observations; 23 countries). Outcomes included mortality from IHD and stroke for adults aged 50 and older. Predictors included per-capita consumption of palm oil and cigarettes and per-capita Gross Domestic Product as well as time trends and an interaction between palm oil consumption and country economic development level. Analyses examined changes in country-level outcomes over time employing linear panel regressions with country-level fixed effects, population weighting, and robust standard errors clustered by country. Sensitivity analyses included further adjustment for other major dietary sources of saturated fat.

Results
In developing countries, for every additional kilogram of palm oil consumed per-capita annually, IHD mortality rates increased by 68 deaths per 100,000 (95% CI [21-115]), whereas, in similar settings, stroke mortality rates increased by 19 deaths per 100,000 (95% CI [-12-49]) but were not significant. For historically high-income countries, changes in IHD and stroke mortality rates from palm oil consumption were smaller (IHD: 17 deaths per 100,000 (95% CI [5.3-29]); stroke: 5.1 deaths per 100,000 (95% CI [-1.2-11.0])). Inclusion of other major saturated fat sources including beef, pork, chicken, coconut oil, milk cheese, and butter did not substantially change the differentially higher relationship between palm oil and IHD mortality in developing countries.

Conclusions
Increased palm oil consumption is related to higher IHD mortality rates in developing countries. Palm oil consumption represents a saturated fat source relevant for policies aimed at reducing cardiovascular disease burdens.
Spinal radiosurgery - efficacy and safety after prior conventional radiotherapy
Authors: Nikolajek Katharina , Kufeld Markus , Muacevic Alexander , Wowra Berndt , Niyazi Maximilian , Ganswindt Ute 
Published: December 2011

Abstract

Background
Conventional external beam radiotherapy is a standard procedure for treatment of spinal metastases. In case of progression spinal cord tolerance limits further radiotherapy in pre-irradiated areas. Spinal stereotactic radiotherapy is a non-invasive option to re-treat pre-irradiated patients. Nevertheless, spinal radiosurgery results in relevant dose deposition within the myelon with potential toxicity. Aim of the study was to retrospectively analyse the efficacy and feasibility for salvage radiosurgery of spinal metastases.

Methods
During a period of 4 years (2005-2009) 70 lesions in 54 patients were treated in 60 radiosurgery sessions and retrospectively analysed. Clinical (pain, sensory and motor deficit) and radiological (CT/MRI) follow-up data were collected prospectively after radiosurgery. Pain - as main symptom - was classified by the Visual Analogue Scale (VAS) score. Every patient received single session radiosurgery after having been treated first-line with conventionally fractionated radiotherapy. Kaplan-Meier method and life tables were used to analyse freedom from local failure and overall survival.

Results
At a median follow-up of 14.5 months the actuarial rates of freedom from local failure at 6/12/18 months were 93%, 88% and 85%, respectively. The median radiosurgery dose was 1 × 18 Gy (range 10-28 Gy) to the median 70% isodose. The VAS score of patients with pain (median 6) dropped significantly (median 4, p = 0.002). In 6 out of 7 patients worse sensory or motor deficit after SRS was caused by local or distant failures (diagnosed by CT/MRI). One patient with metastatic renal cell carcinoma developed a progressive complete paraparesis one year after the last treatment at lumbar level L3. Due to multiple surgery and radiosurgery treatments at the lumbar region and further local progression, the exact reason remained unclear. Apart from that, no CTC grade III or higher toxicity has been observed.

Conclusions
By applying spinal radiosurgery relevant radiation doses can be limited to small parts of the myelon. This prevents myelopathic side effects and makes it an effective and safe treatment option for well-suited patients. Especially for previously irradiated patients with local failure or pain salvage SRS represents a valuable treatment option with high local control rates, low toxicity and significant pain reduction.
Using the Electronic Medical Record to Better Define “No Products of Conception” as a Critical Value in Anatomic Pathology
Authors: Renshaw Andrew 
Published: December 2011

Abstract
At present, the College of American Pathologists checklist requires documentation of communication of critical values in anatomic pathology to caregivers. Recently, our institution has begun using the electronic medical record to document the lack of imminent danger or emergency associated with the case rather than calling the caregiver. I sought to document this trend.
The results of all critical values and all endometrial curettings with a diagnosis of “no products of conception seen” for the last 3 years at 1 hospital were reviewed. During the first 18 months, 0 of 11 critical cases were documented by reference to the electronic medical record. During the second 18 months 5 of 14 cases (36%; P = .02) were documented to have an intrauterine pregnancy by ultrasound and the physician was not notified. In our laboratory, cases without products of conception and a documented intrauterine pregnancy are no longer considered critical values in anatomic pathology.
Documentation of the lack of imminent danger to the patient through reference to the electronic medical record is an increasingly common and acceptable means of ensuring patient safety and more accurately defining critical values in anatomic pathology.
Quantifying the Results of Horizontal Multistage Development in Tight Oil Reservoirs of the Western Canadian Sedimentary Basin: Technical and Economic Case Studies From a Reservoir Evaluator’s Perspective
Authors: Hamm Brian , Struyk Eric 
Published: December 2011

Abstract
Recent advances in horizontal drilling and multistage completion technologies have unlocked vast quantities of previously inaccessible oil reserves. Since 2006, thousands of horizontal multistage wells have been drilled into numerous low permeability oil reservoirs in the Western Canadian Sedimentary Basin including the Bakken, Cardium, Viking and Shaunavon formations. Early horizontal multistage wells had relatively short horizontal sections with two to four completion stages per well and have evolved over time to include wells in certain areas that have up to two mile horizontal sections and over 25 individual completion stages. Along with the technical advancements that have occurred recently, operators are actively seeking new reservoirs in which to apply them.
This paper presents a brief historical look back at a few of the major areas that have been developed to date. Specifically, the light oil developments of the Bakken formation in Saskatchewan, Manitoba and North Dakota, the Cardium formation in Alberta, the Viking formation in Alberta and Saskatchewan and the Lower Shaunavon formation in Saskatchewan are studied in detail and comparisons drawn. Type curves are presented by vintage for each play showing the progression of advancing technology countered by operator desire to push the development into reservoir of diminishing quality. Specific technical metrics regarding initial production rates and decline rates are compared and contrasted. Average expected ultimate recoveries are estimated based on decline analysis and the authors experience completing detailed reserve evaluations for operators in their respective development areas. Based on the statistical study of performance to date and the estimates of ultimate recovery a type well based on current development is generated for each of the areas.
Economic modeling based on the generated type wells and a comparison of the various development areas is presented using a number of financial and industry metrics. Despite vast differences in productivity and recovery per well between the plays, the economic analysis reveals that bigger is not necessarily better.
A Study Examining Coupled Geomechanics and Reservoir Fluid Flow Modelling
Authors: Gu Edward Wei , Sammon Peter , Da Costa Alvaro Maia , Cabral Leonardo , de Souza Luis Carlos , Pao William 
Published: December 2011

Abstract
A comparative study was carried out examining some coupled geomechanics and reservoir fluid flow simulations. The study attempted to answer the questions: "Why do we need coupled geomechanics and reservoir fluid flow analyses" and "How do we do the coupled work"? It is common in reservoir engineering to expect that volumetric deformation in the reservoir may change rock properties such as porosity and permeability, and hence change reservoir flows. However, the effects of shear or deviatory deformation, and stress re-distribution in the reservoir, on the fluid flow have been often neglected. These latter effects will be examined in this paper.
This paper clarifies the notion that shear or non-uniform deformation and stress re-distribution in the reservoir may have significant effects on reservoir fluid flows. Thus, a "fully" coupled or "two-way" coupled analysis is a "must have" approach in a reservoir study where the shear deformation or changes in total stresses in the reservoir can not be ignored. Shear deformation or changes in total stresses, and the resulting stress re-distribution in the reservoir, can be caused by non-uniform reservoir flows; boundary, corner and arching constraints; material nonlinearity; sliding along interfaces or faults; irregular reservoir geometry; among other causes leading to non-uniform deformations.
There are only a few cases in which a reservoir flow analysis can be conducted independently, i.e., without coupled geomechanical calculations, such as when the reservoir flow is occurring under uniaxial deformation or isotropic deformation conditions. The compressibility of the rock phase in these uncoupled reservoir flow simulations has to be selected with caution according to the deformation pattern that will occur in the reservoir. In the cases where no simple deformation pattern can be defined, a "fully" or "two-way" coupled geomechanical analysis has to be conducted along with the reservoir flow analysis. Otherwise, significant errors may occur in prediction of reservoir performance, not only for reservoir deformation, but also for reservoir fluid flows.
Design of Solvent-Assisted SAGD Processes in Heterogeneous Reservoirs Using Hybrid Optimization Techniques
Authors: Al-Gosayir Muhammad , Leung Juliana , Babadagli Tayfun 
Published: December 2011

Abstract
Many Steam Assisted Gravity Drainage (SAGD) optimization studies published in the literature combined numerical simulation with graphical or analytical techniques for design and performance evaluation. There have been numerous efforts that integrated the simulation exercise with global optimization algorithms. Some studies focused on optimization of cumulative steam-to-oil ratio (cSOR) in SAGD by altering steam injection rates, while others focused on optimization of cumulative net energy-to-oil ratio (cEOR) in solvent-additive SAGD by altering injection pressures and fraction of solvent in the injection stream. Several studies also considered total project net present value calculation by changing total project area, capital cost intensities, solvent prices, and risk factors to determine the well spacing and drilling schedule. Optimization techniques commonly used in those studies were scattered search, simulated annealing, and genetic algorithm (GA). However, the applications of hybrid genetic algorithm were rarely found.
In this paper, we focused on optimization of solvent-assisted SAGD using various GA implementations. In our models, hexane was selected to be co-injected with steam. The objective function, defined based on cumulative steam-oil ratio (cSOR) and recovery factor, was optimized by changing injection pressures, production pressures, and injected solvent-to-steam ratio. Techniques including orthogonal arrays (OA) for experimental design (e.g. Taguchi’s arrays) and proxy models for objective function evaluations were incorporated with the GA method to improve computational and convergence efficiency. Results from these hybrid approaches revealed that an optimized solution could be achieved with less CPU time (e.g. fewer number of iterations) compared to the conventional GA method. Sensitivity analysis was also conducted on the choice of proxy model to study the robustness of the proposed methods.
To investigate the effects of heterogeneity in the design process, optimization of solvent-assisted SAGD was performed on various synthetic heterogeneous reservoir models of porosity, permeability, and shale distributions. Our results highlight the potential application of the proposed techniques in other solvent-enhanced heavy oil recovery processes.
Sample Size Effects on the Application of Mercury Injection Capillary Pressure for Determining the Storage Capacity of Tight Gas and Oil Shales
Authors: Comisky J. T. , Santiago M. , McCollom B. , Buddhala A. , Newsham K. E. 
Published: December 2011

Abstract
We measured Mercury Injection Capillary Pressure (MICP) profiles on tight shale samples with a variety of sample sizes. The goal was to optimize the rock preparation and data reduction workflow for determining the storage properties of the rock, particularly porosity, from MICP measurements. The rock material was taken from a whole core in the Cretaceous Eagle Ford Formation in the form of a puck or disc. A horizontal 1 inch core plug was cut from this disc and the remaining material was subsequently crushed and sieved through various mesh sizes. MICP profiles up to 60,000 psia were then measured on the 1 inch plug and all of the various crushed and sieved rock particle sizes. In parallel we subsampled the plug material to measure bulk volume, grain volume, and porosity using a crushed rock helium pycnometry method. These additional measurements provided a comparison set of standard petrophysical properties from which we could compare the MICP results.
In general our MICP profiles show a very strong dependence on sample size due to two reasons: pore accessibility and conformance. We verify the conformance correction approach of Bailey (2009) which specifically accounts for the pore volume compression of the sample before mercury has been injected into the largest set of interconnected pore throats. This new method is preferred over the traditional method of conformance correction when compared to crushed rock helium porosity since the latter is performed at unstressed conditions. Our results using Bailey’s (2009) method reveals that the -20+35 sample size is optimal for determining porosity in the Eagle Ford, and potentially other tight oil and gas shales.
We use mercury injection for determining the various storage properties of tight shale because helium porosimetry is not always possible on fine cuttings samples. There are many instances when limited cuttings may be the only source of rock information available before a whole core is taken. Cuttings profiles also provide a key insight over long formation intervals that may not be available from whole core. Cuttings and core profiles for use in calibrating well logs have proven to be a requirement in these ultra-low perm systems.
Early Results from a Carbonate Steamflood Pilot in 1st Eocene Reservoir, Wafra Field, PZ
Authors: Brown Joel , Deemer Art , Al-Dhafeeri Fahad , Lekia Solomon , Hoadley Steve , Al-Mutairi Ghanim , Al-Yami Falah , Barge David 
Published: December 2011

Abstract
A large scale steamflood pilot test has been underway since 2008 in the first Eocene reservoir in the Wafra Field in the Partitioned Zone (PZ) between Saudi Arabia and Kuwait. The first Eocene is a carbonate reservoir and it is the shallowest reservoir in the Wafra Field with an average depth of 1,000 feet The primary objective of the pilot is to reduce technical and economic risk/uncertainty to determine whether full field steamflood development is feasible.
The pilot consists of sixteen 2.5 acre inverted 5 spot patterns with associated steamflood and production facilities. The injection interval is the 1st Eocene "C" interval at a depth of 1300 ft. This is the first multi-pattern steamflood of a carbonate reservoir in the Middle East.
This presentation will share the early results from the implementation of the pilot project. The production response to carbonate steamflooding will be shown along with examples of individual well production behavior. Early insights into carbonate steamflood response, variability of production response by pattern and the identification of operating issues associated with carbonate steamflooding will be shared.
The success of the pilot test project has huge implications to not only the PZ, but to the entire Middle East region due to the vast amount of oil contained in reservoirs that would be considered targets for the steamflood process.
Conclusions and lessons learned that can be drawn from carbonate steamflooding results to date in the pilot will also be shared in the presentation
Nuclear Spectrometry Logs on High-Viscosity Oil Fields
Authors: Chernoletskiy K. V. , Kartamyshev S. V. , Zhuravlev T. B. , Ursegov S. O. 
Published: December 2011

Abstract
The paper is devoted to the problem and results of applying up-to-date nuclear spectrometry logs including C/O log for high-viscosity oil pool studies. Information about applied measurement technologies, tools, new comprehensive interpretation techniques has been given. Practical examples of the effectiveness of the nuclear logs in formation water salinity evaluation and localization of water flooded zones in oil recovery by thermal methods have been shown. Techniques for reliable forecasting of the characteristics of the inflows obtained in reservoir tests have been developed.
Design Approach and Early Field Performance for a Solvent-Assisted SAGD Pilot at Cold Lake, Canada
Authors: Dickson Jasper L. , Scott Clingman , Dittaro Larry M. , Jaafar Ali E. , Yerian Jeffrey A , Perlau Darrel L. 
Published: December 2011

Abstract
ExxonMobil and its affiliate Imperial Oil Resources are currently operating a Solvent-Assisted Steam-Assisted Gravity Drainage (SA-SAGD) experimental pilot plant at Cold Lake, Canada. During pilot operation, up to 20 percent by volume of a light hydrocarbon solvent will be injected with dry steam in a dual horizontal well SAGD configuration. The pilot scope consists of two horizontal well pairs (four wells total), six observation wells, associated steam and solvent injection facilities, artificial lift, and dedicated production measurement and testing facilities.
Previous experimental and computer modeling work completed by the Alberta Research Council (ARC) (Nasr, 2003), Imperial Oil Resources, and ExxonMobil indicates that the addition of solvent to the dry steam increases bitumen production rates and decreases the steam oil ratio (SOR) relative to conventional SAGD processes. A key objective of this pilot is to safely collect high-quality field data to support these findings and quantify process improvement.
This paper will focus on the pilot design approach taken to ensure that the multi-year pilot is successful as well as highlight early pilot performance and operation. Specific design aspects which will be discussed include the choice for the pilot location, the use of detailed geologic models to design and place the horizontal wells, and solvent measurements. Early field results are consistent with expectations. However, longer term operation is required to make a more quantitative assessment. In addition, the pilot operation has demonstrated excellent control of injection pressure, which is critical to the application of this technology in settings with bottom water or top gas.