bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic and Environmental Conditions Determine Nuclear Genomic Instability in Budding Yeast Lacking Mitochondrial DNA
Authors: Dirick Léon , Bendris Walid , Loubiere Vincent , Gostan Thierry , Gueydon Elisabeth , Schwob Etienne 
Published: January 2014

AbstractMitochondrial dysfunctions are an internal cause of nuclear genome instability. Because mitochondria are key regulators of cellular metabolism, we have investigated a potential link between external growth conditions and nuclear chromosome instability in cells with mitochondrial defects. Using Saccharomyces cerevisiae, we found that cells lacking mitochondrial DNA (rho0 cells) have a unique feature, with nuclear chromosome instability that occurs in nondividing cells and strongly fluctuates depending on the cellular environment. Calorie restriction, lower growth temperatures, growth at alkaline pH, antioxidants (NAC, Tiron), or presence of nearby wild-type cells all efficiently stabilize nuclear genomes of rho0 cells, whereas high glucose and ethanol boost instability. In contrast, other respiratory mutants that still possess mitochondrial DNA (RHO+) keep fairly constant instability rates under the same growth conditions, like wild-type or other RHO+ controls. Our data identify mitochondrial defects as an important driver of nuclear genome instability influenced by environmental factors.
A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments
Authors: Bank Claudia , Hietpas Ryan T , Wong Alex , Bolon Daniel N , Jensen Jeffrey D 
Published: January 2014

Abstract
The role of adaptation in the evolutionary process has been contentious for decades. At the heart of the century-old debate between neutralists and selectionists lies the distribution of fitness effects (DFE)—that is, the selective effect of all mutations. Attempts to describe the DFE have been varied, occupying theoreticians and experimentalists alike. New high-throughput techniques stand to make important contributions to empirical efforts to characterize the DFE, but the usefulness of such approaches depends on the availability of robust statistical methods for their interpretation. We here present and discuss a Bayesian MCMC approach to estimate fitness from deep sequencing data and use it to assess the DFE for the same 560 point mutations in a coding region of Hsp90 in Saccharomyces cerevisiae across six different environmental conditions. Using these estimates, we compare the differences in the DFEs resulting from mutations covering one-, two-, and three-nucleotide steps from the wild type—showing that multiple-step mutations harbor more potential for adaptation in challenging environments, but also tend to be more deleterious in the standard environment. All observations are discussed in the light of expectations arising from Fisher’s geometric model.
The Impact of Accelerating Faster than Exponential Population Growth on Genetic Variation
Authors: Reppell Mark , Boehnke Michael , Zöllner Sebastian 
Published: January 2014

AbstractCurrent human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models’ effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times.
A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number
Authors: Beissinger Timothy M , Hirsch Candice N , Vaillancourt Brieanne , Deshpande Shweta , Barry Kerrie , Buell C Robin , Kaeppler Shawn M , Gianola Daniel , de Leon Natalia 
Published: January 2014

AbstractA genome-wide scan to detect evidence of selection was conducted in the Golden Glow maize long-term selection population. The population had been subjected to selection for increased number of ears per plant for 30 generations, with an empirically estimated effective population size ranging from 384 to 667 individuals and an increase of more than threefold in the number of ears per plant. Allele frequencies at &gt;1.2 million single-nucleotide polymorphism loci were estimated from pooled whole-genome resequencing data, and FST values across sliding windows were employed to assess divergence between the population preselection and the population postselection. Twenty-eight highly divergent regions were identified, with half of these regions providing gene-level resolution on potentially selected variants. Approximately 93% of the divergent regions do not demonstrate a significant decrease in heterozygosity, which suggests that they are not approaching fixation. Also, most regions display a pattern consistent with a soft-sweep model as opposed to a hard-sweep model, suggesting that selection mostly operated on standing genetic variation. For at least 25% of the regions, results suggest that selection operated on variants located outside of currently annotated coding regions. These results provide insights into the underlying genetic effects of long-term artificial selection and identification of putative genetic elements underlying number of ears per plant in maize.
Morphometric Variation Affecting Sexual Size Dimorphism in Neopedies brunneri (Orthoptera: Acrididae)
Authors: Romero María Luciana , Rosetti Natalia , Remis María Isabel 
Published: January 2014

Abstract
Neopedies brunneri (Giglio-Tos, 1894) is a grasshopper belonging to the family Acrididae. This group of insects usually has economic importance in Argentina because of their ability to experience outbreaks, but little is known about them. Insect populations usually differ at the phenotypic level, often according to geographical and environmental variables, which may be a good indicator of some other factors with adaptive significance (such as developmental rate, seasonal resource disposal, and growing seasonal length). The aim of this article is to report the first preliminary analysis of phenotypic variation in natural populations of N. brunneri from central Argentina to study the amount of intra- and interpopulation variation in morphometric traits and their probable association with geographic and climatic variables.Wefound the existence of morphometrical differences among populations and a pattern of geographical variation, with males and females from eastern populations being larger than the ones from the west. Sexual size dimorphism was also detected and found to be correlated to geographical and climactic variation. Moreover, geographic patterns of sexual size dimorphism were determined, helping to clarify differential susceptibility of both sexes to environmental conditions.
Novel Method for Characterizing Single-Phase Polymer Flooding
Authors: Li Kewen , Sun Wenjie , Li Fen , Qu Yantao , Yang Yaozhong 
Published: January 2014

Summary
Polymer flooding has been used to enhance oil production and reduce water cut for a long time. However, there are still many fundamental challenges in characterizing the multiphase-fluid flow, even the single-phase-fluid flow, associated with polymer flooding. For example, it is difficult to measure and calculate two-phase polymer solution/oil relative permeability. One of the difficulties comes from the non-Newtonian and time-dependent properties of polymer solutions; another comes from the change in absolute permeability caused by the adsorption of polymer on rock surfaces. Almost all the methods for computing relative permeability are based on the assumption that the absolute permeability is constant. It may be helpful to further understand the mechanisms and develop more-reliable methods for calculating two-phase polymer solution/oil relative permeability by investigating single-phase polymer flooding more profoundly. In this study, a new method has been developed to calculate the pseudopermeability during single-phase polymer flooding. The non-Newtonian property of the polymer solutions was considered in the new method. Polymer-flooding experiments with different concentrations of polymers were designed and conducted to study the single-phase flow of polymer solution in rocks with different permeabilities. The values of the pseudopermeability of single-phase polymer flooding were then calculated with the method. It has been found that the relationships between the pseudopermeability and the reciprocal of shear rate were linear. The polymer-flooding pseudopermeability extrapolated at the infinite shear rate was close to the brine-flooding permeability after polymer injections in many cases.
Switchable Nonionic to Cationic Ethoxylated Amine Surfactants for CO2 Enhanced Oil Recovery in High-Temperature, High-Salinity Carbonate Reservoirs
Authors: Chen Yunshen , Elhag Amro S. , Poon Benjamin M. , Cui Leyu , Ma Kun , Liao Sonia Y. , Reddy Prathima P. , Worthen Andrew J. , Hirasaki George J. , Nguyen Quoc P. , Biswal Sibani L. , Johnston Keith P. 
Published: January 2014

Summary
To improve sweep efficiency for carbon dioxide (CO2) enhanced oil recovery (EOR) up to 120°C in the presence of high-salinity brine (182 g/L NaCl), novel CO2/water (C/W) foams have been formed with surfactants composed of ethoxylated amine headgroups with cocoalkyl tails. These surfactants are switchable from the nonionic (unprotonated amine) state in dry CO2 to cationic (protonated amine) in the presence of an aqueous phase with a pH less than 6. The high hydrophilicity in the protonated cationic state was evident in the high cloudpoint temperature up to 120°C. The high cloud point facilitated the stabilization of lamellae between bubbles in CO2/water foams. In the nonionic form, the surfactant was soluble in CO2 at 120°C and 3,300 psia at a concentration of 0.2% (w/w). C/W foams were produced by injecting the surfactant into either the CO2 phase or the brine phase, which indicated good contact between phases for transport of surfactant to the interface. Solubility of the surfactant in CO2 and a favorable C/W partition coefficient are beneficial for transport of surfactant with CO2-flow pathways in the reservoir to minimize viscous fingering and gravity override. The ethoxylated cocoamine with two ethylene oxide (EO) groups was shown to stabilize C/W foams in a 30-darcy sandpack with NaCl concentrations up to 182 g/L at 120°C and 3,400 psia, and foam qualities from 50 to 95%. The foam produces an apparent viscosity of 6.2 cp in the sandpack and 6.3 cp in a 762-μm-inner-diameter capillary tube (downstream of the sandpack) in contrast with values well below 1 cp without surfactant present. Moreover, the cationic headgroup reduces the adsorption of ethoxylated alkyl amines on calcite, which is also positively charged in the presence of CO2 dissolved in brine. The surfactant partition coefficients (0 to 0.04) favored the water phase over the oil phase, which is beneficial for minimizing losses of surfactant to the oil phase for efficient surfactant usage. Furthermore, the surfactant was used to form C/W foams, without forming stable/viscous oil/water (O/W) emulsions. This selectivity is desirable for mobility control whereby CO2 will have low mobility in regions in which oil is not present and high contact with oil at the displacement front. In summary, the switchable ethoxylated alkyl amine surfactants provide both high cloudpoints in brine and high interfacial activities of ionic surfactants in water for foam generation, as well as significant solubilities in CO2 in the nonionic dry state for surfactant injection.
Rapid Updating of Stochastic Models by Use of an Ensemble-Filter Approach
Authors: Tavakoli Reza , Srinivasan Sanjay , Wheeler Mary F. 
Published: January 2014

Summary
Applying an ensemble Kalman filter (EnKF) is an effective method for reservoir history matching. The underlying principle is that an initial ensemble of stochastic models can be progressively updated to reflect measured values as they become available. The EnKF performance is only optimal, however, if the prior-state vector is linearly related to the predicted data and if the joint distribution of the prior-state vector is multivariate Gaussian. Therefore, it is challenging to implement the filtering scheme for non-Gaussian random fields, such as channelized reservoirs, in which the continuity of permeability extremes is well-preserved. In this paper, we develop a methodology by combining model classification with multidimensional scaling (MDS) and the EnKF to create rapidly updating models of a channelized reservoir. A dissimilarity matrix is computed by use of the dynamic responses of ensemble members. This dissimilarity matrix is transformed into a lower-dimensional space by use of MDS. Responses mapped in the lower-dimension space are clustered, and on the basis of the distances between the models in a cluster and the actual observed response, the closest models to the observed response are retrieved. Model updates within the closest cluster are performed with EnKF equations. The results of an update are used to resample new models for the next step. Two-dimensional, waterflooding examples of channelized reservoirs are provided to demonstrate the applicability of the proposed method. The obtained results demonstrate that the proposed algorithm is viable both for sequentially updating reservoir models and for preserving channel features after the data-assimilation process.
Tie-Simplex-Based Phase-Behavior Modeling in an IMPEC Reservoir Simulator
Authors: Rezaveisi M.. , Sepehrnoori K.. , Johns R.T.. T. 
Published: January 2014

Summary
Recently, tie-simplex-based phase-behavior modeling in reservoir simulators has been applied and investigated as a potential method for improving the computational speed of equation-of-state (EOS) -based reservoir simulators. We implemented compositional-space adaptive tabulation (CSAT), the most promising tie-simplex-based method, in UTCOMP, the University of Texas' in-house IMPEC compositional reservoir simulator, to investigate its computational efficiency compared with the phase-behavior algorithm in UTCOMP. The results show that applying CSAT only to skip stability analysis does improve computational time, but only when a significant portion of the gridblocks are in the single-phase region and no other technique for avoiding stability analysis is used. However, in most cases, there is little or no computational advantage to use of CSAT when the simple option in UTCOMP is used where stability analysis is skipped for blocks surrounded by single-phase regions. We explore in detail the performance of CSAT, which depends significantly on the specific gas flood modeled, and the number of tie-lines generated during adaptive tabulation. The results shed light on applicability of CSAT in the IMPEC-type compositional reservoir simulators and show that the advantages of CSAT in this type of simulator are not as great as are reported in the literature for fully implicit or adaptive implicit formulations.
Effect of Elemental-Sulfur Deposition on the Rock Petrophysical Properties in Sour-Gas Reservoirs
Authors: Mahmoud M.A.. A. 
Published: January 2014

Summary
The deposition of elemental sulfur as a solid phase results in plugging the pore space available for gas flow and reduces the reservoir productivity. Elemental sulfur also can be deposited as a liquid phase if the reservoir temperature is greater than 115°C. The liquid sulfur restricts the inflow of gas because of the big density difference between liquid sulfur and gas, which could be 20 times or more. For isothermal conditions in the reservoir, the reduction in reservoir pressure to lower than a critical value causes the elemental sulfur to deposit in the formation, and in turn the gas-well productivity is affected. Accurate prediction of sulfur deposition will help better manage sour-gas reservoirs with potential sulfur-deposition problems.
In this paper, a new analytical model was developed to predict the effect of sulfur deposition on the damage of the near-wellbore region. The damage was quantified through the investigation of the effect of sulfur deposition on rock porosity, relative permeability of the gas phase, and the change in rock wettability. The main objective of this model is to investigate the effect of radial distance on formation damage. Different rock- and fluid-property correlations were used in the model. Previous studies did not consider the change in gas properties with pressure, and numerically modeled the sulfur deposition as a condensate in a gas/condensate reservoir. This paper will consider sulfur adsorption, and the actual physical properties of the sulfur will be used in the developed model. The optimum gas-flow velocity that will maximize the sulfur solubility in the gas will be determined. A coreflood experiment was performed to determine the effect of sulfur deposition on the carbonate-rock permeability, porosity, and wettability. The experiment was used to determine the effect of sulfur adsorption on the rock petrophysical properties. The contact angle was measured for a carbonate core saturated with sulfur by use of a pendant-drop tensiometer.
Analytical and numerical solutions showed that the deposition of sulfur was affected by the radial distance from the wellbore and sulfur-solubility changes as a function of the pressure drop. Sulfur deposition was found to have a great effect on the rock wettability, and in turn the gas production will be affected. The model can be used to predict the critical flow velocity that the gas can flow without precipitating sulfur. The optimum gas-flow velocity was estimated to be a range that maximizes the sulfur solubility in the gas. It was confirmed experimentally that the sulfur deposition reduced the carbonate-core porosity and permeability, and changed the contact angle (rock wettability). The contact angle increased, which means sulfur adsorption on the rock surfaces changed the rock toward more-gas-wet rock.
Integration and Assurance of Well Documents and Data—Essential Preparation for Tomorrow
Authors: Sawaryn S.J.. J. , Pirie L.. , Green I.. , Scott A.. , Cosgrove B.. , Emslie I.. 
Published: January 2014

Summary
During the last 4 years, more than 330,000 electronic drilling, completion, and intervention documents have been consolidated in a new document-management system, improving both their accessibility and future worth to the expanding base of users. The system's document structure builds on earlier, engineer-led experience and has contributed to the new companywide standard for managing these documents. At the same time, the document-management project has eliminated more than 180,000 duplicate or obsolete documents.
As part of the migration from the old system to the new one, common well names have been adopted to support integration activities within the wells' functional organization and the subsurface and operations communities. Directional surveys are key links between these communities, and over the same period, an in-depth, field-by-field review of the company's UK directional-survey data has been conducted. This activity is now approximately 67% complete. Together, these activities are seen as essential preparations for the future, and they have already helped streamline some activities in both asset acquisitions and disposals.
These tasks took time, but measured preparation plus a degree of pragmatism have ensured they remain manageable. Care has been taken to maintain the document folder structure so it remains familiar to users while also taking advantage of the superior capabilities, such as search and assurance, available in the new system. This paper contains an outline of the structure and metadata and a description of the project's goals and history, including some of the challenges commonly encountered in preparing, processing, and exporting and importing data. Details of the directional-survey data-verification process are also provided.
This subject is of interest to many companies because of the scale of the exercise and the growing recognition in the industry of its technical and commercial importance.
Properties of a Natural Fracture and Its Skins From Reservoir Well Tests
Authors: Prats M.. , Raghavan R.. 
Published: January 2014

Summary
Two well tests are described that are aimed at the in-situ determination of the flow capacity (permeability-thickness product) of a natural fracture and the flow resistance of its skins at the boundaries with the reservoir matrix. Fracture skins tend to disperse flow, thus affecting the distribution of tracers in reservoir tests and contaminants and trace elements in aquifers. We are unaware of any other analytical procedure aimed at obtaining the properties of a natural fracture and its skins from subsurface measurements. Neither well test has been implemented.
The well tests are modeled after previously reported analytical expressions for the transient pressure distributions in a three-region composite reservoir in a uniform-thickness reservoir in which (1) the natural fracture is represented by a thin middle region of relatively high permeability, (2) the pressure disturbance is caused by producing from a short interval in one of the outer regions, and (3) the response is measured relatively near the fracture. The source and sensor may be on the same side or on opposite sides of the fracture, distinguishing the two tests.
Visualizing special completions in a horizontal well intersecting a natural fracture normally, pressure responses are given for both tests for a wide range of fracture/matrix permeability ratios and skin flow resistances for a source 190 ft from the fracture and 10 ft from the sensor and on either side of the fracture, both at the midplane of the reservoir.
A simple graphical procedure, not intended to replace history matching or regression where field data are available, illustrates how the two unknowns—permeability-thickness product of a natural fracture and the flow resistance of its skins—may be estimated from two representative values of an assumed measured pressure response.
Applying Method of Characteristics to Determine Pressure Distribution in 1D Shale-Gas Samples
Authors: Moghanloo R. Ghanbarnezhad , Javadpour F.. 
Published: January 2014

SummaryThis paper examines application of the method of characteristics (MOC) to determine pressure distribution in a 1D matrix of shale gas. Because of gas expansion and local desorption in shale gas, pressure distribution changes during production. We developed a semianalytic MOC solution of gas flow in shale by use of the analogous-continuum approximation (apparent permeability). The MOC solution is derived with the inclusion of compressibility, gas-slippage effect, and desorption.Through quantitative comparison of pressure profiles and history plots, we used a simulation approach to verify the accuracy of the analytic solution. Results suggest that the simulation results are consistent with our MOC solution, which can also be used to evaluate impacts of different parameters on pressure distribution. Prediction of pressure distribution over time will greatly enhance approximation of reservoir performance.