bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Mendelian Inheritance To Improve High-Throughput SNP Discovery
Authors: Chen Nancy , Van Hout Cristopher V , Gottipati Srikanth , Clark Andrew G 
Published: September 2014

Abstract
Restriction site-associated DNA sequencing or genotyping-by-sequencing (GBS) approaches allow for rapid and cost-effective discovery and genotyping of thousands of single-nucleotide polymorphisms (SNPs) in multiple individuals. However, rigorous quality control practices are needed to avoid high levels of error and bias with these reduced representation methods. We developed a formal statistical framework for filtering spurious loci, using Mendelian inheritance patterns in nuclear families, that accommodates variable-quality genotype calls and missing data—both rampant issues with GBS data—and for identifying sex-linked SNPs. Simulations predict excellent performance of both the Mendelian filter and the sex-linkage assignment under a variety of conditions. We further evaluate our method by applying it to real GBS data and validating a subset of high-quality SNPs. These results demonstrate that our metric of Mendelian inheritance is a powerful quality filter for GBS loci that is complementary to standard coverage and Hardy–Weinberg filters. The described method, implemented in the software MendelChecker, will improve quality control during SNP discovery in nonmodel as well as model organisms.
Deleterious Passengers in Adapting Populations
Authors: Good Benjamin H , Desai Michael M 
Published: September 2014

Abstract
Most new mutations are deleterious and are eventually eliminated by natural selection. But in an adapting population, the rapid amplification of beneficial mutations can hinder the removal of deleterious variants in nearby regions of the genome, altering the patterns of sequence evolution. Here, we analyze the interactions between beneficial “driver” mutations and linked deleterious “passengers” during the course of adaptation. We derive analytical expressions for the substitution rate of a deleterious mutation as a function of its fitness cost, as well as the reduction in the beneficial substitution rate due to the genetic load of the passengers. We find that the fate of each deleterious mutation varies dramatically with the rate and spectrum of beneficial mutations and the deleterious substitution rate depends nonmonotonically on the population size and the rate of adaptation. By quantifying this dependence, our results allow us to estimate which deleterious mutations will be likely to fix and how many of these mutations must arise before the progress of adaptation is significantly reduced.
Health Care-Associated Infections Among Critically Ill Children in the US, 2007–2012
Authors: Patrick Stephen W. , Kawai Alison Tse , Kleinman Ken , Jin Robert , Vaz Louise , Gay Charlene , Kassler William , Goldmann Don , Lee Grace M. 
Published: September 2014

BACKGROUND:
Health care–associated infections (HAIs) are harmful and costly and can result in substantial morbidity for hospitalized children; however, little is known about national trends in HAIs in neonatal and pediatric populations. Our objective was to determine the incidence of HAIs among a large sample of hospitals in the United States caring for critically ill children from 2007 to 2012.

METHODS:
In this cohort study, we included NICUs and PICUs located in hospitals reporting data to the Centers for Disease Control and Prevention’s National Healthcare Safety Network for central line–associated bloodstream infections (CLABSIs), ventilator-associated pneumonias, and catheter-associated urinary tract infections. We used a time-series design to evaluate changes in HAI rates.

RESULTS:
A total of 173 US hospitals provided data from NICUs, and 64 provided data from PICUs. From 2007 to 2012, rates of CLABSIs decreased in NICUs from 4.9 to 1.5 per 1000 central-line days (incidence rate ratio (IRR) per quarter = 0.96, 95% confidence interval 0.94–0.97) and in PICUs from 4.7 to 1.0 per 1000 central-line days (IRR per quarter = 0.96 [0.94–0.98]). Rates of ventilator-associated pneumonias decreased in NICUs from 1.6 to 0.6 per 1000 ventilator days (IRR per quarter = 0.97 [0.93–0.99]) and PICUs from 1.9 to 0.7 per 1000 ventilator-days (IRR per quarter = 0.95 [0.92–0.98]). Rates of catheter-associated urinary tract infections did not change significantly in PICUs.

CONCLUSIONS:
Between 2007 and 2012 there were substantial reductions in HAIs among hospitalized neonates and children.
Growth of Reduced Graphene Oxide
Authors: Huang Jingfeng , Chen Hu , Fam Derrick , Faulkner Steve H. , Niu Wenbin , Larisika Melanie , Nowak Christoph , Nimmo Myra A. , Yoong Tok Alfred Iing 
Published: September 2014

ABSTRACTReduced graphene oxide (RGO) has the advantage of an aqueous and industrial-scalable production route. However, one of the main limitations that prevent the use of RGO in electronics is the high electrical resistance deviation between fabricated chips. In this article, we present the novel growth of RGO which can bridge the gaps in-between existing flakes and thus reduce the electrical resistance standard deviation from 80.5 % to 16.5 %. The average resistivity of the treated RGO of ∼ 3.8 nm thickness was 200 Ω/square. The study uses an atmospheric-pressure chemical vapour deposition (CVD) system with hydrogen and argon gas bubbling through ethanol before entering the furnace. With a treatment of 2 hours, 100 % of the silicon dioxide substrate was covered with RGO from an initial 65 % coverage. This technology could enable large-scale application of RGO use in practical electronic devices.
Annular Pressure Build Up (APB) Analysis-Optimization of Fluid Rheology
Authors: Osgouei R. Ettehadi , Miska S. Z. , Ozbayoglu M. E. , Takach N. E. , Coe D.. , Chen D. C. 
Published: September 2014

AbstractAnnular pressure build up (APB) is an important problem in the area of well design. Different solutions have been proposed to mitigate APB, including vacuum-insulated tubing, silicate foam wellbore insulation techniques, and insulating with completion (packer) fluids. However, proposed solutions that include the optimization of annular fluid rheology of drilling fluids trapped in the outer annuli need further investigation.Convective and conductive heat transfer through fluids placed between the casing strings is a driving force for increasing annular pressure. This study explains how to design and optimize the rheological and thermal properties of drilling fluid to provide a sustainable and reliable insulating performance. The objectives of this study are 1) to develop a better insight of APB in the annulus of casing and 2) to experimentally measure and 3) analytically model the effect of different parameters, such as rheological and thermal properties, on the insulating performance of drilling fluid trapped in annular spaces.By combining the theory of sedimentation and the model proposed for free convective heat transfer of Yield Power Law fluids, a stepwise guideline is proposed to estimate the Nusselt number and thermal conductivity coefficient of annular fluids. A computer code to perform this procedure has been developed. Additionally, a unique experimental apparatus was designed and constructed to investigate the insulating performance of drilling fluids.Experimental observation and model results indicate that compressive yield stress, density difference between the solid and liquid phases of a drilling fluid, solid particle size and annular space geometry, are four important factors that determine sedimentation rate. These criteria can be used to characterize YPL annular fluid properties to minimize sedimentation rate and consequently to reduce free convective flow. The magnitude of the convective heat transfer coefficient is affected by the shear yield stress and density of annular fluid, by the flow behavior index (m), consistency index (k), conductivity coefficient and specific heat of the YPL fluid, and by annular space clearance. This conclusion can be used to quantitatively analyze the reliability and sustainability of the insulating performance of drilling fluids.The sedimentation profile, shear yield stress distribution and effective conductivity coefficient profile as functions of time and depth, as well as the Nusselt number, Nu, as a function of temperature difference in the radial direction can be estimated by the introduced guideline. The most important achievement is that the developed guideline can be used as a design tool in offshore drilling and completion operations to mitigate APB. A practical benefit of this study is demonstrated by the application of its findings in an illustrative example.
Improved Sand-Screen Design for Multi-Joint Flow Control
Authors: Hailey Travis , Cunningham Scott , Novelen Ryan , Kang James 
Published: September 2014

Abstract
A new sand screen design that enables collection and control of production flow from multiple sand-screen joints has been developed; the control in this design is in the form of a sliding-sleeve circulating device that is at a single point and enables flow from multiple joints. This type of functionality was developed previously for use in multiple-zone frac- or gravel-packs as a means of helping to control flows and pressures more efficiently in zones other than the one being packed. However, these early designs were less efficient in use of available geometry than the new design, which uses, 1) tall wire ribs of a wire-wrapped structure to create an annular flow space, and 2) an innovative crimping technology that uses plastic deformation of metal components to connect the annular flow space across connections between sand-screen joints during rig assembly.
Although the initial use of the new screen design was planned to provide an improvement to existing multi-zone packing systems (the new screens are already being planned for use in two deep-water lower tertiary projects in the Gulf of Mexico), alternative uses are now being envisioned for the design. Future uses may be as stand-alone or gravel-packed screens in long (probably horizontal) intervals, where a single circulating sleeve can control a longer portion of the interval. Another improvement being considered is the incorporation of passive inflow-control device (ICDs or AICDs) functionality into the single flow points for multiple screens.
Additionally, with minor modification, it is anticipated that the new screen design will be conducive to installing tracer materials in the channels between ribs of the annular flow space.
Lost Circulation Materials Capability of Sealing Wide Fractures
Authors: Alsaba Mortadha , Nygaard Runar , Saasen Arild , Nes Olav-Magnar 
Published: September 2014

Abstract
Lost circulation prevention or mitigation is a major challenge while drilling. Conventional lost circulation materials (LCM) are often implemented to prevent/cure seepage or partial losses. When it comes to severe losses, often caused by larger fracture sizes, special treatments are being applied. Curing severe losses with specialized treatments requires more time because some treatments can't be applied in the presence of downhole tools, where special equipment and procedures are required. In addition, polymer and cement treatments require time to be activated or cured after being pumped.
Evaluating the performance of LCM and their effectiveness in sealing wide fractures is required in conjunction with an optimized LCM combination to ensure their ability in curing losses. This paper presents investigations about the possibility of sealing relatively large fracture using conventional LCM instead of the other approaches such as cement or hydratable LCM pills. Two specifically developed apparatuses were used to optimize LCM combination and investigate their ability in sealing wide fractures at different pressures. A set of tapered slots that simulate sealable fracture widths with different fracture aperture (2.5 – 5 mm) and tip sizes (1-2 mm) were used in this study.
A total of 160 tests were conducted to optimize LCM combinations and concentrations in addition to 30 tests to evaluate the integrity of the seal formed under elevated pressures with apparatus capability of up to 10,000 psi (69 MPa) fracture differential pressure. The effects of varying LCM's type, concentration, particle size distribution and fracture width were studied with respect to differential pressure and fluid loss. The results showed that LCM's that have irregularity in particles shapes and a degree of deformability such as nut shells are capable of sealing wide fractures when used individually or in combination with other LCM's. In addition, a strong relationship between fluid loss values and the seal integrity was observed, i.e. lower fluid loss, gave higher sealing efficiency.
There is a good potential for conventional LCM's to be reconsidered as a corrective approach for partial or severe losses when the proper LCM's size, type and concentration are selected for a wider range of fracture widths. Curing losses using conventional LCM's for a wider range of fractures widths is advantageous since it can cut time and cost compared to current practices.
A Novel Approach in Locating Single Loss Zone during Deepwater Drilling with Distributed Temperature Measurement
Authors: Chen Yuanhang , Yu Mengjiao , Miska Stefan Z. , Ozbayoglu Evren M. , Takach Nicholas 
Published: September 2014

Abstract
One of the major concerns when drilling deepwater wells is fluid loss since the fracture gradients are typically lower than their onshore counterparts. Failure to minimize the fluid loss can significantly increase the cost of drilling, and even lead to abandonment of the well. Successful management of lost circulation should incorporate accurate estimation of loss zone location, followed by corresponding lost circulation control procedures.
This paper presents an innovative way to estimate the location of mud loss by interpreting distributed temperature measurement which is facilitated by a recently developed drilling microchip technology. Firstly, a transient wellbore thermal model is presented to predict the effect of mud loss on the change in circulating mud temperature profile for tubular fluids. The model is developed based on heat balance equations with variable local flow rates along the wellbore due to the mud loss. The effects of heat transfer above the seabed between riser and the drilling muds are included. Downward shifts in the temperature curves are noted in both the drillpipe and annulus. With distributed temperature measurement data, the derivative of annulus temperature with respect to depth can be used to effectively identify the location of the loss zone. A case study has been conducted to identify the location of a loss zone in a deepwater well. According to the results, a jump in the derivative coincides with the location of loss and is sufficiently significant in magnitude to be identified. The seawater-riser heat transfer has minimum effect on the loss zone prediction; furthermore, the effect of the same amount of loss is more conspicuous if the loss occurs at a shallower depth, in which case the loss zone can be more reliably located.
Investigating the Impact of the "Tool Joint Effect" on Equivalent Circulating Density in Deep-Water Wells
Authors: Vajargah Ali Karimi , Fard Fardis Najafi , Parsi Mazdak , Hoxha Besmir Buranaj 
Published: September 2014

AbstractPrecise prediction of Equivalent Circulating Density (ECD) is one of the most important challenges during drilling operations. This becomes more vital in deep-water offshore wells in which formation pressure is very close to the fracture pressure. In addition, techniques such as Managed Pressure Drilling (MPD) rely on the precise estimation of frictional pressure losses.Although many theoretical and experimental studies have been conducted on fluid flow through pipes and annuli to predict the pressure losses, majority of them undermine or simply ignore the effect of tool joints. A few studies that take the effect of tool joints into account indicate that it can have significant effect on pressure loss. Therefore, there is a strong need to determine the amount of additional pressure loss caused by the tool joints.This paper presents a Computational Fluid Dynamics (CFD) approach to investigate the effect of tool joint on annular pressure losses. The utilized software package in this simulation study uses Finite Volume methods to solve the problem. The effects of important parameters such as flow rate, mud type, mud weight and mesh size are investigated. The pressure loss in the annuli, with and without tool joint, is obtained and additional pressure loss due to presence of tool joint is calculated accordingly.Simulation results show that the ratio of annular pressure loss with tool joints to the pressure loss without tool joints (α) strongly depends on the flow regime. In Laminar flow, this ratio remains relatively constant, regardless of the type of the drilling fluid. In turbulent flow, it increases rapidly with increasing Reynolds number and can be precisely estimated by the proposed correlation. It has been found that in deep offshore wells and high range of operational flow rate, the additional pressure loss due to tool joints can be as high as 30% of the total frictional pressure loss and must be taken into consideration during ECD calculations.
Finite Element Analysis of Casing Drilling Smearing Effect
Authors: Kiran R.. , Salehi S.. , Karimi M.. 
Published: September 2014

AbstractCasing while Drilling (CwD) is a new drilling method where the well is drilled and cased simultaneously. Previous field operations of CwD have shown a decrease in drilling non-productive time as well as improvement in controlling lost circulation and wellbore stability. Although advantages of this technology are well noted in the literature, the mechanisms of improvements were not studied comprehensively. In order to study these mechanisms, one has to understand the formation properties, fluid hydraulics, casing dynamics, and how CwD helps in better hydraulic control and results in strengthening effects. In the previous research works, the factors that were widely discussed and results obtained were related to formation properties. However, while considering the stresses in the wellbore, mechanical factors such as the RPM and contact of casing at different positions in wellbore were usually neglected. In furtherance to this study, the importance of plastering mechanism cannot be ignored. This work includes a new insight towards the underlying mechanism of casing-wellbore contact and changes in the near wellbore stresses while casing rotation. The main objective of this study is to investigate the hypothesis of the increase in hoop stress when the casing contacts wellbore with regard to the formation stresses orientations. To accomplish this objective, finite-element analysis has been conducted to simulate several CwD scenarios. The classical equations used to obtain the wellbore stresses include parameters like the far-field stresses, pore pressure, and wellbore geometry. These equations do not consider the effect of casing pipe contact and eccentricity; therefore finite element simulations can be very helpful to investigate these effects. Casing-wellbore contact in both maximum and minimum in-situ stress directions are considered in this study as well as changing contact length. The study of different cases shows the variation of hoop stress, which can be beneficial if properly implemented in CwD operations.
Profiling Drilling Fluid’s Invasion Using Scanning Electron Microscopy: Implications for Bridging and Wellbore Strengthening Effects
Authors: Salehi Saeed , Hussmann Stefanie , Karimi M.. , Ezeakacha Chinedum , Tavanaei Amirhossien 
Published: September 2014

Abstract
Wellbore stability issues are continually plaguing the industry and it is important to understand the mud properties that contribute to these issues. The effects of mud cake build up and filtration with time aids the understanding of formation damage and wellbore stability. The increase of drilling in high temperature and pressure zones (HTHP) necessitates studies that can predict filtrate invasion, and particle bridging. The most common hydraulically challenged zones are: depleted sands or intervals with very low pore pressure and fracture pressure, wellbore ballooning zones encountered in deep water drilling where surge and swab pressures could be a serious challenge, and complete lost circulation/no return zones.
Filtrate invasion and mud cake build up can be considered as primary factors controlling wellbore stability while drilling. Decreasing the near wellbore permeability by forming an ultra low permeability mud cake can strengthen the wellbore and mitigate further lost circulation problems. Very few studies have investigated filtration and filter cake build up under HPHT situations where the effect of different mud particles and bridging solids can be analyzed.
This paper focuses on experimental methods to investigate the effects of particle bridging, filtrate invasion and permeability on some common water based muds used by the industry. The methodology in this paper is based on using high temperature and pressure (HTHP) filtration tests at different time steps on sandstone cores of 50 mD and 750 mD fitted into Particle Plugging Test (PPT) aparatus. The Scanning Electron Microscope (SEM) and elemental mapping was used to characterize filter cake and further investigating the particles invasion in the core samples. Finally, mud cake permeability of the samples was calculated using analytical models from litreture.
Study of Casing Annulus Pressure for Deepwater Drilling and Completions
Authors: Liu Baosheng , Yang Jin , Zhou Bo , Yan De , Tian Ruirui , Liu Zhengli , Luo Junfeng , Huang Xiaolong 
Published: September 2014

Abstract
Casing collapse and fracture may be caused by the rise of casing annulus temperature and pressure in the initial stage of production and testing of deepwater wells. Based on the casing program and wellbore heat transfer process, a pressure calculation model for casing annulus was established, which provides basis for annulus pressure control.
Fluid trapped in the annulus of subsea wells can cause casing strings to fail. This condition occurs when casing annuli attain a closed-volume circumstance (when a well is cased, cemented, and head seals are set). During production, the heat transfer of the produced fluids to the casing strings causes the trapped fluid to increase in pressure. This condition is magnified in deepwater because annular fluids are cooler due to the cold deepwater environment.
With the annulus between testing string and production casing as an example, a casing annulus temperature calculation method was derived according to the principle of conservation of energy and wellbore heat transfer analysis. The casing annulus pressure prediction model was established for typical deepwater wells according to the volume change of casing annulus fluid with temperature and pressure, and in combination of the casing annulus PVT equation and annulus temperature equation.
The casing annulus temperature and pressure calculation methods were successfully applied in the casing annulus temperature and pressure management operation in deepwater wells in West Africa, and the predicted temperature and pressure were compared with the actual ones, which indicates that casing annulus temperature and pressure prediction methods have good accuracy.