bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competition Between Conjugation and M13 Phage Infection inEscherichia coliin the Absence of Selection Pressure: A Kinetic Study
Authors: Wan Zhenmao , Goddard Noel L 
Published: October 2012

AbstractInter- and intraspecies horizontal gene transfer enabled by bacterial secretion systems is a powerful mechanism for bacterial genome plasticity. The type IV secretion system of Escherichia coli, encoded by the F plasmid, enables cell-to-cell contact and subsequent DNA transfer known as conjugation. Conjugation is compromised by phage infection that specifically targets the secretion machinery. Hence, the use of phages to regulate the spread of genes, such as acquired antibiotic resistance or as general biosanitation agents, has gained interest. To predict the potential efficacy, the competition kinetics must first be understood. Using quantitative PCR to enumerate genomic loci in a resource-limited batch culture, we quantify the infection kinetics of the nonlytic phage M13 and its impact on conjugation in the absence of selection pressure (isogenic set). Modeling the resulting experimental data reveals the cellular growth rate to be reduced to 60% upon phage infection. We also find a maximum phage infection rate of 3×10−11 mL phage−1 min−1 which is only 1 order of magnitude slower than the maximum conjugation rate (3×10−10 mL cell−1 min−1), suggesting phages must be in significant abundance to be effective antagonists to horizontal gene transfer. In the regime where the number of susceptible cells (F+) and phages are equal upon initial infection, we observe the spread of the conjugative plasmid throughout the cell population despite phage infection, but only at 10% of the uninfected rate. This has interesting evolutionary implications, as even in the absence of selection pressure, cells maintain the ability to conjugate despite phage vulnerability and the associated growth consequences.
SlWUS1; An X-linked Gene Having No Homologous Y-Linked Copy inSilene latifolia
Authors: Kazama Yusuke , Nishihara Kiyoshi , Bergero Roberta , Fujiwara Makoto T , Abe Tomoko , Charlesworth Deborah , Kawano Shigeyuki 
Published: October 2012

AbstractThe dioecious plant Silene latifolia has heteromorphic sex chromosomes, and comparison of the positions of sex-linked genes indicates that at least three large inversions have occurred during the evolution of the Y chromosome. In this article, we describe the isolation of a new sex-linked gene from S. latifolia, which provides new information on the evolution of this plant’s young sex chromosomes. By using reverse-transcription polymerase chain reaction degenerate primers based on the Arabidopsis thaliana sequence of WUSCHEL, a flower-development gene, we found two copies in S. latifolia, which we named SlWUS1 and SlWUS2. Southern blot and genetic segregation analysis showed that SlWUS1 is located on the X chromosome and SlWUS2 is autosomal. No Y-linked copy of SlWUS1 was found by either Southern blot analysis under low-stringency conditions or polymerase chain reaction with degenerate primers, so we conclude that SlWUS1 probably has no Y-linked homolog. It is unknown whether the Y chromosome lost the SlWUS1 copy by degeneration of this individual gene or whether deletion of a larger genome region was involved. Several tests lead us to conclude that dosage compensation has not evolved for this sex-linked gene. We mapped the ortholog in the nondioecious relative S. vulgaris (SvWUS1), to compare the location in a species that has no history of having sex chromosomes. SvWUS1 maps to the same linkage group as other fully X-linked genes, indicating that it was not added to the X, but was lost from the Y. Its location differs in the maps from the two species, raising the possibility that the X chromosome, as well as the Y, may have been rearranged.
A Fast and Efficient Approach for Genomic Selection with High-Density Markers
Authors: Pungpapong Vitara , Muir William M , Li Xianran , Zhang Dabao , Zhang Min 
Published: October 2012

AbstractRecent advances in high-throughput genotyping have motivated genomic selection using high-density markers. However, an increasingly large number of markers brings up both statistical and computational issues and makes it difficult to estimate the breeding values. We propose to apply the penalized orthogonal-components regression (POCRE) method to estimate breeding values. As a supervised dimension reduction method, POCRE sequentially constructs linear combinations of markers, i.e. orthogonal components, such that these components are most closely correlated to the phenotype. Such a dimension reduction is able to group highly correlated predictors and allows for collinear or nearly collinear markers. Different from BayesB, which predetermines hyperparameters, POCRE uses an empirical Bayes thresholding method to obtain data-driven optimal hyperparameters and effectively select important markers when constructing each component. Demonstrated through simulation studies, POCRE greatly reduces the computing time compared with BayesB. On the other hand, unlike fBayesB which slightly sacrifices prediction accuracy for fast computation, POCRE provides similar or even better accuracy of predicting breeding values than BayesB in both simulation studies and real data analyses.
Prediction of Inflicted Brain Injury in Infants and Children Using Retinal Imaging
Authors: Minns Robert A. , Jones Patricia A. , Tandon Anamika , Fleck Brian W. , Mulvihill Alan O. , Elton Robert A. 
Published: October 2012

BACKGROUND:Retinal hemorrhages (RHs) occur in inflicted traumatic brain injury (ITBI), accidental traumatic brain injury (ATBI), and some medical conditions, although the reported number, distribution, type, and frequency vary greatly between these different etiologies. We hypothesize that these RH characteristics reliably help to distinguish ITBI from ATBI and nontraumatic etiologies.METHODS:A 6-year prospective observational study using wide-field retinal imaging (RetCam) was conducted within 24 hours of admission to PICU, on serially recruited children with traumatic and nontraumatic encephalopathies. “Definite” and “probable” ITBI cases were confirmed by multiagency child protection case conferences. Image analysis used digital color and grayscale images for retinal “zoning” and “layering” of hemorrhages.RESULTS:Significant differences were found between the mean numbers of hemorrhages in ATBI/ITBI, and ITBI/nontraumatic etiologies for the 3 retinal zones (range, P = .003–.009) and for the dot-blot hemorrhages (range P = .001–.002). The mean numbers of RHs per ITBI patient in the peripapillary, macula, and peripheral zones were 14, 28, and 31 respectively. RHs in ATBI were near the optic disc and more superficial than in ITBI, where hemorrhages involved deeper layers (range, P = .003–.039) and were more peripheral (P = .03). The positive predictive value for ITBI in children &lt;3 years with &gt;25 dot-blot (intraretinal) hemorrhages was 93%.CONCLUSIONS:This prospective study, which included all potential causes of RHs, with objective retinal methodology, has confirmed that a young age and a high dot-blot count are strong predictors of ITBI. This high predictive value may support medicolegal deliberations.
Allowing Adolescents and Young Adults to Plan Their End-of-Life Care
Authors: Wiener Lori , Zadeh Sima , Battles Haven , Baird Kristin , Ballard Elizabeth , Osherow Janet , Pao Maryland 
Published: October 2012

OBJECTIVE:
The objective of this study was to assess and compare the usefulness, helpfulness, and stress associated with reviewing a previously adapted advance care planning guide, My Thoughts, My Wishes, My Voice, in comparison with the widely used adult document Five Wishes by adolescents and young adults (AYAs) living with a serious illness.

METHODS:
Fifty-two participants (age 16–28) living with metastatic or recurrent cancer or HIV infection (acquired at birth or early in life) were presented pages randomly from My Thoughts, My Wishes, My Voice and, Five Wishes, and asked to rank 25 items on several factors, including how likely they would be to complete each statement. Participant opinion on suggested changes in content, design, format, and style was obtained and resulted in development of a new document.

RESULTS:
AYAs living with a life-threatening illness want to be able to choose and record (1) the kind of medical treatment they want and do not want, (2) how they would liked to be cared for, (3) information for their family and friends to know, and (4) how they would like to be remembered.

CONCLUSIONS:
AYA views of what should be included in an advance care planning guide were incorporated into a new document, Voicing My Choices, that provides youth, families and providers an opportunity to reduce the silence around the dying process by allowing an opportunity to share one’s voice. We provide guidance on how to incorporate this tool into care.
Clinical Prognostic Messages From a Systematic Review on Cerebral Palsy
Authors: Novak Iona , Hines Monique , Goldsmith Shona , Barclay Richard 
Published: October 2012

OBJECTIVE:To summarize evidence on the rates of co-occurring impairments, diseases, and functional limitations with cerebral palsy into succinct clinical messages.METHODS:A search was conducted of the databases PubMed, Medline, CINAHL, and PsycINFO, and the results were supplemented with hand searches. Two independent reviewers determined whether retrieved abstracts met the following inclusion criteria: human subjects; &gt;90% were children or adults with cerebral palsy; published after 1999; and population-based data. Articles were appraised, analyzing design, participants, level of evidence, rates of impairments, and functional implications. Methodologic quality was rated by using a standardized checklist.RESULTS:A total of 1366 papers were identified in the search; 82 were appraised and 30 were included in the meta-analyses. High-level evidence existed, as rated on the Oxford 2011 Levels of Evidence: 97% of prevalence studies were level 1. The data were of a moderate to high quality grade (with the exception of sleep disorders), allowing plain English clinical messages to be developed.CONCLUSIONS:Among children with cerebral palsy, 3 in 4 were in pain; 1 in 2 had an intellectual disability; 1 in 3 could not walk; 1 in 3 had a hip displacement; 1 in 4 could not talk; 1 in 4 had epilepsy; 1 in 4 had a behavior disorder; 1 in 4 had bladder control problems; 1 in 5 had a sleep disorder; 1 in 5 dribbled; 1 in 10 were blind; 1 in 15 were tube-fed; and 1 in 25 were deaf.
Numerical Modeling of Induced Fracture Propagation: A Novel Approach for Lost Circulation Materials (LCM) Design in Borehole Strengthening Applications of Deep Offshore Drilling
Authors: Salehi Saeed , Nygaard Runar 
Published: October 2012

Abstract
Lost circulation caused by low fracture gradients is the cause of many drilling related problems. Typically the operational practice when lost circulation occurs is to add loss circulation materials (LCM) to stop mud from flowing into the formations. To improve the treatment for lost circulation caused by low fracture gradients, especially designed materials in mud system are used to seal the induced fractures around the wellbore. This operation is in the literature referred to as wellbore strengthening that has been found to be a very effective in cutting Non-Productive Time (NPT) when drilling deep offshore wells. Size, type and geometry of sealing materials are debating issues when different techniques are applied. Also the phenomenon is not truly understood when these techniques applied in different sedimentary basins.
This paper presents development and simulation results of a three-dimensional Finite-Element Model (FEM) for investigating wellbore strengthening mechanism. This study also describes a procedure for designing Particle Size Distribution (PSD) in field applications. To better understand the numerical results, the paper also reviews the connection between Leak of Tests (LOTs) and wellbore hoop stress and how these LOTs can mislead in fracture gradient determination.
A comprehensive field database was collected from different sedimentary basins for this study. Results demonstrate that the maximum attainable wellbore pressure achieved by wellbore strengthening is strongly controlled by stress anisotropy. Results also show that Particle Size Distribution (PSD) of wellbore strengthening should be designed in order to seal the fractures close to the mouth and at fracture tip. This will result both in maximizing hoop stress restoration and tip-screening effects. In addition this model is able to show the exact fracture geometry formed around the wellbore that will help to optimize the sealing materials design in wellbore strengthening pills. To support numerical modeling results, near wellbore fracture lab experiments on Sandstone and Dolomite samples were also presented. Laboratory experiments results reveal importance of rock permeability, tensile strength and fluid leak-off in wellbore strengthening applications.
Comparison of Stuck-Pipe and Lost-in-Hole Outcomes by Operator and Well Complexity in US Land Taken from a Global Bit Run Dataset
Authors: Robson Robert Ian 
Published: October 2012

Abstract
The loss of bottomhole assemblies (BHAs) in wellbores has always been a problem for drillers. A great deal has been written about the causes of stuck pipe, and many studies have been performed. Much of this work is anecdotal or localized. Until now, there has not been a very large dataset available in a format that allows performance to be compared for identifying causal relationships and risks.
A bit run summary database exists in which directional and measurement service crews can enter data related to the run location, objective, and operational outcome. These bit run summaries from 2005 through 2010, covering jobs run in US land operations (over 27,000 runs), were reviewed and classified. The reviewed data built a statistical picture of run outcomes that can be searched with a wide array of filters, including hole size, region, run length, date, operator, mud system, and combinations thereof.
Examination of these data has yielded several interesting relationships as well as general observations and conclusions. Tripping of pipe in the elevators (i.e., with no pumps) or reaming in and out of hole is seen to be the activity 40% of the time when a stuck or lost incident occurs. Interestingly, the likelihood of losing a BHA once it becomes stuck in US land is much less than the global rate; i.e., approximately one in three stuck BHAs are recovered.
The importance of planning the run with stuck pipe prevention in mind cannot be overstated. This dataset represents a valuable tool for risk analysis and job planning by comparing relative risk factors to both local and global datasets.
A Unique Electrical Submersible Reciprocating Pumping (ESRP) System Design Applied in Unconventional Oilfield
Authors: Wensheng Zhang , Lin Wang , Fengshan Wang , Youquan Huang , Gang Cao , Fengwu Zhang , Huaifeng Ren , Junwen Ge , Weiping Zhang , Ling Liu , Xinmin Wang 
Published: October 2012

Abstract
In recent years, a unique electrical submersible reciprocating pumping system (ESRP) was developed and has been applied in Daqing Oilfields. The main structure of ESRP is similar with ESP, consisting of an electrical submersible motor, pump, tubing and cable. The key equipments of ESRP are the reciprocating motor and the pump. The motor is a novel permanent magnetic line motor consisting of stator and mover. The pump is a special reciprocating pump. In operation, the mover slips in the stator from one end to the other periodically controlled by surface equipment, applying the power to the plunger of the reciprocating pump. Because of its small outerdiameter, the whole system could be run into the horizontal wellbore conveniently.
This unique lifting system was designed mainly for the production of satellite oilfields in Daqing Oilfield. Unlike the properties of the main blocks of Daqing Oilfield with thick pay zones, high permeability and shallow imbedded reservoir, these satellite oilfields distributed discontinuously, the layers are thin and imbedded deeply with poor permeability. The producers’ averaged production is below 35 bpd. Beam pumping system showed poor benefit due to the high investment and operating cost. PCPs and Bailing lifting systems were applied later in a larger scale. But the management was relatively complicated and still limited in horizontal wells. As the result, ESRP showed great advantages both in technical and economic respects in the production.
Till the end of 2010, ESRP has been applied in more than 30 wells in Daqing Oilfield. The longest running life has reached above 400 days. It showed remarkable advantages in the production of low displacement and deep reservoir, especially for horizontal wells.
With the improvement of displacement and other specifications, this unique lifting system design has great potential in the development of unconventional reservoir as well as mature oilfields.
Instilling Realism in Production Forecasting: Dos and Don'ts
Authors: Rajvanshi Avnish K. , Meyling Robert Gmelig , Haaf Danny ten 
Published: October 2012

Abstract
Historically, and across the E&P industry, several projects were found to underperform in their actual performance as compared to the promises made at the time of project approval. Investment decisions on upstream projects rely, to a large extent, on the robustness of the predicted ultimate recovery and production forecast associated with the chosen development concept. A 2010 upstream industry benchmarking consortium reviewed global performance of E&P projects and concluded that the majority of production forecasts presented at project approval were not attained. In many cases, this underdelivery resulted in eroded project economics and reputation damage with stakeholders.
The challenge for the E&P industry is to ensure that project approvals are based on realistic forecasts (P50 case). Modern technology has offered a paradigm shift in the amount of detail which can be included in the subsurface static and dynamic models. However, a universal truth is that no single model is the perfect representation of reality, and the recovery processes based on modelling are, therefore, always approximations of real life situations. Simulation models are guiding tools rather than sources of perfect answers.
This work is intended to increase awareness amongst the forecasters and the decision makers about pitfalls associated with production forecasting (especially those generated by dynamic models). It provides insight into the need to condition model input data or alternatively the model output to ensure that forecasts and resource volumes generated by these models are realistic. Root causes of unrealistic forecasts are identified. Dos and don'ts are described that help instil realism in the forecasting process. Pragmatic techniques to adjust the output obtained from dynamic modelling are illustrated using real-life examples.
This work presents a pragmatic approach to create reliable long-term production forecasts which can form the basis for sound business decisions.
Evaluation of Bakken Performance Using Coreflooding, Well Testing, and Reservoir Simulation
Authors: Kurtoglu Basak , Kazemi Hossein 
Published: October 2012

Abstract
The success of oil production in North Dakota Bakken should be credited to advanced completion and stimulation techniques. The abundance of data on well production, core analyses and flooding, geologic reservoir characterization, and pressure transient testing has enhanced reservoir evaluation. Understanding matrix and fracture contribution to daily oil production is the key to identifying reservoir drivers affecting the lifelong well productivity.
In this paper, we will present an application of core flooding, mini-frac and pressure build-up tests, decline curve analysis and reservoir simulation history matching to achieve reliable long-term reservoir performance predictions. This approach could lead to developing an integrated workflow for determining the performance drivers in the greater Bakken.
Information presented in this paper includes well performance data from several Bakken fields, displacement results on selected cores, mini-frac and pressure transient analyses, and history matching using decline curve analysis and numerical simulation.
Specifically, the matrix permeability from core measurements is on the order of 10-4 md while the permeability from well testing is on the order of 10-2 md. The latter represents the combined contributions of micro-fractures and matrix permeability. Reservoir simulation also shows that a single-porosity system, using only the matrix permeability from the core analysis, is not sufficient for matching well production performance without having a secondary permeability and porosity (micro-fractures). The dual-porosity nature of the reservoir was confirmed by a long-term pressure build-up test.
The Use of Real-Time Downhole Pressure and Distributed Temperature Surveying in Quantifying the Skin Evolution and Zone Coverage in Horizontal Well Stimulation
Authors: Balto Abdulelah A. , Qahtani Hassan B. , Kilany Khaled A , Baez Fernando , Elsherif Tamer 
Published: October 2012

ABSTRACT
Fiber optic enabled coiled tubing (FOECT) has been commonly used in qualitatively evaluating reservoir matrix chemical treatment in real time during the past couple of years. During this period, attempts of transforming qualitative evaluations to quantitative ones were made. The quantitative evaluation is based on two simultaneous criterions. The first one is a downhole pressure diagnostic plot (pressure transient analysis) created instantinuously using real-time acquired data by the downhole gauges. The second is an estimate of the zonal coverage based on the resulting temperature profile plot before, during and after a pumping treatment. Pressure transient analysis gives the skin as a direct output, while the cooling down/warming up DTS profiles identifies where the treatment fluids went in the formation, hence identifying the damaged zones.
It is strongly recommended to combine well testing analysis techniques with zone coverage evaluation in highly deviated and horizontal completed wells in both clastic and non-clastic rocks. Basically, deriving the skin from the injectivity test (pretreatment) and the skin from the post flush (post-treatment) provides an evaluation matrix treatment effectiveness.
A comparison between formation damage "skin" before and after the treatment was performed on the spot, revealing positive results of nearly uniform distribution of treatment fluids, and skin value reduction across the 3400 ft horizontal section.
Following the innovative procedures executed in well-A, different techniques were proposed, providing time and cost savings; raising the operational excellence expectations levels higher than expected for an offshore environment. The application of FOECT technology helped to minimize uncertainties during treatmentevaluation, and enhanced treatment distribution and placement. In addition to establishing more accurate and reliable Nodal Analysis and production forecast models.