bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Team-Based Approach to History Matching a Giant Carbonate Reservoir Using Sector Models with a Domain Decomposition Workflow
Authors: Brantferger M. , Al-Jenaibi H. M. , Patel H. , Al Harbi A. S. , Kompanik G. S. , Mubarak M. 
Published: October 2011

Abstract
Numerical simulation models have been used to optimize oil recovery since the 1960's. Typical steps to create a simulation model include 1) building a static model based on all available geological and petrophysical data; 2) history matching the static model to tune it to the available production and measured data; and 3) using the conditioned model to design drill-wells, predict pressure evolution, and forecast flow streams for business decisions. Today it is generally accepted that the best models result from using interdisciplinary teams to ensure geologic consistency is maintained during the history matching modifications – e.g. Sibley (1997), Landis (2005).
We discuss herein a unique approach to efficiently manage and expedite the history matching of a giant carbonate reservoir using a team of simulation engineers. The workflow was developed based on domain decomposition principles to divide the problem into manageable sector models with coordinated updates between the sector and full field model to obtain the full-field history match. With this approach, dynamic history matching is divided among many simulation engineers in a way that maintains the base geologic model, vets regional modifications, and transmits local lessons to the full-field model.
The workflow relies on fast extraction, creation, and management of sector models (or subdomains) from the full field. Each sector is linked to the full field by incorporating flux boundary conditions obtained from either a larger sector model or the full-field model. The proposed approach allows for the acceleration of the history match by effectively dividing the work among a team of simulation engineers. The "sector" approach of making smaller models from one large model speeds up the model build and run times making it convenient to have the multiple iterations necessary to achieve a satisfactory history match in a complex, high-contrast flow strata geologic environment.
The goal of the work was to reduce the time to achieve the history match to one year, as opposed to the previous experience requiring several years for similarly sized models. Some critical advantages and lessons from the workflow will be discussed through its application using actual history matching examples from a giant offshore, Middle Eastern, carbonate reservoir having over four decades of production history.
Assessing the Learning Needs of South Carolina Nurses by Exploring Their Perceived Knowledge of Emergency Preparedness: Evaluation of a Tool
Authors: McKibbin Anne E. , Sekula Kathleen , Colbert Alison M. , Peltier James W. 
Published: October 2011

Background:
This study assessed South Carolina nurses’ perceived knowledge of emergency preparedness to gain a better understanding of their learning needs and to prioritize continuing education and training efforts based on these needs.

Methods:
Boone’s programming model concept of planning provided the framework for this study, which used a descriptive correlational design and the Emergency Preparedness Information Questionnaire (EPIQ). Data from 207 eligible survey participants were analyzed.

Results:
Nurses showed an overall low level of self-reported knowledge of emergency preparedness. Nurses reported being most familiar with triage and least familiar with clinical decision making in epidemiology and biological agents.

Conclusion:
By prioritizing learning needs based on a needs assessment and accommodating learning preferences, a systematic and planned approach to educating nurses about this extremely important topic can be implemented to significantly strengthen nurses’ ability to respond to disaster events competently and effectively.
The Effectiveness of Nurses’ Ability to Interpret Basic Electrocardiogram Strips Accurately Using Different Learning Modalities
Authors: Spiva LeeAnna , Johnson Kimberly , Robertson Bethany , Barrett Darcy T. , Jarrell Nicole M. , Hunter Donna , Mendoza Inocencia 
Published: October 2011

Background:
Historically, the instructional method of choice has been traditional lecture or face-to-face education; however, changes in the health care environment, including resource constraints, have necessitated examination of this practice.

Methods:
A descriptive pre-/posttest method was used to determine the effectiveness of alternative teaching modalities on nurses’ knowledge and confidence in electrocardiogram (EKG) interpretation. A convenience sample of 135 nurses was recruited in an integrated health care system in the Southeastern United States. Nurses attended an instructor-led course, an online learning (e-learning) platform with no study time or 1 week of study time, or an e-learning platform coupled with a 2-hour post-course instructor-facilitated debriefing with no study time or 1 week of study time. Instruments included a confidence scale, an online EKG test, and a course evaluation.

Results:
Statistically significant differences in knowledge and confidence were found for individual groups after nurses participated in the intervention. Statistically significant differences were found in pre-knowledge and post-confidence when groups were compared.

Conclusion:
Organizations that use various instructional methods to educate nurses in EKG interpretation can use different teaching modalities without negatively affecting nurses’ knowledge or confidence in this skill.
GPS Navigation and Tracking Device
Authors: Khraisat Yahya Salameh , Al-Khateeb Mohammad , Abu-Alreesh Yahya , Ayyash Anas , Lahlouh Osama 
Published: October 2011

Since the introduction of GPS Navigation systems in the marketplace, consumers and businesses have been coming up with innovative ways to use the technology in their everyday life. GPS Navigation and Tracking systems keep us from getting lost when we are in strange locations, they monitor children when they are away from home, keep track of business vehicles and can even let us know where a philandering partner is at all times.
Because of this we attend to build a GPS tracking device to solve the mentioned problems.
Our work consists of the GPS module that collects data from satellites and calculates the position information before transmitting them to the userâ??s PC (of Navigation system) or observers (of Tracking System) using wireless technology (GSM).
Outcomes of Arteriovenous Fistulae Compared with Heparin-Bonded and Conventional Grafts for Hemodialysis Access
Authors: Charlton-Ouw Kristofer M. , Nosrati Naveed , Miller Charles C. , Coogan Sheila M. , Safi Hazim J. , Azizzadeh Ali 
Published: October 2011

Purpose Arteriovenous fistulae (AVF) are the preferred vascular access for hemodialysis patients. However, patients who do not have suitable veins require prosthetic arteriovenous graft (AVG) placement. We analyzed the patency and complication rates of upper extremity brachiocephalic AVF compared to brachioaxillary tapered heparin-bonded AVG and conventional AVG. Methods We performed a retrospective analysis of patients who underwent a permanent vascular access procedure at our tertiary referral center from 2006 to 2008. Factors presumed to affect patency and complication rates including age, body-mass index, dyslipidemia, hypertension, and diabetes were analyzed. Complication rates, re-interventions, primary, primary-assisted, and cumulative patency rates were compared using logistic regression analysis. Results We performed 138 upper extremity access procedures during the study period, including 64 brachiocephalic fistulae, 21 brachioaxillary heparin-bonded, and 21 brachioaxillary conventional AVGs. Nine patients were excluded from long-term follow-up. The 1-year cumulative patency rates for AVF, heparin-bonded, and conventional AVGs were 83%, 44%, and 67%, respectively (P=.0001). On multivariate regression analysis, only use of heparin-bonded AVG affected cumulative patency. Conclusions Although selection bias cannot be excluded in this retrospective study, heparin-bonded AVGs did not perform better than conventional AVGs. Co-morbid conditions did not affect the cumulative patency or complication rates of brachiocephalic AVF or AVG in this analysis. Larger, randomized trials are needed to validate the results of this study.
Micromechanics approach to poroelastic behavior of a jointed rock
Authors: Maghous S. , Dormieux L. , Kondo D. , Shao J. F. 
Published: October 2011

SUMMARYThe formulation of macroscopic poroelastic behavior of a jointed rock is investigated within the framework of a micro–macro approach. The joints are modeled as interfaces, and their behavior is modeled by means of generalized poroelastic state equations. Starting from Hill's lemma extended for a jointed medium and extending the concept of strain concentration to relate the joint displacement jump to macroscopic strain, the overall poroelastic constitutive equations for the jointed rock are formulated. The analysis emphasizes the main differences and similarities of the resulting behavior with respect to that characterizing ordinary porous media. It is shown that, unlike ordinary porous media, conditions on the poroelastic parameters of joints are required for the macroscopic drained stiffness to entirely define the poroelastic behavior. This is achieved, for instance, if the joint network is characterized by a unique Biot coefficient. Extension of the analysis to non‐linear poroelasticity is also outlined. Finally, the theoretical formulation is applied to two particular cases of jointed rock for which explicit expressions of the overall poroelastic parameters are derived. Copyright © 2011 John Wiley & Sons, Ltd.
Distance-based differential analysis of gene curves
Authors: Minas Christopher , Waddell Simon J. , Montana Giovanni 
Published: October 2011

Abstract
Motivation: Time course gene expression experiments are performed to study time-varying changes in mRNA levels of thousands of genes. Statistical methods from functional data analysis (FDA) have recently gained popularity for modelling and exploring such time courses. Each temporal profile is treated as the realization of a smooth function of time, or curve, and the inferred curve becomes the basic unit of statistical analysis. The task of identifying genes with differential temporal profiles then consists of detecting statistically significant differences between curves, where such differences are commonly quantified by computing the area between the curves or the l2 distance.
Results: We propose a general test statistic for detecting differences between gene curves, which only depends on a suitably chosen distance measure between them. The test makes use of a distance-based variance decomposition and generalizes traditional MANOVA tests commonly used for vectorial observations. We also introduce the visual l2 distance, which is shown to capture shape-related differences in gene curves and is robust against time shifts, which would otherwise inflate the traditional l2 distance. Other shape-related distances, such as the curvature, may carry biological significance. We have assessed the comparative performance of the test on realistically simulated datasets and applied it to human immune cell responses to bacterial infection over time.
Availability: R scripts are freely available for download at http://www2.imperial.ac.uk/~gmontana/dbf.htm.
Contact: g.montana@imperial.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
FASTSP: linear time calculation of alignment accuracy
Authors: Mirarab Siavash , Warnow Tandy 
Published: October 2011

Abstract
Motivation: Multiple sequence alignment is a basic part of much biological research, including phylogeny estimation and protein structure and function prediction. Different alignments on the same set of unaligned sequences are often compared, sometimes in order to assess the accuracy of alignment methods or to infer a consensus alignment from a set of estimated alignments.
Three of the standard techniques for comparing alignments, Developer, Modeler and Total Column (TC) scores can be derived through calculations of the set of homologies that the alignments share. However, the brute-force technique for calculating this set is quadratic in the input size. The remaining standard technique, Cline Shift Score, inherently requires quadratic time.
Results: In this article, we prove that each of these scores can be computed in linear time, and we present FastSP, a linear-time algorithm for calculating these scores. Even on the largest alignments we explored (one with 50 000 sequences), FastSP completed &lt;2 min and used at most 2 GB of the main memory. The best alternative is qscore, a method whose empirical running time is approximately the same as FastSP when given sufficient memory (at least 8 GB), but whose asymptotic running time has never been theoretically established. In addition, for comparisons of large alignments under lower memory conditions (at most 4 GB of main memory), qscore uses substantial memory (up to 10 GB for the datasets we studied), took more time and failed to analyze the largest datasets.
Availability: The open-source software and executables are available online at http://www.cs.utexas.edu/~phylo/software/fastsp/.
Contact: tandy@cs.utexas.edu
Computational network analysis of the anatomical and genetic organizations in the mouse brain
Authors: Ji Shuiwang 
Published: October 2011

Abstract
Motivation: The mammalian central nervous system (CNS) generates high-level behavior and cognitive functions. Elucidating the anatomical and genetic organizations in the CNS is a key step toward understanding the functional brain circuitry. The CNS contains an enormous number of cell types, each with unique gene expression patterns. Therefore, it is of central importance to capture the spatial expression patterns in the brain. Currently, genome-wide atlas of spatial expression patterns in the mouse brain has been made available, and the data are in the form of aligned 3D data arrays. The sheer volume and complexity of these data pose significant challenges for efficient computational analysis.
Results: We employ data reduction and network modeling techniques to explore the anatomical and genetic organizations in the mouse brain. First, to reduce the volume of data, we propose to apply tensor factorization techniques to reduce the data volumes. This tensor formulation treats the stack of 3D volumes as a 4D data array, thereby preserving the mouse brain geometry. We then model the anatomical and genetic organizations as graphical models. To improve the robustness and efficiency of network modeling, we employ stable model selection and efficient sparsity-regularized formulation. Results on network modeling show that our efforts recover known interactions and predicts novel putative correlations.
Availability: The complete results are available at the project website: http://compbio.cs.odu.edu/mouse/
Contact: sji@cs.odu.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Separable Fragments and Membrane Tethering of Arabidopsis RIN4 Regulate Its Suppression of PAMP-Triggered Immunity
Authors: Afzal Ahmed J. , da Cunha Luis , Mackey David 
Published: October 2011

Abstract
RPM1-interacting protein 4 (RIN4) is a multifunctional Arabidopsis thaliana protein that regulates plant immune responses to pathogen-associated molecular patterns (PAMPs) and bacterial type III effector proteins (T3Es). RIN4, which is targeted by multiple defense-suppressing T3Es, provides a mechanistic link between PAMP-triggered immunity (PTI) and effector-triggered immunity and effector suppression of plant defense. Here we report on a structure–function analysis of RIN4-mediated suppression of PTI. Separable fragments of RIN4, including those produced when the T3E AvrRpt2 cleaves RIN4 and each containing a plant-specific nitrate-induced (NOI) domain, suppress PTI. The N-terminal and C-terminal NOIs each contribute to PTI suppression and are evolutionarily conserved. Native RIN4 is anchored to the plasma membrane by C-terminal acylation. Nonmembrane-tethered derivatives of RIN4 activate a cell death response in wild-type Arabidopsis and are hyperactive PTI suppressors in a mutant background that lacks the cell death response. Our results indicate that RIN4 is a multifunctional suppressor of PTI and that a virulence function of AvrRpt2 may include cleaving RIN4 into active defense-suppressing fragments.
The ATG1/ATG13 Protein Kinase Complex Is Both a Regulator and a Target of Autophagic Recycling in Arabidopsis
Authors: Suttangkakul Anongpat , Li Faqiang , Chung Taijoon , Vierstra Richard D. 
Published: October 2011

Abstract
Autophagy is an intracellular recycling route in eukaryotes whereby organelles and cytoplasm are sequestered in vesicles, which are subsequently delivered to the vacuole for breakdown. The process is induced by various nutrient-responsive signaling cascades converging on the Autophagy-Related1 (ATG1)/ATG13 kinase complex. Here, we describe the ATG1/13 complex in Arabidopsis thaliana and show that it is both a regulator and a target of autophagy. Plants missing ATG13 are hypersensitive to nutrient limitations and senesce prematurely similar to mutants lacking other components of the ATG system. Synthesis of the ATG12-ATG5 and ATG8-phosphatidylethanolamine adducts, which are essential for autophagy, still occurs in ATG13-deficient plants, but the biogenesis of ATG8-decorated autophagic bodies does not, indicating that the complex regulates downstream events required for autophagosome enclosure and/or vacuolar delivery. Surprisingly, levels of the ATG1a and ATG13a phosphoproteins drop dramatically during nutrient starvation and rise again upon nutrient addition. This turnover is abrogated by inhibition of the ATG system, indicating that the ATG1/13 complex becomes a target of autophagy. Consistent with this mechanism, ATG1a is delivered to the vacuole with ATG8-decorated autophagic bodies. Given its responsiveness to nutrient demands, the turnover of the ATG1/13 kinase likely provides a dynamic mechanism to tightly connect autophagy to a plant's nutritional status.
An Importin β Protein Negatively Regulates MicroRNA Activity in Arabidopsis
Authors: Wang Wei , Ye Ruiqiang , Xin Ying , Fang Xiaofeng , Li Chunlian , Shi Huiqing , Zhou Xueping , Qi Yijun 
Published: October 2011

Abstract
As key components in the eukaryotic gene regulatory network, microRNAs (miRNAs) themselves are regulated at the level of both metabolism and activity. To identify factors that modulate miRNA activity, we used an Arabidopsis thaliana transgenic line expressing an artificial miRNA that causes trichome clustering and performed a screen for mutants with compromised miRNA activity (cma mutants) or enhanced miRNA activity (ema mutants). From this screen, we identified two novel mutant alleles of SERRATE, which is known to be required for miRNA biogenesis and dozens of other cma and ema mutants. In this study, we analyzed ema1. SAD2/EMA1 encodes an Importin β protein. The ema1 mutation had no effects on the accumulation of miRNAs and ARGONAUTE1 (AGO1) or on their cytoplasmic and nuclear distributions. Intriguingly, we found that the miRNA effector complexes purified from ema1 contained a larger amount of miRNAs and displayed elevated mRNA cleavage activities, indicating that EMA1 modulates miRNA activity by influencing the loading of miRNAs into AGO1 complexes. These results implicate EMA1 as a negative regulator of the miRNA pathway and reveal a novel layer of miRNA activity modulation.
Is the glass ceiling cracked in information technology? A qualitative analysis (part 2)
Authors: Appelbaum Steven H. , Asham Neveen , Argheyd Kamal 
Published: October 2011

PurposeThe purpose of this paper is to qualitatively investigate, through literature review of past studies and an in‐field case study, three different hypotheses regarding women working in the IT sector and their career and promotional aspirations.Design/methodology/approachAn online survey was used for data collection from female employees with varying professional specializations across several IT departments within the company. Questions for the survey were designed from the findings of the literature review.FindingsThe results obtained prove that married women who are intrinsically inspired to maintain their work‐family balance face higher stress and more conflicts than those who do not. In addition, the glass ceiling is still evident in today's corporations, but mainly affecting the older generation of women professionals. Also, the results slightly hinted at a ten‐year cutoff period, after which promotional aspiration is lost.Research limitations/implicationsOwing to the limitations of the research conducted, further qualitative studies can be done to compare careers and promotional patterns between men and women in the IT departments; as well as those between women in IT departments and women working in other departments.Practical implicationsEmployers should strive to provide their female employees practical solutions to allow for an easier balancing of work‐family responsibilities, such as flex‐times and telecommuting. At the same time, employers should place female employees in more opportunity‐enhancing positions within the corporation such that they can exploit or utilize their talents and increase their probability of climbing up the corporate ladder.Originality/valueWith a generous response rate, this paper provides a realistic perspective of professional females working within the IT domain as to their career and promotional aspirations.
Contemporary workplace occupations in Britain
Authors: Gall Gregor 
Published: October 2011

PurposeThis paper aims to examine the more militant response of a minority of workers to collective redundancy and restructuring in Britain since 2007.Design/methodology/approachThe paper deploys secondary sources to develop a series of grounded micro‐factors to help explain the presence and absence of the deployment of the occupation tactic.FindingsSome headway is made in explaining why only a limited number of occupations took place against redundancy and restructuring.Practical implicationsThe method of occupation was not shown to be as effective as might have been thought in opposing redundancies.Social implicationsThese concern union strategies and tactics for resistance to redundancy and restructuring.Originality/valueThe paper provides a grounded explanation of the phenomenon and incidence of worker occupations against collective redundancy and closure.