bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Genetics of Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-Hardiness Related Traits
Authors: Eckert Andrew J , Bower Andrew D , Wegrzyn Jill L , Pande Barnaly , Jermstad Kathleen D , Krutovsky Konstantin V , St. Clair J Bradley , Neale David B 
Published: June 2009

Abstract
Adaptation to cold is one of the greatest challenges to forest trees. This process is highly synchronized with environmental cues relating to photoperiod and temperature. Here, we use a candidate gene-based approach to search for genetic associations between 384 single-nucleotide polymorphism (SNP) markers from 117 candidate genes and 21 cold-hardiness related traits. A general linear model approach, including population structure estimates as covariates, was implemented for each marker–trait pair. We discovered 30 highly significant genetic associations [false discovery rate (FDR) Q &lt; 0.10] across 12 candidate genes and 10 of the 21 traits. We also detected a set of 7 markers that had elevated levels of differentiation between sampling sites situated across the Cascade crest in northeastern Washington. Marker effects were small (r2 &lt; 0.05) and within the range of those published previously for forest trees. The derived SNP allele, as measured by a comparison to a recently diverged sister species, typically affected the phenotype in a way consistent with cold hardiness. The majority of markers were characterized as having largely nonadditive modes of gene action, especially underdominance in the case of cold-tolerance related phenotypes. We place these results in the context of trade-offs between the abilities to grow longer and to avoid fall cold damage, as well as putative epigenetic effects. These associations provide insight into the genetic components of complex traits in coastal Douglas fir, as well as highlight the need for landscape genetic approaches to the detection of adaptive genetic diversity.
A Genetic Test for Yeast Two-Hybrid Bait Competency Using RanBPM
Authors: Tucker Chandra L , Peteya Leslie A , Pittman Adrianne M C , Zhong Jing 
Published: June 2009

Abstract
We describe a simple genetic test for assessing the competency of Gal4-based baits prior to a yeast two-hybrid screen, which allows determination of whether a bait protein is expressed appropriately for an interaction to be detected. The novel test, based on interaction with the protein RanBPM, is easier and more predictive than other methods such as Western blotting, allowing identification of ∼80% of incompetent baits prior to screening.
A Drosophila Resource of Transgenic RNAi Lines for Neurogenetics
Authors: Ni Jian-Quan , Liu Lu-Ping , Binari Richard , Hardy Robert , Shim Hye-Seok , Cavallaro Amanda , Booker Matthew , Pfeiffer Barret D , Markstein Michele , Wang Hui , Villalta Christians , Laverty Todd R , Perkins Lizabeth A , Perrimon Norbert 
Published: June 2009

Abstract
Conditional expression of hairpin constructs in Drosophila is a powerful method to disrupt the activity of single genes with a spatial and temporal resolution that is impossible, or exceedingly difficult, using classical genetic methods. We previously described a method (Ni et al. 2008) whereby RNAi constructs are targeted into the genome by the phiC31-mediated integration approach using Vermilion-AttB-Loxp-Intron-UAS-MCS (VALIUM), a vector that contains vermilion as a selectable marker, an attB sequence to allow for phiC31-targeted integration at genomic attP landing sites, two pentamers of UAS, the hsp70 core promoter, a multiple cloning site, and two introns. As the level of gene activity knockdown associated with transgenic RNAi depends on the level of expression of the hairpin constructs, we generated a number of derivatives of our initial vector, called the “VALIUM” series, to improve the efficiency of the method. Here, we report the results from the systematic analysis of these derivatives and characterize VALIUM10 as the most optimal vector of this series. A critical feature of VALIUM10 is the presence of gypsy insulator sequences that boost dramatically the level of knockdown. We document the efficacy of VALIUM as a vector to analyze the phenotype of genes expressed in the nervous system and have generated a library of 2282 constructs targeting 2043 genes that will be particularly useful for studies of the nervous system as they target, in particular, transcription factors, ion channels, and transporters.
Lysophosphatidic acid as a potential target for treatment and molecular diagnosis of epithelial ovarian cancers
Authors: Tanyi János , Rigó Jr. János 
Published: May 2009

Az ováriumtumorok mortalitása a legmagasabb a nőgyógyászati tumorok között. Ez egyrészt a késői diagnózisnak, másrészt a hatásos terápia hiányának következménye. Az ováriumtumorok karcinogenezise és metasztázisképzése egy komplikált genetikai, molekuláris és biokémiai folyamatsor eredménye. A lizofoszfátsav (LPA) termelésének, receptorstátusának és szignáltranszdukciós útvonalának abnormalitása gyakran megtalálható az ováriumtumorokban, ami azt sejteti, hogy az LPA nagyon fontos szerepet játszik ennek a betegségnek a kialakulásában és patofiziológiájában. Így jogosan feltételezhetjük, hogy az LPA-szignálkaszkád számos célpontot szolgáltat a molekuláris kezelési módok kialakítására és jó példát mutat arra, hogyan lehet új diagnosztikus és terápiás módszereket kialakítani egyes betegségek ellen. Az LPA-t lebontó és termelő enzimcsaládoknak csak a közelmúltban történt felfedezése és a receptorspecifikus molekulák kifejlesztése új fejezetet nyithat e potenciálisan halálos betegség kezelésében. Ebben az összefoglaló tanulmányban ismertetjük, hogy a tumorsejtekben lévő LPA-t lebontó enzimek aktivitása csökkent, és ez hozzájárul a tumor progressziójához. Ugyanezen enzimek mesterségesen létrehozott, fokozott aktivitása csökkenti a tumorsejtek növekedését és elősegíti a fiziológiás viszonyok helyreállását. Bemutatjuk azokat az irodalmi adatokat, amelyek egyértelműen bizonyítják, hogy a lipidfoszfát-foszfatáz enzimek hatásukat a sejten kívüli LPA lebontásával érik el. Minthogy ez a lebontás extracellulárisan történik, ez megmagyarázza a „bystander-effect” előfordulását, amit szintén ismertetünk. Az LPA-lebontás és -termelés enzimjei, illetve az LPA-t kötő receptorok kitűnő célpontok új molekuláris terápia kidolgozására. A különböző LPA-izoformák és más lizofoszfolipidek szintváltozásainak korai detektálása segíthet a tumor korai diagnosztizálásában, illetve később a kezelés hatékonyságának követésében. A közelmúlt jelentős LPA-szignálkaszkáddal kapcsolatos kutatási eredményei azt sejtetik, hogy azok jelentős szerepet fognak játszani ennek a még mindig halálos betegségnek a kezelésében, de további kutatások szükségesek a részletek pontos megértéséhez.
Prognostic Factors in Patients with Ovarian Serous Low Malignant Potential (Borderline) Tumors with Peritoneal Implants
Authors: Kane Aminata , Uzan Catherine , Rey Annie , Gouy Sebastien , Camatte Sophie , Pautier Patricia , Lhommé Catherine , Haie-Meder Christrine , Duvillard Pierre , Morice Philippe 
Published: June 2009

Abstract

Background.
The objective of this study was to determine prognostic factors in a large series of patients with stage II or III serous low malignant potential ovarian tumor (LMPOT) and peritoneal implants.

Methods.
Patients with a serous LMPOT and peritoneal implants treated at or referred to our institution were retrospectively reviewed. The slides of ovarian tumors and peritoneal implants were reviewed by the same pathologist.

Results.
From 1969 to 2006, 168 patients were reviewed, 21 of whom had invasive implants. Tumors exhibited a micropapillary pattern in 56 patients. Adjuvant treatment had been administered to 61 patients. The median duration of follow-up was 57 months (range, 1–437). Forty-four patients had relapsed and 10 patients had died. The 5-year overall survival rate was 98%. Among patients with noninvasive and invasive implants, 8% and 10%, respectively, had relapsed at 5 years in the form of invasive disease (p = .08). In a multivariate analysis, the use of conservative treatment was the only prognostic factor.

Interpretation.
The prognosis of serous LMPOT with peritoneal implants remains good. The strongest prognostic factor in patients with an advanced-stage borderline tumor is the use of conservative surgery. In this series, a micropapillary pattern and implant subtype (invasive versus noninvasive) were not prognostic factors.
Systemic Immune Responses in Pregnancy and Periodontitis: Relationship to Pregnancy Outcomes in the Obstetrics and Periodontal Therapy (OPT) Study
Authors: Ebersole Jeffrey L. , Novak M. John , Michalowicz Bryan S. , Hodges James S. , Steffen Michelle J. , Ferguson James E. , DiAngelis Anthony , Buchanan William , Mitchell Dennis A. , Papapanou Panos N. 
Published: June 2009

Background: Our previous studies reported on the obstetric, periodontal, and microbiologic outcomes of women participating in the Obstetrics and Periodontal Therapy (OPT) Study. This article describes the systemic antibody responses to selected periodontal bacteria in the same patients.Methods: Serum samples, obtained from pregnant women at baseline (13 to 16 weeks; 6 days of gestation) and 29 to 32 weeks, were analyzed by enzyme‐linked immunosorbent assay for serum immunoglobulin G (IgG) antibody to Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans), Campylobacter rectus, Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia (previously T. forsythensis), and Treponema denticola.Results: At baseline, women who delivered live preterm infants had significantly lower total serum levels of IgG antibody to the panel of periodontal pathogens (P = 0.0018), to P. gingivalis (P = 0.0013), and to F. nucleatum (P = 0.0200) than women who delivered at term. These differences were not significant at 29 to 32 weeks. Changes in IgG levels between baseline and 29 to 32 weeks were not associated with preterm birth when adjusted for treatment group, clinical center, race, or age. In addition, delivery of low birth weight infants was not associated with levels of antibody at baseline or with antibody changes during pregnancy.Conclusions: Live preterm birth is associated with decreased levels of IgG antibody to periodontal pathogens in women with periodontitis when assessed during the second trimester. Changes in IgG antibody during pregnancy are not associated with birth outcomes.
Periodontal Treatment Needs and Prevalence of Localized Aggressive Periodontitis in a Young Turkish Population
Authors: Ereş Gülden , Sarıbay Aysel , Akkaya Murat 
Published: June 2009

Background: The purpose of this study was to investigate the prevalence of localized aggressive periodontitis (LAgP) among students aged 13 to 19 years at public schools in Ankara.Methods: A total of 3,056 students (1,563 females and 1,493 males) participated in the study. All students were examined at their schools and their mouths coded according to the recommendations of the Community Periodontal Index of Treatment Needs (CPITN) using a mirror, a World Health Organization 621 ball‐tip probe, and daylight for illumination. Among the students examined, 170 had two or more sextants or teeth with code 3 or one sextant with code 4 and were scheduled for radiographs and a full clinical examination. The additional criteria for the diagnosis of LAgP were good general health, radiographically determined bone loss around the first molars bilaterally, and the bone loss must be unproportionally extensive with respect to the low levels of plaque and calculus, contrary to what is usually observed in chronic periodontitis.Results: Among the 3,056 students screened, 170 were scheduled for further examination, and 18 (10 females and eight males) were diagnosed with LAgP. Of 18,336 sextants examined, 6,575 required scaling, and 63 required scaling and further complex treatment.Conclusion: The prevalence of LAgP was 0.6%, with a female/male ratio of 1.25:1.
The Efficacy of Acetaminophen–Caffeine Compared to Ibuprofen in the Control of Postoperative Pain After Periodontal Surgery: A Crossover Pilot Study
Authors: Rashwan Weam A.M. 
Published: June 2009

Background: Previous studies showed that non‐steroidal anti‐inflammatory drugs (NSAIDs) have significant benefits in the control of pain after periodontal surgery. Acetaminophen (centrally acting NSAID) is believed to provide less analgesic efficacy than ibuprofen (centrally and peripherally acting NSAID). This study compared an alternative combination of acetaminophen, 500 mg, with caffeine, 30 mg, to ibuprofen, 400 mg, in pain management after periodontal surgeries.Methods: A prospective, randomized, double‐masked crossover clinical trial was conducted on 15 patients. Open flap debridement was performed on two quadrants with a 3‐week interval in between. Each quadrant was randomly assigned to acetaminophen, 500 mg, with caffeine, 30 mg, or ibuprofen, 400 mg, immediately after surgery and 8 hours after the first dose. Postoperative pain was assessed during the first 8 hours and on the following day using the 101‐point numeric rate scale (NRS‐101) and the four‐point verbal rating scale (VRS‐4).Results: Using the NRS‐101, the acetaminophen‐caffeine group showed statistically significantly lower mean pain scores than the ibuprofen group at 1 and 2 hours (P = 0.002), whereas at 6, 7, and 8 hours, the ibuprofen group showed statistically significantly lower mean pain scores (P <0.001). Using the VRS‐4, there was no statistically significant difference between the two groups at all periods (P >0.05).Conclusion: Acetaminophen, 500 mg, with caffeine, 30 mg, can be used efficiently in controlling postoperative pain after open flap debridement, especially in patients with gastric ulcers or bleeding tendency because acetaminophen is less hazardous than ibuprofen.
In Vitro Evaluation of the Effects of Low‐Intensity Nd:YAG Laser Irradiation on the Inflammatory Reaction Elicited by Bacterial Lipopolysaccharide Adherent to Titanium Dental Implants
Authors: Giannelli Marco , Bani Daniele , Tani Alessia , Pini Alessandro , Margheri Martina , Zecchi‐Orlandini Sandra , Tonelli Paolo , Formigli Lucia 
Published: June 2009

Background:The bacterial endotoxin lipopolysaccharide (LPS) represents a prime pathogenic factor of peri‐implantitis because of its ability to adhere tenaciously to dental titanium implants. Despite this, the current therapeutic approach to this disease remains based mainly on bacterial decontamination, paying little attention to the neutralization of bioactive bacterial products. The purpose of the present study was to evaluate whether irradiation with low‐energy neodymium‐doped:yttrium, aluminum, and garnet (Nd:YAG) laser, in addition to the effects on bacterial implant decontamination, was capable of attenuating the LPS‐induced inflammatory response.Methods:RAW 264.7 macrophages or human umbilical vein endothelial cells were cultured on titanium disks coated withPorphyromonas gingivalisLPS, subjected or not to irradiation with the Nd:YAG laser, and examined for the production of inflammatory cytokines and the expression of morphologic and molecular markers of cell activation.Results:Laser irradiation of LPS‐coated titanium disks significantly reduced LPS‐induced nitric oxide production and cell activation by the macrophages and strongly attenuated intercellular adhesion molecule‐1 and vascular cell adhesion molecule expression, as well as interleukin‐8 production by the endothelial cells.Conclusion:By blunting the LPS‐induced inflammatory response, Nd:YAG laser irradiation may be viewed as a promising tool for the therapeutic management of peri‐implantitis.
A Fractal Model of Production by Spontaneous Water Imbibition
Authors: Zhao Haiyang , Li Kewen 
Published: May 2009

Abstract
A mathematical model was proposed to predict production in rock by spontaneous imbibition. Heterogeneity of rock represented by fractal dimension was considered. This fractal model predicts a power law relationship between spontaneous imbibition rate and time. Experimental data of recovery in gas-water-rock and oil-water-rock systems were used to test the fractal model. Spontaneous water imbibition experiments were conducted in different type of rocks (Berea sandstone, chalk, and The Geysers gray wacke) with permeability ranging from 0.5 to over 1000 md. The results demonstrated that the fractal production model could match the experimental data satisfactorily in the cases studied. The fractal dimension data inferred from the model match were approximately equal to the values of fractal dimension obtained using a different technique (mercury-intrusion capillary pressure) in Berea sandstone.
Complex Well Modeling Workflow Enabling Full Field Optimization and Forward Decisions
Authors: Al-Qahtani Ghazi D. , Elrafie Emad A. , Abbas Raja T. , Ikuku Clara E. , Hogg Martin F. , Rincon Alexander 
Published: May 2009

Abstract
The application of Complex Wells (CW) as a component of an optimized field development strategy at single well, sector model and or small scale multi-well level is generally well understood. In contrast, the application, modeling and optimization of a full field strategy inclusive of CW remains a daunting industry challenge.
This paper describes a highly successful four-step workflow to manage, assess and model the qualification of a CW optimization strategy at a full field model scale. The paper utilizes a field case to illuminate a CW field wide optimization – extended production plateau, increased production rates and CW completion strategies – approach as compared to single, sector and or multi-well level CW model derived field development decisions. In this paper, complex wells include; Multi-laterals (ML) and Maximum Reservoir Contact wells (MRC) inclusive of down-hole Internal Control Devices (ICD), Equalizers (ICD or equalizers) and or Internal Control Valves (ICV).
The workflow starts with reservoir understanding and identifying the need for CW. A sector model is then extracted from the full field model to conduct detailed well level analysis. This is followed by defining well sensitivity cases, that may include a range of field development decision scenarios and a resultant optimization strategy that recommends a combined conventional and CW field optimization approach. From sensitivity cases, the best fit well(s) case scenario is identified. Thereafter, the optimized well(s) strategy is applied to the full field model and evaluated under uncertainty. Detailed analysis is conducted on both the sector and full field models including well location, orientation, placement, length, and target zones for various CW configurations.
The resultant development strategy is an optimized full field CW development decision approach including for example; improved sweep efficiency, delayed water breakthrough, improved oil recovery, reduced water handling expense, reduced produced water, extended oil plateau duration and reduced environmental impact.
Waterflood Recovery Optimization Using Intelligent Wells and Decision Analysis
Authors: Saputelli L. , Ramirez K. , Chegin J. , Cullick S. 
Published: May 2009

Abstract
The many critical decisions in a waterflood recovery process range from well number, architecture, and completion configuration to scheduling and facilities capacity planning. Project success is also affected by subsurface uncertainties, such as reservoir heterogeneity and compartmentalization, as well as surface events including equipment uptime and availability. Managing the complexities of a waterflood recovery is traditionally a sequential and intermittent process in terms of data acquisition, modeling, and workflows. However, traditional project planning, execution, and monitoring may help an operator reach production targets and budgets, but these activities do not necessarily align technical and business goals to create a comprehensive development plan that increases the probability of optimal business success.
This paper describes a process to maximize long-term economic return by optimizing key decisions, such as well number, placement, and use of intelligent wells and operating schedules, as well as evaluating surface capacity parameters, such as export pipeline diameter and pump inlet pressure. An integrated asset model (IAM) simultaneously simulates the reservoir flow, wells, and facilities, and calculates the economics associated with each potential decision scenario. An automated optimization workflow is presented as an efficient procedure to handle a large number of decisions. A well-known industry waterflood case study is discussed in the paper. A development plan that includes processes for maximizing oil recovery and economic return by implementing intelligent-well operational procedures is presented.
The results from this work for the case examples presented show that the number and location of the wells are more significant factors in the success of the field development plan than the selection of export pipeline diameter or pump inlet pressure. The optimum selection of well number, location, and producer to injector ratio could lead to an increase of 136%, when compared to the optimized primary recovery case. In the secondary recovery example, a proactive operating scheduling of intelligent well valves improved the waterflood project value by 130% with respect to the case with no intelligent completion; this was achieved by the efficient reduction in produced (~9%) and injected (~8%) water, and the increase of produced oil (~3%).
Applications of this workflow and integration by professionals from multiple surface and subsurface disciplines provide a means of minimizing the risk of investment and setting optimal surface parameters that maximize production while reducing capital and operating costs. In this way, the return on investment of the project is optimized. The decision framework presented may be applied in any type of hydrocarbon field, from early to mature development, and may be extended to other important decision variables, including the selection of the reservoir recovery process and market strategy.