bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Hypercalciuric Stone-Forming Rats Have a Primary Decrease in BMD and Strength
Authors: Grynpas Marc , Waldman Stephen , Holmyard Douglas , Bushinsky David A 
Published: March 2009

Abstract
Kidney stone patients often have a decrease in BMD. It is unclear if reduced BMD is caused by a primary disorder of bone or dietary factors. To study the independent effects of hypercalciuria on bone, we used genetic hypercalciuric stone-forming (GHS) rats. GHS and control (Ctl) rats were fed a low Ca (0.02% Ca, LCD) or a high Ca (1.2% Ca, HCD) diet for 6 wk in metabolic cages. All comparisons are to Ctl rats. Urine Ca was greater in the GHS rats on both diets. GHS fed HCD had reduced cortical (humerus) and trabecular (L1–L5 vertebrae) BMD, whereas GHS rats fed LCD had a reduction in BMD similar to Ctl. GHS rats fed HCD had a decrease in trabecular volume and thickness, whereas LCD led to a ∼20-fold increase in both osteoid surface and volume. GHS rats fed HCD had no change in vertebral strength (failure stress), ductibility (failure strain), stiffness (modulus), or toughness, whereas in the humerus, there was reduced ductibility and toughness and an increase in modulus, indicating that the defect in mechanical properties is mainly manifested in cortical, rather than trabecular, bone. GHS rat cortical bone is more mineralized than trabecular bone and LCD led to a decrease in the mineralization profile. Thus, the GHS rats, fed an ample Ca diet, have reduced BMD with reduced trabecular volume, mineralized volume, and thickness, and their bones are more brittle and fracture prone, indicating that GHS rats have an intrinsic disorder of bone that is not secondary to diet.
Contribution of the Vertebral Posterior Elements in Anterior–Posterior DXA Spine Scans in Young Subjects
Authors: Lee David C , Campbell Patricia P , Gilsanz Vicente , Wren Tishya AL 
Published: March 2009

Abstract
Because DXA is a projection technique, anterior–posterior (AP) measurements of the spine include the posterior elements and the vertebral body. This may be a disadvantage because the posterior elements likely contribute little to vertebral fracture resistance. This study used QCT to quantify the impact of the posterior elements in DXA AP spine measures. We examined 574 subjects (294 females and 280 males), age 6–25 yr, with DXA and QCT. QCT measures were calculated for the cancellous bone region and for the vertebral body including and excluding the posterior elements. DXA data were analyzed for the entire L3 vertebra and for a 10-mm slice corresponding to the QCT scan region. BMC and BMD were determined and compared using Pearson's correlation. The posterior elements accounted for 51.4 ± 4.2% of the total BMC, with a significant difference between males (49.9 ± 4.0%) and females (52.8 ± 3.9%, p &lt; 0.001). This percentage increased with age in younger subjects of both sexes (p &lt; 0.001) but was relatively consistent after age 17 for males and 16 for females (p &gt; 0.10). DXA areal BMD and QCT volumetric BMD correlated strongly for the whole vertebra including the posterior elements (R = 0.83), with BMC measures showing a stronger relationship (R = 0.93). Relationships were weaker when excluding the posterior elements. We conclude that DXA BMC provides a measure of bone that is most consistent with QCT and that the contribution of the posterior elements is consistent in young subjects after sexual maturity.
Serum IGF-1 Determines Skeletal Strength by Regulating Subperiosteal Expansion and Trait Interactions
Authors: Yakar Shoshana , Canalis Ernesto , Sun Hui , Mejia Wilson , Kawashima Yuki , Nasser Philip , Courtland Hayden-William , Williams Valerie , Bouxsein Mary , Rosen Clifford , Jepsen Karl J 
Published: March 2009

Abstract
Strong correlations between serum IGF-1 levels and fracture risk indicate that IGF-1 plays a critical role in regulating bone strength. However, the mechanism by which serum IGF-1 regulates bone structure and fracture resistance remains obscure and cannot be determined using conventional approaches. Previous analysis of adult liver-specific IGF-1–deficient (LID) mice, which exhibit 75% reductions in serum IGF-1 levels, showed reductions in periosteal circumference, femoral cross-sectional area, cortical thickness, and total volumetric BMD. Understanding the developmental sequences and the resultant anatomical changes that led to this adult phenotype is the key for understanding the complex relationship between serum IGF-1 levels and fracture risk. Here, we identified a unique developmental pattern of morphological and compositional traits that contribute to bone strength. We show that reduced bone strength associated with low levels of IGF-1 in serum (LID mice) result in impaired subperiosteal expansion combined with impaired endosteal apposition and lack of compensatory changes in mineralization throughout growth and aging. We show that serum IGF-1 affects cellular activity differently depending on the cortical surface. Last, we show that chronic reductions in serum IGF-1 indirectly affect bone strength through its effect on the marrow myeloid progenitor cell population. We conclude that serum IGF-1 not only regulates bone size, shape, and composition during ontogeny, but it plays a more fundamental role—that of regulating an individual's ability to adapt its bone structure to mechanical loads during growth and development.
Substrate Durability Guidelines Used in Silicone Structural Attachment
Authors: Carbary Lawrence D. 
Published: March 2009

AbstractThis paper sets forth a procedure for evaluating substrates for durability for use in conjunction with structural silicone glazing (SSG). Lap shear and peel adhesion specimens are evaluated after exposures to various conditions using a modified ASTM C794-06, “Standard Test Method for Adhesion-In-Peel of Elastomeric Joint Sealants,” and ASTM C961-06, “Standard Test Method for Lap Shear Strength of Sealants.” Conditions of exposure include water, sodium hypochlorite (bleach), acetic acid (vinegar), salt fog, UV florescent accelerated weathering device (UVFl), ultraviolet light (UV) exposure, and heat. Evaluation of substrates and the interfaces are completed after tensile testing and visual surface analysis. The silicone structural glazing adhesive used in this evaluation is a high modulus high strength material intended to place the maximum load at the interface. Substrates evaluated include steel, anodized aluminum, galvanized steel, extruded rigid polyvinyl chloride (PVC), glass reinforced thermoplastic resin (fiberglass), and polyvinylidene fluoride (PVDF) painted aluminum. These evaluated substrates are tested to this procedure to show differences in performance and suggest a minimum time frame required for testing. The results and guidelines set forth in this paper provide the foundation for a practice and or a substrate specification for use in conjunction with structural silicone attachment methods.
Methods for Human Demographic Inference Using Haplotype Patterns From Genomewide Single-Nucleotide Polymorphism Data
Authors: Lohmueller Kirk E , Bustamante Carlos D , Clark Andrew G 
Published: March 2009

AbstractWe propose a novel approximate-likelihood method to fit demographic models to human genomewide single-nucleotide polymorphism (SNP) data. We divide the genome into windows of constant genetic map width and then tabulate the number of distinct haplotypes and the frequency of the most common haplotype for each window. We summarize the data by the genomewide joint distribution of these two statistics—termed the HCN statistic. Coalescent simulations are used to generate the expected HCN statistic for different demographic parameters. The HCN statistic provides additional information for disentangling complex demography beyond statistics based on single-SNP frequencies. Application of our method to simulated data shows it can reliably infer parameters from growth and bottleneck models, even in the presence of recombination hotspots when properly modeled. We also examined how practical problems with genomewide data sets, such as errors in the genetic map, haplotype phase uncertainty, and SNP ascertainment bias, affect our method. Several modifications of our method served to make it robust to these problems. We have applied our method to data collected by Perlegen Sciences and find evidence for a severe population size reduction in northwestern Europe starting 32,500–47,500 years ago.
The Genetic Basis of Phenotypic Adaptation I: Fixation of Beneficial Mutations in the Moving Optimum Model
Authors: Kopp Michael , Hermisson Joachim 
Published: March 2009

Abstract
We study the genetic basis of adaptation in a moving optimum model, in which the optimal value for a quantitative trait increases over time at a constant rate. We first analyze a one-locus two-allele model with recurrent mutation, for which we derive accurate analytical approximations for (i) the time at which a previously deleterious allele becomes beneficial, (ii) the waiting time for a successful new mutation, and (iii) the time the mutant allele needs to reach fixation. On the basis of these results, we show that the shortest total time to fixation is for alleles with intermediate phenotypic effect. We derive an approximation for this “optimal” effect, and we show that it depends in a simple way on a composite parameter, which integrates the ecological parameters and the genetic architecture of the trait. In a second step, we use stochastic computer simulations of a multilocus model to study the order in which mutant alleles with different effects go to fixation. In agreement with the one-locus results, alleles with intermediate effect tend to become fixed earlier than those with either small or large effects. However, the effect size of the fastest mutations differs from the one predicted in the one-locus model. We show how these differences can be explained by two specific effects of multilocus genetics. Finally, we discuss our results in the light of three relevant timescales acting in the system—the environmental, mutation, and fixation timescales—which define three parameter regimes leading to qualitative differences in the adaptive substitution pattern.
Characterization of a Novel Thermosensitive Restorer of Fertility for Cytoplasmic Male Sterility in Maize
Authors: Gabay-Laughnan Susan , Kuzmin Evgeny V , Monroe Jessica , Roark Leah , Newton Kathleen J 
Published: March 2009

AbstractS-type cytoplasmic male sterility (CMS-S) in maize is associated with high levels of a 1.6-kb RNA in mitochondria. This RNA contains two chimeric open reading frames (ORFs), orf355 and orf77. The previously described nuclear restorer-of-fertility allele Rf3 causes the processing of all transcripts that contain these chimeric ORFs. The Lancaster Surecrop-derived inbred line A619 carries a restorer that is distinct from Rf3 in that it selectively reduces only the CMS-S-specific 1.6-kb RNA. We have found that 10 additional Lancaster lines carry a single restoring allele traceable to either of two inbred lines, C103 and Oh40B. The C103 and Oh40B restorers are allelic to each other, but not to Rf3. Thus, this restoring allele, designated Rf9, represents a second naturally occurring CMS-S restorer in maize. Rf9 is a less effective restorer of fertility than is Rf3; its expression is influenced by both inbred nuclear background and temperature. Rf9 acts to reduce the amounts of orf355/orf77-containing linear mitochondrial subgenomes, which are generated by recombination of circular subgenomes with CMS-S-specific linear plasmids. The 1.6-kb RNA, which is transcribed only from linear ends, is correspondingly reduced.
Excision ofHelitronTransposons in Maize
Authors: Li Yubin , Dooner Hugo K 
Published: March 2009

AbstractHelitrons are novel transposons discovered by bioinformatic analysis of eukaryotic genome sequences. They are believed to move by rolling circle (RC) replication because their predicted transposases are homologous to those of bacterial RC transposons. We report here evidence of somatic Helitron excision in maize, an unexpected finding suggesting that Helitrons can exhibit an excisive mode of transposition.
Institution of Basal-Bolus Therapy at Diagnosis for Children With Type 1 Diabetes Mellitus
Authors: Adhikari Soumya , Adams-Huet Beverley , Wang Yu-Chi A. , Marks James F. , White Perrin C. 
Published: March 2009

OBJECTIVE. We studied whether the institution of basal-bolus therapy immediately after diagnosis improved glycemic control in the first year after diagnosis for children with newly diagnosed type 1 diabetes mellitus.
METHODS. We reviewed the charts of 459 children ≥6 years of age who were diagnosed as having type 1 diabetes between July 1, 2002, and June 30, 2006 (212 treated with basal-bolus therapy and 247 treated with a more-conventional neutral protamine Hagedorn regimen). We abstracted data obtained at diagnosis and at quarterly clinic visits and compared groups by using repeated-measures, mixed-linear model analysis. We also reviewed the records of 198 children with preexisting type 1 diabetes mellitus of &gt;1-year duration who changed from the neutral protamine Hagedorn regimen to a basal-bolus regimen during the review period.
RESULTS. Glargine-treated subjects with newly diagnosed diabetes had lower hemoglobin A1c levels at 3, 6, 9, and 12 months after diagnosis than did neutral protamine Hagedorn-treated subjects (average hemoglobin A1c levels of 7.05% with glargine and 7.63% with neutral protamine Hagedorn, estimated across months 3, 6, 9, and 12, according to repeated-measures models adjusted for age at diagnosis and baseline hemoglobin A1c levels; treatment difference: 0.58%). Children with long-standing diabetes had no clinically important changes in their hemoglobin A1c levels in the first year after changing regimens.
CONCLUSION. The institution of basal-bolus therapy with insulin glargine at the time of diagnosis of type 1 diabetes was associated with improved glycemic control, in comparison with more-conventional neutral protamine Hagedorn regimens, during the first year after diagnosis.
The Use of Fractional-Flow Theory for Foam Displacement in Presence of Oil
Authors: Mayberry D. J. , Afsharpoor A. , Kam S. I. 
Published: March 2009

Summary
Foam has been extensively used in improved and enhanced oil recovery processes in the petroleum industry over decades. Foam is capable of reducing gas mobility dramatically in porous media, and thus helps keep displacement fronts stable by controlling the mobility ratio between injected gas and reservoir fluids. In this study, models were constructed to investigate the mechanisms of foam displacement in porous media using three-phase fractional-flow theory and ternary diagrams. The strength of foam in the presence of oil was accounted for by using a mobility reduction factor (MRF) for the gas phase that can be routinely measured in laboratory coreflood experiments. The use of MRF is a typical way of describing foam rheology in local steady-state modeling.
Results were analyzed in terms of saturation paths in the ternary diagrams, saturation velocities, sweep efficiency and effluent history. Two different initial conditions were selected to demonstrate the importance of initial saturation on the displacement: one with oil phase dominant ((Sw, So) = (0.2, 0.8)) and the other with water phase dominant ((Sw, So) = (0.8, 0.2)). At low MRF (i.e., no foam or weak foam), the efficiency of foam displacement was primarily governed by fast-moving spreading waves that rapidly broke through the porous medium resulting in poor sweep efficiency. An increase in MRF (i.e., stronger foam) altered the nature of the displacement front by making it more piston-like through the development of "shock" fronts and improved sweep efficiency significantly. Once shock fronts dominated the displacement, the importance of initial saturation on the mechanisms of displacement became less pronounced. Calculations also demonstrated that a decrease in oil viscosity made the oil phase more mobile and the formation of shock fronts more prolific, significantly enhancing sweep efficiency.
The results in this study imply that if basic fluid properties, injection and initial saturation conditions, and MRF are known, one can reliably predict the mechanisms of foam displacement in porous media even in the presence of oil. The solutions obtained from the three-phase fractional-flow analysis were in good agreement with simulation results in a wide range of MRF values and initial core conditions.
Fracture-Face-Skin Evolution During Cleanup
Authors: Gdanski Rick , Fulton Dwight , Shen Chun 
Published: March 2009

Summary
There remains considerable debate about the impact of fracture-face-matrix damage on cleanup and productivity of gas wells. The impact of the Cinco-Ley fracture-face-skin factor has been studied extensively, normally with single-phase-flow examples. Two-phase-flow examples are usually limited to the impact on long-term production. This paper uses a new two-phase-flow simulator to demonstrate the impact of fracture-face-matrix damage on both fracture-treatment cleanup and fracture-face-skin evolution during cleanup and subsequent production. The simulator was validated by comparison of calculated skins with pressure-buildup simulations evaluated by use of a high-end, third-party, pressure-transient-analysis package.
The study has demonstrated that fracture-face skin relative to gas flow can be calculated continually throughout a simulation of fracture-treatment cleanup and production. It was found that at lower matrix permeabilities and subsequent higher capillary pressure curves, the impact of water saturation in the damage zone becomes much more important. Specifically, the effective fracture-face skin relative to gas can be several times higher than expected on the basis of single-phase flow. Furthermore, the simulation results show that at lower matrix permeabilities, the time required to achieve a reasonable fracture-face skin relative to gas flow can require considerable production time, on the order of several weeks, even for moderate damage factors. The results demonstrate that in tight gas reservoirs (≈0.01 md and less), even a moderate amount of matrix damage in a fracture face can result in high fracture-face skins and exceedingly long times for treatment cleanup. As such, it becomes very important to minimize fracture-face-matrix damage during tight gas fracturing treatments.
Identifying the Potential Upside of Hydrocarbon Saturation From Electric Logs
Authors: Worthington Paul F. 
Published: March 2009

Summary
Validated electrical type curves, which collectively describe a continuum of conductivity behavior of fluid-saturated rocks, allow the petrophysical evaluation of hydrocarbon saturation to be set within a generic reference framework. As part of this process, the type curves permit pre-existing data from other reservoirs to be examined as potential analogs. Through the type curves, a reservoir rock can be classified in terms of its electrical character, specifically adherence to, or departures from, classical clean-sand (Archie) conditions and, by corollary, the degree of any shale (non-Archie) effects. The classification guides the approach to future core-data acquisition and to well-log analysis. In particular, in non-Archie reservoirs the type curves indicate whether the formation-water salinity is sufficiently high for the application of shaly-sand equations for the evaluation of hydrocarbon saturation or whether recourse should be made to a (customized) pseudo-Archie approach. Thus, the type curves are used to ensure that interpretative algorithms are appropriate to the petrophysical task at hand.
The application of the type curves, using initializing log data from seven shaly hydrocarbon reservoirs containing relatively fresh formation waters, has illustrated how petrophysical interpretations away from the key intervals can be screened with minimal supporting information through a pseudo-Archie approach. Comparisons of best estimates of hydrocarbon-filled porosity with previously reported values have indicated a potential volumetric upside in all cases, with hydrocarbon saturations being up to 30 saturation units higher for these complex reservoirs. This outcome is attributed to the generic nature of the screening process, which takes account of the electrical character of a reservoir without any of the procedural constraints that are associated with conventional well-log analysis. To reduce further the risk of underestimating hydrocarbon volumes, a set of equivalence charts has been constructed using basic petro-physical properties. The equivalence charts allow a quick-look recognition of any departures from Archie conditions and thence whether the type curves are likely to be required.
The screening process has been synthesized into pragmatic workflows, whose adoption should impart additional quality assurance to the petrophysical evaluation of hydrocarbon volumes.
Efficient Field-Scale Simulation of Black Oil in a Naturally Fractured Reservoir Through Discrete Fracture Networks and Homogenized Media
Authors: Li Liyong , Lee Seong H. 
Published: March 2009

SummaryThis paper describes a hybrid finite volume method, designed to simulate multiphase flow in a field-scale naturally fractured reservoir. Lee et al. (WRR 37:443-455, 2001) developed a hierarchical approach in which the permeability contribution from short fractures is derived in an analytical expression that from medium fractures is numerically solved using a boundary element method. The long fractures are modeled explicitly as major fluid conduits. Reservoirs with well-developed natural fractures include many complex fracture networks that cannot be easily modeled by simple long fracture formulation and/or homogenized single continuity model. We thus propose a numerically efficient hybrid method in which small and medium fractures are modeled by effective permeability, and large fractures are modeled by discrete fracture networks. A simple, systematic way is devised to calculate transport parameters between fracture networks and discretized, homogenized media. An efficient numerical algorithm is also devised to solve the dual system of fracture network and finite volume grid. Black oil formulation is implemented in the simulator to demonstrate practical applications of this hybrid finite volume method.
A Novel Stimulation Technique for Horizontal Openhole Wells in Carbonate Reservoirs—A Case Study in Kuwait
Authors: Liu Hai , Coston Chad , Yassin Mohamed , Uddin Shahab , Dhafeeri Fahad Al 
Published: March 2009

Summary
Effective matrix acidizing in Kuwait's horizontal openhole wells is a big challenge. Reservoir heterogeneity and the length of the horizontal wells make acid placement and diversion difficult, particularly in high-water-cut (WC) wells in which water has broken through as a result of high-permeability streaks or natural fractures. Furthermore, acid penetration is limited by the large surface area of the horizontal wellbore, and this is exacerbated by the relatively small injection rate imposed by the use of coiled tubing (CT). To make matters worse, formation damage in horizontal wells is usually very deep as a result of long exposure times.
This paper discusses the application of a new viscoelastic-surfactant (VES)-based, self-diverting acid system for stimulation of more than 20 horizontal openhole wells in carbonate reservoirs in Kuwait. The application also deployed a new nonparticulate material that forms a highly viscous plug when it contacts water and that degrades when mixed with oil in the formation. The new fluid system is pumped before the acid treatment to effectively prevent the acid from stimulating high-water-saturation sections.
The field results show significant improvement in post-stimulation production, owing to effective diversion and water-production control compared with wells in which a conventional polymer-diversion technique was used in the past with no consideration for water-production control in high-WC cases. The new technique has been selected as the standard stimulation practice in most horizontal openhole carbonate wells in Kuwait.