bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the Influence of Adjacent Gene Orientation on the Evolution of Gene Upstream Regions inArabidopsis thaliana
Authors: He Fei , Chen Wei-Hua , Collins Sinéad , Acquisti Claudia , Goebel Ulrike , Ramos-Onsins Sebastian , Lercher Martin J , de Meaux Juliette 
Published: March 2010

AbstractThe orientation of flanking genes may influence the evolution of intergenic regions in which cis-regulatory elements are likely to be located: divergently transcribed genes share their 5′ regions, resulting either in smaller “private” spaces or in overlapping regulatory elements. Thus, upstream sequences of divergently transcribed genes (bi-directional upstream regions, or URs) may be more constrained than those of uni-directional gene pairs. We investigated this effect by analyzing nucleotide variation segregating within and between Arabidopsis species. Compared to uni-directional URs, bi-directional URs indeed display lower population mutation rate, as well as more low-frequency polymorphisms. Furthermore, we find that bi-directional regions undergo selection for the maintenance of intergenic distance. Altogether, however, we observe considerable variation in evolutionary rates, with putative signatures of selection on two uni-directional upstream regions.
Environmental Factors Influence Early Population Growth of Japanese Stiltgrass (Microstegium vimineum)
Authors: Nord Andrea N. , Mortensen David A. , Rauschert Emily S. J. 
Published: March 2010

AbstractHabitat suitability and disturbance can shape the early stages of biological invasions in important ways. Much that we know about habitat suitability and invasion originates from point-in-time studies, which characterize invasive plant abundance and associated site characteristics. In our study, we tested the influence of habitat suitability by creating small-scale invasions in a range of environments. Seeds of the invasive annual grass Japanese stiltgrass [Microstegium vimineum (Trin.) A. Camus] were planted into six environments in a deciduous forest in central Pennsylvania, and patch growth was monitored for 4 yr. Each of the 30 sites included a subplot subjected to litter disturbance at time of planting. This litter disturbance led to increased seedling recruitment only in the first 2 yr. Although patches were generally larger in wetland and roadside habitats, site influence was highly variable. Environmental variables (soil moisture, ammonium–N, pH, and plant species richness) measured in each plot were better predictors of population success than broad habitat categories. We conclude that risk assessment for species such as M. vimineum should focus not on habitat types but on areas likely to experience the physical changes that release M. vimineum populations.
Invasive Grasses Increase Nitrogen Availability in California Grassland Soils
Authors: Parker Sophie S. , Schimel Joshua P. 
Published: March 2010

AbstractAs Europeans colonized California, they introduced annual grasses from the Mediterranean Basin. These exotic annual grasses eventually invaded grasslands throughout the state, some of which were once dominated by native perennial grass species. Annual grasses differ from perennials in their phenology, longevity, rooting depth, litter chemistry, and interaction with the microbial community. As these traits may influence plant nitrogen (N) use, it is likely that the invasion by annual species resulted in changes in the availability and cycling of N in California grassland systems. We addressed the question of how invasive annual grasses influence rates of N cycling by measuring N pool sizes and rates of net and gross mineralization and nitrification, gross immobilization, and the denitrification potential of soils from experimentally planted annual and perennial-dominated grasslands. With an increase in annual grass cover, we saw increases in ammonium (NH4+) pool sizes and rates of N mineralization, nitrification, and denitrification in soils. These differences in N status suggest that N cycling in California grasslands was altered at sites where native perennial bunchgrasses were invaded by nonnative annual grasses. One consequence of annual grass invasion may be a legacy of NH4+-enriched soils that hinder the reestablishment of native perennial grass species.
Uncertainty in Assessing Value of Oncology Treatments
Authors: Mullins C. Daniel , Montgomery Russ , Tunis Sean 
Published: March 2010

Abstract
Patients, clinicians, payers, and policymakers face an environment of significant evidentiary uncertainty as they attempt to achieve maximum value, or the greatest level of benefit possible at a given level of cost in their respective health care decisions. This is particularly true in the area of oncology, for which published evidence from clinical trials is often incongruent with real-world patient care, and a substantial portion of clinical use is for off-label indications that have not been systematically evaluated. It is this uncertainty in the knowledge of the clinical harms and benefits associated with oncology treatments that prevents postregulatory decision makers from making accurate assessments of the value of these treatments. Because of the incentives inherent in the clinical research enterprise, randomized control trials (RCTs) are designed for the specific purpose of regulatory approval and maximizing market penetration. The pursuit of these goals results in RCT study designs that achieve maximal internal validity at the expense of generalizability to diverse real-world patient populations that may have significant comorbidities and other clinically mitigating factors. As such, systematic reviews for the purposes of coverage and treatment decisions often find relevant and high-quality evidence to be limited or nonexistent. For a number of reasons, including frequent off-label use of medications and the expedited approval process for cancer drugs by the U.S. Food and Drug Administration, this situation is exacerbated in the area of oncology. This paper investigates the convergence of incentives and circumstances that lead to widespread uncertainty in oncology and proposes new paradigms for clinical research, including pragmatic clinical trials, methodological guidance, and coverage with evidence development. Each of these initiatives would support the design of clinical research that is more informative for postregulatory decision makers, and would therefore reduce uncertainty and provide greater confidence in conclusions about the value of these treatments.
The Impact of Inspections on Plant-Level Air Emissions
Authors: Hanna Rema Nadeem , Oliva Paulina 
Published: March 2010

Abstract
Each year, the United States conducts approximately 20,000 inspections of manufacturing plants under the Clean Air Act. This paper compiles a panel dataset on plant-level inspections, fines, and emissions to understand whether these inspections actually reduce air emissions. We find plants reduce air emissions by fifteen percent, on average, following an inspection under the Clean Air Act. Plants that belong to industries that typically have low abatement costs respond more strongly to an inspection than those who belong to industries with high abatement costs.
Minimum Resale Price Maintenance: Some Empirical Evidence from Maryland
Authors: Bailey Elizabeth M , Leonard Gregory K 
Published: March 2010

Abstract
On October 1, 2009, the State of Maryland enacted a statute that prohibits the use of minimum resale price maintenance (RPM). This was in response to the Supreme Court's 2007 Leegin decision that held that RPM should be evaluated under the rule of reason rather than be considered per se illegal. The Maryland statute provides a natural experiment that can be used to analyze the effect of RPM on retail prices. We analyze the effect of the statute on video game prices in Maryland. Video games were used for this analysis because video game manufacturers have been known to impose RPM. Employing a difference-in-differences approach, we find no effect of the Maryland statute on video game prices.
Does slice thickness affect diagnostic performance of 64-slice CT coronary angiography in stable and unstable angina patients with a positive calcium score?
Authors: Meijs Matthijs F.L. , de Vries Jan J.J. , Rutten Annemarieke , Budde Ricardo P.J. , de Vos Alexander M , Meijboom W. Bob , Cramer Maarten J. , de Feyter Pim J. , Doevendans Pieter A. , Prokop Mathias 
Published: March 2010

Background: Coronary calcification can lead to over-estimation of the degree of coronary stenosis. Purpose: To evaluate whether thinner reconstruction thickness improves the diagnostic performance of 64-slice CT coronary angiography (CTCA) in angina patients with a positive calcium score. Material and Methods: We selected 20 scans from a clinical study comparing CTCA to conventional coronary angiography (CCA) in stable and unstable angina patients based on a low number of motion artifacts and a positive calcium score. All images were acquired at 64×0.625 mm and each CTCA scan was reconstructed at slice thickness/increment 0.67 mm/0.33 mm, 0.9 mm/0.45 mm, and 1.4 mm/0.7 mm. Two reviewers blinded for CCA results independently evaluated the scans for the presence of significant coronary artery disease (CAD) in three randomly composed series, with ≥2 weeks in between series. The diagnostic performance of CTCA was compared for the different slice thicknesses using a pooled analysis of both reviewers. Significant CAD was defined as >50% diameter narrowing on quantitative CCA. Image noise (standard deviation of CT numbers) was measured in all scans. Inter-observer variability was assessed with kappa. Results: Significant CAD was present in 8% of 304 available segments. Median total Agatston calcium score was 181.8 (interquartile range 34.9–815.6). Sensitivity at 0.67 mm, 0.9 mm, and 1.4 mm slice thickness was 70% (95% confidence interval 57–83%), 74% (62–86%), and 70% (57–83%), respectively. Specificity was 85% (82–88%), 84% (81–87%), and 84% (81–87%), respectively. The positive predictive value was 30 (21–38%), 29 (21–37%), and 28 (20–36%), respectively. The negative predictive value was 97% (95–98%), 97% (96–99%), and 97% (96–99%), respectively. Kappa for inter-observer agreement was 0.56, 0.58, and 0.59. Noise decreased from 32.9 HU at 0.67 mm, to 23.2 HU at 1.4 mm ( P<0.001). Conclusion: Diagnostic performance of CTCA in angina patients with a positive calcium score was not markedly affected by modest variations in reconstruction slice thickness.
HSP-Mediated Cytoprotection of Mesothelial Cells in Experimental Acute Peritoneal Dialysis
Authors: Bender Thorsten O. , Böhm Michael , Kratochwill Klaus , Lederhuber Hans , Endemann Michaela , Bidmon Bettina , Aufricht Christoph 
Published: March 2010

♦ Background Low biocompatibility of peritoneal dialysis solution (PDS) injures mesothelial cells but also induces heat shock proteins (HSP), the main effectors of the cellular stress response. This study investigated whether overexpression of HSP upon pharmacologic induction results in cytoprotection of mesothelial cells in experimental PD. ♦ Methods Stress response of mesothelial cells upon exposure to PDS was pharmacologically manipulated using glutamine as a co-inducer. In vitro, HSP-mediated cytoprotection was assessed by simultaneous measurements of HSP expression using Western blot analysis and viability testing using release of lactic dehydrogenase in cultured human mesothelial cells. In vivo, detachment of mesothelial cells from their peritoneal monolayer was assessed following exposure to PDS with and without the addition of glutamine in the acute rat model of PD. ♦ Results In vitro, mesothelial cell viability following exposure to PDS was significantly improved upon pharmacologic co-induction of HSP expression by glutamine (226% ± 29% vs 190% ± 19%, p = 0.001). In vivo, mesothelial cell detachment during exposure to PDS was reduced upon pharmacologic induction of HSP expression by glutamine (93 ± 39 vs 38 ± 38 cells, p = 0.044), resulting in reduced peritoneal protein loss (75 ± 7 vs 65 ± 4 mg, p = 0.045). ♦ Conclusion Our results represent the first study of pharmacologic manipulation of HSP expression for cytoprotection of mesothelial cells following acute in vitro and in vivo exposure to PDS. PDS with added glutamine might represent a promising therapeutic approach against low biocompatibility of PDS but needs validation in a chronic PD model.
Electrical resistivity tomography applied to detect contamination on a dairy farm in the Pampean region, Argentina
Authors: Sainato Claudia M. , Losinno Beatriz N. , Malleville Horacio J. 
Published: March 2010

ABSTRACTOn dairy farms, it is important to identify the degree of contamination that different management units, as localized sources, produce on soil and groundwater due to animal effluents. This information may be used to improve management practices in order to maintain not only environmental sustainability but also the standards of milk production. The aim was to test the performance of electrical resistivity tomography to detect anomalies of resistivity and to identify the relative impact, on physicochemical properties of soil and groundwater, produced by the effluents of the different management units of a dairy farm situated in the southern part of Santa Fe Province (Argentina). Twelve electrical resistivity tomography (ERT) profiles were carried out and 2D models of the resistivity distribution were interpreted together with the physicochemical analysis of soil and groundwater samples. At the plots around the milking house, resistivity decreased in the non‐saturated zone between 60–84% relative to the background values, being the maximum value for the feeding zone, the most critical management unit, in agreement with sampling results. The surroundings of the lagoon of effluents showed a decrease of resistivity around 80%, even on the phreatic aquifer, due to flooding events in the past. Electrical resistivity tomography was sensitive enough to evaluate anomalies in the distribution of electrical conductivity associated with an increase of nitrates, sulphates and bicarbonates, in addition to phosphorous in soil and chlorides in groundwater, in all cases probably connected directly or indirectly with the animal waste.
IL-17–Mediated Monocyte Migration Occurs Partially through CC Chemokine Ligand 2/Monocyte Chemoattractant Protein-1 Induction
Authors: Shahrara Shiva , Pickens Sarah R. , Mandelin Arthur M. , Karpus William J. , Huang Qiquan , Kolls Jay K. , Pope Richard M. 
Published: March 2010

Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease that is mediated, in part, by proinflammatory factors produced by RA synovial tissue (ST) fibroblasts and macrophages, resulting in monocyte migration from the blood to the ST. To characterize the potential role of IL-17 in monocyte migration, RA synovial fibroblasts and macrophages were activated with IL-17 and examined for the expression of monocyte chemokines. The two potentially important monocyte chemoattractants identified were CCL20/MIP-3α and CCL2/MCP-1, which were significantly induced in RA synovial fibroblasts and macrophages. However, in vivo, only CCL2/MCP-1 was detectable following adenovirus IL-17 injection. We found that IL-17 induction of CCL2/MCP-1 was mediated by the PI3K, ERK, and JNK pathways in RA ST fibroblasts and by the PI3K and ERK pathways in macrophages. Further, we show that neutralization of CCL2/MCP-1 significantly reduced IL-17–mediated monocyte recruitment into the peritoneal cavity. We demonstrate that local expression of IL-17 in ankle joints was associated with significantly increased monocyte migration and CCL2/MCP-1 levels. Interestingly, we show that RA synovial fluids immunoneutralized for IL-17 and CCL2/MCP-1 have similar monocyte chemotaxis activity as those immunoneutralized for each factor alone. In short, CCL2/MCP-1 produced from cell types present in the RA joint, as well as in experimental arthritis, may be responsible, in part, for IL-17–induced monocyte migration; hence, these results suggest that CCL2/MCP-1 is a downstream target of IL-17 that may be important in RA.
Cutting Edge: IFN-γ Is a Negative Regulator of IL-23 in Murine Macrophages and Experimental Colitis
Authors: Sheikh Shehzad Z. , Matsuoka Katsuyoshi , Kobayashi Taku , Li Fengling , Rubinas Tara , Plevy Scott E. 
Published: March 2010

Abstract
IL-23 regulation is a central event in the pathogenesis of the inflammatory bowel diseases. We demonstrate that IFN-γ has anti-inflammatory properties in the initiation phase of IL-23–mediated experimental colitis. IFN-γ attenuates LPS-mediated IL-23 expression in murine macrophages. Mechanistically, IFN-γ inhibits Il23a promoter activation through altering NF-κB binding and histone modification. Moreover, intestinal inflammation is inhibited by IFN-γ signaling through attenuation of Il23a gene expression. In germ-free wild-type mice colonized with enteric microbiota, inhibition of colonic Il23a temporally correlates with induction of IFN-γ. IFN-γR1/IL-10 double-deficient mice demonstrate markedly increased colonic inflammation and IL23a expression compared with those of IL-10−/− mice. Colonic CD11b+ cells are the primary source of IL-23 and a target for IFN-γ. This study describes an impor-tant anti-inflammatory role for IFN-γ through inhibition of IL-23. Converging genetic and functional findings suggest that IL-23 and IFN-γ are important pathogenic molecules in human inflammatory bowel disease.
Modulation of the African easterly jet by a mesoscale convective system
Authors: Wang Zhuo , Elsberry Russell L. 
Published: March 2010

AbstractThe modulation of the African easterly jet (AEJ) by a mesoscale convective system (MCS) is examined in a numerical simulation. An AEJ with a strong and confined core is simulated before the formation of the MCS north of the AEJ axis, and the jet is ‘split’ with two separate cores after the passage of the MCS. Our diagnosis suggests that the MCS may be triggered by a wave propagating south of the AEJ axis. A momentum budget analysis indicates that the meridional circulation associated with the MCS weakens the jet to its south and forms the secondary jet to its north. Copyright © 2010 Royal Meteorological Society
Pre‐clinical evidence of enhanced oral bioavailability of the P‐glycoprotein substrate talinolol in combination with morin
Authors: Pathak Shriram M. , Udupa N. 
Published: March 2010

AbstractMost known interactions between herbal extracts and drugs involve the inhibition of drug‐metabolizing enzymes, but little is yet known about the possible role of transporters in these interactions. In order to evaluate the effect of one of such prominent flavonoids, morin, on P‐glycoprotein related efflux carriers, measurements of transport characteristics through Ussing chambers, in situ perfusion and in vivo drug absorption studies were performed with the transported, yet not metabolized model compound talinolol.This study investigated the effects of orally administered morin (1.0, 2.5 and 5.0 mg kg−1), on the pharmacokinetics of orally (10 mg kg−1) and intravenously (1.0 mg kg−1) administered talinolol in rats. In the presence of morin, the pharmacokinetic parameters of talinolol were significantly altered in the oral group but not in the intravenous group. The presence of 2.5 and 5.0 mg kg−1 of morin significantly increased (1.8–2.0 fold, p<0.01) the area under the plasma concentration–time curve and the peak plasma concentration (2.3–3.0 fold, p<0.01) of orally administered talinolol. The absolute bioavailability (F %) of talinolol in the rats pretreated with morin was significantly higher (89.09–98.29%, p<0.01) than the control (52.14%). Talinolol demonstrated asymmetric transport across rat ileum with significantly greater basolateral‐to‐apical (B–A) permeability than that in the apical‐to‐basolateral (A–B) direction. The addition of morin resulted in a concentration dependent effect, especially on the secretory transport of talinolol.The present study demonstrates that morin bears the ability to interfere with secretory intestinal transport processes. This might be due to an interaction with P‐glycoprotein. Copyright © 2010 John Wiley & Sons, Ltd.
Derivation, implementation, and initial testing of a compressible wall‐layer model
Authors: Bond R. B. , Blottner Frederick G. 
Published: March 2010

AbstractTraditional wall functions have been used successfully for decades to decrease the computational cost for obtaining solutions to incompressible flows with equilibrium turbulence. However, these traditional, analytic wall functions are poorly suited for more complex flows. The present work describes an alternative approach named the ‘diffusion model’. The diffusion model is a subgrid model developed by Blottner and Bond that solves a system of ODEs in the near‐wall region instead of assuming an analytic profile. The diffusion model has previously been shown to reproduce profiles of various turbulence models through the log layer with fixed outer boundary conditions. This paper documents the implementation and the testing of the diffusion model fully coupled with a 3‐D Reynolds‐averaged Navier–Stokes (RANS) algorithm, using the Spalart–Allmaras model. The results indicate that the coupled algorithm is valid when the interface between diffusion model and the 3‐D RANS algorithm is below the outer edge of the log layer. Although the current work focuses on using steady 3‐D RANS outside of the log layer, modeling assumptions introduced in the current work could be used to derive a diffusion model for coupling with a large eddy simulation region. Published in 2010 by John Wiley & Sons, Ltd.
The Quaternary development of tributary channels to the Nile River at Kom Ombo area, Eastern Desert of Egypt, and their implication for groundwater resources
Authors: El Bastawesy Mohammed , Faid Abdallah , Gammal El Sayed El 
Published: March 2010

AbstractThe dry wadis ‘ephemeral channel’ constituting the main tributaries to the Nile River in Kom Ombo are structurally and tectonically controlled and exhibit complex drainage pattern. This complicated drainage pattern is inherited from the morpho‐tectonic evolution of the ancestral Nile River (‘Protonile’), which drained the Eastern Desert during the Middle Pleistocene. A digital elevation model derived from Shuttle Radar Topography Mission data is used to delineate the contemporary drainage networks and their catchments. Satellite images acquired during a flash flood event were used to validate the delineated watershed divides and flow pathways, particularly where the courses of dry wadis are interlocked. Currently, the westward flow of Wadi Abu‐Suberah is derived from a small area in the Eastern Desert, as the palaeo‐upper reaches of this wadi were captured due to tectonic movements along NW/SE and N/S faults by wadis in the Kharit and Elewa areas. The influence of these tectonic movements on groundwater distribution is also shown where the deep Nubian aquifer discharges its water into the Quaternary aquifer through fault planes. The northward flowing ‘Protonile’ main course has tectonically shifted from the Gallaba plain in the Western Desert, eastward to the current Nile River course. This shift has produced several cut‐off segments of the palaeo‐tributary drainage that was originally flowing westward towards the old ‘Protonile’ main course in the Gallaba plain. However, these segments have reversed their surface run‐off flow directions eastward towards the current Nile course; they could include potential groundwater resources, as their alluvium may be still recharged by the Nile River. Copyright © 2010 John Wiley & Sons, Ltd.