bluuebunny/crossref_metadata_2025_split huggingface dataset:
Residual platelet factor V ensures thrombin generation in patients with severe congenital factor V deficiency and mild bleeding symptoms
Authors: Duckers Connie , Simioni Paolo , Spiezia Luca , Radu Claudia , Dabrilli Paolo , Gavasso Sabrina , Rosing Jan , Castoldi Elisabetta 
Published: October 2009

AbstractCoagulation factor V (FV), present in plasma and platelets, is indispensable to thrombin formation, yet patients with undetectable plasma FV seldom experience major bleeding. We used thrombin generation assays to explore the role of platelet FV in 4 patients with severe congenital FV deficiency (3 with plasma FV clotting activity [FV:C] < 1%). When triggered with tissue factor (TF) concentrations up to 50pM, platelet-poor plasma (PPP) from the patients with undetectable plasma FV showed no thrombin generation, whereas platelet-rich plasma (PRP) formed thrombin already at 1 to 5pM of TF. Thrombin generation in PRP from the FV-deficient patients was enhanced to near-normal levels by platelet activators (collagen or Ca2+-ionophore) and could be completely suppressed by specific FV inhibitors, suggesting FV dependence. Accordingly, platelet FV antigen and activity were measurable in all FV-deficient patients and platelet FVa could be visualized by Western blotting. Normalization of the tissue factor pathway inhibitor (TFPI) level, which is physiologically low in FV-deficient plasma, almost completely abolished thrombin generation in PRP from the FV-deficient patients. In conclusion, patients with undetectable plasma FV may contain functional FV in their platelets. In combination with low TFPI level, residual platelet FV allows sufficient thrombin generation to rescue these patients from fatal bleeding.
High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity
Authors: Zhou Weiyin , Calciano Margaret A , Jordan Heather , Brenner Michael , Johnson Seth , Wu Darong , Lei Lin , Pallares Diego , Beurdeley Pascale , Rouet Fabien , Gill Pritmohinder S , Bracco Laurent , Soucaille Cyril , Einstein Richard 
Published: October 2009

Abstract

Background
Commercially available microarrays have been used in many settings to generate expression profiles for a variety of applications, including target selection for disease detection, classification, profiling for pharmacogenomic response to therapeutics, and potential disease staging. However, many commercially available microarray platforms fail to capture transcript diversity produced by alternative splicing, a major mechanism for driving proteomic diversity through transcript heterogeneity.

Results
The human Genome-Wide SpliceArray™ (GWSA), a novel microarray platform, utilizes an existing probe design concept to monitor such transcript diversity on a genome scale. The human GWSA allows the detection of alternatively spliced events within the human genome through the use of exon body and exon junction probes to provide a direct measure of each transcript, through simple calculations derived from expression data. This report focuses on the performance and validation of the array when measured against standards recently published by the Microarray Quality Control (MAQC) Project. The array was shown to be highly quantitative, and displayed greater than 85% correlation with the HG-U133 Plus 2.0 array at the gene level while providing more extensive coverage of each gene. Almost 60% of splice events among genes demonstrating differential expression of greater than 3 fold also contained extensive splicing alterations. Importantly, almost 10% of splice events within the gene set displaying constant overall expression values had evidence of transcript diversity. Two examples illustrate the types of events identified: LIM domain 7 showed no differential expression at the gene level, but demonstrated deregulation of an exon skip event, while erythrocyte membrane protein band 4.1 -like 3 was differentially expressed and also displayed deregulation of a skipped exon isoform.

Conclusion
Significant changes were detected independent of transcriptional activity, indicating that the controls for transcript generation and transcription are distinct, and require novel tools in order to detect changes in specific transcript quantity. Our results demonstrate that the SpliceArray™ design will provide researchers with a robust platform to detect and quantify specific changes not only in overall gene expression, but also at the individual transcript level.
Comparative study of enteric viruses, coliphages and indicator bacteria for evaluating water quality in a tropical high-altitude system
Authors: Espinosa Ana C , Arias Carlos F , Sánchez-Colón Salvador , Mazari-Hiriart Marisa 
Published: October 2009

AbstractBackgroundBacteria used as indicators for pathogenic microorganisms in water are not considered adequate as enteric virus indicators. Surface water from a tropical high-altitude system located in Mexico City that receives rainwater, treated and non-treated wastewater used for irrigation, and groundwater used for drinking, was studied.MethodsThe presence of enterovirus, rotavirus, astrovirus, coliphage, coliform bacteria, and enterococci was determined during annual cycles in 2001 and 2002. Enteric viruses in concentrated water samples were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). Coliphages were detected using the double agar layer method. Bacteria analyses of the water samples were carried out by membrane filtration.ResultsThe presence of viruses and bacteria in the water used for irrigation showed no relationship between current bacterial indicator detection and viral presence. Coliphages showed strong association with indicator bacteria and enterovirus, but weak association with other enteric viruses. Enterovirus and rotavirus showed significant seasonal differences in water used for irrigation, although this was not clear for astrovirus.ConclusionColiphages proved to be adequate faecal pollution indicators for the irrigation water studied. Viral presence in this tropical high-altitude system showed a similar trend to data previously reported for temperate zones.
Developing capacity in health informatics in a resource poor setting: lessons from Peru
Authors: Kimball Ann Marie , Curioso Walter H , Arima Yuzo , Fuller Sherrilynne , Garcia Patricia J , Segovia-Juarez Jose , Castagnetto Jesus M , Leon-Velarde Fabiola , Holmes King K 
Published: October 2009

Abstract
The public sectors of developing countries require strengthened capacity in health informatics. In Peru, where formal university graduate degrees in biomedical and health informatics were lacking until recently, the AMAUTA Global Informatics Research and Training Program has provided research and training for health professionals in the region since 1999. The Fogarty International Center supports the program as a collaborative partnership between Universidad Peruana Cayetano Heredia in Peru and the University of Washington in the United States of America. The program aims to train core professionals in health informatics and to strengthen the health information resource capabilities and accessibility in Peru. The program has achieved considerable success in the development and institutionalization of informatics research and training programs in Peru. Projects supported by this program are leading to the development of sustainable training opportunities for informatics and eight of ten Peruvian fellows trained at the University of Washington are now developing informatics programs and an information infrastructure in Peru. In 2007, Universidad Peruana Cayetano Heredia started offering the first graduate diploma program in biomedical informatics in Peru.
Genetic and pharmacological inhibition of calcineurin corrects the BDNF transport defect in Huntington's disease
Authors: Pineda Jose R , Pardo Raúl , Zala Diana , Yu Hua , Humbert Sandrine , Saudou Frédéric 
Published: October 2009

AbstractBackgroundHuntington's disease (HD) is an inherited neurogenerative disease caused by an abnormal expansion of glutamine repeats in the huntingtin protein. There is currently no treatment to prevent the neurodegeneration caused by this devastating disorder. Huntingtin has been shown to be a positive regulator of vesicular transport, particularly for neurotrophins such as brain-derived neurotrophic factor (BDNF). This function is lost in patients with HD, resulting in a decrease in neurotrophic support and subsequent neuronal death. One promising line of treatment is therefore the restoration of huntingtin function in BDNF transport.ResultsThe phosphorylation of huntingtin at serine 421 (S421) restores its function in axonal transport. We therefore investigated whether inhibition of calcineurin, thebona fidehuntingtin S421 phosphatase, restored the transport defects observed in HD. We found that pharmacological inhibition of calcineurin by FK506 led to sustained phosphorylation of mutant huntingtin at S421. FK506 restored BDNF transport in two complementary models: rat primary neuronal cultures expressing mutant huntingtin and mouse cortical neurons fromHdhQ111/Q111HD knock-in mice. This effect was the result of specific calcineurin inhibition, as calcineurin silencing restored both anterograde and retrograde transport in neurons fromHdhQ111/Q111mice. We also observed a specific increase in calcineurin activity in the brain ofHdhQ111/Q111mice potentially accounting for the selective loss of huntingtin phosphorylation and contributing to neuronal cell death in HD.ConclusionOur results validate calcineurin as a target for the treatment of HD and provide the first demonstration of the restoration of huntingtin function by an FDA-approved compound.
Glucose Promotes the Production of Interleukine-1β and Cyclooxygenase-2 in Mesangial Cells via Enhanced (Pro)Renin Receptor Expression
Authors: Huang Jiqian , Siragy Helmy M. 
Published: October 2009

Abstract(Pro)renin receptor (PRR) is present in renal glomeruli, and its expression is up-regulated in diabetes. Similarly, renal inflammation is increased in the presence of hyperglycemia. The linkage between PRR and renal inflammation is not well established. We hypothesized that glucose-induced up-regulation of PRR leads to increased production of the proinflammatory factors IL-1β and cyclooxygenase-2 (COX-2). Studies were conducted in rat mesangial cells (RMCs) exposed to 30 mmd-glucose for 2 wk followed by PRR small interfering RNA knockdown, IL-1 receptor blockade with IL-1 receptor antagonist or angiotensin II type 1 receptor blockade with valsartan. The results showed that d-glucose treatment up-regulates prorenin, renin, angiotensin II, PRR, IL-1β, and COX-2 mRNA and protein expression and increases phosphorylation of ERK1/2, c-Jun N-terminal kinase, c-Jun, and nuclear factor-κB (NF-κB) p65 (serine 276,468 and 536), respectively. PRR small interfering RNA attenuated PRR, IL-1β, and COX-2 mRNA and protein expressions and significantly decreased angiotensin II production and phosphorylation of ERK1/2 and NF-κB p65 associated with high glucose exposure. Similarly, IL-1 receptor antagonist significantly reduced COX-2 mRNA and protein expression induced by high glucose. COX-2 inhibition reduced high-glucose-induced PRR expression. We conclude that glucose induces the up-regulation of PRR and its ligands prorenin and renin, leading to increased IL-1β and COX-2 production via the angiotensin II-dependent pathway. It is also possible that PRR could enhance the production of these inflammatory cytokines through direct stimulation of ERK1/2-NF-κB signaling cascade.
The sense of the interface: Applying semiotics to HCI research
Authors: Scolari Carlos 
Published: October 2009

Abstract
The objective of this article is to reflect on the application of Semiotics to Human-Computer Interaction (HCI) and interface analysis. To accomplish the objective the article presents an example of semiotic analysis of a blog interface but the methodology proposed, conveniently adapted, may be applied to any kind of digital interactive environment. The analysis reconstructs the interface sense production device (including the surface of the page and the link architecture), identifies implied users and exchange scenes of the blog and concludes with some reflections on interface evolution and hybridation. Finally, the article proposes future trends for a Semiotics of HCI.
Geoengineering and Economic Assessment of a Potential Carbon Capture and Storage Site in Southeast Queensland, Australia
Authors: Cinar Y. , Neal P. R. , Allinson W. G. , Sayers J. 
Published: October 2009

Summary
This paper presents geoengineering and economic sensitivity analyses and assessments of the Wunger Ridge flank carbon capture and storage (CCS) site. Both geoengineering and economics are needed to derive the number of wells required to inject a certain amount of CO2 for a given period.
A numerical reservoir simulation examines injection rates ranging from 0.5 to 1.5 million tonnes of CO2 year for 25 years of injection. Primary factors affecting the ability to inject CO2 include permeability, formation fracture gradient, aquifer strength, and multiphase flow functions. Secondary factors include the solubility of CO2 in the formation brine, injection well location with respect to the flow barriers/low-permeability aquifers, model geometry including faults, grid size and refinement, and injection well type. Less significant factors include hydrodynamic effects.
The economics are assessed using an internally developed tech-noeconomic model. The model optimizes the CO2 injection cost on the basis of geoengineering data and recent equipment costs. The overall costs depend on the initial costs of CO2 separation and source-to-sink distances and their associated pipeline costs. Secondary cost variations are highly dependent on fracture gradient, permeability, and CO2 injection rates. Depending on the injection characteristics, the specific cost of CO2 avoided is between AUS 62 and 80 per tonne.
A New Method for Vertical Leak Detection in Low to Moderate Permeability Flooded Reservoirs
Authors: Walser D. W. , Astakhov D. K. , Stanley G. R. 
Published: October 2009

Summary
Rising commodity prices have resulted in an increase in secondary recovery projects that are associated with lower permeability reservoirs. These processes often inject fluids above the parting pressure for the duration of the life of the flood, and pressurization takes place as fluids leak off from the exposed surface area of the induced fracture into the surrounding moderate or low-permeability reservoir matrix. The primary difference between these situations and conventional flooding is that matrix fluid migration is initiating off an induced fracturing plane, as opposed to point-source initiation.
During the early history of a flood, mass-balance issues are often ignored, as average reservoir pressures are typically low, and injection rates can dramatically exceed production. As pressures rise, some localized portions of the reservoir not only can exceed virgin static pressures, but volumes near existing induced fractures can approach or equal the pressure in those fractures. When this occurs, vertical fracturing initiates within the reservoir, and can migrate either above or below the reservoir, depending upon the location of the closest lower stress interval.
A new method to detect the location of vertical "leakage" has been developed. This method uses existing surface tiltmeter (STM) technologies and a new surface deformation calculation regime to zero in on volumetric changes that occur above or below the limits of the given reservoir. This method uses measured surface deformation from observed tilt to extrapolate the volumetric change at different specified depths. With a number of constraints and using a linear geophysical model based on poroelastic equations, an inversion routine is used to find the reservoir compaction or expansion at different depths. When volumetric change best fits the measured deformation data (or tilt) at the surface, the depth and aerial location is then correlated to the area near a specific well or wells.
Line-Tension-Based Modification of Young's Equation for Rock/Oil/Brine Systems
Authors: Saini Dayanand , Rao Dandina N. 
Published: October 2009

Summary
The two-century-old Young's equation has been widely used in petroleum engineering to depict the reservoir wettability in terms of contact angle, which is a function of surface free energies of the system. For solid/liquid/vapor (S/L/V) systems, Young's equation has been modified in the recent literature to include a line-tension term. This modification was sought to accommodate the imbalance of intermolecular forces experienced by the three-phase confluence zone. Also, Young's equation does not account for the vertical component of liquid/vapor surface tension. The present study aims to experimentally investigate the applicability of the line-tension-based modification of Young's equation to solid/liquid/liquid (rock/ oil/brine) (S/L/L) systems of interest to the petroleum industry.
Both the ambient- and reservoir-condition optical cells were used, with stock-tank and live oil, respectively, to determine the drop-size dependence of dynamic contact angle subtended by the oil/brine interface with the rock surface. The experimental data were correlated with the modified Young's equation to determine the magnitude of line tension for different rock/oil/brine systems. To the best of our knowledge, this is the first attempt to apply the modified Young's equation to rock/oil/brine systems and to measure line tension for a rock/live-crude-oil/brine system at reservoir conditions of pressure and temperature.
The measured line tension for S/L/L systems, while being positive and of the same order of magnitude as in S/L/V systems, correlates well with the water-advancing contact angle and the adhesion number, a ratio of adhesion force to capillary force. This experimental study indicates that the extent of deviation from Young's equation exhibited by rock/oil/brine systems may be directly related to the rock/oil adhesion interaction. This study reinforces the need to include the rock/oil adhesion force in our consideration of rock/fluid interactions, wettability, and their impact on enhanced-oil-recovery (EOR)/improved-oil-recovery (IOR) processes.
Injectivity Characteristics of EOR Polymers
Authors: Seright R. S. , Seheult Mac , Talashek Todd 
Published: October 2009

Summary
For applications in which enhanced-oil-recovery (EOR) polymer solutions are injected, we estimate injectivity losses (relative to water injectivity) if fractures are not open. We also consider the degree of fracture extension that may occur if fractures are open. Three principal EOR polymer properties are examined that affect injectivity: (1) debris in the polymer, (2) polymer rheology in porous media, and (3) polymer mechanical degradation. An improved test was developed to measure the tendency of EOR polymers to plug porous media. The new test demonstrated that plugging tendencies varied considerably among both partially hydrolyzed polyacrylamide (HPAM) and xanthan polymers.
Rheology and mechanical degradation in porous media were quantified for a xanthan and an HPAM polymer. Consistent with previous work, we confirmed that xanthan solutions show pseudoplastic behavior in porous rock that closely parallels that in a viscometer. Xanthan was remarkably resistant to mechanical degradation, with a 0.1% xanthan solution (in seawater) experiencing only a 19% viscosity loss after flow through 102-md Berea sandstone at a pressure gradient of 24,600 psi/ft.
For 0.1% HPAM in both 0.3% NaCl brine and seawater in 573-md Berea sandstone, Newtonian behavior was observed at low to moderate fluid fluxes, while pseudodilatant behavior was seen at moderate to high fluxes. No evidence of pseudoplastic behavior was seen in the porous rock, even though one solution exhibited a power-law index of 0.64 in a viscometer. For this HPAM in both brines, the onset of mechanical degradation occurred at a flux of 14 ft/d in 573-md Berea.
Considering the polymer solutions investigated, satisfactory injection of more than 0.1 pore volume (PV) in field applications could only be expected for the cleanest polymers (i.e., that do not plug before 1,000 cm3/cm2 throughput), without inducing fractures (or formation parts for unconsolidated sands). Even in the absence of face plugging, the viscous nature of the solutions investigated requires that injectivity must be less than one-fifth that of water if formation parting is to be avoided (unless the injectant reduces the residual oil saturation and substantially increases the relative permeability to water). Since injectivity reductions of this magnitude are often economically unacceptable, fractures or fracture-like features are expected to open and extend significantly during the course of most polymer floods. Thus, an understanding of the orientation and growth of fractures may be crucial for EOR projects in which polymer solutions are injected.
Inaccessible Drilling Targets and Completions Operation Made Possible by the Alleviation of Excessive Torque and Drag
Authors: Long Tim Parker , McCormick John Edward , Frilot Melissa Anne 
Published: October 2009

Abstract
This paper describes the factors contributing to excessive torque and drag that necessitated the use of sub-based mechanical friction-reduction tools in one land and two offshore wells. The software modeling of torque and drag is presented with the predicted and actual results. The paper also describes how the friction-reduction tools were run and how they work.
Applications related to this paper include any well with torque or drag challenges limiting the reach of a well or the options available for completions operations, extended-reach wells (ERWs), and any drilling, fishing, or other operation restricted by torque or drag challenges.
Effective planning and running of specialized tools are required for success. All three wells discussed had higher than expected torque and drag forces. The first and second wells experienced excessive torque, which threatened to halt drilling before reaching total depth (TD). In both cases the torque was reduced significantly, enabling drilling to continue to the target depths. In the third well, drag was reduced sufficiently to take advantage of an otherwise unavailable well-completion method, resulting in increased production and earlier financial recovery of drilling and completion costs.
This paper helps familiarize the reader with the technology and function of sub-based, rolling mechanical, friction-reduction tools, techniques, and information required to run a torque and drag model, as well as the benefits of using roller tools in drilling and completions operations.