bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees
Authors: Toleno Donna M , Renaud Gabriel , Wolfsberg Tyra G , Islam Munirul , Wildman Derek E , Siegmund Kimberly D , Hacia Joseph G 
Published: March 2009

AbstractBackgroundCross-species gene expression analyses using oligonucleotide microarrays designed to evaluate a single species can provide spurious results due to mismatches between the interrogated transcriptome and arrayed probes. Based on the most recent human and chimpanzee genome assemblies, we developed updated and accessible probe masking methods that allow human Affymetrix oligonucleotide microarrays to be used for robust genome-wide expression analyses in both species. In this process, only data from oligonucleotide probes predicted to have robust hybridization sensitivity and specificity for both transcriptomes are retained for analysis.ResultsTo characterize the utility of this resource, we applied our mask protocols to existing expression data from brains, livers, hearts, testes, and kidneys derived from both species and determined the effects probe numbers have on expression scores of specific transcripts. In all five tissues, probe sets with decreasing numbers of probes showed non-linear trends towards increased variation in expression scores. The relationships between expression variation and probe number in brain data closely matched those observed in simulated expression data sets subjected to random probe masking. However, there is evidence that additional factors affect the observed relationships between gene expression scores and probe number in tissues such as liver and kidney. In parallel, we observed that decreasing the number of probes within probe sets lead to linear increases in both gained and lost inferences of differential cross-species expression in all five tissues, which will affect the interpretation of expression data subject to masking.ConclusionWe introduce a readily implemented and updated resource for human and chimpanzee transcriptome analysis through a commonly used microarray platform. Based on empirical observations derived from the analysis of five distinct data sets, we provide novel guidelines for the interpretation of masked data that take the number of probes present in a given probe set into consideration. These guidelines are applicable to other customized applications that involve masking data from specific subsets of probes.
Micropitting of carburized gears lubricated with biodegradable low-toxicity oils
Authors: Cardoso N F R , Martins R C , Seabra J H O 
Published: March 2009

Environmental issues are leading to a growing interest in bio-lubricants, which can have similar or even better performance than mineral and synthetic oils. In this work, the biodegradability and toxicity characteristics of ester-based gear oils are presented and their physical, chemical, and wear properties are compared with those of a commercial mineral oil. In an earlier work, power loss tests were performed on the FZG test rig, using carburized gears and several different lubricants. The operating temperatures of the oil and of the FZG gearbox wall were measured for different values of the input torque and speed. An energetic model of the FZG test gearbox was developed, taking into account the power loss mechanisms inside the gearbox and the heat flow mechanisms from the gearbox to the surrounding environment. Using this model it was possible to quantify the influence of lubricant formulation on the average friction coefficient between gear teeth. Gear micropitting tests were performed on the FZG test rig, using carburized gears and different oils. Post-test analysis included the mass loss measurement of the gear, the ferrometric analysis of lubricant samples collected during the tests, and the visual inspection of the gears. The tooth flanks were inspected using surface topography measurements to assess the number and depth of micropits. In comparison with the gear lubricated with mineral oil, the gears lubricated with ester-based oil showed significantly higher mass loss (3—4 times higher), smaller number of micropits, and less deep micropits. If carefully formulated, biodegradable low-toxicity ester-based gear oils, beside their environmental advantages, enhance gear performance when compared with the mineral lubricant providing (a) lower friction coefficients and lower operating temperatures of gearboxes and (b) lower number of micro-pits (with depths greater than 4 μm). One of the ester-based gear oils passed the FVA gear micropitting criterion.
Abundance of Immunologically Active Alanine Aminotransferase in Sera of Liver Cirrhosis and Hepatocellular Carcinoma Patients
Authors: Kim Hyun Jeong , Oh Sang Wook , Kim Dong Joon , Choi Eui Yul 
Published: March 2009

Abstract
Background: Although alanine aminotransferase (ALT) is a widely used indicator of liver function, ALT enzymatic activity may not always reflect the degree of liver damage. Improved methods or approaches would be useful.
Methods: Monoclonal antibodies (mAbs) to ALT were generated to develop a sandwich enzyme immunoassay system. We used an immunoassay to measure ALT mass concentration and a common biochemical analyzer to assay ALT enzymatic activity in serum samples from patients with liver diseases and healthy individuals. The results from the 2 methods were compared and analyzed by ROC curve analysis.
Results: The ALT sandwich enzyme immunoassay system demonstrated reliable performance in linearity, recovery, and imprecision studies. The ALT activity assay exhibited a higher diagnostic accuracy in acute hepatitis (AH) patients, but the ALT immunoassay exhibited higher sensitivity and specificity in patients with chronic liver diseases. The areas under the ROC curve for ALT mass and enzymatic activity were 0.82 and 0.98, respectively, in AH, 0.99 and 0.52 in hepatocellular carcinoma (HCC), and 0.94 and 0.45 in liver cirrhosis (LC). Serum samples from HCC and LC patients had higher amounts of ALT–immunoglobulin complexes [median A450, 1.7 (interquartile range, 1.4–1.9)] than the other groups [1.3 (interquartile range, 0.9–1.6)].
Conclusions: Our analysis of sera from the HCC and LC patient groups revealed considerable amounts of immunologically active but catalytically inactive ALT. The amount of the ALT–immunoglobulin complex increased with the severity of the liver disease. The 2-site immunoassay method may be useful in the differential diagnosis of some causes of liver disease.
New ELISA for Detecting Primary Biliary Cirrhosis–Specific Antimitochondrial Antibodies
Authors: Dähnrich Cornelia , Pares Albert , Caballeria Llorenç , Rosemann Anke , Schlumberger Wolfgang , Probst Christian , Mytilinaiou Maria , Bogdanos Dimitrios , Vergani Diego , Stöcker Winfried , Komorowski Lars 
Published: March 2009

Abstract
Background: Antimitochondrial antibodies specific for primary biliary cirrhosis (PBC) target the E2 subunits of 2-oxo acid dehydrogenase complexes, in particular the pyruvate dehydrogenase complex (PDC)-E2. Their antigen-specific detection relies on conventional ELISA using purified PDC. More recent assays have employed a hybrid containing the 3 E2-subunits (MIT3). Some PBC sera react with one or the other preparation, suggesting the presence of nonoverlapping epitopes.
Methods: We have developed an ELISA (anti-M2-3E) using a mixture of purified PDC and MIT3 as antigenic targets. We compared this assay to anti-MIT3 alone, conventional anti-PDC, and indirect immunofluorescence using 173 PBC and 247 disease controls.
Results: The anti-M2-3E ELISA showed a 93.6% diagnostic sensitivity compared with 91.3%, 83.8%, and 87.3% for MIT3, purified PDC, or indirect immunofluorescence, respectively, when all specificities are set to 98.8%. By immunoblotting, anti-M2-3E–positive sera unreactive to purified PDC recognized recombinant E2-subunits of the other 2 complexes, whereas those with no reactivity to MIT3 immunofixed PDC subunits E1α or E1β.
Conclusions: The diagnostic accuracy of the anti-M2-3E ELISA for detection of antibodies to 2-oxo acid dehydrogenase complexes exceeds that of conventional ELISA and IFL; its novelty derives from the combination of the MIT3 hybrid and purified PDC.
Standardizing and Harmonizing Terminology: Theory and Practice
Authors: Wright SE , Strehlow RA 
Published: March 2009

Description
The question of terminology harmonization within the framework of data exchange and information retrieval is likely to dominate concerns in the field well beyond the turn of the next century. STP 1223 follows in a series of publications resulting from symposia that has been recognized in the world wide terminology community for its excellence, timeliness and relevance.
16 peer-reviewed papers in 5 sections:
• Concept Congruence--Theory and Practice of Terminology
• Design and Management of Terminologies--Varieties and Types
• Harmonization in a Multilingual Environment
• Computer Aided Terminology Work
• Roundtable Discussion.
Special Applications and Advanced Techniques for Crack Size Determination
Authors: Ruschau JJ , Donald JK 
Published: March 2009

Description
Presents a compelling range of unique approaches to non-visual crack size measurement. Up-to-date improvements over standard, well-used methods are also discussed. Ten comprehensive, peer-reviewed papers that explore original and advanced methodology for crack measuring techniques on a variety of materials. Some of the procedures explored include use of: Alternating Current Potential Difference Technique • Improved Load Ration Methods • Ultrasonic Microscopy • AC Magnetic Bridge Device.
Mode I and Mode II Delamination Growth of Interlayer Toughened Carbon/Epoxy (T800H/3900-2) Composite System
Authors: Kageyama K , Kimpara I , Ohsawa I , Hojo M , Kabashima S 
Published: March 2009

Delamination is one of the most critical failure modes in a laminated composite structure. In order to improve the interlaminar fracture toughness, the concept of “interlayer” has been applied to thermoset composite materials. In the present paper, the static and fatigue interlaminar fracture characteristics of a interlayer toughened carbon/epoxy, T800H/3900-2, were examined and compared with those of a thermoplastic composite, APC2, as a reference.
Fracture region transition, which is deflection of the crack path from interlayer to intralaminar, is observed in the static Mode I interlaminar crack growth of T800H/3900-2. Mode I interlaminar fracture toughness, GIR, decreases during the propagation in relation to the decrease of the interlayer fracture surface area.
The Mode II crack growth resistance curve (R-curve) was obtained under the constant CSD rate by applying the stabilized ENF test. The remarkable fracture region transition is not observed in the Mode II R-curve of T800H/3900-2, and the toughened carbon/epoxy composite exhibits excellent crack growth resistance under Mode II loading.
The Mode I fatigue crack growth rate of T800H/3900-2 was expressed as a function of the maximum energy release rate during cyclic loading. The fracture region transition is also observed. The transition in the fatigue test was completed after a shorter crack extension than that in the static test.
Atmospheric Corrosion of Bolted Lap Joints Made of Weathering Steel
Authors: Knotkova D , Vlckova J 
Published: March 2009

For certain types of steel structures the application of weathering steels is especially suitable. These are electrical transmission towers, masts, bridges and other structures, used in outdoor exposure, where brown color is appreciated and no maintenance is necessary.
Proposals for the use of weathering steels for various types of steel structures are based mainly on the results of field corrosion tests (outdoor and under sheds) in which a significantly higher corrosion resistence of weathering steels as compared to that of plain carbon structural steel, has been proved in the atmospheres of low or medium aggressivness.
At bolted joints of certain design exposed to a more corrosive environment, significant defects were found in the crevices which cause even deformation of the joints. After dismantling and pickling, these phenomena were quantified. Recommendations were prepared to minimize these corrosion effects, and also possibilities were considered of increasing the lifetime of structures already affected by crevice corrosion.
Investigation of the Relationship Between Field Performance and Laboratory Aging Properties of Asphalt Mixtures
Authors: Kliewer JE , Bell CA , Sosnovske DA 
Published: March 2009

Short- and long-term aging procedures were developed at Oregon State University under the Strategic Highway Research Program (SHRP) A-003A project. Several alternative methods for short- and long-term aging of asphalt-aggregate were examined. These were subjected to extensive laboratory and field validation test programs. Laboratory validation was done with an extensive testing program using 8 asphalts and 4 aggregates. Field validation utilized 20 test sites and compared the modulus of field aged and laboratory aged specimens.
For short-term aging a procedure of curing the loose mix in a forced draft oven at 135°C for 4 hours was recommended. For long-term aging, oven aging at 85°C for 4 days was recommended to represent projects of about 10 years old. Alternative procedures may be appropriate in some situations. Long-term oven aging for 2 days at 100°C could be used for stiff mixes, whereas a low pressure procedure of 4 days at 85°C may be necessary for soft mixes.
The results of the asphalt-aggregate mixture testing presented herein show that the aging of the mixture is dependant on both the asphalt and the aggregate. Also, it appears, from the evaluation of data from other SHRP contractors, that the aging and subsequent testing of asphalt alone is not a good predictor of how a mixture will behave due to the effect of the asphalt-aggregate interaction.
Continued monitoring of field projects is needed, particularly for Dry-No Freeze and Wet-No Freeze zones. Increasing the number of sites and total number of specimens tested will facilitate the use of regression analyses to develop performance prediction models.
An Assessment of Oil-spill Effects on Pink Salmon Populations Following the Exxon Valdez Oil Spill—Part 2: Adults and Escapement
Authors: Maki AW , Brannon EJ , Gilbertson LG , Moulton LL , Skalski JR 
Published: March 2009

This paper presents results of a field program designed to monitor the status of wildstock pink salmon populations in Prince William Sound following the Exxon Valdez oil spill. Field counts of spawning salmon were conducted each year from 1989 through 1992 to test for spill effects on the distribution and abundance of pink salmon adults spawning in selected streams in the southwestern portion of Prince William Sound, including streams from the most heavily oiled areas. Counts of whole-stream and intertidal escapement density were statistically compared for 40 study streams in 1989 and for a subset of those streams in successive years. Measurements of residual hydrocarbons were made from stream-bed sediments to test for correlations with spawning behavior.
Adult pink salmon in the postspill years of 1990 and 1991, progeny of the year classes considered most vulnerable to the oil spill, returned in high numbers, with the wildstock spawners exceeding their parent year returns. In 1989, adult returns reflected the relatively weak run for that year with a mean spawner density of 0.68 fish/m2 in reference streams and 0.69 fish/m2 in oiled streams. In 1990, mean escapement density for reference streams was 1.40 fish/m2 and 1.55 fish/m2 for oiled streams, indicating the strongest run of the four study years. Trends in polycyclic aromatic hydrocarbon (PAH) concentrations for the majority of oiled streams show a general decline from 1989 to background levels by 1990. The measured PAH concentrations indicate low-level exposure to residual hydrocarbons that have not produced detectable differences in spawning behavior or escapement between streams from oiled areas compared with unoiled streams.
In Part 1 of this paper, elements of the early lifestage survival of potentially affected year classes of pink salmon were examined by Brannon et al. (this volume). Conclusions indicate measures of early lifestages were largely indistinguishable between oiled and unoiled streams. The early lifestage data, in combination with observations of the strength of postspill returns and analyses of escapement reported herein, are the basis for the conclusion that changes in the wildstock pink salmon population in Prince William Sound could not be attributed to the oil spill.
Study of the Effect of Inhibitor on Erosion-Corrosion in CO2-Saturated Condition With Sand
Authors: Neville A. , Wang C. 
Published: March 2009

Summary
CO2 corrosion inhibitors are widely adopted in production and processing facilities in the oil and gas industry. The challenge is that under multiphase flow (liquid/sand) and high shear-stress conditions, successful application of inhibitors can be difficult. Under such severe erosion-corrosion conditions, the total material damage is identified as being associated with electrochemical corrosion, solid particle erosion, and synergistic effects between the two.
To investigate the possibility of using corrosion inhibitors to reduce erosion-corrosion, this study has characterized the corrosion phenomena occurring at the carbon steel-electrolyte interface under erosion-corrosion conditions. AC impedance was used to provide mechanistic information of corrosion with absence and presence of a commercial corrosion inhibitor in erosion-corrosion conditions in a CO2-saturated brine. Experiments were conducted using a rotating cylinder electrode cell containing sand at different temperatures, rotational speeds and with various inhibitor concentrations. Four commercial inhibitors have been investigated.
In this work, the potential for applying corrosion inhibitors for the reduction of material loss in erosion–corrosion is assessed and the role of the inhibitor in reducing corrosion, erosion, and interactive mass-loss mechanisms is discussed.
Investigation of Swirl Flows Applied to the Oil and Gas Industry
Authors: Surendra Meher , Falcone Gioia , Teodoriu Catalin 
Published: March 2009

Summary
The work presented in this paper is part of a larger research project which is aimed at finding solutions to problems associated with liquid loading, erosion at pipe bends caused by sand particles, and phase separation. The work uses computational fluid dynamics (CFD) to design solutions that can reduce or eliminate the aforementioned problems. Here, the results from CFD simulations of two-phase air and water flows are critically analyzed through comparison with the results from experiments carried out by Falcone et al. (2003) using the ANUMET concept.† The entire experimental setup is modeled within the CFD simulation and flow rates for water and air are taken from the data used for the experiments. Important variables such as pressure drop and fluid film thickness, which were monitored closely during the experiments, are obtained from the CFD simulations and compared with the experimental results. The results presented in this paper provide insights into the physics of two-phase swirl flows, identifying areas of research that still need to be addressed.
Paraffin Cleanout in a Single Subsea Flowline Using Xylene
Authors: Bailey J. Claire , Allenson Stephan J. 
Published: March 2009

Summary
Paraffin deposition was found in the RedHawk #2 subsea flowline and was successfully removed using a xylene slug swept by produced gas from the well. Testing indicated that the problem resulted from the interaction between glycol and produced condensate. Overtreatment with glycol and low produced water volumes contributed to the precipitation of paraffin and eventual plugging of the flowline.
The objective of this procedure was to clear the restriction by pumping a slug of xylene into the flowline and producing the well to carry the solids to surface. Glycol can react negatively with the condensate in some dry gas wells, resulting in paraffin precipitation. When there is sufficient water present to mix with the glycol the problem does not occur; however, a lack of water causes the glycol to react with the condensate and form paraffin. Clearing the restriction would eliminate a pressure drop in the flowline, thus allowing the well to produce at optimal rate and prolonging the well's life. All work was performed from the host spar facility using temporary separation equipment and platform methanol pumps.
The RedHawk flowline restriction was successfully removed using two 25-bbl xylene slugs which were swept from the flowline with produced gas from the well. With the restriction removed, 982 psi of frictional loss was regained and the well was returned to optimal production. The deposition appears to be reoccurring, although at a much slower rate than before. However, any further reduction in glycol usage would not guarantee effective hydrate inhibition. Changing hydrate inhibitors is impractical because of platform equipment, and annual cleanouts are a more cost effective option.
It is quickly becoming critical to develop means of cleaning single flowline systems with highly efficient and low-cost methods. By understanding new problems that arise and putting new solutions into practice, operators can extend the life of some wells and avoid significant downtime and workover costs.
Mucosal Eosinophils and L-Selectin Ligands are Associated with Invasive and Noninvasive Sinus Surgery Outcomes
Authors: Myller Jyri P. , Toppila-Salmi Sanna K. , Toppila Esko M. , Torkkeli Tommi V.M. , Numminen Jura E.A. , Renkonen Risto L.O. , Rautiainen Markus E.P. 
Published: March 2009

Background Chronic rhinosinusitis (CRS) is characterized by persistent inflammation of the nasal and paranasal mucosa with numerous emigrated leukocytes. L-Selectin on leukocytes and its endothelial glycosylated ligands initiate leukocyte infiltration into inflamed tissues. Endoscopic sinus surgery (ESS) is the major approach for restoring sinus physiology after failure of conservative therapy; however, the effect of enlarging the maxillary sinus ostium is still unknown. Here, we compared two histological markers of local inflammation, the number of mucosal eosinophils, and the expression of endothelial L-selectin ligands, with clinical outcomes after enlarging or saving the maxillary sinus ostium. Methods Twenty-three patients with CRS underwent uncinectomy on one side and additional middle meatal antrostomy on the other side. Maxillary sinus mucosa biopsy specimens from these patients and nine healthy subjects were taken for immunohistochemical evaluations of the number of mucosal eosinophils and endothelial L-selectin ligands. Also, symptoms and mucociliary clearance were measured. Results The postoperative reduction of the endothelial L-selectin ligands was independent of the operation technique. There was a correlation between postoperative number of mucosal eosinophils and symptom score, which was also independent of the surgical technique. The postoperative decrease of mucosal eosinophils, as well as the correlation of the intraoperative eosinophils with the postoperative symptom score, was found only on antrostomy side. Conclusion ESS decreases the expression of endothelial L-selectin ligands, which might lead to decreased eosinophil traffic into maxillary sinus mucosa, putatively more when enlarging the maxillary sinus ostium. Both intra- and postoperative low number of eosinophils seem to be indicators of good subjective recovery.