bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Thyroid Hormone-Inactivating Deiodinase Functions as a Homodimer
Authors: Sagar G. D. Vivek , Gereben Balázs , Callebaut Isabelle , Mornon Jean-Paul , Zeöld Anikó , Curcio-Morelli Cyntia , Harney John W. , Luongo Cristina , Mulcahey Michelle A. , Larsen P. Reed , Huang Stephen A. , Bianco Antonio C. 
Published: March 2008

AbstractThe type 3 deiodinase (D3) inactivates thyroid hormone action by catalyzing tissue-specific inner ring deiodination, predominantly during embryonic development. D3 has gained much attention as a player in the euthyroid sick syndrome, given its robust reactivation during injury and/or illness. Whereas much of the structure biology of the deiodinases is derived from studies with D2, a dimeric endoplasmic reticulum obligatory activating deiodinase, little is known about the holostructure of the plasma membrane resident D3, the deiodinase capable of thyroid hormone inactivation. Here we used fluorescence resonance energy transfer in live cells to demonstrate that D3 exists as homodimer. While D3 homodimerized in its native state, minor heterodimerization was also observed between D3:D1 and D3:D2 in intact cells, the significance of which remains elusive. Incubation with 0.5–1.2 m urea resulted in loss of D3 homodimerization as assessed by bioluminescence resonance energy transfer and a proportional loss of enzyme activity, to a maximum of approximately 50%. Protein modeling using a D2-based scaffold identified potential dimerization surfaces in the transmembrane and globular domains. Truncation of the transmembrane domain (ΔD3) abrogated dimerization and deiodinase activity except when coexpressed with full-length catalytically inactive deiodinase, thus assembled as ΔD3:D3 dimer; thus the D3 globular domain also exhibits dimerization surfaces. In conclusion, the inactivating deiodinase D3 exists as homo- or heterodimer in living intact cells, a feature that is critical for their catalytic activities.
Single‐point incremental forming and formability—failure diagrams
Authors: Silva M B , Skjoedt M , Atkins A G , Bay N , Martins P A F 
Published: March 2008

In recent work, the present authors constructed a closed‐form analytical model that is capable of dealing with the fundamentals of single‐point incremental forming (SPIF) and explaining the experimental and numerical results published in the literature over the past couple of years. The model is based on membrane analysis with in‐plane contact frictional forces but is limited to plane strain, rotationally symmetric conditions. The aim of the present paper is twofold: first, to extend the previous closed‐form analytical model into a theoretical framework that can easily be applied to the different modes of deformation that are commonly found in general single‐point incremental forming processes and, second, to investigate the formability limits of SPIF in terms of ductile damage mechanics and the question of whether necking does, or does not, precede fracture. Experimentation by the present authors, together with data retrieved from the literature, confirms that the proposed theoretical framework is capable of successfully addressing the influence of the major parameters of the SPIF process. It is demonstrated that neck formation is suppressed in SPIF, so that traditional forming limit diagrams are inapplicable to describe failure. Instead fracture forming limit diagrams should be employed.
A ramp—heated plate method for measuring heat and water vapour transport in seats
Authors: Ratts E B 
Published: March 2008

In this paper, an experimental ramp method is presented which was used to quantify the capability of an automotive seat to move heat and moisture away from its surface. The method involved placing an indenter on a seat cushion for a fixed time period. Average heat and mass transfer rates were measured to compare seats. In addition, an effective effusivity was defined and measured to quantify the seat's thermal property. The ramp method was used to compare the difference in dry ventilated and dry non—ventilated seats. An increase of 82 per cent in heat transfer was observed. The ventilated and non—ventilated seat effusivities were 440 W s1/2/m2 K and 292 W s1/2/m2 K respectively. In comparing wet ventilated with wet non—ventilated seats, an increase of 60–94 per cent in mass transfer was observed. Also, the method was used to compare the difference in positive—pressure and negative—pressure ventilation systems. The positive—pressure system demonstrated an increase over the negative—pressure system in dry heat transfer rate of 32 per cent. Both were comparable in terms of mass transfer capability.
A one-dimensional lean NOx trap model with a global kinetic mechanism that includes NH3 and N2O
Authors: Depcik C , Assanis D , Bevan K 
Published: March 2008

Eaton has developed an aftertreatment system for medium- and heavy-duty diesel engines in response to the US 2010 regulations. This system consists of a fuel reformer, a lean NO x trap (LNT), and an ammonia selective catalytic reduction (SCR) catalyst in series. A transient, one-dimensional model of the system was developed to improve system performance, reduce experimental testing, and optimize system design. In this paper, the LNT portion of this model is presented. The model simulates flow, heat transfer, and chemical reactions in the LNT catalyst. A global LNT chemical kinetic mechanism was developed to simulate the key catalytic processes with the minimum number of reactions. The model can be used to predict LNT catalyst performance over a range of operating conditions and driving cycles. Simulated species concentrations and gas temperatures at the LNT outlet were compared with experimental data at three steady state engine conditions over a 13-mode test. The conditions were chosen to develop and test the model over a range of gas temperatures, space velocities, and species concentrations. The LNT model predicts species trends and magnitudes with reasonable accuracy in comparison with experimental data. The simulated LNT NO x conversion efficiency over the 13-mode test was 67 per cent, compared with 63 per cent for the experiment.
Unsteady wall heat flux in spark-ignited, homogeneous charge engines fuelled with reformer gas/gasoline blends
Authors: Conte E , Boulouchos K 
Published: March 2008

On-board partial oxidation of gasoline to produce reformer gas seems to be an attractive strategy to abate pollutant emissions from internal combustion engines. The engine behaviour in terms of efficiency and combustion process can be better understood by means of in-cylinder heat flux measurements. The study of the unsteady wall heat transfer, supported by previous studies of flame propagation and flame speed through ion sensors and optical fibres, reveals a limited influence of the reformer gas upon the heat transfer coefficient and possibly upon the flame-quenching distance, which is estimated in three different and independent ways. A detailed statistical analysis of single-cycle heat flux shows that the cycle-to-cycle variation remains large when the fraction of reformer gas in the fuel blend increases, even if the global engine stability improves. The comparison of numerous data shows how the chemical energy is released partly within the flame and partly within the post-flame region. This last can account for as much as 30 per cent of the total energy release. The analysis of slow and fast-burning cycles with different fuel blends shows that this fraction of energy is released only when, during the expansion stroke, the cylinder temperature decreases below a certain threshold, allowing radicals to recombine and carbon monoxide (CO) completely to oxidize to CO 2.
Pollutant formation modelling in natural gas SI engines using a level set based flamelet model
Authors: Dahms R , Peters N , Stanton D W , Tan Z , Ewald J 
Published: March 2008

The level set flamelet model for turbulent premixed combustion was recently extended to improve the modelling of the spark ignition process, to incorporate the influence of unsteady flame kernel development on turbulent flame propagation, to embrace flame—wall interaction, and to comprise pollutant prediction models. The formation of nitrogen oxides (NO x) is predicted using the extended Zeldovich mechanism. The concentrations of the involved intermediate species are determined using a chemical equilibrium assumption. The formation of engine-out unburnt hydrocarbons (UHCs) and carbon monoxides (COs) is directly linked to incomplete combustion due to flame quenching at the time the flame hits the wall. In this paper, the new model is used for the analysis of combustion in a homogeneous charged natural gas SI engine operating on lean conditions. The investigated engine operating (PAM) points differ in the applied equivalence ratio, ignition timing, and rate of exhaust gas recirculation. The influence of the load on the peak pressures, peak pressure locations, and pollutant formations is discussed in detail. A good agreement with experimental data was obtained among all engine operating points.
Exon-Level Expression Profiling: A Comprehensive Transcriptome Analysis of Oral Fluids
Authors: Hu Zhanzhi , Zimmermann Bernhard G , Zhou Hui , Wang Jianghua , Henson Bradley S , Yu Weixia , Elashoff David , Krupp Guido , Wong David T 
Published: March 2008

Abstract
Background: The application of global gene expression profiling to saliva samples is hampered by the presence of partially fragmented and degraded RNAs that are difficult to amplify and detect with the prevailing technologies. Moreover, the often limited volume of saliva samples is a challenge to quantitative PCR (qPCR) validation of multiple candidates. The aim of this study was to provide proof-of-concept data on the combination of a universal mRNA-amplification method with exon arrays for candidate selection and a multiplex preamplification method for easy validation.
Methods: We used a universal mRNA–specific linear-amplification strategy in combination with Affymetrix Exon Arrays to amplify salivary RNA from 18 healthy individuals on the nanogram scale. Multiple selected candidates were preamplified in one multiplex reverse transcription PCR reaction, cleaned up enzymatically, and validated by qPCR.
Results: We defined a salivary exon core transcriptome (SECT) containing 851 transcripts of genes that have highly similar expression profiles in healthy individuals. A subset of the SECT transcripts was verified by qPCR analysis. Informatics analysis of the SECT revealed several functional clusters and sequence motifs. Sex-specific salivary exon biomarkers were identified and validated in tests with samples from healthy individuals.
Conclusions: It is feasible to use samples containing fragmented RNAs to conduct high-resolution expression profiling with coverage of the entire transcriptome and to validate multiple targets from limited amounts of sample.
Genetic Variants of Tumor Necrosis Factor Superfamily, Member 4 (TNFSF4), and Risk of Incident Atherothrombosis and Venous Thromboembolism
Authors: Mälarstig Anders , Eriksson Per , Rose Lynda , Diehl Kirsti A , Hamsten Anders , Ridker Paul M , Zee Robert Y L 
Published: March 2008

AbstractBackground: Recent data have implicated tumor necrosis factor (ligand) superfamily, member 4 (TNFSF4) gene variation in myocardial infarction in women; however, no prospective data are available on either incident arterial or venous disorders.Methods: We evaluated 2 previously characterized TNFSF4 gene variants (−921C&gt;T and dbSNP rs3850641) with a) incident arterial events using a prospective case-cohort design with 344 incident CVD cases and 2254 control participants, all white, drawn from the Women’s Health Study cohort with 10 years of follow-up, and b) venous thromboembolism (VTE) risk using a nested, matched case-control design of 108 white male pairs (drawn from the Physicians’ Health Study cohort) and a case-cohort design of white female participants consisting of 125 cases and 2269 controls (drawn from the Women’s Health Study cohort), analyzed separately.Results: Genotype distributions were in Hardy-Weinberg equilibrium. Results from a marker-by-marker regression analysis, adjusting for traditional risk factors, showed a significant association of −921C&gt;T with an increased risk of VTE in women (additive: odds ratio 1.86; 95% CI 1.17–2.92, P = 0.008) in women. Furthermore, using a haplotype-based regression analysis, haplotype C-G was associated with a reduced risk of VTE relative to the referent haplotype, C-A (odds ratio 0.50; 95% CI 0.27–0.92; P = 0.02). In contrast, we found little evidence for an association of the variants/haplotypes with risk of VTE in men or CVD risk in women (as previously reported).Conclusions: Our present findings, if corroborated in other prospective investigations, suggest that the TNFSF4 variants tested may be useful indicators for assessing the risk of venous thromboembolism.
Screening Autoantibody Profiles in Systemic Rheumatic Disease with a Diagnostic Protein Microarray That Uses a Filtration-Assisted Nanodot Array Luminometric Immunoassay (NALIA)
Authors: McBride Jeffrey D , Gabriel Francis Guy , Fordham John , Kolind Torsten , Barcenas-Morales Gabriela , Isenberg David A , Swana Marlene , Delves Peter J , Lund Torben , Cree Ian A , Roitt Ivan M 
Published: March 2008

Abstract
Background: We developed a cost-efficient modular system for multiplex analysis of the multiple autoantibodies that characterize systemic rheumatoid diseases.
Methods: The nanodot array luminometric immunoassay (NALIA) system consists of conventional 96-well membrane-bottomed plates in which antigens or antibodies are adsorbed onto the underside of the membrane. Current arrays use a 5 × 5 format (25 dots/well), which allows 10 analytes to be measured in duplicate: double-stranded DNA (dsDNA), centromere protein B (CENP-B), PCNA, Sm, Sm ribonucleoprotein (Sm-RNP), U1-snRNP, Scl70, SSA/Ro, SSB/La, Jo-1, and controls. The test fluid, control sera, and subsequent reagents are drawn through the membrane. The captured analytes are quantified by monitoring chemiluminescence with a charge-coupled device (CCD) and analyzed with commercial array software.
Results: The assay can detect &lt;20 × 103 IU/L of anti-dsDNA. The interwell CV was 10%–14%. There was an 83% concordance (κ = 0.56) between the NALIA results obtained for anti-dsDNA assayed by β-testing in a routine immunology diagnostic laboratory and the results obtained with a conventional ELISA reagent set. The concordance values for Ro, La, Sm, and RNP were 98% (κ, 0.92), 93% (κ, 0.41), 97% (κ, 0.62), and 97% (κ, 0.73), respectively.
Conclusion: The NALIA approach promises to provide a highly economical platform for a wide range of applications that require assays of multiple analytes. The degree of concordance of our results with a conventional reagent set was no less than that occurring between different commercial products. A sample of serum from a finger stick provides a volume sufficient to perform the array assay.
Association of Serum Interleukin-6 Concentration with a Functional IL6 −6331T&gt;C Polymorphism
Authors: Smith Andrew J P , D’Aiuto Francesco , Palmen Jutta , Cooper Jackie A , Samuel Jane , Thompson Simon , Sanders Julie , Donos Nikos , Nibali Luigi , Brull David , Woo Pat , Humphries Steve E 
Published: March 2008

AbstractBackground: Interleukin-6 (IL-6) concentrations vary substantially among individuals. This study aimed to identify novel genetic markers to explain these differences.Methods: We sequenced a region 6-kb upstream of the IL6 [interleukin 6 (interferon, beta 2)] transcription start site in a search for functional variants and detected 3 common variants: −6331T&gt;C, −6101A&gt;T, and −5617/−5616C/A&gt;T/G. IL6 −6331T&gt;C (C allele frequency, 0.20; 95% confidence interval, 0.16–0.24) showed strong negative linkage disequilibrium with −174G&gt;C (D′ = −0.97) and was studied further in 309 individuals who underwent coronary artery bypass grafting.Results: Patients with the TT genotype had higher IL-6 concentrations 6 h after surgery than those with the CC genotype (mean, 199.4 ng/L vs 114.9 ng/L; P = 0.02). A similar association was seen in a cohort of 173 patients who underwent intensive periodontal therapy: Individuals with the CC genotype had significantly lower IL-6 concentrations 24 h after therapy than TT patients (mean, 0.78 ng/L vs 5.00 ng/L; P &lt; 0.0001). A similar trend was observed in 203 healthy individuals from northern Europe (1.29 ng/L for the TT genotype vs 0.89 ng/L for the CC genotype; P = 0.07). Reporter assays that used a sequence flanking the −6331 single-nucleotide polymorphism spliced upstream to the IL-6 minimal promoter driving luciferase gene expression demonstrated a 1.3-fold increase in promoter activity (P &lt; 0.01) for constructs containing −6331T. Electrophoretic mobility shift assays revealed enhanced binding of transcription factor Oct-1 to the T allele.Conclusions: IL6 −6331T is associated with increased IL-6 concentrations in an acute inflammatory state via a mechanism involving binding of the Oct-1 transcription factor. This finding may help resolve conflicting studies based on the IL6 −174G&gt;C variant.
“Die Ochsen am Berge”: Franz Xaver Süssmayr and the Orchestration of Mozart's Requiem, K. 626
Authors: Keefe Simon P. 
Published: March 2008

AbstractFranz Xaver Süssmayr's letter to the publisher Härtel (1800) about his involvement in completing Mozart's Requiem implicitly and explicitly asks its recipient to take his contribution seriously. Positive appraisals of the entire Requiem in the early decades of the nineteenth century, read alongside this letter, invite reevaluation of Süssmayr's orchestration of the work. Early writings on Mozart's orchestration clarify that Süssmayr's countless musical decisions, large and small, would have carried genuine aesthetic resonance. Süssmayr's view that the winds should function primarily as support for the voices derives from Mozart's orchestration of the Introit, and manifests itself especially in voice doublings and frequent segues between vocal statements. The origin of his shaping of orchestration toward climactic points in the Lacrymosa, Sanctus, and Benedictus, however, is less clearly attributable to Mozart. Süssmayr's entitlement to a vision of his own for the completion of the work, one that may not follow Mozart's intentions in every respect, encourages us to consider putative “transgressions” evidence of active engagement with the work itself, rather than of musical misjudgment. Examining the Sanctus and Benedictus (for which no materials in Mozart's hand are extant) as well as the Sequence, reveals the consistency and coherence of Süssmayr's vision across the Requiem as a whole.
Autocrine Fibroblast Growth Factor 2 Increases the Multipotentiality of Human Adipose-Derived Mesenchymal Stem Cells
Authors: Rider David A. , Dombrowski Christian , Sawyer Amber A. , Ng Grace H. B. , Leong David , Hutmacher Dietmar W. , Nurcombe Victor , Cool Simon M. 
Published: March 2008

Abstract
Multipotent mesenchymal stem cells (MSCs), first identified in the bone marrow, have subsequently been found in many other tissues, including fat, cartilage, muscle, and bone. Adipose tissue has been identified as an alternative to bone marrow as a source for the isolation of MSCs, as it is neither limited in volume nor as invasive in the harvesting. This study compares the multipotentiality of bone marrow-derived mesenchymal stem cells (BMSCs) with that of adipose-derived mesenchymal stem cells (AMSCs) from 12 age- and sex-matched donors. Phenotypically, the cells are very similar, with only three surface markers, CD106, CD146, and HLA-ABC, differentially expressed in the BMSCs. Although colony-forming units-fibroblastic numbers in BMSCs were higher than in AMSCs, the expression of multiple stem cell-related genes, like that of fibroblast growth factor 2 (FGF2), the Wnt pathway effectors FRAT1 and frizzled 1, and other self-renewal markers, was greater in AMSCs. Furthermore, AMSCs displayed enhanced osteogenic and adipogenic potential, whereas BMSCs formed chondrocytes more readily than AMSCs. However, by removing the effects of proliferation from the experiment, AMSCs no longer out-performed BMSCs in their ability to undergo osteogenic and adipogenic differentiation. Inhibition of the FGF2/fibroblast growth factor receptor 1 signaling pathway demonstrated that FGF2 is required for the proliferation of both AMSCs and BMSCs, yet blocking FGF2 signaling had no direct effect on osteogenic differentiation.
Disclosure of potential conflicts of interest is found at the end of this article.
Derivation and Cloning of a Novel Rhesus Embryonic Stem Cell Line Stably Expressing Tau-Green Fluorescent Protein
Authors: Wianny Florence , Bernat Agnieszka , Huissoud Cyril , Marcy Guillaume , Markossian Suzy , Cortay Véronique , Giroud Pascale , Leviel Vincent , Kennedy Henry , Savatier Pierre , Dehay Colette 
Published: March 2008

Abstract
Embryonic stem cells (ESC) have the ability of indefinite self-renewal and multilineage differentiation, and they carry great potential in cell-based therapies. The rhesus macaque is the most relevant preclinical model for assessing the benefit, safety, and efficacy of ESC-based transplantations in the treatment of neurodegenerative diseases. In the case of neural cell grafting, tracing both the neurons and their axonal projections in vivo is essential for studying the integration of the grafted cells in the host brain. Tau-Green fluorescent protein (tau-GFP) is a powerful viable lineage tracer, allowing visualization of cell bodies, dendrites, and axons in exquisite detail. Here, we report the first rhesus monkey ESC line that ubiquitously and stably expresses tau-GFP. First, we derived a new line of rhesus monkey ESC (LYON-ES1) that show marker expression and cell cycle characteristics typical of primate ESCs. LYON-ES1 cells are pluripotent, giving rise to derivatives of the three germ layers in vitro and in vivo through teratoma formation. They retain all their undifferentiated characteristics and a normal karyotype after prolonged culture. Using lentiviral infection, we then generated a monkey ESC line stably expressing tau-GFP that retains all the characteristics of the parental wild-type line and is clonogenic. We show that neural precursors derived from the tau-GFP ESC line are multipotent and that their fate can be precisely mapped in vivo after grafting in the adult rat brain.
Disclosure of potential conflicts of interest is found at the end of this article.
Conditional Stabilization ofβ-Catenin Expands the Pool of Lung Stem Cells
Authors: Reynolds Susan D. , Zemke Anna C. , Giangreco Adam , Brockway Brian L. , Teisanu Roxana M. , Drake Jeffrey A. , Mariani Thomas , Di Peter Y.P. , Taketo Mark M. , Stripp Barry R. 
Published: March 2008

AbstractMaintenance of classic stem cell hierarchies is dependent upon stem cell self-renewal mediated in part by Wnt/β-catenin regulation of the cell cycle. This function is critical in rapidly renewing tissues due to the obligate role played by the tissue stem cell. However, the stem cell hierarchy responsible for maintenance of the conducting airway epithelium is distinct from classic stem cell hierarchies. The epithelium of conducting airways is maintained by transit-amplifying cells in the steady state; rare bronchiolar stem cells are activated to participate in epithelial repair only following depletion of transit-amplifying cells. Here, we investigate how signaling through β-catenin affects establishment and maintenance of the stem cell hierarchy within the slowly renewing epithelium of the lung. Conditional potentiation of β-catenin signaling in the embryonic lung results in amplification of airway stem cells through attenuated differentiation rather than augmented proliferation. Our data demonstrate that the differentiation-modulating activities of stabilized β-catenin account for expansion of tissue stem cells.Disclosure of potential conflicts of interest is found at the end of this article.