bluuebunny/crossref_metadata_2025 huggingface dataset:
Time Characterization of the Anodic Loop of a Pressurized Solid Oxide Fuel Cell System
Authors: Traverso A. , Trasino F. , Magistri L. , Massardo A. F.
Published: March 2008

A dynamic solid oxide fuel cell (SOFC) model was integrated with other system components (i.e., reformer, anodic off-gas burner, anodic ejector) to build a system model that can simulate the time response of the anode side of an integrated 250kW pressurized SOFC hybrid system. After model description and data on previous validation work, this paper describes the results obtained for the dynamic analysis of the anodic loop, taking into account two different conditions for the fuel flow input: in the first case (I), the fuel flow follows with no delay the value provided by the control system, while in the second case (II), the flow is delayed by a volume between the regulating valve and the anode ejector, this being a more realistic case. The step analysis was used to obtain information about the time scales of the investigated phenomena: such characteristic times were successfully correlated to the results of the subsequent frequency analysis. This is expected to provide useful indications for designing robust anodic loop controllers. In the frequency analysis, most phase values remained in the 0–180deg range, thus showing the expected delay-dominated behavior in the anodic loop response to the input variations in the fuel and current. In Case I, a threshold frequency of 5Hz for the pressure and steam to carbon ratio and a threshold frequency of 31Hz for the anodic flow were obtained. In the more realistic Case II, natural gas pipe delay dominates, and a threshold frequency of 1.2Hz was identified, after which property oscillations start to decrease toward null values.
Last Stage Performance Considerations in Low-Pressure Turbines of Power Plants: A Case Study
Authors: Sunder Raj Komandur S.
Published: March 2008

The last stage blades (LSBs) of low-pressure (LP) turbine power plants have been historically specified and designed on the basis of optimization studies by matching the turbine to the condenser/cooling system for a specified unit rating. LSB sizes for U.S. nuclear applications currently range from 38 in. to 52 in. for unit ratings of 600 MWe to 1200 MWe. LP turbine arrangements usually consist of two or three double-flow sections in parallel. Last stage end loadings (last stage mass flow divided by the last stage annulus area) vary from approximately 8000lb∕hsqftto14,000lb∕hsqft, with corresponding unit loadings (electrical output in megawatts divided by last stage annulus area) of 1.1 MWe∕sqftto2.1MWe∕sqft. Several power plants have been upgrading/replacing their LP turbines. Considerations include efficiency, reliability, power uprates, operating license renewals (nuclear), aging, inspection, and maintenance. In some cases, LP turbine rotors are being replaced with new rotors, blading, and steam path. Others are replacing LP turbines with new and advanced designs incorporating improved technology, better materials, optimized steam paths, more efficient blading, longer LSB sizes, redesigned exhaust hoods, etc. Unlike the other stages in the LP turbine, the last stage performance is affected by both the upstream (load) and downstream (condenser) conditions. While the LP turbines are being upgraded or replaced, no major modifications or upgrades are being made to the condensers. To address vibration effects due to increased flows and velocities from power uprates, the condenser tubes may be staked. Circulating water pumps may or may not be upgraded depending upon the particular application. Consequently, while improvements in LP turbines lead to more efficient utilization of the available energy and higher output, the last stage performance may be out of synchronization with the existing condenser/cooling system. Undersized or oversized LSB sizes in relation to the unit rating and end loading may result in less than optimum performance depending upon the design and operating range of the condenser/cooling system. This paper examines the various factors that affect last stage performance of LP turbines. Using a case study, it discusses the relationships between the last stage, the unit rating, the end loading, and the operating range of the condenser/cooling system. It examines different last stage exhaust loss curves and provides recommendations for selection of LSB sizes for optimum performance.
Robust Strategies for Forced Response Reduction of Bladed Disks Based on Large Mistuning Concept
Authors: Nikolic M. , Petrov E. P. , Ewins D. J.
Published: March 2008

In this paper, robust maximum forced response reduction strategies based on a “large mistuning” concept are introduced, including both (i) random and (ii) deterministic approaches. An industrial bladed fan disk serves as an application example for a reliability assessment of the aforementioned strategies using two well-established tools for uncertainty analysis: (i) statistics and (ii) sensitivity and robustness. The feasibility and other practical aspects of implementing large mistuning as a means of preventing excessive forced response levels caused by random mistuning and ensuring the predictability of the response are discussed.
Identification of Rotordynamic Forces in a Flexible Rotor System Using Magnetic Bearings
Authors: Zutavern Zachary S. , Childs Dara W.
Published: March 2008

A method is presented for parameter identification of an annular gas seal on a flexible-rotor test rig. Dynamic loads are applied by magnetic bearings (MBs) that support the rotor. MB forces are measured using fiber-optic strain gauges that are bonded to the poles of the MBs. In addition to force and position measurements, a finite element rotor model is required for the identification algorithm. The FE rotor model matches free-free characteristics of the test rotor. The addition of smooth air sealed to the system introduces stiffness and damping terms for identification that are representative of reaction forces in turbomachines. Tests are performed to experimentally determine seal stiffness and damping coefficients for different running speeds and preswirl conditions. Stiffness and damping coefficients are determined using a frequency domain identification method. This method uses an iterative approach to minimize error between theoretical and experimental transfer functions. Test results produce seal coefficients with low uncertainties.
Vortex Breakdown in Swirling Fuel Injector Flows
Authors: Spencer Adrian , McGuirk James J. , Midgley Kris
Published: March 2008

It is well known that the process of vortex breakdown plays an important role in establishing the near-field aerodynamic characteristics of fuel injectors, influencing fuel/air mixing and flame stability. The precise nature of the vortex breakdown can take on several forms, which have been shown in previous papers to include both a precessing vortex core (PVC) and the appearance of multiple helical vortices formed in the swirl stream shear layer. The unsteady dynamics of these particular features can play an important role in combustion induced oscillations. The present paper reports an experimental investigation, using particle image velocimetry (PIV) and hot-wire anemometry, to document variations in the relative strength of PVC and helical vortex patterns as the configuration of a generic fuel injector is altered. Examples of geometric changes that have been investigated include: the combination of an annular swirl stream with and without a central jet; variation in geometric details of the swirler passage, e.g., alteration in the swirler entry slots to change swirl number, and variations in the area ratio of the swirler passage. The results show that these geometric variations can influence: the axial location of the origin of the helical vortices (from inside to outside the fuel injector), and the strength of the PVC. For example, in a configuration with no central jet (swirl number S=0.72), the helical vortex pattern was much less coherent, but the PVC was much stronger than when a central jet was present. These changes modify the magnitude of the turbulence energy in the fuel injector near field dramatically, and hence have an important influence on fuel air mixing patterns.
Critical Analysis of the Available Ammonia Horizontal In-Tube Flow Boiling Heat Transfer Correlations for Liquid Overfeed Evaporators
Authors: Ablanque N. , Rigola J. , Oliet C. , Castro J.
Published: March 2008

The aim of this work is to present a critical examination of both the available experimental data and the performance of the available heat transfer correlations for oil-free ammonia horizontal in-tube boiling at fin-and-tube-type air-to-refrigerant liquid overfeed evaporation conditions. First, a selection and comparison of the experimental database found in the open literature at the mentioned working conditions is presented. Subsequently, after a short description of the most relevant heat transfer correlations, and in accordance with the selected data, a detailed analysis of the performance of each correlation is carried out. Results show an important divergence between the experimental data sets and conclude that the presently available correlations show considerable discrepancies in heat transfer coefficients within the selected conditions.
Finite Element Simulation on Natural Convection Flow in a Triangular Enclosure Due to Uniform and Nonuniform Bottom Heating
Authors: Roy S. , Basak Tanmay , Thirumalesha Ch. , Krishna Ch. Murali
Published: March 2008

A penalty finite element analysis with biquadratic elements has been carried out to investigate natural convection flows within an isosceles triangular enclosure with an aspect ratio of 0.5. Two cases of thermal boundary conditions are considered with uniform and nonuniform heating of bottom wall. The numerical solution of the problem is illustrated for Rayleigh numbers (Ra), 103⩽Ra⩽105 and Prandtl numbers (Pr), 0.026⩽Pr⩽1000. In general, the intensity of circulation is found to be larger for nonuniform heating at a specific Pr and Ra. Multiple circulation cells are found to occur at the central and corner regimes of the bottom wall for a small Prandtl number regime (Pr=0.026−0.07). As a result, the oscillatory distribution of the local Nusselt number or heat transfer rate is seen. In contrast, the intensity of primary circulation is found to be stronger, and secondary circulation is completely absent for a high Prandtl number regime (Pr=0.7–1000). Based on overall heat transfer rates, it is found that the average Nusselt number for the bottom wall is 2 times that of the inclined wall, which is well, matched in two cases, verifying the thermal equilibrium of the system. The correlations are proposed for the average Nusselt number in terms of the Rayleigh number for a convection dominant region with higher Prandtl numbers (Pr=0.7 and 10).
Numerical Study of Dielectric Fluid Bubble Behavior Within Diverging External Electric Fields
Authors: Pearson Matthew R. , Seyed-Yagoobi Jamal
Published: March 2008

A three-dimensional mathematical model is presented that models bubble deformation of a dielectric fluid due to the presence of a nonuniform electric field and calculates the net dielectrophoretic force that is exerted by the electric field on the bubble. The study includes the development of a method of predicting the shape of a bubble based on the arbitrary distribution of stresses over its surface without requiring an axisymmetric configuration. The reciprocal effect of the bubble’s presence on the electric field is also incorporated into the model, and dimensional analysis is used to obtain a single key parameter that governs the bubble deformation phenomenon. Numerical implementation of the mathematical model shows that the bubble deformation can be significant. Furthermore, bubble deformation and electric field distortion can have significant effects on the dielectrophoretic behavior of bubbles in nonuniform fields, especially within small-scale devices where the bubble size and electrode spacing are similar in magnitude.
Numerical Investigation on the Effects of Pressure Drop on Thermal Behavior of Porous Burners
Authors: El-Hossaini M. Khosravy , Maerefat M. , Mazaheri K.
Published: March 2008

This article aims to study the effect of pressure drop on the thermal behavior of porous burners. Since the reticulated ceramics are used in the burners’ construction, in the previous researches pressure drop arising from flow velocity was ignored. This research has showed that due to the increase of speed resulting from combustion, the consequence pressure drop creates considerable effects on the thermal performance of porous burners. To study this subject, the temperature of a point on the burner axis has been taken to be constant. The burned gas and exit surface temperature were obtained almost the same for two conditions, one with the pressure held constant and the other with a pressure drop. Results show that the firing rate was decreased up to 18%, compared to the constant pressure case. The thermal radiative efficiency of radiant porous burners, in which the pressure drop has been considered, was increased about 3–5% for the studied equivalence ratio of methane-air combustion.
Heterogeneous Nucleation Experiments Bridging the Scale from Molecular Ion Clusters to Nanoparticles
Authors: Winkler Paul M. , Steiner Gerhard , Vrtala Aron , Vehkamäki Hanna , Noppel Madis , Lehtinen Kari E. J. , Reischl Georg P. , Wagner Paul E. , Kulmala Markku
Published: March 2008

Generation, investigation, and manipulation of nanostructured materials are of fundamental and practical importance for several disciplines, including materials science and medicine. Recently, atmospheric new particle formation in the nanometer-size range has been found to be a global phenomenon. Still, its detailed mechanisms are mostly unknown, largely depending on the incapability to generate and measure nanoparticles in a controlled way. In our experiments, an organic vapor (
n
-propanol) condenses on molecular ions, as well as on charged and uncharged inorganic nanoparticles, via initial activation by heterogeneous nucleation. We found a smooth transition in activation behavior as a function of size and activation to occur well before the onset of homogeneous nucleation. Furthermore, nucleation enhancement for charged particles and a substantial negative sign preference were quantitatively detected.
Hepatic Glucose Sensing via the CREB Coactivator CRTC2
Authors: Dentin Renaud , Hedrick Susan , Xie Jianxin , Yates John , Montminy Marc
Published: March 2008

Chronic hyperglycemia contributes to the development of diabetes-associated complications. Increases in the concentration of circulating glucose activate the hexosamine biosynthetic pathway (HBP) and promote the O-glycosylation of proteins by O-glycosyl transferase (OGT). We show that OGT triggered hepatic gluconeogenesis through the O-glycosylation of the transducer of regulated cyclic adenosine monophosphate response element–binding protein (CREB) 2 (TORC2 or CRTC2). CRTC2 was O-glycosylated at sites that normally sequester CRTC2 in the cytoplasm through a phosphorylation-dependent mechanism. Decreasing amounts of O-glycosylated CRTC2 by expression of the deglycosylating enzyme O-GlcNAcase blocked effects of glucose on gluconeogenesis, demonstrating the importance of the HBP in the development of glucose intolerance.
Complexities of a Continent
Authors: Abimiku Alash'le G.
Published: March 2008

HIV/AIDS, Illness, and African Well-Being
.
Toyin Falola and Matthew M. Heaton, Eds.
. University of Rochester Press, Rochester, NY, 2007. 428 pp. $75. ISBN 9781580462402.Rochester Studies in African History and the Diaspora.

The authors discuss the historical and contemporary contexts of health challenges (especially AIDS) in Africa.
Prevalence of Hepatitis E Virus Infection in Children in the Northeast of Spain
Authors: Buti Maria , Plans Pere , Domínguez Angela , Jardi Rossend , Frias Francisco Rodriguez , Esteban Rafael , Salleras Luis , Plasencia Antoni
Published: March 2008

The prevalence of immunoglobulin G (IgG) anti-hepatitis E virus (anti-HEV) antibodies was studied with a representative sample of 1,249 healthy children aged between 6 and 15 years. IgG anti-HEV antibodies were detected in 57 (4.6%) of the 1,249 samples analyzed, suggesting that some children are exposed to HEV in early childhood.
Measuring Immunoglobulin G Antibodies to Tetanus Toxin, Diphtheria Toxin, and Pertussis Toxin with Single-Antigen Enzyme-Linked Immunosorbent Assays and a Bead-Based Multiplex Assay
Authors: Reder Sabine , Riffelmann Marion , Becker Christian , Wirsing von König Carl Heinz
Published: March 2008

Bead-based assay systems offer the possibility of measuring several specific antibodies in one sample simultaneously. This study evaluated a vaccine panel of a multianalyte system that measures antibodies to tetanus toxin, diphtheria toxin, and pertussis toxin (PT) from
Bordetella pertussis
. The antibody concentrations of human immunoglobulin G (IgG) to PT, tetanus toxin, and diphtheria toxin were measured in 123 serum pairs (total of 246 sera) from a vaccine study. The multianalyte bead assay was compared to a standardized in-house IgG- anti-PT enzyme-linked immunosorbent assay (ELISA) of the German reference laboratory for bordetellae, as well as to various commercially available ELISAs for anti-PT IgG, anti-tetanus IgG, and anti-diphtheria IgG. The results of the multiplex assay regarding the antibodies against diphtheria toxin compared favorably with a regression coefficient of 0.938 for values obtained with an ELISA from the same manufacturer used as a reference. Similarly, antibodies to tetanus toxin showed a correlation of 0.910 between the reference ELISA and the multianalyte assay. A correlation coefficient of 0.905 was found when an “in-house” IgG anti-PT and the multiplex assay were compared. Compared to single ELISA systems from two other manufacturers, the multiplex assay performed similarly well or better. The multianalyte assay system was a robust system with fast and accurate results, analyzing three parameters simultaneously in one sample. The system was well suited to quantitatively determine relevant vaccine induced antibodies compared to in-house and commercially available single-antigen ELISA systems.
Agammaglobulinemia and
Staphylococcus aureus
Botryomycosis in a Cohort of Related Sentinel Swiss Webster Mice
Authors: Bridgeford Erin C. , Fox James G. , Nambiar Prashant R. , Rogers Arlin B.
Published: March 2008

Sentinel mouse seroconversion to infectious agents is critical for laboratory animal facility disease monitoring. We report spontaneous emergence of non-sex-linked agammaglobulinemia with B-cell deficiency and cutaneous
Staphylococcus aureus
granulomatosis (botryomycosis) in a cohort of related Swiss Webster sentinel mice. Our experience reinforces the importance of immunocompetency validation in surveillance programs.
High-Throughput Genotyping of
Salmonella enterica
Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia
Authors: Baker Stephen , Holt Kathryn , van de Vosse Esther , Roumagnac Philippe , Whitehead Sally , King Emma , Ewels Philip , Keniry Andrew , Weill François-Xavier , Lightfoot Diane , van Dissel Jaap T. , Sanderson Kenneth E. , Farrar Jeremy , Achtman Mark , Deloukas Panagiotis , Dougan Gordon
Published: March 2008

High-throughput epidemiological typing systems that provide phylogenetic and genotypic information are beneficial for tracking bacterial pathogens in the field. The incidence of
Salmonella enterica
serovar Typhi infection in Indonesia is high and is associated with atypical phenotypic traits such as expression of the j and the z66 flagellum antigens. Utilizing a high-throughput genotyping platform to investigate known nucleotide polymorphisms dispersed around the genome, we determined the haplotypes of 140 serovar Typhi isolates associated with Indonesia. We identified nine distinct serovar Typhi haplotypes circulating in Indonesia for more than 30 years, with eight of these present in a single Jakarta suburb within a 2-year period. One dominant haplotype, H59, is associated with j and z66 flagellum expression, representing a potential pathotype unique to Indonesia. Phylogenetic analysis suggests that H59 z66
+
, j
+
isolates emerged relatively recently in terms of the origin of serovar Typhi and are geographically restricted. These data demonstrate the potential of high-throughput genotyping platforms for analyzing serovar Typhi populations in the field. The study also provides insight into the evolution of serovar Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, that is internet friendly, and that has global utility.
Evaluation of Different Techniques for Identification of Human Papillomavirus Types of Low Prevalence
Authors: Sabol Ivan , Salakova Martina , Smahelova Jana , Pawlita Michal , Schmitt Markus , Gašperov Nina Milutin , Grce Magdalena , Tachezy Ruth
Published: March 2008

Human papillomaviruses (HPVs) have been recognized as etiologic factors in a variety of diseases. Due to the large number of HPV types, methods for HPV genotyping are difficult to standardize. Despite this fact, several methods exist, and some of them are available commercially. In this study, we evaluated the Roche Diagnostics linear array (LA) HPV genotyping assay, the Innogenetics INNO-LiPA (line probe assay [LiPA]), and two noncommercial reverse line blot (RLB) assays based on either primers GP5+ and GP6+ (GP) or newly designed broad-spectrum primers BSGP5+ and BSGP6+ (BS). The reliabilities of these assays were tested with a wide spectrum of HPV types less prevalent in cervical samples. This is the first study to compare the performance of the most widely used HPV genotyping methods with selected samples positive for low-prevalence HPV types. We focused on interassay agreement, both overall and type specific, in cases with single and/or multiple HPV infections. Interassay agreement was moderate in cases of single HPV infections and poor in cases of multiple HPV infections. The LA and the BS-based RLB assays found a higher rate of cases positive for multiple HPV types than LiPA and the GP-based RLB assay. The weakest capability in detecting multiple HPV infections was observed for LiPA. The use of only one assay in epidemiological and clinical studies might lead to biased conclusions. Therefore, a universally evaluated and agreed upon HPV typing assay or a combination of current assays is needed for possible clinical applications, and knowledge of their limitations is advised.
Evaluation of the New Micronaut-
Candida
System Compared to the API ID32C Method for Yeast Identification
Authors: Szabó Z. , Tóth B. , Kovács M. , Kardos G. , Maráz A. , Rozgonyi F. , Majoros L.
Published: March 2008

A new system, Micronaut-
Candida
, was compared to API ID32C to identify 264 yeast (
Candida albicans
,
C. parapsilosis
,
C. tropicalis
,
C. krusei
,
C. inconspicua
,
C. norvegensis
,
C. lusitaniae
,
C. guilliermondii
,
C. dubliniensis
,
C. pulcherrima
,
C. famata
,
C. rugosa
,
C. glabrata
,
C. kefyr
,
C. lipolytica
,
C. catenulata
,
C. neoformans
,
Geotrichum
and
Trichosporon
species,
Rhodotorula glutinis
, and
Saccharomyces cerevisiae
) clinical isolates. Results were in concordance in 244 cases. Eighteen out of the 20 of discordant results were correctly identified by Micronaut-
Candida
but not by API ID32C, as confirmed by PCR ribotyping.
Mutations in the Human Immunodeficiency Virus Type 1 Polypurine Tract (PPT) Reduce the Rate of PPT Cleavage and Plus-Strand DNA Synthesis
Authors: McWilliams M. J. , Julias J. G. , Hughes S. H.
Published: March 2008

Previously, we analyzed the effects of point mutations in the human immunodeficiency virus type 1 (HIV-1) polypurine tract (PPT) and found that some mutations affected both titer and cleavage specificity. We used HIV-1 vectors containing two PPTs and the D116N integrase active-site mutation in a cell-based assay to measure differences in the relative rates of PPT processing and utilization. The relative rates were measured by determining which of the two PPTs in the vector is used to synthesize viral DNA. The results indicate that mutations that have subtle effects on titer and cleavage specificity can have dramatic effects on rates of PPT generation and utilization.
Human Cytomegalovirus UL97 Kinase Activity Is Required for the Hyperphosphorylation of Retinoblastoma Protein and Inhibits the Formation of Nuclear Aggresomes
Authors: Prichard Mark N. , Sztul Elizabeth , Daily Shannon L. , Perry Amie L. , Frederick Samuel L. , Gill Rachel B. , Hartline Caroll B. , Streblow Daniel N. , Varnum Susan M. , Smith Richard D. , Kern Earl R.
Published: March 2008

Cells infected with human cytomegalovirus in the absence of UL97 kinase activity produce large nuclear aggregates that sequester considerable quantities of viral proteins. A transient expression assay suggested that pp71 and IE1 were also involved in this process, and this suggestion was significant, since both proteins have been reported to interact with components of promyelocytic leukemia (PML) bodies (ND10) and also interact functionally with retinoblastoma pocket proteins (RB). PML bodies have been linked to the formation of nuclear aggresomes, and colocalization studies suggested that viral proteins were recruited to these structures and that UL97 kinase activity inhibited their formation. Proteins associated with PML bodies were examined by Western blot analysis, and pUL97 appeared to specifically affect the phosphorylation of RB in a kinase-dependent manner. Three consensus RB binding motifs were identified in the UL97 kinase, and recombinant viruses were constructed in which each was mutated to assess a potential role in the phosphorylation of RB and the inhibition of nuclear aggresome formation. The mutation of either the conserved LxCxE RB binding motif or the lysine required for kinase activity impaired the ability of the virus to stabilize and phosphorylate RB. We concluded from these studies that both UL97 kinase activity and the LxCxE RB binding motif are required for the phosphorylation and stabilization of RB in infected cells and that this effect can be antagonized by the antiviral drug maribavir. These data also suggest a potential link between RB function and the formation of aggresomes.
Distinct Ex Vivo Susceptibility of B-Cell Subsets to Epstein-Barr Virus Infection According to Differentiation Status and Tissue Origin
Authors: Dorner Marcus , Zucol Franziska , Berger Christoph , Byland Rahel , Melroe Gregory T. , Bernasconi Michele , Speck Roberto F. , Nadal David
Published: March 2008

Epstein-Barr virus (EBV) uses tonsils as the portal of entry to establish persistent infection. EBV is found in various B-cell subsets in tonsils but exclusively in memory B cells in peripheral blood. The in vitro susceptibilities of B-cell subsets to EBV infection have been studied solely qualitatively. In this work, we examined quantitatively the in vitro susceptibilities of various B-cell subsets from different tissue origins to EBV infection. First, we established a centrifugation-based inoculation protocol (spinoculation) that resulted in a significantly increased proportion of infected cells compared to that obtained by conventional inoculation, enabling a detailed susceptibility analysis. Importantly, B-cell infection occurred via the known EBV receptors and infected cells showed EBV mRNA expression patterns similar to those observed after conventional inoculation, validating our approach. Tonsillar naïve and memory B cells were infected ex vivo at similar frequencies. In contrast, memory B cells from blood, which represent B cells from various lymphoid tissues, were infected at lower frequencies than their naïve counterparts. Immunoglobulin A (IgA)-positive or IgG-positive tonsillar memory B cells were significantly more susceptible to EBV infection than IgM-positive counterparts. Memory B cells were transformed with lower efficiency than naïve B cells. This result was paralleled by lower proliferation rates. In summary, these data suggest that EBV exploits the B-cell differentiation status and tissue origin to establish persistent infection.
Mitochondrial Dysfunction in Lyssavirus-Induced Apoptosis
Authors: Gholami Alireza , Kassis Raïd , Real Eléonore , Delmas Olivier , Guadagnini Stéphanie , Larrous Florence , Obach Dorothée , Prevost Marie-Christine , Jacob Yves , Bourhy Hervé
Published: March 2008

Lyssaviruses are highly neurotropic viruses associated with neuronal apoptosis. Previous observations have indicated that the matrix proteins (M) of some lyssaviruses induce strong neuronal apoptosis. However, the molecular mechanism(s) involved in this phenomenon is still unknown. We show that for Mokola virus (MOK), a lyssavirus of low pathogenicity, the M (M-MOK) targets mitochondria, disrupts the mitochondrial morphology, and induces apoptosis. Our analysis of truncated M-MOK mutants suggests that the information required for efficient mitochondrial targeting and dysfunction, as well as caspase-9 activation and apoptosis, is held between residues 46 and 110 of M-MOK. We used a yeast two-hybrid approach, a coimmunoprecipitation assay, and confocal microscopy to demonstrate that M-MOK physically associates with the subunit I of the cytochrome
c
(cyt-
c
) oxidase (CcO) of the mitochondrial respiratory chain; this is in contrast to the M of the highly pathogenic Thailand lyssavirus (M-THA). M-MOK expression induces a significant decrease in CcO activity, which is not the case with M-THA. M-MOK mutations (K77R and N81E) resulting in a similar sequence to M-THA at positions 77 and 81 annul cyt-
c
release and apoptosis and restore CcO activity. As expected, the reverse mutations, R77K and E81N, introduced in M-THA induce a phenotype similar to that due to M-MOK. These features indicate a novel mechanism for energy depletion during lyssavirus-induced apoptosis.
Virion-Wide Protein Interactions of Kaposi's Sarcoma-Associated Herpesvirus
Authors: Rozen Ramona , Sathish Narayanan , Li Yong , Yuan Yan
Published: March 2008

Herpesvirus virions are highly organized structures built through specific protein-protein interactions. Thus, revelation of the protein interactions among virion proteins will shed light on the processes and the mechanisms of virion formation. Recently, we identified 24 virion proteins of Kaposi's sarcoma-associated herpesvirus (KSHV), using a proteomic approach (F. X. Zhu et al., J. Virol. 79:800-811, 2005). In the current study, a comprehensive analysis of protein-protein interaction between KSHV virion proteins was carried out using yeast two-hybrid (Y2H) and coimmunoprecipitation (co-IP) approaches. Every pairwise combination between KSHV tegument and capsid proteins, between tegument and envelope proteins, and among tegument proteins was tested for possible binary interaction. Thirty-seven protein-protein interactions were identified by both Y2H and co-IP analyses. The results revealed interactions between tegument and capsid proteins such as that of open reading frame 64 (ORF64) with ORF25 (major capsid protein [MCP]), ORF62 (triplex-1 [TRI-1]), and ORF26 (TRI-2). Many interactions were detected among the tegument proteins. ORF64 was found to interact with several tegument proteins including ORF11, ORF21, ORF33, ORF45, ORF63, ORF75, and ORF64 itself, suggesting that ORF64 may serve as a hub protein and play a role in recruiting tegument proteins during tegumentation and virion assembly. Our investigation also revealed redundant interactions between tegument proteins and envelope glycoproteins. These interactions are believed to contribute to final envelopment in virion assembly. Overall, this study allows us to establish a virion-wide protein interaction map, which provides insight into the architecture of the KSHV virion and sets up a foundation for exploring the functions of these proteins in viral particle assembly.
Expression of Gamma Interferon-Dependent Genes Is Blocked Independently by Virion Host Shutoff RNase and by US3 Protein Kinase
Authors: Liang Li , Roizman Bernard
Published: March 2008

Gamma interferon receptor α (IFN-γRα) is stable but posttranslationally modified in herpes simplex virus 1(F) [HSV-1(F)]-infected cells. Studies with antibody directed to the phosphorylation site indicate that IFN-γRα is phosphorylated by the US3 kinase. The modification is abolished in cells infected with ΔUS3, ΔUL13, or Δ(US3/UL13) mutant virus. Transcripts of the IFN-γ-dependent genes do not accumulate in cells transduced with the US3 protein kinase and treated with IFN-γ. In contrast, the accumulation of IFN-γ-dependent gene transcripts is suppressed in cells infected with the wild-type virus, in cells infected with the ΔUS3 mutant virus, and to a lesser extent in the ΔUL41 virus-infected cells. The accumulation of IFN-γ-dependent gene transcripts in ΔUL41-infected cells could be due at least in part to a significant delay and reduction in the accumulation of the US3 protein. The results suggest that the expression of IFN-γ-dependent genes is blocked independently by the degradation of IFN-γ-dependent gene transcripts—a function of the virion host shutoff RNase—and by posttranslational modification of the IFN-γRα protein.
Synthesis of Some Impurities and/or Degradation Products of Atorvastatin
Authors: Stach Jan , Havlíček Jaroslav , Plaček Lukáš , Rádl Stanislav
Published: March 2008

Synthesis of some impurities and/or degradation products of atorvastatin, calcium (3R,5R)-7- [2-(4-fluorophenyl)-5-isopropyl-3-phenyl-4-(phenylcarbamoyl)pyrrol-1-yl]-3,5-dihydroxyheptanoate, is described. These include its desfluoro analog, the corresponding (3S,5S)- and (3S,5R)-epimers, atorvastatin lactone, and some other potential impurities. The synthesized compounds as well as the corresponding intermediates were characterized by 1H NMR, 13C NMR and MS.
Synthesis and Reactions of 5-Methylthieno[2',3':5,6]pyrimido[2,1-a]isoindol-4(5H)-one
Authors: Kysil Andriy I. , Voitenko Zoia V. , Wolf Jean-Gérard
Published: March 2008

The reaction of 2-(bromomethyl)benzonitrile with methyl 3-aminothiophene-2-carboxylate results in two tautomeric thienopyrimidoisoindolones. Their methylation yields 5-methylthieno[2',3':5,6]pyrimido[2,1-a]isoindol-4(5H)-one which reacts with N-substituted maleimides and dimethyl acetylenedicarboxylate.
Automated immunostaining of cell smears: an alternative to flow cytometry
Authors: Happerfield L C , Saward R , Grimwade L , Bloxham D , Erber W N
Published: March 2008

Aims:

To assess the applicability of an automated tissue immunostainer machine for the phenotypic analysis of peripheral blood and bone marrow aspirate smears.

Methods:

Air-dried smears of peripheral blood and bone marrow from normal individuals and 14 patients with haematological malignancies were stained, following fixation, with a range of antibodies to haemopoietic antigens using both immunoperoxidase and immuno-alkaline phosphatase methods on the Bond-maX (Leica Microsystems) automated immunostaining machine.

Results:

Automated protocols used for staining formalin-fixed paraffin-embedded tissue could be applied to cell smears, giving high quality staining with excellent cytological detail and antigenic preservation for an extensive antibody panel. Optimal quality (morphological preservation and antigen detection without background staining) was obtained with an alkaline phosphatase method and Fast Red chromogenic substrate. Both cell surface and intracellular (cytoplasmic and nuclear) antigens could be detected and gave the expected reactivity.

Conclusions:

Automated immunostaining is possible for haematological smears. It generates consistent high quality staining, with the exception of surface immunoglobulin, and is applicable to haematological and, potentially, cytological smears. It provides a practical alternative to flow cytometry and will have particular application when smears are available and there is no suitable sample for flow cytometry.
SYNCHRONIZATION OF SYSTEMS WITH MULTIPLICATIVE NOISE
Authors: CARABALLO TOMÁS , KLOEDEN PETER E. , NEUENKIRCH ANDREAS
Published: March 2008

The synchronization of Stratonovich stochastic differential equations (SDE) with a one-sided dissipative Lipschitz drift and linear multiplicative noise is investigated by transforming the SDE to random ordinary differential equations (RODE) and synchronizing their dynamics. In terms of the original SDE, this gives synchronization only when the driving noises are the same. Otherwise, the synchronization is modulo exponential factors involving Ornstein–Uhlenbeck processes corresponding to the driving noises. Moreover, this occurs no matter how large the intensity coefficients of the noise.
MARKOV ATTRACTORS: A PROBABILISTIC APPROACH TO MULTIVALUED FLOWS
Authors: FLANDOLI FRANCO , LANGA JOSÉ A.
Published: March 2008

Deterministic ordinary differential equations without uniqueness may be studied in the framework of Markov selections. This motivates a concept of Markov attractor, namely a set which attracts, in a suitable probabilistic sense, a Markov kernel. The relationship with respect to global attractors for multivalued flows in the sense of Ball [4] or Melnik and Valero [18] is also established.
STABILIZING WITH A HAMMER
Authors: SANZ-SERNA J. M.
Published: March 2008

We show that, with high probability, the undamped, nonlinear inverted pendulum may be "stabilized" over bounded time-intervals if subjected to random shocks.
PROTEIN STRUCTURE–STRUCTURE ALIGNMENT WITH DISCRETE FRÉCHET DISTANCE
Authors: JIANG MINGHUI , XU YING , ZHU BINHAI
Published: March 2008

Matching two geometric objects in two-dimensional (2D) and three-dimensional (3D) spaces is a central problem in computer vision, pattern recognition, and protein structure prediction. In particular, the problem of aligning two polygonal chains under translation and rotation to minimize their distance has been studied using various distance measures. It is well known that the Hausdorff distance is useful for matching two point sets, and that the Fréchet distance is a superior measure for matching two polygonal chains. The discrete Fréchet distance closely approximates the (continuous) Fréchet distance, and is a natural measure for the geometric similarity of the folded 3D structures of biomolecules such as proteins. In this paper, we present new algorithms for matching two polygonal chains in two dimensions to minimize their discrete Fréchet distance under translation and rotation, and an effective heuristic for matching two polygonal chains in three dimensions. We also describe our empirical results on the application of the discrete Fréchet distance to protein structure–structure alignment.
USING FORMAL CONCEPT ANALYSIS FOR MICROARRAY DATA COMPARISON
Authors: CHOI V. , HUANG Y. , LAM V. , POTTER D. , LAUBENBACHER R. , DUCA K.
Published: March 2008

Microarray technologies, which can measure tens of thousands of gene expression values simultaneously in a single experiment, have become a common research method for biomedical researchers. Computational tools to analyze microarray data for biological discovery are needed. In this paper, we investigate the feasibility of using formal concept analysis (FCA) as a tool for microarray data analysis. The method of FCA builds a (concept) lattice from the experimental data together with additional biological information. For microarray data, each vertex of the lattice corresponds to a subset of genes that are grouped together according to their expression values and some biological information related to gene function. The lattice structure of these gene sets might reflect biological relationships in the dataset. Similarities and differences between experiments can then be investigated by comparing their corresponding lattices according to various graph measures. We apply our method to microarray data derived from influenza-infected mouse lung tissue and healthy controls. Our preliminary results show the promise of our method as a tool for microarray data analysis.
FITTING PROTEIN CHAINS TO CUBIC LATTICE IS NP-COMPLETE
Authors: MAŇUCH JÁN , GAUR DAYA RAM
Published: March 2008

It is known that folding a protein chain into a cubic lattice is an NP-complete problem. We consider a seemingly easier problem: given a three-dimensional (3D) fold of a protein chain (coordinates of its C α atoms), we want to find the closest lattice approximation of this fold. This problem has been studied under names such as "lattice approximation of a protein chain", "the protein chain fitting problem", and "building of protein lattice models". We show that this problem is NP-complete for the cubic lattice with side close to 3.8 Å and coordinate root mean square deviation.
LIKELIHOOD OF A PARTICULAR ORDER OF GENETIC MARKERS AND THE CONSTRUCTION OF GENETIC MAPS
Authors: TEWARI S. , ARNOLD J. , BHANDARKAR S. M.
Published: March 2008

We model the recombination process of fungal systems via chromatid exchange in meiosis, which accounts for any type of bivalent configuration in a genetic interval in any specified order of genetic markers, for both random spore and tetrad data. First, a probability model framework is developed for two genes and then generalized for an arbitrary number of genes. Maximum likelihood estimators (MLEs) for both random and tetrad data are developed. It is shown that the MLE of recombination for tetrad data is uniformly more efficient over that from random spore data by a factor of at least 4 usually. The MLE for the generalized probability framework is computed using the expectation-maximization (EM) algorithm. Pearson's chi-squared statistic is computed as a measure of goodness of fit using a product-multinomial setup. We implement our model with genetic marker data on the whole genome of Neurospora crassa. Simulated annealing is used to search for the best order of genetic markers for each chromosome, and the goodness of fit value is evaluated for model assumptions. Inferred map orders are corroborated by genomic sequence, with the exception of linkage groups I, II, and V.
Constitutive nitric oxide differentially regulates Na-H and Na-glucose cotransport in intestinal epithelial cells
Authors: Coon Steven , Kekuda Ramesh , Saha Prosenjit , Talukder Jamilur R. , Sundaram Uma
Published: March 2008

Previous in vivo studies suggest that constitutive nitric oxide (cNO) can regulate Na- glucose cotransport (SGLT1) and Na-H exchange (NHE3) in rabbit intestinal villus cells. Whether these two primary Na absorbing pathways are directly regulated by cNO and the mechanisms of this regulation in the enterocyte is not known. Thus nontransformed rat small intestinal epithelial cells (IEC-18) were treated with NG-nitro-l-arginine methyl ester (l-NAME), which directly decreased cNO in these cells. l-NAME treatment decreased SGLT1 in IEC-18 cells. Kinetic studies demonstrated that the mechanism of inhibition was secondary to a decrease in the affinity of the cotransporter for glucose without a change in the number of cotransporters. In contrast, l-NAME treatment increased NHE3 in IEC-18 cells. Kinetic studies demonstrated that the mechanism of stimulation was by increasing the number of the exchangers without a change in the affinity for Na. Quantitative RT-PCR (RTQ-PCR) and Western blot analysis of SGLT1 demonstrated no change in mRNA and protein, respectively. RTQ-PCR and Western blot analysis of NHE3 indicated that NHE3 was increased by l-NAME treatment by an increase in mRNA and protein, respectively. These results indicate that decreased cNO levels directly mediate the inhibition of SGLT1 and stimulation of NHE3 in intestinal epithelial cells. Thus cNO directly but uniquely regulates the two primary Na-absorptive pathways in the mammalian small intestine.
Differential sympathetic drive to adipose tissues after food deprivation, cold exposure or glucoprivation
Authors: Brito Nilton A. , Brito Márcia N. , Bartness Timothy J.
Published: March 2008

Surplus energy is principally stored in white adipose tissue (WAT) as triacylglycerol and mobilized via lipolysis through norepinephrine (NE) released from sympathetic nervous system terminals innervating WAT. We demonstrated that central melanocortin receptor agonism provokes differential sympathetic drives across WAT pads and interscapular brown adipose tissue (IBAT). Here we tested for differential WAT and IBAT sympathetic drive to known lipolytic stimuli {glucoprivation [2-deoxy-d-glucose (2-DG)], cold exposure (5°C), food deprivation (16 h), or both cold exposure and food deprivation} by measuring NE turnover (NETO). Only inguinal WAT NETO significantly increased across all stimuli. Dorsal subcutaneous WAT NETO only increased with glucoprivation. Retroperitoneal WAT NETO increased with glucoprivation, cold and cold + food deprivation, but not by food deprivation. Epididymal WAT NETO was unaffected by glucoprivation but increased with cold, cold + food deprivation or food deprivation, but to a small significant degree. IBAT NETO was unaffected by glucoprivation or food deprivation, but increased with cold and cold + food deprivation. Plasma glucose decreased with food deprivation and increased with 2-DG administration or cold exposure. Plasma glycerol was increased with food deprivation, cold, and their combination but not with 2-DG, whereas plasma free fatty acids increased with food deprivation, cold + food deprivation, and 2-DG. These data show differential sympathetic drive to WAT and BAT for four different lipolytic stimuli, exemplifying the fat pad-specific pattern of WAT sympathetic drive across lipid-mobilizing conditions and emphasizing the need to analyze multiple adipose depots for measures of NETO and likely most measures.
Potent cardiovascular actions of homologous adrenomedullins in eels
Authors: Nobata Shigenori , Ogoshi Maho , Takei Yoshio
Published: March 2008

Adrenomedullin (AM), known as a multifunctional hormone in mammals, forms a unique family of five paralogous peptides in teleost fish. To examine their cardiovascular effects using homologous AMs in eels, we isolated cDNAs encoding four eel AMs, and named AM1 (ortholog of mammalian AM), AM2, AM3 (paralog of AM2 generated only in teleost lineage), and AM5 according to the known teleost AM sequences. Unlike pufferfish, not only AM1 but AM2/3 and AM5 were expressed ubiquitously in various eel tissues. Synthetic mature AM1, AM2, and AM5 exhibited vasodepressor effects after intra-arterial injections, and the effects were more potent at dorsal aorta than at ventral aorta. This indicates that AMs preferentially act on peripheral resistance vessels rather than on branchial arterioles. The potency was in the order of AM2 = AM5 ≫ AM1 in both freshwater (FW) and seawater (SW) eels, which is different from the result of mammals in which AM1 is as potent as, or more potent than, AM2 when injected peripherally. The minimum effective dose of AM2 and AM5 in eels was 1/10 that of AM1 in mammals. The hypotension reached 50% at 1.0 nmol/kg of AM2 and AM5, which is much greater than atrial natriuretic peptide (20%), another potent vasodepressor hormone. Even with such hypotension, AMs did not change heart rate in eels. In addition, AM1 increased blood pressure at ventral aorta and dorsal aorta immediately after an initial hypotension at 5.0 nmol/kg, but not with AM2 and AM5. These data strongly suggest that specific receptors for AM2 and AM5 exist in eels, which differ from the AM1 receptors identified in mammals.