bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Characterization of Equine Rotavirus in Ireland
Authors: Collins P. J. , Cullinane A. , Martella V. , O'Shea H. 
Published: August 2008

ABSTRACTGroup A rotaviruses are important causative agents of severe, acute dehydrating diarrhea in foals. A total of 86 rotavirus-positive fecal samples, collected from diarrheic foals from 11 counties in three of the four provinces of Ireland, were obtained from the Irish Equine Centre in Kildare during a 7-year (1999 to 2005) passive surveillance study and were characterized molecularly to establish the VP7 (G type) and VP4 (P type) antigenic specificities. Fifty-eight samples (67.5%) were found to contain G3 viruses, while in 26 samples (30.2%) the rotaviruses were typed as G14 and in 2 samples (2.3%) there was a mixed infection, G3 plus G14. All samples except for two, which were untypeable, were characterized as P[12]. Fifty-eight percent of the samples were obtained from County Kildare, the center of the Irish horse industry, where an apparent shift from G3P[12] to G14P[12] was observed in 2003. By sequence analysis of the VP7 protein, the G3 Irish strains were shown to resemble viruses of the G3A subtype (H2-like) (97.1 to 100% amino acid [aa] identity), while the G14 Irish strains displayed 93.9 to 97.1% aa identity to other G14 viruses. In the VP8* fragment of the VP4 protein, the P[12] Irish viruses displayed high conservation (92.3 to 100% aa) with other equine P[12] viruses. Worldwide, G3P[12] and G14P[12] are the most prevalent equine rotavirus strains, and G3P[12] vaccines have been developed for prevention of rotavirus-associated diarrhea in foals. Investigations of the VP7/VP4 diversity of the circulating equine viruses and the dynamics of strain replacement are important for better assessing the efficacies of the vaccines.
Kinetic Analysis by Real-Time PCR of Hepatitis C Virus (HCV)-Specific T Cells in Peripheral Blood and Liver after Challenge with HCV
Authors: Ramalingam Ramesh K. , Meyer-Olson Dirk , Shoukry Naglaa H. , Bowen David G. , Walker Christopher M. , Kalams Spyros A. 
Published: August 2008

ABSTRACT

Intrahepatic virus-specific CD8
+
T cells are thought to be important for the control of hepatitis C virus (HCV) infection, yet the precise kinetics for the expansion of epitope-specific T cells over the course of infection are difficult to determine with currently available methods. We used a real-time PCR assay to measure the frequency of clonotypic HCV-specific CD8
+
T cells in peripheral blood and snap-frozen liver biopsy specimens of two chimpanzees (
Pan troglodytes
) with previously resolved HCV infection who were rechallenged with HCV. In response to rechallenge, the magnitude of each clonotypic response was 10-fold higher in the liver than in the blood, and the peak clonotype frequency was concurrent with the peak viral load. The higher frequency of HCV-specific clonotypes in the liver than in peripheral blood was maintained for at least 3 months after the clearance of viremia. After antibody-mediated CD8
+
T-cell depletion and another viral challenge, the rebound of these clonotypes was seen prior to an appreciable reconstitution of CD8
+
T-cell values and, again, at higher frequencies in the liver than in peripheral blood. These data demonstrate the importance of intrahepatic virus-specific CD8
+
T cells for the clearance of infection and the rapid kinetics of expansion after virus challenge.
Hidden Virulence Determinants in a Viral Quasispecies In Vivo
Authors: Sanz-Ramos Marta , Díaz-San Segundo Fayna , Escarmís Cristina , Domingo Esteban , Sevilla Noemí 
Published: August 2008

ABSTRACT
The characterization of virulence determinants of pathogenic agents is of utmost relevance for the design of disease control strategies. So far, two classes of virulence determinants have been characterized for viral populations: those imprinted in the nucleotide sequence of some specific genomic regions and those that depend on the complexity of the viral population as such. Here we provide evidence of a virulence determinant that depends neither on a genomic sequence nor on detectable differences in population complexity. Foot-and-mouth disease virus is lethal for C57BL/6 mice showing the highest viral load in pancreas. Virus isolated from pancreas after one passage in mice showed an attenuated phenotype, with no lethality even at the highest dose tested. By contrast, virus from sera of the same mice displayed a virulence similar to that of the parental wild-type clone and virus isolated from spleen displayed an intermediate phenotype. However, viral populations from pancreas, spleen, and serum showed indistinguishable consensus genomic nucleotide sequences and mutant spectrum complexities, as quantified according to the mutation frequencies of both entire genomic nucleotide sequences of biological clones. The results show that the populations with differing virulences cannot be distinguished either by the consensus sequence or by the average complexity of the mutant spectrum. Differential harvesting of virus generated by cell transfection of RNA from serum and pancreas failed to reveal genetic differences between subpopulations endowed with differing virulences. In addition to providing evidence of hidden virulence determinants, this study underlines the capacity of a clone of an RNA virus to rapidly diversify phenotypically in vivo.
Insertion of an EYFP-pp71 (UL82) Coding Sequence into the Human Cytomegalovirus Genome Results in a Recombinant Virus with Enhanced Viral Growth
Authors: Tavalai Nina , Kraiger Martina , Kaiser Nina , Stamminger Thomas 
Published: August 2008

ABSTRACT
The human cytomegalovirus (HCMV) UL82-encoded tegument protein pp71 has recently been shown to activate viral immediate-early (IE) gene expression by neutralizing a cellular intrinsic immune defense instituted by the ND10 protein hDaxx. Pp71 localizes to ND10 upon infection and induces the degradation of hDaxx. Here, we report the successful generation of a recombinant HCMV expressing enhanced yellow fluorescent protein (EYFP) fused to the N terminus of pp71. Intriguingly, insertion of the EYFP-UL82 coding sequence into the HCMV AD169 genome gave rise to a recombinant virus, termed AD169/EYFP-pp71, that replicates to significantly higher titers than wild-type AD169. In particular, we noticed strongly increased protein levels of pp71 after AD169/EYFP-pp71 inoculation. Although the high abundance of pp71 resulted in augmented packaging of the tegument protein into viral particles, no increased hDaxx degradation was detectable upon AD169/EYFP-pp71 infection. In contrast, further investigation revealed a significantly enhanced viral DNA replication compared to wild-type AD169. Thus, we hypothesize that an as-yet-unidentified function of pp71 contributes to the enhanced infectivity of AD169/EYFP-pp71. This assumption is additionally supported by the observation that increased early and late gene expression after AD169/EYFP-pp71 infection occurs independent of elevated IE protein levels. Finally, immunofluorescence analyses confirmed that hDaxx determines the ND10-localization of pp71 upon infection, since pp71 exhibited a nucleolar distribution in the absence of hDaxx. Taken together, we generated a recombinant HCMV that constitutes a useful tool not only to dissect the in vivo dynamics of pp71 subnuclear localization more precisely but also to explore new features of this viral transactivator.
Identification of Direct Transcriptional Targets of the Kaposi's Sarcoma-Associated Herpesvirus Rta Lytic Switch Protein by Conditional Nuclear Localization
Authors: Bu Wei , Palmeri Diana , Krishnan Raghu , Marin Roxana , Aris Virginie M. , Soteropoulos Patricia , Lukac David M. 
Published: August 2008

ABSTRACT
Lytic reactivation from latency is critical for the pathogenesis of Kaposi's sarcoma-associated herpesvirus (KSHV). We previously demonstrated that the 691-amino-acid (aa) KSHV Rta transcriptional transactivator is necessary and sufficient to reactivate the virus from latency. Viral lytic cycle genes, including those expressing additional transactivators and putative oncogenes, are induced in a cascade fashion following Rta expression. In this study, we sought to define Rta's direct targets during reactivation by generating a conditionally nuclear variant of Rta. Wild-type Rta protein is constitutively localized to cell nuclei and contains two putative nuclear localization signals (NLSs). Only one NLS (NLS2; aa 516 to 530) was required for the nuclear localization of Rta, and it relocalized enhanced green fluorescent protein exclusively to cell nuclei. The results of analyses of Rta NLS mutants demonstrated that proper nuclear localization of Rta was required for transactivation and the stimulation of viral reactivation. RTA with NLS1 and NLS2 deleted was fused to the hormone-binding domain of the murine estrogen receptor to generate an Rta variant whose nuclear localization and ability to transactivate and induce reactivation were tightly controlled posttranslationally by the synthetic hormone tamoxifen. We used this strategy in KSHV-infected cells treated with protein synthesis inhibitors to identify direct transcriptional targets of Rta. Rta activated only eight KSHV genes in the absence of de novo protein synthesis. These direct transcriptional targets of Rta were transactivated to different levels and included the genes nut-1/PAN, ORF57/Mta, ORF56/Primase, K2/viral interleukin-6 (vIL-6), ORF37/SOX, K14/vOX, K9/vIRF1, and ORF52. Our data suggest that the induction of most of the KSHV lytic cycle genes requires additional protein expression after the expression of Rta.
Persistent Propagation of Variant Creutzfeldt-Jakob Disease Agent in Murine Spleen Stromal Cell Culture with Features of Mesenchymal Stem Cells
Authors: Akimov Sergey , Yakovleva Oksana , Vasilyeva Irina , McKenzie Carroll , Cervenakova Larisa 
Published: August 2008

ABSTRACT
The transmission of variant Creutzfeldt-Jakob disease (vCJD) through blood transfusions has created new concerns about the iatrogenic spread of transmissible spongiform encephalopathies (TSEs)/prion diseases through blood and plasma-derived products and has increased the need to develop efficient methods for detection of the agent in biologics. Here, we report the first successful generation of spleen-derived murine stromal cell cultures that persistently propagate two mouse-adapted isolates of human TSE agents, mouse-adapted vCJD, and Fukuoka 1. These new cell cultures can be used efficiently for studies of the pathogenesis of the disease, for development of diagnostics and therapeutics, and as a rapid ex vivo assay for TSE inactivation/removal procedures.
Structural Rearrangement within an Enveloped Virus upon Binding to the Host Cell
Authors: Meckes David G. , Wills John W. 
Published: August 2008

ABSTRACT

We have made the surprising discovery that the interactions of herpes simplex virus with its initial cell attachment receptor induce a rapid and highly efficient structural change in the tegument, the region of the virion situated between the membrane and the capsid. It has been known for nearly a decade that viruses can trigger host signaling pathways when they bind to receptors on the cell surface; however, until now there has been no evidence that a signal can be sent in reverse—from the “outside in”—across a viral membrane. Evidence for this signaling event was found during studies of UL16, a tegument protein that is conserved among all the herpesviruses. Previous work has demonstrated that UL16 is bound to capsids isolated from the cytoplasm of infected cells, but this interaction is destabilized during subsequent egress steps, leading to release of the extracellular virion. Pretreatment with
N
-ethylmaleimide, a small, membrane-permeating compound that covalently modifies free cysteines, restabilizes the interaction, thereby permitting the capsid-UL16 complex to be isolated following disruption of virions with NP-40. In the experiments described here, we found that the natural signal for release of UL16 from capsids is sent when virions merely bind to cells at 4°C. The internal change was also observed upon binding to immobilized heparin in a manner that requires viral glycoprotein C. This represents the first example of signaling across a viral envelope following receptor binding.
Analysis of the Interaction between the UL11 and UL16 Tegument Proteins of Herpes Simplex Virus
Authors: Yeh Pei-Chun , Meckes David G. , Wills John W. 
Published: August 2008

ABSTRACT

The UL11 and UL16 tegument proteins of herpes simplex virus are conserved throughout the herpesvirus family. Previous studies have shown that these proteins interact, perhaps to link UL16-bound nucleocapsids to UL11, which resides on the cytoplasmic face of the
trans
-Golgi network, where maturation budding occurs. Little is known about the interaction except that it requires the leucine-isoleucine (LI) and acidic cluster motifs in UL11 and that no other viral proteins are involved. In particular, the important question of whether these two proteins bind to each other directly has not been addressed. Accordingly, UL11 and UL16 were expressed in bacteria, and the purified proteins were found to retain the ability to interact in a manner that was dependent upon the LI and acidic cluster. In an attempt to map the UL11-binding site contained in UL16, a large number of deletion mutants were constructed. The first 40 (nonconserved) amino acids were found to be dispensable, but all the other constructs failed to bind UL11 or had poor expression in transfected cells, suggesting that UL16 is very sensitive to alterations and probably lacks a multidomain structure. As an alternative strategy for identifying residues that are important for the interaction, the cysteines of UL16 were investigated, because many of these are highly conserved. Approximately half of the 20 cysteines in UL16 have been shown to be covalently modified by
N
-ethylmaleimide, and this treatment was found to block the interaction with UL11. Moreover, individual serine replacements of six of the most conserved cysteine residues were made, and four of these disrupted the interaction with UL11 without affecting protein stability. However, the UL11-UL16 interaction does not involve the formation of interspecies disulfide bonds, because binding occurred even when all the cysteines in UL11 were eliminated. Thus, UL16 directly interacts with UL11 and does so in a manner that requires free cysteines.
Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations
Authors: Mitsuya Yumi , Varghese Vici , Wang Chunlin , Liu Tommy F. , Holmes Susan P. , Jayakumar Prerana , Gharizadeh Baback , Ronaghi Mostafa , Klein Daniel , Fessel W. Jeffrey , Shafer Robert W. 
Published: August 2008

ABSTRACTT215 revertant mutations such as T215C/D/E/S that evolve from the nucleoside reverse transcriptase (RT) inhibitor mutations T215Y/F have been found in about 3% of human immunodeficiency virus type 1 (HIV-1) isolates from newly diagnosed HIV-1-infected persons. We used a newly developed sequencing method—ultradeep pyrosequencing (UDPS; 454 Life Sciences)—to determine the frequency with which T215Y/F or other RT inhibitor resistance mutations could be detected as minority variants in samples from untreated persons that contain T215 revertants (“revertant” samples) compared with samples from untreated persons that lack such revertants (“control” samples). Among the 22 revertant and 29 control samples, UDPS detected a mean of 3.8 and 4.8 additional RT amino acid mutations, respectively. In 6 of 22 (27%) revertant samples and in 4 of 29 control samples (14%;P= 0.4), UDPS detected one or more RT inhibitor resistance mutations. T215Y or T215F was not detected in any of the revertant or control samples; however, 4 of 22 revertant samples had one or more T215 revertants that were detected by UDPS but not by direct PCR sequencing. The failure to detect viruses with T215Y/F in the 22 revertant samples in this study may result from the overwhelming replacement of transmitted T215Y variants by the more fit T215 revertants or from the primary transmission of a T215 revertant in a subset of persons with T215 revertants.
Minimal response time design for linear multivariable sampled-data control systems
Authors: Steel G.K. , Puri S.N. 
Published: August 2008

The method of minimum, finite settling time design used for single-loop systems is extended to cover multivariable systems. Sensitivity analysis is applied and results of considerable generality are derived which indicate the effects of gain changes and pole or zero movement in the plant transfer functions. A design policy is developed which satisfies the need for low sensitivity in implementation. Further development evolves a design technique in which speed of response can be systematically traded for sensitivity. At the same time the technique satisfies the need to achieve a digital control algorithm of minimal complexity. The method of design has been shown to be particularly relevant to systems with lightly damped open-loop modes and an example of this type of system is analysed in detail.
Ultrasonic flowmeters
Authors: Lynnworth Lawrence C. 
Published: August 2008

Recent accounts of ultrasonic flowmeters usually concentrate on either transit time or Doppler types. Although these are the most common types in use today, at least six other types exist. Part 1 of this two-part paper describes the physical principles of eight types of ultrasonic flowmeters, along with some general considerations (flow profile, accuracy, response time) applicable to any flowmeter. Part 2 deals mainly with single-path transit time ultrasonic flowmeters for liquids, but discusses in a more general sense ultrasonic propagation starting at the transmitting transducer, continuing across impedance mismatches and attenuating media, and including the effects of reflection, refraction and diffraction. Application of these ultrasonic propagation principles is illustrated by various flow cell designs such as the axial offset type for pipe diameters down to a few mm; the square-hole zigzag type for in-line area-averaging; clamp-on and wetted-transducer installations on conventional pipes; and special cells. Finally, the use of microprocessor technology is illustrated with respect to improving accuracy and reliability, and for calculating fluid-or flow-related parameters such as sound speed, temperature, density, viscosity, Reynolds number, Mach number, standard deviation of the flow velocity, and mass flow rate.
Some observations on resistance/ temperature characteristics of platinum resistance thermometers
Authors: Atherton A. 
Published: August 2008

This paper seeks to highlight the unexploited potential of industrial platinum resistance thermometers by investigating calibration measurements over the range of temperature between ice-point and zinc-point. Indications are that adherence to the IPTS-68 definition might depend to a greater extent on assembling thermometers in such a manner as to realise a prescribed unique value of the coefficient δ than on requiring the temperature coefficient a to be in excess of a particular specified value. Moreover, implications arise that apparent deviations from an IPTS-68-type characteristic, and the consequent observed variability in δ, are attributable to heat conduction along thermometer stems. No attempt has yet been made to elucidate the reason for the above empirically inferred constancy of the ratio of the coefficients of terms of first and second degree in the quadratic equation relatitig resistance to the modified temperature t'. It appears that the 'fixed' correction polynomial used to convert t' into t 68 , which was defined to achieve compatibility with the thermodynamic temperature scale, represents the behaviour of a certain type of thermometer rather than of the sensing element itself; although of academic interest only, the 'bare' element would require a different, individually assigned, numerical factor in the polynomial in order to restore agreement. It might also be feasible to adopt the same procedure as a means of overcoming any discrepancy arising for a thermometer whose materials and manner of construction have resulted in a 'non-ideal' value of δ.
Measurement and estimation in catalytic reactors for partial oxidation
Authors: Kershenbaum L. , Lopez-Isunza F. 
Published: August 2008

An appropriate simplified model has been developed to describe the steady-state and dynamic behaviour of a fixed-bed catalytic reactor for the oxidation of o-xylene to phthalic anhydride. Predictions have been compared with experiments in a single-tube reactor of industrial dimensions, using measurements of temperature and composition at 26 axial positions. Experiments point out the existence of regions of moderate or high sensitivity to changes in operating conditions; the model predicts the same behaviour. However, variations in catalyst activity as a function of both time and position can lead to some ambiguity in the interpretation of results.
Pharmaceutical care in an inpatient pediatric hematopoietic stem cell transplant service
Authors: Prot-Labarthe Sonia , Therrien Roxane , Demanche Colette , Larocque Diane , Bussières Jean-François 
Published: August 2008

Introduction. Hematopoietic stem cell transplant patients represent a population at high risk for drug-related problems. Our objective is to describe pharmacist interventions in a hematopoietic stem cell transplant pediatric unit. Methods and Patients. The Hematopoietic Stem Cell Transplant Unit of the Centre Hospitalier Universitaire Sainte-Justine performs around 50 hematopoietic stem cell transplants per year. During a pharmaceutical care specialized residency program, a French pharmacist participated in certain clinical activities. Drug-related problems and clinical interventions were compiled over 31 nonconsecutive days using a tool developed by the Société Française de Pharmacie Clinique. Data concerning patients, drugs, intervention, documentation, approval (if needed), and estimated impact were compiled. Results. During the 31-day period, 525 interventions were collected (16.9 ± 3.7 per day), targeting 29 patients. The main drug-related problems were adverse drug reactions (N = 125, 23.8%), untreated indication (N = 92, 17.5%) and failure to receive drug (N = 89, 17.0%). The pharmacist's interventions concerned mainly dose adjustment (N = 174, 33.1%) and drug monitoring (N = 132, 25.1%). Among the 324 (61.7%) interventions requiring a physician's approval, 302 (93.2%) were accepted without any change. Conclusion. A pharmacist is able to perform clinically relevant interventions in a hematopoietic stem cell transplant unit, given the complexity of the pharmacotherapy. Our description of drug-related problems and interventions may help other pharmacists already working or developing pharmaceutical care in a hematopoietic stem cell transplant unit to compare their practice and it is one of the few reported in the literature. J Oncol Pharm Practice (2008) 14: 147—152.