bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction of Numerical Parameter Dependencies in Diesel Spray Models
Authors: Abani Neerav , Munnannur Achuth , Reitz Rolf D. 
Published: April 2008

Abstract
Numerical grid and time-step dependencies of discrete droplet Lagrangian spray models are identified. The two main sources of grid dependency are due to errors in predicting the droplet-gas relative velocity and errors in describing droplet-droplet collision and coalescence processes. For reducing grid dependency due to the relative velocity effects, a gas-jet theory is proposed and applied to model diesel sprays. For the time-step dependency, it is identified that the collision submodel results in drop size variation in the standard spray model. A proposed spray model based on the gas-jet theory is found to improve the time-step independency also along with the mesh independency. The use of both Eulerian (collision mesh) and Lagrangian (radius of influence) collision models along with the gas-jet theory is found to provide mesh-independent results.
Comparison of Nasal Swabs with Nose Blowing for Community-Based Pneumococcal Surveillance of Healthy Children
Authors: Leach Amanda Jane , Stubbs Elizabeth , Hare Kim , Beissbarth Jemima , Morris Peter Stanley 
Published: April 2008

ABSTRACT

The nasopharynx (NP) is the preferred site for detection of
Streptococcus pneumoniae
in young children, but NP sampling is not well tolerated. We compared nose blowing with paired nasal swabs. The sensitivity of nose blowing was 46% (95% confidence interval [CI] 38 to 56%), which increased to 94% (95% CI, 85 to 98%) for children with visible secretions.
Evaluation of Novel Broad-Range Real-Time PCR Assay for Rapid Detection of Human Pathogenic Fungi in Various Clinical Specimens
Authors: Vollmer Tanja , Störmer Melanie , Kleesiek Knut , Dreier Jens 
Published: April 2008

ABSTRACT

In the present study, a novel broad-range real-time PCR was developed for the rapid detection of human pathogenic fungi. The assay targets a part of the 28S large-subunit ribosomal RNA (rDNA) gene. We investigated its application for the most important human pathogenic fungal genera, including
Aspergillus, Candida, Cryptococcus, Mucor, Penicillium, Pichia, Microsporum, Trichophyton
, and
Scopulariopsis
. Species were identified in PCR-positive reactions by direct DNA sequencing. A noncompetitive internal control was applied to prevent false-negative results due to PCR inhibition. The minimum detection limit for the PCR was determined to be one 28S rDNA copy per PCR, and the 95% detection limit was calculated to 15 copies per PCR. To assess the clinical applicability of the PCR method, intensive-care patients with artificial respiration and patients with infective endocarditis were investigated. For this purpose, 76 tracheal secretion samples and 70 heart valve tissues were analyzed in parallel by real-time PCR and cultivation. No discrepancies in results were observed between PCR analysis and cultivation methods. Furthermore, the application of the PCR method was investigated for other clinical specimens, including cervical swabs, nail and horny skin scrapings, and serum, blood, and urine samples. The combination of a broad-range real-time PCR and direct sequencing facilitates rapid screening for fungal infection in various clinical specimens.
Is the Sequenced
Bordetella pertussis
Strain Tohama I Representative of the Species?
Authors: Caro Valérie , Bouchez Valérie , Guiso Nicole 
Published: April 2008

ABSTRACT

Subtractive hybridization was carried out to identify differences between the sequenced genome of
Bordetella pertussis
Tohama I and those of two recently collected isolates. We identified genetic regions specific to recent isolates, old isolates, and isolates of
B. parapertussis
and
B. bronchiseptica
species. We conclude that Tohama I strain is not representative of the
B. pertussis
species.
West Nile Virus Entry Requires Cholesterol-Rich Membrane Microdomains and Is Independent of αvβ3 Integrin
Authors: Medigeshi Guruprasad R. , Hirsch Alec J. , Streblow Daniel N. , Nikolich-Zugich Janko , Nelson Jay A. 
Published: April 2008

ABSTRACT
West Nile virus (WNV) has been the leading cause of viral encephalitis in the United States since 1999. The endocytic processes involved in the internalization of infectious WNV by various cell types are not well characterized, and the involvement of cholesterol-rich membrane microdomains, or lipid rafts, in the life cycle of WNV has not been investigated previously. In this study, we found that the depletion of cellular cholesterol levels by brief treatment with methyl-β-cyclodextrin resulted in a 100-fold reduction of the titers of infectious WNV released into the culture supernatant, as well as a reduction in the number of WNV genome copies in the cholesterol-depleted cells. The addition of exogenous cholesterol to cholesterol-depleted cells reversed this effect. Cholesterol depletion postinfection did not affect WNV growth, suggesting that the effect occurs at the level of WNV entry. We also showed that while WNV entry did not require αvβ3 integrin and focal adhesion kinase, WNV particles failed to be internalized by cholesterol-depleted cells. Finally, we showed the colocalization of the WNV envelope protein and cholera toxin B, which is internalized in a lipid raft-dependent pathway, in microdomain clusters at the plasma membrane. These data suggest that WNV utilizes lipid rafts during initial stages of internalization and that the lipid rafts may contain a factor(s) that may enhance WNV endocytosis.
Characterization of a Rhesus Monkey Calicivirus Representing a New Genus of
Caliciviridae
Authors: Farkas Tibor , Sestak Karol , Wei Chao , Jiang Xi 
Published: April 2008

ABSTRACT

In this study, we report the characterization of a novel calicivirus (CV), the Tulane virus (TV), which was isolated from stool samples of captive juvenile rhesus macaques (
Macaca mulatta
) of the Tulane National Primate Research Center. The complete genome of TV contains 6,714 nucleotides plus a poly(A) tail and is organized into three open reading frames (ORFs) that encode the nonstructural (NS) polyprotein (ORF1); the capsid protein (ORF2), with an estimated molecular mass of 57.9 kDa; and a possible minor structural protein (ORF3), with an isoelectric point (pI) of 10.0 and a calculated molecular mass of 22.8 kDa. The NS polyprotein revealed all typical CV amino acid motifs, including GXXGXGKT (NTPase), EYXEX (Vpg), GDCG (protease), and GLPSG and YGDD (polymerase). Phylogenetic trees constructed for the NS polyprotein, NTPase, protease, polymerase, and capsid protein sequences consistently placed the TV on a branch rooted with
Norovirus
, but with distances equal to those between other genera. The TV can be cultured in a monkey kidney cell line (LLC-MK2) with the appearance of typical cytopathic effect. TV exhibits a typical CV morphology, with a diameter of 36 nm, and has a buoyant density of 1.37 g/ml. According to these physicochemical and genetic characteristics, TV represents a new CV genus for which we propose the name “Recovirus” (rhesus enteric CV). Although the pathogenicity of TV in rhesus macaques remains to be elucidated, the likelihood of TV causing intestinal infection and the availability of a tissue culture system make this virus a valuable surrogate for human CVs.
Characterization of the Follicular Dendritic Cell Reservoir of Human Immunodeficiency Virus Type 1
Authors: Keele Brandon F. , Tazi Loubna , Gartner Suzanne , Liu Yiling , Burgon Trever B. , Estes Jacob D. , Thacker Tyler C. , Crandall Keith A. , McArthur Justin C. , Burton Gregory F. 
Published: April 2008

ABSTRACT
Throughout the natural course of human immunodeficiency virus (HIV) infection, follicular dendritic cells (FDCs) trap and retain large quantities of particle-associated HIV RNA in the follicles of secondary lymphoid tissue. We have previously found that murine FDCs in vivo could maintain trapped virus particles in an infectious state for at least 9 months. Here we sought to determine whether human FDCs serve as an HIV reservoir, based on the criteria that virus therein must be replication competent, genetically diverse, and archival in nature. We tested our hypothesis using postmortem cells and tissues obtained from three HIV-infected subjects and antemortem blood samples obtained from one of these subjects. Replication competence was determined using coculture, while genetic diversity and the archival nature of virus were established using phylogenetic and population genetics methods. We found that FDC-trapped virus was replication competent and demonstrated greater genetic diversity than that of virus found in most other tissues and cells. Antiretrovirus-resistant variants that were not present elsewhere were also detected on FDCs. Furthermore, genetic similarity was observed between FDC-trapped HIV and viral species recovered from peripheral blood mononuclear cells obtained 21 and 22 months antemortem, but was not present in samples obtained 4 and 18 months prior to the patient's death, indicating that FDCs can archive HIV. These data indicate that FDCs represent a significant reservoir of infectious and diverse HIV, thereby providing a mechanism for viral persistence for months to years.
Demyelinating and Nondemyelinating Strains of Mouse Hepatitis Virus Differ in Their Neural Cell Tropism
Authors: Das Sarma Jayasri , Iacono Kathryn , Gard Lilli , Marek Ryan , Kenyon Lawrence C. , Koval Michael , Weiss Susan R. 
Published: April 2008

ABSTRACTSome strains of mouse hepatitis virus (MHV) can induce chronic inflammatory demyelination in mice that mimics certain pathological features of multiple sclerosis. We have examined neural cell tropism of demyelinating and nondemyelinating strains of MHV in order to determine whether central nervous system (CNS) cell tropism plays a role in demyelination. Previous studies demonstrated that recombinant MHV strains, isogenic other than for the spike gene, differ in the extent of neurovirulence and the ability to induce demyelination. Here we demonstrate that these strains also differ in their abilities to infect a particular cell type(s) in the brain. Furthermore, there is a correlation between the differential localization of viral antigen in spinal cord gray matter and that in white matter during acute infection and the ability to induce demyelination later on. Viral antigen from demyelinating strains is detected initially in both gray and white matter, with subsequent localization to white matter of the spinal cord, whereas viral antigen localization of nondemyelinating strains is restricted mainly to gray matter. This observation suggests that the localization of viral antigen to white matter during the acute stage of infection is essential for the induction of chronic demyelination. Overall, these observations suggest that isogenic demyelinating and nondemyelinating strains of MHV, differing in the spike protein expressed, infect neurons and glial cells in different proportions and that differential tropism to a particular CNS cell type may play a significant role in mediating the onset and mechanisms of demyelination.
Multimerization of Tegument Protein pp28 within the Assembly Compartment Is Required for Cytoplasmic Envelopment of Human Cytomegalovirus
Authors: Seo Jun-Young , Britt William J. 
Published: April 2008

ABSTRACT
Human cytomegalovirus (HCMV) UL99-encoded pp28 is an essential tegument protein required for envelopment and production of infectious virus. Nonenveloped virions accumulate in the cytoplasm of cells infected with recombinant viruses with the UL99 gene deleted. Previous results have suggested that a key function of pp28 in the envelopment of infectious HCMV is expressed after the protein localizes in the assembly compartment (AC). In this study, we investigated the potential role of pp28 multimerization in the envelopment of the infectious virion. Our results indicated that pp28 multimerized during viral infection and that interacting domains responsible for self-interaction were localized in the amino terminus of the protein (amino acids [aa] 1 to 43). The results from transient-expression and/or infection assays indicated that the self-interaction took place in the AC. A mutant pp28 molecule containing only the first 35 aa failed to accumulate in the AC, did not interact with pp28 in the AC, and could not support virus replication. In contrast, the first 50 aa of pp28 was sufficient for the self-interaction within the AC and the assembly of infectious virus. Recombinant viruses encoding an in-frame deletion of aa 26 to 33 of pp28 were replication competent, whereas infectious virus was not recovered from HCMV BACs lacking aa 26 to 43. These findings suggested that the accumulation of pp28 was a prerequisite for multimerization of pp28 within the AC and that pp28 multimerization in the AC represented an essential step in the envelopment and production of infectious virions.
Plasmacytoid Dendritic Cell Dynamics and Alpha Interferon Production during Simian Immunodeficiency Virus Infection with a Nonpathogenic Outcome
Authors: Diop Ousmane M. , Ploquin Mickaël J.-Y. , Mortara Lorenzo , Faye Abdourahmane , Jacquelin Béatrice , Kunkel Désirée , Lebon Pierre , Butor Cécile , Hosmalin Anne , Barré-Sinoussi Françoise , Müller-Trutwin Michaela C. 
Published: April 2008

ABSTRACT
We addressed the role of plasmacytoid dendritic cells (PDC) in protection against AIDS in nonpathogenic simian immunodeficiency virus (SIVagm) infection in African green monkeys (AGMs). PDC were monitored in blood and lymph nodes (LNs) starting from day 1 postinfection. We observed significant declines in blood during acute infection. However, PDC then returned to normal levels, and chronically infected AGMs showed no decrease of PDC in blood. There was a significant increase of PDC in LNs during acute infection. Blood PDC displayed only weak alpha interferon (IFN-α) responses to TLR9 agonist stimulation before infection. However, during acute infection, both blood and LN PDC showed a transiently increased propensity for IFN-α production. Bioactive IFN-α was detected in plasma concomitant with the peak of viremia, though levels were only low to moderate in some animals. Plasma interleukin 6 (IL-6) and IL-12 were not increased. In conclusion, PDC were recruited to the LNs and displayed increased IFN-α production during acute infection. However, increases in IFN-α were transient. Together with the lack of inflammatory cytokine responses, these events might play an important role in the low level of T-cell activation which is associated with protection against AIDS in nonpathogenic SIVagm infection.
Paucity of CD4
+
CCR5
+
T Cells May Prevent Transmission of Simian Immunodeficiency Virus in Natural Nonhuman Primate Hosts by Breast-Feeding
Authors: Pandrea Ivona , Onanga Richard , Souquiere Sandrine , Mouinga-Ondéme Augustin , Bourry Olivier , Makuwa Maria , Rouquet Pierre , Silvestri Guido , Simon François , Roques Pierre , Apetrei Cristian 
Published: April 2008

ABSTRACT

Simian immunodeficiency virus (SIV) persistence in wild populations of African nonhuman primates (NHPs) may occur through horizontal and vertical transmission. However, the mechanism(s) and timing of the latter type of transmission have not been investigated to date. Here we present the first study of SIV transmissibility by breast-feeding in an African NHP host. Six mandrill dames were infected with plasma containing 300 50% tissue culture infective doses of SIVmnd-1 on the day after delivery. All female mandrills became infected, as demonstrated by both plasma viral loads (VLs) and anti-SIVmnd-1 seroconversion. Neither fever nor lymphadenopathy was observed. At the peak of SIVmnd-1 viral replication (days 7 to 10 postinoculation), plasma VLs were high (8 × 10
6
to 8 × 10
8
RNA copies/ml) and paralleled the high VLs in milk (4.7 × 10
4
to 5.6 × 10
5
RNA/ml). However, at the end of the breast-feeding period, after 6 months of follow-up, no sign of infection was observed for the offspring. Later on, during a 4-year follow-up examination, two of the offspring showed virological evidence of SIVmnd-1 infection. Both animals seroconverted at least 6 months after the interruption of lactation. In conclusion, despite extensive viral replication in mandrill mothers and high levels of free virus in milk, no SIVmnd-1 transmission was detectable at the time of breast-feeding or during the following months. Since we observed a markedly lower expression of CCR5 on the CD4
+
T cells of young mandrills and African green monkeys than on those of adults, we propose that low levels of this viral coreceptor on CD4
+
T cells may be involved in the lack of breast-feeding transmission in natural hosts of SIVs.
Natural Resistance of Human Immunodeficiency Virus Type 1 to the CD4bs Antibody b12 Conferred by a Glycan and an Arginine Residue Close to the CD4 Binding Loop
Authors: Duenas-Decamp Maria José , Peters Paul , Burton Dennis , Clapham Paul R. 
Published: April 2008

ABSTRACT
The human monoclonal antibody b12 recognizes a conserved epitope on gp120 that overlaps the CD4 binding site. b12 has neutralizing activity against diverse human immunodeficiency virus type 1 (HIV-1) strains. However, we recently reported that b12 sensitivity of HIV-1 envelopes amplified from patient tissues without culture varied considerably. For two subjects, there was clear modulation of b12 sensitivity, with lymph node-derived envelopes being essentially resistant while those from brain tissue were sensitive. Here, we have mapped envelope determinants of b12 resistance by constructing chimeric envelopes from resistant and sensitive envelopes derived from lymph node and brain tissue, respectively. Residues on the N-terminal flank of the CD4 binding loop conferred partial resistance. However, a potential glycosylation site at residue N386 completely modulated b12 resistance but required the presence of an arginine at residue 373. Moreover, the introduction of R373 into b12-sensitive NL4.3 and AD8 envelopes, which carry N386, also conferred b12 resistance. Molecular modeling suggests that R373 and the glycan at N386 may combine to sterically exclude the benzene ring of b12 W100 from entering a proximal pocket. In summary, we identify residues on either side of the CD4 binding loop that contribute to b12 resistance in immune tissue in vivo. Our data have relevance for the design of vaccines that aim to elicit neutralizing antibodies.
Transformation by Bovine Papillomavirus Type 1 E6 Requires Paxillin
Authors: Wade Ramon , Brimer Nicole , Vande Pol Scott 
Published: April 2008

ABSTRACT
Papillomavirus E6 proteins are adapters that change the function of cellular regulatory proteins. The bovine papillomavirus type 1 E6 (BE6) binds to LXXLL peptide sequences termed LD motifs (consensus sequence LDXLLXXL) on the cellular protein paxillin that is a substrate of Src and focal adhesion kinases. Anchorage-independent transformation induced by BE6 required both paxillin and BE6-binding LD motifs on paxillin but was independent of the major tyrosine phosphorylation sites of paxillin. The essential role of paxillin in transformation by BE6 highlights the role of paxillin in the transduction of cellular signals that result in anchorage-independent cell proliferation.
Are the take-off and landing phase dynamics of the volleyball spike jump related to patellar tendinopathy?
Authors: Bisseling R W , Hof A L , Bredeweg S W , Zwerver J , Mulder T 
Published: April 2008

Objective:The causal mechanism of the chronic sports injury patellar tendinopathy is not well understood. The aim of the present study was to compare ankle and knee joint dynamics during the performance of the volleyball spike jump between healthy volleyball players (n = 8) and asymptomatic volleyball players with previous patellar tendinopathy (n = 7).Design:Cross-sectional.Methods:Inverse dynamics were used to estimate ankle and knee joint dynamics. From these multiple biomechanical variables, a logistic regression was performed to estimate the probability of the presence or absence of previous patellar tendinopathy among the volleyball players studied.Results:Several biomechanical variables improved the prediction of the presence or absence of previous patellar tendinopathy. For landing, ankle plantar flexion at the time of touch-down, and knee range of motion during the first part of impact, and for take-off, loading rate of the knee extensor moment during the eccentric countermovement phase of take-off were predictive. As interaction effects, the presence or absence of previous patellar tendinopathy were correctly predicted by ankle and knee range of motion during the first part of impact, by loading rate of the knee extensor moment during the eccentric phases of take-off and landing, and by knee angular velocity during the eccentric phases of take-off and landing.Conclusion:Smaller joint flexion during the first part of landing impact , and higher rate of knee moment development during the eccentric phases of the spike-jump landing sequence, together with higher knee angular velocities, might be risk factors in the development of patellar tendinopathy in volleyball players.
MRI evaluation of body composition changes in wrestlers undergoing rapid weight loss
Authors: Kukidome T , Shirai K , Kubo J , Matsushima Y , Yanagisawa O , Homma T , Aizawa K 
Published: April 2008

Purpose:Changes in body composition of college wrestlers undergoing rapid weight reduction were evaluated over time using magnetic resonance imaging (MRI).Methods:This study evaluated 12 wrestlers (male, 18–22 years of age) who participated in Japan’s 2005 intercollegiate wrestling tournament. For this study, MRI (of the right femoral region and the trunk), as well as measurements of body weight, body fat percentage and body water content, were performed 1 month and 1 week prior to the weigh-in, on the day of the weigh-in, on the day of the match (after the match), and 1 week after the weigh-in. A survey of food and fluid intake was also conducted.Results:Several variables were significantly lower on the day of the weigh-in than one month prior: body weight (p<0.01, −7.3% (SD 1.6%)); body fat (p<0.05, −9.3 (5.8)%); body water content (p<0.01, −5.9 (1.6)%); trunk cross-section (p<0.01, −13.2 (4.4)%), including separate measurements of trunk viscera, trunk muscle, and trunk fat; quadriceps muscle; lower subcutaneous; and food intake (p<0.01, 122 (20)). At 1 week after the match, all metrics had recovered to their levels measured 1 month before the weigh-in. Certain variables that were highly sensitive to hydration recovered more rapidly: they had reached their initial levels when measured immediately after the match.Conclusion:Rapid weight reduction reduced the wrestlers’ cross-sectional areas of muscle and fat tissues, which tended to recover through rehydration after the weigh-in. These results suggest that rapid weight reduction of wrestlers induced changes in different regions of the body.