bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Cox rings of K3 surfaces
Authors: Artebani Michela , Hausen Jürgen , Laface Antonio 
Published: March 2010

AbstractWe study Cox rings of K3 surfaces. A first result is that a K3 surface has a finitely generated Cox ring if and only if its effective cone is rational polyhedral. Moreover, we investigate degrees of generators and relations for Cox rings of K3 surfaces of Picard number two, and explicitly compute the Cox rings of generic K3 surfaces with a non-symplectic involution that have Picard number 2 to 5 or occur as double covers of del Pezzo surfaces.
Interlaboratory Comparison of Three Multiplexed Bead-Based Immunoassays for Measuring Serum Antibodies to Pneumococcal Polysaccharides
Authors: Whaley Melissa J. , Rose Charles , Martinez Joseph , Laher Gouri , Sammons Deborah L. , Smith Jerry P. , Snawder John E. , Borrow Ray , Biagini Raymond E. , Plikaytis Brian , Carlone George M. , Romero-Steiner Sandra 
Published: March 2010

ABSTRACT

Serotype-specific IgG, as quantified by a standardized WHO enzyme-linked immunosorbent assay (ELISA), is a serologic end point used to evaluate pneumococcal polysaccharide-based vaccine immunogenicity. Antibodies to each vaccine polysaccharide in licensed multivalent vaccines are quantified separately; this is laborious and consumes serum. We compared three bead-based immunoassays: a commercial assay (xMAP Pneumo14; Luminex) and two in-house assays (of the Health Protection Agency [HPA] and Centers for Disease Control and Prevention [CDC]), using the WHO-recommended standard reference and reference sera (
n
= 11) from vaccinated adults. Multiple comparisons of the IgG concentrations for seven conjugate vaccine serotypes were performed by sample (percent error), serotype (equivalency testing), and laboratory (concordance correlation coefficient [CCC]). When comparing concentrations by sample, bead-based immunoassays generally yielded higher antibody concentrations than the ELISA and had higher variability for serotypes 6B, 18C, and 23F. None of the three assays met the current WHO recommendation of 75% of sera falling within 40% of the assigned antibody concentrations for all seven serotypes. When compared by serotype, the CDC and HPA tests were equivalent for five of seven serotypes, whereas the Luminex assay was equivalent for four of seven serotypes. When overall mean IgG concentrations were compared by laboratory, a higher level of agreement (CCC close to 1) was found among bead-based immunoassays than between the assays and WHO assignments. When compared to WHO assignments, the HPA assay outperformed the other assays (
r
= 0.920; CCC = 0.894; coefficient of accuracy = 0.972). Additional testing with sera from immunogenicity studies should demonstrate the applicability of this methodology for vaccine evaluation.
High Levels of β-
d
-Glucan in Immunocompromised Children with Proven Invasive Fungal Disease
Authors: Mularoni Alessandra , Furfaro Elisa , Faraci Maura , Franceschi Alessia , Mezzano Paola , Bandettini Roberto , Viscoli Claudio , Castagnola Elio 
Published: March 2010

ABSTRACT

The plasmatic levels of 1,3-β-
d
-glucan (BDG) were >523 pg/ml in 4 children, 2 low-birth-weight neonates and 2 stem cell transplant recipients, with the following invasive fungal diseases (IFD) proven apart from this BDG test: 3 cases of
Candida parapsilosis
candidemias and 1 case of disseminated aspergillosis. The BDG test may be useful for identification of IFD in pediatrics.
Isolation and Phylogenetic Analysis of Sindbis Viruses from Mosquitoes in Germany
Authors: Jöst Hanna , Bialonski Alexandra , Storch Volker , Günther Stephan , Becker Norbert , Schmidt-Chanasit Jonas 
Published: March 2010

ABSTRACT

A molecular survey of 16,057 mosquitoes captured in Southwest Germany during the summer of 2009 demonstrated the presence of Sindbis virus (SINV) in
Culex
spp. and
Anopheles maculipennis
sensu lato. Phylogenetic analysis of the German SINV strains linked them with Swedish SINV strains, the causative agent of Ockelbo disease in humans.
Characterization and Persistence of
Staphylococcus aureus
Strains Isolated from the Anterior Nares and Throats of Healthy Carriers in a Mexican Community
Authors: Hamdan-Partida Aída , Sainz-Espuñes Teresita , Bustos-Martínez Jaime 
Published: March 2010

ABSTRACT

Healthy carriers of
Staphylococcus aureus
strains have an important role in the dissemination of this bacterium. To investigate the presence of
S. aureus
in the throat and anterior nares, samples from 1,243 healthy volunteers in a Mexican community were examined. The percentage of healthy carriers was 59.8%. Results showed that colonization of the throat occurred more frequently than that of the nares (46.5% versus 37.1%,
P
< 0.0001). Of the
S. aureus
carriers, 22.2% were exclusive nasal carriers and 38% were exclusive throat carriers. A total of 1,039 strains were isolated; 12.6% were shown to be methicillin-resistant
S. aureus
(MRSA). Of MRSA strains, 32.1% were isolated from exclusive throat carriers. Most of the strains isolated from the anterior nares and throat of the same carriers were the same or related; however, some were different. Pulsed-field gel electrophoresis (PFGE) pattern analysis of the MRSA strains isolated from the exclusive nasal carriers or exclusive throat carriers showed that they belong to different clusters. A 6-year prospective study was performed to investigate the persistence of
S. aureus
in the throat. Results showed that 13% of subjects were persistent carriers. Most of them were colonized with the same clone of
S. aureus
throughout the time of the study, and just three had different clones. Antimicrobial susceptibility testing showed that 91.1% of the strains were penicillin resistant. The presence of
mecA
and
nucA
genes (in order to confirm methicillin resistance) and of thermostable nuclease of
S. aureus
was examined. This study showed that some strains of
S. aureus
regularly colonized the throats of healthy people and could persist for years.
Mathematical Modeling of Ultradeep Sequencing Data Reveals that Acute CD8
+
T-Lymphocyte Responses Exert Strong Selective Pressure in Simian Immunodeficiency Virus-Infected Macaques but Still Fail To Clear Founder Epitope Sequences
Authors: Love Tanzy M. T. , Thurston Sally W. , Keefer Michael C. , Dewhurst Stephen , Lee Ha Youn 
Published: March 2010

ABSTRACT

The prominent role of antiviral cytotoxic CD8
+
T-lymphocytes (CD8-TL) in containing the acute viremia of human and simian immunodeficiency viruses (HIV-1 and SIV) has rationalized the development of T-cell-based vaccines. However, the presence of escape mutations in the acute stage of infection has raised a concern that accelerated escape from vaccine-induced CD8-TL responses might undermine vaccine efficacy. We reanalyzed previously published data of 101,822 viral genomes of three CD8-TL epitopes, Nef
103-111
RM9 (RM9), Tat
28-35
SL8 (SL8), and Gag
181-189
CM9 (CM9), sampled by ultradeep pyrosequencing from eight macaques. Multiple epitope variants appeared during the resolution of acute viremia, followed by the predominance of a single mutant epitope. By fitting a mathematical model, we estimated the first acute escape rate as 0.36 day
−1
within escape-prone epitopes, RM9 and SL8, and the chronic escape rate as 0.014 day
−1
within the CM9 epitope. Our estimate of SIV acute escape rates was found to be comparable to very early HIV-1 escape rates. The timing of the first escape was more highly correlated with the timing of the peak CD8-TL response than with the magnitude of the CD8-TL response. The transmitted epitope decayed more than 400 times faster during the acute viral decline stage than predicted by a neutral evolution model. However, the founder epitope persisted as a minor population even at the viral set point; in contrast, the majority of acute escape epitopes were completely cleared. Our results suggest that a reservoir of SIV infection is preferentially formed by virus with the transmitted epitope.
Geographical Spread of Highly Pathogenic Avian Influenza Virus H5N1 during the 2006 Outbreak in Austria
Authors: Fink Maria , Fernández Sandra Revilla , Schobesberger Hermann , Koefer Josef 
Published: March 2010

ABSTRACT

In spring 2006, highly pathogenic avian influenza virus (HPAIV) of subtype H5N1 was detected in Austria in 119 dead wild birds. The hemagglutinin cleavage site showed that the amino acid sequence motif was identical to that of the Qinghai lineage. For detailed analysis, the hemagglutinin (HA) and neuraminidase (NA) genes of 27 selected Austrian H5N1 viruses originating from different regions and wild bird species were analyzed phylogenetically, which revealed two clearly separated Austrian subclusters, both belonging to European cluster EMA-1. Subcluster
South
(
SCS
) contains virus isolates from the south of Austria as well as from Slovenia, Turkey, Egypt, and Nigeria. The second subcluster,
Northwest
(
SCN
), covered a larger group of viruses originating from different locations and wild bird species in the northern and very western parts of Austria, as well as from Bavaria and Switzerland. Surprisingly, virus isolates originating from two mute swans and one wild duck found on the north side of the Alps did not cluster with
SCN
but with
SCS
. Together with isolates from Bavarian, the Czech Republic, Italy, and Slovakia, they form a genuine subgroup, named subgroup
Bavaria
(
SGB
). This subgroup forms a link to
SCN
, indicating a spread of the virus from south to north. There has been a general assumption that the generic HPAI introduction route into Europe was from Russia to north Germany, introducing cluster EMA-2 into Europe. Interestingly, our findings support the assumption of an alternative introduction of the HPAI H5N1 virus from Turkey to central Europe, where it spread as cluster EMA-1 during the outbreak of 2006.
Rotaviruses Associate with Cellular Lipid Droplet Components To Replicate in Viroplasms, and Compounds Disrupting or Blocking Lipid Droplets Inhibit Viroplasm Formation and Viral Replication
Authors: Cheung Winsome , Gill Michael , Esposito Alessandro , Kaminski Clemens F. , Courousse Nathalie , Chwetzoff Serge , Trugnan Germain , Keshavan Nandita , Lever Andrew , Desselberger Ulrich 
Published: March 2010

ABSTRACT
Rotaviruses are a major cause of acute gastroenteritis in children worldwide. Early stages of rotavirus assembly in infected cells occur in viroplasms. Confocal microscopy demonstrated that viroplasms associate with lipids and proteins (perilipin A, ADRP) characteristic of lipid droplets (LDs). LD-associated proteins were also found to colocalize with viroplasms containing a rotaviral NSP5-enhanced green fluorescent protein (EGFP) fusion protein and with viroplasm-like structures in uninfected cells coexpressing viral NSP2 and NSP5. Close spatial proximity of NSP5-EGFP and cellular perilipin A was confirmed by fluorescence resonance energy transfer. Viroplasms appear to recruit LD components during the time course of rotavirus infection. NSP5-specific siRNA blocked association of perilipin A with NSP5 in viroplasms. Viral double-stranded RNA (dsRNA), NSP5, and perilipin A cosedimented in low-density gradient fractions of rotavirus-infected cell extracts. Chemical compounds interfering with LD formation (isoproterenol plus isobutylmethylxanthine; triacsin C) decreased the number of viroplasms and inhibited dsRNA replication and the production of infectious progeny virus; this effect correlated with significant protection of cells from virus-associated cytopathicity. Rotaviruses represent a genus of another virus family utilizing LD components for replication, pointing at novel therapeutic targets for these pathogens.
Interleukin-15 Is Critical in the Pathogenesis of Influenza A Virus-Induced Acute Lung Injury
Authors: Nakamura Risa , Maeda Naoyoshi , Shibata Kensuke , Yamada Hisakata , Kase Tetsuo , Yoshikai Yasunobu 
Published: March 2010

ABSTRACT

Highly pathogenic influenza A viruses cause acute severe pneumonia to which the occurrence of “cytokine storm” has been proposed to contribute. Here we show that interleukin-15 (IL-15) knockout (KO) mice exhibited reduced mortality after infection with influenza virus A/FM/1/47 (H1N1, a mouse-adapted strain) albeit the viral titers of these mice showed no difference from those of control mice. There were significantly fewer antigen-specific CD44
+
CD8
+
T cells in the lungs of infected IL-15 KO mice, and adoptive transfer of the CD8
+
T cells caused reduced survival of IL-15 KO mice following influenza virus infection. Mice deficient in β
2
-microglobulin by gene targeting and those depleted of CD8
+
T cells by
in vivo
administration of anti-CD8 monoclonal antibody displayed a reduced mortality rate after infection. These results indicate that IL-15-dependent CD8
+
T cells are at least partly responsible for the pathogenesis of acute pneumonia caused by influenza A virus.
Enhanced Anti-HIV Functional Activity Associated with Gag-Specific CD8 T-Cell Responses
Authors: Julg B. , Williams K. L. , Reddy S. , Bishop K. , Qi Y. , Carrington M. , Goulder P. J. , Ndung'u T. , Walker B. D. 
Published: March 2010

ABSTRACT

Effective HIV-specific T-cell immunity requires the ability to inhibit virus replication in the infected host, but the functional characteristics of cells able to mediate this effect are not well defined. Since Gag-specific CD8 T cells have repeatedly been associated with lower viremia, we examined the influence of Gag specificity on the ability of unstimulated CD8 T cells from chronically infected persons to inhibit virus replication in autologous CD4 T cells. Persons with broad (≥6;
n
= 13) or narrow (≤1;
n
= 13) Gag-specific responses, as assessed by gamma interferon enzyme-linked immunospot assay, were selected from 288 highly active antiretroviral therapy (HAART)-naive HIV-1 clade C-infected South Africans, matching groups for total magnitude of HIV-specific CD8 T-cell responses and CD4 T-cell counts. CD8 T cells from high Gag responders suppressed
in vitro
replication of a heterologous HIV strain in autologous CD4 cells more potently than did those from low Gag responders (
P
< 0.003) and were associated with lower viral loads
in vivo
(
P
< 0.002). As previously shown in subjects with low viremia, CD8 T cells from high Gag responders exhibited a more polyfunctional cytokine profile and a stronger ability to proliferate in response to HIV stimulation than did low Gag responders, which mainly exhibited monofunctional CD8 T-cell responses. Furthermore, increased polyfunctionality was significantly correlated with greater inhibition of viral replication
in vitro
. These data indicate that enhanced suppression of HIV replication is associated with broader targeting of Gag. We conclude that it is not the overall magnitude but rather the breadth, magnitude, and functional capacity of CD8 T-cell responses to certain conserved proteins, like Gag, which predict effective antiviral HIV-specific CD8 T-cell function.
Bocavirus Infection Induces Mitochondrion-Mediated Apoptosis and Cell Cycle Arrest at G2/M Phase
Authors: Chen Aaron Yun , Luo Yong , Cheng Fang , Sun Yuning , Qiu Jianming 
Published: March 2010

ABSTRACTBocavirusis a newly classified genus of the familyParvovirinae. Infection withBocavirusminute virus of canines (MVC) produces a strong cytopathic effect in permissive Walter Reed/3873D (WRD) canine cells. We have systematically characterized the MVC infection-produced cytopathic effect in WRD cells, namely, the cell death and cell cycle arrest, and carefully examined how MVC infection induces the cytopathic effect. We found that MVC infection induces an apoptotic cell death characterized by Bax translocalization to the mitochondrial outer membrane, disruption of the mitochondrial outer membrane potential, and caspase activation. Moreover, we observed that the activation of caspases occurred only when the MVC genome was replicating, suggesting that replication of the MVC genome induces apoptosis. MVC infection also induced a gradual cell cycle arrest from the S phase in early infection to the G2/M phase at a later stage, which was confirmed by the upregulation of cyclin B1 and phosphorylation of cdc2. Cell cycle arrest at the G2/M phase was reproduced by transfection of a nonreplicative NS1 knockout mutant of the MVC infectious clone, as well as by inoculation of UV-irradiated MVC. In contrast with other parvoviruses, only expression of the MVC proteins by transfection did not induce apoptosis or cell cycle arrest. Taken together, our results demonstrate that MVC infection induces a mitochondrion-mediated apoptosis that is dependent on the replication of the viral genome, and the MVC genomeper seis able to arrest the cell cycle at the G2/M phase. Our results may shed light on the molecular pathogenesis ofBocavirusinfection in general.
Efficient Generation of Mucosal and Systemic Antigen-Specific CD8+T-Cell Responses following Pulmonary DNA Immunization
Authors: Bivas-Benita Maytal , Bar Liat , Gillard Geoffrey O. , Kaufman David R. , Simmons Nathaniel L. , Hovav Avi-Hai , Letvin Norman L. 
Published: March 2010

ABSTRACTAlthough mucosal CD8+T-cell responses are important in combating mucosal infections, the generation of such immune responses by vaccination remains problematic. In the present study, we evaluated the ability of plasmid DNA to induce local and systemic antigen-specific CD8+T-cell responses after pulmonary administration. We show that the pulmonary delivery of plasmid DNA formulated with polyethyleneimine (PEI-DNA) induced robust systemic CD8+T-cell responses that were comparable in magnitude to those generated by intramuscular (i.m.) immunization. Most importantly, we observed that the pulmonary delivery of PEI-DNA elicited a 10-fold-greater antigen-specific CD8+T-cell response in lungs and draining lymph nodes of mice than that of i.m. immunization. The functional evaluation of these pulmonary CD8+T cells revealed that they produced type I cytokines, and pulmonary immunization with PEI-DNA induced lung-associated antigen-specific CD4+T cells that produced higher levels of interleukin-2 than those induced by i.m. immunization. Pulmonary PEI-DNA immunization also induced CD8+T-cell responses in the gut and vaginal mucosa. Finally, pulmonary, but not i.m., plasmid DNA vaccination protected mice from a lethal recombinant vaccinia virus challenge. These findings suggest that pulmonary PEI-DNA immunization might be a useful approach for immunizing against pulmonary pathogens and might also protect against infections initiated at other mucosal sites.
Children in health research: a matter of trust
Authors: Woodgate Roberta L , Edwards Marie 
Published: March 2010

BackgroundCentral to the involvement of children in health research is the notion of risk. In this paper we present one of the factors, a matter of trust, that shaped Canadian parents' and children's perceptions and assessments of risk in child health research.Participants and methodsPart of a larger qualitative research study, 82 parents took part an in-depth qualitative interview, with 51 parents having children who had participated in health research and 31 having children with no research history. 51 children ranging from 6 to 19 years of age were also interviewed, with 28 having a history of participation in child health research and 23 having no history. Children also took part in 3 focus groups interviews. Themes emerged through a grounded theory analysis of coded interview transcripts.FindingsThe presence or absence of trust was not only perceived by parents and children as a contributing factor to involving children in health research, but also shaped their perceptions and assessments of risk. Three interrelated subthemes identified were: (1) relationships of trust; (2) placing trust in symbols of authority; and (3) the continuum of trust.ConclusionsOur study reinforces that trust is an important factor when parents assess risk in child health research and shows that children use the language of trust in relation to risk. More discussion regarding trust in training researchers is warranted given the trust in researchers and institutions evident in this study. We also recommend further study of the continuum of trust in child health research.
Ethics committees for biomedical research in some African emerging countries: which establishment for which independence? A comparison with the USA and Canada
Authors: Rwabihama Jean-Paul , Girre Catherine , Duguet Anne-Marie 
Published: March 2010

ContextThe conduct of medical research led by Northern countries in developing countries raises ethical questions. The assessment of research protocols has to be twofold, with a first reading in the country of origin and a second one in the country where the research takes place. This reading should benefit from an independent local ethical review of protocols. Consequently, ethics committees for medical research are evolving in Africa.ObjectiveTo investigate the process of establishing ethics committees and their independence.MethodDescriptive study of 25 African countries and two North American countries. Data were recorded by questionnaire and interviews. Two visits of ethics committee meetings were conducted on the ground: over a period of 3 months in Kigali (Rwanda) and 2 months in Washington DC (USA).Results22 countries participated in this study, 20 from Africa and two from North America. The response rate was 80%. 75% of local African committees developed into national ethics committees. During the last 5 years, these national committees have grown on a structural level. The circumstances of creation and the general context of underdevelopment remain the major challenges in Africa. Their independence could not be ensured without continuous training and efficient funding mechanisms. Institutional ethics committees are well established in USA and in Canada, whereas ethics committees in North America are weakened by the institutional affiliation of their members.ConclusionThe process of establishing ethics committees could affect their functioning and compromise their independence in some African countries and in North America.
AN ATLAS OF ROBUST, STABLE, HIGH-DIMENSIONAL LIMIT CYCLES
Authors: WILDS ROY , GLASS LEON 
Published: March 2010

We present a method for constructing dynamical systems with robust, stable limit cycles in arbitrary dimensions. Our approach is based on a correspondence between dynamics in a class of differential equations and directed graphs on the n-dimensional hypercube (n-cube). When the directed graph contains a certain type of cycle, called a cyclic attractor, then a stable limit cycle solution of the differential equations exists. A novel method for constructing regulatory systems that we call minimal regulatory networks from directed graphs facilitates investigation of limit cycles in arbitrarily high dimensions.We identify two families of cyclic attractors that are present for all dimensions n ≥ 3: cyclic negative feedback and sequential disinhibition. For each, we obtain explicit representations for the differential equations in arbitrary dimension. We also provide a complete listing of minimal regulatory networks, a representative differential equation, and a bifurcation analysis for each cyclic attractor in dimensions 3–5. This work joins discrete concepts of symmetry and classification with analysis of differential equations useful for understanding dynamics in complex biological control networks.