bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Cepheid Xpert GBS Assay for Rapid Detection of Group B Streptococci in Amniotic Fluids from Pregnant Women with Premature Rupture of Membranes
Authors: Bourgeois-Nicolaos Nadege , Cordier Anne-Gael , Guillet-Caruba Christelle , Casanova François , Benachi Alexandra , Doucet-Populaire Florence 
Published: February 2013

ABSTRACT
The Xpert GBS real-time PCR assay for the detection of group B streptococci (GBS) in antepartum screening samples was evaluated on amniotic fluid samples collected from 139 women with premature rupture of membrane at term. When any intrapartum positive result from the Xpert GBS or culture was considered a true positive, the sensitivities of the Xpert GBS and culture were 92.3% and 84.6%, respectively. This assay could enhance exact identification of candidates for intrapartum antibiotic prophylaxis.
Mapping of Sequences in Pseudorabies Virus pUL34 That Are Required for Formation and Function of the Nuclear Egress Complex
Authors: Paßvogel Lars , Trübe Patricia , Schuster Franziska , Klupp Barbara G. , Mettenleiter Thomas C. 
Published: February 2013

ABSTRACT
The nuclear egress complex (NEC) is required for efficient translocation of newly synthesized herpesvirus nucleocapsids from the nucleus to the cytosol. It consists of the type II membrane protein pUL34 which interacts with pUL31 at the inner nuclear membrane (INM). To map regions within pUL34 required for nuclear membrane targeting and pUL31 interaction, we constructed deletion/substitution mutations. Previously, we showed that 50 C-terminal amino acids (aa) of pseudorabies virus (PrV) pUL34, including the transmembrane domain, could be functionally replaced by cellular lamina-associated polypeptide 2β (Lap2β) sequences. In contrast, replacement of the C-terminal 100 aa abrogated complementation but not pUL31 interaction. To further delineate essential sequences within this region, C-terminal pUL34 truncations of 60, 70, 80, 85, and 90 aa fused to Lap2β sequences were generated. While truncations up to 85 aa were functional, deletion of the C-terminal 90 aa abrogated function, which indicates that the important region is located between aa 171 and 176. Amino acids 173 to 175 represent RQR, a motif suggested to mediate INM targeting. Mutagenesis to RQG revealed that the mutant protein exhibited pronounced Golgi localization, but a fraction still reached the INM. Deletion mutations in the N-terminal domain of pUL34 demonstrated that absence of the first 4 aa was tolerated, while removal of 9 or more residues resulted in a nonfunctional protein. In addition, mutation of three conserved cysteines did not abrogate pUL34 function, whereas alteration of a conserved glutamine/tyrosine sequence yielded a nonfunctional protein.
The Transcription Factors TBX2 and TBX3 Interact with Human Papillomavirus 16 (HPV16) L2 and Repress the Long Control Region of HPVs
Authors: Schneider Marc A. , Scheffer Konstanze D. , Bund Timo , Boukhallouk Fatima , Lambert Carsten , Cotarelo Cristina , Pflugfelder Gert O. , Florin Luise , Spoden Gilles A. 
Published: February 2013

ABSTRACT
The minor capsid protein L2 of human papillomaviruses (HPVs) has multiple functions during the viral life cycle. Although L2 is required for effective invasion and morphogenesis, only a few cellular interaction partners are known so far. Using yeast two-hybrid screening, we identified the transcription factor TBX2 as a novel interaction partner of HPV type 16 (HPV16) L2. Coimmunoprecipitations and immunofluorescence analyses confirmed the L2-TBX2 interaction and revealed that L2 also interacts with TBX3, another member of the T-box family. Transcription of the early genes during HPV infection is under the control of an upstream enhancer and early promoter region, the long control region (LCR). In promoter-reporter gene assays, we observed that TBX2 and TBX3 repress transcription from the LCR and that this effect is enhanced by L2. Repression of the HPV LCR by TBX2/3 seems to be a conserved mechanism, as it was also observed with the LCRs of different HPV types. Finally, interaction of TBX2 with the LCR was detected by chromatin immunoprecipitation, and we found a strong colocalization of L2 and TBX2 in HPV16-positive cervical intraepithelial neoplasia (CIN) I-II tissue sections. These results suggest that TBX2/3 might play a role in the regulation of HPV gene expression during the viral life cycle.
Genetic Variability and the Classification of Hepatitis E Virus
Authors: Smith Donald B. , Purdy Michael A. , Simmonds Peter 
Published: February 2013

ABSTRACT

The classification of hepatitis E virus (HEV) variants is currently in transition without agreed definitions for genotypes and subtypes or for deeper taxonomic groupings into species and genera that could incorporate more recently characterized viruses assigned to the
Hepeviridae
family that infect birds, bats, rodents, and fish. These conflicts arise because of differences in the viruses and genomic regions compared and in the methodology used. We have reexamined published sequences and found that synonymous substitutions were saturated in comparisons between and within virus genotypes. Analysis of complete genome sequences or concatenated ORF1/ORF2 amino acid sequences indicated that HEV variants most closely related to those infecting humans can be consistently divided into six genotypes (types 1 to 4 and two additional genotypes from wild boar). Variants isolated from rabbits, closely related to genotype 3, occupy an intermediate position. No consistent criteria could be defined for the assignment of virus subtypes. Analysis of amino acid sequences from these viruses with the more divergent variants from chickens, bats, and rodents in three conserved subgenomic regions (residues 1 to 452 or 974 to 1534 of ORF1 or residues 105 to 458 of ORF2) provided consistent support for a division into 4 groups, corresponding to HEV variants infecting humans and pigs, those infecting rats and ferrets, those from bats, and those from chickens. This approach may form the basis for a future genetic classification of HEV into four species, with the more divergent HEV-like virus from fish (cutthroat trout virus) representing a second genus.
Characterization of Ovine Nectin-4, a Novel Peste des Petits Ruminants Virus Receptor
Authors: Birch Jamie , Juleff Nicholas , Heaton Michael P. , Kalbfleisch Ted , Kijas James , Bailey Dalan 
Published: February 2013

ABSTRACT
Small ruminants infected with peste des petits ruminants virus exhibit lesions typical of epithelial infection and necrosis. However, the only established host receptor for this virus is the immune cell marker signaling lymphocyte activation molecule (SLAM). We have confirmed that the ovine Nectin-4 protein, when overexpressed in epithelial cells, permits efficient replication of PPRV. Furthermore, this gene was predominantly expressed in epithelial tissues and encoded by multiple haplotypes in sheep breeds from around the world.
Novel Biopanning Strategy To Identify Epitopes Associated with Vaccine Protection
Authors: Bachler Barbara C. , Humbert Michael , Palikuqi Brisa , Siddappa Nagadenahalli B. , Lakhashe Samir K. , Rasmussen Robert A. , Ruprecht Ruth M. 
Published: February 2013

ABSTRACTIdentifying immune correlates of protection is important to develop vaccines against infectious diseases. We designed a novel, universally applicable strategy to profile the antibody (Ab) repertoire of protected vaccine recipients, using recombinant phages encoding random peptide libraries. The new approach, termed “protection-linked (PL) biopanning,” probes the Ab paratopes of protected vaccinees versus those with vaccine failure. As proof of concept, we screened plasma samples from vaccinated rhesus macaques (RMs) that had completely resisted multiple mucosal challenges with R5-tropic simian-human immunodeficiency viruses (SHIVs). The animals had been immunized with a multicomponent vaccine (multimeric HIV-1 gp160, HIV-1 Tat, and SIV Gag-Pol particles). After PL biopanning, we analyzed the phagotopes selected for amino acid homologies; in addition to the expected Env mimotopes, one recurring motif reflected the neutralizing Ab epitope at the N terminus (NT) of HIV-1 Tat. Subsequent binding and functional assays indicated that anti-Tat NT Abs were present only in completely or partially protected RMs; peak viremia of the latter was inversely correlated with anti-Tat NT Ab titers. In contrast, highly viremic, unvaccinated controls did not develop detectable Abs against the same epitope. Based upon the protective effect observedin vivo, we suggest that Tat should be included in multicomponent HIV-1 vaccines. Our data highlight the power of the new PL-biopanning strategy to identify Ab responses with significant association to vaccine protection, regardless of the mechanism(s) or targets of the protective Abs. PL biopanning is also unbiased with regard to pathogens or disease model, making it a universal tool.
Amoebae as Battlefields for Bacteria, Giant Viruses, and Virophages
Authors: Slimani Meriem , Pagnier Isabelle , Raoult Didier , La Scola Bernard 
Published: February 2013

ABSTRACT

When amoebae are simultaneously infected with
Acanthamoeba polyphaga Mimivirus
(APM) and the strictly intracellular BABL1 bacterium, the latter is always lost after serial subculturing. We showed that the virophage Sputnik 1, by reducing APM fitness, preserved BABL1 growth in acute and chronic models. This capability of a virophage to modulate the virulence of mimiviruses highlights the competition that occurs between them during natural host infection.
Hamster-Adapted Sin Nombre Virus Causes Disseminated Infection and Efficiently Replicates in Pulmonary Endothelial Cells without Signs of Disease
Authors: Safronetz David , Prescott Joseph , Haddock Elaine , Scott Dana P. , Feldmann Heinz , Ebihara Hideki 
Published: February 2013

ABSTRACT
To date, a laboratory animal model for the study of Sin Nombre virus (SNV) infection or associated disease has not been described. Unlike infection with Andes virus, which causes lethal hantavirus pulmonary syndrome (HPS)-like disease in hamsters, SNV infection is short-lived, with no viremia and little dissemination. Here we investigated the effect of passaging SNV in hamsters. We found that a host-adapted SNV achieves prolonged and disseminated infection in hamsters, including efficient replication in pulmonary endothelial cells, albeit without signs of disease.
Evolution of Equine Influenza Virus in Vaccinated Horses
Authors: Murcia Pablo R. , Baillie Gregory J. , Stack J. Conrad , Jervis Carley , Elton Debra , Mumford Jennifer A. , Daly Janet , Kellam Paul , Grenfell Bryan T. , Holmes Edward C. , Wood James L. N. 
Published: February 2013

ABSTRACT

Influenza A viruses are characterized by their ability to evade host immunity, even in vaccinated individuals. To determine how prior immunity shapes viral diversity
in vivo
, we studied the intra- and interhost evolution of equine influenza virus in vaccinated horses. Although the level and structure of genetic diversity were similar to those in naïve horses, intrahost bottlenecks may be more stringent in vaccinated animals, and mutations shared among horses often fall close to putative antigenic sites.
Alphavirus Genome Delivery Occurs Directly at the Plasma Membrane in a Time- and Temperature-Dependent Process
Authors: Vancini Ricardo , Wang Gongbo , Ferreira Davis , Hernandez Raquel , Brown Dennis T. 
Published: February 2013

ABSTRACT
It is widely held that arboviruses such as the alphavirus Sindbis virus gain entry into cells by a process of receptor-mediated endocytosis followed by membrane fusion in the acid environment of the endosome. We have used an approach of direct observation of Sindbis virus entry into cells by electron microscopy and immunolabeling of virus proteins with antibodies conjugated to gold beads. We found that upon attaching to the cell surface, intact RNA-containing viruses became empty shells that could be identified only by antibody labeling. We found that the rate at which full particles were converted to empty particles increased with time and temperature. We found that this entry event takes place at temperatures that inhibit both endosome formation and membrane fusion. We conclude that entry of alphaviruses is by direct penetration of cell plasma membranes through a pore structure formed by virus and, possibly, host proteins.
Splenic Priming of Virus-Specific CD8 T Cells following Influenza Virus Infection
Authors: Turner Damian L. , Bickham Kara L. , Farber Donna L. , Lefrançois Leo 
Published: February 2013

ABSTRACTIn healthy individuals, influenza virus (IAV) infection generally remains localized to the epithelial cells of the respiratory tract. Previously, IAV-specific effector CD8 T cells found systemically during the course of IAV infection were thought to have been primed in lung-draining lymph nodes with subsequent migration to other tissues. However, little is known about whether other lymphoid sites participate in the generation of virus-specific CD8 T cells during localized IAV infection. Here, we present evidence of early CD8 T cell priming in the spleen following respiratory IAV infection independent of lung-draining lymph node priming of T cells. Although we found early indications of CD8 T cell activation in the lymph nodes draining the respiratory tract, we also saw evidence of virus-specific CD8 T cell activation in the spleen. Furthermore, CD8 T cells primed in the spleen differentiated into memory cells of equivalent longevity and with similar recall capacity as CD8 T cells primed in the draining lymph nodes. These data showed that the spleen contributes to the virus-specific effector and memory CD8 T cell populations that are generated in response to respiratory infection.
Determining the frequency and preventability of adverse drug reaction-related admissions to an Irish University Hospital: a cross-sectional study
Authors: Ahern Fiona , Sahm Laura J , Lynch Deirdre , McCarthy Suzanne 
Published: February 2013

BackgroundAdverse drug reactions (ADR) cause considerable morbidity and mortality.MethodsThis 4-week study was undertaken in Cork University Hospital, Ireland, for all admissions from the emergency department (ED). A panel independently reviewed patients with suspected ADRs. Causality assessment was performed using the Naranjo ADR probability scale and the Hallas criteria was used to assess preventability of the ADRs.ResultsDuring the study period, 1258 patients were admitted from the ED; of these, 856 patients were included in the study; 75 patients (8.8%) had an ADR-related admission. Over half were deemed to be ‘possibly’ or ‘definitely’ avoidable. The level of agreement between reviewers using the Naranjo and Hallas criteria was very low.In the ADR group (n=75), 50.7% were men compared with 53.1% in the non-ADR group (n=781). The median age for patients in the ADR group was 73 years compared with 45 years in the non-ADR group. The average number of prescribed drugs per patient in the ADR group was 7.5 (SD±3.8) compared with 2.4 (SD±3.6) in the non-ADR group. Classified by drug type, 74.2% of the ADRs were attributed to cardiovascular and central nervous system drugs.ConclusionsThis study estimated the incidence of ADR-related admissions to an Irish hospital at 8.8%, with 57.3% of these deemed to have been potentially avoidable. Older patients were more likely to have an ADR-related admission. Prescribers must be aware of this increased likelihood of an ADR when prescribing new drugs to this patient population, and regularly review treatment.
Is air transport of stroke patients faster than ground transport? A prospective controlled observational study
Authors: Hesselfeldt Rasmus , Gyllenborg Jesper , Steinmetz Jacob , Do Hien Quoc , Hejselbæk Julie , Rasmussen Lars S 
Published: February 2013

BackgroundHelicopters are widely used for interhospital transfers of stroke patients, but the benefit is sparsely documented. We hypothesised that helicopter transport would reduce system delay to thrombolytic treatment at the regional stroke centre.MethodsIn this prospective controlled observational study, we included patients referred to a stroke centre if their ground transport time exceeded 30 min, or they were transported by a secondarily dispatched, physician-staffed helicopter. The primary endpoint was time from telephone contact to triaging neurologist to arrival in the stroke centre. Secondary endpoints included modified Rankin Scale at 3 months, 30-day and 1-year mortality.ResultsA total of 330 patients were included; 265 with ground transport and 65 with helicopter, of which 87 (33%) and 22 (34%), received thrombolysis, respectively (p=0.88). Time from contact to triaging neurologist to arrival in the regional stroke centre was significantly shorter in the ground group (55 (34–85) vs 68 (40–85) min, p<0.01). The distance from scene to stroke centre was shorter in the ground group (67 (42–136) km) than in the helicopter group (83 (46–143) km) (p<0.01). We did not detect significant differences in modified Rankin Scale at 3 months, in 30-day (9.4% vs 0%; p=0.20) nor 1-year (18.8% vs 13.6%; p=0.76) mortality between ground and helicopter transport.ConclusionsWe found significantly shorter time from contact to triaging neurologist to arrival in the regional stroke centre if stroke patients were transported by primarily dispatched ground ambulance compared with a secondarily dispatched helicopter.
Vaccinations and the Animal Welfare Act
Authors: Whiting Martin 
Published: February 2013

Articles in this series give readers the opportunity to consider and contribute to discussion of some of the ethical dilemmas that can arise in veterinary practice. Each month, a case scenario is presented, followed by discussion of some of the issues involved. In addition, a possible way forward is suggested; however, there is rarely a cut‐and‐dried answer in such cases, and readers may wish to suggest an alternative approach. This month's dilemma, ‘Vaccinations and the Animal Welfare Act’, is presented and discussed by Martin Whiting. Readers with comments to contribute are invited to send them as soon as possible, so that they can be considered for publication in the next issue. Discussion of the dilemma ‘A corneal cat‐astrophe?’, which was published in the January issue of In Practice, appears on page 103.The series is being coordinated by Siobhan Mullan, of the University of Bristol. It is hoped it will provide a framework that will help practices find solutions when facing similar dilemmas.
DISTRIBUTED RELIABLE RENDERING METHOD FOR PARAMETRIC MODELING
Authors: SKALA TIBOR , TODOROVAC MIRSAD , SKALA KAROLJ 
Published: February 2013

Paper presents the achievement on parallelized distributed reliable rendering method shown on 3D electromotor designed to be performed on Cluster computer system. In this paper we will describe a proof of concept model of rendering using parametric POVRay model, client-server on-demand rendering architecture with RFC 822 + 1 SMTP and HTTP like keep-alive extensible protocol, using open source elements, configurable rendering architecture, available to use at no cost added to cost of hardware, with new solutions for simple configuration file mechanisms, and resilient behavior of software, based on best effort strategy of work distribution. The paper presents an innovative way of creating distributed reliable rendering method using huge range of computers for parametric modeling. The main aim of this paper is to present a solution that will use existing resources in order to make modeling method more sufficient and for applying complex computer services/jobs under distributed architecture. The implementation also includes logistics and support for automatic computer clustering and for service/job programs execution. The primary goal is to use existing resources for useful applications in the 3D parametric modeling, image programming and simulation rendering.
Geochronology (Ar/Ar and K–Ar) of the South Atlantic post-break-up magmatism
Authors: Geraldes M. C. , Motoki A. , Costa A. , Mota C. E. , Mohriak W. U. 
Published: February 2013

Abstract
This work integrates the available geological information and geochronology data for the Cretaceous–Recent magmatism in the South Atlantic, represented by onshore and offshore magmatic events, including the oceanic islands along the transform faults and near the mid-ocean ridge. The analysis of the igneous rocks and their tectonic settings allows new insights into the evolution of the African and Brazilian continental margins during the South Atlantic opening. Following the abundant volcanism in the Early Cretaceous, the magmatic quiescence during the Aptian–Albian times is a common characteristic of almost all Brazilian and West African marginal basins. However, rocks ascribed to the Cabo Granite (104 Ma) are observed in NE Brazil. In West Africa, sparse Aptian–Albian ages are observed in a few coastal igneous centres. In the SE Brazilian margin, an east–west alkaline magmatic trend is observed from Poços de Caldas to Cabo Frio, comprising igneous intrusions dated from 87 to 64 Ma. Mafic dyke swarms trending NW also occur in the region extending from the Cabo Frio Province towards the Central Brazilian Craton. On the West African side, Early Cretaceous–Recent volcanism is observed in the Walvis Ridge (139 Ma), the St Helena Ridge (81 Ma) and the Cameroon Volcanic Line (Early Tertiary–Recent). Volcanic islands such as Ascencion (1.0–0.65 Ma), Tristão da Cunha (2.5–0.13 Ma) and the St Helena islands (12 Ma) most probably correspond to mantle plumes or hot spots presently located near the mid-Atlantic spreading centre. Within the South America platform and deep oceanic regions, the following volcanic islands are observed: the Rio Grande Rise (88–86 Ma), Abrolhos (54–44 Ma), the Vitória–Trindade Chain (no age), Trindade (2.8–1.2 Ma) and Fernando de Noronha (12–1.5 Ma). There are several volcanic features along the NW–SE-trending Cruzeiro do Sul Lineament from Cabo Frio to the Rio Grande Rise, but they have not been dated. The only known occurrence of serpentinized mantle rocks in the South Atlantic margin is associated with the Saint Peter and Saint Paul Rocks located along the São Paulo Fracture Zone. The Cameroon Volcanic Line in NW Africa is related to the magmatism that started in the Late Cretaceous and shows local manifestations up to the Present. The compilation of all available magmatic ages suggests an asymmetrical evolution between the African and South America platforms with more pre-break-up and post-break-up magmatism observed in the Brazilian margin. This is most likely to have resulted from the different geological processes operating during the South Atlantic Ocean opening, shifts in the spreading centre, and, possibly, the rising and waning of mantle plumes.

Supplementary material:

A complete table with radiometric dates that have been obtained by universities, government agencies and research groups is available at:
www.geolsoc.org.uk/SUP18596
Targeting the HGF/c-MET Pathway in Hepatocellular Carcinoma
Authors: Goyal Lipika , Muzumdar Mandar D. , Zhu Andrew X. 
Published: February 2013

Abstract
Hepatocellular carcinoma (HCC) is a significant cause of cancer-related morbidity and mortality worldwide. Despite improvements in local therapies, including surgical resection, liver transplantation, and transarterial embolization, the prognosis remains poor for the majority of patients who develop recurrence or present with advanced disease. Systemic therapy with the tyrosine kinase inhibitor sorafenib represents a milestone in advanced HCC but provides a limited survival benefit. Ongoing efforts to study hepatocarcinogenesis have identified an important role for c-MET signaling in the promotion of tumor growth, angiogenesis, and metastasis. In this review, we summarize the preclinical data from human tissue, cell lines, and animal models that implicate c-MET in the pathogenesis of HCC. We also evaluate potential biomarkers that may estimate prognosis or predict response to c-MET inhibitors for more rational clinical trial design. Finally, we discuss the latest clinical trials of c-MET inhibitors in advanced HCC. Clin Cancer Res; 19(9); 2310–8. ©2013 AACR.