bluuebunny/crossref_metadata_2025_split huggingface dataset:
An accretion disc origin for the ‘X-ray broad-line region’ in 1H0707-495
Authors: Blustin A. J. , Fabian A. C. 
Published: September 2009

Abstract
We use a 380-ks X-ray Multi-Mirror Mission–Newton (XMM–Newton) high-resolution Reflection Grating Spectrometer (RGS) spectrum to look for narrow spectral features from the nuclear environment of 1H0707-495. We do not find any evidence of a line-of-sight ionized wind (warm absorber). We do, however, detect broad emission lines, of width ∼5000 kms−1, consistent with Oviii Lyα, Nvii Lyα, Cvi Lyα and an Fexix/Fexx/Neix Heα blend. Intriguingly, these lines have both blueshifted and redshifted components, whose velocity shifts are consistent with an origin in an accretion disc at ∼1600 Rg from the black hole. The features can be interpreted as the narrow-line cores of the disc reflection spectrum, thus providing independent support for the discline interpretation of the X-ray spectrum of 1H0707-495. We discuss the relevance of our findings for the ‘X-ray broad-line region’ in other Seyferts, and for the origins of the optical broad-line region itself.
Comparison of Real-Time PCR and Conventional Biochemical Methods for Identification of
Staphylococcus lugdunensis
Authors: Pinsky Benjamin A. , Samson Divinia , Ghafghaichi Laleh , Baron Ellen J. , Banaei Niaz 
Published: September 2009

ABSTRACT

Staphylococcus lugdunensis
is an aggressive, virulent member of the coagulase-negative staphylococci (CoNS) that is responsible for severe, rapidly progressive skin and soft tissue infections and native valve endocarditis. To facilitate prompt identification and appropriate therapy, we describe here a rapid and robust multiplex real-time PCR assay that is able to definitively distinguish
S. lugdunensis
from other staphylococci. Using melting curve analysis, the assay also identifies
Staphylococcus aureus
and CoNS other than
S. lugdunensis
and determines MecA-dependent resistance to methicillin (meticillin). When applied to a panel of well-characterized staphylococcal reference strains, as well as 165 clinical isolates previously identified by conventional methods, the assay was both sensitive and specific for
S. lugdunensis
, correctly identifying the reference strain and all 47
S. lugdunensis
isolates without inappropriate amplification of other staphylococci. Furthermore, rapid biochemical identification using the WEE-TAB system to detect ornithine decarboxylase activity was found to be unsuitable as an alternative to PCR identification, displaying just 31% sensitivity and 77% specificity when tested on a subset (90 isolates) of the clinical strains. We therefore propose that this simple, accurate PCR approach will allow for the routine and timely identification of
S. lugdunensis
in the clinical microbiology laboratory.
False-Positive PCR Detection of
Tropheryma whipplei
in Cerebrospinal Fluid and Biopsy Samples from a Child with Chronic Lymphocytic Meningitis
Authors: Goyo Daniel , Camacho Ana , Gómez Carmen , de las Heras Rogelio Simón , Otero Joaquín R. , Chaves Fernando 
Published: September 2009

ABSTRACT

We report the case of a teenager with chronic lymphocytic meningitis for whom
Tropheryma whipplei
16S rRNA PCR results were positive in two cerebrospinal fluid samples and one duodenal biopsy specimen. PCR targeting another specific sequence of
Tropheryma whipplei
and sequencing of the initially amplified 16S rRNA fragment did not confirm the results.
The EmsB Tandemly Repeated Multilocus Microsatellite: a New Tool To Investigate Genetic Diversity of
Echinococcus granulosus
Sensu Lato
Authors: Maillard S. , Gottstein B. , Haag K. L. , Ma S. , Colovic I. , Benchikh-Elfegoun M. C. , Knapp J. , Piarroux R. 
Published: September 2009

ABSTRACT

Cystic echinococcosis (CE) is a widespread and severe zoonotic disease caused by infection with the larval stage of the eucestode
Echinococcus granulosus
sensu lato. The polymorphism exhibited by nuclear and mitochondrial markers conventionally used for the genotyping of different parasite species and strains does not reach the level necessary for the identification of genetic variants linked to restricted geographical areas. EmsB is a tandemly repeated multilocus microsatellite that proved its usefulness for the study of genetic polymorphisms within the species
E. multilocularis
, the causative agent of alveolar echinococcosis. In the present study, EmsB was used to characterize
E. granulosus
sensu lato samples collected from different host species (sheep, cattle, dromedaries, dogs, and human patients) originating from six different countries (Algeria, Mauritania, Romania, Serbia, Brazil, and the People's Republic of China). The conventional mitochondrial
cox1
and
nad1
markers identified genotypes G1, G3, G5, G6, and G7, which are clustered into three groups corresponding to the species
E. granulosus
sensu stricto,
E. ortleppi
, and
E. canadensis
. With the same samples, EmsB provided a higher degree of genetic discrimination and identified variations that correlated with the relatively small-scale geographic origins of the samples. In addition, one of the Brazilian single hydatid cysts presented a hybrid genotypic profile that suggested genetic exchanges between
E. granulosus
sensu stricto and
E. ortleppi
. In summary, the EmsB microsatellite exhibits an interesting potential for the elaboration of a detailed map of the distribution of genetic variants and therefore for the determination and tracking of the source of CE.
Infections with VIM-1 Metallo-β-Lactamase-Producing
Enterobacter cloacae
and Their Correlation with Clinical Outcome
Authors: Falcone Marco , Mezzatesta Maria Lina , Perilli Mariagrazia , Forcella Chiara , Giordano Alessandra , Cafiso Viviana , Amicosante Gianfranco , Stefani Stefania , Venditti Mario 
Published: September 2009

ABSTRACT

The aim of this study was to ascertain the incidence and clinical significance of metallo-β-lactamases among
Enterobacter
strains isolated from patients with nosocomial infections. We prospectively collected data on patients with
Enterobacter
infection during a 13-month period. All of the strains were investigated for antibiotic susceptibility, the presence and expression of metallo-β-lactamases, and clonality. Of 29 infections (11 involving the urinary tract, 7 pneumonias, 3 skin/soft tissue infections, 3 intra-abdominal infections, 3 bacteremias, and 2 other infections), 7 (24%) were caused by
Enterobacter cloacae
strains harboring a
bla
VIM-1
gene associated or not with a
bla
SHV12
gene. Infections caused by VIM-1-producing strains were more frequently associated with a recent prior hospitalization (
P
= 0.006), cirrhosis (
P
= 0.03), relapse of infection (
P
< 0.001), and more prolonged duration of antibiotic therapy (
P
= 0.01) than were other infections. All of the isolates were susceptible to imipenem and meropenem and had
bla
VIM-1
preceded by a weak P1 promoter and inactivated P2 promoters. Most VIM-1-producing
Enterobacter
isolates belonged to a main clone, but four different clones were found. Multiclonal VIM-1-producing
E. cloacae
infections are difficult to diagnose due to an apparent susceptibility to various beta-lactams, including carbapenems, and are associated with a high relapse rate and a more prolonged duration of antibiotic therapy.
Phylogenetic Analysis of Human Parvovirus B19 Sequences from Eleven Different Countries Confirms the Predominance of Genotype 1 and Suggests the Spread of Genotype 3b
Authors: Hübschen Judith M. , Mihneva Zefira , Mentis Andreas F. , Schneider François , Aboudy Yair , Grossman Zehava , Rudich Hagit , Kasymbekova Kalia , Sarv Inna , Nedeljkovic Jasminka , Tahita Marc C. , Tarnagda Zekiba , Ouedraogo Jean-Bosco , Gerasimova A. G. , Moskaleva T. N. , Tikhonova Nina T. , Chitadze Nazibrola , Forbi J. C. , Faneye Adedayo O. , Otegbayo Jesse A. , Charpentier Emilie , Muller Claude P. 
Published: September 2009

ABSTRACT
Phylogenetic analysis of 166 human parvovirus B19 sequences from 11 different countries attributed 91.57% to genotype 1, 5.42% to genotype 3b, and 3.01% to genotype 3a. Very similar viruses of genotype 1 circulated widely in Europe and Israel. Genotype 3b seems to show an increasing spread outside of Africa.
Comparison of a Commercial Multiplex Real-Time PCR to the Cell Cytotoxicity Neutralization Assay for Diagnosis of
Clostridium difficile
Infections
Authors: Huang Haihui , Weintraub Andrej , Fang Hong , Nord Carl Erik 
Published: September 2009

ABSTRACT

A commercial multiplex real-time PCR assay (Cepheid Xpert
C. difficile
assay) for the diagnosis of
Clostridium difficile
infection was evaluated. The sensitivity and specificity of the Cepheid assay were 97.1% and 93.0% for fresh stools, using the cell cytotoxicity neutralization assay as the reference. Using PCR ribotyping as the reference for ribotype 027 strains, the corresponding figures were 100% and 98.1%, respectively.
Transmission of an Extended-Spectrum-Beta-Lactamase-Producing
Escherichia coli
(Sequence Type ST131) Strain between a Father and Daughter Resulting in Septic Shock and Emphysematous Pyelonephritis
Authors: Ender Peter T. , Gajanana Deepakraj , Johnston Brian , Clabots Connie , Tamarkin Frank J. , Johnson James R. 
Published: September 2009

ABSTRACT

Probable transmission of an extended-spectrum-beta-lactamase-producing
Escherichia coli
strain (sequence type ST131) between a father and daughter was documented. The father developed severe, recurrent pyelonephritis with multiple small abscesses; the daughter later developed septic shock, bacteremia, and extensive emphysematous pyelonephritis. This multidrug-resistant
E. coli
clone appears to be highly pathogenic and transmissible.
Molecular Characteristics of German G8P[4] Rotavirus Strain GER1H-09 Suggest that a Genotyping and Subclassification Update Is Required for G8
Authors: Pietsch C. , Petersen L. , Patzer L. , Liebert U. G. 
Published: September 2009

ABSTRACT
A rare G8P[4] rotavirus, designated GER1H-09, was detected in a stool sample from an infant suffering from repeated episodes of emesis for 2 days without diarrhea. Sequencing of all genomic RNA segments was performed, and complete coding sequences were determined. The VP7 amino acid sequence revealed a close phylogenetic relationship to human G8P[6] and G8P[8] isolates from Slovenia and Africa. GER1H-09 shared typical amino acid residues within variable regions VR3 to VR7 with those strains, and their subclassification as lineage G8-II rotaviruses is proposed. The variability in VR3 was identified as the likely reason for the failure in genotyping G8-II rotaviruses by commonly used multiplex PCR. Furthermore, the sequences of associated structural and nonstructural proteins showed high amino acid identities to DS-1-like rotaviruses. The genotype composition of GER1H-09 (G8-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) suggests the occurrence of reassortment events between G8 genotypes and human DS-1-like G2P[4] rotaviruses.
Rapid SYBR Green I and Modified Probe Real-Time Reverse Transcription-PCR Assays Identify Influenza H1N1 Viruses and Distinguish between Pandemic and Seasonal Strains
Authors: Yang Ji-Rong , Lo Je , Liu Jian-Liang , Lin Chao-Hua , Ho Yu-Lin , Chen Chun-Jung , Wu Ho-Sheng , Liu Ming-Tsan 
Published: September 2009

ABSTRACT
A rapid SYBR green I real-time reverse transcription-PCR (RT-PCR) assay was developed to identify pandemic influenza H1N1 virus from clinical specimens in less than 1 h. Probe real-time RT-PCR influenza A/B, H1/H3, and swNP/swHA assays were modified into the same PCR program, which allows for rapid and simultaneous typing and subtyping of influenza viruses.
Expansion, Reexpansion, and Recall-Like Expansion of Vγ2Vδ2 T Cells in Smallpox Vaccination and Monkeypox Virus Infection
Authors: Shao Lingyun , Huang Dan , Wei Huiyong , Wang Richard C. , Chen Crystal Y. , Shen Ling , Zhang Wenhong , Jin Jialin , Chen Zheng W. 
Published: September 2009

ABSTRACT
Little is known about the in vivo kinetics of T-cell responses in smallpox/monkeypox. We showed that macaque Vγ2Vδ2 T cells underwent 3-week-long expansion after smallpox vaccine immunization and displayed simple reexpansion in association with sterile anti-monkeypox virus (anti-MPV) immunity after MPV challenge. Virus-activated Vγ2Vδ2 T cells exhibited gamma interferon-producing effector function after phosphoantigen stimulation. Surprisingly, like αβ T cells, suboptimally primed Vγ2Vδ2 T cells in vaccinia virus/cidofovir-covaccinated macaques mounted major recall-like expansion after MPV challenge. Finally, Vγ2Vδ2 T cells localized in inflamed lung tissues for potential regulation. Our studies provide the first in vivo evidence that viruses, despite their inability to produce exogenous phosphoantigen, can induce expansion, reexpansion, and recall-like expansion of Vγ2Vδ2 T cells and stimulate their antimicrobial cytokine response.
Human Endogenous Retroviral Long Terminal Repeat Sequences as Cell Type-Specific Promoters in Retroviral Vectors
Authors: Schön Ulrike , Diem Olivia , Leitner Laura , Günzburg Walter H. , Mager Dixie L. , Salmons Brian , Leib-Mösch Christine 
Published: September 2009

ABSTRACT
The human genome contains more than half a million human endogenous retrovirus (HERV) long terminal repeats (LTRs) that can be regarded as mobile regulatory modules. Many of these HERV LTRs have been recruited during evolution as transcriptional control elements for cellular gene expression. We have cloned LTR sequences from two HERV families, HERV-H and HERV-L, differing widely in their activity and tissue specificity into a murine leukemia virus (MLV)-based promoter conversion vector (ProCon). Various human cell lines were infected with the HERV-MLV hybrid vectors, and cell type-specific expression of the reporter gene was compared with the promoter specificity of the corresponding HERV LTRs in transient-transfection assays. Transcription start site analysis of HERV-MLV hybrid vectors revealed preferential use of the HERV promoter initiation site. Our data show that HERV LTRs function in the context of retroviral vectors in certain cell types and have the potential to be useful as cell type-specific promoters in vector construction.
Differences in the Regulatory and Functional Effects of the Us3 Protein Kinase Activities of Herpes Simplex Virus 1 and 2
Authors: Morimoto Tomomi , Arii Jun , Tanaka Michiko , Sata Tetsutaro , Akashi Hiroomi , Yamada Masao , Nishiyama Yukihiro , Uema Masashi , Kawaguchi Yasushi 
Published: September 2009

ABSTRACTUs3 protein kinases encoded by herpes simplex virus 1 (HSV-1) and 2 (HSV-2) are serine/threonine protein kinases and play critical roles in viral replication and pathogenicity in vivo. In the present study, we investigated differences in the biological properties of HSV-1 and HSV-2 Us3 protein kinases and demonstrated that HSV-2 Us3 did not have some of the HSV-1 Us3 kinase functions, including control of nuclear egress of nucleocapsids, localization of UL31 and UL34, and cell surface expression of viral envelope glycoprotein B. In agreement with the observations that HSV-2 Us3 was less important for these functions, the effect of HSV-2 Us3 kinase activity on virulence in mice following intracerebral inoculation was much lower than that of HSV-1 Us3. Furthermore, we showed that alanine substitution in HSV-2 Us3 at a site (aspartic acid at position 147) corresponding to one that can be autophosphorylated in HSV-1 Us3 abolished HSV-2 Us3 kinase activity. Thus, the regulatory and functional effects of Us3 kinase activity are different between HSV-1 and HSV-2.
Long-Term Administration of Valacyclovir Reduces the Number of Epstein-Barr Virus (EBV)-Infected B Cells but Not the Number of EBV DNA Copies per B Cell in Healthy Volunteers
Authors: Hoshino Yo , Katano Harutaka , Zou Ping , Hohman Patricia , Marques Adriana , Tyring Stephen K. , Follmann Dean , Cohen Jeffrey I. 
Published: September 2009

ABSTRACT

Epstein-Barr virus (EBV) establishes a latent infection in B cells in the blood, and the latent EBV load in healthy individuals is generally stable over time, maintaining a “set point.” It is unknown if the EBV load changes after long-term antiviral therapy in healthy individuals. We treated volunteers with either valacyclovir (valaciclovir) or no antiviral therapy for 1 year and measured the amount of EBV DNA in B cells every 3 months with a novel, highly sensitive assay. The number of EBV-infected B cells decreased in subjects receiving valacyclovir (half-life of 11 months;
P
= 0.02) but not in controls (half-life of 31 years;
P
= 0.86). The difference in the slopes of the lines for the number of EBV-infected B cells over time for the valacyclovir group versus the control group approached significance (
P
= 0.054). In contrast, the number of EBV DNA copies per B cell remained unchanged in both groups (
P
= 0.62 and
P
= 0.92 for the control and valacyclovir groups, respectively). Valacyclovir reduces the frequency of EBV-infected B cells when administered over a long period and, in theory, might allow eradication of EBV from the body if reinfection does not occur.
The First Transmembrane Domain of the Hepatitis B Virus Large Envelope Protein Is Crucial for Infectivity
Authors: Lepère-Douard Charlotte , Trotard Maud , Le Seyec Jacques , Gripon Philippe 
Published: September 2009

ABSTRACT
The early steps of the hepatitis B virus (HBV) life cycle are still poorly understood. Indeed, neither the virus receptor at the cell surface nor the mechanism by which nucleocapsids are delivered to the cytosol of infected cells has been identified. Extensive mutagenesis studies in pre-S1, pre-S2, and most of the S domain of envelope proteins revealed the presence of two regions essential for HBV infectivity: the 77 first residues of the pre-S1 domain and a conformational motif in the antigenic loop of the S domain. In addition, at the N-terminal extremity of the S domain, a putative fusion peptide, partially overlapping the first transmembrane (TM1) domain and preceded by a PEST sequence likely containing several proteolytic cleavage sites, was identified. Since no mutational analysis of these two motifs potentially implicated in the fusion process was performed, we decided to investigate the ability of viruses bearing contiguous deletions or substitutions in the putative fusion peptide and PEST sequence to infect HepaRG cells. By introducing the mutations either in the L and M proteins or in the S protein, we demonstrated the following: (i) that in the TM1 domain of the L protein, three hydrophobic clusters of four residues were necessary for infectivity; (ii) that the same clusters were critical for S protein expression; and, finally, (iii) that the PEST sequence was dispensable for both assembly and infection processes.
Human Papillomavirus (HPV) Type 18 Induces Extended Growth in Primary Human Cervical, Tonsillar, or Foreskin Keratinocytes More Effectively than Other High-Risk Mucosal HPVs
Authors: Lace Michael J. , Anson James R. , Klingelhutz Aloysius J. , Lee John H. , Bossler Aaron D. , Haugen Thomas H. , Turek Lubomir P. 
Published: September 2009

ABSTRACT
Mucosal high-risk (HR) human papillomaviruses (HPVs) that cause cervical and other anogenital cancers also are found in ∼25% of head and neck carcinomas (HNCs), especially those arising in the oropharynx and the tonsils. While many HR HPV types are common in anogenital cancer, over 90% of HPV-positive HNCs harbor HPV type 16 (HPV-16). Using a quantitative colony-forming assay, we compared the ability of full-length mucosal HPV genomes, i.e., the low-risk HPV-11 and HR HPV-16, -18, and -31, to persist in and alter the growth of primary human keratinocytes from the foreskin, cervix, and tonsils. The HR HPV types led to the formation of growing keratinocyte colonies in culture independent of the site of epithelial origin. However, HPV-18 induced colony growth in all keratinocytes >4-fold more effectively than HPV-16 or HPV-31 and >20-fold more efficiently than HPV-11 or controls. HPV-11-transfected or control colonies failed to expand beyond 32 to 36 population doublings postexplantation. In contrast, individual HR HPV-transfected clones exhibited no apparent slowdown of growth or “crisis,” and many maintained HPV plasmid persistence beyond 60 population doublings. Keratinocyte clones harboring extrachromosomal HR HPV genomes had shorter population doubling times and formed dysplastic stratified epithelia in organotypic raft cultures, mirroring the pathological features of higher-grade intraepithelial lesions, yet did not exhibit chromosomal instability. We conclude that, in culture, the HR HPV type, rather than the site of epithelial origin of the cells, determines the efficacy of inducing continued growth of individual keratinocytes, with HPV-18 being the most aggressive mucosal HR HPV type tested.
A dynamic population-based model for the development of work-related respiratory health effects among bakery workers
Authors: Warren N , Meijster T , Heederik D , Tielemans E 
Published: September 2009

Objectives:This paper presents a dynamic population-based model for the development of sensitisation and respiratory symptoms in bakery workers. The model simulates a population of individual workers longitudinally and tracks the development of work-related sensitisation and respiratory symptoms in each worker.Methods:The model has three components: a multi-stage disease model describing the development of sensitisation and respiratory symptoms in each worker over time; an exposure model describing occupational exposure to flour dust and allergens; and a basic population model describing the length of a worker’s career in the bakery sector and the influx of new workers. Each worker’s disease state is modelled independently using a discrete time Markov Chain, updated yearly using each individual’s simulated exposure. A Bayesian analysis of data from a recent epidemiological study provided estimates of the yearly transition probabilities between disease states.Results:For non-atopic/non-sensitised workers the estimated probabilities of developing moderate (upper respiratory) symptoms and progression to severe (lower respiratory) symptoms are 0.4% (95% CI 0.3 to 0.5%) and 1.1% (95% CI 0.6 to 1.9%) per mg/m3/year of flour dust, respectively, and approximately twice these for atopic workers. The model predicts that 36% (95% CI 26 to 46%) of workers with severe symptoms are sensitised to wheat and 22% (95% CI 12 to 37%) to α-amylase. The predicted mean latency period for respiratory symptoms was 10.3 years (95% CI 8.3 to 12.3).Conclusions:While the model provides a valuable population-level representation of the mechanisms contributing to respiratory diseases in bakers, it was primarily developed for use in quantitative health impact assessment. Future research will use the model to evaluate a range of workplace interventions, including achievable reductions in exposure and health surveillance. The general methodology is applicable to other diseases such as chronic obstructive pulmonary disease, silicosis and musculoskeletal disorders and could be particularly valuable for forecasting changes in long latency diseases.
Monstrous Births and Medical Networks: Debates over Forensic Evidence, Generation Theory, and Obstetrical Authority in France, ca. 1780-1815
Authors: Quinlan Sean 
Published: September 2009

AbstractIn France between 1780 and 1815, doctors opened a broad correspondence with medical faculties and public officials about foetal anomalies ("monstrosities"). Institutional and legal reforms forced doctors to encounter monstrous births with greater frequency, and they responded by developing new ideas about heredity and embryology to explain malformations to public officials. Though doctors achieved consensus on pathogenesis, they struggled to apply these ideas in forensic cases, especially with doubtful sex. Medical networks simultaneously allowed doctors to explore obstetrical techniques, as licensing regulations forced practitioners into emotional encounters with child anomalies. Doctors thus developed a new ethics for treating monstrosities, viewing them as pathological specimens, forensic objects, and obstetrical tragedies.