bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social inequalities in preterm birth in Scotland 1980–2003: findings from an area‐based measure of deprivation
Authors: Gray R , Bonellie SR , Chalmers J , Greer I , Jarvis S , Williams C 
Published: December 2007

Objective  The preterm birth rate in Scotland has been increasing in recent years. Although preterm birth rates show a social gradient, it is unclear how this gradient has been affected by the overall increase. We examined time trends in singleton live preterm birth rates in relation to area‐based socio‐economic indicators.Design  Population‐based retrospective cohort study.Setting  Scotland.Participants  All singleton live births delivered in Scottish hospitals between 1980 and 2003 (n= 1 423 993).Main outcome measures  Singleton live preterm birth rates in each deprivation quintile were derived. Subgroup analyses of those born moderately preterm (32–36 weeks), very preterm (28–31 weeks) and extremely preterm (24–27 weeks) were performed.Results  The rate of singleton live preterm births increased from 49.7 per 1000 live births in the 5‐year period 1980–84 to 56.1 per 1000 in the 4‐year period 2000–03, a relative increase of 12.9%. A marked social gradient was apparent at all time periods: relative indices of inequality were 1.63 (95% CI 1.38–1.92) in 1980–84 and 1.55 (1.44–1.66) in 2000–03. Similar social gradients existed for all gestational age subgroups. Smoking status at first antenatal contact and increased obstetric intervention, possibly reflecting improvements in fetal monitoring and neonatal care, appeared to explain some but not all the social gradient.Conclusions  Social inequalities in preterm birth were apparent in Scotland between 1980 and 2003. In addition to helping pregnant women to stop smoking, other means to reduce social inequalities are required.
Molecular Characterization of a Novel Fastidious Mycobacterium Causing Lepromatous Lesions of the Skin, Subcutis, Cornea, and Conjunctiva of Cats Living in Victoria, Australia
Authors: Fyfe J. A. , McCowan C. , O'Brien C. R. , Globan M. , Birch C. , Revill P. , Barrs V. R. D. , Wayne J. , Hughes M. S. , Holloway S. , Malik R. 
Published: December 2007

ABSTRACT

Between 1999 and 2006, 15 cats were diagnosed with disease attributable to a novel mycobacterial species. The infections consisted of granulomatous lesions in the skin, subcutis, and ocular or periocular tissues with an indolent but progressive clinical course. Lesions typically were found in facial regions or on the distal limbs. Cats of all ages and both sexes were affected. Infections often were challenging to treat, although they could be cured using surgery in concert with combination antimicrobial therapy. Microscopically, lesions were granulomatous to pyogranulomatous and contained numerous acid-fast bacilli. Scanty cultures of the causal microorganisms occasionally could be obtained in mycobacterial broth, but subculture to solid media failed. When cultures were not available, DNA was extracted from fresh tissue, lyophilized material, and formalin-fixed, paraffin-embedded tissues from lesions. PCR amplification of the 5′ end of the 16S rRNA gene and regions within four additional loci (ITS1,
hsp65
,
rpoB
, and
sodA
) was performed with various efficiencies using mycobacterial primers. Nucleotide sequences were unique for each locus tested. Nucleotide sequences obtained from individual cases were identical for each locus for which the amplification was successful. Phylogenetic analysis performed using concatenated partial 16S rRNA and
hsp65
gene sequences indicated that this novel mycobacterial species from Victoria is a member of the
Mycobacterium simiae
-related group, taxonomically related to the mycobacterium causing leproid granulomas in dogs throughout the world. Based on the clustering of cases, we refer to this novel species as
Mycobacterium
sp. strain Tarwin.
Development of a Species-Specific
fur
Gene-Based Method for Identification of the
Burkholderia cepacia
Complex
Authors: Lynch Karlene H. , Dennis Jonathan J. 
Published: December 2007

ABSTRACT

Burkholderia
is an important bacterial genus with a complex taxonomy that contains species of both ecological and pathogenic importance, including nine closely related species collectively termed the
Burkholderia cepacia
complex (BCC). Unfortunately, 16S rRNA gene analysis has proven to be not sensitive enough to discriminate between species of the BCC. Alternative species identification strategies such as
recA
-based PCR followed by restriction fragment length polymorphism analysis, although initially useful, have proven to be inaccurate with the increasing species diversity of the BCC.
recA
gene sequence analysis is more discriminatory and corroborates other biochemical and polyphasic means of taxonomic differentiation. However, it is limited by the fact that certain BCC species are subdivided into discrete
recA
sequence subgroups that may confuse clinical diagnoses. In this study, an effective approach is described for the rapid differentiation of BCC species from both environmental and clinical sources by means of a single-locus sequencing and PCR assay using
fur
as a target gene that provides sequence phylogenies that are species specific and, with few exceptions, not divided into subspecies clusters. This assay is specific and can be used to correctly determine the species status of BCC strains tested following sequencing and amplification of the
fur
gene by both general and species-specific primers. Based on our results, this typing strategy is simpler than and as sensitive as established tests currently in use clinically. This assay is useful for the rapid, definitive identification of all nine current BCC species and potentially novel species groups.
Multilocus Sequence Typing Reveals that the Population Structure of
Candida dubliniensis
Is Significantly Less Divergent than That of
Candida albicans
Authors: McManus Brenda A. , Coleman David C. , Moran Gary , Pinjon Emmanuelle , Diogo Dorothée , Bougnoux Marie-Elisabeth , Borecká-Melkusova Silvia , Bujdákova Helena , Murphy Philip , d'Enfert Christophe , Sullivan Derek J. 
Published: December 2007

ABSTRACT

The pathogenic yeast
Candida dubliniensis
is phylogenetically very closely related to
Candida albicans
, and both species share many phenotypic and genetic characteristics. DNA fingerprinting using the species-specific probe Cd25 and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal gene cluster previously showed that
C. dubliniensis
is comprised of three major clades comprising four distinct ITS genotypes. Multilocus sequence typing (MLST) has been shown to be very useful for investigating the epidemiology and population biology of
C. albicans
and has identified many distinct major and minor clades. In the present study, we used MLST to investigate the population structure of
C. dubliniensis
for the first time. Combinations of 10 loci previously tested for MLST analysis of
C. albicans
were assessed for their discriminatory ability with 50 epidemiologically unrelated
C. dubliniensis
isolates from diverse geographic locations, including representative isolates from the previously identified three Cd25-defined major clades and the four ITS genotypes. Dendrograms created by using the unweighted pair group method with arithmetic averages that were generated using the data from all 10 loci revealed a population structure which supports that previously suggested by DNA fingerprinting and ITS genotyping. The MLST data revealed significantly less divergence within the
C. dubliniensis
population examined than within the
C. albicans
population. These findings show that MLST can be used as an informative alternative strategy for investigating the population structure of
C. dubliniensis
. On the basis of the highest number of genotypes per variable base, we recommend the following eight loci for MLST analysis of
C. dubliniensis
: Cd
AAT1b
, Cd
ACC1
, Cd
ADP1
, Cd
MPIb
, Cd
RPN2
, Cd
SYA1
, exCd
VPS13
, and exCd
ZWF1b
, where “Cd” indicates
C. dubliniensis
and “ex” indicates extended sequence.
Prediction of Methicillin-Resistant
Staphylococcus aureus
Involvement in Disease Sites by Concomitant Nasal Sampling
Authors: Robicsek Ari , Suseno Mira , Beaumont Jennifer L. , Thomson Richard B. , Peterson Lance R. 
Published: December 2007

ABSTRACT

Nasal colonization with methicillin-resistant
Staphylococcus aureus
(MRSA) is believed to precede disease. It is therefore reasonable to expect that testing for nasal MRSA colonization could provide guidance in the choice of empirical therapy for infections. We conducted a retrospective review of 5,779 nasal MRSA tests performed within a 24-h period before or after a clinical culture showed the growth of any organism. A positive nasal MRSA test strongly predicted MRSA involvement at a clinical site (relative risk, 12.9 times higher than in the remainder of the population; 95% confidence intervals [CI], 10.4, 16.1). Nasal MRSA colonization also strongly predicted antimicrobial resistance in other organisms. A negative nasal test was less useful; only 217 of 323 patients (67.2%; 95% CI, 61.8, 72.3) with clinical cultures involving MRSA had detectable, concomitant nasal MRSA colonization. Patients with clindamycin-susceptible MRSA infections were less likely (59%) to have nasal colonization than those with clindamycin-resistant MRSA infections (71%;
P
= 0.042). Patients nasally colonized with MRSA were substantially more likely to have antibiotic-resistant floras in clinical specimens, and this should be considered when initiating therapy. However, nearly a third of MRSA-infected patients were not nasally colonized, suggesting that nasal colonization need not precede disease and that a negative test for nasal colonization would not rule out MRSA disease in settings of moderate or high prevalence.
The Microbicide Tenofovir Does Not Inhibit Nucleic Acid Amplification Tests for Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
in Urine Samples
Authors: Wood Billie Jo , Rizzo-Price Patricia , Holden Jeff , Hardick Andrew , Quinn Thomas C. , Gaydos Charlotte A. 
Published: December 2007

ABSTRACT

The potential inhibitory effects of tenofovir and a placebo were examined using the Becton Dickinson ProbeTec, Gen-Probe Aptima Combo 2, and Roche Amplicor tests to detect
Chlamydia trachomatis
and
Neisseria gonorrhoeae
. Concentrations of 5% to 0% of tenofovir and the placebo were added to dilutions of
C. trachomatis
and
N. gonorrhoeae
. No appreciable inhibition was observed.
Association of
Mycoplasma ovipneumoniae
Infection with Population-Limiting Respiratory Disease in Free-Ranging Rocky Mountain Bighorn Sheep (
Ovis canadensis canadensis
)
Authors: Besser Thomas E. , Cassirer E. Frances , Potter Kathleen A. , VanderSchalie John , Fischer Allison , Knowles Donald P. , Herndon David R. , Rurangirwa Fred R. , Weiser Glen C. , Srikumaran Subramaniam 
Published: December 2007

ABSTRACT

Bronchopneumonia is a population-limiting disease in bighorn sheep in much of western North America. Previous investigators have isolated diverse bacteria from the lungs of affected sheep, but no single bacterial species is consistently present, even within single epizootics. We obtained high-quality diagnostic specimens from nine pneumonic bighorn sheep in three populations and analyzed the bacterial populations present in bronchoalveolar lavage specimens of seven by using a culture-independent method (16S rRNA gene amplification and clone library analyses).
Mycoplasma ovipneumoniae
was detected as a predominant member of the pneumonic lung flora in lambs with early lesions of bronchopneumonia. Specific PCR tests then revealed the consistent presence of
M. ovipneumoniae
in the lungs of pneumonic bighorn sheep in this study, and
M. ovipneumoniae
was isolated from lung specimens of five of the animals. Retrospective application of
M. ovipneumoniae
PCR to DNA extracted from archived formalin-fixed, paraffin-embedded lung tissues of historical adult bighorn sheep necropsy specimens supported the association of this agent with bronchopneumonia (16/34 pneumonic versus 0/17 nonpneumonic sheep were PCR positive [
P
< 0.001]). Similarly, a very strong association was observed between the presence of one or more
M. ovipneumoniae
antibody-positive animals and the occurrence of current or recent historical bronchopneumonia problems (seropositive animals detected in 9/9 versus 0/9 pneumonic and nonpneumonic populations, respectively [
P
< 0.001]).
M. ovipneumoniae
is strongly associated with bronchopneumonia in free-ranging bighorn sheep and is a candidate primary etiologic agent for this disease.
Equine Infectious Anemia Virus Entry Occurs through Clathrin-Mediated Endocytosis
Authors: Brindley Melinda A. , Maury Wendy 
Published: December 2007

ABSTRACT

Entry of wild-type lentivirus equine infectious anemia virus (EIAV) into cells requires a low-pH step. This low-pH constraint implicates endocytosis in EIAV entry. To identify the endocytic pathway involved in EIAV entry, we examined the entry requirements for EIAV into two different cells: equine dermal (ED) cells and primary equine endothelial cells. We investigated the entry mechanism of several strains of EIAV and found that both macrophage-tropic and tissue culture-adapted strains utilize clathrin-coated pits for entry. In contrast, a superinfecting strain of EIAV, EIAV
vMA-1c
, utilizes two mechanisms of entry. In cells such as ED cells that EIAV
vMA-1c
is able to superinfect, viral entry is pH independent and appears to be mediated by plasma membrane fusion, whereas in cells where no detectable superinfection occurs, EIAV
vMA-1c
entry that is low-pH dependent occurs through clathrin-coated pits in a manner similar to wild-type virus. Regardless of the mechanism of entry being utilized, the internalization kinetics of EIAV is rapid with 50% of cell-associated virions internalizing within 60 to 90 min. Cathepsin inhibitors did not prevent EIAV entry, suggesting that the low-pH step required by wild-type EIAV is not required to activate cellular cathepsins.
Cooperative Effect of the Attenuation Determinants Derived from Poliovirus Sabin 1 Strain Is Essential for Attenuation of Enterovirus 71 in the NOD/SCID Mouse Infection Model
Authors: Arita Minetaro , Ami Yasushi , Wakita Takaji , Shimizu Hiroyuki 
Published: December 2007

ABSTRACT
Enterovirus 71 (EV71) is a causative agent of hand, foot, and mouth disease and is also associated with serious neurological disorders. An attenuated EV71 strain [EV71(S1-3′)] has been established in the cynomolgus monkey infection model; this strain contains the attenuation determinants derived from the type 1 poliovirus vaccine strain, Sabin 1 [PV1(Sabin)], in the 5′ nontranslated region (NTR), 3D polymerase, and 3′ NTR. In this study, we analyzed the effect of the attenuation determinants of PV1(Sabin) on EV71 infection in a NOD/SCID mouse infection model. We isolated a mouse-adapted EV71 strain [EV71(NOD/SCID)] that causes paralysis of the hind limbs in 3- to 4-week-old NOD/SCID mice by adaptation of the virulent EV71(Nagoya) strain in the brains of NOD/SCID mice. A single mutation at nucleotide 2876 that caused an amino acid change in capsid protein VP1 (change of the glycine at position 145 to glutamic acid) was essential for the mouse-adapted phenotype in NOD/SCID mice. Next, we introduced attenuation determinants derived from PV1(Sabin) along with the mouse adaptation mutation into the EV71(Nagoya) genome. In 4-week-old mice, the determinants in the 3D polymerase and 3′ NTR, which are the major temperature-sensitive determinants, had a strong effect on attenuation. In contrast, the effect of individual determinants was weak in 3-week-old NOD/SCID mice, and all the determinants were required for substantial attenuation. These results suggest that a cooperative effect of the attenuation determinants of PV1(Sabin) is essential for attenuated neurovirulence of EV71.
Patterns of CD8+Immunodominance May Influence the Ability ofMamu-B*08-Positive Macaques To Naturally Control Simian Immunodeficiency Virus SIVmac239 Replication
Authors: Loffredo John T. , Bean Alex T. , Beal Dominic R. , León Enrique J. , May Gemma E. , Piaskowski Shari M. , Furlott Jessica R. , Reed Jason , Musani Solomon K. , Rakasz Eva G. , Friedrich Thomas C. , Wilson Nancy A. , Allison David B. , Watkins David I. 
Published: December 2007

ABSTRACTCertain major histocompatibility complex (MHC) class I alleles are strongly associated with control of human immunodeficiency virus and simian immunodeficiency virus (SIV). CD8+T cells specific for epitopes restricted by these molecules may be particularly effective. Understanding how CD8+T cells contribute to control of viral replication should yield important insights for vaccine design. We have recently identified an Indian rhesus macaque MHC class I allele,Mamu-B*08, associated with elite control and low plasma viremia after infection with the pathogenic isolate SIVmac239. Here, we infected fourMamu-B*08-positive macaques with SIVmac239 to investigate why some of these macaques control viral replication. Three of the four macaques controlled SIVmac239 replication with plasma virus concentrations below 20,000 viral RNA copies/ml at 20 weeks postinfection; two of four macaques were elite controllers (ECs). Interestingly, two of the four macaques preserved their CD4+memory T lymphocytes during peak viremia, and all four recovered their CD4+memory T lymphocytes in the chronic phase of infection. Mamu-B*08-restricted CD8+T-cell responses dominated the acute phase and accounted for 23.3% to 59.6% of the total SIV-specific immune responses. Additionally, the ECs mounted strong and broad CD8+T-cell responses against several epitopes in Vif and Nef. Mamu-B*08-specific CD8+T cells accounted for the majority of mutations in the virus at 18 weeks postinfection. Interestingly, patterns of viral variation in Nef differed between the ECs and the other two macaques. Natural containment of AIDS virus replication inMamu-B*08-positive macaques may, therefore, be related to a combination of immunodominance and viral escape from CD8+T-cell responses.
Activation of p90 Ribosomal S6 Kinase by ORF45 of Kaposi's Sarcoma-Associated Herpesvirus and Its Role in Viral Lytic Replication
Authors: Kuang Ersheng , Tang Qiyi , Maul Gerd G. , Zhu Fanxiu 
Published: December 2007

ABSTRACTThe extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) pathway is essential for infection by a variety of viruses. The p90 ribosomal S6 kinases (RSKs) are direct substrates of ERK and functional mediators of ERK MAPK signaling, but their roles in viral infection have never been examined. We demonstrate that ORF45 of Kaposi's sarcoma-associated herpesvirus (KSHV) interacts with RSK1 and RSK2 and strongly stimulates their kinase activities. The activation of RSK by ORF45 is correlated with ERK activation but does not require MEK. We further demonstrate that RSK1/RSK2 is activated during KSHV primary infection and reactivation from latency; a subset of RSK1/RSK2 is present in the viral replication compartment in the nucleus. Depletion of RSK1/RSK2 by small interfering RNA or the specific inhibitor BI-D1870 suppresses KSHV lytic gene expression and progeny virion production, suggesting an essential role of RSK1/RSK2 in KSHV lytic replication.
Lipid Intermediates in the Biosynthesis of Bacterial Peptidoglycan
Authors: van Heijenoort Jean 
Published: December 2007

SUMMARY
This review is an attempt to bring together and critically evaluate the now-abundant but dispersed data concerning the lipid intermediates of the biosynthesis of bacterial peptidoglycan. Lipid I, lipid II, and their modified forms play a key role not only as the specific link between the intracellular synthesis of the peptidoglycan monomer unit and the extracytoplasmic polymerization reactions but also in the attachment of proteins to the bacterial cell wall and in the mechanisms of action of antibiotics with which they form specific complexes. The survey deals first with their detection, purification, structure, and preparation by chemical and enzymatic methods. The recent important advances in the study of transferases MraY and MurG, responsible for the formation of lipids I and II, are reported. Various modifications undergone by lipids I and II are described, especially those occurring in gram-positive organisms. The following section concerns the cellular location of the lipid intermediates and the translocation of lipid II across the cytoplasmic membrane. The great efforts made since 2000 in the study of the glycosyltransferases catalyzing the glycan chain formation with lipid II or analogues are analyzed in detail. Finally, examples of antibiotics forming complexes with the lipid intermediates are presented.
Elastic dislocation modelling for prediction of small-scale fault and fracture network characteristics
Authors: Dee S. J. , Yielding G. , Freeman B. , Healy D. , Kusznir N. J. , Grant N. , Ellis P. 
Published: December 2007

Abstract
Predicting the effects of small-scale faults and fractures on reservoir behaviour requires a definition of their spatial distribution, orientation and mode. Elastic dislocation (ED) theory can predict the distribution of displacement, strain and stress in the rock volume surrounding major faults, from mapping of fault geometry and slip distribution in 3D seismic-reflection datasets. The intensity of small-scale faulting can be related to the predicted local strain, or the degree to which the shear stresses exceeded the rock failure envelope. We illustrate the methodology with three case studies: (i) a relatively-simple thrust anticline from Venezuela, where hydrocarbons are trapped in Pliocene sandstones within the faulted hanging wall anticline; (ii) the Gull-faks Field and of the North Sea; and (iii) the Miskar Field, offshore Tunisia, where large seismically mapped normal faults are forward-modelled to predict small-scale fault characteristics for comparison with detailed interpretation and seismic attribute analysis. Key requirements for the development of a robust predictive model of the small-scale fault and fracture network are a geometrically consistent framework model, judicious choice of mechanical properties, and a reasonable estimate of regional background strain.
Fold amplification and style transition involving fractured dip-domain boundaries: buckling experiments in brittle paraffin wax multilayers and comparison with natural examples
Authors: Bazalgette L. , Petit J.-P. 
Published: December 2007

Abstract
Experiments aiming to study the conditions of fracture localization during buckle folding in brittle sedimentary layers of the upper crust were conducted using brittle paraffin wax multilayers submitted to axial and vertical load. The particular aim was to understand the mechanisms of development of subtle features often observed in apparently rounded natural folds. These consist of scarcely visible discontinuous fractured zones, more or less parallel to the fold axis, that separate domains of constant dip. These zones are of great interest for fluid dynamics in folded fractured reservoirs. It is shown that such axial kink boundaries referred to as dip-domain boundaries (DDBs) play a major role in the development of curvature in fractured buckle folds. DDBs observed in experiments consist of the localization and coalescence of tensile fractures along axial planes after the elastic instability stage. The tested physical parameters were (1) the intensity of the vertical load, (2) the bed thickness within a mechanical unit of constant thickness, (3) the stiff (multilayer)-soft (embedding material) thickness ratio and (4) the interlayer friction. In low interlayer friction conditions DDBs remain relatively localized during shortening, leading to chevron-style folds. With high interlayer friction conditions, DDBs tend to multiply laterally from an initial chevron fold. The latter phenomenon leads towards a more rounded fold, but one that still shows discontinuous curvature comparable to that observed in natural conditions. Fold models of flexural slip and tangential longitudinal strain (orthogonal flexure) are discussed under the influence of tensile failure in multilayer materials.