bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymicrobial periodontal pathogen transcriptomes in calvarial bone and soft tissue
Authors: Bakthavatchalu V. , Meka A. , Mans J.J. , Sathishkumar S. , Lopez M.C. , Bhattacharyya I. , Boyce B.F. , Baker H.V. , Lamont R.J. , Ebersole J.L. , Kesavalu L. 
Published: July 2011

SummaryPorphyromonas gingivalis, Treponema denticola, and Tannerella forsythia are consistently associated with adult periodontitis. This study sought to document the host transcriptome to a P. gingivalis, T. denticola, and T.forsythia challenge as a polymicrobial infection using a murine calvarial model of acute inflammation and bone resorption. Mice were infected with P. gingivalis, T. denticola, and T. forsythia over the calvaria, after which the soft tissues and calvarial bones were excised. A Murine GeneChip® array analysis of transcript profiles showed that 6997 genes were differentially expressed in calvarial bones (P < 0.05) and 1544 genes were differentially transcribed in the inflamed tissues after the polymicrobial infection. Of these genes, 4476 and 1035 genes in the infected bone and tissues were differentially expressed by upregulation. Biological pathways significantly impacted by the polymicrobial infection in calvarial bone included leukocyte transendothelial migration (LTM), cell adhesion molecules, adherens junction, major histocompatibility complex antigen, extracellular matrix–receptor interaction, and antigen processing and presentation resulting in inflammatory/cytokine/chemokine transcripts stimulation in bone and soft tissue. Intense inflammation and increased activated osteoclasts were observed in calvarias compared with sham‐infected controls. Quantitative real‐time RT‐PCR analysis confirmed that the mRNA level of selected genes corresponded with the microarray expression. The polymicrobial infection regulated several LTM and extracellular membrane pathway genes in a manner distinct from mono‐infection with P. gingivalis, T. denticola, or T. forsythia. To our knowledge, this is the first definition of the polymicrobially induced transcriptome in calvarial bone and soft tissue in response to periodontal pathogens.
Predicting alcohol consumption and binge drinking in company employees: An application of planned behaviour and self‐determination theories
Authors: Hagger Martin S. , Lonsdale Adam J. , Hein Vello , Koka Andre , Lintunen Taru , Pasi Heidi , Lindwall Magnus , Rudolfsson Lisa , Chatzisarantis Nikos L. D. 
Published: July 2011

Objectives.  This study tested an integrated model of the psychosocial determinants of alcohol‐related behaviour among company employees from four nations. A motivational sequence was proposed in which motivational orientations from self‐determination theory influenced intentions to consume alcohol within guideline limits and alcohol‐related behaviour via the mediation of the theory of planned behaviour variables of attitude, subjective norms, and perceived behavioural control (PBC).Design.  A three‐wave prospective design using self‐reported psychological and behavioural measures.Methods.  Company employees (N= 486, males = 225, females = 261; M age = 30.41, SD= 8.31) from four nations (Estonia, Finland, Sweden, and UK) completed measures of autonomous and controlled motivation from self‐determination theory, attitudes, subjective norms, PBC, intentions from the theory of planned behaviour, and self‐reported measures of past alcohol consumption and binge‐drinking occasions at the first time point (time 1). Follow‐up psychological and behavioural measures were taken one month later (time 2) and follow‐up behavioural measures taken a further 2 months later (time 3).Results.  Path analyses supported the motivational sequence with identified regulation (time 1), predicting intentions (time 1), and alcohol units consumed (time 2). The effects were indirect via the mediation of attitudes and PBC (time 1). A similar pattern of effects was found for the effect of time 2 psychological variables on time 3 units of alcohol consumed. There was little support for the effects of the psychological variables on binge‐drinking behaviour.Conclusions.  Findings provide new information on the psychosocial determinants of alcohol behaviour in company employees and the processes involved. Results may provide impetus for the development of interventions to reduce alcohol consumption.
Easy Strategy To Increase Salt Resistance of Antimicrobial Peptides
Authors: Yu Hui-Yuan , Tu Chih-Hsiung , Yip Bak-Sau , Chen Heng-Li , Cheng Hsi-Tsung , Huang Kuo-Chun , Lo Hsiu-Jung , Cheng Jya-Wei 
Published: July 2011

ABSTRACT
The efficacies of many antimicrobial peptides are greatly reduced under high salt concentrations, limiting their development as pharmaceutical compounds. Here, we describe an easy strategy to increase salt resistance of antimicrobial peptides by replacing tryptophan or histidine residues with the bulky amino acids β-naphthylalanine and β-(4,4′-biphenyl)alanine. The activities of the salt-sensitive peptide P-113 were diminished at high salt concentrations, whereas the activities of its β-naphthylalanine and β-(4,4′-biphenyl)alanine-substituted variant were less affected.
Cryptic Species and Azole Resistance in the Aspergillus niger Complex
Authors: Howard Susan J. , Harrison Elizabeth , Bowyer Paul , Varga Janos , Denning David W. 
Published: July 2011

ABSTRACT

Aspergillus niger
is a common clinical isolate. Multiple species comprise the
Aspergillus
section
Nigri
and are separable using sequence data. The antifungal susceptibility of these cryptic species is not known. We determined the azole MICs of 50 black aspergilli, 45 from clinical specimens, using modified EUCAST (mEUCAST) and Etest methods. Phylogenetic trees were prepared using the internal transcribed spacer, beta-tubulin, and calmodulin sequences to identify strains to species level and the results were compared with those obtained with
cyp51A
sequences. We attempted to correlate
cyp51A
mutations with azole resistance. Etest MICs were significantly different from mEUCAST MICs (
P
< 0.001), with geometric means of 0.77 and 2.79 mg/liter, respectively. Twenty-six of 50 (52%) isolates were itraconazole resistant by mEUCAST (MICs > 8 mg/liter), with limited cross-resistance to other azoles. Using combined beta-tubulin/calmodulin sequences, the 45 clinical isolates grouped into 5 clades,
A. awamori
(55.6%),
A. tubingensis
(17.8%),
A. niger
(13.3%),
A. acidus
(6.7%), and an unknown group (6.7%), none of which were morphologically distinguishable. Itraconazole resistance was found in 36% of the isolates in the
A. awamori
group, 90% of the
A. tubingensis
group, 33% of the
A. niger
group, 100% of the
A. acidus
group, and 67% of the unknown group. These data suggest that
cyp51A
mutations in section
Nigri
may not play as important a role in azole resistance as in
A. fumigatus
, although some mutations (G427S, K97T) warrant further study. Numerous cryptic species are found in clinical isolates of the
Aspergillus
section
Nigri
and are best reported as “
A. niger
complex” by clinical laboratories. Itraconazole resistance was common in this data set, but azole cross-resistance was unusual. The mechanism of resistance remains obscure.
Residual Activity of Two HIV Antiretroviral Regimens Prescribed without Virological Monitoring
Authors: Dunn D. T. , Goodall R. L. , Munderi P. , Kityo C. , Ranopa M. , Bacheler L. , Van Houtte M. , Gilks C. , Kaleebu P. , Pillay D. 
Published: July 2011

ABSTRACTVirological residual activity (VRA) denotes the degree of HIV RNA suppression achieved by antiretroviral therapy in the presence of resistant virus. This concept is particularly important in resource-limited settings, where rapid switching after detection of virological failure may not be feasible. Using data from the NORA trial, we estimated VRA for two regimens—zidovudine-lamivudine-abacavir (ZDV-3TC-ABC) and zidovudine-lamivudine-nevirapine (ZDV-3TC-NVP)—and related this to the phenotypic drug sensitivity of the component drugs in the two regimens. Plasma samples at weeks 0, 48, and 96 were retrospectively assayed for HIV-1 RNA, and genotypic/phenotypic resistance testing was performed if HIV-1 RNA exceeded 1,000 copies/ml. Virological residual activity (VRA) was defined as the difference between log10(HIV RNA) at week 48 or 96 and week 0 and related to 50% inhibitory concentration (IC50) relative to wild-type virus for ZDV and ABC (fold change [FC]). Twenty-seven samples in the ZDV-3TC-NVP group and 56 in the ZDV-3TC-ABC group contributed to the analysis. Mean VRA was significantly higher in the ZDV-3TC-ABC group than in the ZDV-3TC-NVP at week 48 (1.62 versus 0.90) and week 96 (1.29 versus 0.78). There was a weak and nonsignificant relationship between VRA and ZDV FC, with VRA decreasing by 0.1 log10copies/ml per 2-fold increase in ZDV. The association with ABC FC was much stronger, with a marked reduction in VRA occurring at ABC FC values greater than approximately 2. This information should be considered in future treatment guidelines relevant to resource-poor settings.
Pyrazinamide Susceptibility Testing in Mycobacterium tuberculosis: a Systematic Review with Meta-Analyses
Authors: Chang Kwok Chiu , Yew Wing Wai , Zhang Ying 
Published: July 2011

ABSTRACT

Standard culture-based testing of the susceptibility of
Mycobacterium tuberculosis
to pyrazinamide is difficult to perform. This systematic review with meta-analyses evaluated the roles of molecular assays targeting
pncA
and of pyrazinamidase assays. PubMed and Embase were searched for relevant publications in English. Sensitivity and specificity were estimated in bivariate random-effects models. Of 128 articles identified, 73 sets of data involving culture isolates were initially included in meta-analyses. Summary estimates of sensitivity and specificity, respectively, were 87% and 93% for PCR-DNA sequencing (
n
= 29), 75% and 95% for PCR-single-stranded conformation polymorphism (SSCP) (
n
= 5), 96% and 97% for a mixture of other molecular assays (
n
= 6), and 89% and 97% for pyrazinamidase assays using the Wayne method (
n
= 33). The median prevalence (range) of pyrazinamide resistance was 51% (31% to 89%) in multidrug-resistant
M. tuberculosis
isolates and 5% (0% to 9%) in non-multidrug-resistant isolates. Excluding studies with possibly considerable false resistance in the reference assay gave the following estimates of sensitivity and specificity, respectively: 92% and 93% for PCR-DNA sequencing (
n
= 20), 98% and 96% for other molecular assays (
n
= 5), and 91% and 97% for the Wayne assay (
n
= 27). The Wayne assay had significant funnel plot asymmetry, so the test performance might have been overestimated. Considering the prevalence of pyrazinamide resistance in different clinical settings, PCR-DNA sequencing, and possibly other molecular assays targeting
pncA
, can detect pyrazinamide resistance in multidrug-resistant
M. tuberculosis
isolates, with predictive values largely exceeding 90%, and rule out pyrazinamide resistance in non-multidrug-resistant isolates, with predictive values exceeding 99%. Molecular assays are probably the way forward for detecting pyrazinamide resistance.
Expression of an Mg
2+
-Dependent HIV-1 RNase H Construct for Drug Screening
Authors: Farias Richard V. , Vargas Deborah A. , Castillo Andres E. , Valenzuela Beatriz , Coté Marie L. , Roth Monica J. , Leon Oscar 
Published: July 2011

ABSTRACT

A single polypeptide of the HIV-1 reverse transcriptase that reconstituted Mg
2+
-dependent RNase H activity has been made. Using molecular modeling, the construct was designed to encode the p51 subunit joined by a linker to the thumb (T), connection (C), and RNase H (R) domains of p66. This p51-G-TCR construct was purified from the soluble fraction of an
Escherichia coli
strain, MIC2067(DE3), lacking endogenous RNase HI and HII. The p51-G-TCR RNase H construct displayed Mg
2+
-dependent activity using a fluorescent nonspecific assay and showed the same cleavage pattern as HIV-1 reverse transcriptase (RT) on substrates that mimic the tRNA removal required for second-strand transfer reactions. The mutant E706Q (E478Q in RT) was purified under similar conditions and was not active. The RNase H of the p51-G-TCR RNase H construct and wild type HIV-1 RT had similar

K
m

s for an RNA-DNA hybrid substrate and showed similar inhibition kinetics to two known inhibitors of the HIV-1 RT RNase H.
Observational Study of the Clinical Efficacy of Voriconazole and Its Relationship to Plasma Concentrations in Patients
Authors: Troke Peter F. , Hockey Hans P. , Hope William W. 
Published: July 2011

ABSTRACT

Voriconazole is approved for treating invasive fungal infections. We examined voriconazole exposure-response relationships for patients from nine published clinical trials. The relationship between the mean voriconazole plasma concentration (
C
avg
) and clinical response and between the free
C
avg
/MIC ratio versus the clinical response were explored using logistic regression. The impact of covariates on response was also assessed. Monte Carlo simulation was used to estimate the relationship between the trough concentration/MIC ratio and the probability of response. The covariates individually related to response were as follows: study (
P
< 0.001), therapy (primary/salvage,
P
< 0.001), primary diagnosis (
P
< 0.001), race (
P
= 0.004), baseline bilirubin (
P
< 0.001), baseline alkaline phosphatase (
P
= 0.014), and pathogen (yeast/mold,
P
< 0.001). The
C
avg
for 72% of the patients was 0.5 to 5.0 μg/ml, with the maximum response rate (74%) at 3.0 to 4.0 μg/ml. The
C
avg
showed a nonlinear relationship to response (
P
< 0.003), with a lower probability at the extremes. For patients with
C
avg
< 0.5 μg/ml, the response rate was 57%. The lowest response rate (56%) was seen with a
C
avg
≥ 5.0 μg/ml (18% of patients) and was associated with significantly lower mold infection responses compared to yeasts (
P
< 0.001) but not with voriconazole toxicity. Higher free
C
avg
/MIC ratios were associated with a progressively higher probability of response. Monte Carlo simulation suggested that a trough/MIC ratio of 2 to 5 is associated with a near-maximal probability of response. The probability of response is lower at the extremes of
C
avg
. Patients with higher free
C
avg
/MIC ratios have a higher probability of clinical response. A trough/MIC ratio of 2 to 5 can be used as a target for therapeutic drug monitoring.
Mutations of the Listeria monocytogenes PeptidoglycanN-Deacetylase andO-Acetylase Result in Enhanced Lysozyme Sensitivity, Bacteriolysis, and Hyperinduction of Innate Immune Pathways
Authors: Rae Chris S. , Geissler Aimee , Adamson Paul C. , Portnoy Daniel A. 
Published: July 2011

ABSTRACTListeria monocytogenesis a Gram-positive intracellular pathogen that is naturally resistant to lysozyme. Recently, it was shown that peptidoglycan modification by N-deacetylation or O-acetylation confers resistance to lysozyme in various Gram-positive bacteria, includingL. monocytogenes.L. monocytogenespeptidoglycan is deacetylated by the action ofN-acetylglucosamine deacetylase (Pgd) and acetylated byO-acetylmuramic acid transferase (Oat). We characterized Pgd−, Oat−, and double mutants to determine the specific role ofL. monocytogenespeptidoglycan acetylation in conferring lysozyme sensitivity during infection of macrophages and mice. Pgd−and Pgd−Oat−double mutants were attenuated approximately 2 and 3.5 logs, respectively,in vivo. In bone-marrow derived macrophages, the mutants demonstrated intracellular growth defects and increased induction of cytokine transcriptional responses that emanated from a phagosome and the cytosol. Lysozyme-sensitive mutants underwent bacteriolysis in the macrophage cytosol, resulting in AIM2-dependent pyroptosis. Each of thein vitrophenotypes was rescued upon infection of LysM−macrophages. The addition of extracellular lysozyme to LysM−macrophages restored cytokine induction, host cell death, andL. monocytogenesgrowth inhibition. This surprising observation suggests that extracellular lysozyme can access the macrophage cytosol and act on intracellular lysozyme-sensitive bacteria.
Role for the Burkholderia pseudomallei Type Three Secretion System Cluster 1
bpscN
Gene in Virulence
Authors: D'Cruze Tanya , Gong Lan , Treerat Puthayalai , Ramm Georg , Boyce John D. , Prescott Mark , Adler Ben , Devenish Rodney J. 
Published: July 2011

ABSTRACT

Burkholderia pseudomallei
, the causal agent of melioidosis, employs a number of virulence factors during its infection of mammalian cells. One such factor is the type three secretion system (TTSS), which is proposed to mediate the transport and secretion of bacterial effector molecules directly into host cells. The
B. pseudomallei
genome contains three TTSS gene clusters (designated TTSS1, TTSS2, and TTSS3). Previous research has indicated that neither TTSS1 nor TTSS2 is involved in
B. pseudomallei
virulence in a hamster infection model. We have characterized a
B. pseudomallei
mutant lacking expression of the predicted TTSS1 ATPase encoded by
bpscN
. This mutant was significantly attenuated for virulence in a respiratory melioidosis mouse model of infection. In addition, analyses
in vitro
showed diminished survival and replication in RAW264.7 cells and an increased level of colocalization with the autophagy marker protein LC3 but an unhindered ability to escape from phagosomes. Taken together, these data provide evidence that the TTSS1
bpscN
gene product plays an important role in the intracellular survival of
B. pseudomallei
and the pathogenesis of murine infection.
Two DHH Subfamily 1 Proteins Contribute to Pneumococcal Virulence and Confer Protection against Pneumococcal Disease
Authors: Cron L. E. , Stol K. , Burghout P. , van Selm S. , Simonetti E. R. , Bootsma H. J. , Hermans P. W. M. 
Published: July 2011

ABSTRACT

Streptococcus pneumoniae
is an important human bacterial pathogen, causing such infections as pneumonia, meningitis, septicemia, and otitis media. Current capsular polysaccharide-based conjugate vaccines protect against a fraction of the over 90 serotypes known, whereas vaccines based on conserved pneumococcal proteins are considered promising broad-range alternatives. The pneumococcal genome encodes two conserved proteins of an as yet unknown function, SP1298 and SP2205, classified as DHH (Asp-His-His) subfamily 1 proteins. Here we examined their contribution to pneumococcal pathogenesis using single and double knockout mutants in three different strains: D39, TIGR4, and BHN100. Mutants lacking both SP1298 and SP2205 were severely impaired in adherence to human epithelial Detroit 562 cells. Importantly, the attenuated phenotypes were restored upon genetic complementation of the deleted genes. Single and mixed mouse models of colonization, otitis media, pneumonia, and bacteremia showed that bacterial loads in the nasopharynx, middle ears, lungs, and blood of mice infected with the mutants were significantly reduced from those of wild-type-infected mice, with an apparent additive effect upon deletion of both genes. Minor strain-specific phenotypes were observed, i.e., deletion of SP1298 affected host-cell adherence in BHN100 only, and deletion of SP2205 significantly attenuated virulence in lungs and blood in D39 and BHN100 but not TIGR4. Finally, subcutaneous vaccination with a combination of both DHH subfamily 1 proteins conferred protection to nasopharynx, lungs, and blood of mice infected with TIGR4. We conclude that SP1298 and SP2205 play a significant role at several stages of pneumococcal infection, and importantly, these proteins are potential candidates for a multicomponent protein vaccine.
Importance of Antibodies to Lipopolysaccharide in Natural and Vaccine-Induced Serum Bactericidal Activity against Neisseria meningitidis Group B
Authors: Schmiel Deborah H. , Moran Elizabeth E. , Keiser Paul B. , Brandt Brenda L. , Zollinger Wendell D. 
Published: July 2011

ABSTRACTAnalysis of the specificity of bactericidal antibodies in normal, convalescent, and postvaccination human sera is important in understanding human immunity to meningococcal infections and can aid in the design of an effective group B vaccine. A collection of human sera, including group C and group B convalescent-phase sera, normal sera with naturally occurring cross-reactive bactericidal activity, and some postvaccination sera, was analyzed to determine the specificity of cross-reactive bactericidal antibodies. Analysis of human sera using a bactericidal antibody depletion assay demonstrated that a significant portion of the bactericidal activity could be removed by purified lipopolysaccharide (LPS). LPS homologous to that expressed on the bactericidal test strain was most effective, but partial depletion by heterologous LPS suggested the presence of antibodies with various degrees of cross-reactivity. Binding of anti-L3,7 LPS bactericidal antibodies was affected by modification of the core structure, suggesting that these functional antibodies recognized epitopes consisting of both core structures and lacto-N-neotetraose (LNnT). When the target strain was grown with 5′-cytidinemonophospho-N-acetylneuraminic acid (CMP-NANA) to increase LPS sialylation, convalescent-phase serum bactericidal titers were decreased by only 2- to 4-fold, and most remaining bactericidal activity was still depleted by LPS. Highly sialylated LPS was ineffective in depleting bactericidal antibodies. We conclude that natural infections caused by strains expressing L3,7 LPS induce persistent, protective bactericidal antibodies and appear to be directed against nonsialylated bacterial epitopes. Additionally, subsets of these bactericidal antibodies are cross-reactive, binding to several different LPS immunotypes, which is a useful characteristic for an effective group B meningococcal vaccine antigen.
Stratified assessment of the role of inhaled hypertonic saline in reducing cystic fibrosis pulmonary exacerbations: a retrospective analysis
Authors: Dmello Dayton , Nayak Ravi P , Matuschak George M 
Published: July 2011

ObjectiveLimited data exist concerning the role of inhaled hypertonic saline (HS) in decreasing pulmonary exacerbations in cystic fibrosis (CF), especially as more advanced stages of CF lung disease were excluded in prior studies. Herein, the authors retrospectively determined the efficacy of inhaled HS in reducing CF pulmonary exacerbations when stratified according to the severity of CF lung disease. Stratification was based on the framework of the Pulmonary Therapeutics Committee's published gradation of obstructive lung physiology in CF, that is, mild (FEV1>70%), moderate (FEV140–70%) and severe (FEV1<40%) lung disease, respectively.DesignA retrospective review of the Port CF database over a 3-year period performed at an academic CF care centre.Results340 pulmonary exacerbations were identified; inhaled HS was being used in 99 of these cases. Univariate analysis demonstrated a significant reduction in pulmonary exacerbations only in mild obstruction (OR=0.09, CI 0.01 to 0.81, p=0.012); however, multivariate logistic regression that adjusted for confounding variables showed a reduction in pulmonary exacerbations across the entire spectrum of obstructive lung disease when using inhaled HS, that is, mild obstructive CF lung disease (OR=0.17, CI 0.05 to 0.58, p=0.004), moderate obstructive CF lung disease (OR=0.39, CI 0.16 to 0.93, p=0.034), as well as severe obstructive CF lung disease (OR=0.02, CI 0.001 to 0.45, p=0.015). Moreover, inhaled HS appeared reasonably well tolerated across all stages of lung-disease severity, and was discontinued in only 7% of cases (n=4) with severe lung disease.ConclusionIn this study, inhaled HS appeared to reduce pulmonary exacerbations in CF lung disease at all stages of obstruction. This underscores the importance of therapeutic inhaled HS in CF lung disease, regardless of the severity of lung obstruction.