bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeneXpert MTB/RIF Version G4 for Identification of Rifampin-Resistant Tuberculosis in a Programmatic Setting
Authors: Osman Muhammad , Simpson John A. , Caldwell Judy , Bosman Marlein , Nicol Mark P. 
Published: November 2013

ABSTRACT
A recent Cochrane review estimated GeneXpert MTB/RIF specificity for rifampin resistance as 98% (95% confidence interval [CI], 97 to 99), based on results from earlier test versions. The measured positive predictive value of the new generation test from programmatic implementation in Cape Town, South Africa, was 99.5% (95% CI, 98.5 to 100), confirming excellent specificity.
Ethambutol Resistance as Determined by Broth Dilution Method Correlates Better than Sequencing Results with
embB
Mutations in Multidrug-Resistant Mycobacterium tuberculosis Isolates
Authors: Zhang Zhijian , Wang Yufeng , Pang Yu , Kam Kai Man 
Published: November 2013

ABSTRACT

We evaluated the correlation of phenotypic ethambutol (EMB) susceptibility as determined by two drug susceptibility methods with
embB
mutations in multidrug-resistant (MDR)
Mycobacterium tuberculosis
strains. The concordance rate for EMB resistance between broth dilution method and sequencing results (83.6%) was significantly higher than between the proportion method and sequencing results (61.7%) (
P
= 0.004). Of the
embB
mutants, 75.4% (46/61) possessed a mutation at
embB306
. Our results demonstrated that ethambutol resistance determined by broth dilution method reveals better correlation with
embB
mutations than the proportion method in MDR isolates.
Cellular Vimentin Regulates Construction of Dengue Virus Replication Complexes through Interaction with NS4A Protein
Authors: Teo Catherine Su Hui , Chu Justin Jang Hann 
Published: November 2013

ABSTRACT
Dengue virus (DENV) interacts with host cellular factors to construct a more favorable environment for replication, and the interplay between DENV and the host cellular cytoskeleton may represent one of the potential antiviral targeting sites. However, the involvement of cellular vimentin intermediate filaments in DENV replication has been explored less. Here, we revealed the direct interaction between host cellular vimentin and DENV nonstructural protein 4A (NS4A), a known component of the viral replication complex (RC), during DENV infection using tandem affinity purification, coimmunoprecipitation, and scanning electron microscopy. Furthermore, the dynamics of vimentin-NS4A interaction were demonstrated by using confocal three-dimensional (3D) reconstruction and proximity ligation assay. Most importantly, we report for the first time the discovery of the specific region of NS4A that interacts with vimentin lies within the first 50 amino acid residues at the cytosolic N-terminal domain of NS4A (N50 region). Besides identifying vimentin-NS4A interaction, vimentin reorganization and phosphorylation by calcium calmodulin-dependent protein kinase II occurs during DENV infection, signifying that vimentin reorganization is important in maintaining and supporting the DENV RCs. Interestingly, we found that gene silencing of vimentin by small interfering RNA induced a significant alteration in the distribution of RCs in DENV-infected cells. This finding further supports the crucial role of intact vimentin scaffold in localizing and concentrating DENV RCs at the perinuclear site, thus facilitating efficient viral RNA replication. Collectively, our findings implicate the biological and functional significance of vimentin during DENV replication, as we propose that the association of DENV RCs with vimentin is mediated by DENV NS4A.
Genetic Resistance to Scrapie Infection in Experimentally Challenged Goats
Authors: Lacroux Caroline , Perrin-Chauvineau Cécile , Corbière Fabien , Aron Naima , Aguilar-Calvo Patricia , Torres Juan Maria , Costes Pierrette , Brémaud Isabelle , Lugan Séverine , Schelcher François , Barillet Francis , Andréoletti Olivier 
Published: November 2013

ABSTRACT

In goats, several field studies have identified coding mutations of the gene encoding the prion protein (I/M
142
, N/D
146
, S/D
146
, R/Q
211
, and Q/K
222
) that are associated with a lower risk of developing classical scrapie. However, the data related to the levels of resistance to transmissible spongiform encephalopathies (TSEs) of these different
PRNP
gene mutations are still considered insufficient for developing large-scale genetic selection against scrapie in this species. In this study, we inoculated wild-type (WT)
PRNP
(I
142
R
154
R
211
Q
222
) goats and homozygous and/or heterozygous I/M
142
, R/H
154
, R/Q
211
, and Q/K
222
goats with a goat natural scrapie isolate by either the oral or the intracerebral (i.c.) route. Our results indicate that the I/M
142
PRNP
polymorphism does not provide substantial resistance to scrapie infection following intracerebral or oral inoculation. They also demonstrate that H
154
, Q
211
, and K
222
PRNP
allele carriers are all resistant to scrapie infection following oral exposure. However, in comparison to WT animals, the H
154
and Q
211
allele carriers displayed only moderate increases in the incubation period following i.c. challenge. After i.c. challenge, heterozygous K
222
and a small proportion of homozygous K
222
goats also developed the disease, but with incubation periods that were 4 to 5 times longer than those in WT animals. These results support the contention that the K
222
goat prion protein variant provides a strong but not absolutely protective effect against classical scrapie.
Identification and Characterization of Antibody-Binding Epitopes on the Norovirus GII.3 Capsid
Authors: Mahar Jackie E. , Donker Nicole C. , Bok Karin , Talbo Gert H. , Green Kim Y. , Kirkwood Carl D. 
Published: November 2013

ABSTRACT
Genotype II.3 (GII.3) noroviruses are a major cause of sporadic gastroenteritis, particularly in children. The greater incidence of GII.3 noroviruses in the pediatric population compared to the adult demographic suggests development of herd immunity to this genotype, possibly as a consequence of limited evolution of immune epitopes. This study aimed to identify and characterize immune epitopes on the GII.3 capsid protein and to determine the level of immune cross-reactivity within the genotype. A panel of seven GII.3 virus-like particles (VLPs), representing norovirus strains isolated during 1975 to 2008, was tested by enzyme-linked immunosorbent assay (ELISA) for reactivity with human sera and a rabbit anti-GII.3 strain-specific polyclonal serum generated against the 2008 GII.3 VLP. Immunoprecipitation of protease-digested GII.3 VLPs and sequencing of bound peptides via mass spectrometry were used to locate epitopes on the capsid. Two epitopes were investigated further using Mimotopes technology. Serum binding studies demonstrated complete intragenotype GII.3 cross-reactivity using both human and rabbit serum. Six immunoreactive regions containing epitopes were located on the GII.3 capsid protein, two within each capsid domain. Epitopes in the S and P1 domains were highly conserved within GII.3 noroviruses. P2 domain epitopes were variable and contained evolutionarily important residues and histo-blood group antigen (HBGA) binding residues. In conclusion, anti-GII.3 antibody-binding epitopes are highly cross-reactive and mostly conserved within GII.3 strains. This may account for the limited GII.3 prevalence in adults and suggests that a GII.3 strain may be a valuable inclusion in a multivalent pediatric targeted VLP vaccine. Exploration of norovirus immune epitopes is vital for effective vaccine design.

IMPORTANCE
This study represents an important contribution to the understanding of norovirus immunology in a pediatric genotype. The high cross-reactivity and conservation of GII.3 epitopes suggest development of herd immunity against GII.3 and indicate that a GII.3 strain would be a valuable inclusion in a pediatric targeted multivalent vaccine. Immunological understanding of pediatric norovirus strains is important since norovirus vaccines will likely target high-risk groups such as the pediatric population.
Therapeutic Depletion of Natural Killer Cells Controls Persistent Infection
Authors: Waggoner Stephen N. , Daniels Keith A. , Welsh Raymond M. 
Published: November 2013

ABSTRACTPersistent viral infections are associated with host and viral factors that impair effective antiviral immunity. Natural killer (NK) cells contribute to establishment of persistent lymphocytic choriomeningitis virus (LCMV) infection in mice through suppression of virus-specific T cell responses during the first few days of infection, but NK cell depletion during those early time points can enable severe T cell-mediated immune pathology and death of the host. Here we show that long after their peak in cytolytic activation, NK cells continue to support viral persistence at later times of infection. Delayed depletion of NK cells, 2 to 3 weeks after infection, enhanced virus-specific T cell responses and viral control. This enhancing effect of delayed NK cell depletion on antiviral immunity, in contrast to early NK cell depletion, was not associated with increased morbidity and mortality, and mice quickly regained weight after treatment. The efficacy of the depletion depended in part upon the size of the original virus inoculum, the viral load at the time of depletion, and the presence of CD4 T cells. Each of these factors is an important contributor to the degree of CD8 T cell dysfunction during viral persistence. Thus, NK cells may continuously contribute to exhaustion of virus-specific T cells during chronic infection, possibly by depleting CD4 T cells. Targeting of NK cells could thus be considered in combination with blockade of other immunosuppressive pathways, such as the interleukin-10 (IL-10) and programmed death 1 (PD-1) pathways, as a therapy to cure chronic human infections, including those with HIV or hepatitis C virus.IMPORTANCEPersistent virus infections are a major threat to global human health. The capacity of viruses, including HIV and hepatitis C virus, to overwhelm or subvert host immune responses contributes to a prolonged state of dampened antiviral immune functionality, which in turn facilitates viral persistence. Recent efforts have focused on therapeutics that can restore the effector functions of these functionally exhausted virus-specific T cells in order to expedite viral clearance. Here we establish that natural killer (NK) cells actively contribute to immune dysfunction and viral persistence at later stages of infection. This previously undescribed mechanism of immune suppression during chronic infection provides a vital clue for the design of novel therapeutic strategies targeting NK cell immunosuppressive activity in order to restore immune function and enhance viral control in chronically infected individuals.
A Bromodomain-Containing Host Protein Mediates the Nuclear Importation of a Satellite RNA of Cucumber Mosaic Virus
Authors: Chaturvedi Sonali , Kalantidis Kriton , Rao A. L. N. 
Published: November 2013

ABSTRACT

Replication of the satellite RNA (satRNA) of
Cucumber Mosaic Virus
is dependent on replicase proteins of helper virus (HV). However, we recently demonstrated that like with
Potato spindle tuber viroid
(PSTVd), a satRNA associated with
Cucumber Mosaic Virus
strain Q (Q-satRNA) has the propensity to localize in the nucleus and generate multimers that subsequently serve as templates for HV-dependent replication. But the mechanism regulating the nuclear importation of Q-satRNA is unknown. Here we show that the nuclear importation of Q-satRNA is mediated by a bromodomain-containing host protein (BRP1), which is also apparently involved in the nuclear localization of PSTVd. A comparative analysis of nuclear and cytoplasmic fractions from
Nicotiana benthamiana
plants coinfected with Q-satRNA and its HV confirmed the association of Q-satRNA but not HV with the nuclear compartment. A combination of the MS2-capsid protein-based RNA tagging assay and confocal microscopy demonstrated that the nuclear localization of Q-satRNA was completely blocked in transgenic lines of
Nicotiana benthamiana
(ph5.2nb) that are defective in BRP1 expression. This defect, however, was restored when the ph5.2nb lines of
N. benthamiana
were
trans
-complemented by ectopically expressed BRP1. The binding specificity of BRP1 with Q-satRNA was confirmed
in vivo
and
in vitro
by coimmunoprecipitation and electrophoretic mobility shift assays, respectively. Finally, infectivity assays involving coexpression of Q-satRNA and its HV in wild-type and ph5.2nb lines of
N. benthamiana
accentuated a biological role for BRP1 in the Q-satRNA infection cycle. The significance of these results in relation to a possible evolutionary relationship to viroids is discussed.
Protection Provided by a Herpes Simplex Virus 2 (HSV-2) Glycoprotein C and D Subunit Antigen Vaccine against Genital HSV-2 Infection in HSV-1-Seropositive Guinea Pigs
Authors: Awasthi Sita , Balliet John W. , Flynn Jessica A. , Lubinski John M. , Shaw Carolyn E. , DiStefano Daniel J. , Cai Michael , Brown Martha , Smith Judith F. , Kowalski Rose , Swoyer Ryan , Galli Jennifer , Copeland Victoria , Rios Sandra , Davidson Robert C. , Salnikova Maya , Kingsley Susan , Bryan Janine , Casimiro Danilo R. , Friedman Harvey M. 
Published: November 2013

ABSTRACTA prophylactic vaccine for genital herpes disease remains an elusive goal. We report the results of two studies performed collaboratively in different laboratories that assessed immunogenicity and vaccine efficacy in herpes simplex virus 1 (HSV-1)-seropositive guinea pigs immunized and subsequently challenged intravaginally with HSV-2. In study 1, HSV-2 glycoproteins C (gC2) and D (gD2) were produced in baculovirus and administered intramuscularly as monovalent or bivalent vaccines with CpG and alum. In study 2, gD2 was produced in CHO cells and given intramuscularly with monophosphoryl lipid A (MPL) and alum, or gC2 and gD2 were produced in glycoengineeredPichia pastorisand administered intramuscularly as a bivalent vaccine with Iscomatrix and alum to HSV-1-naive or -seropositive guinea pigs. In both studies, immunization boosted neutralizing antibody responses to HSV-1 and HSV-2. In study 1, immunization with gC2, gD2, or both immunogens significantly reduced the frequency of genital lesions, with the bivalent vaccine showing the greatest protection. In study 2, both vaccines were highly protective against genital disease in naive and HSV-1-seropositive animals. Comparisons between gD2 and gC2/gD2 in study 2 must be interpreted cautiously, because different adjuvants, gD2 doses, and antigen production methods were used; however, significant differences invariably favored the bivalent vaccine. Immunization of naive animals with gC2/gD2 significantly reduced the number of days of vaginal shedding of HSV-2 DNA compared with that for mock-immunized animals. Surprisingly, in both studies, immunization of HSV-1-seropositive animals had little effect on recurrent vaginal shedding of HSV-2 DNA, despite significantly reducing genital disease.
Chronic health conditions and poverty: a cross-sectional study using a multidimensional poverty measure
Authors: Callander Emily J , Schofield Deborah J , Shrestha Rupendra N 
Published: November 2013

ObjectivesTo identify the chronic health conditions associated with multidimensional poverty.DesignCross-sectional study of the nationally representativeSurvey of Disability, Ageing and Carers,conducted by the Australian Bureau of Statistics.SettingAustralian population in 2003.Participants35 704 individuals randomly selected from the Australian population by the Australian Bureau of Statistics.Outcome measuresMultidimensional poverty status, costs of disability, short form 6D health utility score, income, education attainment.ResultsAmong those who were multidimensionally poor, 75% had a chronic health condition and the most common health conditions were back problems (11% of those in multidimensional poverty had back problems) and arthritis (11%). The conditions with the highest proportion of individuals in multidimensional poverty were depression/mood affecting disorders (26% in multidimensional poverty) and mental and behavioural disorders (22%). Those with depression/mood affecting disorders were nearly seven times (OR 6.60, 95% CI 5.09 to 8.55, p<0.0001) more likely to be multidimensionally poor than those with no health condition. Equivalising for the additional costs of disability increased the proportion of individuals in multidimensional poverty for all conditions and the conditions with the highest proportion of individuals in multidimensional poverty changed.ConclusionsOwing to the influence of certain health conditions on poverty status, health interventions have the potential to improve national living standards and poverty rates in a similar way that ‘traditional’ policy responses such as changes to welfare payment currently do. Using a multidimensional poverty measure reveals the health conditions that should be the focus of such efforts.
A population-based survival analysis describing the association of body mass index on time to revision for total hip and knee replacements: results from the UK general practice research database
Authors: Culliford David , Maskell Joe , Judge Andy , Arden Nigel K ,   the COAST Study group
Published: November 2013

ObjectivesAgainst a backdrop of rising levels of obesity, we describe and estimate associations of body mass index (BMI), age and gender with time to revision for participants undergoing primary total hip (THR) or knee (TKR) replacement in the UK.DesignPopulation-based cohort study.SettingRoutinely collected primary care data from a representative sample of general practices, including linked data on all secondary care events.ParticipantsPopulation-based cohort study of 63 162 patients with THR and 54 276 with TKR in the UK General Practice Research Database between 1988 and 2011.Primary and secondary outcomesRisk of THR and TKR revision associated with BMI, age and gender, after adjusting for the competing risk of death.ResultsThe 5-year cumulative incidence rate for THR was 2.2% for men and 1.8% for women (TKR 2.3% for men, 1.6% for women). The adjusted overall subhazard ratio (SHR) for patients with THR undergoing subsequent hip revision surgery, with a competing risk of death, were estimated at 1.020 (95% CI 1.009 to 1.032) per additional unit (kg/m2) of BMI, 1.23 (95% CI 1.10 to 1.38) for men compared with women and 0.970 (95% CI 0.967 to 0.973) per additional year of age. For patients with TKR, the equivalent estimates were 1.015 (95% CI 1.002 to 1.028) for BMI; 1.51 (95% CI 1.32 to 1.73) for gender and 0.957 (95% CI 0.951 to 0.962) for age. Morbidly obese patients with THR had a 65.5% increase (95% CI 15.4% to 137.3%, p=0.006) in the subhazard of revision versus the normal BMI group (18.5–25). The effect for TKR was smaller (a 43.9% increase) and weaker (95% CI 2.6% to 103.9%, p=0.040).ConclusionsBMI is estimated to have a small but statistically significant association with the risk of hip and knee revision, but absolute numbers are small. Further studies are needed in order to distinguish between effects for specific revision surgery indications.
A standardised storage solution for venepuncture/cannulation equipment could save an NHS hospital the equivalent of a whole junior doctor
Authors: Lindley Steven , Robertson Ian 
Published: November 2013

AbstractJunior doctors, nursing staff, and phlebotomists spend a large proportion of their time taking blood samples and siting (venous) cannulae. Approximately 350 blood samples are taken daily across 25 wards at the Royal United Hospital Bath NHS Trust. There is no standard storage solution for venepuncture or cannulation equipment. On-call junior doctors cover most of the hospital’s wards. Time is wasted locating essential equipment on unfamiliar wards and nurses are frequently interrupted to assist. These delays can compromise patient safety in emergencies as well as contributing to a source of daily inefficiency.Junior doctors were timed collecting equipment needed for venepuncture and cannulation on unfamiliar wards. Initial results suggested large variation between timings on different wards. The medical admissions unit (MAU), which organises items for venepuncture and cannulation on a single trolley, was 4 times quicker than the mean of all other wards. MAU mean time 21.0s vs. Non-standardised wards mean time 103.0s (p<0.0001). Estimates suggest approximately 47 hours per week (the equivalent of a fulltime doctor) could be saved by implementing a standard trust-wide storage solution.We set out to introduce the MAU trolley format to all adult inpatient wards. All ward managers agreed to implement the trolley. 18 wards (72% of adult inpatient wards) already possessed the ‘MAU style’ trolley, which we standardised using an easy-to-follow inventory and laminated draw inlays. Feedback was very positive from doctors and ward staff alike. We repeated timings to validate the change and successfully presented a business case to senior management for a further 10 trolleys (£3623.78) for full adult inpatient ward coverage.As junior doctors, we identified a common problem, tested solutions, and made early simple affordable changes. Initial work helped us present a compelling case for patient safety and efficiency improvements, releasing money to implement modest trust-wide quality improvement changes.
p53-Induced miR-15a/16-1 and AP4 Form a Double-Negative Feedback Loop to Regulate Epithelial–Mesenchymal Transition and Metastasis in Colorectal Cancer
Authors: Shi Lei , Jackstadt Rene , Siemens Helge , Li Huihui , Kirchner Thomas , Hermeking Heiko 
Published: November 2013

Abstract
The transcription factor AP4 mediates epithelial–mesenchymal transition (EMT) in colorectal cancer but its control in this setting is not fully understood. Here, we report the definition of a double-negative feedback loop involving AP4 and miR-15a/16-1 that regulates EMT and metastatic progression. In colorectal cancer cells, AP4 was downregulated by DNA damage in a p53-dependent manner. AP4 downregulation by p53 was mediated indirectly by the tumor-suppressive microRNAs miR-15a and miR-16-1, which targeted the 3′ untranslated region (3′-UTR) of AP4 mRNA, induced mesenchymal–epithelial transition (MET), and inhibited colorectal cancer cell migration and invasion. The downregulation of AP4 was necessary for induction of MET and cell cycle arrest by miR-15a/16-1. In tumor xenoplants, ectopic miR-15a/16-1 suppressed formation of lung metastases. Furthermore, AP4 directly suppressed expression of miR-15a/16-1. In clinical specimens of colorectal cancer, miR-15a levels inversely correlated with AP4 protein levels shown previously to correlate with distant metastasis and poor survival. In summary, our results define a double-negative feedback loop involving miR-15a/16-1 and AP4 that stabilizes epithelial and mesenchymal states, respectively, which may determine metastatic prowess. Cancer Res; 74(2); 532–42. ©2013 AACR.