bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multicenter Evaluation of the LightCycler Methicillin-Resistant
Staphylococcus aureus
(MRSA) Advanced Test as a Rapid Method for Detection of MRSA in Nasal Surveillance Swabs
Authors: Peterson Lance R. , Liesenfeld Oliver , Woods Christopher W. , Allen Stephen D. , Pombo David , Patel Parul A. , Mehta Maitry S. , Nicholson Bradly , Fuller DeAnna , Onderdonk Andrew 
Published: March 2010

ABSTRACT

The rate of methicillin-resistant
Staphylococcus aureus
(MRSA) infection continues to rise in many health care settings. Rapid detection of MRSA colonization followed by appropriate isolation can reduce transmission and infection. We compared the performance of the new Roche LightCycler MRSA advanced test to that of the BD GeneOhm MRSA test and culture. Double-headed swabs were used to collect anterior nasal specimens from each subject. For both tests, DNA was extracted and real-time PCR was performed according to manufacturer's instructions. For culture, one swab of the pair was plated directly to CHROMagar MRSA. The swab paired with the BD GeneOhm MRSA test was also placed into an enrichment broth and then plated to CHROMagar MRSA. Colonies resembling staphylococci were confirmed as
S. aureus
by standard methods. Discrepant specimens had further testing with additional attempts to grow MRSA as well as sample amplicon sequencing. Agreement between results for the two swabs was 99.3% for those with valid results. A total of 1,402 specimens were tested using direct culture detection of MRSA as the gold standard; 187 were culture positive for MRSA. The LightCycler MRSA advanced test had relative sensitivity and specificity of 95.2% (95% confidence interval [CI]: 91.1% to 97.8%) and 96.4% (95% CI: 95.2% to 97.4%), respectively. The BD GeneOhm assay had relative sensitivity and specificity of 95.7% (95% CI: 91.7% to 98.1%) and 91.7% (95% CI: 90.0% to 93.2%), respectively. Following discrepancy analysis, the relative sensitivities of the LightCycler MRSA advanced test and the BD GeneOhm MRSA assay were 92.2 and 93.2%, respectively; relative specificities were 98.9 and 94.2%, respectively. Specificity was significantly better (
P
< 0.001) with the LightCycler MRSA advanced test. The sensitivity of direct culture was 80.4%. The LightCycler MRSA advanced test is a useful tool for sensitive and rapid detection of MRSA nasal colonization.
Evaluation of Blood Agar Microtiter Plates for Culturing
Leishmania
Parasites To Titrate Parasite Burden in Spleen and Peripheral Blood of Patients with Visceral Leishmaniasis
Authors: Maurya Radheshyam , Mehrotra Sanjana , Prajapati Vijay Kumar , Nylén Susanne , Sacks David , Sundar Shyam 
Published: March 2010

ABSTRACT

Serial dilution of blood and spleen biopsy specimens, plated on Novy-MacNeal-Nicolle (NNN) blood agar using microtiter culture plates, is a sensitive and reproducible method for detection and growth of
Leishmania
parasites. Plates could be easily monitored, and growth could be rapidly detected. Moreover, parasite number may be estimated using this technique.
Enhanced Discrimination of Highly Clonal ST22-Methicillin-Resistant
Staphylococcus aureus
IV Isolates Achieved by Combining
spa
,
dru
, and Pulsed-Field Gel Electrophoresis Typing Data
Authors: Shore Anna C. , Rossney Angela S. , Kinnevey Peter M. , Brennan Orla M. , Creamer Eilish , Sherlock Orla , Dolan Anthony , Cunney Robert , Sullivan Derek J. , Goering Richard V. , Humphreys Hilary , Coleman David C. 
Published: March 2010

ABSTRACT

ST22-methicillin-resistant
Staphylococcus aureus
type IV (ST22-MRSA-IV) is endemic in Irish hospitals and is designated antibiogram-resistogram type-pulsed-field group (AR-PFG) 06-01. Isolates of this highly clonal strain exhibit limited numbers of pulsed-field gel electrophoresis (PFGE) patterns and
spa
types. This study investigated whether combining PFGE and
spa
typing with DNA sequencing of the staphylococcal cassette chromosome
mec
element (SCC
mec
)-associated direct repeat unit (
dru
typing) would improve isolate discrimination. A total of 173 MRSA isolates recovered in one Irish hospital during periods in 2007 and 2008 were investigated using antibiogram-resistogram (AR), PFGE,
spa
,
dru
, and SCC
mec
typing. Isolates representative of each of the 17 pulsed-field group 01 (PFG-01)
spa
types identified underwent multilocus sequence typing, and all isolates were ST22. Ninety-seven percent of isolates (168 of 173) exhibited AR-PFG 06-01 or closely related AR patterns, and 163 of these isolates harbored SCC
mec
type IVh. The combination of PFGE,
spa
, and
dru
typing methods significantly improved discrimination of the 168 PFG-01 isolates, yielding 65 type combinations with a Simpson's index of diversity (SID) of 96.53, compared to (i) pairwise combinations of s
pa
and
dru
typing,
spa
and PFGE typing, and
dru
and PFGE typing, which yielded 37, 44, and 43 type combinations with SIDs of 90.84, 91.00, and 93.57, respectively, or (ii) individual
spa
,
dru
, and PFGE typing methods, which yielded 17, 17, and 21 types with SIDs of 66.9, 77.83, and 81.34, respectively. Analysis of epidemiological information for a subset of PFG-01 isolates validated the relationships inferred using combined PFGE,
spa
, and
dru
typing data. This approach significantly enhances discrimination of ST22-MRSA-IV isolates and could be applied to epidemiological investigations of other highly clonal MRSA strains.
Comparison of European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Etest Methods with the CLSI Broth Microdilution Method for Echinocandin Susceptibility Testing of
Candida
Species
Authors: Pfaller M. A. , Castanheira M. , Diekema D. J. , Messer S. A. , Moet G. J. , Jones R. N. 
Published: March 2010

ABSTRACT

The antifungal broth microdilution (BMD) method of the European Committee on Antibiotic Susceptibility Testing (EUCAST) and the Etest agar diffusion method were compared with the Clinical and Laboratory Standards Institute (CLSI) BMD method M27-A3 for anidulafungin, caspofungin, and micafungin susceptibility testing of 133 clinical isolates of
Candida
species. The isolates were characterized for the presence or absence of
fks1
and/or
fks2
gene mutations and included 34 isolates of
C. glabrata
(4 mutant strains), 32 of
C. albicans
(1 mutant strain), 25 of
C. parapsilosis
, 19 of
C. guilliermondii
, 12 of
C. tropicalis
(2 mutant strains), and 11 of
C. krusei
. Excellent essential agreement (EA; within 2 dilutions) between the CLSI and EUCAST and CLSI and Etest MIC results was observed. The overall EA between the EUCAST and CLSI results ranged from 89.5% (caspofungin) to 99.2% (micafungin), whereas the EA between the Etest and CLSI results ranged from 90.2% (caspofungin) to 93.2% (anidulafungin). The categorical agreement (CA) between methods for each antifungal agent was assessed using previously determined epidemiological cutoff values (ECVs). Excellent CA (>90%) was observed for all comparisons between the EUCAST and CLSI results with the exceptions of
C. glabrata
and caspofungin (85.3%) and
C. krusei
and caspofungin (54.5%). The CA between the Etest and CLSI results was also excellent for all comparisons, with the exception of
C. krusei
and caspofungin (81.8%). All three methods were able to differentiate wild-type (WT) strains from those with
fks
mutations. With anidulafungin as the test reagent, the CLSI method identified 5 of 7 mutant strains, whereas the EUCAST method and the Etest identified 6 of 7 mutant strains. With either caspofungin or micafungin as the test reagent, the CLSI method identified all 7 mutant strains and the EUCAST method identified 6 of 7 mutant strains. The Etest identified all 7 mutant strains using caspofungin as the reagent. All three test methods showed a high level of agreement and of ability to distinguish
fks
mutant strains of
Candida
species from WT strains using each of the echinocandins.
Human Picobirnaviruses Identified by Molecular Screening of Diarrhea Samples
Authors: van Leeuwen Marije , Williams Marisol M. W. , Koraka Penelope , Simon James H. , Smits Saskia L. , Osterhaus Albert D. M. E. 
Published: March 2010

ABSTRACT
The global threat of (re)emerging infectious viruses requires a more effective approach regarding virus surveillance and diagnostic assays, as current diagnostics are often virus species specific and not able to detect highly divergent or unknown viruses. A systematic exploration of viruses that infect humans is the key to effectively counter the potential public health threat caused by new and emerging infectious diseases. The human gut is a known reservoir of a wide variety of microorganisms, including viruses. In this study, Dutch clinical diarrhea samples for which no etiological agent could be identified by available cell culture, serological, or nucleic acid-based tests were gathered. Large-scale molecular RNA virus screening based on host nucleic acid depletion, sequence-independent amplification, and sequencing of partially purified viral RNA from a limited number of clinical diarrhea samples revealed four eukaryotic virus species. Among the detected viruses were a rhinovirus and a new picobirnavirus variant. In total, ∼20% of clinical diarrhea samples contained human picobirnavirus sequences. The Dutch picobirnaviruses belonged to different phylogenetic clades and did not group with other picobirnaviruses according to year of isolation or host species. Interestingly, the average age of patients infected with picobirnavirus was significantly higher than that of uninfected patients. Our data show that sequence-independent amplification of partially purified viral RNA is an efficient procedure for identification of known and highly divergent new RNA viruses in clinical diarrhea samples.
A Five-Year Longitudinal Analysis of Sooty Mangabeys Naturally Infected with Simian Immunodeficiency Virus Reveals a Slow but Progressive Decline in CD4+T-Cell Count Whose Magnitude Is Not Predicted by Viral Load or Immune Activation
Authors: Taaffe Jessica , Chahroudi Ann , Engram Jessica , Sumpter Beth , Meeker Tracy , Ratcliffe Sarah , Paiardini Mirko , Else James , Silvestri Guido 
Published: March 2010

ABSTRACTNatural simian immunodeficiency virus (SIV) infection in sooty mangabeys (SMs) typically does not result in AIDS, despite high-level viremia and significant depletion of mucosal CD4+T cells. Here, we report the results of the first longitudinal study of a large cohort of SMs naturally infected with SIV (n= 78) housed at the Yerkes National Primate Research Center from which samples were obtained three times over a 5-year period. In this study, we observed (i) no signs of simian AIDS, (ii) stable SIV loads, (iii) a slow but progressive decline in CD4+T-cell counts (from a mean of 1,067.0 cells/mm3at time point 1 to 764.8 cells/mm3at time point 3) and increases in the numbers of animals with CD4+T-cell levels below 500 and 200 cells/mm3(from 8 to 28 of 78 and from 1 to 4 of 78, respectively), (iv) progressive declines in percentages of naïve CD4+and CD8+T cells (from 37.7 to 24.8% and from 21.0 to 13.0%, respectively), and (v) stably low levels of activated/proliferating T cells as well as CD4+CCR5+T cells. Since the level of total CD4+T cells and the fraction of naïve T cells in SIV-uninfected SMs also declined, it is possible that some of these observations are related to aging, as the SIV-infected animals were significantly older than the uninfected animals. In contrast to the decline in CD4+T cell counts in individuals infected with human immunodeficiency virus (HIV), the decline in CD4+T cell counts in SMs naturally infected with SIV over a 5-year period was not predicted by either plasma viremia or levels of T-cell activation. Taken together, these results confirm that natural SIV infection is nonprogressive from a clinical, virological, and immunological point of view and that stable levels of viremia associated with persistently low-level immune activation represent key differences from the natural course of HIV infection in humans.
Role of Complex Carbohydrates in Human Immunodeficiency Virus Type 1 Infection and Resistance to Antibody Neutralization
Authors: Binley James M. , Ban Yih-En Andrew , Crooks Emma T. , Eggink Dirk , Osawa Keiko , Schief William R. , Sanders Rogier W. 
Published: March 2010

ABSTRACT

Complex N-glycans flank the receptor binding sites of the outer domain of HIV-1 gp120, ostensibly forming a protective “fence” against antibodies. Here, we investigated the effects of rebuilding this fence with smaller glycoforms by expressing HIV-1 pseudovirions from a primary isolate in a human cell line lacking
N
-acetylglucosamine transferase I (GnTI), the enzyme that initiates the conversion of oligomannose N-glycans into complex N-glycans. Thus, complex glycans, including those that surround the receptor binding sites, are replaced by fully trimmed oligomannose stumps. Conversely, the untrimmed oligomannoses of the silent domain of gp120 are likely to remain unchanged. For comparison, we produced a mutant virus lacking a complex N-glycan of the V3 loop (N301Q). Both variants exhibited increased sensitivities to V3 loop-specific monoclonal antibodies (MAbs) and soluble CD4. The N301Q virus was also sensitive to “nonneutralizing” MAbs targeting the primary and secondary receptor binding sites. Endoglycosidase H treatment resulted in the removal of outer domain glycans from the GnTI- but not the parent Env trimers, and this was associated with a rapid and complete loss in infectivity. Nevertheless, the glycan-depleted trimers could still bind to soluble receptor and coreceptor analogs, suggesting a block in post-receptor binding conformational changes necessary for fusion. Collectively, our data show that the antennae of complex N-glycans serve to protect the V3 loop and CD4 binding site, while
N
-glycan stems regulate native trimer conformation, such that their removal can lead to global changes in neutralization sensitivity and, in extreme cases, an inability to complete the conformational rearrangements necessary for infection.
Membrane Insertion and Biogenesis of the
Turnip Crinkle Virus
p9 Movement Protein
Authors: Martínez-Gil Luis , Johnson Arthur E. , Mingarro Ismael 
Published: March 2010

ABSTRACT

Plant viral infection and spread depends on the successful introduction of a virus into a cell of a compatible host, followed by replication and cell-to-cell transport. The movement proteins (MPs) p8 and p9 of
Turnip crinkle virus
are required for cell-to-cell movement of the virus. We have examined the membrane association of p9 and found that it is an integral membrane protein with a defined topology in the endoplasmic reticulum (ER) membrane. Furthermore, we have used a site-specific photo-cross-linking strategy to study the membrane integration of the protein at the initial stages of its biosynthetic process. This process is cotranslational and proceeds through the signal recognition particle and the translocon complex.
In Vitro
Reconstitution Reveals Key Intermediate States of Trimer Formation by the Dengue Virus Membrane Fusion Protein
Authors: Liao Maofu , Martín Claudia Sánchez-San , Zheng Aihua , Kielian Margaret 
Published: March 2010

ABSTRACT

The flavivirus dengue virus (DV) infects cells through a low-pH-triggered membrane fusion reaction mediated by the viral envelope protein E. E is an elongated transmembrane protein with three domains and is organized as a homodimer on the mature virus particle. During fusion, the E protein homodimer dissociates, inserts the hydrophobic fusion loop into target membranes, and refolds into a trimeric hairpin in which domain III (DIII) packs against the central trimer. It is clear that E refolding drives membrane fusion, but the steps in hairpin formation and their pH requirements are unclear. Here, we have used truncated forms of the DV E protein to reconstitute trimerization
in vitro
. Protein constructs containing domains I and II (DI/II) were monomeric and interacted with membranes to form core trimers. DI/II-membrane interaction and trimerization occurred efficiently at both neutral and low pH. The DI/II core trimer was relatively unstable and could be stabilized by binding exogenous DIII or by the formation of mixed trimers containing DI/II plus E protein with all three domains. The mixed trimer had unoccupied DIII interaction sites that could specifically bind exogenous DIII at either low or neutral pH. Truncated DV E proteins thus reconstitute hairpin formation and define properties of key domain interactions during DV fusion.
High-Resolution X-Ray Structure and Functional Analysis of the Murine Norovirus 1 Capsid Protein Protruding Domain
Authors: Taube Stefan , Rubin John R. , Katpally Umesh , Smith Thomas J. , Kendall Ann , Stuckey Jeanne A. , Wobus Christiane E. 
Published: March 2010

ABSTRACT

Murine noroviruses (MNV) are closely related to the human noroviruses (HuNoV), which cause the majority of nonbacterial gastroenteritis. Unlike HuNoV, MNV grow in culture and in a small-animal model that represents a tractable model to study norovirus biology. To begin a detailed investigation of molecular events that occur during norovirus binding to cells, the crystallographic structure of the murine norovirus 1 (MNV-1) capsid protein protruding (P) domain has been determined. Crystallization of the bacterially expressed protein yielded two different crystal forms (Protein Data Bank identifiers [PDB ID], 3LQ6 and 3LQE). Comparison of the structures indicated a large degree of structural mobility in loops on the surface of the P2 subdomain. Specifically, the A′-B′ and E′-F′ loops were found in open and closed conformations. These regions of high mobility include the known escape mutation site for the neutralizing antibody A6.2 and an attenuation mutation site, which arose after serial passaging in culture and led to a loss in lethality in STAT1
−/−
mice, respectively. Modeling of a Fab fragment and crystal structures of the P dimer into the cryoelectron microscopy three-dimensional (3D) image reconstruction of the A6.2/MNV-1 complex indicated that the closed conformation is most likely bound to the Fab fragment and that the antibody contact is localized to the A′-B′ and E′-F′ loops. Therefore, we hypothesize that these loop regions and the flexibility of the P domains play important roles during MNV-1 binding to the cell surface.
Cellular and Viral Control over the Initial Events of Human Cytomegalovirus Experimental Latency in CD34+Cells
Authors: Saffert Ryan T. , Penkert Rhiannon R. , Kalejta Robert F. 
Published: March 2010

ABSTRACTHuman cytomegalovirus (HCMV) persists for the life of its host by establishing a latent infection. The identification of viral and cellular determinants of latency is the first step toward developing antiviral treatments that target and might clear or control the reservoir of latent virus. HCMV latency is established in CD34+cells when expression of viral immediate early (IE) proteins that initiate lytic infection is silenced. Viral IE gene expression during lytic infection is controlled by a cellular intrinsic immune defense mediated by promyelocytic leukemia nuclear body (PML-NB) proteins such as Daxx and histone deacetylases (HDACs). This defense is inactivated at the start of lytic infection by the HCMV virion tegument protein pp71, which upon viral entry traffics to the nucleus and induces Daxx degradation. Here we show that a similar defense is present, active, and not neutralized during experimental latency in CD34+cells infectedin vitrobecause tegument-delivered pp71 remains in the cytoplasm. Artificial inactivation of this defense by HDAC inhibition or Daxx knockdown rescues viral IE gene expression upon infection of CD34+cells with a laboratory-adapted viral strain but not with clinical strains. Interestingly, coinfection of CD34+cells with clinical viral strains blocked the ability of an HDAC inhibitor to activate IE1 and early protein expression during infection with a laboratory-adapted strain. This suggests that in addition to the intrinsic defense, HCMV clinical strains contribute an HDAC-independent,trans-acting dominant means of control over viral gene expression during the early stages of experimental HCMV latency modeledin vitroin CD34+cells.
Some principles of Islamic ethics as found in Harrisian philosophy
Authors: Aksoy Sahin 
Published: March 2010

John Harris is one of the prominent philosophers and bioethicists of our time. He has published tens of books and hundreds of papers throughout his professional life. This paper aims to take a ‘deep-look’ at Harris' works to argue that it is possible to find some principles of Islamic ethics in Harrisian philosophy, namely in his major works, as well as in his personal life.This may be surprising, or thought of as a ‘big’ and ‘groundless’ claim, since John Harris has nothing to do with any religion in his intellectual works. The major features of Harrisian philosophy could be defined as consequentialism or utilitarianism with liberal overtones. Despite some significant and fundamental differences in the application of principles (ie, abortion, euthanasia), the similarities between the major principles in Harrisian philosophy and Islamic ethics are greater at some points than the similarities between Islamic ethics and some other religious ethics (ie, Christian, Judaism).In this study I compare Harrisian teachings with major Islamic principles on ‘Responsibility’, ‘Side-effects and Double-effects’, ‘Equality’, ‘Vicious choice, guilt and innocence’, ‘Organ transplantation and property rights’ and ‘Advance directives’.
Dutch experience of monitoring active ending of life for newborns: Table 1
Authors: Buiting Hilde M , Karelse Maartje A C , Brouwers Hens A A , Onwuteaka-Philipsen Bregje D , van der Heide Agnes , van Delden Johannes J M 
Published: March 2010

IntroductionIn 2007, a national review committee was instituted in The Netherlands to review cases of active ending of life for newborns. It was expected that 15–20 cases would be reported. To date, however, only one case has been reported to this committee. Reporting is essential to obtain societal control and transparency; the possible explanations for this lack of reporting were therefore explored.MethodsData on end-of-life decision-making were scrutinised from Dutch nation-wide studies (1995, 2001 and 2005), before institution of the committee. Physicians received a questionnaire about their medical decision-making for stratified samples of deceased infants up to 1 year, drawn from the central death registry.ResultsIn 2005, 58% of all deaths were preceded by an end-of-life decision, compared with 68% in 2001 and 62% in 1995. The use of drugs with a possible life-shortening effect tended to be lower. In 2005, all four cases in the study in which an infants' life was actively ended were preceded by a decision to forego life-prolonging treatment. In three cases, the infant's life expectancy was short; one case involved a longer life expectancy.DiscussionThe expected number of cases is probably an overestimation due to changes in medical practice such as the tendency to attribute less life-shortening effects to opioids. The lack of reports is probably also associated with requirements in the regulation; it may be difficult to fulfil them due either to time constraints or the nature of the suffering that is addressed. If societal control of active ending of life is considered useful, changes in the regulation may be needed.