bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-Scale Evaluation of the Immuno-Mycologics Lateral Flow and Enzyme-Linked Immunoassays for Detection of Cryptococcal Antigen in Serum and Cerebrospinal Fluid
Authors: Hansen Jessica , Slechta E. Susan , Gates-Hollingsworth Marcellene A. , Neary Brandon , Barker Adam P. , Bauman Sean , Kozel Thomas R. , Hanson Kimberly E. 
Published: November 2012

ABSTRACT

Cryptococcosis is a systemic infection caused by the pathogenic yeasts
Cryptococcus neoformans
and
C. gattii
. Detection of cryptococcal capsular antigen (CrAg) in serum and cerebrospinal fluid (CSF) plays an important diagnostic role. We prospectively compared the new Immuno-Mycologics Inc. (IMMY) lateral flow assay (LFA) and enzyme immunoassay (EIA) to our current CrAg test (Premier EIA; Meridian Bioscience Inc.). Discordant samples were retested with the latex-
Cryptococcus
antigen test (IMMY) and using serotype-specific monoclonal antibodies (MAbs). A total of 589 serum and 411 CSF specimens were tested in parallel. Qualitative agreement across assays was 97.7%. In all, 56 (41 serum and 15 CSF) samples were positive and 921 (527 serum and 394 CSF) samples were negative by all three assays. The 23 discrepant specimens were all Meridian EIA negative. Of 23 discordant specimens, 20 (87.0%) were positive by both the IMMY LFA and EIA, 2 were LFA positive only, and 1 was EIA positive only. Eleven discrepant specimens had adequate volume for latex agglutination (LA) testing; 8 were LA positive, and 3 were LA negative. LA-negative samples (2 CSF samples and 1 serum) had low IMMY LFA/EIA titers (≤1:10). Serotype-specific MAb analysis of the LA-positive samples suggested that these specimens contained CrAg epitopes similar to those of serotype C strains. In conclusion, the IMMY assays showed excellent overall concordance with the Meridian EIA. Assay performance differences were related to issues of analytic sensitivity and possible serotype bias. Incomplete access to patient-level data combined with low specimen volumes limited our ability to fully resolve discrepant results.
Population Dynamics of Tuberculous Bacilli in Cameroon as Assessed by Spoligotyping
Authors: Koro Koro Francioli , Kamdem Simo Yannick , Piam Félix Fotso , Noeske Jurgen , Gutierrez Cristina , Kuaban Christopher , Eyangoh Sara Irène 
Published: November 2012

ABSTRACT

Genetic assessment by spoligotyping of 565
Mycobacterium tuberculosis
complex strains collected from the Western Region of Cameroon between 2004 and 2005 has confirmed the establishment of the “Cameroon family” as the leading cause of tuberculosis in 45.9% of cases and evidenced the rapid quasi extinction of
Mycobacterium africanum
, isolated in 3.3% of tuberculosis cases.
Analysis of Mutations in theSGene of Hepatitis B Virus Strains in Patients with Chronic Infection by Online Bioinformatics Tools
Authors: Simon Benedikt , Kundi Michael , Puchhammer Elisabeth 
Published: November 2012

ABSTRACTHepatitis B virus (HBV) genomes show a high rate of mutations. This can lead to a variety of amino acid changes in the surface and polymerase genes, causing changes in viral protein conformation that can result in diminished antibody binding or decreased secretion of surface antigen (HBsAg). HBV monitoring increasingly relies on HBsAg detection and quantification, and therefore epidemiological data on HBsAg mutations are needed. We therefore analyzed the frequency of HBsAg mutations possibly influencing the quantification of HBsAg (MUPIQHs) in an unselected patient collective. To this end, we determined the HBV surface and polymerase gene sequences of an unselected patient collective of 237 individuals chronically infected with HBV and analyzed the MUPIQHs in these sequences using three different online HBV sequence analysis tools. We found that 17 or 34% of the patients, depending on the online interpretation algorithm used, harbored MUPIQHs and that MUPIQHs were not significantly associated with the duration of disease, treatment, or HBV genotype. Thus, this study shows that a substantial amount of HBV sequences derived from unselected patients chronically infected with HBV carry MUPIQHs, and therefore the reliability of routine quantitative and qualitative HBsAg tests needs to be reevaluated.
Comparison of Sequencing (Barcode Region) and Sequence-Tagged-Site PCR for Blastocystis Subtyping
Authors: Stensvold Christen Rune 
Published: November 2012

ABSTRACT

Blastocystis
is the most common nonfungal microeukaryote of the human intestinal tract and comprises numerous subtypes (STs), nine of which have been found in humans (ST1 to ST9). While efforts continue to explore the relationship between human health status and subtypes, no consensus regarding subtyping methodology exists. It has been speculated that differences detected in subtype distribution in various cohorts may to some extent reflect different approaches.
Blastocystis
subtypes have been determined primarily in one of two ways: (i) sequencing of small subunit rRNA gene (SSU-rDNA) PCR products and (ii) PCR with subtype-specific sequence-tagged-site (STS) diagnostic primers. Here, STS primers were evaluated against a panel of samples (
n
= 58) already subtyped by SSU-rDNA sequencing (barcode region), including subtypes for which STS primers are not available, and a small panel of DNAs from four other eukaryotes often present in feces (
n
= 18). Although the STS primers appeared to be highly specific, their sensitivity was only moderate, and the results indicated that some infections may go undetected when this method is used. False-negative STS results were not linked exclusively to certain subtypes or alleles, and evidence of substantial genetic variation in STS loci was obtained. Since the majority of DNAs included here were extracted from feces, it is possible that STS primers may generally work better with DNAs extracted from
Blastocystis
cultures. In conclusion, due to its higher applicability and sensitivity, and since sequence information is useful for other forms of research, SSU-rDNA barcoding is recommended as the method of choice for
Blastocystis
subtyping.
AMP-Activated Protein Kinase Is Required for the Macropinocytic Internalization of Ebolavirus
Authors: Kondratowicz Andrew S. , Hunt Catherine L. , Davey Robert A. , Cherry Sara , Maury Wendy J. 
Published: November 2012

ABSTRACT

Identification of host factors that are needed for Zaire Ebolavirus (EBOV) entry provides insights into the mechanism(s) of filovirus uptake, and these factors may serve as potential antiviral targets. In order to identify novel host genes and pathways involved in EBOV entry, gene array findings in the National Cancer Institute's NCI-60 panel of human tumor cell lines were correlated with permissivity for EBOV glycoprotein (GP)-mediated entry. We found that the gene encoding the γ2 subunit of AMP-activated protein kinase (AMPK) strongly correlated with EBOV transduction in the tumor panel. The AMPK inhibitor compound C inhibited infectious EBOV replication in Vero cells and diminished EBOV GP-dependent, but not Lassa fever virus GPC-dependent, entry into a variety of cell lines in a dose-dependent manner. Compound C also prevented EBOV GP-mediated infection of primary human macrophages, a major target of filoviral replication
in vivo
. Consistent with a role for AMPK in filovirus entry, time-of-addition studies demonstrated that compound C abrogated infection when it was added at early time points but became progressively less effective when added later. Compound C prevented EBOV pseudovirion internalization at 37°C as cell-bound particles remained susceptible to trypsin digestion in the presence of the inhibitor but not in its absence. Mouse embryonic fibroblasts lacking the AMPKα1 and AMPKα2 catalytic subunits were significantly less permissive to EBOV GP-mediated infection than their wild-type counterparts, likely due to decreased macropinocytic uptake. In total, these findings implicate AMPK in macropinocytic events needed for EBOV GP-dependent entry and identify a novel cellular target for new filoviral antivirals.
The West Nile Virus Capsid Protein Blocks Apoptosis through a Phosphatidylinositol 3-Kinase-Dependent Mechanism
Authors: Urbanowski Matt D. , Hobman Tom C. 
Published: November 2012

ABSTRACT
West Nile virus (WNV) is a mosquito-transmitted pathogen that can cause serious disease in humans. Our laboratories are focused on understanding how interactions between WNV proteins and host cells contribute to virus replication and pathogenesis. WNV replication is relatively slow, and on the basis of earlier studies, the virus appears to activate survival pathways that delay host cell death during virus replication. The WNV capsid is the first viral protein produced in infected cells; however, its role in virus assembly is not required until after replication of the genomic RNA. Accordingly, from a temporal perspective, it is perfectly suited to block host cell apoptosis during virus replication. In the present study, we provide evidence that the WNV capsid protein blocks apoptosis through a phosphatidylinositol (PI) 3-kinase-dependent pathway. Specifically, expression of this protein in the absence of other viral proteins increases the levels of phosphorylated Akt, a prosurvival kinase that blocks apoptosis through multiple mechanisms. Treatment of cells with the PI 3-kinase inhibitor LY294002 abrogates the protective effects of the WNV capsid protein.
Cumulative Impact of Host and Viral Factors on HIV-1 Viral-Load Control during Early Infection
Authors: Yue Ling , Prentice Heather A. , Farmer Paul , Song Wei , He Dongning , Lakhi Shabir , Goepfert Paul , Gilmour Jill , Allen Susan , Tang Jianming , Kaslow Richard A. , Hunter Eric 
Published: November 2012

ABSTRACT

In HIV-1 infection, the early set-point viral load strongly predicts both viral transmission and disease progression. The factors responsible for the wide spectrum of set-point viral loads are complex and likely reflect an interplay between the transmitted virus and genetically defined factors in both the transmitting source partner and the seroconverter. Indeed, analysis of 195 transmission pairs from Lusaka, Zambia, revealed that the viral loads in transmitting source partners contributed only ∼2% of the variance in early set-point viral loads of seroconverters (
P
= 0.046 by univariable analysis). In multivariable models, early set-point viral loads in seroconverting partners were a complex function of (i) the viral load in the source partner, (ii) the gender of the seroconverter, (iii) specific HLA class I alleles in the newly infected partner, and (iv) sharing of HLA-I alleles between partners in a transmission pair. Each of these factors significantly and independently contributed to the set-point viral load in the newly infected partner, accounting for up to 37% of the variance observed and suggesting that many factors operate in concert to define the early virological phenotype in HIV-1 infection.
Complete Nucleotide Sequence of Avian Paramyxovirus Type 6 Strain JL Isolated from Mallard Ducks in China
Authors: Tian Zhige , Chai Hongliang , Li Fengyong , Sun Jing , Chen Guang , Hu Xiaoliang , Hua Yuping , Xiang Wenhua 
Published: November 2012

ABSTRACT
A new strain of avian paramyxovirus type 6 (APMV-6), JL, has been isolated from mallard ducks in China, and its complete genome has been sequenced and analyzed. This work is the first announced complete genome sequence of APMV-6 from mallards.
Complete Genome Sequence of a Velogenic Neurotropic Avian Paramyxovirus 1 Isolated from Peacocks (Pavo cristatus) in a Wildlife Park in Pakistan
Authors: Munir Muhammad , Shabbir Muhammad Z. , Yaqub Tahir , Shabbir Muhammad A. B. , Mukhtar Nadia , Khan Muhammad R. , Berg Mikael 
Published: November 2012

ABSTRACT

Avian paramyxovirus serotype 1 (APMV-1) was isolated from an acute and highly contagious outbreak in peacocks (
Pavo cristatus
) in a wildlife park in Pakistan. A velogenic neurotropic form of APMV-1 caused a 100% case fatality rate and killed 190 peacocks within a week. Biological and serological characterizations showed features of a velogenic strain of APMV-1, and these results were further confirmed by sequence analysis of the cleavage site in the fusion protein. The complete genome of one of the isolates was sequenced, and phylogenetic analysis was conducted. The analysis showed that this isolate belonged to genotype VII, specifically, to subgenotype VIIa, and clustered closely with isolates characterized from Indonesia in the 1990s. Interestingly, the isolate showed significant differences from previously characterized APMV-1 isolates from commercial and rural chickens in Pakistan. The work presented here is the first complete genome sequence of any APMV-1 isolate from wild birds in the region and therefore highlights the need for increased awareness and surveillance in such bird species.
Full Genome Sequence of Bluetongue Virus Serotype 4 from China
Authors: Yang Heng , Zhu Jianbo , Li Huachun , Xiao Lei , Wang Jinpin , Li Nan , Zhang Nianzu , Kirkland Peter. D. 
Published: November 2012

ABSTRACT
The complete genomic sequence of a bluetongue virus serotype 4 (BTV-4) strain (strain YTS-4), isolated from sentinel cattle in Yunnan Province, China, is reported here. This work is the first to document the complete genomic sequence of a BTV-4 strain from China. The sequence information will help determine the geographic origin of Chinese BTV-4 and provide data to facilitate future analyses of the genetic diversity and phylogenetic relationships of BTV strains.
Complete Genome Sequence of a Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Variant
Authors: Wang Lianghai , Hou Jun , Zhang Hexiao , Feng Wen-hai 
Published: November 2012

ABSTRACT
Highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRS) emerged in China in 2006, and HP-PRRS virus (HP-PRRSV) has evolved continuously. Here, the complete genomic sequence of a novel HP-PRRSV field strain, JX, is reported. The present finding will contribute to further studies focusing on the evolutionary mechanism of PRRSV.
Complete Genome Sequence of Bacteriophage phiAC-1 Infecting Acinetobacter soli Strain KZ-1
Authors: Kim Ji Hyung , Oh Chulhong , Choresca Casiano H. , Shin Sang Phil , Han Jee Eun , Jun Jin Woo , Heo Soo-Jin , Kang Do-Hyung , Park Se Chang 
Published: November 2012

ABSTRACT

To date, a number of bacteriophages (phages) infecting
Acinetobacter
species have been reported and characterized. However,
Acinetobacter
phages which infect
A. soli
have not been investigated yet. Here, we report the complete genome sequence of
Acinetobacter
phage phiAC-1, which belongs to the
Myoviridae
, infecting
Acinetobacter soli
strain KZ-1.
A Second CRM1-Dependent Nuclear Export Signal in the Influenza A Virus NS2 Protein Contributes to the Nuclear Export of Viral Ribonucleoproteins
Authors: Huang Shengping , Chen Jingjing , Chen Quanjiao , Wang Huadong , Yao Yanfeng , Chen Jianjun , Chen Ze 
Published: November 2012

ABSTRACT
Influenza A virus NS2 protein, also called nuclear export protein (NEP), is crucial for the nuclear export of viral ribonucleoproteins. However, the molecular mechanisms of NEP mediation in this process remain incompletely understood. A leucine-rich nuclear export signal (NES2) in NEP, located at the predicted N2 helix of the N-terminal domain, was identified in the present study. NES2 was demonstrated to be a transferable NES, with its nuclear export activity depending on the nuclear export receptor chromosome region maintenance 1 (CRM1)-mediated pathway. The interaction between NEP and CRM1 is coordinately regulated by both the previously reported NES (NES1) and now the new NES2. Deletion of the NES1 enhances the interaction between NEP and CRM1, and deletion of the NES1 and NES2 motifs completely abolishes this interaction. Moreover, NES2 interacts with CRM1 in the mammalian two-hybrid system. Mutant viruses containing NES2 alterations generated by reversed genetics exhibit reduced viral growth and delay in the nuclear export of viral ribonucleoproteins (vRNPs). The NES2 motif is highly conserved in the influenza A and B viruses. The results demonstrate that leucine-rich NES2 is involved in the nuclear export of vRNPs and contributes to the understanding of nucleocytoplasmic transport of influenza virus vRNPs.
Sudden cardiac death screening in adolescent athletes: an evaluation of compliance with national guidelines
Authors: Madsen Nicolas L , Drezner Jonathan A , Salerno Jack C 
Published: November 2012

ObjectiveIn the USA, the preparticipation physical evaluation (PPE) is the standard of care for screening eight million high-school athletes for their risk of sudden cardiac death (SCD). Our aim was to evaluate both physician and school compliance with national guidelines for SCD screening.MethodsWe conducted a confidential survey of the Washington Chapter of the American Academy of Pediatrics (AAP), the Washington Academy of Family Physicians (WAFP) and Washington State high-school athletic directors. Responses were evaluated for compliance with the American Heart Association (AHA) guidelines for SCD screening.ResultsWe received a response rate of 72% (559/776) from the AAP, 56% (554/990) from the WAFP and 78% (317/409) from the athletic directors. Only 6% of all providers and 0% of schools were in compliance with AHA guidelines. In addition, 47% of the physicians and 6% of athletic directors reported awareness of the guidelines. There was no difference in compliance between physician specialties (p=0.20). Physician location, years of experience and exposure to SCD were not significantly associated with compliance. Provider knowledge of the guidelines, number of PPE/month and frequency of referrals to cardiology were all positively associated with improved overall compliance (p<0.05).ConclusionsDespite the unaltered presence of the AHA SCD screening guidelines for the past 15 years, compliance with the recommendations is poor. Lack of compliance does not reflect clinical experience, but rather lack of knowledge of the guidelines themselves. New directions for provider education and policy requirements are needed to improve this implementation gap.
Reported medication events in a paediatric emergency research network: sharing to improve patient safety
Authors: Shaw Kathy N , Lillis Kathleen A , Ruddy Richard M , Mahajan Prashant V , Lichenstein Richard , Olsen Cody S , Chamberlain James M ,   for the Pediatric Emergency Care Applied Research Network
Published: November 2012

ObjectiveMedication errors are an important cause of preventable morbidity, especially in children in emergency department (ED) settings. Internal use of voluntary incident reporting (IR) is common within hospitals, with little external reporting or sharing of this information across institutions. We describe the analysis of paediatric medication events (ME) reported in 18 EDs in a paediatric research network in 2007–2008.MethodsConfidential, deidentified incident reports (IRs) were collected, and MEs were independently categorised by two investigators. Discordant responses were resolved by consensus.ResultsMEs (597) accounted for 19% of all IRs, with reporting rates varying 25-fold across sites. Anti-infective agents were the most commonly reported, followed by analgesics, intravenous fluids and respiratory medicines. Of the 597 MEs, 94% were medication errors and 6% adverse reactions; further analyses are reported for medication errors. Incorrect medication doses were related to incorrect weight (20%), duplicate doses (21%), and miscalculation (22%). Look-alike/sound-alike MEs were 36% of incorrect medications. Human factors contributed in 85% of reports: failure to follow established procedures (41%), calculation (13%) or judgment (12%) errors, and communication failures (20%). Outcomes were: no deaths or permanent disability, 13% patient harm, 47% reached patient (no harm), 30% near miss or unsafe conditions, and 9% unknown.ConclusionsME reporting by the system revealed valuable data across sites on medication categories and potential human factors. Harm was infrequently reported. Our analyses identify trends and latent systems issues, suggesting areas for future interventions to reduce paediatric ED medication errors.
Relationships between fatty acid composition and bile tolerance in lactobacillus isolates from plants and from non-plant materials
Authors: Kimoto-Nira Hiromi , Suzuki Shigenori , Yakabe Takafumi , Suzuki Chise 
Published: November 2012

Twenty plant-derived and 18 non-plant-derived strains of Lactobacillus casei were compared for their growth in tryptone – yeast extract – glucose broth containing 0.3% bile by measuring absorbance at a wavelength of 620 nm after 24 h of incubation at 37 °C. Bile tolerance — a fundamental probiotic property — was calculated by dividing the experimental data by control values (growth without bile). We found that bile tolerance was strain specific but that the average bile tolerance of the plant-derived strains was significantly (P < 0.05) lower than that of the non-plant-derived strains tested. All tested strains could not deconjugate sodium taurocholate, indicating that the difference in bile tolerance was not due to the ability to deconjugate bile. The fatty acid compositions of the test strains with and without exposure to 0.3% bile were investigated, and a statistical correlation analysis between these compositions and their bile tolerance was conducted. The fatty acids correlated with bile tolerance differed between plant and non-plant lactobacilli. This is the first report to show that the origin (i.e., growth environment) of lactobacilli affects their fatty acid composition, which in turn, appears to be related to their bile tolerance.
Seismic interpretation and attribute analysis of the Herodotus and the Levantine Basin, offshore Cyprus and Lebanon
Authors: Skiple C. , Anderson E. , Fürstenau J. 
Published: November 2012

Giant gas discoveries in the vicinity have sparked increased interest in the petroleum potential of the Eastern Mediterranean. However, a lack of well data from the area means that a number of crucial unknowns about the region remain. Many of these unknowns relate to uncertainties regarding the sedimentary infill of the main basins, including the sediment provenance areas and elastic properties.
The petroleum potential of this region has been investigated through the acquisition and analysis of multiple 2D and 3D seismic surveys offshore Cyprus and Lebanon and a thorough review of available literature regarding the regional geology. An amplitude extraction study indicates sourcing of probable clastic sediments from the NE, from present-day Syria. In addition evidence of conduits coming off onshore Lebanon can be seen in the seismic data. Use of released data from one of the closest wells penetrating the same stratigraphy as the new discoveries enabled us to build a synthetic model over one of these discoveries (Tamar discovery) and to perform a fluid-substitution over this model. Comparison of these results with characteristics of identified leads and prospects in the northern, undrilled part of the Levantine Basin may improve our understanding of the rock properties in this area as similarities in between these may also indicate similarities in the elastic properties.