bluuebunny/crossref_metadata_2025_split huggingface dataset:
External Quality Assessment for Enterovirus 71 and Coxsackievirus A16 Detection by Reverse Transcription-PCR Using Armored RNA as a Virus Surrogate
Authors: Song Liqiong , Sun Shipeng , Li Bo , Pan Yang , Li Wenli , Zhang Kuo , Li Jinming 
Published: August 2011

ABSTRACT

Three armored RNAs (virus-like particles [VLPs]) containing target sequences from enterovirus 71 (EV71) and coxsackievirus A16 (CA16) and a pan-enterovirus (pan-EV) sequence were constructed and used in an external quality assessment (EQA) to determine the performance of laboratories in the detection of EV71 and CA16. The EQA panel, which consisted of 20 samples, including 14 positive samples with different concentrations of EV and either EV71 or CA16 armored RNAs, 2 samples with all 3 armored RNAs, and 4 negative-control samples (NaN
3
-preserved minimal essential medium [MEM] without VLPs), was distributed to 54 laboratories that perform molecular diagnosis of hand, foot, and mouth disease (HFMD) virus infections. A total of 41 data sets from 41 participants were returned; 5 (12.2%) were generated using conventional in-house reverse transcription-PCR (RT-PCR) assays, and 36 (87.8%) were generated using commercial real-time RT-PCR assays. Performance assessments of laboratories differed; 12 (29.3%) showed a need for improvement. Surprisingly, 4 laboratories were unable to detect EV71 RNA in any samples, even those containing the highest concentration of 10
7
IU/ml. Furthermore, the detection sensitivity for EV71 among all laboratories (82.1%) was substantially lower than that for EV (97.4%) or CA16 (95.1%). Overall, the results of the present study indicate that EQA should be performed periodically to help laboratories monitor their ability to detect HFMD viruses and to improve the comparability of results from different laboratories.
Diagnostic Strategy Used To Establish Etiologies of Encephalitis in a Prospective Cohort of Patients in England
Authors: Ambrose H. E. , Granerod J. , Clewley J. P. , Davies N. W. S. , Keir G. , Cunningham R. , Zuckerman M. , Mutton K. J. , Ward K. N. , Ijaz S. , Crowcroft N. S. , Brown D. W. G. ,   on behalf of the UK Aetiology of Encephalitis Study Group
Published: August 2011

ABSTRACT

The laboratory diagnostic strategy used to determine the etiology of encephalitis in 203 patients is reported. An etiological diagnosis was made by first-line laboratory testing for 111 (55%) patients. Subsequent testing, based on individual case reviews, resulted in 17 (8%) further diagnoses, of which 12 (71%) were immune-mediated and 5 (29%) were due to infection. Seventy-five cases were of unknown etiology. Sixteen (8%) of 203 samples were found to be associated with either
N
-methyl-
d
-aspartate receptor or voltage-gated potassium channel complex antibodies. The most common viral causes identified were herpes simplex virus (HSV) (19%) and varicella-zoster virus (5%), while the most important bacterial cause was
Mycobacterium tuberculosis
(5%). The diagnostic value of testing cerebrospinal fluid (CSF) for antibody was assessed using 139 samples from 99 patients, and antibody was detected in 46 samples from 37 patients. Samples collected at 14 to 28 days were more likely to be positive than samples taken 0 to 6 days postadmission. Three PCR-negative HSV cases were diagnosed by the presence of virus-specific antibody in the central nervous system (CNS). It was not possible to make an etiological diagnosis for one-third of the cases; these were therefore considered to be due to unknown causes. Delayed sampling did not contribute to these cases. Twenty percent of the patients with infections with an unknown etiology showed evidence of localized immune activation within the CNS, but no novel viral DNA or RNA sequences were found. We conclude that a good standard of clinical investigation and thorough first-line laboratory testing allows the diagnosis of most cases of infectious encephalitis; testing for CSF antibodies allows further cases to be diagnosed. It is important that testing for immune-mediated causes also be included in a diagnostic algorithm.
High-Resolution Melting Approach to Efficient Identification and Quantification of H275Y Mutant Influenza H1N1/2009 Virus in Mixed-Virus-Population Samples
Authors: Lee Hong Kai , Lee Chun Kiat , Loh Tze Ping , Tang Julian Wei-Tze , Tambyah Paul Anantharajah , Koay Evelyn Siew-Chuan 
Published: August 2011

ABSTRACT

The single-nucleotide variation 823C to T (His275Tyr), responsible for oseltamivir drug resistance has been detected in some isolates of the influenza A/H1N1/2009 virus. Early detection of the presence of this oseltamivir-resistant strain allows prompt consideration of alternative treatment options. An isolated-probe–asymmetric amplification PCR (Roche LightCycler v2.0) and high-resolution melting (HRM) method using unlabeled probes and amplified products (Idaho LightScanner 32) was designed and optimized to detect and estimate the proportion of H275Y mutants in influenza A/H1N1/2009 virus samples. The lower limit of quantification within the linear range of PCR assay detection was 200 copies/reaction. The melting peaks of the H275Y-specific unlabeled probe for the wild-type A/H1N1/2009 and H275Y mutant viruses were clearly distinguishable at 65.5°C and 69.0°C, respectively, at various ratios of wild-type/mutant virus population standards. The 95% detection limit for the 10% mutant sample pool was 1,200 copies/reaction (95% confidence interval, 669.7 to 3,032.6 copies/reaction). This HRM assay was tested with 116 archived clinical specimens. The quantitative HRM results obtained with samples containing mixed mutant–wild-type virus populations, at threshold cycle (

C
T

) values of <29, compared well to those obtained with a pyrosequencing method performed by an independent laboratory. The quantitative feature of this assay allows the proportions of mutant and wild-type viral populations to be determined, which may assist in the conventional clinical management of infected patients and potentially more preemptive clinical management. This validated quantitative HRM method, with its low running cost, is well positioned as a rapid, high-throughput screening tool for oseltamivir resistance mutations in influenza A/H1N1/2009 virus-infected patients, with the potential to be adapted to other influenza virus species.
Emergence of a Novel Shiga Toxin-Producing Escherichia coli O Serogroup Cross-Reacting with Shigella boydii Type 10
Authors: Iguchi Atsushi , Iyoda Sunao , Seto Kazuko , Ohnishi Makoto ,   on behalf of the EHEC Study Group
Published: August 2011

ABSTRACT

This is the first report of the isolation of Shiga toxin-producing
Escherichia coli
(STEC) strains whose O antigens were genetically and serologically identical to those of
Shigella boydii
type 10, from human feces. The novel STEC O serogroup may be widespread in Japan and associated with diarrhea and hemorrhagic colitis.
Evidence for Alteration of EZH2, BMI1, and KDM6A and Epigenetic Reprogramming in Human Papillomavirus Type 16 E6/E7-Expressing Keratinocytes
Authors: Hyland Paula L. , McDade Simon S. , McCloskey Rachel , Dickson Glenda J. , Arthur Ken , McCance Dennis J. , Patel Daksha 
Published: August 2011

ABSTRACT

A number of epigenetic alterations occur in both the virus and host cellular genomes during human papillomavirus (HPV)-associated carcinogenesis, and investigations of such alterations, including changes in chromatin proteins and histone modifications, have the potential to lead to therapeutic epigenetic reversion. We report here that transformed HPV16 E6/E7-expressing primary human foreskin keratinocytes (HFKs) (E6/E7 cells) demonstrate increased expression of the PRC2 methyltransferase EZH2 at both the mRNA and protein levels but do not exhibit the expected increase in trimethylated H3K27 (H3K27me3) compared to normal keratinocytes. In contrast, these cells show a reduction in global H3K27me3 levels
in vitro
, as well as upregulation of the KDM6A demethylase. We further show for the first time that transformation with the HPV16 E6 and E7 oncogenes also results in an increase in phosphorylated EZH2 serine 21 (P-EZH2-Ser21), mediated by active Akt, and in a downregulation of the PRC1 protein BMI1 in these cells. High-grade squamous cervical intraepithelial lesions also showed a loss of H3K27me3 in the presence of increased expression of EZH2. Correlating with the loss of H3K27me3, E6/E7 cells exhibited derepression of specific EZH2-, KMD6A-, and BMI1-targeted HOX genes. These results suggest that the observed reduction in H3K27me3 may be due to a combination of reduced activities/levels of specific polycomb proteins and increases in demethylases. The dysregulation of multiple chromatin proteins resulting in the loss of global H3K27me3 and the transcriptional reprogramming in HPV16 E6/E7-infected cells could provide an epigenetic signature associated with risk and/or progression of HPV16-associated cancers, as well as the potential for epigenetic reversion in the future.
Alphavirus-Induced Encephalomyelitis: Antibody-Secreting Cells and Viral Clearance from the Nervous System
Authors: Metcalf Talibah U. , Griffin Diane E. 
Published: August 2011

ABSTRACTSindbis virus (SINV) infection of the central nervous system (CNS) provides a model for understanding the role of the immune response in recovery from alphavirus infection of neurons. Virus clearance occurred in three phases: clearance of infectious virus (days 3 to 7), clearance of viral RNA (days 8 to 60), and maintenance of low levels of viral RNA (>day 60). The antiviral immune response was initiated in the cervical lymph nodes with rapid extrafollicular production of plasmablasts secreting IgM, followed by germinal center production of IgG-secreting and memory B cells. The earliest inflammatory cells to enter the brain were CD8+T cells, followed by CD4+T cells and CD19+B cells. During the clearance of infectious virus, effector lymphocytes in the CNS were primarily CD8+T cells and IgM antibody-secreting cells (ASCs). During the clearance of viral RNA, there were more CD4+than CD8+T cells, and B cells included IgG and IgA ASCs. At late times after infection, ASCs in the CNS were primarily CD19+CD38+CD138−Blimp-1+plasmablasts, with few fully differentiated CD38−CD138+Blimp-1+plasma cells. CD19+CD38+surface Ig+memory B cells were also present. The level of antibody to SINV increased in the brain over time, and the proportion of SINV-specific ASCs increased from 15% of total ASCs at day 14 to 90% at 4 to 6 months, suggesting specific retention in the CNS during viral RNA persistence. B cells in the CNS continued to differentiate, as evidenced by accumulation of IgA ASCs not present in peripheral lymphoid tissue and downregulation of major histocompatibility complex (MHC) class II expression on plasmablasts. However, there was no evidence of germinal center activity or IgG avidity maturation within the CNS.
Systems Analysis of Immune Responses in Marek's Disease Virus-Infected Chickens Identifies a Gene Involved in Susceptibility and Highlights a Possible Novel Pathogenicity Mechanism
Authors: Smith Jacqueline , Sadeyen Jean-Remy , Paton Ian R. , Hocking Paul M. , Salmon Nigel , Fife Mark , Nair Venugopal , Burt David W. , Kaiser Pete 
Published: August 2011

ABSTRACT

Marek's disease virus (MDV) is a highly contagious oncogenic alphaherpesvirus that causes disease that is both a cancer model and a continuing threat to the world's poultry industry. This comprehensive gene expression study analyzes the host response to infection in both resistant and susceptible lines of chickens and inherent expression differences between the two lines following the infection of the host. A novel pathogenicity mechanism, involving the downregulation of genes containing HIC1 transcription factor binding sites as early as 4 days postinfection, was suggested from this analysis. HIC1 drives antitumor mechanisms, suggesting that MDV infection switches off genes involved in antitumor regulation several days before the expression of the MDV oncogene
meq
. The comparison of the gene expression data to previous QTL data identified several genes as candidates for involvement in resistance to MD. One of these genes, IRG1, was confirmed by single nucleotide polymorphism analysis to be involved in susceptibility. Its precise mechanism remains to be elucidated, although the analysis of gene expression data suggests it has a role in apoptosis. Understanding which genes are involved in susceptibility/resistance to MD and defining the pathological mechanisms of the disease gives us a much greater ability to try to reduce the incidence of this virus, which is costly to the poultry industry in terms of both animal welfare and economics.
Dynamic Antibody Specificities and Virion Concentrations in Circulating Immune Complexes in Acute to Chronic HIV-1 Infection
Authors: Liu Pinghuang , Overman R. Glenn , Yates Nicole L. , Alam S. Munir , Vandergrift Nathan , Chen Yue , Graw Frederik , Freel Stephanie A. , Kappes John C. , Ochsenbauer Christina , Montefiori David C. , Gao Feng , Perelson Alan S. , Cohen Myron S. , Haynes Barton F. , Tomaras Georgia D. 
Published: August 2011

ABSTRACT
Understanding the interactions between human immunodeficiency virus type 1 (HIV-1) virions and antibodies (Ab) produced during acute HIV-1 infection (AHI) is critical for defining antibody antiviral capabilities. Antibodies that bind virions may prevent transmission by neutralization of virus or mechanically prevent HIV-1 migration through mucosal layers. In this study, we quantified circulating HIV-1 virion-immune complexes (ICs), present in approximately 90% of AHI subjects, and compared the levels and antibody specificity to those in chronic infection. Circulating HIV-1 virions coated with IgG (immune complexes) were in significantly lower levels relative to the viral load in acute infection than in chronic HIV-1 infection. The specificities of the antibodies in the immune complexes differed between acute and chronic infection (anti-gp41 Ab in acute infection and anti-gp120 in chronic infection), potentially suggesting different roles in immunopathogenesis for complexes arising at different stages of infection. We also determined the ability of circulating IgG from AHI to bind infectious versus noninfectious virions. Similar to a nonneutralizing anti-gp41 monoclonal antibody (MAb), purified plasma IgG from acute HIV-1 subjects bound both infectious and noninfectious virions. This was in contrast to the neutralizing antibody 2G12 MAb that bound predominantly infectious virions. Moreover, the initial antibody response captured acute HIV-1 virions without selection for different HIV-1 envelope sequences. In total, this study demonstrates that the composition of immune complexes are dynamic over the course of HIV-1 infection and are comprised initially of antibodies that nonselectively opsonize both infectious and noninfectious virions, likely contributing to the lack of efficacy of the antibody response during acute infection.
Factors associated with use of slip-resistant shoes in US limited-service restaurant workers
Authors: Verma Santosh K , Courtney Theodore K , Corns Helen L , Huang Yueng-Hsiang , Lombardi David A , Chang Wen-Ruey , Brennan Melanye J , Perry Melissa J 
Published: August 2011

ObjectivesSlips and falls are a leading cause of injury at work. Several studies have indicated that slip-resistant shoes can reduce the risk of occupational slips and falls. Few studies, however, have examined the determinants of slip-resistant shoe use. This study examined the individual and workplace factors associated with slip-resistant shoe use.Methods475 workers from 36 limited-service restaurants in the USA participated in a study of workplace slipping. Demographic and job characteristic information about each participant was collected. Restaurant managers provided information on whether slip-resistant shoes were provided and paid for by the employer and whether any guidance was given regarding slip-resistant shoe use when they were not provided. Kitchen floor coefficient of friction was measured. Slip-resistant status of the shoes was determined by noting the presence of a ‘slip-resistant’ marking on the sole. Poisson regression with robust SE was used to calculate prevalence ratios.Results320 participants wore slip-resistant shoes (67%). In the multivariate analysis, the prevalence of slip-resistant shoe use was lowest in 15–19-year age group. Women were more likely to wear slip-resistant shoes (prevalence ratio 1.18, 95% CI 1.07 to 1.31). The prevalence of slip-resistant shoe use was lower when no guidance regarding slip-resistant shoes was given as compared to when they were provided by the employer (prevalence ratio 0.66, 95% CI 0.55 to 0.79). Education level, job tenure and the mean coefficient of friction had no significant effects on the use of slip-resistant shoes.ConclusionProvision of slip-resistant shoes was the strongest predictor of their use. Given their effectiveness and low cost, employers should consider providing slip-resistant shoes at work.
Long-term effect of nutritional counselling on desired gain in body mass and lean body mass in elite athletes
Authors: Garthe Ina , Raastad Truls , Sundgot-Borgen Jorunn 
Published: August 2011

Lean body mass (LBM) is important in power-related sports. In athletes with heavy training loads and competitions, it may be difficult to increase and maintain LBM during the season. The purpose of this study was to evaluate the long-term effects on body composition after an 8–12 week weight-gain period with or without nutritional guidance. Twenty-one elite athletes where randomized to 1 of 2 groups: the nutritional counselling group (NCG; n = 12, 18.5 ± 1.7 y, 67.8 ± 7.4 kg) and the ad libitum group (ALG; n = 9, 19.6 ± 2.7 y, 74.2 ± 5.7 kg). The NCG followed a meal plan that provided a surplus of 506 ± 84 kcal·day–1, whereas the ALG had an ad libitum energy intake (EI) during the strength-training (4 sessions per week) intervention. Body mass (BM) and body composition were measured pre- and postintervention, and 6 and 12 months after the intervention. EI in the NCG was normalized after 12 months, whereas EI in the ALG was unchanged during or after the intervention. BM increased more in the NCG than in the ALG during the intervention (4.3% ± 0.9% vs. 1.0% ± 0.6%) and after 12 months (6.0% ± 0.9% vs. 1.8% ± 0.7%). LBM increased in the NCG during the intervention (2.8% ± 0.5%) and after 12 months (4.4% ± 1.0%), whereas LBM in the ALG was unchanged. The NCG managed to maintain and increase BM and LBM after the intervention period. Hence, the focus on nutritional guidance, in addition to strength training, seems to be preferable for obtaining the long-term effect of weight gain in athletes.
Anti-thrombotic effects of selective estrogen receptor modulator tamoxifen
Authors: Nayak Manasa , Singh Sunil , Roy Arnab , Prakash Vivek , Kumar Anand , Dash Debabrata 
Published: August 2011

SummaryTamoxifen is a known anti-cancer drug and established estrogen receptor modulator. Few clinical studies have earlier implicated the drug in thrombotic complications attributable to lower anti-thrombin and protein S levels in plasma. However, action of tamoxifen on platelet signalling machinery has not been elucidated in detail. In the present report we show that tamoxifen is endowed with significant inhibitory property against human platelet aggregation. From a series of in vivo and in vitro studies tamoxifen was found to inhibit almost all platelet functions, prolong tail bleeding time in mouse and profoundly prevent thrombus formation at injured arterial wall in mice, as well as on collagen matrix perfused with platelet-rich plasma under arterial shear against the vehicle dimethylsulfoxide (DMSO). These findings strongly suggest that tamoxifen significantly downregulates platelet responses and holds potential as a promising anti-platelet / anti-thrombotic agent.
Mast cells in atherosclerosis
Authors: Biessen Erik , Bot Ilze 
Published: August 2011

SummaryThe mast cell, a potent inflammatory cell type, is widely distributed over several tissues, but particularly prominent at the interface exposed to the environment to act in the first line of defense against pathogens. Upon activation mast cells release granules, which contain a large panel of mediators, including neutral proteases (e.g. chymase and tryptase), cathepsins, heparin, histamine and a variety of cytokines and growth factors. While mast cells have been demonstrated to be critically involved in a number of Th2 dominated diseases such as asthma and allergy, recent investigations have now also implicated mast cells in the pathogenesis of atherosclerosis and acute cardiovascular syndromes. In this review, we will discuss the contribution of mast cells to the initiation and progression of atherosclerosis and gauge the therapeutic opportunities of mast cell targeted intervention in acute cardiovascular syndromes.
Ontogeny stage-independent and high-level clonal expansion in vitro of mouse hematopoietic stem cells stimulated by an engineered NUP98-HOX fusion transcription factor
Authors: Sekulovic Sanja , Gasparetto Maura , Lecault Véronique , Hoesli Corinne A. , Kent David G. , Rosten Patty , Wan Adrian , Brookes Christy , Hansen Carl L. , Piret James M. , Smith Clayton , Eaves Connie J. , Humphries R. Keith 
Published: August 2011

Abstract
Achieving high-level expansion of hematopoietic stem cells (HSCs) in vitro will have an important clinical impact in addition to enabling elucidation of their regulation. Here, we couple the ability of engineered NUP98-HOXA10hd expression to stimulate > 1000-fold net expansions of murine HSCs in 10-day cultures initiated with bulk lin−Sca-1+c-kit+ cells, with strategies to purify fetal and adult HSCs and analyze their expansion clonally. We find that NUP98-HOXA10hd stimulates comparable expansions of HSCs from both sources at ∼ 60% to 90% unit efficiency in cultures initiated with single cells. Clonally expanded HSCs consistently show balanced long-term contributions to the lymphoid and myeloid lineages without evidence of leukemogenic activity. Although effects on fetal and adult HSCs were indistinguishable, NUP98-HOXA10hd–transduced adult HSCs did not thereby gain a competitive advantage in vivo over freshly isolated fetal HSCs. Live-cell image tracking of single transduced HSCs cultured in a microfluidic device indicates that NUP98-HOXA10hd does not affect their proliferation kinetics, and flow cytometry confirmed the phenotype of normal proliferating HSCs and allowed reisolation of large numbers of expanded HSCs at a purity of 25%. These findings point to the effects of NUP98-HOXA10hd on HSCs in vitro being mediated by promoting self-renewal and set the stage for further dissection of this process.