bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Generalized Constraint Model for Two-Dimensional Beam Flexures: Nonlinear Strain Energy Formulation
Authors: Awtar Shorya , Sen Shiladitya 
Published: August 2010

Abstract
The beam constraint model (BCM), presented previously, captures pertinent nonlinearities to predict the constraint characteristics of a generalized beam flexure in terms of its stiffness and error motions. In this paper, a nonlinear strain energy formulation for the beam flexure, consistent with the transverse-direction load-displacement and axial-direction geometric constraint relations in the BCM, is presented. An explicit strain energy expression, in terms of beam end displacements, that accommodates generalized loading conditions, boundary conditions, initial curvature, and beam shape, is derived. Using energy-based arguments, new insight into the BCM is elucidated by fundamental relations among its stiffness, constraint, and energy coefficients. The presence of axial load in the geometric constraint and strain energy expressions—a unique attribute of distributed compliance flexures that leads to the elastokinematic effect—is highlighted. Using the principle of virtual work, this strain energy expression for a generalized beam is employed in determining the load-displacement relations, and therefore constraint characteristics, of a flexure mechanism comprising multiple beams. The benefit of this approach is evident in its mathematical efficiency and succinctness, which is to be expected with the use of energy methods. All analytical results are validated to a high degree of accuracy via nonlinear finite element analysis.
Serological Protection Induced by
Haemophilus influenzae
Type b Conjugate Vaccine in Mexican Children: Is a Booster Dose of the Vaccine Needed?
Authors: Rodriguez Romeo S. , Mascarenas Cesar , Conde-Glez Carlos J. , Inostroza Jaime , Villanueva Sonia , Velázquez María Elena , Sánchez-Alemán Miguel Angel , Echániz Gabriela 
Published: August 2010

ABSTRACT
We determined the seroprevalence of protective antibodies against Hib in Mexican children under the age of five using a standardized enzyme-linked immunosorbent assay. Hib antibodies (≥0.15 μg/ml) were present in 95.34% (±1.14% [seroprevalence ± standard error]) of samples. Fewer children aged 30 to 47 months had protective Hib antibody levels (91.45% ± 2.60%) than children from 12 to 29 and 48 to 59 months (97.3% ± 1.34% and 97.44% ± 1.80%, respectively).
Mycoplasma genitalium
PCR: Does Freezing of Specimens Affect Sensitivity?
Authors: Carlsen Katrina Hutton , Jensen Jorgen Skov 
Published: August 2010

ABSTRACT

Mycoplasma genitalium
is an established cause of sexually transmitted infections. Studies of disease associations are often performed on archived specimens, but little is known about the effect of storage of specimens on the detection of
M. genitalium.
Genital swab and first-void urine specimens submitted for detection of
M. genitalium
were tested on the day of receipt. Remnants of positive original specimens as well as DNA preparations were stored at −20°C for up to 18 months. A total of 361
M. genitalium
-positive specimens were available. PCR after repeat DNA preparation was performed for 262 specimens. The sensitivity after repeat DNA preparation was 90%, and the median decrease in DNA load was 155 genome equivalents (geq) (
P
< 0.0001). For 327 specimens, PCR could be repeated on the primary DNA preparation. The sensitivity of PCR after storage was 95%, and the median decrease in DNA load was 13.5 geq (
P
< 0.0001). The specimens yielding negative results at repeat testing had a significantly lower median DNA load in the primary analysis than those with a repeat positive test (
P
< 0.0001). For 228 specimens, PCR could be performed both on the primary DNA preparation and after repeat DNA preparation. The median DNA load was lower after repeat DNA extraction than after repeat testing of the stored DNA extract (
P
< 0.0001). In conclusion, the
M. genitalium
DNA load as well as the detection rate decreased after storage. This was more pronounced in clinical specimens stored frozen than in stored DNA extracts, particularly in those with an initial low DNA load.
Strains of
Mycobacterium tuberculosis
from Western Maharashtra, India, Exhibit a High Degree of Diversity and Strain-Specific Associations with Drug Resistance, Cavitary Disease, and Treatment Failure
Authors: Chatterjee Anirvan , D'Souza Desiree , Vira Tina , Bamne Arun , Ambe Gurish T. , Nicol Mark P. , Wilkinson Robert J. , Mistry Nerges 
Published: August 2010

ABSTRACT

We performed spoligotyping of
Mycobacterium tuberculosis
isolates from 833 systematically sampled pulmonary tuberculosis (TB) patients in urban Mumbai, India (723 patients), and adjacent rural areas in western India (110 patients). The urban cohort consisted of two groups of patients, new cases (646 patients) and first-time treatment failures (77 patients), while only new cases were recruited in the rural areas. The isolates from urban new cases showed 71% clustering, with 168 Manu1, 62 CAS, 22 Beijing, and 30 EAI-5 isolates. The isolates from first-time treatment failures were 69% clustered, with 14 Manu1, 8 CAS, 8 Beijing, and 6 EAI-5 isolates. The proportion of Beijing strains was higher in this group than in urban new cases (odds ratio [OR], 3.29; 95% confidence limit [95% CL], 1.29 to 8.14;
P
= 0.003). The isolates from rural new cases showed 69% clustering, with 38 Manu1, 7 CAS, and 1 EAI-5 isolate. Beijing was absent in the rural cohort. Manu1 was found to be more common in the rural cohort (OR, 0.67; 95% CL, 0.42 to 1.05;
P
= 0.06). In total, 71% of isolates were clustered into 58 spoligotypes with 4 predominant strains, Manu1 (26%), CAS (9%), EAI-5 (4%), and Beijing (4%), along with 246 unique spoligotypes. In the isolates from urban new cases, we found Beijing to be associated with multidrug resistance (MDR) (OR, 3.40; 95% CL, 1.20 to 9.62;
P
= 0.02). CAS was found to be associated with pansensitivity (OR, 1.83; 95% CL, 1.03 to 3.24;
P
= 0.03) and cavities as seen on chest radiographs (OR, 2.72; 95% CL, 1.34 to 5.53;
P
= 0.006). We recorded 239 new spoligotypes yet unreported in the global databases, suggesting that the local TB strains exhibit a high degree of diversity.
Simultaneous Genotyping and Quantification of Hepatitis B Virus for Genotypes B and C by Real-Time PCR Assay
Authors: Zhao Yao , Zhang Xiu-Yu , Guo Jin-Jun , Zeng Ai-Zhong , Hu Jie-Li , Huang Wen-Xiang , Shan You-Lan , Huang Ai-Long 
Published: August 2010

ABSTRACTHepatitis B virus (HBV) is an important cause of human chronic liver diseases and is a major public health problem. Viral load and HBV genotype play critical roles in determining clinical outcomes and response to antiviral treatment in hepatitis B patients. Viral genotype detection and quantification assays are currently in use with different levels of effectiveness. In this study, the performance of a real-time genotyping and quantitative PCR (GQ-PCR)-based assay was evaluated. Through the use of genotype-specific primers and probes, this assay provides simultaneous identification and quantification of genotypes B and C in a single reaction. Our GQ-PCR correctly identified all predefined genotypes B and C, and no cross-reaction between genotypes B and C were observed. The GQ-PCR identified more cases of HBV infections with mixed genotypes B and C than direct sequencing did. Samples from 127 HBV-infected Chinese patients were genotyped with GQ-PCR, revealing 56.7% HBV as genotype B, 13.4% as genotype C, and 29.8% as mixed genotypes B and C. This assay provides a reliable, efficient, and cost-effective means for quantification of the B and C genotypes of HBV in single or mixed infections. This assay is suitable for sequential monitoring of viral load levels and for determining the relationship between the genotype viral load and stage of disease in Asians.
Containment of Bioaerosol Infection Risk by the Xpert MTB/RIF Assay and Its Applicability to Point-of-Care Settings
Authors: Banada Padmapriya P. , Sivasubramani Satheesh K. , Blakemore Robert , Boehme Catharina , Perkins Mark D. , Fennelly Kevin , Alland David 
Published: August 2010

ABSTRACT

The recently introduced Xpert MTB/RIF assay (Xpert) has point-of-care potential, but its capacity for biohazard containment remained to be studied. We compared the bioaerosols generated by the Xpert assay to acid-fast bacillus (AFB) microscope slide smear preparation. The Xpert assay sample treatment reagent (SR) was also studied for its sterilizing capacity, stability, and effect on assay sensitivity after prolonged treatment. During the preparation of AFB smears, sputum samples spiked with
Mycobacterium bovis
BCG at 5 × 10
8
CFU/ml produced 16 and 325 CFU/m
3
air measured with an Andersen impactor or BioSampler, respectively. In contrast, neither the sample preparation steps for the Xpert assay nor its automated processing produced any culturable bioaerosols. In testing of SR sterilizing capacity, clinical sputum samples from strongly smear-positive tuberculosis patients treated with SR at a 2:1 ratio eliminated
Mycobacterium tuberculosis
growth in all but 1/39 or 3/45 samples cultured on solid or liquid medium, respectively. These few unsterilized samples had a mean 13.1-day delay in the time to positive culture. SR treatment at a 3:1 ratio eliminated growth in all samples. SR retained a greater than 6-log-unit killing capacity despite storage at temperatures spanning 4 to 45°C for at least 3 months. The effect of prolonged SR sample treatment was also studied. Spiked sputum samples could be incubated in SR for up to 3 days without affecting Xpert sensitivity for
M. tuberculosis
detection and up to 8 h without affecting specificity for rifampin resistance detection. These results suggest that benchtop use of the Xpert MTB/RIF assay limits infection risk to the user.
Performance of Version 2.0 of the Cobas AmpliPrep/Cobas TaqMan Real-Time PCR Assay for Hepatitis B Virus DNA Quantification
Authors: Chevaliez Stéphane , Bouvier-Alias Magali , Laperche Syria , Hézode Christophe , Pawlotsky Jean-Michel 
Published: August 2010

ABSTRACT

The detection and quantification of hepatitis B virus (HBV) DNA are essential for the diagnosis and treatment of chronic HBV infection. The use of real-time PCR assays for HBV DNA quantification is strongly recommended. The goal of this study was to evaluate the intrinsic characteristics and clinical performance of version 2.0 (v2.0) of the Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) assay, a fully automated platform for HBV DNA quantification in serum or in plasma with a claimed lower limit of detection of 20 IU/ml and a claimed upper limit of quantification of 1.7 × 10
8
IU/ml. The specificity of the assay was 99% (95% confidence interval, 94.7 to 100%). Intra-assay and interassay coefficients of variation ranged from 0.21% to 2.67% and from 0.65% to 2.25%, respectively. The calibration of the assay was found to be satisfactory. Study of blood specimens from patients infected with HBV genotypes A to F showed good correspondence between HBV DNA levels measured by the CAP/CTM v2.0 assay, version 1.0 of the same assay, and the third-generation “branched DNA” assay. The CAP/CTM v2.0 assay quantified HBV DNA levels in serum or plasma from the same patients equally. In conclusion, the new version of the CAP/CTM assay is sensitive, specific, and reproducible. It accurately quantifies HBV DNA levels in patients chronically infected with HBV genotypes A to F. Improvements made to ensure equal quantification of HBV DNA in serum and plasma have been successful. Overall, the CAP/CTM assay, version 2.0, is well suited to monitoring clinical HBV DNA levels according to current clinical practice guidelines.
Polymicrobial Bloodstream Infection with
Eggerthella lenta
and
Desulfovibrio desulfuricans
Authors: Liderot Karin , Larsson Martin , Boräng Stina , Özenci Volkan 
Published: August 2010

ABSTRACT

The advancement in culture identification methods has made possible the culture and identification of slow-growing anaerobic bacteria in clinical samples. Here, we describe a case of polymicrobial bloodstream infection (BSI) caused by
Eggerthella lenta
and
Desulfovibrio desulfuricans
, identified by API 20A and Vitek 2 systems and by 16S rRNA sequencing.
Proteasome Activator REGγ Enhances Coxsackieviral Infection by Facilitating p53 Degradation
Authors: Gao Guang , Wong Jerry , Zhang Jingchun , Mao Ivy , Shravah Jayant , Wu Yan , Xiao Allen , Li Xiaotao , Luo Honglin 
Published: August 2010

ABSTRACT

Coxsackievirus B3 (CVB3) is a small RNA virus associated with diseases such as myocarditis, meningitis, and pancreatitis. We have previously demonstrated that proteasome inhibition reduces CVB3 replication and attenuates virus-induced myocarditis. However, the underlying mechanisms by which the ubiquitin/proteasome system regulates CVB replication remain unclear. In this study, we investigated the role of REGγ, a member of the 11S proteasome activator, in CVB3 replication. We showed that overexpression of REGγ promoted CVB3 replication but that knockdown of REGγ led to reduced CVB3 replication. We further demonstrated that REGγ-mediated p53 proteolysis contributes, as least in part, to the proviral function of REGγ. Although total protein levels of REGγ remained unaltered after CVB3 infection, virus infection induced a redistribution of REGγ from the nucleus to the cytoplasm, rendering an opportunity for a direct interaction of REGγ with viral proteins and/or host proteins (e.g., p53), which controls viral growth and thereby enhances viral infectivity. Further analyses suggested a potential modification of REGγ by SUMO following CVB3 infection, which was verified by both
in vitro
and
in vivo
sumoylation assays. Sumoylation of REGγ may play a role in its nuclear export during CVB3 infection. Taken together, our results present the first evidence that the host REGγ pathway is utilized and modified during CVB3 infection to promote efficient viral replication.
Poxvirus Complement Control Proteins Are Expressed on the Cell Surface through an Intermolecular Disulfide Bridge with the Viral A56 Protein
Authors: DeHaven Brian C. , Girgis Natasha M. , Xiao Yuhong , Hudson Paul N. , Olson Victoria A. , Damon Inger K. , Isaacs Stuart N. 
Published: August 2010

ABSTRACTThe vaccinia virus (VACV) complement control protein (VCP) is an immunomodulatory protein that is both secreted from and expressed on the surface of infected cells. Surface expression of VCP occurs though an interaction with the viral transmembrane protein A56 and is dependent on a free N-terminal cysteine of VCP. Although A56 and VCP have been shown to interact in infected cells, the mechanism remains unclear. To investigate if A56 is sufficient for surface expression, we transiently expressed VCP and A56 in eukaryotic cell lines and found that they interact on the cell surface in the absence of other viral proteins. Since A56 contains three extracellular cysteines, we hypothesized that one of the cysteines may be unpaired and could therefore form a disulfide bridge with VCP. To test this, we generated a series of A56 mutants in which each cysteine was mutated to a serine, and we found that mutation of cysteine 162 abrogated VCP cell surface expression. We also tested the ability of other poxvirus complement control proteins to bind to VACV A56. While the smallpox homolog of VCP is able to bind VACV A56, the ectromelia virus (ECTV) VCP homolog is only able to bind the ECTV homolog of A56, indicating that these proteins may have coevolved. Surface expression of poxvirus complement control proteins may have important implications in viral pathogenesis, as a virus that does not express cell surface VCP is attenuatedin vivo. This suggests that surface expression of VCP may contribute to poxvirus pathogenesis.
Culturing the Unculturable: Human Coronavirus HKU1 Infects, Replicates, and Produces Progeny Virions in Human Ciliated Airway Epithelial Cell Cultures
Authors: Pyrc Krzysztof , Sims Amy C. , Dijkman Ronald , Jebbink Maarten , Long Casey , Deming Damon , Donaldson Eric , Vabret Astrid , Baric Ralph , van der Hoek Lia , Pickles Raymond 
Published: August 2010

ABSTRACT

Culturing newly identified human lung pathogens from clinical sample isolates can represent a daunting task, with problems ranging from low levels of pathogens to the presence of growth suppressive factors in the specimens, compounded by the lack of a suitable tissue culture system. However, it is critical to develop suitable
in vitro
platforms to isolate and characterize the replication kinetics and pathogenesis of recently identified human pathogens. HCoV-HKU1, a human coronavirus identified in a clinical sample from a patient with severe pneumonia, has been a major challenge for successful propagation on all immortalized cells tested to date. To determine if HCoV-HKU1 could replicate in
in vitro
models of human ciliated airway epithelial cell cultures (HAE) that recapitulate the morphology, biochemistry, and physiology of the human airway epithelium, the apical surfaces of HAE were inoculated with a clinical sample of HCoV-HKU1 (Cean1 strain). High virus yields were found for several days postinoculation and electron micrograph, Northern blot, and immunofluorescence data confirmed that HCoV-HKU1 replicated efficiently within ciliated cells, demonstrating that this cell type is infected by all human coronaviruses identified to date. Antiserum directed against human leukocyte antigen C (HLA-C) failed to attenuate HCoV-HKU1 infection and replication in HAE, suggesting that HLA-C is not required for HCoV-HKU1 infection of the human ciliated airway epithelium. We propose that the HAE model provides a ready platform for molecular studies and characterization of HCoV-HKU1 and in general serves as a robust technology for the recovery, amplification, adaptation, and characterization of novel coronaviruses and other respiratory viruses from clinical material.
The C-Terminal α-Helix Domain of Apolipoprotein E Is Required for Interaction with Nonstructural Protein 5A and Assembly of Hepatitis C Virus
Authors: Cun Wei , Jiang Jieyun , Luo Guangxiang 
Published: August 2010

ABSTRACT

We have recently demonstrated that human apolipoprotein E (apoE) is required for the infectivity and assembly of hepatitis C virus (HCV) (K. S. Chang, J. Jiang, Z. Cai, and G. Luo, J. Virol. 81:13783-13793, 2007; J. Jiang and G. Luo, J. Virol. 83:12680-12691, 2009). In the present study, we have determined the molecular basis underlying the importance of apoE in HCV assembly. Results derived from mammalian two-hybrid studies demonstrate a specific interaction between apoE and HCV nonstructural protein 5A (NS5A). The C-terminal third of apoE
per se
is sufficient for interaction with NS5A. Progressive deletion mutagenesis analysis identified that the C-terminal α-helix domain of apoE is important for NS5A binding. The N-terminal receptor-binding domain and the C-terminal 20 amino acids of apoE are dispensable for the apoE-NS5A interaction. The NS5A-binding domain of apoE was mapped to the middle of the C-terminal α-helix domain between amino acids 205 and 280. Likewise, deletion mutations disrupting the apoE-NS5A interaction resulted in blockade of HCV production. These findings demonstrate that the specific apoE-NS5A interaction is required for assembly of infectious HCV. Additionally, we have determined that using different major isoforms of apoE (E2, E3, and E4) made no significant difference in the apoE-NS5A interaction. Likewise, these three major isoforms of apoE are equally compatible with infectivity and assembly of infectious HCV, suggesting that apoE isoforms do not differentially modulate the infectivity and/or assembly of HCV in cell culture.
RNA Structures Required for Production of Subgenomic Flavivirus RNA
Authors: Funk Anneke , Truong Katherine , Nagasaki Tomoko , Torres Shessy , Floden Nadia , Balmori Melian Ezequiel , Edmonds Judy , Dong Hongping , Shi Pei-Yong , Khromykh Alexander A. 
Published: August 2010

ABSTRACT

Flaviviruses are a group of single-stranded, positive-sense RNA viruses causing ∼100 million infections per year. We have recently shown that flaviviruses produce a unique, small, noncoding RNA (∼0.5 kb) derived from the 3′ untranslated region (UTR) of the genomic RNA (gRNA), which is required for flavivirus-induced cytopathicity and pathogenicity (G. P. Pijlman et al., Cell Host Microbe, 4: 579-591, 2008). This RNA (subgenomic flavivirus RNA [sfRNA]) is a product of incomplete degradation of gRNA presumably by the cellular 5′-3′ exoribonuclease XRN1, which stalls on the rigid secondary structure stem-loop II (SL-II) located at the beginning of the 3′ UTR. Mutations or deletions of various secondary structures in the 3′ UTR resulted in the loss of full-length sfRNA (sfRNA1) and production of smaller and less abundant sfRNAs (sfRNA2 and sfRNA3). Here, we investigated in detail the importance of West Nile virus Kunjin (WNV
KUN
) 3′ UTR secondary structures as well as tertiary interactions for sfRNA formation. We show that secondary structures SL-IV and dumbbell 1 (DB1) downstream of SL-II are able to prevent further degradation of gRNA when the SL-II structure is deleted, leading to production of sfRNA2 and sfRNA3, respectively. We also show that a number of pseudoknot (PK) interactions, in particular PK1 stabilizing SL-II and PK3 stabilizing DB1, are required for protection of gRNA from nuclease degradation and production of sfRNA. Our results show that PK interactions play a vital role in the production of nuclease-resistant sfRNA, which is essential for viral cytopathicity in cells and pathogenicity in mice.
Swine Influenza H1N1 Virus Induces Acute Inflammatory Immune Responses in Pig Lungs: a Potential Animal Model for Human H1N1 Influenza Virus
Authors: Khatri Mahesh , Dwivedi Varun , Krakowka Steven , Manickam Cordelia , Ali Ahmed , Wang Leyi , Qin Zhuoming , Renukaradhya Gourapura J. , Lee Chang-Won 
Published: August 2010

ABSTRACTPigs are capable of generating reassortant influenza viruses of pandemic potential, as both the avian and mammalian influenza viruses can infect pig epithelial cells in the respiratory tract. The source of the current influenza pandemic is H1N1 influenza A virus, possibly of swine origin. This study was conducted to understand better the pathogenesis of H1N1 influenza virus and associated host mucosal immune responses during acute infection in humans. Therefore, we chose a H1N1 swine influenza virus, Sw/OH/24366/07 (SwIV), which has a history of transmission to humans. Clinically, inoculated pigs had nasal discharge and fever and shed virus through nasal secretions. Like pandemic H1N1, SwIV also replicated extensively in both the upper and lower respiratory tracts, and lung lesions were typical of H1N1 infection. We detected innate, proinflammatory, Th1, Th2, and Th3 cytokines, as well as SwIV-specific IgA antibody in lungs of the virus-inoculated pigs. Production of IFN-γ by lymphocytes of the tracheobronchial lymph nodes was also detected. Higher frequencies of cytotoxic T lymphocytes, γδ T cells, dendritic cells, activated T cells, and CD4+and CD8+T cells were detected in SwIV-infected pig lungs. Concomitantly, higher frequencies of the immunosuppressive T regulatory cells were also detected in the virus-infected pig lungs. The findings of this study have relevance to pathogenesis of the pandemic H1N1 influenza virus in humans; thus, pigs may serve as a useful animal model to design and test effective mucosal vaccines and therapeutics against influenza virus.