bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lumped Parameter Analysis of an Enclosed Incompressible Squeeze Film and a Central Gas Bubble
Authors: Anderson M. , Richards C. , Richards R. , Bahr D. 
Published: February 2008

Abstract
A lumped-parameter dynamic model for an enclosed incompressible squeeze film with a central gas bubble has been derived. A new approach was applied to derive closed-form expressions for the lumped-parameter mass and damping coefficients caused by liquid motion. It was assumed that plate motions were small and the fluid behaved as a continuum. The values of the lumped-parameter mass and damping were found to depend on the aspect ratio and nondimensional squeeze-film thickness. The nondimensional thickness was given by the ratio of the actual squeeze-film thickness to the viscous penetration depth of the liquid. A nondimensional squeeze-film thickness of a value of 5 was found to divide between categories of thick and thin incompressible squeeze films. Amplification of the liquid mass and damping over and above squeeze films open to the atmosphere at the edges was found. The amplification was attributed to converging flow caused by enclosed boundaries. Comparisons between the lumped-parameter model predictions and finite-element computations showed a surprising degree of accuracy for the lumped-parameter model despite large liquid velocities in the squeeze film.
HLA Class II Haplotypes Distinctly Associated with Vaso-Occlusion in Children with Sickle Cell Disease
Authors: Mahdi Najat , Al-Ola Khadija , Al-Subaie Abeer M. , Ali Muhallab E. , Al-Irhayim Zaid , Al-Irhayim A. Qader , Almawi Wassim Y. 
Published: February 2008

ABSTRACT

We investigated the association of HLA class II alleles and haplotypes with sickle cell anemia vaso-occlusive crisis (VOC).
DRB1*100101
was positively associated, while
DRB1*140101
,
DRB1*150101
, and
DQB1*060101
were negatively associated, with VOC. Both susceptible (
DRB1*100101
-
DQB1*050101
) and protective (
DRB1*110101
-
DQB1*030101
and
DRB1*150101
-
DQB1*060101
) haplotypes were identified, indicating that HLA class II haplotypes influence VOC risk.
Smallpox Virus Resequencing GeneChips Can Also Rapidly Ascertain Species Status for Some Zoonotic Non-
Variola
Orthopoxviruses
Authors: Sulaiman Irshad M. , Sammons Scott A. , Wohlhueter Robert M. 
Published: February 2008

ABSTRACT

We recently developed a set of seven resequencing GeneChips for the rapid sequencing of
Variola
virus strains in the WHO Repository of the Centers for Disease Control and Prevention. In this study, we attempted to hybridize these GeneChips with some known non-
Variola
orthopoxvirus isolates, including monkeypox, cowpox, and vaccinia viruses, for rapid detection.
Variation of a Newcastle Disease Virus Hemagglutinin-Neuraminidase Linear Epitope
Authors: Cho Sun-Hee , Kwon Hyuk-Joon , Kim Tae-Eun , Kim Jae-Hong , Yoo Han-Sang , Kim Sun-Joong 
Published: February 2008

ABSTRACT
Fifty-six Newcastle disease virus strains collected from 2000 to 2006 could be grouped into subgenotype VIId. However, they displayed cumulative mutations in and around the linear epitope of hemagglutinin-neuraminidase (residues 345 to 353) with time. The antigenicities of the variants that became predominant in Korea differ from each other and from the wild type.
Salmonella enterica
Serovar Senftenberg Human Clinical Isolates Lacking SPI-1
Authors: Hu Qinghua , Coburn Bryan , Deng Wanyin , Li Yuling , Shi Xiaolu , Lan Quanxue , Wang Bing , Coombes Brian K. , Finlay B. Brett 
Published: February 2008

ABSTRACT

Nontyphoidal
Salmonella
species cause gastrointestinal disease worldwide. The prevailing theory of
Salmonella
enteropathogenesis is that bacterial invasion of the intestinal epithelium is essential for virulence and that this requires the virulence-associated genomic region
Salmonella
pathogenicity island 1 (SPI-1). Recent studies of
Salmonella enterica
infection models have demonstrated that enterocolitis and diarrhea in mice and cows can occur independently of SPI-1. In this study, we sought to confirm whether two
S. enterica
serovar Senftenberg clinical isolates lacked genes essential for SPI-1 function. Two clinical strains were isolated and identified as being
S. enterica
serovar Senftenberg from four stool samples from a food-borne disease outbreak affecting seven individuals in Shenzhen, Guangdong Province, China, using conventional methods, pulsed-field gel electrophoresis and multilocus sequence typing. The possibility of coinfection with other potential bacteria or usual viruses was excluded. Two isolates were analyzed for the presence of
invA
,
sipA
,
ssaR
,
sifA
, and
sopE2
by PCR and Southern blotting and were then assayed for the presence of SPI-1 by PCR and long-range PCR for
fhlA-hilA
,
hilA-spaP
, and
spaP-invH
and Southern blot analysis. A long-range PCR fragment from
fhlA
to
mutS
covering the 5′ and 3′ flanks of SPI-1 was also amplified from the two clinical isolates and sequenced. In addition, the two clinical isolates were assayed for enteroinvasiveness in vitro. Murine infection models were also examined. Biochemical tests and serotyping confirmed that the two clinical isolates are
S. enterica
serovar Senftenberg. However, they lacked genes critical for SPI-1 function but contained SPI-2 genes and were attenuated for the invasion of cultured intestinal epithelial cells. In conclusion, clinical
S. enterica
serovar Senftenberg strains isolated from a food-borne disease outbreak lack the invasion-associated locus SPI-1, indicating that SPI-1 is not essential for human gastroenteritis.
Detection of Cytomegalovirus (CMV) DNA in EDTA Whole-Blood Samples: Evaluation of the Quantitative
artus
CMV LightCycler PCR Kit in Conjunction with Automated Sample Preparation
Authors: Michelin Birgit D. A. , Hadžisejdić Ita , Bozic Michael , Grahovac Maja , Hess Markus , Grahovac Blaženka , Marth Egon , Kessler Harald H. 
Published: February 2008

ABSTRACT

Whole blood has been found to be a reliable matrix for the detection and quantitation of cytomegalovirus (CMV) DNA. In this study, the performance of the
artus
CMV LightCycler (LC) PCR kit in conjunction with automated sample preparation on a BioRobot EZ1 workstation was evaluated. The accuracy, linearity, analytical sensitivity, and inter- and intra-assay variations were determined. A total of 102 clinical EDTA whole-blood samples were investigated, and results were compared with those obtained with the in vitro diagnostics (IVD)/Conformité Européene (CE)-labeled CMV HHV6,7,8 R-gene quantification kit. When the accuracy of the new kit was tested, seven of eight results were found to be within ±0.5 log
10
unit of the expected panel results. Determination of linearity resulted in a quasilinear curve over more than 5 log units. The lower limit of detection of the assay was determined to be 139 copies/ml in EDTA whole blood. The interassay variation ranged from 15 to 58%, and the intra-assay variation ranged from 7 to 35%. When clinical samples were tested and the results were compared with those of the routinely used IVD/CE-labeled assay, 53 samples tested positive and 13 samples tested negative by both of the assays. One sample was found to be positive with the
artus
CMV LC PCR kit only, and 35 samples tested positive with the routinely used assay only. The majority of discrepant results were found with low-titer samples. In conclusion, use of the
artus
CMV LC PCR kit in conjunction with automated sample preparation on the BioRobot EZ1 workstation may be suitable for the detection and quantitation of CMV DNA in EDTA whole blood in the routine low-throughput laboratory; however, low-positive results may be missed by this assay.
Clinical Evaluation of NucliSENS Magnetic Extraction and NucliSENS Analyte-Specific Reagents for Real-Time Detection of Human Metapneumovirus in Pediatric Respiratory Specimens
Authors: Ginocchio Christine C. , Manji Ryhana , Lotlikar Madhavi , Zhang Fan 
Published: February 2008

ABSTRACT

In this study, we evaluated the NucliSENS miniMAG (MM) and easyMAG (EM) nucleic acid extraction platforms (bioMérieux, Durham, NC) in combination with the NucliSENS EasyQ basic kit and analyte-specific reagents (ASRs) (bioMérieux) for the detection of human metapneumovirus (hMPV) in respiratory samples. Total nucleic acids from pediatric clinical samples (
n
= 653) and an hMPV-specific inhibition control (h-IC) were coextracted using the MM and/or the EM. Nucleic acid sequence-based amplification and real-time molecular beacon detection of hMPV were performed using a NucliSENS EasyQ analyzer (bioMérieux). Positive results were confirmed using an in-house-validated reverse transcriptase PCR ASR-based assay. The inclusion of the h-IC monitored the entire process, including the efficiency of nucleic acid extraction, amplification, and detection. The percentages of samples with inhibited amplification of the h-IC after initial NA extraction by EM and MM were 1.88% and 3.17%, respectively. After reprocessing of a new aliquot, the final h-IC inhibition rates were 0% (EM) and 1.06% (MM). The limit of detection of the assay was between 2 (EM extraction) and 10 (MM extraction) RNA copies/reaction, and specificity was 100% when testing viral respiratory isolates and clinical samples. hMPV was detected in 5.6% of pediatric samples tested and was also detected in three coinfections with respiratory syncytial virus (RSV). hMPV was the second most frequently detected respiratory virus in children of 0 to 2 years of age, after RSV. In summary, NucliSENS extraction and ASRs provided a sensitive and specific method for the detection of hMPV in respiratory samples.
Validation of the BrockTB Stat-Pak Assay for Detection of Tuberculosis in Eurasian Badgers (
Meles meles
) and Influence of Disease Severity on Diagnostic Accuracy
Authors: Chambers Mark A. , Crawshaw Tim , Waterhouse Sue , Delahay Richard , Hewinson R. Glyn , Lyashchenko Konstantin P. 
Published: February 2008

ABSTRACT

A lateral-flow immunoassay (BrockTB Stat-Pak) for detecting tuberculosis in Eurasian badgers was 49% sensitive and 93% specific against culture for
M. bovis
(
n
= 1,464) at necropsy. However, the sensitivity was significantly higher (66 to 78%) in animals with more severe tuberculosis, indicating that the BrockTB Stat-Pak may be useful for the detection of badgers with the greatest risk of transmitting disease.
High-Resolution Genotyping of
Campylobacter
Species by Use of PCR and High-Throughput Mass Spectrometry
Authors: Hannis James C. , Manalili Sheri M. , Hall Thomas A. , Ranken Raymond , White Neill , Sampath Rangarajan , Blyn Lawrence B. , Ecker David J. , Mandrell Robert E. , Fagerquist Clifton K. , Bates Anna H. , Miller William G. , Hofstadler Steven A. 
Published: February 2008

ABSTRACT

In this work we report on a high-throughput mass spectrometry-based technique for the rapid high-resolution identification of
Campylobacter jejuni
strain types. This method readily distinguishes
C. jejuni
from
C. coli
, has a resolving power comparable to that of multilocus sequence typing (MLST), is applicable to mixtures, and is highly automated. The strain typing approach is based on high-performance mass spectrometry, which “weighs” PCR amplicons with enough mass accuracy to unambiguously determine the base composition of each amplicon (i.e., the numbers of A's, G's, C's, and T's). Amplicons are derived from PCR primers which amplify short (<140-bp) regions of the housekeeping genes used by conventional MLST strategies. The results obtained with a challenge panel that comprised 25 strain types of
C. jejuni
and 25 strain types of
C. coli
are presented. These samples were parsed and resolved with demonstrated sensitivity down to 10 genomes/PCR from pure isolates.
New Immuno-PCR Assay for Detection of Low Concentrations of Shiga Toxin 2 and Its Variants
Authors: Zhang Wenlan , Bielaszewska Martina , Pulz Matthias , Becker Karsten , Friedrich Alexander W. , Karch Helge , Kuczius Thorsten 
Published: February 2008

ABSTRACT

Shiga toxin (Stx)-producing
Escherichia coli
(STEC) strains secrete toxins that are major virulence factors and diagnostic targets, but some STEC strains secrete Stx in amounts that cannot be detected using conventional cell cytotoxicity or immunological assays. Therefore, there is an urgent need for more-sensitive Stx detection methods. We describe the development of an assay that can detect low concentrations of Stx2 and its variants. An immuno-PCR Stx2 assay was developed based on an enzyme immunoassay (EIA) combining antibody capture and DNA amplification to increase the signal. The immuno-PCR assay detected 10 pg/ml of purified Stx2, compared to 1 ng/ml Stx2 detected by commercial EIA. Consequently, immuno-PCR detected Stx2 and its variants in STEC strains that produce the toxins at levels that are nondetectable by using the EIA, as well as the Stx2 in EIA-negative enriched stool cultures from patients. Our data demonstrate that the immuno-PCR developed here is a highly sensitive and specific method for the detection of trace amounts of Stx2 and Stx2 variants. It is therefore suitable for use by clinical microbiological laboratories to improve the toxin detection in clinical samples.
Emergence of G12 Rotavirus Strains in Delhi, India, in 2000 to 2007
Authors: Sharma S. , Ray P. , Gentsch J. R. , Glass R. I. , Kalra V. , Bhan M. K. 
Published: February 2008

ABSTRACT
The prospect that rotavirus diarrhea in children may soon be prevented by vaccines has placed a new priority on understanding the diversity of rotavirus strains and the mechanism by which these strains evolve over time. We have characterized a total of 465 rotavirus strains collected in North India from 2000 to 2007 for G and P types by reverse transcription-PCR and sequencing. The novel G12 rotavirus strains recently detected in other countries were first detected in India in 2001 and have emerged as the predominant strains in Delhi, India, during 2005 to 2007. While the VP7 sequence was highly homologous among G12 strains isolated in Delhi, suggesting recent emergence from a common ancestor, the strains had a diverse constellation of other gene segments, demonstrating substantial reassortment. For the entire period, the common rotavirus G types G1 (26%), G2 (25%), and G9 (14%) comprised 65% of the strains, and common P types, P[4] (19%), P[6] (22%), and P[8] (35%), comprised 76% of the total P types. Of note, we detected a high percentage of unusual (17%) strains and fecal specimens with mixed (12% G and 15% P) rotavirus infections having a variety of genomic constellations. For the first time, we identified two novel rotavirus strains with unusual G/P combinations, G2P[11] and G3P[11], in patients with diarrhea. The study highlights the great diversity among rotaviruses isolated from Indian children, the opportunity for genetic reassortment between strains, and the emergence of a novel G12 strain in our country. Due to the demonstrated effect of antigenic diversity on rotavirus vaccines, it will be important to continue careful monitoring of these strains as rotavirus vaccine programs are implemented in India.
Vaccine Protection by Live, Attenuated Simian Immunodeficiency Virus in the Absence of High-Titer Antibody Responses and High-Frequency Cellular Immune Responses Measurable in the Periphery
Authors: Mansfield Keith , Lang Sabine M. , Gauduin Marie-Claire , Sanford Hannah B. , Lifson Jeffrey D. , Johnson R. Paul , Desrosiers Ronald C. 
Published: February 2008

ABSTRACT

An attenuated derivative of simian immunodeficiency virus strain 239 deleted of V1-V2 sequences in the envelope gene (SIV239ΔV1-V2) was used for vaccine/challenge experiments in rhesus monkeys. Peak levels of viral RNA in plasma of 10
4
to 10
6.5
copies/ml in the weeks immediately following inoculation of SIV239ΔV1-V2 were 10- to 1,000-fold lower than those observed with parental SIV239 (∼10
7.3
copies/ml). Viral loads consistently remained below 200 copies/ml after 8 weeks of infection by the attenuated SIV239ΔV1-V2 strain. Viral localization experiments revealed large numbers of infected cells within organized lymphoid nodules of the colonic gut-associated lymphoid tissue at 14 days; double-labeling experiments indicated that 93.5% of the virally infected cells at this site were positive for the macrophage marker CD68. Cellular and humoral immune responses measured principally by gamma interferon enzyme-linked immunospot and neutralization assays were variable in the five vaccinated monkeys. One monkey had responses in these assays comparable to or only slightly less than those observed in monkeys infected with parental, wild-type SIV239. Four of the vaccinated monkeys, however, had low, marginal, or undetectable responses in these same assays. These five vaccinated monkeys and three naïve control monkeys were subsequently challenged intravenously with wild-type SIV239. Three of the five vaccinated monkeys, including the one with strong anti-SIV immune responses, were strongly protected against the challenge on the basis of viral load measurements. Surprisingly, two of the vaccinated monkeys were strongly protected against SIV239 challenge despite the presence of cellular anti-SIV responses of low-frequency and low-titer anti-SIV antibody responses. These results indicate that high-titer anti-SIV antibody responses and high-frequency anti-SIV cellular immune responses measurable by standard assays from the peripheral blood are not needed to achieve strong vaccine protection, even against a difficult, neutralization-resistant strain such as SIV239.
Standardized and Highly Efficient Expansion of Epstein-Barr Virus-Specific CD4
+
T Cells by Using Virus-Like Particles
Authors: Adhikary Dinesh , Behrends Uta , Feederle Regina , Delecluse Henri-Jacques , Mautner Josef 
Published: February 2008

ABSTRACT

Epstein-Barr virus (EBV)-specific T-cell lines generated by repeated stimulation with EBV-immortalized lymphoblastoid B-cell lines (LCL) have been successfully used to treat EBV-associated posttransplant lymphoproliferative disease (PTLD) in hematopoietic stem cell transplant recipients. However, PTLD in solid-organ transplant recipients and other EBV-associated malignancies respond less efficiently to this adoptive T-cell therapy. LCL-stimulated T-cell preparations are polyclonal and contain CD4
+
and CD8
+
T cells, but the composition varies greatly between lines. Because T-cell lines with higher CD4
+
T-cell proportions show improved clinical efficacy, we assessed which factors might compromise the expansion of this T-cell population. Here we show that spontaneous virus production by LCL and, hence, the presentation of viral antigens varies intra- and interindividually and is further impaired by acyclovir treatment of LCL. Moreover, the stimulation of T cells with LCL grown in medium supplemented with fetal calf serum (FCS) caused the expansion of FCS-reactive CD4
+
T cells, whereas human serum from EBV-seropositive donors diminished viral antigen presentation. To overcome these limitations, we used peripheral blood mononuclear cells pulsed with nontransforming virus-like particles as antigen-presenting cells. This strategy facilitated the specific and rapid expansion of EBV-specific CD4
+
T cells and, thus, might contribute to the development of standardized protocols for the generation of T-cell lines with improved clinical efficacy.
Human APOBEC3G Can Restrict Retroviral Infection in Avian Cells and Acts Independently of both UNG and SMUG1
Authors: Langlois Marc-André , Neuberger Michael S. 
Published: February 2008

ABSTRACT
APOBEC3 proteins are mammal-specific cytidine deaminases that can restrict retroviral infection. The exact mechanism of the restriction remains unresolved, but one model envisions that uracilated retroviral cDNA, generated by cytidine deamination, is the target of cellular glycosylases. While restriction is unaffected by UNG deficiency, it has been suggested that the SMUG1 glycosylase might provide a backup. We found that retroviral restriction can be achieved by introducing human APOBEC3G into chicken cells (consistent with the components necessary for APOBEC3-mediated restriction predating mammalian evolution) and used this assay to show that APOBEC3G-mediated restriction can occur in cells deficient in both UNG and SMUG1.
Role of Dendritic Cells in Antibody-Dependent Enhancement of Dengue Virus Infection
Authors: Boonnak Kobporn , Slike Bonnie M. , Burgess Timothy H. , Mason Randall M. , Wu Shuenn-Jue , Sun Peifang , Porter Kevin , Rudiman Irani Fianza , Yuwono Djoko , Puthavathana Pilaipan , Marovich Mary A. 
Published: February 2008

ABSTRACTDengue viruses (DV), composed of four distinct serotypes (DV1 to DV4), cause 50 to 100 million infections annually. Durable homotypic immunity follows infection but may predispose to severe subsequent heterotypic infections, a risk conferred in part by the immune response itself. Antibody-dependent enhancement (ADE), a process best described in vitro, is epidemiologically linked to complicated DV infections, especially in Southeast Asia. Here we report for the first time the ADE phenomenon in primary human dendritic cells (DC), early targets of DV infection, and human cell lines bearing Fc receptors. We show that ADE is inversely correlated with surface expression of DC-SIGN (DC-specificintercellular adhesion molecule-3-grabbingnonintegrin) and requires Fc gamma receptor IIa (FcγRIIa). Mature DC exhibited ADE, whereas immature DC, expressing higher levels of DC-SIGN and similar FcγRIIa levels, did not undergo ADE. ADE results in increased intracellular de novo DV protein synthesis, increased viral RNA production and release, and increased infectivity of the supernatants in mature DC. Interestingly, tumor necrosis factor alpha and interleukin-6 (IL-6), but not IL-10 and gamma interferon, were released in the presence of dengue patient sera but generally only at enhancement titers, suggesting a signaling component of ADE. FcγRIIa inhibition with monoclonal antibodies abrogated ADE and associated downstream consequences. DV versatility in entry routes (FcγRIIa or DC-SIGN) in mature DC broadens target options and suggests additional ways for DC to contribute to the pathogenesis of severe DV infection. Studying the cellular targets of DV infection and their susceptibility to ADE will aid our understanding of complex disease and contribute to the field of vaccine development.
A Bispecific Antibody Composed of a Nonneutralizing Antibody to the gp41 Immunodominant Region and an Anti-CD89 Antibody Directs Broad Human Immunodeficiency Virus Destruction by Neutrophils
Authors: Duval Mark , Posner Marshall R. , Cavacini Lisa A. 
Published: February 2008

ABSTRACTIn addition to the direct neutralization of virus, there is a broader potential for antibody-mediated inhibition of human immunodeficiency virus (HIV) by targeting HIV to effector cells. We demonstrate here that a bispecific antibody incorporating a broadly reactive anti-gp41 antibody, F240, and an anti-IgA receptor (CD89) antibody is effective at directing neutrophils to destroy HIV. Not only are neutrophils the predominant type of white blood cells and very efficient at mediating cell cytotoxicity, they are relatively resistant to infection with HIV. Therefore, they represent a significant weapon against infection if they can be directed and armed to destroy HIV and infected cells.