bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Specificity of Pneumococcal Polysaccharide Enzyme-Linked Immunosorbent Assay and the Effect of Serum Adsorption Based on Standard Pneumococcal Serogroup- or Serotype-Specific Rabbit Antisera
Authors: Slotved Hans-Christian , Guttmann Christina , Pedersen Charlotte Demuth , Jacobsen Jasper Neergaard , Krogfelt Karen Angeliki 
Published: July 2009

ABSTRACT

Worldwide,
Streptococcus pneumoniae
(pneumococcus) is a major cause of morbidity and mortality, especially in infants and elderly people. Pneumococcal capsular polysaccharides are well characterized, and more than 90 different serotypes have been identified. Serotype-specific antibodies against the capsular polysaccharide are produced during infection. Detection of antibodies against pneumococci by enzyme-linked immunosorbent assay (ELISA) is performed according to WHO guidelines, using antigens provided by ATCC. However, testing the ELISA for specificity is challenging due to the difficulty in obtaining human naïve serum with pneumococcal antibodies as well as human serum with antibodies against a single serotype. The application of well-defined serotype-specific sera produced in animals to evaluate the specificity of the ATCC antigens and the effect of adsorption with cell wall and 22F polysaccharides has not been performed before, to our knowledge. In this study, the specificity of ATCC antigens (serotypes 4, 6B, 9V, 14, 18C, 19F, and 23F) was tested by using commercial serotype-, serogroup-, and pool-specific pneumococcal rabbit antisera.
Assessment ofMycobacterium tuberculosisOmpATb as a Novel Antigen for the Diagnosis of Bovine Tuberculosis
Authors: Schiller Irene , Vordermeier H. Martin , Waters W. Ray , Palmer Mitchell , Thacker Tyler , Whelan Adam , Hardegger Roland , Marg-Haufe Beatrice , Raeber Alex , Oesch Bruno 
Published: July 2009

ABSTRACTIn the search for better tools to control bovine tuberculosis, the development of diagnostic tests with improved specificity and sensitivity has a high priority. We chose to search for novel immunodiagnostic reagents. In this study, Rv0899 (outer membrane protein A ofMycobacterium tuberculosis[OmpATb]) was evaluated as a stimulation antigen in a gamma interferon (IFN-γ) release assay to diagnose bovine tuberculosis. OmpATb induced IFN-γ responses in cattle experimentally infected withM. bovisas early and as persistently as ESAT-6 and CFP-10, the current lead diagnostic antigens. In naturally infected cattle, OmpATb stimulated IFN-γ production in 22 of 26 animals (85%). Importantly, OmpATb detected a portion ofM. bovis-infected cattle which did not respond to ESAT-6 and CFP-10 (five of six cattle). The combined diagnostic sensitivity of OmpATb, ESAT-6, and CFP-10 for a preselected group consisting of naturally infected cattle with an overrepresentation of ESAT-6/CFP-10 nonresponders was 96% (25 of 26 animals). The specificity of OmpATb for uninfected cattle was 100% (27 cattle were tested; 12 of them gave false-positive results with tuberculins). In summary, our results indicate that OmpATb has the potential to enhance the sensitivity of previously described diagnostic tests based on ESAT-6 and CFP-10 and that the combined use of OmpATb, ESAT-6, CFP-10, and other proteins may achieve at least equal sensitivity to that obtained with purified protein derivative, but at a higher specificity. Further studies evaluating the diagnostic performance of OmpATb in combination with other proteins are ongoing.
Vesicular Stomatitis Virus Induces Apoptosis Primarily through Bak Rather than Bax by Inactivating Mcl-1 and Bcl-X
L
Authors: Pearce Alicia F. , Lyles Douglas S. 
Published: July 2009

ABSTRACT

Vesicular stomatitis virus (VSV) induces apoptosis via the mitochondrial pathway. The mitochondrial pathway is regulated by the Bcl-2 family of proteins, which consists of both pro- and antiapoptotic members. To determine the relative importance of the multidomain proapoptotic Bcl-2 family members Bak and Bax, HeLa cells were transfected with Bak and/or Bax small interfering RNA (siRNA) and subsequently infected with recombinant wild-type VSV. Our results showed that Bak is more important than Bax for the induction of apoptosis in this system. Bak is regulated by two antiapoptotic Bcl-2 proteins, Mcl-1, which is rapidly turned over, and Bcl-X
L
, which is relatively stable. Inhibition of host gene expression by the VSV M protein resulted in the degradation of Mcl-1 but not Bcl-X
L
. However, inactivation of both Mcl-1 and Bcl-X
L
was required for cells to undergo apoptosis. While inactivation of Mcl-1 was due to inhibition of its expression, inactivation of Bcl-X
L
indicates a role for one or more BH3-only Bcl-2 family members. VSV-induced apoptosis was inhibited by transfection with siRNA against Bid, a BH3-only protein that is normally activated by the cleavage of caspase-8, the initiator caspase associated with the death receptor pathway. Similarly, treatment with an inhibitor of caspase-8 inhibited VSV-induced apoptosis. These results indicate a role for cross talk from the death receptor pathway in the activation of the mitochondrial pathway by VSV.
The Linear Plasmid Prophage Vp58.5 of
Vibrio parahaemolyticus
Is Closely Related to the Integrating Phage VHML and Constitutes a New Incompatibility Group of Telomere Phages
Authors: Zabala Beatriz , Hammerl Jens A. , Espejo Romilio T. , Hertwig Stefan 
Published: July 2009

ABSTRACT

Vibrio parahaemolyticus
O3:K6 pandemic strains recovered in Chile frequently possess a 42-kb plasmid which is the prophage of a myovirus. We studied the prototype phage VP58.5 and show that it does not integrate into the host cell chromosome but replicates as a linear plasmid (Vp58.5) with covalently closed ends (telomeres). The Vp58.5 replicon coexists with other plasmid prophages (N15, PY54, and ΦKO2) in the same cell and thus belongs to a new incompatibility group of telomere phages. We determined the complete nucleotide sequence (42,612 nucleotides) of the VP58.5 phage DNA and compared it with that of the plasmid prophage. The two molecules share the same nucleotide sequence but are 35% circularly permuted to each other. In contrast to the hairpin ends of the plasmid, VP58.5 phage DNA contains 5′-protruding ends. The VP58.5 sequence is 92% identical to the sequence of phage VHML, which was reported to integrate into the host chromosome. However, the gene order and termini of the phage DNAs are different. The VHML genome exhibits the same gene order as does the Vp58.5 plasmid. VHML phage DNA has been reported to contain terminal inverted repeats. This repetitive sequence is similar to the telomere resolution site (
telRL
) of VP58.5 which, after processing by the phage protelomerase, forms the hairpin ends of the Vp58.5 prophage. It is discussed why these closely related phages may be so different in terms of their genome ends and their lifestyle.
A 49-Kilodalton Isoform of the Adenovirus Type 5 Early Region 1B 55-Kilodalton Protein Is Sufficient To Support Virus Replication
Authors: Kindsmüller Kathrin , Schreiner Sabrina , Leinenkugel Florian , Groitl Peter , Kremmer Elisabeth , Dobner Thomas 
Published: July 2009

ABSTRACT

The adenovirus type 5 (Ad5) early region 1B 55-kDa (E1B-55K) protein is a multifunctional regulator of cell-cycle-independent virus replication that participates in many processes required for maximal virus production. As part of a study of E1B-55K function, we generated the Ad5 mutant H5
pm
4133, carrying stop codons after the second and seventh codons of the E1B reading frame, thereby eliminating synthesis of the full-length 55K product and its smaller derivatives. Unexpectedly, phenotypic studies revealed that H5
pm
4133 fully exhibits the characteristics of wild-type (wt) Ad5 in all assays tested. Immunoblot analyses demonstrated that H5
pm
4133 and wt Ad5 produce very low levels of two distinct polypeptides in the 48- to 49-kDa range, which lack the amino-terminal region but contain segments from the central and carboxy-terminal part of the 55K protein. Genetic and biochemical studies with different Ad5 mutants show that at least one of these isoforms consists of two closely migrating polypeptides of 433 amino acid residues (433R) and 422R, which are produced by translation initiation at two downstream AUG codons of the 55K reading frame. Significantly, a virus mutant producing low levels of the 433R isoform alone replicated to levels comparable to those of wt Ad5, demonstrating that this polypeptide provides essentially all functions of E1B-55K required to promote maximal virus growth in human tumor cells. Altogether, these results extend previous findings that the wt Ad5 E1B region encodes a series of smaller isoforms of E1B-55K and demonstrate that very low levels of at least one of these novel proteins (E1B-433R) are sufficient for a productive infection.
A One-Plasmid System To Generate Influenza Virus in Cultured Chicken Cells for Potential Use in Influenza Vaccine
Authors: Zhang Xiangmin , Kong Wei , Ashraf Shamaila , Curtiss Roy 
Published: July 2009

ABSTRACT
Influenza virus has a set of ribonucleoproteins (RNPs) consisting of viral RNAs, influenza virus polymerase subunits, and nucleoprotein. Intracellular reconstitution of the whole set of RNPs via plasmid transfection results in the generation of influenza virus. By the use of reverse genetics and dual promoters, we constructed a 23.6-kb eight-unit plasmid that contains all the required constituents to generate influenza virus in chicken cells. Our “one-plasmid” system generated higher titers of influenza virus in chicken cells than the “eight-plasmid” system, enabling a simpler approach for generating vaccine seeds. Our study identified plasmid size as a potential limiting factor affecting transfection efficiency and hence the influenza viral yield from chicken cells.
Dynamic Host Energetics and Cytoskeletal Proteomes in Human Immunodeficiency Virus Type 1-Infected Human Primary CD4 Cells: Analysis by Multiplexed Label-Free Mass Spectrometry
Authors: Chan Eric Y. , Sutton Jennifer N. , Jacobs Jon M. , Bondarenko Andrey , Smith Richard D. , Katze Michael G. 
Published: July 2009

ABSTRACTWe report on a proteomic analysis of ex vivo human immunodeficiency virus (HIV) type 1 infection in human primary CD4 cells by shotgun liquid chromatography-tandem mass spectrometry analysis, revealing two distinct proteomic profiles at two phases of virus replication. Relative to mock-infected cells, 168 signature proteins exhibited abundance changes at the first sign of Gag p24 production (8 h postinfection [p.i.]) or the peak of virus replication (24 h p.i.); interestingly, most of the changes were exclusive to only one phase of virus replication. Based on characterization by functional ontology and known human-HIV protein interactions, we observed the enrichment for protein abundance increases pertaining to protein synthesis and nucleasomal reorganization amid an otherwise placid cellular proteome at the first sign of HIV replication. In contrast, we observed indications of decreased protein turnover, concomitant with heightened DNA repair activities and preludes to apoptosis, in the presence of robust virus replication. We also observed hints of disruptions in protein and small molecule trafficking. Our label-free proteomic strategy allowed us to perform multiplexed comparisons—we buttressed our detection specificity with the use of a reverse transcriptase inhibitor as a counterscreen, enabling highlighting of cellular protein abundance changes unique to robust virus replication as opposed to viral entry. In conjunction with complementary high-throughput screens for cellular partners of HIV, we put forth a model pinpointing specific rerouting of cellular biosynthetic, energetic, and trafficking pathways as HIV replication accelerates in human primary CD4 cells.
Defining APOBEC3 Expression Patterns in Human Tissues and Hematopoietic Cell Subsets
Authors: Koning Fransje A. , Newman Edmund N. C. , Kim Eun-Young , Kunstman Kevin J. , Wolinsky Steven M. , Malim Michael H. 
Published: July 2009

ABSTRACT

Human APOBEC3 enzymes are cellular DNA cytidine deaminases that inhibit and/or mutate a variety of retroviruses, retrotransposons, and DNA viruses. Here, we report a detailed examination of human
APOBEC3
gene expression, focusing on APOBEC3G (A3G) and APOBEC3F (A3F), which are potent inhibitors of human immunodeficiency virus type 1 (HIV-1) infection but are suppressed by HIV-1 Vif. A3G and A3F are expressed widely in hematopoietic cell populations, including T cells, B cells, and myeloid cells, as well as in tissues where mRNA levels broadly correlate with the lymphoid cell content (gonadal tissues are exceptions). By measuring mRNA copy numbers, we find that
A3G
mRNA is ∼10-fold more abundant than
A3F
mRNA, implying that A3G is the more significant anti-HIV-1 factor in vivo.
A3G
and
A3F
levels also vary between donors, and these differences are sustained over 12 months. Responses to T-cell activation or cytokines reveal that
A3G
and
A3F
mRNA levels are induced ∼10-fold in macrophages and dendritic cells (DCs) by alpha interferon (IFN-α) and ∼4-fold in naïve CD4
+
T cells. However, immunoblotting revealed that A3G protein levels are induced by IFN-α in macrophages and DCs but not in T cells. In contrast, T-cell activation and IFN-γ had a minimal impact on
A3G
or
A3F
expression. Finally, we noted that
A3A
mRNA expression and protein expression are exquisitely sensitive to IFN-α induction in CD4
+
T cells, macrophages, and DCs but not to T-cell activation or other cytokines. Given that A3A does not affect HIV-1 infection, these observations imply that this protein may participate in early antiviral innate immune responses.
Chapter 12 Two-Photon Physics
Authors: Bian Jian-Ming , Bytev Vladimir , Chen Ying , Jin Hong-Ying , Jin Shan , Qin Hu , Shen Xiao-Yan , Wu Ning , Xu Guo-Fa , Zhang Zhen-Xia , Zhao Qiang , Zhemchugov Alexey , Zheng Han-Qing , Zhu Shi-Lin , Zou Bing-Song 
Published: July 2009

The following sections are included: Introduction Experimental Status of Two-Photon Processes Measurement of Two-Photon Processes at BES-III Summary
The Impact of Type 2 Diabetes on the Development of Hepatocellular Carcinoma in Different Viral Hepatitis Statuses
Authors: Wang Chong-Shan , Yao Wei-Jen , Chang Ting-Tsung , Wang Shan-Tair , Chou Pesus 
Published: July 2009

Abstract
Background: The risk of type 2 diabetes on the development of hepatocellular carcinoma remains inconclusive in different hepatitis statuses.
Methods: We prospectively followed a community-based cohort with 5,929 persons in southern Taiwan from January 1997 through December 2004, made up of 4,117 seronegative, 982 anti–hepatitis C virus–positive [HCV(+)], 696 hepatitis B surface antigen–positive [HBsAg(+)], and 134 coinfected persons. Before the study, 546 participants had developed diabetes. Hepatocellular carcinoma diagnoses were from the National Cancer Registry.
Results: After 50,899 person-years of follow-up, 111 individuals had developed hepatocellular carcinoma. The highest risk of hepatocellular carcinoma, compared with seronegative individuals without diabetes, was in anti-HCV(+) individuals with diabetes [incidence rate ratio (IRR), 76.0], then coinfected (IRR, 46.0), anti-HCV(+) without diabetes (IRR, 26.1), HBsAg(+) with diabetes (IRR, 21.4), and seronegative with diabetes (IRR, 7.2; P &lt; 0.001). Anti-HCV(+) (n = 132) and seronegative individuals (n = 352) with diabetes had a higher cumulative incidence rate of hepatocellular carcinoma than those without diabetes (log-rank test, P &lt; 0.001). Multivariate Cox proportional hazards analysis showed that gender, age, body mass index ≥30, HBsAg(+) [hazards ratio (HR), 12.6], anti-HCV(+) (HR, 18.8), coinfection (HR, 25.9), and diabetes [HR, 2.7; 95% confidence interval (95% CI), 1.7-4.3] were independent predictors of hepatocellular carcinoma (P &lt; 0.05). After stratifying hepatitis status in multivariate Cox analysis, diabetes was significant for seronegative (HR, 5.4; 95% CI, 1.7-17.1) and anti-HCV(+) individuals (HR, 3.1; 95% CI, 1.7-5.4). Body mass index ≥30 was significant for HBsAg(+) individuals (HR, 3.3; 95% CI, 1.3-8.1).
Conclusion: Type 2 diabetes is a strong independent predictor of hepatocellular carcinoma in anti-HCV(+) and seronegative individuals but not in HBsAg(+) individuals. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2054–60)
Screening for HIV-Associated Anal Cancer: Correlation of HPV Genotypes, p16, and E6 Transcripts with Anal Pathology
Authors: Salit Irving E. , Tinmouth Jill , Chong Sylvia , Raboud Janet , Diong Christina , Su DeSheng , Sano Marie , Lytwyn Alice , Chapman William , Mahony James 
Published: July 2009

AbstractBackground: HIV-positive men with a history of anal-receptive intercourse are at risk for anal cancer. We determined whether human papilloma virus (HPV) biomarkers were correlated with anal pathology in these men.Methods: HPV genotype was determined by PCR/line blot assay. Real-time PCR assays were done for viral load, E6 transcripts for HPV genotypes 16, 18, and 31, and p16 transcripts.Results: The most common oncogenic HPV types were HPV 16 (38%), 18 (19%), 45 (22%), and 52 (19%). HPV types 16, 18, 31, 52, 59, and 68 were associated with high-grade histology. The number of HPV genotypes per anal swab was higher for anal intraepithelial neoplasia (AIN) 2/3 than for normal or AIN 1 histology [median, 5 types (interquartile range) (IQR), 3-7 versus 3.5 (IQR), 2-6; P = 0.0005]. HPV 16 viral load was also associated with AIN 2/3 histology. There was no difference in p16 or E6 transcripts between histologic grades. In the multivariable logistic regression model, HPV genotypes 16 [odds ratio, 2.58; 95% confidence interval (95% CI), 1.31-5.08; P = 0.006] and 31 (odds ratio, 4.74; 95% CI, 2.00-11.22; P = 0.0004), baseline CD4 count &lt; 400 cells/mm3 (odds ratio, 2.96; 95% CI, 1.46-5.99; P = 0.0025), and Acquired Immunodeficiency Syndrome (AIDS)-defining illness (odds ratio, 2.42; 95% CI, 1.22-4.82; P = 0.01) were associated with high-grade histology after adjusting for age.Conclusions: The presence of high-grade anal pathology (AIN 2/3) in HIV-positive men was associated with multiple HPV genotypes, HPV genotypes 16 and 31, and HPV 16 viral load. (Cancer Epidemiol Biomarkers Prev 2009;18(7):1986–92)
Genetic Variants and Prostate Cancer Risk: Candidate Replication and Exploration of Viral Restriction Genes
Authors: Breyer Joan P. , McReynolds Kate M. , Yaspan Brian L. , Bradley Kevin M. , Dupont William D. , Smith Jeffrey R. 
Published: July 2009

Abstract
The genetic variants underlying the strong heritable component of prostate cancer remain largely unknown. Genome-wide association studies of prostate cancer have yielded several variants that have significantly replicated across studies, predominantly in cases unselected for family history of prostate cancer. Additional candidate gene variants have also been proposed, many evaluated within familial prostate cancer study populations. Such variants hold great potential value for risk stratification, particularly for early-onset or aggressive prostate cancer, given the comorbidities associated with current therapies. Here, we investigate a Caucasian study population of 523 independent familial prostate cancer cases and 523 age-matched controls without a personal or family history of prostate cancer. We replicate identified associations at genome-wide association study loci 8q24, 11q13, and 2p15 (P = 2.9 × 10−4 to P = 4.7 × 10−5), showing study population power. We also find evidence to support reported associations at candidate genes RNASEL, EZH2, and NKX3-1 (P = 0.031 to P = 0.0085). We further explore a set of candidate genes related to RNASEL and to its role in retroviral restriction, identifying nominal associations at XPR1 and RBM9. The effects at 8q24 seem more pronounced for those diagnosed at an early age, whereas at 2p15 and RNASEL the effects were more pronounced at a later age. However, these trends did not reach statistical significance. The effects at 2p15 were statistically significantly more pronounced for those diagnosed with aggressive disease. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2137–44)
Relationship between Migraine History and Breast Cancer Risk among Premenopausal and Postmenopausal Women
Authors: Li Christopher I. , Mathes Robert W. , Malone Kathleen E. , Daling Janet R. , Bernstein Leslie , Marchbanks Polly A. , Strom Brian L. , Simon Michael S. , Press Michael F. , Deapen Dennis , Burkman Ronald T. , Folger Suzanne G. , McDonald Jill A. , Spirtas Robert 
Published: July 2009

Abstract
Both migraine and breast cancer are hormonally mediated diseases, and it is biologically plausible that women with a history of migraine may have a reduced breast cancer risk. However, this relationship has only been assessed in a single relatively small study that was unable to assess the effect of migraine triggers, which are also well-established breast cancer risk factors (e.g., use of alcohol and exogenous hormones), on the inverse association observed. Utilizing data on 4,568 breast cancer cases and 4,678 controls who participated in a multicenter population-based case-control study in the United States, we evaluated the association between migraine history and breast cancer risk using unconditional logistic regression. Migraine history data were obtained from structured in-person interviews. Women with a history of migraine had a reduced risk of breast cancer [odds ratio, 0.74; 95% confidence interval (CI), 0.66-0.82]. This risk did not differ by menopausal status, age at migraine diagnosis, use of prescription migraine medications, or when analyses were restricted to women who avoided various migraine triggers (including alcohol, exogenous hormones, and smoking). These data support a previous finding that a history of migraine may be associated with a reduced risk of breast cancer. It extends the prior report in observing that this relationship holds for both premenopausal and postmenopausal women and is independent of exposure to common migraine triggers. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2030–4)
Enriched Analyses with Assimilation of SALLJEX Data
Authors: García Skabar Yanina , Nicolini Matilde 
Published: July 2009

Abstract
This paper aims at generating a set of enriched analyses by assimilating the data collected during the South American Low-Level Jet Experiment (SALLJEX) in southeastern South America during the summer season 2002/03. The analyses are generated with the Brazilian Regional Atmospheric Modeling System (BRAMS) using all available observations and achieving 20-km horizontal resolution and 3-h temporal resolution. This paper describes the methods used to generate and evaluate the analyses. The results indicate that the method is appropriate because data assimilation provides an improved fit between analyses and observations. In addition, enriched analyses show a better representation of mesoscale structure in case studies. This satisfactory evaluation allows one to use the set of analyses to perform case studies at higher resolution than is currently available, with the certainty that these analyses reproduce the atmospheric conditions better than those that do not assimilate data.