bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monoclonal Antibodies to VP1 Recognize a Broad Range of Enteroviruses
Authors: Miao Lynn Yihong , Pierce Christina , Gray-Johnson Jennifer , DeLotell Jill , Shaw Carl , Chapman Nate , Yeh Elaine , Schnurr David , Huang Yung T. 
Published: August 2009

ABSTRACT
Enteroviruses (EVs) are common seasonal viruses that are associated with a variety of diseases. High-quality monoclonal antibodies (MAbs) are needed to improve the accuracy of EV diagnosis in clinical laboratories. In the present study, the full-length VP1 genes of poliovirus 1 (Polio 1) and coxsackievirus B3 (Cox B3) were cloned, and the encoded proteins were expressed and used as antigens in an attempt to raise broad-spectrum MAbs to EVs. Two pan-EV MAbs were isolated: one raised against Polio 1 VP1 and the other against Cox B3 VP1. The binding sites of both pan-EV MAbs were mapped to an amino acid sequence within a conserved region in the N terminus of Polio 1 VP1 by peptide and competition enzyme-linked immunosorbent assay. Two additional MAbs, an EV70-specific MAb and an EV71/Cox A16-bispecific MAb, developed against EV70 and 71 VP1 proteins, were pooled with the two pan-EV MAbs (pan-EV MAb mix) and tested for their sensitivity and specificity in the staining of various virus-infected cells. The pan-EV MAb mix detected all 40 prototype EVs tested and showed no cross-reactivity to 18 different non-EV human viruses. Compared with two commercially available EV tests, the pan-EV MAb mix exhibited higher specificity than one test and broader spectrum reactivity than the other. Thus, our study demonstrates that full-length Polio 1 VP1 and Cox B3 VP1 can serve as effective antigens for developing a pan-EV MAb and that the pan-EV MAb mix can be used for the laboratory diagnosis of a wide range of EV infections.
Validation of Vitek 2 Nonfermenting Gram-Negative Cards and Vitek 2 Version 4.02 Software for Identification and Antimicrobial Susceptibility Testing of Nonfermenting Gram-Negative Rods from Patients with Cystic Fibrosis
Authors: Otto-Karg Ines , Jandl Stefanie , Müller Tobias , Stirzel Beate , Frosch Matthias , Hebestreit Helge , Abele-Horn Marianne 
Published: August 2009

ABSTRACT
Accurate identification and antimicrobial susceptibility testing (AST) of nonfermenters from cystic fibrosis patients are essential for appropriate antimicrobial treatment. This study examined the ability of the newly designed Vitek 2 nonfermenting gram-negative card (NGNC) (new gram-negative identification card; bioMérieux, Marcy-l'Ètoile, France) to identify nonfermenting gram-negative rods from cystic fibrosis patients in comparison to reference methods and the accuracy of the new Vitek 2 version 4.02 software for AST compared to the broth microdilution method. Two hundred twenty-four strains for identification and 138 strains for AST were investigated. The Vitek 2 NGNC identified 211 (94.1%) of the nonfermenters correctly. Among morphologically atypical microorganisms, five strains were misidentified and eight strains were determined with low discrimination, requiring additional tests which raised the correct identification rate to 97.8%. Regarding AST, the overall essential agreement of Vitek 2 was 97.6%, and the overall categorical agreement was 92.9%. Minor errors were found in 5.1% of strains, and major and very major errors were found in 1.6% and 0.3% of strains, respectively. In conclusion, the Vitek NGNC appears to be a reliable method for identification of morphologically typical nonfermenters and is an improvement over the API NE system and the Vitek 2 GNC database version 4.01. However, classification in morphologically atypical nonfermenters must be interpreted with care to avoid misidentification. Moreover, the new Vitek 2 version 4.02 software showed good results for AST and is suitable for routine clinical use. More work is needed for the reliable testing of strains whose MICs are close to the breakpoints.
Cerebral Aspergillosis Caused by
Aspergillus granulosus
Authors: Sutton Deanna A. , Wickes Brian L. , Romanelli Anna M. , Rinaldi Michael G. , Thompson Elizabeth H. , Fothergill Annette W. , Dishop Megan K. , Elidemir Okan , Mallory George B. , Moonnamakal Siby P. , Adesina Adekunle M. , Schecter Marc G. 
Published: August 2009

ABSTRACT

Disseminated disease by
Aspergillus granulosus
has been reported only once previously in a cardiac transplant recipient. We report a fatal central nervous system infection in a lung transplant recipient. Key features of this species in the section
Usti
include growth at 37°C and large, randomly spaced aggregates of variably shaped Hülle cells.
Comparison of Nine Commercially Available
Clostridium difficile
Toxin Detection Assays, a Real-Time PCR Assay for
C
.
difficile tcdB
, and a Glutamate Dehydrogenase Detection Assay to Cytotoxin Testing and Cytotoxigenic Culture Methods
Authors: Eastwood Kerrie , Else Patrick , Charlett André , Wilcox Mark 
Published: August 2009

ABSTRACT

The continuing rise in the incidence of
Clostridium difficile
infection is a cause for concern, with implications for patients and health care systems. Laboratory diagnosis largely relies on rapid toxin detection kits, although assays detecting alternative targets, including glutamate dehydrogenase (GDH) and toxin genes, are now available. Six hundred routine diagnostic diarrheal samples were tested prospectively using nine commercial toxin detection assays, cytotoxin assay (CYT), and cytotoxigenic culture (CYTGC) and retrospectively using a GDH detection assay and PCR for the toxin B gene. The mean sensitivity and specificity for toxin detection assays were 82.8% (range, 66.7 to 91.7%) and 95.4% (range, 90.9 to 98.8%), respectively, in comparison with CYT and 75.0% (range, 60.0 to 86.4%) and 96.1% (91.4 to 99.4%), respectively, in comparison with CYTGC. The sensitivity and specificity of the GDH assay were 90.1% and 92.9%, respectively, compared to CYT and 87.6% and 94.3%, respectively, compared to CYTGC. The PCR assay had the highest sensitivity of all the tests in comparison with CYT (92.2%) and CYTGC (88.5%), and the specificities of the PCR assay were 94.0% and 95.4% compared to CYT and CYTGC, respectively. All kits had low positive predictive values (range, 48.6 to 86.8%) compared with CYT, assuming a positive sample prevalence of 10% (representing the hospital setting), which compromises the clinical utility of single tests for the laboratory diagnosis of
C
.
difficile
infection. The optimum rapid single test was PCR for toxin B gene, as this had the highest negative predictive value. Diagnostic algorithms that optimize test combinations for the laboratory diagnosis of
C
.
difficile
infection need to be defined.
Comparative Evaluation of a Commercially Available Automated System for Extraction of Viral DNA from Whole Blood: Application to Monitoring of Epstein-Barr Virus and Cytomegalovirus Load
Authors: Pillet Sylvie , Bourlet Thomas , Pozzetto Bruno 
Published: August 2009

ABSTRACT
The NucliSENS easyMAG automated system was compared to the column-based Qiagen method for Epstein-Barr virus (EBV) or cytomegalovirus (CMV) DNA extraction from whole blood before viral load determination using the corresponding R-gene amplification kits. Both extraction techniques exhibited a total agreement of 81.3% for EBV and 87.2% for CMV.
Variability of Immediate-Early Gene 62 in German Varicella-Zoster Virus Wild-Type Strains
Authors: Sauerbrei A. , Bohn K. , Zell R. , Wutzler P. 
Published: August 2009

ABSTRACT
Varicella-zoster virus strains of European genotypes have developed a high variability of open reading frame (ORF) 62 during their occurrence over many years in Germany. M1 strains in Germany display a uniform ORF 62 pattern, suggesting that these strains were introduced from Africa and/or Asia via few sources during the last years.
Carriage Rate of
Enterocytozoon bieneusi
in an Orphanage in Bangkok, Thailand
Authors: Pagornrat Watcharee , Leelayoova Saovanee , Rangsin Ram , Tan-Ariya Peerapan , Naaglor Tawee , Mungthin Mathirut 
Published: August 2009

ABSTRACT

This study was performed to evaluate the incidence of and risk factors for
E
nterocytozoon bieneusi
carriage in an orphanage in Bangkok, Thailand.
E. bieneusi
has been identified by PCR every 2 consecutive months since June 2003. The incidence ranged between 0.6 and 4.7/100 person-months. Person-to-person transmission was indicated by risk factor analysis and genotyping information.
Analysis of Nucleotide Sequences of Human Parvovirus B19 Genome Reveals Two Different Modes of Evolution, a Gradual Alteration and a Sudden Replacement: a Retrospective Study in Sapporo, Japan, from 1980 to 2008
Authors: Suzuki Masashi , Yoto Yuko , Ishikawa Aki , Tsutsumi Hiroyuki 
Published: August 2009

ABSTRACT
There have been no long-term systematic analyses of the molecular epidemiology of human parvovirus B19 (B19V). We investigated the variations of nucleotide sequences of B19V strains collected in Sapporo, Japan, from 1980 to 2008. In that period, six outbreaks of erythema infectiosum occurred regularly at 5-year intervals. The B19V strains collected successively, regardless of the outbreak, were analyzed for nucleotide variation in the subgenomic NS1-VP1u junction. The isolated strains can be classified into 10 subgroups. Two patterns of change of endemic strains were observed. One was a dynamic replacement of strains that occurred almost every 10 years, and the other was a gradual change consisting of an accumulation of point mutations.
The Epstein-Barr Virus Protein Kinase BGLF4 and the Exonuclease BGLF5 Have Opposite Effects on the Regulation of Viral Protein Production
Authors: Feederle Regina , Mehl-Lautscham Anja M. , Bannert Helmut , Delecluse Henri-Jacques 
Published: August 2009

ABSTRACT
The Epstein-Barr virus BGLF4 and BGLF5 genes encode a protein kinase and an alkaline exonuclease, respectively. Both proteins were previously found to regulate multiple steps of virus replication, including lytic DNA replication and primary egress. However, while inactivation of BGLF4 led to the downregulation of several viral proteins, the absence of BGLF5 had the opposite effect. Using recombinant viruses that lack both viral enzymes, we confirm and extend these initial observations, e.g., by showing that both BGLF4 and BGLF5 are required for proper phosphorylation of the DNA polymerase processivity factor BMRF1. We further found that neither BGLF4 nor BGLF5 is required for baseline viral protein production. Complementation with BGLF5 downregulated mRNA levels and translation of numerous viral genes, though to various degrees, whereas BGLF4 had the opposite effect. BGLF4 and BGLF5 influences on viral expression were most pronounced for BFRF1 and BFLF2, two proteins essential for nuclear egress. For most viral genes studied, cotransfection of BGLF4 and BGLF5 had only a marginal influence on their expression patterns, showing that BGLF4 antagonizes BGLF5-mediated viral gene shutoff. To be able to exert its functions on viral gene expression, BGLF4 must be able to escape BGLF5's shutoff activities. Indeed, we found that BGLF5 stimulated the BGLF4 gene's transcription through an as yet uncharacterized molecular mechanism. The BGLF4/BGLF5 enzyme pair builds a regulatory loop that allows fine-tuning of virus protein production, which is required for efficient viral replication.
Involvement of SSRP1 in Latent Replication of Kaposi's Sarcoma-Associated Herpesvirus
Authors: Hu Jianhong , Liu Eugene , Renne Rolf 
Published: August 2009

ABSTRACT

Kaposi's sarcoma-associated herpesvirus (also named human herpesvirus 8) is a γ-herpesvirus that undergoes both lytic and latent infection. During latent infection, two viral elements are required: latency-associated nuclear antigen (LANA), which functions as an origin binding protein, and the latent origin, which resides within the terminal repeats (TRs) of the viral genome. Previously, we identified two
cis
-elements within the TRs which are required for latent DNA replication: two LANA binding sites (LBS1 and LBS2 [LBS1/2]) and a GC-rich replication element (RE) upstream of LBS1/2. To further characterize the RE, we constructed a 71-bp minimal replicon (MR) and performed a detailed mutational analysis. Our data indicate that the first 8 nucleotides within the RE are critical for replication. Moreover, both the position and the distance between the RE and LBS1/2 can affect origin replication activity, suggesting that the RE may function as a loading pad for cellular proteins involved in replication. Using biotinylated DNA fragments of wild-type or mutant MRs as probes, we identified 30 proteins that preferentially bind to the origin. Among these proteins, structure-specific recognition protein 1 (SSRP1), a subunit of the FACT complex, and telomeric repeat binding factor 2 (TRF2) formed complexes with LANA at the MR region. Furthermore, the small interfering RNA-based knockdown of SSRP1, but not the dominant-negative-based knockdown of TRF2, significantly decreased the efficiency of LANA-dependent DNA replication. These results indicate that SSRP1 is a novel cellular protein involved in LANA-dependent DNA replication.
Murine Gammaherpesvirus 68 Infection of Gamma Interferon-Deficient Mice on a BALB/c Background Results in Acute Lethal Pneumonia That Is Dependent on Specific Viral Genes
Authors: Lee Katherine S. , Cool Carlyne D. , van Dyk Linda F. 
Published: August 2009

ABSTRACT
Gamma interferon (IFN-γ) is critical for the control of chronic infection with murine gammaherpesvirus 68 (γHV68). Current data indicate that IFN-γ has a lesser role in the control of acute replication of γHV68. Here, we show that IFN-γ-deficient mice on the BALB/c genetic background poorly control acute viral replication and succumb to early death by acute pneumonia. Notably, this acute, lethal pneumonia was dependent not only on the viral dose, but also on specific viral genes including the viral cyclin gene, previously identified to be important in promoting optimal chronic infection and reactivation from latency.
Dynamin- and Lipid Raft-Dependent Entry of Decay-Accelerating Factor (DAF)-Binding and Non-DAF-Binding Coxsackieviruses into Nonpolarized Cells
Authors: Patel Kunal P. , Coyne Carolyn B. , Bergelson Jeffrey M. 
Published: August 2009

ABSTRACT
Group B coxsackieviruses (CVB) use the CVB and adenovirus receptor (CAR) to enter and infect cells. Some CVB also bind to decay-accelerating factor (DAF), but that interaction alone is insufficient for infection. We previously found that CVB3 entry into polarized human intestinal cells (Caco-2) occurs by a caveolin-dependent but dynamin-independent mechanism that requires DAF-mediated tyrosine kinase signals. In this study, we examined how CVB enter and infect nonpolarized HeLa cells and how DAF binding affects these processes. Using immunofluorescence microscopy and a combination of dominant-negative proteins, small interfering RNAs, and drugs targeting specific endocytic pathways, we found that both DAF-binding and non-DAF-binding virus isolates require dynamin and lipid rafts to enter and infect cells. Unlike what we observed in Caco-2 cells, CVB3 entered HeLa cells with CAR. We found no role for clathrin, endosomal acidification, or caveolin. Inhibition of tyrosine kinases blocked an early event in infection but did not prevent entry of virus into the cell. These results indicate that CVB3 entry into nonpolarized HeLa cells differs significantly from entry into polarized Caco-2 cells and is not influenced by virus binding to DAF.
Mutational Analysis Reveals a Noncontractile but Interactive Role of Actin and Profilin in Viral RNA-Dependent RNA Synthesis
Authors: Harpen Mary , Barik Tiasha , Musiyenko Alla , Barik Sailen 
Published: August 2009

ABSTRACT
As obligatory parasites, viruses co-opt a variety of cellular functions for robust replication. The expression of the nonsegmented negative-strand RNA genome of respiratory syncytial virus (RSV), a significant pediatric pathogen, absolutely requires actin and is stimulated by the actin-regulatory protein profilin. As actin is a major contractile protein, it was important to determine whether the known functional domains of actin and profilin were important for their ability to activate RSV transcription. Analyses of recombinant mutants in a reconstituted RSV transcription system suggested that the divalent-cation-binding domain of actin is critically needed for binding to the RSV genome template and for the activation of viral RNA synthesis. In contrast, the nucleotide-binding domain and the N-terminal acidic domain were needed neither for template binding nor for transcription. Specific surface residues of actin, required for actin-actin contact during filamentation, were also nonessential for viral transcription. Unlike actin, profilin did not directly bind to the viral template but was recruited by actin. Mutation of the interactive residues of actin or profilin, resulting in the loss of actin-profilin binding, also abolished profilin's ability to stimulate viral transcription. Together, these results suggest that actin acts as a classical transcription factor for the virus by divalent-cation-dependent binding to the viral template and that profilin acts as a transcriptional cofactor, in part by associating with actin. This essential viral role of actin is independent of its contractile cellular role.
Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family
Leviviridae
)
Authors: Friedman Stephanie D. , Genthner Fred J. , Gentry Jennifer , Sobsey Mark D. , Vinjé Jan 
Published: August 2009

ABSTRACT

Male-specific single-stranded RNA (FRNA) coliphages belong to the family
Leviviridae
. They are classified into two genera (
Levivirus
and
Allolevivirus
), which can be subdivided into four genogroups (genogroups I and II in
Levivirus
and genogroups III and IV in
Allolevivirus
). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10
Levivirus
strains and 9
Allolevivirus
strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of
Levivirus
genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of
Allolevivirus
genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in
Levivirus
genogroup I and that the MX1 and M11 strains belong in
Allolevivirus
genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3′ end of the genome distinguishes leviviruses (5′ ACCACCCA 3′) from alloleviviruses (5′ TCCTCCCA 3′).
Rhodium(I)–(N-heterocyclic carbene)–diphosphine complexes
Authors: Sun Hongsui , Yu Xiao-Yan , Marcazzan Paolo , Patrick Brian O. , James Brian R. 
Published: August 2009

Reactions of [RhCl(COE)(IPr)]2 (1) and [RhCl(COE)(IMes)]2 (2) (COE = cyclooctene; IPr = N,N′-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene; IMes = N,N′-bis(2,4,6-trimethylphenyl)imidazolin-2-ylidene) with the diphosphines Ph2P(CH2)nPPh2 and 1,2-bis(diphenylphosphino)benzene (dppbz) give the N-heterocyclic carbene (NHC) – diphosphine – rhodium(I) complexes: RhCl(NHC)[Ph2P(CH2)nPPh2] [NHC = IPr, n = 1 (3); NHC = IMes, n = 1 (4); NHC = IPr, n = 2 (5); NHC = IMes, n = 2 (6); NHC = IPr, n = 4 (7); NHC = IMes, n = 4 (8)] and RhCl(NHC)(dppbz) [NHC = IPr (9); NHC = IMes (10)]. All the complexes are characterized by 1H, 31P{1H}, and 13C{1H} NMR spectroscopy, elemental analysis, and mass spectrometry. Complexes 3, 7, and 9 are also characterized crystallographically. In benzene solution, the complexes decompose in the presence of O2 with formation of the diphosphine dioxide, whereas reaction with CO leads to replacement of the NHC ligand to give known carbonyl–diphosphine complexes.
ON RECTANGULAR COVERING PROBLEMS
Authors: PORSCHEN STEFAN 
Published: August 2009

Many applications like image processing, data compression or pattern recognition require a covering of a set of n points most often located in the (discrete) plane by rectangles due to specific cost constraints. In this paper we provide exact dynamic programming algorithms for covering point sets by regular rectangles, that have to obey certain boundary conditions, namely all rectangles must have lengths of at least k, which is a prescribed problem parameter. The concrete objective function underlying our optimization problem is the sum of area, circumference and a constant over all rectangles forming a covering. This objective function can be motivated by requirements of numerically solving PDE's by discretization over (adaptive multi-)grids. More precisely, we propose exact deterministic algorithms for such problems based on a (set theoretic) dynamic programming approach yielding a time bound of O(n23n). In a second step this bound is (asymptotically) decreased to O(n62n) by exploiting some structural features. Finally, a generalization of the problem and its solution methods is discussed for the case of arbitrary (finite) space dimension.
Simulation of Snow on Arctic Sea Ice Using a Coupled Snow–Ice Model
Authors: Chung Yi-Ching , Bélair Stéphane , Mailhot Jocelyn 
Published: August 2009

Abstract
The new Recherche Prévision Numérique (NEW-RPN) model, a coupled system including a multilayer snow thermal model (SNTHERM) and the sea ice model currently used in the Meteorological Service of Canada (MSC) operational forecasting system, was evaluated in a one-dimensional mode using meteorological observations from the Surface Heat Budget of the Arctic Ocean (SHEBA)’s Pittsburgh site in the Arctic Ocean collected during 1997/98. Two parameters simulated by NEW-RPN (i.e., snow depth and ice thickness) are compared with SHEBA’s observations and with simulations from RPN, MSC’s current coupled system (the same sea ice model and a single-layer snow model). Results show that NEW-RPN exhibits better agreement for the timing of snow depletion and for ice thickness. The profiles of snow thermal conductivity in NEW-RPN show considerable variability across the snow layers, but the mean value (0.39 W m−1 K−1) is within the range of reported observations for SHEBA. This value is larger than 0.31 W m−1 K−1, which is commonly used in single-layer snow models. Of particular interest in NEW-RPN’s simulation is the strong temperature stratification of the snowpack, which indicates that a multilayer snow model is needed in the SHEBA scenario. A sensitivity analysis indicates that snow compaction is also a crucial process for a realistic representation of the snowpack within the snow/sea ice system. NEW-RPN’s overestimation of snow depth may be related to other processes not included in the study, such as small-scale horizontal variability of snow depth and blowing snow processes.