bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Throughput Genotyping of
Salmonella enterica
Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia
Authors: Baker Stephen , Holt Kathryn , van de Vosse Esther , Roumagnac Philippe , Whitehead Sally , King Emma , Ewels Philip , Keniry Andrew , Weill François-Xavier , Lightfoot Diane , van Dissel Jaap T. , Sanderson Kenneth E. , Farrar Jeremy , Achtman Mark , Deloukas Panagiotis , Dougan Gordon 
Published: March 2008

ABSTRACT

High-throughput epidemiological typing systems that provide phylogenetic and genotypic information are beneficial for tracking bacterial pathogens in the field. The incidence of
Salmonella enterica
serovar Typhi infection in Indonesia is high and is associated with atypical phenotypic traits such as expression of the j and the z66 flagellum antigens. Utilizing a high-throughput genotyping platform to investigate known nucleotide polymorphisms dispersed around the genome, we determined the haplotypes of 140 serovar Typhi isolates associated with Indonesia. We identified nine distinct serovar Typhi haplotypes circulating in Indonesia for more than 30 years, with eight of these present in a single Jakarta suburb within a 2-year period. One dominant haplotype, H59, is associated with j and z66 flagellum expression, representing a potential pathotype unique to Indonesia. Phylogenetic analysis suggests that H59 z66
+
, j
+
isolates emerged relatively recently in terms of the origin of serovar Typhi and are geographically restricted. These data demonstrate the potential of high-throughput genotyping platforms for analyzing serovar Typhi populations in the field. The study also provides insight into the evolution of serovar Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, that is internet friendly, and that has global utility.
Evaluation of Different Techniques for Identification of Human Papillomavirus Types of Low Prevalence
Authors: Sabol Ivan , Salakova Martina , Smahelova Jana , Pawlita Michal , Schmitt Markus , Gašperov Nina Milutin , Grce Magdalena , Tachezy Ruth 
Published: March 2008

ABSTRACT
Human papillomaviruses (HPVs) have been recognized as etiologic factors in a variety of diseases. Due to the large number of HPV types, methods for HPV genotyping are difficult to standardize. Despite this fact, several methods exist, and some of them are available commercially. In this study, we evaluated the Roche Diagnostics linear array (LA) HPV genotyping assay, the Innogenetics INNO-LiPA (line probe assay [LiPA]), and two noncommercial reverse line blot (RLB) assays based on either primers GP5+ and GP6+ (GP) or newly designed broad-spectrum primers BSGP5+ and BSGP6+ (BS). The reliabilities of these assays were tested with a wide spectrum of HPV types less prevalent in cervical samples. This is the first study to compare the performance of the most widely used HPV genotyping methods with selected samples positive for low-prevalence HPV types. We focused on interassay agreement, both overall and type specific, in cases with single and/or multiple HPV infections. Interassay agreement was moderate in cases of single HPV infections and poor in cases of multiple HPV infections. The LA and the BS-based RLB assays found a higher rate of cases positive for multiple HPV types than LiPA and the GP-based RLB assay. The weakest capability in detecting multiple HPV infections was observed for LiPA. The use of only one assay in epidemiological and clinical studies might lead to biased conclusions. Therefore, a universally evaluated and agreed upon HPV typing assay or a combination of current assays is needed for possible clinical applications, and knowledge of their limitations is advised.
Evaluation of the New Micronaut-
Candida
System Compared to the API ID32C Method for Yeast Identification
Authors: Szabó Z. , Tóth B. , Kovács M. , Kardos G. , Maráz A. , Rozgonyi F. , Majoros L. 
Published: March 2008

ABSTRACT

A new system, Micronaut-
Candida
, was compared to API ID32C to identify 264 yeast (
Candida albicans
,
C. parapsilosis
,
C. tropicalis
,
C. krusei
,
C. inconspicua
,
C. norvegensis
,
C. lusitaniae
,
C. guilliermondii
,
C. dubliniensis
,
C. pulcherrima
,
C. famata
,
C. rugosa
,
C. glabrata
,
C. kefyr
,
C. lipolytica
,
C. catenulata
,
C. neoformans
,
Geotrichum
and
Trichosporon
species,
Rhodotorula glutinis
, and
Saccharomyces cerevisiae
) clinical isolates. Results were in concordance in 244 cases. Eighteen out of the 20 of discordant results were correctly identified by Micronaut-
Candida
but not by API ID32C, as confirmed by PCR ribotyping.
Mutations in the Human Immunodeficiency Virus Type 1 Polypurine Tract (PPT) Reduce the Rate of PPT Cleavage and Plus-Strand DNA Synthesis
Authors: McWilliams M. J. , Julias J. G. , Hughes S. H. 
Published: March 2008

ABSTRACT
Previously, we analyzed the effects of point mutations in the human immunodeficiency virus type 1 (HIV-1) polypurine tract (PPT) and found that some mutations affected both titer and cleavage specificity. We used HIV-1 vectors containing two PPTs and the D116N integrase active-site mutation in a cell-based assay to measure differences in the relative rates of PPT processing and utilization. The relative rates were measured by determining which of the two PPTs in the vector is used to synthesize viral DNA. The results indicate that mutations that have subtle effects on titer and cleavage specificity can have dramatic effects on rates of PPT generation and utilization.
Human Cytomegalovirus UL97 Kinase Activity Is Required for the Hyperphosphorylation of Retinoblastoma Protein and Inhibits the Formation of Nuclear Aggresomes
Authors: Prichard Mark N. , Sztul Elizabeth , Daily Shannon L. , Perry Amie L. , Frederick Samuel L. , Gill Rachel B. , Hartline Caroll B. , Streblow Daniel N. , Varnum Susan M. , Smith Richard D. , Kern Earl R. 
Published: March 2008

ABSTRACT
Cells infected with human cytomegalovirus in the absence of UL97 kinase activity produce large nuclear aggregates that sequester considerable quantities of viral proteins. A transient expression assay suggested that pp71 and IE1 were also involved in this process, and this suggestion was significant, since both proteins have been reported to interact with components of promyelocytic leukemia (PML) bodies (ND10) and also interact functionally with retinoblastoma pocket proteins (RB). PML bodies have been linked to the formation of nuclear aggresomes, and colocalization studies suggested that viral proteins were recruited to these structures and that UL97 kinase activity inhibited their formation. Proteins associated with PML bodies were examined by Western blot analysis, and pUL97 appeared to specifically affect the phosphorylation of RB in a kinase-dependent manner. Three consensus RB binding motifs were identified in the UL97 kinase, and recombinant viruses were constructed in which each was mutated to assess a potential role in the phosphorylation of RB and the inhibition of nuclear aggresome formation. The mutation of either the conserved LxCxE RB binding motif or the lysine required for kinase activity impaired the ability of the virus to stabilize and phosphorylate RB. We concluded from these studies that both UL97 kinase activity and the LxCxE RB binding motif are required for the phosphorylation and stabilization of RB in infected cells and that this effect can be antagonized by the antiviral drug maribavir. These data also suggest a potential link between RB function and the formation of aggresomes.
Distinct Ex Vivo Susceptibility of B-Cell Subsets to Epstein-Barr Virus Infection According to Differentiation Status and Tissue Origin
Authors: Dorner Marcus , Zucol Franziska , Berger Christoph , Byland Rahel , Melroe Gregory T. , Bernasconi Michele , Speck Roberto F. , Nadal David 
Published: March 2008

ABSTRACTEpstein-Barr virus (EBV) uses tonsils as the portal of entry to establish persistent infection. EBV is found in various B-cell subsets in tonsils but exclusively in memory B cells in peripheral blood. The in vitro susceptibilities of B-cell subsets to EBV infection have been studied solely qualitatively. In this work, we examined quantitatively the in vitro susceptibilities of various B-cell subsets from different tissue origins to EBV infection. First, we established a centrifugation-based inoculation protocol (spinoculation) that resulted in a significantly increased proportion of infected cells compared to that obtained by conventional inoculation, enabling a detailed susceptibility analysis. Importantly, B-cell infection occurred via the known EBV receptors and infected cells showed EBV mRNA expression patterns similar to those observed after conventional inoculation, validating our approach. Tonsillar naïve and memory B cells were infected ex vivo at similar frequencies. In contrast, memory B cells from blood, which represent B cells from various lymphoid tissues, were infected at lower frequencies than their naïve counterparts. Immunoglobulin A (IgA)-positive or IgG-positive tonsillar memory B cells were significantly more susceptible to EBV infection than IgM-positive counterparts. Memory B cells were transformed with lower efficiency than naïve B cells. This result was paralleled by lower proliferation rates. In summary, these data suggest that EBV exploits the B-cell differentiation status and tissue origin to establish persistent infection.
Mitochondrial Dysfunction in Lyssavirus-Induced Apoptosis
Authors: Gholami Alireza , Kassis Raïd , Real Eléonore , Delmas Olivier , Guadagnini Stéphanie , Larrous Florence , Obach Dorothée , Prevost Marie-Christine , Jacob Yves , Bourhy Hervé 
Published: March 2008

ABSTRACT

Lyssaviruses are highly neurotropic viruses associated with neuronal apoptosis. Previous observations have indicated that the matrix proteins (M) of some lyssaviruses induce strong neuronal apoptosis. However, the molecular mechanism(s) involved in this phenomenon is still unknown. We show that for Mokola virus (MOK), a lyssavirus of low pathogenicity, the M (M-MOK) targets mitochondria, disrupts the mitochondrial morphology, and induces apoptosis. Our analysis of truncated M-MOK mutants suggests that the information required for efficient mitochondrial targeting and dysfunction, as well as caspase-9 activation and apoptosis, is held between residues 46 and 110 of M-MOK. We used a yeast two-hybrid approach, a coimmunoprecipitation assay, and confocal microscopy to demonstrate that M-MOK physically associates with the subunit I of the cytochrome
c
(cyt-
c
) oxidase (CcO) of the mitochondrial respiratory chain; this is in contrast to the M of the highly pathogenic Thailand lyssavirus (M-THA). M-MOK expression induces a significant decrease in CcO activity, which is not the case with M-THA. M-MOK mutations (K77R and N81E) resulting in a similar sequence to M-THA at positions 77 and 81 annul cyt-
c
release and apoptosis and restore CcO activity. As expected, the reverse mutations, R77K and E81N, introduced in M-THA induce a phenotype similar to that due to M-MOK. These features indicate a novel mechanism for energy depletion during lyssavirus-induced apoptosis.
Virion-Wide Protein Interactions of Kaposi's Sarcoma-Associated Herpesvirus
Authors: Rozen Ramona , Sathish Narayanan , Li Yong , Yuan Yan 
Published: March 2008

ABSTRACT
Herpesvirus virions are highly organized structures built through specific protein-protein interactions. Thus, revelation of the protein interactions among virion proteins will shed light on the processes and the mechanisms of virion formation. Recently, we identified 24 virion proteins of Kaposi's sarcoma-associated herpesvirus (KSHV), using a proteomic approach (F. X. Zhu et al., J. Virol. 79:800-811, 2005). In the current study, a comprehensive analysis of protein-protein interaction between KSHV virion proteins was carried out using yeast two-hybrid (Y2H) and coimmunoprecipitation (co-IP) approaches. Every pairwise combination between KSHV tegument and capsid proteins, between tegument and envelope proteins, and among tegument proteins was tested for possible binary interaction. Thirty-seven protein-protein interactions were identified by both Y2H and co-IP analyses. The results revealed interactions between tegument and capsid proteins such as that of open reading frame 64 (ORF64) with ORF25 (major capsid protein [MCP]), ORF62 (triplex-1 [TRI-1]), and ORF26 (TRI-2). Many interactions were detected among the tegument proteins. ORF64 was found to interact with several tegument proteins including ORF11, ORF21, ORF33, ORF45, ORF63, ORF75, and ORF64 itself, suggesting that ORF64 may serve as a hub protein and play a role in recruiting tegument proteins during tegumentation and virion assembly. Our investigation also revealed redundant interactions between tegument proteins and envelope glycoproteins. These interactions are believed to contribute to final envelopment in virion assembly. Overall, this study allows us to establish a virion-wide protein interaction map, which provides insight into the architecture of the KSHV virion and sets up a foundation for exploring the functions of these proteins in viral particle assembly.
Expression of Gamma Interferon-Dependent Genes Is Blocked Independently by Virion Host Shutoff RNase and by US3 Protein Kinase
Authors: Liang Li , Roizman Bernard 
Published: March 2008

ABSTRACTGamma interferon receptor α (IFN-γRα) is stable but posttranslationally modified in herpes simplex virus 1(F) [HSV-1(F)]-infected cells. Studies with antibody directed to the phosphorylation site indicate that IFN-γRα is phosphorylated by the US3 kinase. The modification is abolished in cells infected with ΔUS3, ΔUL13, or Δ(US3/UL13) mutant virus. Transcripts of the IFN-γ-dependent genes do not accumulate in cells transduced with the US3 protein kinase and treated with IFN-γ. In contrast, the accumulation of IFN-γ-dependent gene transcripts is suppressed in cells infected with the wild-type virus, in cells infected with the ΔUS3 mutant virus, and to a lesser extent in the ΔUL41 virus-infected cells. The accumulation of IFN-γ-dependent gene transcripts in ΔUL41-infected cells could be due at least in part to a significant delay and reduction in the accumulation of the US3 protein. The results suggest that the expression of IFN-γ-dependent genes is blocked independently by the degradation of IFN-γ-dependent gene transcripts—a function of the virion host shutoff RNase—and by posttranslational modification of the IFN-γRα protein.
Synthesis of Some Impurities and/or Degradation Products of Atorvastatin
Authors: Stach Jan , Havlíček Jaroslav , Plaček Lukáš , Rádl Stanislav 
Published: March 2008

Synthesis of some impurities and/or degradation products of atorvastatin, calcium (3R,5R)-7- [2-(4-fluorophenyl)-5-isopropyl-3-phenyl-4-(phenylcarbamoyl)pyrrol-1-yl]-3,5-dihydroxyheptanoate, is described. These include its desfluoro analog, the corresponding (3S,5S)- and (3S,5R)-epimers, atorvastatin lactone, and some other potential impurities. The synthesized compounds as well as the corresponding intermediates were characterized by 1H NMR, 13C NMR and MS.
Automated immunostaining of cell smears: an alternative to flow cytometry
Authors: Happerfield L C , Saward R , Grimwade L , Bloxham D , Erber W N 
Published: March 2008

Aims:To assess the applicability of an automated tissue immunostainer machine for the phenotypic analysis of peripheral blood and bone marrow aspirate smears.Methods:Air-dried smears of peripheral blood and bone marrow from normal individuals and 14 patients with haematological malignancies were stained, following fixation, with a range of antibodies to haemopoietic antigens using both immunoperoxidase and immuno-alkaline phosphatase methods on the Bond-maX (Leica Microsystems) automated immunostaining machine.Results:Automated protocols used for staining formalin-fixed paraffin-embedded tissue could be applied to cell smears, giving high quality staining with excellent cytological detail and antigenic preservation for an extensive antibody panel. Optimal quality (morphological preservation and antigen detection without background staining) was obtained with an alkaline phosphatase method and Fast Red chromogenic substrate. Both cell surface and intracellular (cytoplasmic and nuclear) antigens could be detected and gave the expected reactivity.Conclusions:Automated immunostaining is possible for haematological smears. It generates consistent high quality staining, with the exception of surface immunoglobulin, and is applicable to haematological and, potentially, cytological smears. It provides a practical alternative to flow cytometry and will have particular application when smears are available and there is no suitable sample for flow cytometry.
A Generalized Subsurface Flow Parameterization Considering Subgrid Spatial Variability of Recharge and Topography
Authors: Huang Maoyi , Liang Xu , Leung L. Ruby 
Published: March 2008

Abstract
Subsurface flow is an important hydrologic process and a key component of the water budget. Through its direct impacts on soil moisture, it can affect water and energy fluxes at the land surface and influence the regional climate and water cycle. In this study, a new subsurface flow formulation is developed that incorporates the spatial variability of both topography and recharge. It is shown through theoretical derivation and case studies that the power-law and exponential subsurface flow parameterizations and the parameterization proposed by Woods et al. are all special cases of the new formulation. The subsurface flows calculated using the new formulation compare well with values derived from observations at Tulpehocken Creek, Pennsylvania, and Walnut Creek, Iowa. Sensitivity studies show that when the spatial variability of topography or recharge, or both is increased, the subsurface flows increase at the two aforementioned sites and at the Maimai hillslope, New Zealand. This is likely due to enhancement of interactions between the groundwater table and the land surface that reduce the flow path. An important conclusion of this study is that the spatial variability of recharge alone, and/or in combination with the spatial variability of topography can substantially alter the behaviors of subsurface flows. This suggests that in macroscale hydrologic models or land surface models, subgrid variations of recharge and topography can make significant contributions to the grid mean subsurface flow and must be accounted for in regions with large surface heterogeneity. This is particularly true for regions with humid climate and a relatively shallow groundwater table where the combined impacts of spatial variability of recharge and topography are shown to be more important. For regions with an arid climate and a relatively deep groundwater table, simpler formulations, for example, the power law, for subsurface flow can work well, and the impacts of subgrid variations of recharge and topography may be ignored.
Performance of ventilators for noninvasive positive-pressure ventilation in children
Authors: Fauroux B. , Leroux K. , Desmarais G. , Isabey D. , Clément A. , Lofaso F. , Louis B. 
Published: March 2008

The aim of the present study was to evaluate the performance characteristics of all the ventilators proposed for home noninvasive positive-pressure ventilation in children in France.The ventilators (one volume-targeted, 12 pressure-targeted and four dual) were evaluated on a bench which simulated six different paediatric ventilatory patterns. For each ventilator, the quality of the inspiratory and expiratory trigger and the ability to reach and maintain the preset pressures and volumes were evaluated with the six patient profiles.The performance of the ventilators showed great variability, and depended upon the type of trigger (flow or pressure), type of circuit and patient profile. Differences were observed between the preset and measured airway pressure and between the tidal volume measured by the ventilator and on the bench. Leaks were associated with an inability to detect the patient’s inspiratory effort or autotriggering. No single ventilator was able to adequately ventilate the six paediatric profiles. Only a few ventilators were able to ventilate the profiles simulating the youngest patients.A systematic paediatric bench evaluation is recommended for every ventilator proposed for home ventilation, in order to detect any dysfunction and guide the choice of the appropriate ventilator for a specific patient.
Extracellular matrix components and regulators in the airway smooth muscle in asthma
Authors: Araujo B. B. , Dolhnikoff M. , Silva L. F. F. , Elliot J. , Lindeman J. H. N. , Ferreira D. S. , Mulder A. , Gomes H. A. P. , Fernezlian S. M. , James A. , Mauad T. 
Published: March 2008

There is an intimate relationship between the extracellular matrix (ECM) and smooth muscle cells within the airways. Few studies have comprehensively assessed the composition of different ECM components and its regulators within the airway smooth muscle (ASM) in asthma.With the aid of image analysis, the fractional areas of total collagen and elastic fibres were quantified within the ASM of 35 subjects with fatal asthma (FA) and compared with 10 nonfatal asthma (NFA) patients and 22 nonasthmatic control cases. Expression of collagen I and III, fibronectin, versican, matrix metalloproteinase (MMP)-1, -2, -9 and -12 and tissue inhibitor of metalloproteinase-1 and -2 was quantified within the ASM in 22 FA and 10 control cases.In the large airways of FA cases, the fractional area of elastic fibres within the ASM was increased compared with NFA and controls. Similarly, fibronectin, MMP-9 and MMP-12 were increased within the ASM in large airways of FA cases compared with controls. Elastic fibres were increased in small airways in FA only in comparison with NFA cases.There is altered extracellular matrix composition and a degradative environment within the airway smooth muscle in fatal asthma patients, which may have important consequences for the mechanical and synthetic functions of airway smooth muscle.
Ranking analysis of F-statistics for microarray data
Authors: Tan Yuan-De , Fornage Myriam , Xu Hongyan 
Published: March 2008

AbstractBackgroundMicroarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Methods for large-scale statistical analyses have been developed but most of them are applicable to two-sample or two-condition data.ResultsWe developed a large-scale multiple-groupF-test based method, named ranking analysis ofF-statistics (RAF), which is an extension of ranking analysis of microarray data (RAM) for two-sample t-test. In this method, we proposed a novel random splitting approach to generate the null distribution instead of using permutation, which may not be appropriate for microarray data. We also implemented a two-simulation strategy to estimate the false discovery rate. Simulation results suggested that it has higher efficiency in finding differentially expressed genes among multiple classes at a lower false discovery rate than some commonly used methods. By applying our method to the experimental data, we found 107 genes having significantly differential expressions among 4 treatments at <0.7% FDR, of which 31 belong to the expressed sequence tags (ESTs), 76 are unique genes who have known functions in the brain or central nervous system and belong to six major functional groups.ConclusionOur method is suitable to identify differentially expressed genes among multiple groups, in particular, when sample size is small.