bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computed tomography‐guided transthoracic fine‐needle aspiration in diagnosis of lung cancer: A comparison of single‐pass needle and multiple‐pass coaxial needle systems and the value of immediate cytological assessment
Authors: KÜÇÜK ÇAğla Uyanusta , YILMAZ Adnan , YILMAZ Aynur , AKKAYA Esen 
Published: September 2004

Objectives:  The aim of the present study was to compare single‐pass needle and multiple‐pass coaxial needle systems and to evaluate the value of immediate cytological assessment during the procedure in the diagnosis of lung cancer with CT‐guided transthoracic fine‐needle aspiration.Methodology:  One hundred and forty‐three consecutive patients who underwent CT‐guided transthoracic fine‐needle aspiration were divided into three groups. In the first group (group A, 48 patients), a single‐pass needle was used for aspiration, but immediate cytological examination was not performed. In the second group (group B, 48 patients), a single‐pass needle was used for aspiration and a pathologist immediately assessed the adequacy of the sample obtained. In the third group (group C, 47 patients), a multiple‐pass coaxial needle was used for aspiration and a pathologist immediately assessed the adequacy of the sample obtained.Results:  The mean number of fine‐needle aspirations was 1.25 in group A, 1.39 in group B and 1.34 in group C (group A vs group B, P = 0.08). The diagnostic accuracy was 83.3, 97.9 and 100.0%, respectively (group A vs group B, P = 0.03; group B vs group C, P > 0.05). Although immediate cytological assessment resulted in adequate samples being obtained from all patients in groups B and C, adequate samples were obtained in 41 of 48 patients (85.4%) in group A (P = 0.004). There was no statistically significant difference among the groups with respect to the rate of pneumothorax.Conclusions:  A single‐pass needle technique in transthoracic fine‐needle aspiration is preferred because there is no significant difference between single‐pass needle and multiple‐pass coaxial needle systems with respect to the diagnostic accuracy and the complication rate and, in addition, the single‐pass needle has a lower cost. The results of the present study suggest that immediate cytological assessment during the procedure reduces an inadequate sampling rate, thus increasing the diagnostic accuracy of the procedure.
Defining, Measuring, and Comparing Organisational Cultures
Authors: Van Den Berg Peter T. , Wilderom Celeste P.M. 
Published: September 2004

La littérature portant sur la culture des organisations souffre d’un manque manifeste d’enquêtes extensives débouchant sur des études comparatives. Afin de rendre plus comparables les cultures organisationnelles, nous proposons une définition et une série de dimensions. La culture organisationnelle renverrait aux perceptions communes des pratiques de travail dans le cadre des unités constitutives des organisations. A l’examen d’études empiriques, les cinq dimensions suivantes nous sont apparues: autonomie, orientation externe, coordination interdépartementale, orientation vers les ressources humaines et orientation vers le développement. L’utilisation de cette définition et de ces dimensions générales devrait faciliter la comparaison des cultures organisationnelles et l’accumulation de résultats.Within the body of organisation culture literature, there is a conspicuous absence of large‐scale studies reporting on comparative studies. In order to increase comparability of organisational cultures we propose a definition and a set of dimensions. Organisational culture is defined as shared perceptions of organisational work practices within organisational units. On the basis of empirical studies we discerned the following five dimensions: autonomy, external orientation, interdepartmental coordination, human resource orientation, and improvement orientation. Use of this definition and a set of such generic dimensions would facilitate the comparison of organisational cultures and the accumulation of research findings.
Identification of Candidate Gammaherpesvirus 68 Genes Required for Virus Replication by Signature-Tagged Transposon Mutagenesis
Authors: Moorman Nathaniel J. , Lin Chie Yu , Speck Samuel H. 
Published: September 2004

ABSTRACT

Current methods for determining the role of a given gene product in the gammaherpesvirus 68 (γHV68) life cycle require generation of a specific mutation by either homologous recombination in mammalian cells or bacterial artificial chromosome-mediated mutagenesis in
Escherichia coli
. The mutant virus is then compared to wild-type virus, and the role of the gene in the viral life cycle is deduced from its phenotype. This process is both time-consuming and labor intensive. Here we present the use of random, transposon-mediated signature-tagged mutagenesis for the identification of candidate viral genes involved in virus replication. Pools of viral mutants, each containing a random insertion of a transposon, were generated with a transposon donor library in which each transposon contains a unique sequence identifier. These pools were transfected into mammalian cells, and the ability of each mutant to replicate was assessed by comparing the presence of virus in the output pool to that present in the input pool of viral genomes. With this approach we could rapidly screen up to 96 individual mutants simultaneously. The location of the transposon insertion was determined by sequencing individual clones with a common primer specific for the transposon end. Here we present the characterization of 53 distinct viral mutants that correspond to insertions in 29 open reading frames within the γHV68 genome. To confirm the results of the signature-tagged mutagenesis screen, we quantitated the ability of each mutant to replicate compared to wild-type γHV68. From these analyses we identified 16 γHV68 open reading frames that, when disrupted by transposon insertions, score as essential for virus replication, and six other open reading frames whose disruption led to significant attenuation of virus replication. In addition, transposon insertion in five other γHV68 open reading frames did not affect virus replication. Notably, all but one of the candidate essential replication genes identified in this screen have been shown to be essential for the replication of at least one other herpesvirus.
Direct Evidence for a Chronic CD8+-T-Cell-Mediated Immune Reaction to Tax within the Muscle of a Human T-Cell Leukemia/Lymphoma Virus Type 1-Infected Patient with Sporadic Inclusion Body Myositis
Authors: Ozden Simona , Cochet Madeleine , Mikol Jacqueline , Teixeira Antonio , Gessain Antoine , Pique Claudine 
Published: September 2004

ABSTRACTHuman T-cell leukemia/lymphoma virus type 1 (HTLV-1) infection can lead to the development of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), concomitantly with or without other inflammatory disorders such as myositis. These pathologies are considered immune-mediated diseases, and it is assumed that migration within tissues of both HTLV-1-infected CD4+T cells and anti-HTLV-1 cytotoxic T cells represents a pivotal event. However, although HTLV-1-infected T cells were found in inflamed lesions, the antigenic specificity of coinfiltrated CD8+T cells remains to be determined. In this study, we performed both ex vivo and in situ analyses using muscle biopsies obtained from an HTLV-1-infected patient with HAM/TSP and sporadic inclusion body myositis. We found that both HTLV-1-infected CD4+T cells and CD8+T cells directed to the dominant Tax antigen can be amplified from muscle cell cultures. Moreover, we were able to detect in two successive muscle biopsies bothtaxmRNA-positive mononuclear cells and T cells recognized by the Tax11-19/HLA-A*02 tetramer and positive for perforin. These findings provide the first direct demonstration that anti-Tax cytotoxic T cells are chronically recruited within inflamed tissues of an HTLV-1 infected patient, which validates the cytotoxic immune reaction model for the pathogenesis of HTLV-1-associated inflammatory disease.
ORF73 of Herpesvirus Saimiri, a Viral Homolog of Kaposi's Sarcoma-Associated Herpesvirus, Modulates the Two Cellular Tumor Suppressor Proteins p53 and pRb
Authors: Borah Sumit , Verma Subhash C. , Robertson Erle S. 
Published: September 2004

ABSTRACT
All known DNA tumor viruses are known to target and inactivate two main cell cycle regulatory proteins, retinoblastoma protein (pRb) and p53. Inactivation of pRb promotes host cell cycle progression into S phase, and inactivation of p53 promotes cell immortalization. The DNA tumor virus Kaposi's sarcoma associated herpesvirus (KSHV)-encoded latency-associated nuclear antigen (LANA) was shown to target and inactivate pRb as well as p53. In this report we provide evidence that these functions are conserved in the homologous protein encoded by the related gammaherpesvirus herpesvirus saimiri (HVS). ORF73, the HVS homologue of LANA, is shown to bind both p53 and pRb in vitro and in vivo, to colocalize with p53 in human T cells infected with HVS, and in cells overexpressing both ORF73 and p53, as well as to adversely influence pRB/E2F and p53 transcriptional regulation. The C terminus of LANA, the region most highly conserved in ORF73, is shown to be responsible for both pRb and p53 interactions, supporting the hypothesis that these functions are conserved in both homologues. Finally, the region of p53 targeted by LANA (and ORF73) maps to the domain required for tetramerization. However, preliminary cross-linking studies do not detect disruption of p53 tetramerization by either LANA or HVS-encoded ORF73, suggesting that p53 inactivation may be by a mechanism independent of tetramer disruption.
Latency-Associated Nuclear Antigen of Kaposi's Sarcoma-Associated Herpesvirus Up-Regulates Transcription of Human Telomerase Reverse Transcriptase Promoter through Interaction with Transcription Factor Sp1
Authors: Verma Subhash C. , Borah Sumit , Robertson Erle S. 
Published: September 2004

ABSTRACT
Telomerase is required for the maintenance of telomere length and is an important determinant for cell immortalization. In human cells, telomerase activity is due to the expression of its enzymatic subunit, human telomerase reverse transcriptase (hTERT). The expression of hTERT is not typically detectable in healthy somatic human cells but is present in cancerous tissues and immortalized cells. We have previously shown that hTERT promoter activity is up-regulated by the Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded latency-associated nuclear antigen (LANA). LANA is expressed in all forms of human malignancies associated with KSHV. The hTERT promoter sequence located at positions −130 to +5 contains several Sp1 binding motifs and was shown be important for up-regulation by LANA. In this report, we demonstrate that hTERT promoter activity is due to the direct interaction of LANA with Sp1. The interaction of LANA with Sp1 was demonstrated through in vitro binding experiments and coimmunoprecipitation and is supported by the colocalization of these two molecules in the nuclei of KSHV-infected cells. Moreover, LANA modulates Sp1-mediated transcription in transient GAL4 fusion reporter assays. Mapping of the regions involved in binding and transcriptional activation showed that the amino terminus of LANA is the major site for interaction and up-regulation but that it can cooperate with the carboxy terminus to enhance these functions. An analysis of Sp1 binding to its cognate sequence corroborated the binding data. Together, our results suggest that the interaction of LANA with Sp1 up-regulates the telomerase promoter, potentially contributing to the immortalization of KSHV-infected cells.
Human Cytomegalovirus UL84 Insertion Mutant Defective for Viral DNA Synthesis and Growth
Authors: Xu Yiyang , Cei Sylvia A. , Huete Alicia Rodriguez , Pari Gregory S. 
Published: September 2004

ABSTRACT

Human cytomegalovirus (HCMV) UL84 is required for
ori
Lyt-dependent DNA replication, and evidence from transient transfection assays suggests that UL84 directly participates in DNA synthesis. In addition, because of its apparent interaction with IE2, UL84 is implicated as a possible regulatory protein. To address the role of UL84 in the context of the viral genome, we generated a recombinant HCMV bacterial artificial chromosome (BAC) construct that did not express the UL84 gene product. This construct, BAC-IN84/Ep, displayed a null phenotype in that it failed to produce infectious virus after transfection into human fibroblast cells, whereas a revertant virus readily produced viral plaques and, subsequently, infectious virus. Real-time quantitative PCR showed that BAC-IN84/Ep was defective for DNA synthesis in that no increase in the accumulation of viral DNA was observed in transfected cells. We were unable to complement BAC-IN84/Ep in
trans
; however,
ori
Lyt-dependent DNA replication was observed by the cotransfection of UL84 and BAC-IN84/Ep. An analysis of viral mRNA by real-time PCR indicated that, even in the absence of DNA synthesis, all representative kinetic classes of genes were expressed in cells transfected with BAC-IN84/Ep. The detection of UL44 and IE2 by immunofluorescence in BAC-IN84/Ep-transfected cells showed that these proteins failed to partition into replication compartments, indicating that UL84 expression is essential for the formation of these proteins into replication centers within the context of the viral genome. These results show that UL84 provides an essential DNA replication function and influences the subcellular localization of other viral proteins.
Timing and Reconstruction of the Most Recent Common Ancestor of the Subtype C Clade of Human Immunodeficiency Virus Type 1
Authors: Travers Simon A. A. , Clewley Jonathan P. , Glynn Judith R. , Fine Paul E. M. , Crampin Amelia C. , Sibande Felix , Mulawa Dominic , McInerney James O. , McCormack Grace P. 
Published: September 2004

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) subtype C is responsible for more than 55% of HIV-1 infections worldwide. When this subtype first emerged is unknown. We have analyzed all available
gag
(p17 and p24) and
env
(C2-V3) subtype C sequences with known sampling dates, which ranged from 1983 to 2000. The majority of these sequences come from the Karonga District in Malawi and include some of the earliest known subtype C sequences. Linear regression analyses of sequence divergence estimates (with four different approaches) were plotted against sample year to estimate the year in which there was zero divergence from the reconstructed ancestral sequence. Here we suggest that the most recent common ancestor of subtype C appeared in the mid- to late 1960s. Sensitivity analyses, by which possible biases due to oversampling from one district were explored, gave very similar estimates.
The Raft-Promoting Property of Virion-Associated Cholesterol, but Not the Presence of Virion-Associated Brij 98 Rafts, Is a Determinant of Human Immunodeficiency Virus Type 1 Infectivity
Authors: Campbell Shahan , Gaus Katharina , Bittman Robert , Jessup Wendy , Crowe Suzanne , Mak Johnson 
Published: September 2004

ABSTRACT
Lipid rafts are enriched in cholesterol and sphingomyelin and are isolated on the basis of insolubility in detergents, such as Brij 98 and Triton X-100. Recent work by Holm et al. has shown that rafts insoluble in Brig 98 can be found in human immunodeficiency virus type 1 (HIV-1) virus-like particles, although it is not known whether raft-like structures are present in authentic HIV-1 and it is unclear whether a virion-associated raft-like structure is required for HIV replication. Independently, it was previously reported that virion-associated cholesterol is critical for HIV-1 infectivity, although the specific requirement of virion cholesterol in HIV-1 was not examined. In the present study, we have demonstrated that infectious wild-type HIV-1 contains Brij 98 rafts but only minimal amounts of Triton X-100 rafts. To directly assess the functional requirement of virion-associated rafts and various features of cholesterol on HIV-1 replication, we replaced virion cholesterol with exogenous cholesterol analogues that have demonstrated either raft-promoting or -inhibiting capacity in model membranes. We observed that variable concentrations of exogenous analogues are required to replace a defined amount of virion-associated cholesterol, showing that structurally diverse cholesterol analogues have various affinities toward HIV-1. We found that replacement of 50% of virion cholesterol with these exogenous cholesterol analogues did not eliminate the presence of Brij 98 rafts in HIV-1. However, the infectivity levels of the lipid-modified HIV-1s directly correlate with the raft-promoting capacities of these cholesterol analogues. Our data provide the first direct assessment of virion-associated Brij 98 rafts in retroviral replication and illustrate the importance of the raft-promoting property of virion-associated cholesterol in HIV-1 replication.
Enhanced Cytoplasmic Sequestration of the Nuclear Export Receptor CRM1 by NS2 Mutations Developed in the Host Regulates Parvovirus Fitness
Authors: López-Bueno Alberto , Valle Noelia , Gallego Jesús M. , Pérez Joel , Almendral José M. 
Published: September 2004

ABSTRACT
To investigate whether a DNA virus can evade passive immunotherapy with a polyclonal antiserum, we analyzed the protection of a neutralizing capsid antiserum against a lethal infection of the immunosuppressive strain of the parvovirus minute virus of mice (MVMi) in 42 immunodeficient mice over a period of 200 days. A few mice were effectively protected, but most developed a delayed lethal leukopenic syndrome during the treatment or weeks afterwards. Unexpectedly, viruses isolated from treated but also from control leukopenic mice showed no amino acid changes throughout the entire capsid coding region, although the viral populations were genetically heterogeneous, mainly in the second exon of the coding sequence of the NS2 nonstructural protein. The NS2 point amino acid changes (T88A, K96E, L103P, and L153 M) that were consistently selected in several mice clustered within the nuclear exportin CRM1 binding domain, in a reading frame that did not alter the overlapping NS1 coding region. These mutations endowed emerging viruses with an increased fitness that was demonstrable by their relative resistance to the neutralizing capsid antiserum in a postentry plaque-forming assay, the rapid overgrowth of a competing wild-type (wt) population in culture, and a larger yield of infectious particles. Mutant NS2 proteins interacted with a higher affinity and sequestered CRM1 in the perinuclear region of the cytoplasm more efficiently than the wt. Correspondingly this phenomenon, as well as the following timely ordered release of the NS1 nonstructural protein and the empty capsid from the nucleus to the cytoplasm, occurred markedly earlier in the infection cycle of the mutant viruses. We hypothesize that the enhanced cytoplasmic sequestration of CRM1 by the NS2 mutations selected in mice may trigger pleiotropic effects leading to an accelerated MVMi life cycle and thus to increased fitness. These results strengthen our earlier report on the rapid evolutionary capacity of this mammalian-specific DNA virus in vivo and indicate that the NS2-CRM1 interaction is an important determinant of parvovirus virulence that can be modulated in nature, hampering the effectiveness of passive antibody therapies in the long term.
Mapping the Golgi Targeting and Retention Signal of Bunyamwera Virus Glycoproteins
Authors: Shi Xiaohong , Lappin David F. , Elliott Richard M. 
Published: September 2004

ABSTRACT

The membrane glycoproteins (Gn and Gc) of
Bunyamwera virus
(BUN; family
Bunyaviridae
) accumulate in the Golgi complex, where virion maturation occurs. The Golgi targeting and retention signal has previously been shown to reside within the Gn protein. A series of truncated Gn and glycoprotein precursor cDNAs were constructed by progressively deleting the coding region of the transmembrane domain (TMD) and the cytoplasmic tail. We also constructed chimeric proteins of BUN Gc, enhanced green fluorescent protein (EGFP), and human respiratory syncytial virus (HRSV) fusion (F) protein that contain the Gn TMD with various lengths of its adjacent cytoplasmic tails. The subcellular localization of mutated BUN glycoproteins and chimeric proteins was investigated by double-staining immunofluorescence with antibodies against BUN glycoproteins or the HRSV F protein and with antibodies specific for the Golgi complex. The results revealed that Gn and all truncated Gn proteins that contained the intact TMD (residues 206 to 224) were able to translocate to the Golgi complex and also rescued the Gc protein, which is retained in the endoplasmic reticulum when expressed alone, to this organelle. The rescued Gc proteins acquired endo-β-
N
-acetylglucosaminidase H resistance. The Gn TMD could also target chimeric EGFP to the Golgi and retain the F protein, which is characteristically expressed on the surface of HRSV-infected cells, in the Golgi. However, chimeric BUN Gc did not translocate to the Golgi, suggesting that an interaction with Gn is involved in Golgi retention of the Gc protein. Collectively, these data demonstrate that the Golgi targeting and retention signal of BUN glycoproteins resides in the TMD of the Gn protein.
A Riboswitch Regulates RNA Dimerization and Packaging in Human Immunodeficiency Virus Type 1 Virions
Authors: Ooms Marcel , Huthoff Hendrik , Russell Rodney , Liang Chen , Berkhout Ben 
Published: September 2004

ABSTRACT

The genome of retroviruses, including human immunodeficiency virus type 1 (HIV-1), consists of two identical RNA strands that are packaged as noncovalently linked dimers. The core packaging and dimerization signals are located in the downstream part of the untranslated leader of HIV-1 RNA—the Ψ and the dimerization initiation site (DIS) hairpins. The HIV-1 leader can adopt two alternative conformations that differ in the presentation of the DIS hairpin and consequently in their ability to dimerize in vitro. The branched multiple-hairpin (BMH) structure folds the poly(A) and DIS hairpins, but these domains are base paired in a long distance interaction (LDI) in the most stable LDI conformation. This LDI-BMH riboswitch regulates RNA dimerization in vitro. It was recently shown that the Ψ hairpin structure is also presented differently in the LDI and BMH structures. Several detailed in vivo studies have indicated that sequences throughout the leader RNA contribute to RNA packaging, but how these diverse mutations affect the packaging mechanism is not known. We reasoned that these effects may be due to a change in the LDI-BMH equilibrium, and we therefore reanalyzed the structural effects of a large set of leader RNA mutations that were presented in three previous studies (J. L. Clever, D. Mirandar, Jr., and T. G. Parslow, J. Virol.
76:
12381-12387, 2002; C. Helga-Maria, M. L. Hammarskjold, and D. Rekosh, J. Virol.
73:
4127-4135, 1999; R. S. Russell, J. Hu, V. Beriault, A. J. Mouland, M. Laughrea, L. Kleiman, M. A. Wainberg, and C. Liang, J. Virol.
77:
84-96, 2003). This analysis revealed a strict correlation between the status of the LDI-BMH equilibrium and RNA packaging. Furthermore, a correlation is apparent between RNA dimerization and RNA packaging, and these processes may be coordinated by the same LDI-BMH riboswitch mechanism.