bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation of routinely used coagulation parameters and presence of portal vein thrombosis in patients with liver cirrhosis
Authors: Weber Andreas , Krebs Stephanie , Lenhardt Cosima , Wagenpfeil Stefan , Schmid Roland M. , Schulte‐Frohlinde Ewert 
Published: July 2009

Aim:  Portal vein thrombosis (PVT) is a serious complication in patients with liver cirrhosis. In patients with advanced stages of liver cirrhosis plasmatic coagulation and platelet count are often reduced. However, patients with normal coagulation status might carry a high risk for developing PVT. A correlation between coagulation status used in clinical routine and the incidence of PVT in patients with liver cirrhosis has been evaluated in the present retrospective analysis.Methods:  88 patients with liver cirrhosis were identified by screening a database. Of these patients, 23 suffered from PVT. Patients were classified according to the Child–Pugh classification. Patients were subdivided into early stages (Child A) and advanced stages (Child B/C) of liver cirrhosis.Results:  In patients with Child–Pugh A cirrhosis, there was no difference in activated partial thromboplastin time (apTT), international normalized ratio (INR), and platelet count between the PVT (n = 7) and the control group (n = 35). In contrast, the median apTT and INR were significantly lower in patients with Child B/C cirrhosis and PVT (n = 16) in comparison with patients without PVT (37 s vs 43 s [P = 0.017] and 1.25 vs 1.40 [P = 0.022]), respectively. Platelet count did not differ significantly in patients with advanced liver cirrhosis and PVT from those without PVT.Conclusion:  Patients with advanced liver cirrhosis and PVT displayed lower apTT and INR compared with those without PVT. Therefore, patients with advanced liver cirrhosis and almost normal coagulation parameters might be at particular risk of developing PVT. The results suggest that regular monitoring using Doppler‐ultrasound should be carried out in these patients, especially when liver transplantation is intended.
Bicentric Evaluation of Six Anti-Toxoplasma Immunoglobulin G (IgG) Automated Immunoassays and Comparison to the Toxo II IgG Western Blot
Authors: Maudry Arnaud , Chene Gautier , Chatelain Rémi , Patural Hugues , Bellete Bahrie , Tisseur Bernard , Hafid Jamal , Raberin Hélène , Beretta Sophie , Tran Manh Sung Roger , Belot Georges , Flori Pierre 
Published: July 2009

ABSTRACT

A comparative study of the Toxoplasma IgG
I
and IgG
II
Access (Access I and II, respectively; Beckman Coulter Inc.), AxSYM Toxo IgG (AxSYM; Abbott Diagnostics), Vidas Toxo IgG (Vidas; bioMerieux, Marcy l'Etoile, France), Immulite Toxo IgG (Immulite; Siemens Healthcare Diagnostics Inc.), and Modular Toxo IgG (Modular; Roche Diagnostics, Basel, Switzerland) tests was done with 406 consecutive serum samples. The Toxo II IgG Western blot (LDBio, Lyon, France) was used as a reference technique in the case of intertechnique discordance. Of the 406 serum samples tested, the results for 35 were discordant by the different techniques. Using the 175 serum samples with positive results, we evaluated the standardization of the titrations obtained (in IU/ml); the medians (second quartiles) obtained were 9.1 IU/ml for the AxSYM test, 21 IU/ml for the Access I test, 25.7 IU/ml for the Access II test, 32 IU/ml for the Vidas test, 34.6 IU/ml for the Immulite test, and 248 IU/ml for the Modular test. For all the immunoassays tested, the following relative sensitivity and specificity values were found: 89.7 to 100% for the Access II test, 89.7 to 99.6% for the Immulite test, 90.2 to 99.6% for the AxSYM test, 91.4 to 99.6% for the Vidas test, 94.8 to 99.6% for the Access I test, and 98.3 to 98.7% for the Modular test. Among the 406 serum samples, we did not find any false-positive values by two different tests for the same serum sample. Except for the Modular test, which prioritized sensitivity, it appears that the positive cutoff values suggested by the pharmaceutical companies are very high (either for economical or for safety reasons). This led to imperfect sensitivity, a large number of unnecessary serological follow-ups of pregnant women, and difficulty in determining the serological status of immunosuppressed individuals.
Prevalence of CTX-M β-Lactamases in Philadelphia, Pennsylvania
Authors: McGettigan Shannon E. , Hu Baofeng , Andreacchio Kathleen , Nachamkin Irving , Edelstein Paul H. 
Published: July 2009

ABSTRACT

CTX-M β-lactamases were thought to be rare in the United States, but a recent study in Texas showed that up to 70% of extended-spectrum β-lactamase (ESBL)-containing members of the
Enterobacteriaceae
family were CTX-M positive (J. S. Lewis, M. Herrera, B. Wickes, J. E. Patterson, and J. H. Jorgensen, Antimicrob. Agents Chemother. 51:4015-4021, 2007). We used PCR to detect CTX-M in all 291 extended-spectrum cephalosporin-resistant gram-negative bacteria isolated in our laboratory during 2007. Thirty (48%)
Escherichia coli
isolates, 6 (3%)
Klebsiella
sp. isolates, and 7 (100%)
Proteus mirabilis
isolates tested were CTX-M positive, with 15% of all
Enterobacteriaceae
tested being positive. The
E. coli
CTX-M groups were I (57%), IV (37%), II (3%), and not groupable (3%); three of the group IV isolates were positive for CTX-M-18, and three of the group I isolates were positive for CTX-M-15. One of seven positive
P. mirabilis
isolates was in group II, with the remainder being positive for a CTX-M-25-like β-lactamase; and 33% of the
Klebsiella
sp. isolates were in group I or IV, with the remainder not being in groups I to IV. CTX-M-producing bacteria were isolated from urine (
n
= 13), blood (
n
= 13), wounds (
n
= 12), and the respiratory tract (
n
= 4). All 31 CTX-M-positive isolates tested for the presence of ESBL were confirmed to produce ESBLs by the use of tests recommended by the CLSI. Pulsed-field gel electrophoresis of the CTX-M-positive isolates showed that six
P. mirabilis
isolates were clonal and that there were seven different
E. coli
clusters. Five of seven
P. mirabilis
isolates were from blood cultures. The CLSI tests for the confirmation of ESBL production reliably detect these isolates if both cefotaxime and ceftazidime are tested, but only about half would be classified as a possible CTX-M producers on the basis of the antibiogram alone. A new panprimer set increases the ability to detect CTX-M-producing strains. CTX-M-positive bacteria are common in our geographic region, are often invasive, and, with the exception of
P. mirabilis
, are multiclonal.
Rapid and Highly Sensitive Neuraminidase Subtyping of Avian Influenza Viruses by Use of a Diagnostic DNA Microarray
Authors: Gall Astrid , Hoffmann Bernd , Harder Timm , Grund Christian , Ehricht Ralf , Beer Martin 
Published: July 2009

ABSTRACT
Rapid neuraminidase subtyping of avian influenza viruses from diagnostic samples is crucial considering the existence of permanently emerging and evolving strains. Here we report an easy-to-use, low-cost microarray for neuraminidase subtyping following fragment amplification by a generic, neuraminidase-specific reverse transcription-PCR (RT-PCR). This method enables highly specific characterization with a sensitivity equal to that of matrix gene-specific real-time RT-PCR.
Naturally Occurring Hepatitis C Virus Subgenomic Deletion Mutants Replicate Efficiently in Huh-7 Cells and Are
trans
-Packaged In Vitro To Generate Infectious Defective Particles
Authors: Pacini Laura , Graziani Rita , Bartholomew Linda , De Francesco Raffaele , Paonessa Giacomo 
Published: July 2009

ABSTRACT

Naturally occurring hepatitis C virus (HCV) subgenomic RNAs have been found in several HCV patients. These subgenomic deletion mutants, mostly lacking the genes encoding envelope glycoproteins, were found in both liver and serum, where their relatively high abundance suggests that they are capable of autonomous replication and can be packaged and secreted in viral particles, presumably harboring the envelope proteins from wild type virus coinfecting the same cell. We recapitulated some of these natural subgenomic deletions in the context of the isolate JFH-1 and confirmed these hypotheses in vitro. In Huh-7.5 cells, these deletion-containing genomes show robust replication and can be efficiently
trans
-packaged and infect naïve Huh-7.5 cells when cotransfected with the full-length wild-type J6/JFH genome. The genome structure of these natural subgenomic deletion mutants was dissected, and the maintenance of both core and NS2 regions was proven to be significant for efficient replication and
trans
-packaging. To further explore the requirements needed to achieve
trans
-complementation, we provided different combinations of structural proteins in
trans
. Optimal
trans
-complementation was obtained when fragments of the polyprotein encompassing core to p7 or E1 to NS2 were expressed. Finally, we generated a stable helper cell line, constitutively expressing the structural proteins from core to p7, which efficiently supports
trans
-complementation of a subgenomic deletion encompassing amino acids 284 to 732. This cell line can produce and be infected by defective particles, thus representing a powerful tool to investigate the life cycle and relevance of natural HCV subgenomic deletion mutants in vivo.
The Genome of Human Parvovirus B19 Can Replicate in Nonpermissive Cells with the Help of Adenovirus Genes and Produces Infectious Virus
Authors: Guan Wuxiang , Wong Susan , Zhi Ning , Qiu Jianming 
Published: July 2009

ABSTRACTHuman parvovirus B19 (B19V) is a member of the genusErythrovirusin the familyParvoviridae. In vitro, autonomous B19V replication is limited to human erythroid progenitor cells and in a small number of erythropoietin-dependent human megakaryoblastoid and erythroid leukemic cell lines. Here we report that the failure of B19V DNA replication in nonpermissive 293 cells can be overcome by adenovirus infection. More specifically, the replication of B19V DNA in the 293 cells and the production of infectious progeny virus were made possible by the presence of the adenovirus E2a, E4orf6, and VA RNA genes that emerged during the transfection of the pHelper plasmid. Using this replication system, we identified the terminal resolution site and the nonstructural protein 1 (NS1) binding site on the right terminal palindrome of the viral genome, which is composed of a minimal origin of replication spanning 67 nucleotides. Plasmids or DNA fragments containing an NS1 expression cassette and this minimal origin were able to replicate in both pHelper-transfected 293 cells and B19V-semipermissive UT7/Epo-S1 cells. Our results have important implications for our understanding of native B19V infection.
Differential Incorporation of Cholesterol by Sindbis Virus Grown in Mammalian or Insect Cells
Authors: Hafer Amanda , Whittlesey Rebecca , Brown Dennis T. , Hernandez Raquel 
Published: July 2009

ABSTRACT

Cholesterol has been shown to be essential for the fusion of alphaviruses with artificial membranes (liposomes). Cholesterol has also been implicated as playing an essential and critical role in the processes of entry and egress of alphaviruses in living cells. Paradoxically, insects, the alternate host for alphaviruses, are cholesterol auxotrophs and contain very low levels of this sterol. To further evaluate the role of cholesterol in the life cycle of alphaviruses, the cholesterol levels of the alphavirus Sindbis produced from three different mosquito (
Aedes albopictus
) cell lines; one other insect cell line, Sf21 from
Spodoptera frugiperda
; and BHK (mammalian) cells were measured. Sindbis virus was grown in insect cells under normal culture conditions and in cells depleted of cholesterol by growth in serum delipidated by using Cab-O-sil, medium treated with methyl-β-cyclodextrin, or serum-free medium. The levels of cholesterol incorporated into the membranes of the cells and into the virus produced from these cells were determined. Virus produced from these treated and untreated cells was compared to virus grown in BHK cells under standard conditions. The ability of insect cells to produce Sindbis virus after delipidation was found to be highly cell specific and not dependent on the level of cholesterol in the cell membrane. A very low level of cholesterol was required for the generation of wild-type levels of infectious Sindbis virus from delipidated cells. The data show that one role of the virus membrane is structural, providing the stability required for infectivity that may not be provided by the delipidated membranes in some cells. These data show that the amount of cholesterol in the host cell membrane in and of itself has no effect on the process of virus assembly or on the ability of virus to infect cells. Rather, these data suggest that the cholesterol dependence reported for infectivity and assembly of Sindbis virus is a reflection of differences in the insect cell lines used and the methods of delipidation.
The Immune Adaptor Molecule SARM Modulates Tumor Necrosis Factor Alpha Production and Microglia Activation in the Brainstem and Restricts West Nile Virus Pathogenesis
Authors: Szretter Kristy J. , Samuel Melanie A. , Gilfillan Susan , Fuchs Anja , Colonna Marco , Diamond Michael S. 
Published: July 2009

ABSTRACTSterile alpha and HEAT/Armadillo motif (SARM) is a highly conserved Toll/interleukin-1 receptor (TIR)-containing adaptor protein that is believed to negatively regulate signaling of the pathogen recognition receptors Toll-like receptor 3 (TLR3) and TLR4. To test its physiological function in the context of a microbial infection, we generated SARM−/−mice and evaluated the impact of this deficiency on the pathogenesis of West Nile virus (WNV), a neurotropic flavivirus that requires TLR signaling to restrict infection. Although SARM was preferentially expressed in cells of the central nervous system (CNS), studies with primary macrophages, neurons, or astrocytes showed no difference in viral growth kinetics. In contrast, viral replication was increased specifically in the brainstem of SARM−/−mice, and this was associated with enhanced mortality after inoculation with a virulent WNV strain. A deficiency of SARM was also linked to reduced levels of tumor necrosis factor alpha (TNF-α), decreased microglia activation, and increased neuronal death in the brainstem after WNV infection. Thus, SARM appears to be unique among the TIR adaptor molecules, since it functions to restrict viral infection and neuronal injury in a brain region-specific manner, possibly by modulating the activation of resident CNS inflammatory cells.
Modification and Reorganization of the Cytoprotective Cellular Chaperone Hsp27 during Herpes Simplex Virus Type 1 Infection
Authors: Mathew Shomita S. , Della Selva Megan P. , Burch April D. 
Published: July 2009

ABSTRACTChaperone-enriched domains are formed in the nuclei of cells lytically infected with herpes simplex virus type 1 (HSV-1). These domains, called VICE, forvirusinducedchaperoneenriched, contain Hsc70, Hsp70, Hsp40, Hsp90, polyubiquitinated proteins, and components of the proteasome machinery. Accumulating evidence indicates that these sites may be utilized during infection to sequester misfolded, modified, or otherwise unwanted proteins away from viral replication compartments, sites of robust transcription, DNA synthesis, and capsid maturation. To further explore the role of cellular chaperones and VICE domains during HSV-1 infection, we have analyzed the cytoprotective chaperone Hsp27. Here we present evidence that Hsp27, which is known to possess several antioxidant functions, is rapidly reorganized and modified at early stages in response to HSV-1 infection and signaling from the mitogen-activated protein kinase p38. Immunofluorescence analysis and fractionation experiments reveal disparate subcellular localizations of nonphosphorylated and phosphorylated forms of Hsp27 during wild-type HSV-1 infection. Unmodified forms of Hsp27 are localized in nuclear foci that are outside of replication compartments, adjacent to VICE domains, and in the cytoplasm. Conversely, we find that phosphorylated forms of Hsp27 are localized exclusively in the cytoplasm. Last, in cells depleted of all forms of Hsp27, virus replication is significantly reduced.
Estimation of standing dead tree class distributions in northwest coastal forests using lidar remote sensing
Authors: Bater Christopher W. , Coops Nicholas C. , Gergel Sarah E. , LeMay Valerie , Collins Denis 
Published: July 2009

The amount and variability of living and dead wood in a forest stand are important indicators of forest biodiversity, as it relates to structural heterogeneity and habitat availability. In this study, we investigate whether light detection and ranging (lidar) can be used to estimate the distribution of standing dead tree classes within forests. Twenty-two field plots were established in which each stem (DBH >10 cm) was assigned to a wildlife tree (WT) class. For each plot, a suite of lidar-derived predictor variables were extracted. Ordinal regression using a negative log–log link function was then employed to predict the cumulative proportions of stems within the WT classes. Results indicated that the coefficient of variation of the lidar height data was the best predictor variable (χ2 = 106.11, p < 0.00; Wald = 4.83, p = 0.028). The derived relationships allowed for the prediction of the cumulative proportion of stems within WT classes (r = 0.90, RMSE = 6.0%) and the proportion of dead stems within forest plots (r = 0.61, RMSE = 16.8%). Our research demonstrates the capacity of lidar remote sensing to estimate the relative abundances of standing living and dead trees in forest stands and its ability to characterize vegetation structure across large spatial extents.
Temporal dynamics of large woody debris in small streams of the Alberta foothills, Canada
Authors: Powell S.R. , Daniels L.D. , Jones T.A. 
Published: July 2009

Large woody debris (LWD) is a key link between riparian forests and streams; however, the temporal dynamics of in-stream wood remains poorly quantified. Using dendrochronology, we evaluated the dynamics of five Pinus -dominated and five Picea -dominated riparian forests in the foothills of Alberta and cross-dated the ring widths of 186 pieces of LWD. Time since death of LWD ranged from 2 to 143 years, with maximums of 86 and 143 years for Pinus and Picea, respectively. Recruitment of Pinus LWD was influenced by stand-replacing fires followed by self-thinning about 40 years after stand establishment. In uneven-aged Picea-dominated forests, tree mortality and LWD recruitment were due to fine-scale disturbances. Time since death increased significantly with decay and position classes, which resulted in changes in LWD function through time. LWD persisted in the bridge position for about 30 years. Bridged LWD was least decayed, was significantly longer, and had greater volume than LWD in other positions. LWD remained in partial bridge and loose positions about 15 years and >80 years when submerged in water and buried in sediment. Given the persistence of LWD, we conclude that management that alters wood abundance and recruitment has short- and long-term implications for the structure and function of small streams.
REVIEW OF PROPERTIES OF THE TOP QUARK FROM MEASUREMENTS AT THE TEVATRON
Authors: PLEIER MARC-ANDRÉ 
Published: July 2009

This review summarizes the program in the physics of the top quark being pursued at Fermilab's Tevatron proton–antiproton collider at a center-of-mass energy of 1.96 TeV. More than a decade after the discovery of the top quark at the two collider detectors CDF and D0, the Tevatron has been the only accelerator to produce top quarks and to study them directly.The Tevatron's increased luminosity and center-of-mass energy offer the possibility to scrutinize the properties of this heaviest fundamental particle through new measurements that were not feasible before, such as the first evidence for electroweak production of top quarks and the resulting direct constraints on the involved couplings. Better measurements of top quark properties provide more stringent tests of predictions from the SM of elementary particle physics. In particular, the improvement in measurements of the mass of the top quark, with the latest uncertainty of 0.7% marking the most precisely measured quark mass to date, further constrains the prediction of the mass of the still to be discovered Higgs boson.
Tissue Microarray Validation: A Methodologic Study with Special Reference to Lung Cancer
Authors: Karlsson Christina , Bodin Lennart , Piehl-Aulin Karin , Karlsson Mats G. 
Published: July 2009

Abstract
Background: Although tissue microarray (TMA) studies of histopathologic material have been frequently reported in studies of malignant diseases, the question of sample size (i.e., the diameter and the number of tissue cylinders investigated) has been rarely discussed. This study addresses the methodologic question of sample size in a variety of tumor types.
Material and Methods: Material from 29 cases of lung carcinoma (small cell, squamous cell, and adenocarcinomas) was examined immunohistochemically for Ki-67 and p53 expression in virtually constructed cylinders of different diameters. The influence of tissue sample size (i.e., different numbers of virtual cylinders) was also investigated. Results from Ki-67 evaluation were analyzed as a continuous variable, whereas p53 expression was scored. p53 evaluations based on scoring in cylinders versus scoring of whole sections were also compared. Furthermore, 10 cases of endometrial and breast carcinomas were evaluated for estrogen receptor, Ki-67, and HER2 by scoring up to five cylinders.
Results and Conclusions: Tissue cylinders of 0.6 and 1.0 mm diameters were compared and found equally informative about Ki-67 expression (intraclass correlation, 0.96). A statistical approach considering intraindividual and interindividual variation data is presented, indicating that in this specific setting three cylinders per case is an adequate sample size for TMA studies. Further sampling yields only a small gain in accuracy as determined by Ki-67 quantification and p53 scoring (κ-coefficient, 0.9). For endometrial and breast tissues, TMA scoring of three cylinders yielded excellent agreement (κ, &gt;0.75) compared with whole-section scoring. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2014–21)