bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils
Authors: Wu Xiao‐Lei , Friedrich Michael W. , Conrad Ralf 
Published: September 2005

SummaryTemperate rice field soil from Vercelli (Italy) contains moderately thermophilic methanogens of the yet uncultivated rice cluster I (RC‐I), which become prevalent upon incubation at temperatures of 45–50°C. We studied whether such thermophilic methanogens were ubiquitously present in anoxic soils. Incubation of different rice field soils (from Italy, China and the Philippines) and flooded riparian soils (from the Netherlands) at 45°C resulted in vigorous CH4 production after a lag phase of about 10 days. The archaeal community structure in the soils was analysed by terminal restriction fragment length polymorphism (T‐RFLP) targeting the SSU rRNA genes retrieved from the soil, and by cloning and sequencing. Clones of RC‐I methanogens mostly exhibited T‐RF of 393 bp, but also terminal restriction fragment (T‐RF) of 158 and 258 bp length, indicating a larger diversity than previously assumed. No RC‐I methanogens were initially found in flooded riparian soils. However, these archaea became abundant upon incubation of the soil at 45°C. Thermophilic RC‐I methanogens were also found in the rice field soils from Pavia, Pila and Gapan. However, the archaeal communities in these soils also contained other methanogenic archaea at high temperature. Rice field soil from Buggalon, on the other hand, only contained thermophilic Methanomicrobiales rather than RC‐I methanogens, and rice field soil from Jurong mostly Methanomicrobiales and only a few RC‐I methanogens. The archaeal community of rice field soil from Zhenjiang almost exclusively consisted of Methanosarcinaceae when incubated at high temperature. Our results show that moderately thermophilic methanogens are common in temperate soils. However, RC‐I methanogens are not always dominating or ubiquitous.
The effect of combination antiretroviral therapy on CD5 B‐ cells, B‐cell activation and hypergammaglobulinaemia in HIV‐1‐infected patients
Authors: Redgrave BE , Stone SF , French MAH , Krueger R , James IR , Price P 
Published: September 2005

ObjectivesThis study assessed B‐cell activation, CD5 B‐cells and circulating immunoglobulin levels in HIV‐infected patients treated with combination antiretroviral therapy (CART).MethodsMeasurement of plasma immunoglobulin levels and electrophoresis of plasma proteins, and analyses of total numbers of B‐cells and B‐cells expressing CD38 and CD5 in whole blood, were undertaken in 47 consecutive HIV‐1‐infected patients attending an out‐patient clinic.ResultsAll HIV‐infected patients had similar percentages and numbers of B‐cells. Proportions of CD5 B‐cells in all HIV‐infected patients were significantly lower than those in HIV‐negative controls. Aviraemic HIV‐infected patients on CART had lower percentages of CD5, CD38 and CD5 CD38 B‐cell subsets and lower plasma levels of immunoglobulin G (IgG) and immunoglobulin A (IgA) than viraemic HIV‐infected patients (untreated or on CART). However, 33–37% of aviraemic HIV‐infected patients had IgG and IgA levels above the 95th percentile of the normal range defined in HIV‐seronegative donors. In aviraemic HIV‐infected patients, plasma IgA levels correlated only with proportions of activated (CD38) B‐cells. IgG levels did not correlate with the proportions of B‐cell subsets or any marker of HIV disease activity. Monoclonal immunoglobulins were not detected in any plasma sample.ConclusionsAviraemic HIV‐infected patients on CART have lower plasma levels of IgG and IgA than viraemic HIV‐infected patients, but levels are often above the normal range. CD5 B‐cell numbers are depressed, so these cells are unlikely to contribute to hypergammaglobulinaemia in HIV‐infected patients.
Laser scanning as a tool for assessment of HIV‐related facial lipoatrophy: evaluation of accuracy and reproducibility
Authors: Yang Y , Paton NI 
Published: September 2005

Background
Facial lipoatrophy (LA) is a common complication of highly active antiretroviral therapy (HAART). Research into causes and treatment of facial LA is hindered by the lack of an objective measurement tool.Objective
To evaluate the accuracy and reproducibility of three‐dimensional laser scanning (LS) for estimating cheek volume changes.Methods
Paired laser scans were performed and the images superimposed using commercial software. The volume difference between images was computed within a circle of radius 25 mm placed in a standardized position over the cheek area. Accuracy was tested by scanning before and after known volumes of plasticine (0.5–5 mL) were applied to the cheek area of a mannequin to simulate volume change. Reproducibility was tested by repeated scanning of the mannequin with and without 2 mL of plasticine, and repeated scanning of 10 healthy subjects over the course of 1 week.Results
The mean difference between actual and estimated volume change was small across the range of volumes tested [mean difference 0.08 mL; 95% confidence interval (CI)–0.36 to 0.20 mL). The coefficient of variation for repeated measurements of 2‐mL volume change was 5.8%. The intraclass correlation coefficient for scan‐to‐scan variability was 0.812 (95% CI 0.515–0.947) and for day‐to‐day variability it was 0.764 (95% CI 0.332–0.935).Conclusions
LS is an accurate and reproducible method for estimating cheek volume changes. It may be useful as an objective tool for assessment of facial LA in clinical research studies.
The long‐term pharmacokinetics and safety of adding low‐dose ritonavir to a nelfinavir 1250 mg twice‐daily regimen in HIV‐infected patients
Authors: Justesen US , Hansen IM , Andersen ÅB , Klitgaard NA , Black FT , Gerstoft J , Mathiesen LR , Pedersen C 
Published: September 2005

ObjectivesTo evaluate the long‐term pharmacokinetics and safety of adding ritonavir 100 mg twice‐daily to a nelfinavir 1250 mg twice‐daily regimen in HIV‐infected patients.MethodsThis was a prospective, randomized, open‐label, controlled 24‐week study. Sixteen patients receiving a nelfinavir 1250 mg twice‐daily regimen with plasma viral load <1000 HIV‐1 RNA copies/mL were randomized to continue treatment or to have ritonavir 100 mg twice‐daily added. Safety, including fasting lipid levels, was evaluated at weeks 4, 12 and 24. Patients who were randomized to have ritonavir added (n=9) participated in three 12‐h pharmacokinetic evaluations at baseline, week 4 and week 24.ResultsIncreases in median nelfinavir steady‐state plasma concentrations at 12 h (C12) from 512 to 773 ng/mL [median difference 450 ng/mL; 95% confidence interval (CI) 116–1510 ng/mL] and in median active nelfinavir metabolite M8 C12 from 107 to 603 ng/mL (median difference 545 ng/mL; 95% CI 370–891) were seen after the addition of low‐dose ritonavir (baseline to week 24). There were no differences between the nelfinavir or M8 pharmacokinetic parameters at weeks 4 and 24. No significant changes or differences in the concentration of fasting total cholesterol, low‐density lipoprotein (LDL) cholesterol or total triglycerides or in the occurrence of adverse events were observed within or between the two groups.ConclusionsNelfinavir and especially M8 concentrations are increased when low‐dose ritonavir is added to a nelfinavir‐containing regimen. The combination seems to be safe and the nelfinavir/ritonavir regimen could be an option in patients with low nelfinavir+M8 concentrations.
A randomized controlled trial investigating the efficacy and safety of switching from a protease inhibitor to nevirapine in patients with undetectable viral load
Authors: Arranz Caso JA , López JC , Santos I , Estrada V , Castilla V , Sanz J , Sanz J , Molina JP , Fernández Guerrero M , Górgolas M 
Published: September 2005

ObjectiveTo assess the antiviral efficacy and safety of switching from a protease inhibitor (PI) to nevirapine in patients with long‐term HIV‐1 RNA suppression on PI‐containing regimens, and to assess its influence in the adherence to treatment.MethodsIn an open‐label multicentre study, 160 HIV‐infected patients with undetectable viral load for at least 6 months on a PI‐containing regimen were randomized to either continue with their PI regimen (n=79) or replace PI with nevirapine (n=81). Clinical assessment included plasma HIV‐1 RNA, blood chemistry, haematology, lymphocyte counts and adverse events reports. Adherence to treatment and lipodystrophy syndrome were assessed by patient self‐reporting.ResultsTreatment efficacy was equivalent in the two arms, for patients with viral loads either above or below 100 000 HIV‐1 RNA copies/mL. The increase in CD4 cell count was significant in both arms (P<0.00001) but the average CD4 cell count at 48 weeks was slightly higher in the nevirapine arm (596 vs. 569; P=0.1588). The number of patients with severe hypertriglyceridaemia (>400 mg/dL) after 48 weeks of treatment decreased in the nevirapine arm (from 11 to six), but increased in the PI arm (from four to 11) and led to treatment discontinuation in two patients. Lipodystrophy changes increased in 15% of patients in the PI arm but decreased in 4% of patients in the nevirapine arm. Finally, although adherence was similar in the two arms, patients reported that it required significantly less effort to stay on treatment in the nevirapine arm.ConclusionsThe results indicate that switching from PI to nevirapine is as effective as continuing with PI for maintaining viral control, even in patients with baseline viral load above 100 000 copies/mL. In addition, reductions in hypertriglyceridaemia and lipodystrophy and in the effort required to stay on treatment were observed.
Mitochondrial impairment induced by poly(ADP‐ribose) polymerase‐1 activation in cortical neurons after oxygen and glucose deprivation
Authors: Tanaka Seigo , Takehashi Masanori , Iida Shinya , Kitajima Takashi , Kamanaka Yoshihisa , Stedeford Todd , Banasik Marek , Ueda Kunihiro 
Published: September 2005

AbstractNeuronal cells injured by ischemia and reperfusion to a certain extent are committed to death in necrotic or apoptotic form. Necrosis is induced by gross ATP depletion or ‘energy crisis’ of the cell, whereas apoptosis is induced by a mechanism still to be defined in detail. Here, we investigated this mechanism by focusing on a DNA damage‐sensor, poly(ADP‐ribose) polymerase‐1 (PARP‐1). A 2‐h oxygen and glucose deprivation (OGD) followed by reoxygenation (Reox) induced apoptosis, rather than necrosis, in rat cortical neurons. During the Reox, PARP‐1 was much activated and autopoly(ADP‐ribosyl)ated, consuming the substrate, NAD+. Induction of apoptosis by OGD/Reox was suppressed by overexpression of Bcl‐2, indicating mitochondrial impairment in this induction process. Mitochondrial permeability transition (MPT), or membrane depolarization, and a release of proapoptotic proteins, i.e. cytochrome c, apoptosis‐inducing factor and endonuclease G, from mitochondria were observed during the Reox. These apoptotic changes of mitochondria and the nucleus were attenuated by PARP‐1 inhibitors, 1,5‐dihydroxyisoquinoline and benzamide, and also by small interfering RNA specific for PARP‐1. These results indicated that PARP‐1 plays a principal role in inducing mitochondrial impairment that ultimately leads to apoptosis of neurons after cerebral ischemia.
Proteomic analysis of parkin knockout mice: alterations in energy metabolism, protein handling and synaptic function
Authors: Periquet Magali , Corti Olga , Jacquier Sandrine , Brice Alexis 
Published: September 2005

Abstract Parkin knockout (KO) mice show behavioural and biochemical changes that reproduce some of the presymptomatic aspects of Parkinson's disease, in the absence of neuronal degeneration. To provide insight into the pathogenic mechanisms underlying the preclinical stages of parkin‐related parkinsonism, we searched for possible changes in the brain proteome of parkin KO mice by means of fluorescence two‐dimensional difference gel electrophoresis and mass spectrometry. We identified 87 proteins that differed in abundance between wild‐type and parkin KO mice by at least 45%. A high proportion of these proteins were related to energy metabolism. The levels of several proteins involved in detoxification, stress‐related chaperones and components of the ubiquitin–proteasome pathway were also altered. These differences might reflect adaptive mechanisms aimed at compensating for the presence of reactive oxygen species and the accumulation of damaged proteins in parkin KO mice. Furthermore, the up‐regulation of several members of the membrane‐associated guanylate kinase family of synaptic scaffold proteins and several septins, including the Parkin substrate cell division control related protein 1 (CDCRel‐1), may contribute to the abnormalities in neurotransmitter release previously observed in parkin KO mice. This study provides clues into possible compensatory mechanisms that protect dopaminergic neurones from death in parkin KO mice and may help us understand the preclinical deficits observed in parkin‐related parkinsonism.
GRB 050223: a faint gamma-ray burst discovered by Swift
Authors: Page K. L. , Rol E. , Levan A. J. , Zhang B. , Osborne J. P. , O'Brien P. T. , Beardmore A. P. , Burrows D. N. , Campana S. , Chincharini G. , Cummings J. R. , Cusumano G. , Gehrels N. , Giommi P. , Goad M. R. , Godet O. , Mangano V. , Tagliaferri G. , Wells A. A. 
Published: September 2005

Abstract
GRB 050223 was discovered by the Swift Gamma-Ray Burst Explorer on 2005 February 23 and was the first gamma-ray burst (GRB) to be observed by both Swift and XMM–Newton. At the time of writing (2005 May), it has one of the faintest GRB afterglows ever observed. The spacecraft could not slew immediately to the burst, so the first X-ray and optical observations occurred approximately 45 min after the trigger. Although no optical emission was found by any instrument, both Swift and XMM–Newton detected the fading X-ray afterglow. Combined data from both of these observatories show the afterglow to be fading monotonically as 0.99+0.15−0.12 over a time-frame between 45 min and 27 h post-burst. Spectral analysis, allowed largely by the higher throughput of XMM–Newton, implies a power law with a slope of Γ= 1.75+0.19−0.18 and shows no evidence for absorption above the Galactic column of 7 × 1020 cm−2.
From the X-ray decay and spectral slopes, a low electron power-law index of p= 1.3–1.9 is derived; the slopes also imply that a jet-break has not occurred up to 27 h after the burst. The faintness of GRB 050223 may be due to a large jet opening or viewing angle or a high redshift.
LNFPIII/LeX-Stimulated Macrophages Activate Natural Killer Cells via CD40-CD40L Interaction
Authors: Atochina Olga , Harn Donald 
Published: September 2005

ABSTRACTLacto-N-fucopentaose III (LNFPIII) is a human milk sugar containing the biologically active Lewis X (LeX) trisaccharide. LNFPIII/LeX is also expressed by immunosuppressive helminth parasites, by bacteria, and on a number of tumor/cancer cells. In this report, we first demonstrate that LNFPIII activates macrophages in vitro as indicated by upregulation of Gr-1 expression on F4/80+cells. Further, we investigated the effect of LNFPIII-activated macrophages on NK cell activity. We found that LNFPIII-stimulated F4/80+cells were able to activate NK cells, inducing upregulation of CD69 expression and gamma interferon (IFN-γ) production. The experiments show that NK cell activation is macrophage dependent, since NK cells alone did not secrete IFN-γ in response to LNFPIII. Furthermore, we found that activation of NK cells by glycan-stimulated macrophages required cell-cell contact. As part of the cell-cell contact mechanism, we determined that CD40-CD40L interaction was critical for IFN-γ secretion by NK cells, as the addition of anti-CD40L antibodies to the coculture blocked IFN-γ production. We also demonstrated that LNFPIII-stimulated macrophages secrete prostaglandin E2, interleukin-10 (IL-10), and tumor necrosis factor alpha (TNF-α) but a very low level of IL-12. Interestingly, addition of anti-TNF-α, anti-IL-10, or anti-IL-12 monoclonal antibodies did not significantly alter NK cell activity. Our data show that these soluble mediators are not critical for LNFPIII-stimulated macrophage activation of NK cells and provide further evidence for the importance of cell-cell contact and CD40-CD40L interactions between macrophages and NK cells.
Diagnosis of Tetanus Immunization Status: Multicenter Assessment of a Rapid Biological Test
Authors: Colombet Isabelle , Saguez Colette , Sanson-Le Pors Marie-José , Coudert Benoît , Chatellier Gilles , Espinoza Pierre ,   the Scientific Committee of the TetaQuick 1000 Study
Published: September 2005

ABSTRACT
Diagnosis of tetanus immunization status by medical interview of patients with wounds is poor. Many protected patients receive unnecessary vaccine or immunoglobulin, and unprotected patients may receive nothing. The aim of this study is to evaluate the feasibility and accuracy of the Tetanos Quick Stick (TQS) rapid finger prick stick test in the emergency department for determining immunization status. We designed a prospective multicenter study for blinded comparison of TQS with an enzyme-linked immunosorbent assay (ELISA). Adults referred for open wounds in 37 French hospital emergency departments had the TQS after receiving standard care (emergency-TQS). TQS was also performed in the hospital laboratory on total blood (blood/lab-TQS) and serum (serum/lab-TQS). ELISA was performed with the same blood sample at a central laboratory. We assessed concordance between emergency-TQS and blood/lab-TQS by the kappa test and the diagnostic accuracy (likelihood ratios) of medical interview, emergency-TQS, and lab-TQS. ELISA was positive in 94.6% of the 988 patients included. Concordance between blood/emergency-TQS and blood/lab-TQS results was moderate (κ = 0.6), with a high proportion of inconclusive blood/emergency-TQS tests (9.8%). Likelihood ratios for immunization were 3.0 (95% confidence interval [CI], 1.8 to 5.1), 36.6 (95% CI, 5.3 to 255.3), 89.1 (95% CI, 5.6 to 1,405.0), and 92.7 (95% CI, 5.9 to 1,462.0) for medical interview, blood/emergency-TQS, blood/lab-TQS, and serum/lab-TQS, respectively. The sensitivity of the blood/emergency-TQS was 76.7%, and the specificity was 98% by reference to the ELISA. TQS use in the emergency room could make tetanus prevention more accurate if its technical feasibility were improved, and our assessment will be supplemented by a cost effectiveness study.
Endogenous Superantigens Shape Response to Exogenous Superantigens
Authors: Rajagopalan Govindarajan , Singh Manisha , Sen Moon M. , Murali Narayana S. , Nath Karl A. , David Chella S. 
Published: September 2005

ABSTRACT

Endogenous superantigen-mediated thymic negative selection resulted in a paucity of mature T cells bearing T-cell receptor (TCR) Vβ8 in the periphery. Consequently, the magnitude of immune response to exogenous superantigen staphylococcal enterotoxin B, which activates TCR Vβ8
+
T cells, was significantly reduced and conferred protection from superantigen-induced mortality.
Patients with Pulmonary Tuberculosis Develop a Strong Humoral Response against Methylated Heparin-Binding Hemagglutinin
Authors: Zanetti Stefania , Bua Alessandra , Delogu Giovanni , Pusceddu Cinzia , Mura Maristella , Saba Franca , Pirina Piero , Garzelli Carlo , Vertuccio Cono , Sechi Leonardo A. , Fadda Giovanni 
Published: September 2005

ABSTRACT

Reactivities of human sera against selected recombinant
Mycobacterium tuberculosis
antigens were assessed by enzyme-linked immunosorbent assay. The results obtained indicate that patients with tuberculosis (TB) do not develop a strong humoral response against PE_PGRS and PPE proteins or against the Ag85B and heparin-binding hemagglutinin (HBHA) recombinant antigens. Conversely, purified methylated HBHA was strongly recognized by sera obtained from TB patients compared to controls.
Clinical Utility of Commercial Enzyme Immunoassays during the Inaugural Season of West Nile Virus Activity, Alberta, Canada
Authors: Tilley Peter A. G. , Walle Roberta , Chow Anthony , Jayaraman Gayatri C. , Fonseca Kevin , Drebot Michael A. , Preiksaitis Jutta , Fox Julie 
Published: September 2005

ABSTRACT
West Nile virus (WNV) has spread rapidly across North America, creating a need for rapid and accurate laboratory diagnosis on a large scale. Immunoglobulin M (IgM) capture enzyme immunoassays (EIA) became commercially available in the summer of 2003, but limited data are available on their clinical performance. Consolidated human WNV diagnostic testing for the province of Alberta, Canada, at the public health laboratory permitted a large-scale evaluation of the assays, covering a wide clinical spectrum. Two thousand nine hundred sixty-nine sera were tested, from 2,553 Alberta residents, and 266 cases were identified. Sensitivities of the Focus assay and first-generation Panbio IgM capture EIA were 79 and 80%, respectively. During the first week of illness only 53 to 58% of cases were positive, but sensitivity was 96 to 97% after day 8. Sensitivity for neurological cases was 92% overall. Specificity was high for the Focus kit at 98.9%, but only 82.9% for the first Panbio kit. A positive Focus WNV IgG result with a twofold rise in IgG index was a reliable indicator of acute flavivirus infection (67/67 WNV). Agreement between the IgG test and hemagglutinin inhibition titers in paired sera was at least 82%. Commercial IgM and IgG EIA proved useful for WNV diagnosis, provided follow-up sera were collected after 8 days of illness.
Mumps Virus-Specific Antibody Titers from Pre-Vaccine Era Sera: Comparison of the Plaque Reduction Neutralization Assay and Enzyme Immunoassays
Authors: Mauldin Jeremy , Carbone Kathryn , Hsu Henry , Yolken Robert , Rubin Steven 
Published: September 2005

ABSTRACTMumps virus-neutralizing antibodies are believed to be the most predictable surrogate marker of protective immunity. However, assays used to detect neutralizing antibodies, such as the plaque reduction neutralization (PRN) assay, are labor- and time-intensive and consequently are often supplanted by the more rapid and inexpensive enzyme immunoassay (EIA) technique. For virus infections for which international antibody standards exist and are bridged to clinical studies of protection (e.g., measles and rubella), the EIA has been successfully used to determine immune surrogate endpoints, yet no such international reference exists for mumps serology. Since both virus-neutralizing and nonneutralizing antibodies are measured in the EIA, in the absence of a mumps serological standard, the EIA may be prone to yielding false-positive results when utilized for assessing surrogate markers of protective immunity. Moreover, since mumps virus-specific antibody titers are generally low in comparison to antibody levels induced by other viruses and EIA procedures often employ relatively high serum dilution factors, the EIA may be prone to yielding false-negative results. To examine these issues, a PRN assay and two commercially available EIA kits were used to evaluate wild-type mumps virus serological responses in human serum samples from the pre-mumps vaccine era. Our results indicate that the PRN assay is a more sensitive and specific method of measuring serological responses to wild-type mumps virus.
Extrinsic Allergic Alveolitis (Hypersensitivity Pneumonitis) Caused by
Sphingobacterium spiritivorum
from the Water Reservoir of a Steam Iron
Authors: Kämpfer Peter , Engelhart S. , Rolke M. , Sennekamp J. 
Published: September 2005

ABSTRACT

A case of extrinsic allergic alveolitis (EAA) caused by
Sphingobacterium spiritivorum
is described. The symptoms were associated with the use of a steam iron. The water reservoir was heavily contaminated with
S. spiritivorum
(10
6
CFU ml
−1
). This is the first report of
S. spiritivorum
as a causative agent of EAA.