bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategy To Characterize the Number and Type of Repeating EPIYA Phosphorylation Motifs in the Carboxyl Terminus of CagA Protein inHelicobacter pyloriClinical Isolates
Authors: Panayotopoulou Effrosini G. , Sgouras Dionyssios N. , Papadakos Konstantinos , Kalliaropoulos Antonios , Papatheodoridis George , Mentis Andreas F. , Archimandritis Athanasios J. 
Published: December 2006

ABSTRACTCytotoxin-associated gene A (CagA) diversity with regard to EPIYA-A, -B, -C, or -D phosphorylation motifs may play an important role inHelicobacter pyloripathogenesis, and therefore determination of these motifs inH. pyloriclinical isolates can become a useful prognostic tool. We propose a strategy for the accurate determination of CagA EPIYA motifs in clinical strains, based upon one-step PCR amplification using primers that flank the EPIYA coding region. We thus analyzed 135H. pyloriisolates derived from 75 adults and 60 children Greek patients. A total of 34 cases were found to be EPIYA PCR negative and were consequently verified ascagAnegative bycagA-specific PCR, empty-sitecagAPCR, and Western blotting. Sequencing of the remaining 101 PCR-positive amplicons confirmed that an accurate prediction of the number of EPIYA motifs on the basis of size distribution of the PCR products was feasible in all cases. Furthermore, our assay could identify closely relatedH. pylorisubclones within the same patient, harboring different numbers of EPIYA repeats. The prevalence of CagA proteins with three EPIYA motifs (ABC) or four EPIYA motifs (ABCC) was the same within the adult and children groups. However, CagA species with more than four EPIYA motifs were observed exclusively within adults (8.6%), suggesting that CagA-positive strains may acquire additional EPIYA-C motifs throughout adulthood. Our strategy requires no initialcagAscreening of the clinical isolates and can accurately predict the number of EPIYA repeats in single or multiple closely related subclones bearing different numbers of EPIYA motifs in their CagA, which may coexist within the same patient.
Use of Enzyme-Linked Immunosorbent Assay and Dipstick Assay for Detection of
Strongyloides stercoralis
Infection in Humans
Authors: van Doorn H. Rogier , Koelewijn Rob , Hofwegen Henk , Gilis Henk , Wetsteyn Jose C. F. M. , Wismans Pieter J. , Sarfati Claudine , Vervoort Tony , van Gool Tom 
Published: December 2006

ABSTRACT

A homemade enzyme-linked immunosorbent assay (ELISA) (Academic Medical Center ELISA [AMC-ELISA]) and a dipstick assay for the detection of anti-
Strongyloides stercoralis
antibodies in serum were developed and evaluated together with two commercially available ELISAs (IVD-ELISA [IVD Research, Inc.] and Bordier-ELISA [Bordier Affinity Products SA]) for their use in the serodiagnosis of imported strongyloidiasis. Both commercially available ELISAs have not been evaluated previously. The sensitivities of the assays were evaluated using sera from 90 patients with parasitologically proven intestinal strongyloidiasis and from 9 patients with clinical larva currens. The sensitivities of the AMC-ELISA, dipstick assay, IVD-ELISA, and Bordier-ELISA were 93, 91, 89, and 83%, respectively, for intestinal strongyloidiasis. In all tests, eight of nine sera from patients with larva currens were positive. The specificity was assessed using a large serum bank of 220 sera from patients with various parasitic, bacterial, viral, and fungal infectious diseases; sera containing autoimmune antibodies; and sera from healthy blood donors. The specificities of AMC-ELISA, dipstick assay, IVD-ELISA, and Bordier-ELISA were 95.0, 97.7, 97.2, and 97.2%, respectively. Our data suggest that all four assays are sensitive and specific tests for the diagnosis of both intestinal and cutaneous strongyloidiasis.
Human Immunodeficiency Virus (HIV) Antibody Avidity Testing To Identify Recent Infection in Newly Diagnosed HIV Type 1 (HIV-1)-Seropositive Persons Infected with Diverse HIV-1 Subtypes
Authors: Chawla A. , Murphy G. , Donnelly C. , Booth C. L. , Johnson M. , Parry J. V. , Phillips A. , Geretti A. M. 
Published: December 2006

ABSTRACT
A guanidine-based antibody avidity assay for the identification of recently acquired human immunodeficiency virus type 1 (HIV-1) infection was evaluated. The kinetics of maturation of antibody avidity were determined prospectively in 23 persons undergoing acute seroconversion followed for up to 1,075 days. Avidity indices (AI) of ≤0.75 and ≤0.80 reproducibly identified seroconversion within the previous 125 (95% confidence interval [CI], 85 to 164) and 142 (95% CI, 101 to 183) days, respectively. To validate the assay, 432 serum samples from newly diagnosed patients were tested by both the avidity assay and the detuned assay. Results were highly concordant (kappa value for agreement, 0.85). The avidity assay was subsequently used to screen 134 consecutive newly diagnosed patients, including 55/134 (41%) infected with non-B subtypes (A, C, D, G, CRF01, CRF02, CRF06, CRF13, and CRF16). In this cohort, 25/79 (32%) persons with the B subtype and 7/55 (13%) with non-B subtypes showed an AI of ≤0.75, and there were 16/25 (64%) and 3/7 (43%) persons, respectively, with a documented history of acute seroconversion illness within the predicted seroconversion interval. An AI of ≤0.75 was also observed for four patients (three with the B subtype and one with a non-B subtype) who presented with AIDS-defining conditions. In multivariate analysis, an AI of ≤0.75 was associated with younger age, higher HIV-1 plasma RNA load, and being born in the United Kingdom or Ireland rather than in Africa but not with gender, ethnicity, risk group, HIV-1 subtype, or CD4 counts. In conclusion, HIV antibody avidity testing provides a reliable method for identifying recently acquired HIV-1 infection. Results are affected by advanced disease and should therefore be interpreted in the context of other clinical parameters.
Human T-Cell Leukemia Virus Type 1 (HTLV-1) bZIP Protein Interacts with the Cellular Transcription Factor CREB To Inhibit HTLV-1 Transcription
Authors: Lemasson Isabelle , Lewis Matthew R. , Polakowski Nicholas , Hivin Patrick , Cavanagh Marie-Hélène , Thébault Sabine , Barbeau Benoit , Nyborg Jennifer K. , Mesnard Jean-Michel 
Published: December 2006

ABSTRACT
The complex human T-cell leukemia virus type 1 (HTLV-1) retrovirus encodes several proteins that are unique to the virus within its 3′-end region. Among them, the viral transactivator Tax and posttranscriptional regulator Rex are well characterized, and both positively regulate HTLV-1 viral expression. Less is known about the other regulatory proteins encoded in this region of the provirus, including the recently discovered HBZ protein. HBZ has been shown to negatively regulate basal and Tax-dependent HTLV-1 transcription through its ability to interact with specific basic-leucine zipper (bZIP) proteins. In the present study, we found that HBZ reduces HTLV-1 transcription and virion production. We then characterized the interaction between HBZ and the cellular transcription factor CREB. CREB plays a critical role in Tax-mediated HTLV-1 transcription by forming a complex with Tax that binds to viral cyclic AMP-response elements (CREs) located within the viral promoter. We found that HBZ and CREB interact in vivo and directly in vitro, and this interaction occurs through the bZIP domain of each protein. We also found that CREM-Ia and ATF-1, which share significant homology in their bZIP domains with the bZIP domain of CREB, interact with HBZ-bZIP. The interaction between CREB and HBZ prevents CREB binding to the viral CRE elements in vitro and in vivo, suggesting that the reduction in HTLV-1 transcription by HBZ is partly due to the loss of CREB at the promoter. We also found that HBZ displaces CREB from a cellular CRE, suggesting that HBZ may deregulate CREB-dependent cellular gene expression.
Quantitating the Magnitude of the Lymphocytic Choriomeningitis Virus-Specific CD8 T-Cell Response: It Is Even Bigger than We Thought
Authors: Masopust David , Murali-Krishna Kaja , Ahmed Rafi 
Published: December 2006

ABSTRACTMeasuring the magnitudes and specificities of antiviral CD8 T-cell responses is critical for understanding the dynamics and regulation of adaptive immunity. Despite many excellent studies, the accurate measurement of the total CD8 T-cell response directed against a particular infection has been hampered by an incomplete knowledge of all CD8 T-cell epitopes and also by potential contributions of bystander expansion among CD8 T cells of irrelevant specificities. Here, we use several techniques to provide a more complete accounting of the CD8 T-cell response generated upon infection of C57BL/6 mice with lymphocytic choriomeningitis virus (LCMV). Eight days following infection, we found that 85 to 95% of CD8 T cells exhibit an effector phenotype as indicated by granzyme B, 1B11, CD62L, CD11a, and CD127 expression. We demonstrate that CD8 T-cell expansion is due to cells that divide >7 times, whereas heterologous viral infections only elicited <3 divisions among bystander memory CD8 T cells. Furthermore, we found that approximately 80% of CD8 T cells in spleen were specific for ten different LCMV-derived epitopes at the peak of primary infection. These data suggest that following a single LCMV infection, effector CD8 T cells divide ≥15 times and account for at least 80%, and possibly as much as 95%, of the CD8 T-cell pool. Moreover, the response targeted a very broad array of peptide major histocompatibility complexes (MHCs), even though we examined epitopes derived from only two of the four proteins encoded by the LCMV genome and C57BL/6 mice only have two MHC class I alleles. These data illustrate the potential enormity, specificity, and breadth of CD8 T-cell responses to viral infection and demonstrate that bystander activation does not contribute to CD8 T-cell expansion.
Foot-and-Mouth Disease Virus Mutant with Decreased Sensitivity to Ribavirin: Implications for Error Catastrophe
Authors: Sierra Macarena , Airaksinen Antero , González-López Claudia , Agudo Rubén , Arias Armando , Domingo Esteban 
Published: December 2006

ABSTRACT
The nucleoside analogue ribavirin (R) is mutagenic for foot-and-mouth disease virus (FMDV). Passage of FMDV in the presence of increasing concentrations of R resulted in the selection of FMDV with the amino acid substitution M296I in the viral polymerase (3D). Measurements of progeny production and viral fitness with chimeric viruses in the presence and absence of R documented that the 3D substitution M296I conferred on FMDV a selective replicative advantage in the presence of R but not in the absence of R. In polymerization assays, a purified mutant polymerase with I296 showed a decreased capacity to use ribavirin triphosphate as a substrate in the place of GTP and ATP, compared with the wild-type enzyme. The results suggest that M296I has been selected because it attenuates the mutagenic activity of R with FMDV. Replacement M296I is located within a highly conserved stretch in picornaviral polymerases which includes residues that interact with the template-primer complex and probably also with the incoming nucleotide, according to the three-dimensional structure of FMDV 3D. Given that a 3D substitution, distant from M296I, was associated with resistance to R in poliovirus, the results indicate that picornaviral polymerases include different domains that can alter the interaction of the enzyme with mutagenic nucleoside analogues. Implications for lethal mutagenesis are discussed.
Influences of Glycosylation on Antigenicity, Immunogenicity, and Protective Efficacy of Ebola Virus GP DNA Vaccines
Authors: Dowling William , Thompson Elizabeth , Badger Catherine , Mellquist Jenny L. , Garrison Aura R. , Smith Jeffery M. , Paragas Jason , Hogan Robert J. , Schmaljohn Connie 
Published: December 2006

ABSTRACT
The Ebola virus (EBOV) envelope glycoprotein (GP) is the primary target of protective immunity. Mature GP consists of two disulfide-linked subunits, GP1 and membrane-bound GP2. GP is highly glycosylated with both N- and O-linked carbohydrates. We measured the influences of GP glycosylation on antigenicity, immunogenicity, and protection by testing DNA vaccines comprised of GP genes with deleted N-linked glycosylation sites or with deletions in the central hypervariable mucin region. We showed that mutation of one of the two N-linked GP2 glycosylation sites was highly detrimental to the antigenicity and immunogenicity of GP. Our data indicate that this is likely due to the inability of GP2 and GP1 to dimerize at the cell surface and suggest that glycosylation at this site is required for achieving the conformational integrity of GP2 and GP1. In contrast, mutation of two N-linked sites on GP1, which flank previously defined protective antibody epitopes on GP, may enhance immunogenicity, possibly by unmasking epitopes. We further showed that although deleting the mucin region apparently had no effect on antigenicity in vitro, it negatively impacted the elicitation of protective immunity in mice. In addition, we confirmed the presence of previously identified B-cell and T-cell epitopes in GP but show that when analyzed individually none of them were neither absolutely required nor sufficient for protective immunity to EBOV. Finally, we identified other potential regions of GP that may contain relevant antibody or T-cell epitopes.
Visual Object Recognition: Do We Know More Now Than We Did 20 Years Ago?
Authors: Peissig Jessie J. , Tarr Michael J. 
Published: December 2006

Abstract We review the progress made in the field of object recognition over the past two decades. Structural-description models, making their appearance in the early 1980s, inspired a wealth of empirical research. Moving to the 1990s, psychophysical evidence for view-based accounts of recognition challenged some of the fundamental assumptions of structural-description theories. The 1990s also saw increased interest in the neurophysiological study of high-level visual cortex, the results of which provide some constraints on how objects may be represented. By 2000, neuroimaging arose as a viable means for connecting neurons to behavior. One of the most striking fMRI results has been category selectivity, which provided further constraints for models of object recognition. Despite this progress, the field is still faced with the challenge of developing a comprehensive theory that integrates this ever-increasing body of results and explains how we perceive and recognize objects.
Active Vibration and Noise Control using Smart Foam
Authors: Akl W. , Baz A. 
Published: December 2006

A new class of smart foam is developed and attached to a flexible aluminum plate coupled with a rigid acoustic cavity in an attempt to evaluate its effectiveness in controlling the structural acoustics of the plate/cavity system. The proposed foam consists of a passive foam layer bonded to one surface of an active piezoelectric composite whose other surface is bonded to the surface of the vibrating plate. In this manner, the active piezoelectric composite can control from one side the porosity and the acoustic absorption characteristics of the foam and from the other side can suppress the vibration of the flexible plate. With such capabilities, the proposed smart foam can simultaneously control structural and acoustic cavity modes over a broad frequency range. A finite element model is presented for the behavior of the smart foam when coupled with a plate/cavity system. The predictions of the model are validated experimentally using vibration and/or sound pressure level feedback control strategies. The obtained experimental results are found to be in good agreement with the predictions of the finite element model. Furthermore, it is found that vibration and noise attenuations of about 90% are obtained with control voltages of less than 180 volts for both vibration and sound pressure feedback.
Clay minerals formed from micas and chlorites in some New Zealand soils
Authors: Churchman G. J. 
Published: December 2006

AbstractClay mineralogical differences between eight soils in South Island, New Zealand, are related to differences in climate, vegetation, and formation time. Alteration of chlorite follows the sequence chlorite→interlayered hydrousmica→chlorite-swelling chlorite→chlorite-vermiculite, with increased weathering leading to the destruction of the chloritic layers. Mica (muscovite) follows two alteration sequences depending on the overlying vegetation. Under tussock grassland the sequence is mica→mica-vermiculite→mica-beidellite→beidellite. This sequence is also followed under beech forest, together with the sequence of mica→vermiculite→beidellite, with pedogenic chlorite forming when the pH is > 4·5. All but one of the interstratified products (the interlayered hydrous mica) appear to be based on a 1:1 regular interlayering of the two components.
The occurrence of palygorskite in Quaternary sediments of the coastal plain of north-west Egypt
Authors: Hassouba H. , Shaw H. F. 
Published: December 2006

AbstractSediments from a Quaternary beach ridge complex along the coastal plain of north-west Egypt have been examined by X-ray diffraction and optical and scanning electron microscopy. Palygorskite was identified in the caliche capping the beach ridges and in the gypsiferous marls between the ridges; petrographic evidence indicated that this had formed authigenically in both environments. Examples are thus provided of the pedogenic and evaporative in situ formation of palygorskite.
The transformation of feldspars and muscovite to clay minerals in (Ca,Mg)-carbonate bearing hydrothermal media
Authors: Frank-Kamenetskii V. A. , Kotov N. V. , Rjumin A. A. 
Published: December 2006

AbstractExperimental transformations of feldspars and muscovites following additions of magnesite and dolomite have been studied at PH2O = 1 kbar, T = 200–600°C. Formation of layer silicates such as smectite, 7 Å (Mg,Al)-serpentine, some mixed-layer phases and other minerals is shown to be a function of the composition of the starting materials, temperature and run duration. It is established that 1 M- and 2 M1-phlogopites are formed from 1 M- and 2 M1-muscovites, respectively, under Mg-bearing hydrothermal conditions. Some causes of variations in the composition of 7 Å (Mg,Al)-serpentines at elevated temperature as a function of the composition of hydrothermal media are given. These data may be used to explain the main characteristics of clay mineral formation from feldspar- and muscovite-bearing sedimentary rocks during their alteration in postdiagenetic and metasomatic processes.
X-ray diffraction from partially disordered layer structures: General case
Authors: Ray B. K. , De A. K. , Bhattacherjee S. 
Published: December 2006

AbstractA general expression for diffracted intensities from partially ordered layer structures with a ‘mistake’ has been calculated. The ‘mistake’ consists of a shift of a layer parallel to adjacent layers by any arbitrary fraction b/q along the b axis, q being any integer. The expression is free from any simplifying approximations.
Further studies of a ferrous iron doped synthetic kaolin: dosimetry of X-ray induced defects
Authors: Cuttler A. H. 
Published: December 2006

AbstractThe structure of kaolin has been examined together with aspects of dosimetry and energy loss mechanisms of radiation to explain the formation of g = 2 EPR centres. The analysis points to the formation of a trapped hole on the ‘inner layer’ oxygen atoms of kaolin located at the boundaries between divalent ion and trivalent ion ‘cells’, in particular at the boundaries with excess negative charge. Direct interaction of X-rays with atoms and the possibility of proton recoil are eliminated. The means of production appears to be by transfer of charge following ionization of atoms by secondary electrons, with transfer of vacancies ultimately to the oxygen ions. Mechanisms which result in a decrease in signal strength with increase in concentration are examined. It is concluded that the cell mechanisms discussed are consistent with the rates of production and that at 20 Mrad (air) the number of centres should be reaching saturation.
IR spectra of powder hematite: effects of particle size and shape
Authors: Rendon Jose L. , Serna Carlos J. 
Published: December 2006

AbstractHematites obtained by heating goethite gave different IR absorption spectra depending on the temperature of formation. Hematites formed between 250–600°C consisted of lath-like crystals (average size 0.4 ×0.08 µm) and showed, in accordance with theoretical predictions, very similar IR spectra whose absorption bands could all be assigned to surface mode vibrations. However, significantly different IR spectra were given by hematites formed between 700–950°C, the differences being correlated with variations in the size and shape of the particles. Differences observed in the IR spectra of powder hematite do not therefore justify new names for the mineral, as have been proposed in the literature.
A method to eliminate the background in X-ray diffraction patterns of oriented clay mineral samples
Authors: Van Der Gaast S. J. , Vaars A. J. 
Published: December 2006

AbstractA method is described for calculating, and then subtracting, the background from X-ray diffraction patterns of oriented clay mineral samples. Ti-Kα radiation is used and, to minimize the absorption of this radiation by air, a vacuum and helium-flushed device has been developed. This device can be used with other X-ray sources, offering a considerable increase of intensity—e.g. Co-Kα radiation is increased by 125%. With the background-eliminated patterns a better semi-quantitative estimate of the composition of clay mineral mixtures is possible. Small differences in composition of two samples can be identified by subtracting one of the background-eliminated patterns from the other. Using this method, peak maxima of smectite-group minerals can also be accurately determined.
Etude d'une smectite magnesienne de transition, a caracteristiques di et trioctahedriques et derivee de l'evolution superficielle d'une trachydolerite de Provence
Authors: Chevalier Y. , Dejou J. 
Published: December 2006

ResumeLa phase <2 µm issue de l'évolution géochimique superficielle d'une trachydolérite de Provence s'est révélée être presque exclusivement constituée d'une smectite. Son examen, grâce à plusieurs techniques, et notamment l'identification des produits de recristallisation à haute température, montre qu'il s'agit d'un minéral 2/1, surtout magnésien. L'établissement de sa formule structurale approchée, calculée sur la base de 11 oxygènes, en ferait un minéral intermédiaire entre les smectites diet trioctaédriques, avec une occupation de 2.55 cations en sites octaédriques. Cette smectite de Provence n'est pas une saponite au sens strict, compte-tenu du nombre des cations R3+ = 0.94 en position octaédrique, plus élevé que celui de ces minéraux, tandis que la part des cations R2+ en ces mêmes sites est inférieure au seuil de 85%.
X-ray photoelectron diffraction studies of lepidolite
Authors: Evans S. , Raftery E. 
Published: December 2006

AbstractX-ray photoelectron diffraction data for three cleavage surfaces from a crystal of a Norwegian lepidolite containing 2·3% Rb and 3% Mn are reported and interpreted. Rubidium is shown to occupy anhydrous interlayer sites equivalent to those of potassium, and to be distributed uniformly throughout the crystals. Cleavage occurs in Mn-rich regions in which the manganese(II) is located in octahedral sites essentially equivalent to those of lithium. The octahedral Al sites can readily be distinguished from the Li,Mn sites and it is concluded that Al occupies predominantly M(2), cis sites while Li and Mn(II) prefer M(1), trans sites. Photoelectron diffraction data also indicate that 40 ± 5% of the Al is tetrahedrally coordinated, compared with a figure of ∼34% deduced independently from a surface analysis.