bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution and Evolution of T-Cell Receptor Vβ Repertoire on Peripheral Blood Lymphocytes of Newborn Infants of Human Immunodeficiency Virus (HIV)-Infected Mothers: Differential Display on CD4 and CD8 T Cells and Effect of HIV Infection
Authors: Borkowsky William , Chen Song-He , Belitskaya-Levy Ilana 
Published: July 2007

ABSTRACTNeonatal human peripheral blood mononuclear cells from 12 human immunodeficiency virus (HIV)-infected and 84 uninfected children were assessed for their distribution of T-cell receptors (TCRs) by flow cytometry employing monoclonal antibodies to 14 Vβ types. Vβ 2, 5c, and 13 were the most commonly found on CD4 cells (in that order). There was a bimodal distribution of Vβ 2, being most common in 48% of individuals but in limiting frequency (<2% of CD4) in 21%. Vβ 2, 3, 8b, and 13 were most commonly expressed on CD8 cells at similar frequencies. There was little difference in the pattern displayed among the infected compared to that of the uninfected. The variation of the distribution over time was studied in 12 infants (7 infected). Only a single HIV-infected child had a significant difference in the interquartile range; none of the HIV-negative patients showed a significant difference. In conclusion, newborns demonstrate different distributions of TCR Vβ types on CD4 and CD8 cells. HIV infection produces no change in neonatal TCR and little change over the course of 2 years compared to that seen in the uninfected.
Quality Assurance Program for Peripheral Blood Mononuclear Cell Cryopreservation
Authors: Weinberg Adriana , Louzao Raul , Mussi-Pinhata Marisa M. , Cruz Maria L. S. , Pinto Jorge A. , Huff Maria F. , de Castro Andrea C. , Sucupira Maria C. , Denny Thomas N. 
Published: July 2007

ABSTRACT
Seven Brazilian sites participating in the Pediatric AIDS Clinical Trials Group international cryopreservation quality assurance pilot program cryopreserved and shipped peripheral blood mononuclear cells (PBMC) to a central U.S. laboratory for analysis. Cell viability and recovery significantly increased over time. A wet-laboratory training session conducted at the central laboratory significantly improved the quality of the cryopreserved PBMC.
Evaluation of Four Whole-Cell
Leptospira
-Based Serological Tests for Diagnosis of Urban Leptospirosis
Authors: McBride Alan J. A. , Santos Balbino L. , Queiroz Adriano , Santos Andréia C. , Hartskeerl Rudy A. , Reis Mitermayer G. , Ko Albert I. 
Published: July 2007

ABSTRACT
Four serologic assays for leptospirosis had sensitivities of 72 to 88% and specificities of 88 to 100% in the setting of highly endemic urban transmission, indicating that assays using enzyme-linked immunosorbency and rapid formats may be used as alternatives to the microscopic agglutination test for diagnosing urban leptospirosis. Testing a second sample will be required in cases with an initial negative result, since sensitivity was low (46 to 68%) during the first week of illness.
PrimaTB STAT-PAK Assay, a Novel, Rapid Lateral-Flow Test for Tuberculosis in Nonhuman Primates
Authors: Lyashchenko Konstantin P. , Greenwald Rena , Esfandiari Javan , Greenwald David , Nacy Carol A. , Gibson Susan , Didier Peter J. , Washington Marc , Szczerba Peter , Motzel Sherri , Handt Larry , Pollock John M. , McNair James , Andersen Peter , Langermans Jan A. M. , Verreck Frank , Ervin Sean , Ervin Frank , McCombs Candace 
Published: July 2007

ABSTRACTTuberculosis (TB) is the most important zoonotic bacterial disease in nonhuman primates (NHP). The current diagnostic method, the intradermal palpebral tuberculin test, has serious shortcomings. We characterized antibody responses in NHP againstMycobacterium tuberculosisto identify immunodominant antigens and develop a rapid serodiagnostic test for TB. A total of 422 NHP were evaluated, including 243 rhesus (Macaca mulatta), 46 cynomolgus (Macaca fascicularis), and 133 African green (Cercopithecus aethiops sabaeus) monkeys at five collaborative centers. Of those, 50 monkeys of the three species were experimentally inoculated withM. tuberculosis. Antibody responses were monitored every 2 to 4 weeks for up to 8 months postinfection by MultiAntigen Print ImmunoAssay with a panel of 12 recombinant antigens. All of the infected monkeys produced antibodies at various levels and with different antigen recognition patterns. ESAT-6 and MPB83 were the most frequently recognized proteins during infection. A combination of selected antigens which detected antibodies in all of the infected monkeys was designed to develop the PrimaTB STAT-PAK assay by lateral-flow technology. Serological evaluation demonstrated high diagnostic sensitivity (90%) and specificity (99%). The highest rate of TB detection was achieved when the skin test was combined with the PrimaTB STAT-PAK kit. This novel immunoassay provides a simple, rapid, and accurate test for TB in NHP.
Extraintestinal Pathogenic
Escherichia coli
Strains of Avian and Human Origin: Link between Phylogenetic Relationships and Common Virulence Patterns
Authors: Moulin-Schouleur Maryvonne , Répérant Maryline , Laurent Sylvie , Brée Annie , Mignon-Grasteau Sandrine , Germon Pierre , Rasschaert Denis , Schouler Catherine 
Published: July 2007

ABSTRACT

Extraintestinal pathogenic
Escherichia coli
(ExPEC) strains of human and avian origin show similarities that suggest that the avian strains potentially have zoonotic properties. However, the phylogenetic relationships between avian and human ExPEC strains are poorly documented, so this possibility is difficult to assess. We used PCR-based phylotyping and multilocus sequence typing (MLST) to determine the phylogenetic relationships between 39 avian pathogenic
E. coli
(APEC) strains of serogroups O1, O2, O18, and O78 and 51 human ExPEC strains. We also compared the virulence genotype and pathogenicity for chickens of APEC strains and human ExPEC strains. Twenty-eight of the 30 APEC strains of serogroups O1, O2, and O18 were classified by MLST into the same subcluster (B2-1) of phylogenetic group B2, whereas the 9 APEC strains of serogroup O78 were in phylogenetic groups D (3 strains) and B1 (6 strains). Human ExPEC strains were closely related to APEC strains in each of these three subclusters. The 28 avian and 25 human strains belonging to phylogenetic subcluster B2-1 all expressed the K1 antigen and presented no significant differences concerning the presence of other virulence factors. Moreover, human strains of this phylogenetic subcluster were highly virulent for chicks, so no host specificity was identified. Thus, APEC strains of serotypes O1:K1, O2:K1, and O18:K1 belong to the same highly pathogenic clonal group as human
E. coli
strains of the same serotypes isolated from cases of neonatal meningitis, urinary tract infections, and septicemia. These APEC strains constitute a potential zoonotic risk.
Development of a Real-Time Fluorescence Resonance Energy Transfer PCR To Detect
Arcobacter
Species
Authors: Abdelbaqi Khalil , Buissonnière Alice , Prouzet-Mauleon Valérie , Gresser Jessica , Wesley Irene , Mégraud Francis , Ménard Armelle 
Published: July 2007

ABSTRACT

A real-time PCR targeting the gyrase A subunit gene outside the quinolone resistance-determining region has been developed to detect
Arcobacter
species. The species identification was done by probe hybridization and melting curve analysis, using fluorescence resonance energy transfer technology. Discrimination between
Arcobacter
species was straightforward, as the corresponding melting points showed significant differences with the characteristic melting temperatures of 63.5°C, 58.4°C, 60.6°C, and 51.8°C for the
Arcobacter butzleri
,
Arcobacter cryaerophilus
,
Arcobacter cibarius
, and
Arcobacter nitrofigilis
type strains, respectively. The specificity of this assay was confirmed with pure cultures of 106
Arcobacter
isolates from human clinical and veterinary specimens identified by phenotypic methods and 16S rRNA gene sequencing. The assay was then used to screen 345 clinical stool samples obtained from patients with diarrhea. The assay detected
A. butzleri
in four of these clinical samples (1.2%). These results were confirmed by a conventional PCR method targeting the 16S rRNA gene with subsequent sequencing of the PCR product. In conclusion, this real-time assay detects and differentiates
Arcobacter
species in pure culture as well as in the competing microbiota of the stool matrix. The assay is economical since only one biprobe is used and multiple
Arcobacter
species are identified in a single test.
Multicenter Evaluation of the BD Phoenix Automated Microbiology System for Antimicrobial Susceptibility Testing of
Streptococcus
Species
Authors: Richter Sandra S. , Howard Wanita J. , Weinstein Melvin P. , Bruckner David A. , Hindler Janet F. , Saubolle Michael , Doern Gary V. 
Published: July 2007

ABSTRACT

This multicenter study evaluated the BD Phoenix Automated Microbiology System STREP panel (BD Diagnostic Systems). Antimicrobial susceptibility testing (AST) with 13 agents was performed on 2,013 streptococci (938
Streptococcus pneumoniae
isolates; 396 group B streptococci [GBS]; 369 viridans group streptococci [VGS]; 290 beta-hemolytic streptococcus groups A, C, and G; and 20 other streptococci) with the Phoenix system and a broth microdilution reference method. Clinical and challenge isolates were tested against cefepime, cefotaxime (CTX), ceftriaxone (CTR), clindamycin (CLI), erythromycin (ERY), gatifloxacin, levofloxacin, linezolid, meropenem, penicillin (PEN), tetracycline (TET), trimethoprim-sulfamethoxazole, and vancomycin. Clinical isolates with major errors or very major errors (VMEs) were retested in duplicate by both methods. The final results for clinical isolates showed the following trends. For all of the organism-antimicrobial agent combinations tested, categorical agreement (CA) was 92 to 100%, with one exception—VGS-PEN (87% CA; all errors were minor). For
S. pneumoniae
, there was one major error with CLI (0.1%) and one or two VMEs with CTX (4%), CTR (4.5%), ERY (0.9%), and TET (0.7%). For groups A, C, and G, the CA was 97 to 100% and the only VMEs were resolved by additional reference laboratory testing. For GBS, there was only one VME (TET, 0.3%) and D-zone testing of 23 isolates with CLI major errors (one isolate unavailable) revealed inducible CLI resistance. For VGS, the major error rates were 0 to 3% and VMEs occurred with seven agents (3.5 to 7.1%). The mean times required for organism groups to generate results ranged from 8.4 to 9.4 h. The Phoenix system provided reliable and rapid AST results for most of the organism-antimicrobial agent combinations tested.
Transduction of Human Immunodeficiency Virus Type 1 Vectors Lacking Encapsidation and Dimerization Signals
Authors: Laham-Karam Nihay , Bacharach Eran 
Published: July 2007

ABSTRACTThe encapsidation signal (Ψ) and the nested dimerization initiation site are important for efficient packaging of human immunodeficiency virus type 1 (HIV-1) genomic RNA dimers. Consequently, these signals are included in all HIV-1 vectors. Here, we provide evidence demonstrating that these elements in such vectors are not absolutely required for vector transduction. In single-cycle infection assays, vectors with Ψ deleted (ΔΨ) were transduced with only a two- to fivefold reduction compared to the wild type. The transduction of ΔΨ showed typical products of reverse transcription and vector integration; however, in vitro and in vivo dimerization assays demonstrated the lack of normal dimerization of the ΔΨ vector. The reduction in transduction reflected a similar reduction in packaging. Nevertheless, a relatively high specificity of packaging was retained, as the ΔΨ vector was encapsidated at a level 4 orders of magnitude higher than that for overexpressed, nonretroviral cellular mRNA and 15 orders of magnitude higher than that for a murine leukemia virus (MLV)-based vector, all containing the same reporter gene, suggesting a Ψ-independent mechanism of packaging. The fact that HIV-1 and MLV vectors were encapsidated with a much higher level of efficiency than the cellular RNA suggests that the genomic RNAs of different retroviruses share common features and/or pathways that target them to encapsidation. Overall, these results formally demonstrate that packaging and dimerization signals are not required for the early stages of infection and can be deleted without risking a total loss of vector transduction. Deletion of these signals should enhance the safety of these vectors.
Primary Isolates of Human Immunodeficiency Virus Type 1 Are Usually Dominated by the Major Variants Found in Blood
Authors: Voronin Yegor , Chohan Bhavna , Emerman Michael , Overbaugh Julie 
Published: July 2007

ABSTRACT
The isolation of primary strains of human immunodeficiency virus (HIV) is an invaluable tool for assessing properties of viruses replicating in HIV-infected subjects. A common method for obtaining a primary isolate is coculture of peripheral blood mononuclear cells (PBMCs) from HIV-infected subjects with PBMCs from uninfected donors. However, such in vitro expansion may disturb the composition (identities and relative proportions of constituting viral species) of the original viral population. We developed a GeneScan assay to monitor HIV populations by detecting variants that differ in the length of the V1/V2 coding region of the envelope gene. This assay was used to compare proviral DNAs from the PBMCs of eight subjects to the corresponding primary isolates. Major variants found in uncultured PBMCs usually persisted during culturing, while the minor variants frequently disappeared, resulting in a reduction in viral diversity. The outgrowth of the initial (2 to 4 days) viral population appeared to be determined by random events. However, subsequent changes in the population were deterministic, and as a result, the compositions of primary isolates from parallel cultures were often very similar. For two of three subjects studied, the source of HIV-negative PBMCs had little effect on the composition of primary isolates, while for the third subject donor-dependent effects were observed. Overall, our results show that most primary isolates accurately represent the major viruses found in a subject's blood and that rapid population-based genotyping methods are useful for detecting isolates with perturbed viral populations.
Structural evolution of the Achnashellach Culmination, southern Moine Thrust Belt: testing the duplex model
Authors: Butler R. W. H. , Matthews S. J. , Morgan R. K. 
Published: July 2007

Abstract
The Achnashellach Culmination is one of the major structures of the Moine Thrust Belt. As with other culminations in the belt, it is formed by a stack of imbricate thrusts. Up to 1 km of Torridon Group sediments, together with a further 200–250 m of Cambrian strata, are repeated up to 10 times, but with ramp-on-ramp thrust geometries. Thus structural thickening was chiefly achieved by thick thrust sheets with individually and aggregated displacements that are substantially lower than elsewhere in the thrust belt. The culmination is limited on its flanks by lateral ramps that climb section out of Torridon Group and up into Cambrian strata. To the north the imbricate thrusts may be deduced to branch onto the major Kinlochewe Thrust. To the south the imbricates are represented only by stacked Durness Limestone. The northward-climbing lateral ramp coincides with a major Precambrian structure, the Loch Maree Fault, which controls the thickness of Torridonian strata preserved beneath the sub-Cambrian unconformity, a rare example of basement influence on thrust system geometry within the Moine Thrust Belt. The imbricates of the Achnashellach Culmination show back-steepening and have bulged up the overriding Kishorn and Kinlochewe thrust sheets. However, these structurally higher level tectonic units slice across imbricate structures in their footwalls. Elsewhere high-level thrusts are folded by some parts of underlying imbricates. Collectively these relationships are not compatible with classical duplex models. They are explained better by models of quasi-synchronous slip on imbricate thrusts. Discordant relationships beneath major thrust sheets, including those that cut down stratigraphic section in the transport direction, can be explained by such models without necessitating low-angle extensional faulting within the thrust belt.
Tectonic stratigraphy and structural continuity of the northernmost Moine Thrust Zone and Moine Nappe, Scottish Caledonides
Authors: Holdsworth R. E. , Alsop G. I. , Strachan R. A. 
Published: July 2007

Abstract

The Moine Thrust Zone and overlying Moine Nappe represent classic ground in Scottish geology in which Neoproterozoic Moine metasedimentary rocks were translated towards the WNW over the Laurentian foreland comprising Lewisian basement gneisses and a Cambrian cover succession during Caledonian orogenesis at
c.
430 Ma. Systematic mapping of both the Moine Nappe and underlying Moine Thrust Zone in the Loch Hope to Whiten Head region of Sutherland extends the tectonic stratigraphy developed in other parts of the thrust zone to the little-studied north coast section. An apparent continuum of deformation is recognized from the Moine Nappe down into the underlying thrust zone with a consistent gently ESE-dipping foliation associated with down-dip mineral and extension lineations. The polyphase fold history present within the Moine Nappe and the thrust zone results from progressive deformation during thrusting. Thrust-related fold axes and bedding-cleavage intersections are typically subparallel to the transport direction in high-strain zones, whereas gently north- or south-plunging attitudes are common in lower strain portions of the thrust zone. Thrusts are commonly deformed by folds developed within their footwalls, consistent with a foreland-propagating sequence of deformation. The newly defined Lochan Riabhach Thrust is interpreted as an ‘out-of-sequence’ structure that sliced at low angles across the thrust zone and toward the WNW after initial thrust stacking. Comparison with the downfaulted segment of the Moine Nappe and thrust zone exposed on the foreland at Faraid Head demonstrates cross-strike continuity of the thrust sheet template and structural history for at least 15 km to the NW.
Constrictional extensional tectonics in the northern Oman mountains, its role in culmination development and the exhumation of the subducted Arabian continental margin
Authors: Al-Wardi Mohammed , Butler Robert W. H. 
Published: July 2007

Abstract
The NE margin of the Arabian continent was overthrust by ‘exotic’ sheets of oceanic and continental margin units (the Semail Ophiolite allochthon) in the Late Cretaceous. Although parts of this margin (Saih Hatat Massif) were deeply buried, through subduction, to depths suitable for eclogite-facies metamorphism, other parts are unmetamorphosed (Jebel Akhdar Massif). Hence an almost continuous metamorphic gradient is preserved. This forms an ideal setting within which to relate shallow and deeper-seated tectonic processes within an orogen. Structural data are presented from the Jebal Akhdar Massif, a composite antiformal structure that contains a network of structures that post-date allochthon emplacement. These include down-to-the-NNE layer-extensional shears and steeper faults. Layer-extensional shears contain open to close folds with hinge lines parallel to regional elongation directions. Larger-scale NNE-trending folds include the regional Jebel Nakhl Antiform. The same kinematic style can be traced into the exhumed high-pressure metamorphic terrane of Saih Hatat. Coeval orthogonal layer contraction and layer-thinning and elongation describes bulk constrictional 3D strain. Although this might be indicative of regional transtension, large-scale strike-slip faults, active during the extension, as predicted by general transtensional models are not evident. Consequently, it is inferred that constriction was the result of laterally varying crustal extension whereby top-to-the-NNE extension was locally combined with left-lateral shearing. Exhumation of the metamorphic series occurred under a carapace of extending allochthons, defining an elongate ‘pip’ of material returning to shallow crustal levels. There is, however, an imbalance between net extension and possible contraction within the Arabian continent that requires deformation within a volume of net-divergent tectonics. Thus crustal extension continued after the end of convergent tectonics in the region.
Tectonic evolution of the South Tethyan ocean: evidence from the Eastern Taurus Mountains (Elaziğ region, SE Turkey)
Authors: Robertson A. H. F. , Parlak O. , Rízaoğlu T. , Ünlügenç Ü. , İnan N. , Tasli K. , Ustaömer T. 
Published: July 2007

Abstract

Geological information from the Eastern Taurus Mountains, part of the Tethyan (South Neotethyan) suture zone exposed in the Elaziğ region, is used here to test existing tectonic hypotheses and to develop a new tectonic model. Five main tectonic stages are identified: (1) Mid-Late Triassic rifting-spreading of Southern Neotethys; (2) Late Cretaceous northward subduction-accretion of ophiolites and arc-related units; (3) Mid-Eocene subduction-related extension; (4) Early-Mid-Miocene collision and southward thrusting over the Arabian Foreland; (6) Plio-Quaternary, post-collisional left-lateral tectonic escape. During the Late Cretaceous (
c.
90 Ma) northward intra-oceanic subduction generated regionally extensive oceanic lithosphere as the İspendere, Kömürhan, Guleman and Killan ophiolites of supra-subduction zone type. A northward-dipping subduction zone was activated along the northern margin of the ocean basin (Keban Platform), followed by accretion of Upper Cretaceous ophiolites in latest Cretaceous time. As subduction continued the accreted ophiolites and overriding northern margin (Keban Platform) were intruded by calc-alkaline plutons, still during latest Cretaceous time. The northern margin was covered by shallow-marine mixed clastic-carbonate sediments in latest Cretaceous-Early Palaeogene time. Northward subduction during the Mid-Eocene was accompanied by extension of the northern continental margin, generating large fault-bounded, extensional basins that were infilled with shallow- to deep-water sediments and subduction-influenced volcanic rocks (Maden Group). Thick debris flows (‘olistostromes’) accumulated along the oceanward edge of the active margin. The partly assembled allochthon finally collided with the Arabian continental margin to the south during Early-Mid-Miocene time in response to oblique convergence; the entire thrust stack was then emplaced southwards over the downflexed Arabian Foreland. Left-lateral strike-slip (tectonic escape) along the East Anatolian Fault Zone ensued.