bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of Reduced Susceptibility to Glycopeptides among Methicillin-Resistant
Staphylococcus aureus
Isolates from Patients in Ireland and Evaluation of Agar Screening Methods for Detection of Heterogeneously Glycopeptide-Intermediate
S. aureus
Authors: Fitzgibbon Margaret M. , Rossney Angela S. , O'Connell Brian 
Published: August 2007

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) isolates (
n
= 3,189) from 2,990 patients were investigated by agar screening and by the Etest macromethod for reduced susceptibility to glycopeptide. No vancomycin-resistant
S. aureus
or glycopeptide-intermediate
S. aureus
(GISA) isolates were detected, but 178 isolates were confirmed as hetero-GISA (hGISA) by vancomycin population analysis profile (vPAP)-area under the curve (AUC) ratio determination and/or teicoplanin PAP (tPAP) methods. Of 139 isolates detected using the recommended Etest macromethod cutoff values of ≥8 mg/liter for both vancomycin and teicoplanin or ≥12 mg/liter for teicoplanin alone, 73 were confirmed as hGISA by vPAP-AUC, 95 were confirmed as hGISA by tPAP, and 108 were confirmed as hGISA by both methods. An Etest macromethod cutoff value of 8 mg/liter for teicoplanin alone detected a further 70 hGISA (17 were confirmed by vPAP-AUC and 70 were confirmed by tPAP). Agar screening utilizing brain heart infusion (BHI) agar containing 6 mg of vancomycin/liter (BHIV6) and Mueller-Hinton (MH) agar containing 8 mg of teicoplanin/liter (MHT8) failed to detect hGISA. MH agar containing 5 mg of teicoplanin/liter (MHT5) and BHI containing 5 mg of teicoplanin/liter (BHIT5) were evaluated using 10-μl volumes of three inoculum concentrations (with densities equivalent to 0.5 and 2.0 McFarland turbidity standards and stationary-phase BHI broth subcultures [MHT5
0.5
, MHT5
2.0
, MHT5
S
, BHIT5
0.5
, BHIT5
2.0
, and BHIT5
S
]). The sensitivity of all methods except MHT5
0.5
and MHT5
2.0
was 100%. The specificity ranged from 4 to 82%. BHIT5
0.5
yielded the best performance, with a specificity of 84% for detecting isolates with teicoplanin Etest macromethod values of ≥8 mg/liter. Screening on BHIT5
0.5
is useful where screen-positive isolates are investigated with the Etest macromethod and confirmed by vPAP-AUC and tPAP. The prevalence of hGISA among patients with blood culture isolates recovered in Irish hospitals between 1999 and 2003 was 2.6%, whereas the prevalence among patients with isolates from all specimen sites collected during a 2-week survey in 1999 was 12%. The prevalence in one hospital decreased from 5.3% in 2003 to 1.5% in 2004.
Dolosigranulum pigrum
Causing Nosocomial Pneumonia and Septicemia
Authors: Lécuyer Hervé , Audibert Juliette , Bobigny Astrid , Eckert Catherine , Jannière-Nartey Caroline , Buu-Hoï Annie , Mainardi Jean-Luc , Podglajen Isabelle 
Published: August 2007

ABSTRACT

We report a case of non-ventilator-associated nosocomial pneumonia and septicemia due to
Dolosigranulum pigrum
, a rare gram-positive opportunistic pathogen. The organism was isolated from bronchoalveolar lavage fluid and blood of a debilitated patient.
D. pigrum
was identified after 16S rRNA gene sequencing.
Evaluation of the Invader Assay with the BACTEC MGIT 960 System for Prompt Isolation and Identification of Mycobacterial Species from Clinical Specimens
Authors: Ichimura Sadahiro , Nagano Makoto , Ito Nobuko , Shimojima Masahiro , Egashira Toru , Miyamoto Chikara , Ohkusu Kiyofumi , Ezaki Takayuki 
Published: August 2007

ABSTRACT
Rapid and accurate identification of mycobacterial species is essential for patient management. We describe the use of the Invader assay in conjunction with the BACTEC MGIT 960 system that together provide an efficient procedure for clinical use. This assay discriminates single-base differences (e.g., genotyping single-nucleotide polymorphisms) under homogeneous and isothermal conditions and can measure directly on genomic DNA without prior target DNA amplification. To identify a wide variety of mycobacterial species, 20 Invader probes were designed to target the 16S rRNA gene and the 16S-23S rRNA gene internal transcribed spacer 1 (ITS-1) region. To validate the Invader probes, we used 78 ATCC strains, and 607 clinical mycobacterial strains, which were identified by DNA sequencing of the 16S rRNA gene and ITS-1. The Invader assay could accurately identify and differentiate these strains according to target sequences. Moreover, it could detect and identify 116 (95.1%) of 122 positive liquid cultures from the BACTEC MGIT 960 system and did not react to 83 contaminated MGIT cultures. Species identification takes 6.5 h by the Invader assay: 2.0 h for DNA extraction, 0.5 h for handling, and up to 4 h for the Invader reaction. The Invader assay has the speed, ease of use, and accuracy to be an effective procedure for the bacteriological diagnosis of mycobacterial infections.
Multilocus Analysis of
Cryptosporidium hominis
and
Cryptosporidium parvum
Isolates from Sporadic and Outbreak-Related Human Cases and
C. parvum
Isolates from Sporadic Livestock Cases in the United Kingdom
Authors: Leoni Francesca , Mallon Marianne E. , Smith Huw V. , Tait Andy , McLauchlin Jim 
Published: August 2007

ABSTRACT

Cryptosporidium parvum
and
Cryptosporidium hominis
isolates from sporadic, drinking water-associated, and intrafamilial human cases together with
C. parvum
isolates from sporadic cases in livestock were collected in the United Kingdom between 1995 and 1999. The isolates were characterized by analysis of three microsatellite markers (ML1, GP15, and MS5) using PCR amplification. Within
C. hominis
, four alleles were detected within the GP15 and MS5 loci, and a single type was detected with ML1.
C. parvum
was more polymorphic; 12 alleles were detected with GP15, 6 were detected with MS5, and 3 were detected with ML1. Multilocus analysis of polymorphisms within the three microsatellite loci was combined with those reported previously for an extrachromosomal small double-stranded RNA. Forty multilocus types were detected within these two species: 9 were detected in
C. hominis
, and 31 were detected in
C. parvum
. In
C. hominis
, heterogeneity was almost exclusively found in samples from sporadic cases. Similarity analysis identified three main groups within
C. parvum
, and the group that predominated in human infection was also found in livestock. Multilocus types of
C. parvum
previously identified only in humans were not detected in livestock. Isolates of both
C. hominis
and
C. parvum
from separate waterborne outbreaks were genetically homogeneous, suggesting preferential or point source transmission of certain types of these two species of parasites.
Epstein-Barr Virus (EBV)-Encoded RNA 2 (EBER2) but Not EBER1 Plays a Critical Role in EBV-Induced B-Cell Growth Transformation
Authors: Wu Yi , Maruo Seiji , Yajima Misako , Kanda Teru , Takada Kenzo 
Published: August 2007

ABSTRACT
Epstein-Barr virus (EBV)-encoded RNA 1 (EBER1) and EBER2 are untranslated RNAs and the most abundant viral transcripts in latently EBV-infected cells. We previously reported that EBERs play a critical role in efficient EBV-induced growth transformation of primary B cells. To investigate whether EBER1 and EBER2 have distinct roles in B-cell growth transformation, recombinant EBVs carrying either EBER1 or EBER2 were generated. The transforming ability of recombinant EBVs expressing EBER2 was as high as that of EBVs expressing both EBER1 and EBER2. In contrast, the transforming ability of recombinant EBVs carrying EBER1 was impaired and was similar to that of EBV lacking both EBER1 and EBER2. Lymphoblastoid cell lines (LCLs) established with EBVs carrying EBER2 proliferated at low cell densities, while LCLs established with EBVs carrying EBER1 did not. Interleukin 6 (IL-6) production in LCLs expressing EBER2 was more abundant than in those lacking EBER2. The growth of LCLs lacking EBER2 was enhanced by the addition of recombinant IL-6 to the cell culture, while the growth of EBER2-expressing LCLs was inhibited by a neutralizing anti-IL-6 antibody. These results demonstrate that EBER2, but not EBER1, contributes to efficient B-cell growth transformation. We conclude that EBER1 and EBER2, despite their structural similarity, have different functions in latently infected lymphoblastoid cells.
Symptomatic and Asymptomatic Viral Recrudescence in Solid-Organ Transplant Recipients and Its Relationship with the Antigen-Specific CD8
+
T-Cell Response
Authors: Crough Tania , Fazou Chrysa , Weiss Julissa , Campbell Scott , Davenport Miles P. , Bell Scott C. , Galbraith Andrew , McNeil Keith , Khanna Rajiv 
Published: August 2007

ABSTRACT

Using ex vivo antigen-specific T-cell analysis, we found that symptomatic cytomegalovirus recrudescence in transplant recipients was coincident with reduced expression of gamma interferon (IFN-γ) by virus-specific CD8
+
T cells and an up-regulation of CD38 expression on these T cells, although there was no significant change in the absolute number of virus-specific cells (as assessed by major histocompatibility complex-peptide multimers). In contrast, HLA class I-matched transplant patients with asymptomatic viral recrudescence showed increased expansion of antigen-specific T cells and highly stable IFN-γ expression by epitope-specific T cells. These studies suggest that a strong functional T-cell response plays a crucial role in defining the clinical outcome of acute viral recrudescence.
Inhibition of Transfer to Secondary Receptors by Heparan Sulfate-Binding Drug or Antibody Induces Noninfectious Uptake of Human Papillomavirus
Authors: Selinka Hans-Christoph , Florin Luise , Patel Hetal D. , Freitag Kirsten , Schmidtke Michaela , Makarov Vadim A. , Sapp Martin 
Published: August 2007

ABSTRACT

Infection with various human papillomaviruses (HPVs) induces cervical cancers. Cell surface heparan sulfates (HS) have been shown to serve as primary attachment receptors, and molecules with structural similarity to cell surface HS, like heparin, function as competitive inhibitors of HPV infection. Here we demonstrate that the
N
,
N
′-bisheteryl derivative of dispirotripiperazine, DSTP27, efficiently blocks papillomavirus infection by binding to HS moieties, with 50% inhibitory doses of up to 0.4 μg/ml. In contrast to short-term inhibitory effects of heparin, pretreatment of cells with DSTP27 significantly reduced HPV infection for more than 30 h. Using DSTP27 and heparinase, we furthermore demonstrate that HS moieties, rather than laminin 5, present in the extracellular matrix (ECM) secreted by keratinocytes are essential for infectious transfer of ECM-bound virions to cells. Prior binding to ECM components, especially HS, partially alleviated the requirement for cell surface HS. DSTP27 blocks infection by cell-bound virions by feeding into a noninfectious entry pathway. Under these conditions, virus colocalized with HS moieties in endocytic vesicles. Similarly, postattachment treatment of cells with heparinase, cytochalasin D, or neutralizing antibodies resulted in uptake of virions without infection, indicating that deviation into a noninfectious entry pathway is a major mode of postattachment neutralization. In untreated cells, initial colocalization of virions with HS on the cell surface and in endocytic vesicles was lost with time. Our data suggest that initial attachment of HPV to HS proteoglycans (HSPGs) must be followed by secondary interaction with additional HS side chains and transfer to a non-HSPG receptor for successful infection.
Sheeppox Virus Kelch-Like Gene
SPPV-019
Affects Virus Virulence
Authors: Balinsky C. A. , Delhon G. , Afonso C. L. , Risatti G. R. , Borca M. V. , French R. A. , Tulman E. R. , Geary S. J. , Rock D. L. 
Published: August 2007

ABSTRACT

Sheeppox virus (SPPV), a member of the
Capripoxvirus
genus of the
Poxviridae
, is the etiologic agent of a significant disease of sheep in the developing world. Genomic analysis of pathogenic and vaccine capripoxviruses identified genes with potential roles in virulence and host range, including three genes with similarity to kelch-like genes of other poxviruses and eukaryotes. Here, a mutant SPPV with a deletion in the
SPPV-019
kelch-like gene, ΔKLP, was derived from the pathogenic strain SPPV-SA. ΔKLP exhibited in vitro growth characteristics similar to those of SPPV-SA and revertant virus (RvKLP). ΔKLP-infected cells exhibited a reduction in Ca
2+
-independent cell adhesion, suggesting that
SPPV-019
may modulate cellular adhesion. When inoculated in sheep by the intranasal or intradermal routes, ΔKLP was markedly attenuated, since all ΔKLP-infected lambs survived infection. In contrast, SPPV-SA and RvKLP induced mortality approaching 100%. Lambs inoculated with ΔKLP exhibited marked reduction or delay in fever response, gross lesions, viremia, and virus shedding compared to parental and revertant viruses. Together, these findings indicate that
SPPV-019
is a significant SPPV virulence determinant in sheep.
Pseudorabies Virus Us9 Directs Axonal Sorting of Viral Capsids
Authors: Lyman M. G. , Feierbach B. , Curanovic D. , Bisher M. , Enquist L. W. 
Published: August 2007

ABSTRACT
Pseudorabies virus (PRV) mutants lacking the Us9 gene cannot spread from presynaptic to postsynaptic neurons in the rat visual system, although retrograde spread remains unaffected. We sought to recapitulate these findings in vitro using the isolator chamber system developed in our lab for analysis of the transneuronal spread of infection. The wild-type PRV Becker strain spreads efficiently to postsynaptic neurons in vitro, whereas the Us9-null strain does not. As determined by indirect immunofluorescence, the axons of Us9-null infected neurons do not contain the glycoproteins gB and gE, suggesting that their axonal sorting is dependent on Us9. Importantly, we failed to detect viral capsids in the axons of Us9-null infected neurons. We confirmed this observation by using three different techniques: by direct fluorescence of green fluorescent protein-tagged capsids; by transmission electron microscopy; and by live-cell imaging in cultured, sympathetic neurons. This finding has broad impact on two competing models for how virus particles are trafficked inside axons during anterograde transport and redefines a role for Us9 in viral sorting and transport.
Crystal Structure and Structural Mechanism of a Novel Anti-Human Immunodeficiency Virus andd-Amino Acid-Containing Chemokine
Authors: Liu Dongxiang , Madani Navid , Li Ying , Cao Rong , Choi Won-Tak , Kawatkar Sameer P. , Lim Mi Youn , Kumar Santosh , Dong Chang-Zhi , Wang Jun , Russell Julie D. , Lefebure Caroline R. , An Jing , Wilson Scott , Gao Yi-Gui , Pallansch Luke A. , Sodroski Joseph G. , Huang Ziwei 
Published: August 2007

ABSTRACTChemokines and their receptors play important roles in normal physiological functions and the pathogeneses of a wide range of human diseases, including the entry of human immunodeficiency virus type 1 (HIV-1). However, the use of natural chemokines to probe receptor biology or to develop therapeutic drugs is limited by their lack of selectivity and the poor understanding of mechanisms in ligand-receptor recognition. We addressed these issues by combining chemical and structural biology in research into molecular recognition and inhibitor design. Specifically, the concepts of chemical biology were used to develop synthetically and modularly modified (SMM) chemokines that are unnatural and yet have properties improved over those of natural chemokines in terms of receptor selectivity, affinity, and the ability to explore receptor functions. This was followed by using structural biology to determine the structural basis for synthetically perturbed ligand-receptor selectivity. As a proof-of-principle for this combined chemical and structural-biology approach, we report a noveld-amino acid-containing SMM-chemokine designed based on the natural chemokine called viral macrophage inflammatory protein II (vMIP-II). The incorporation of unnaturald-amino acids enhanced the affinity of this molecule for CXCR4 but significantly diminished that for CCR5 or CCR2, thus yielding much more selective recognition of CXCR4 than wild-type vMIP-II. Thisd-amino acid-containing chemokine also showed more potent and specific inhibitory activity against HIV-1 entry via CXCR4 than natural chemokines. Furthermore, the high-resolution crystal structure of thisd-amino acid-containing chemokine and a molecular-modeling study of its complex with CXCR4 provided the structure-based mechanism for the selective interaction between the ligand and chemokine receptors and the potent anti-HIV activity ofd-amino acid-containing chemokines.
Radiometric dating of Late Precambrian times
Authors: Odin G. S. , Gale N. H. , Doré F. 
Published: August 2007

Abstract

Between about 1979 and 1981 new radiometric data relevant to the numerical age of the Precambrian-Cambrian boundary became available. Based on this it was suggested in a recent review (Odin
et al.
1983) that the numerical age for that boundary was probably much younger than usually accepted, lying probably in the interval of time 520-540 Ma rather than at about 580-600 Ma. This new estimate has provoked discussions which essentially concern the stratigraphical location appropriate to these modern dates. In addition, it has been argued that this new view of the location of the Precambrian-Cambrian boundary did not take into account all the available geochronological results. We consider this last remark as unfounded at the time when our review was submitted for publication (at the beginning of 1982). However, one result of our review seems to have been to rejuvenate interest in the subject so that there is now more data to be discussed. Although the scarcity of fully published results still permits one at present only to propose tentative conclusions, some facts seem well enough established; conversely, in our opinion, other data are certainly not as soundly based as some authors aver. The present comment tries to give complementary information to enable others to judge both our own arguments as well as those of our colleagues.

A fundamental new contribution to this problem is in progress, i.e. a formal definition of the Precambrian-Cambrian boundary within the Meishucun stage of China (apparently now strongly advocated by the IUGS-IGCP Working Group
Remarks on the numerical scale of Ordovician to Devonian times
Authors: Odin G. S. 
Published: August 2007

Summary

The Early Palaeozoic is the most difficult portion of the time-scale to calibrate due to the low number of precise calibration points although knowledge has greatly increased during the last few years. Thus, two-thirds of the data selected by McKerrow
et al.
(this volume) had not been published in 1980. These new data permit a reassessment of the preceding proposals. The location of some boundaries is still somewhat subjective; this explains differences in recommended or preferred numbers proposed by different authors. However, the correct assessment of the available data by the different authors allow one to define
intervals of time
(better than just numbers), and some sort of 'non disagreement' is now obtained which was not the case earlier. The present comment intends to show the points of agreement, to underline some differences of interpretation, and discuss some data not considered by McKerrow
et al.
Comments on the geochronology of the Carboniferous to Triassic times
Authors: Odin G. S. 
Published: August 2007

Abstract
Thanks to the relatively numerous and more or less reliable radiometric dates obtained from the Carboniferous to Triassic sequences it is possible to choose the best calibration points before trying to draw a picture of the corresponding numerical time-scale. In this context, the analysis of Forster & Warrington in the introduction to their chapter is a most welcome reminder of the criteria for data selection, sometimes neglected or forgotten by other authors.
Taking this into account, one may be sure that the portion of the time-scale proposed is probably one of the most objectively founded in this book for: (1) The authors are fully aware of the various uncertainties arising in the exercise of assessing a calibration point. (2) They actually use their own recommendations, when possible, and try to discuss each of the different areas of uncertainty (i.e.) the stratigraphical and the geochemical as well as the analytical ones in order to weight the reliability of a given date. (3) They have found in the literature a large number of data from which they selected 45. These are supported by other results which, although only briefly mentioned and less significant, are useful to reinforce their arguments.
The result of this considerable work is a time-scale which certainly is a very good reference. The minor remarks proposed here must be considered therefore as a modest complement of information to emphasize some of the limited differences between this work and the synthesis edited by the author in 1982 (Odin 1982).
Concerning the numerical ages proposed for the Jurassic and Cretaceous geochronology
Authors: Odin G. S. 
Published: August 2007

Abstract
In the presentation by Drs Hallam and Hancock some numbers are proposed to calibrate the Middle and Late Mesozoic time. For this period some (if not all) stage boundaries are actually not precisely located from a purely stratigraphical point of view, and, strictly speaking, no definitive numbers can be assigned to them. Consequently, different acceptable solutions can be proposed concerning the numerical age of these boundaries. However, some considerations developed by Hallam and Hancock do not correspond to the present state of knowledge resulting, in my view, in either incomplete or sometimes obsolete conclusions. These considerations are discussed below.
The Neogene: Part 2 Neogene geochronology and chronostratigraphy
Authors: Berggren W. A. , Kent D. V. , van Couvering J. A. 
Published: August 2007

SummaryWe present a revised Neogene geochronology based upon a best fit to selected high temperature radiometric dates on a number of identified magnetic polarity chrons (within the late Cretaceous, Paleogene, and Neogene) which minimizes apparent accelerations in sea-floor spreading. An assessment of first order correlations of calcareous plankton biostratigraphic datum events to magnetic polarity stratigraphy yields the following estimated magnetobiochronology of major chronostratigraphic boundaries: Oligocene/Miocene (Chron C6CN): 23.7 Ma; Miocene/Pliocene (slightly younger than Gilbert/Chron 5 boundary): 5.3 Ma; Pliocene/Pleistocene (slightly younger than Olduvai Subchron): 1.6 Ma.Changes to the marine time-scale are relatively minor in terms of recent and current usage except in the interval of the middle Miocene where new DSDP data reveal that previous correlations of magnetic anomalies 5 and 5A to magnetic polarity Chrons 9 and 11, respectively, are incorrect. Our revized magnetobiostratigraphic correlations result in a 1.5-2 m.y. shift towards younger magnetobiochronologic age estimate in the middle Miocene. Radiometric dates correlated to bio- and magnetostratigraphy in continental section generally support the revized marine magnetobiochronology presented here. Major changes, however, are made in marine-non-marine correlations in the Miocene in Eurasia which indicate African-Eurasian migrations through the Persian Gulf as early as 20 Ma. The 12.5 Ma estimate of theHippariondatum is supported by recent taxonomic revisions of the hipparions and magnetobiostratigraphic correlations which show that primitive hipparions first arrived in Eurasia and North Africa atc.12.5 Ma and a second wave in the tropics (i.e. Indian and central Africa) atc.10 Ma.