bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus aureus
Isolates Carrying Panton-Valentine Leucocidin Genes in England and Wales: Frequency, Characterization, and Association with Clinical Disease
Authors: Holmes A. , Ganner M. , McGuane S. , Pitt T. L. , Cookson B. D. , Kearns A. M. 
Published: May 2005

ABSTRACT

Staphylococcus aureus
isolates carrying the genes that encode for Panton-Valentine leucocidin (PVL), a highly potent toxin, have been responsible for recent outbreaks of severe invasive disease in previously healthy children and adults in the United States of America and Europe. To determine the frequency of PVL-positive isolates sent to the Staphylococcus Reference Unit (United Kingdom) for epidemiological purposes, we tested 515 isolates of
S. aureus
, and 8 (1.6%) were positive for the PVL locus. A further 470 isolates were selected to explore the association of PVL-positive
S. aureus
with clinical disease. Of these, 23 (4.9%) were PVL positive and most were associated with skin and soft tissue infections (especially abscesses). The PVL genes were also detected in isolates responsible for community-acquired pneumonia, burn infections, bacteremia, and scalded skin syndrome. Genotyping by pulsed-field gel electrophoresis and multilocus sequence typing revealed that the PVL-positive isolates were from diverse genetic backgrounds, although one prevalent clone of 12 geographically dispersed methicillin-resistant
S. aureus
(MRSA) isolates was identified (ST80). All 12 isolates were stapylococcal cassette chromosome
mec
type IVc, had an
agr
3 allele, and shared a common toxin gene profile (
sea-see
,
seg-sej
,
eta
,
etb
, and
tst
negative but
etd
positive). ST80 strains with similar genetic characteristics have been responsible for community-acquired infections in France and Switzerland. The remaining PVL-positive isolates were mostly methicillin-sensitive
S. aureus
and belonged to 12 different sequence types, including ST22 and ST30, which are closely related to the most prevalent MRSA clones in United Kingdom hospitals, EMRSA-15 and EMRSA-16, respectively.
Multilocus Sequence Typing of
Streptococcus uberis
Provides Sensitive and Epidemiologically Relevant Subtype Information and Reveals Positive Selection in the Virulence Gene
pauA
Authors: Zadoks Ruth N. , Schukken Ynte H. , Wiedmann Martin 
Published: May 2005

ABSTRACT

Control of the bovine mastitis pathogen
Streptococcus uberis
requires sensitive and epidemiologically meaningful subtyping methods that can provide insight into this pathogen's epidemiology and evolution. Development of a multilocus sequence typing (MLST) scheme based on six housekeeping and virulence genes allowed differentiation of 40 sequence types among 50
S. uberis
isolates from the United States (
n
= 30) and The Netherlands (
n
= 20). MLST was more discriminatory than EcoRI or PvuII ribotyping and provided subtype data with better epidemiological relevance, e.g., by discriminating isolates with identical ribotypes obtained from different farms. Phylogenetic analyses of MLST data revealed indications of reticulate evolution between genes, preventing construction of a core phylogeny based on concatenated DNA sequences. However, all individual gene phylogenies clearly identified a distinct
pauA
-negative subtaxon of
S. uberis
for which housekeeping alleles closely resembled those of
Streptococcus parauberis
. While the average GC content for five genes characterized was between 0.38 and 0.40,
pauA
showed a considerably lower GC content (0.34), suggesting acquisition through horizontal transfer.
pauA
also showed a higher nonsynonymous/synonymous rate ratio (

d
N

/

d
S

) (1.2) compared to the other genes sequenced (

d
N

/

d
S

< 0.12), indicating positive selection in this virulence gene. In conclusion, our data show that (i) MLST provides for highly discriminatory and epidemiologically relevant subtyping of
S. uberis
; (ii)
S. uberis
has a recombinatorial population structure; (iii) phylogenetic analysis of MLST data reveals an
S. uberis
subtaxon resembling
S. parauberis
; and (iv) horizontal gene transfer and positive selection contribute to evolution of certain
S. uberis
genes, such as the virulence gene
pauA
.
Interrelationship between Polymorphisms ofincA, Fusogenic Properties ofChlamydia trachomatisStrains, and Clinical Manifestations in Patients in The Netherlands
Authors: Pannekoek Yvonne , Spaargaren Joke , Langerak Ankie A. J. , Merks Judith , Morré Servaas A. , van der Ende Arie 
Published: May 2005

ABSTRACTIncA variation among DutchChlamydia trachomatisisolates was investigated. Of 98 strains, two carried anincAwith a premature stop codon, lacked IncA, and were nonfusogenic, while 96 contained an intactincA, expressed IncA, and were fusogenic. Among these 96 strains, nine IncA sequence types were found, of which the three most frequently encountered (88% of the strains) were randomly distributed among symptomatic and asymptomatic patients.
Prevalence of Derepressed AmpC Mutants and Extended-Spectrum β-Lactamase Producers among Clinical Isolates of
Citrobacter freundii
,
Enterobacter
spp., and
Serratia marcescens
in Korea: Dissemination of CTX-M-3, TEM-52, and SHV-12
Authors: Kim Jungmin , Lim Yu-Mi 
Published: May 2005

ABSTRACT

The resistance mechanism of extended-spectrum cephalosporins in clinical isolates of
Citrobacter freundii
,
Enterobacter
spp., and
Serratia marcescens
was studied. Of 152 isolates, 45 isolates (29.6%) were derepressed AmpC mutants and 39 isolates (25.7%) produced extended-spectrum β-lactamase (ESBLs). The most prevalent ESBLs were CTX-M enzymes, followed by TEM-52 and SHV-12.
Use of a Commercial Reagent Leads to Reduced Germ Tube Production by
Candida dubliniensis
Authors: Davis Leigh E. , Shields Christine E. , Merz William G. 
Published: May 2005

ABSTRACT

The goal of this study was to determine the factor(s) explaining our inability to detect
Candida dubliniensis
. When germ tube-positive yeasts were tested for
C. dubliniensis
, no
C. dubliniensis
was detected; however, 58
C. dubliniensis
strains were detected when germ tube-negative
Candida albicans
strains were tested further. Since all 58
C. dubliniensis
strains detected were germ tube negative, these data implied that false-negative germ tube tests occurred with germ tube solution (GTS; Remel, Lenexa, KS). All 41 known
C. dubliniensis
strains tested were negative with GTS, whereas 40 were positive with rabbit serum (RS; Sigma-Aldrich, St. Louis, MO). Results for
C. albicans
were equivalent in GTS and RS. In conclusion, GTS cannot be used for the detection of
C. dubliniensis
, and switching from yeast to hyphae in
C. dubliniensis
is more restricted than in
C. albicans
.
Identification of
Shigella sonnei
Biotype
g
Isolates Carrying Class 2 Integrons in Italy (2001 to 2003)
Authors: Mammina Caterina , Pontello Mirella , Dal Vecchio Anna , Nastasi Antonino ,   the Shigella sonnei Working Group
Published: May 2005

ABSTRACT

Phenotyping and genotyping have been carried out on 64 epidemic and sporadic isolates of
Shigella sonnei
identified in Italy in the years 2001 to 2003. Class 2 integron carriage has been also investigated. Isolates from four of the five outbreaks and four of six sporadic cases were biotype
g
, pulsed-field gel electrophoresis type B, and class 2 integron positive, suggesting emergence and spread of an epidemic clone in Italy.
Comparison of Six Methods of Extracting
Mycobacterium tuberculosis
DNA from Processed Sputum for Testing by Quantitative Real-Time PCR
Authors: Aldous Wade K. , Pounder June I. , Cloud Joann L. , Woods Gail L. 
Published: May 2005

ABSTRACT

Six methods of extracting
Mycobacterium tuberculosis
DNA from sputum for testing by quantitative PCR were compared: Tris-EDTA (TE) buffer, PrepMan Ultra, 2% sodium dodecyl sulfate (SDS)-10% Triton X with and without sonication, Infectio Diagnostics, Inc. (IDI) lysing tubes, and QIAGEN QIAamp DNA mini kit; all included a 15-min boiling step. Pooled digested and decontaminated sputum was spiked with
M. tuberculosis
ATCC 27294. Each extraction method was repeated eight times. Quantitative PCR was performed on the Smart Cycler and Rotor-Gene 3000 using primers targeting an 83-bp fragment of IS
6110
. An minor grove binding Eclipse probe with a fluorescent label was used for detection. An internal control was included to detect amplification inhibition. The limit of detection of
M. tuberculosis
DNA was 0.5 fg with both instruments. Calculated DNA concentrations (picograms) extracted using IDI, PrepMan, QIAGEN, and TE were 42.8, 30.4, 28.2, and 7.4, respectively, when run on the Smart Cycler, and 51.7, 20.1, 14.9, and 8.6, respectively, when run on Rotor-Gene. All extractions using SDS/Triton X with or without sonication were inhibited. Of the extraction methods evaluated, IDI lysis tubes provided the greatest yield of mycobacterial DNA, and the procedure can be completed in less than 1 h versus 2.5−3 h for the QIAGEN extraction.
Streptococcus pneumoniaeAntigen Test Using Positive Blood Culture Bottles as an Alternative Method To Diagnose Pneumococcal Bacteremia
Authors: Petti Cathy A. , Woods Christopher W. , Reller L. Barth 
Published: May 2005

ABSTRACTRecovery ofStreptococcus pneumoniaefrom positive blood culture bottles may be difficult due to autolysis of pneumococci. Therefore, we evaluated the performance of the Binax NOWS. pneumoniaeantigen test with samples from positive blood culture bottles and defined the duration of detectable pneumococcal antigen in these bottles. Use of theS. pneumoniaeantigen test is an alternative method for identifyingS. pneumoniaefrom positive blood culture bottles and may enable a diagnosis of pneumococcal bacteremia despite negative subcultures.
Rahnella aquatilis
Bacteremia from a Suspected Urinary Source
Authors: Tash Kaley 
Published: May 2005

ABSTRACT

A 76-year-old male with prostatic hyperplasia presented with acute pyelonephritis. Blood cultures yielded
Rahnella aquatilis
. Treatment with intravenous followed by oral levofloxacin resulted in cure. Important characteristics of this organism include its biochemical similarities to
Enterobacter agglomerans
, its apparent ability to cause bacteremia from a renal focus, and its response to quinolone therapy.
Haploinsufficiency, rather than the effect of an excessive production of soluble CD95 (CD95ΔTM), is the basis for ALPS Ia in a family with duplicated 3′ splice site AG in CD95 intron 5 on one allele
Authors: Roesler Joachim , Izquierdo Jose-Maria , Ryser Martin , Rösen-Wolff Angela , Gahr Manfred , Valcarcel Juan , Lenardo Michael J. , Zheng Lixin 
Published: May 2005

AbstractAutoimmune lymphoproliferative syndrome type Ia (ALPS Ia) is caused by mutations in the CD95/APO1/FAS (TN-FRSF6) gene, which lead to a defective CD95 ligand (CD95L)–induced apoptosis. Soluble CD95 (sCD95) has been suggested to play an important role in the pathogenesis of diverse autoimmune and malignant diseases by antagonizing CD95L. Here we evaluate a family with 4 of its 5 members harboring an ex-6–3C→G mutation that affects the splice cis regulatory region (cctacag/ex-6→cctagag/ex-6) of the CD95 gene. The mutation causes skipping of exon-6, which encodes the transmembrane region of CD95, and thereby leads to an excessive production of sCD95 in all 4 affected individuals. The mutation is associated with a low penetrance of disease phenotype and caused mild and transient ALPS in one male patient whereas all other family members are completely healthy. In all family members with the mutation we found that the cell surface expression of CD95 was low and the activated T cells were resistant to CD95-induced apoptosis. Unexpectedly, excessive production or addition of sCD95 had no effect on the CD95-induced apoptosis in diverse cells. In contrast, increasing the surface expression of CD95 was able to correct the defect in apoptosis. Thus we conclude that the ALPS in the one male patient was caused by haploinsufficiency of membrane CD95 expression. Our data challenge the hypothesis that sCD95 causes autoimmunity.
High-dose chemotherapy and autologous stem cell transplantation for primary refractory or relapsed Hodgkin lymphoma: long-term outcome in the first 100 patients treated in Vancouver
Authors: Lavoie Julye C. , Connors Joseph M. , Phillips Gordon L. , Reece Donna E. , Barnett Michael J. , Forrest Donna L. , Gascoyne Randy D. , Hogge Donna E. , Nantel Stephen H. , Shepherd John D. , Smith Clayton A. , Song Kevin W. , Sutherland Heather J. , Toze Cynthia L. , Voss Nicholas J. S. , Nevill Thomas J. 
Published: May 2005

AbstractBeginning in 1985, patients in British Columbia with Hodgkin lymphoma (HL) that was not controlled by conventional chemotherapy routinely underwent high-dose chemotherapy and autologous stem cell transplantation (HD-ASCT). Long-term complications of HD-ASCT have become apparent as more patients survive without recurrence of HL. Data were obtained retrospectively on the first 100 patients that underwent HD-ASCT for HL in Vancouver, focusing on relapse, treatment-related complications, and the occurrence of late events. Fifty-three patients remain alive (median follow-up, 11.4 years [range, 10.0-17.4 years]) with an overall survival (OAS) of 54% at 15 years. OAS was significantly better in patients in first relapse (67%) than in patients with primary refractory-induction failure (39%) and advanced disease (29%) (P = .002). The major cause of death was progression of HL (32% at 15 years). Treatment-related mortality, including death from second malignancy, was 17% at 15 years. Cumulative risk of a second malignancy was 9% at 15 years. Karnofsky performance status was at least 90% in 47 patients although hypogonadism (20 patients), hypothyroidism (12 patients), unusual infections (10 patients), anxiety or depression (7 patients), and cardiac disease (5 patients) were not uncommon in survivors. HD-ASCT can lead to durable remissions in relapsed or refractory HL with acceptable but definite late toxicity. The occurrence of late events necessitates lifelong medical surveillance. (Blood. 2005;106:1473-1478)
Critical variables in the conversion of marrow cells to skeletal muscle
Authors: Abedi Mehrdad , Greer Deborah A. , Foster Bethany M. , Colvin Gerald A. , Harpel Joshua A. , Demers Delia A. , Pimentel Jeffery , Dooner Mark S. , Quesenberry Peter J. 
Published: May 2005

AbstractWe have studied conversion of marrow cells to skeletal muscle in cardiotoxin-injured anterior tibialis muscle in a green fluorescent protein (GFP) to C57BL/6 transplantation model and ascertained that total body irradiation (TBI) with establishment of chimerism is a critical factor. Local irradiation has little effect in lower doses and was detrimental at higher doses. Whole body (1000 cGy) with shielding of the leg or a combination of 500 cGy TBI and 500 cGy local radiations was found to give the best results. In non-obese diabetic-severe combined immunodeficient (NOD-SCID) recipients, we were able to show that conversion could occur without radiation, albeit at relatively lower levels. Within 3 days of cardiotoxin injury, GFP-positive mononuclear cells were seen in the muscle, and within 2 weeks GFP-positive muscle fibers were identified. Conversion rates were increased by increasing donor-cell dose. Timing of the cardiotoxin injury relative to the transplantation was critical. These studies show that variables in transplantation and injury are critical features of marrow-to-muscle conversions. Irradiation primarily effects conversion by promoting chimerism. These data may explain the differences in the literature for the frequency of marrow-to-skeletal muscle conversion and can set a platform for future models and perhaps clinical protocols. (Blood. 2005;106:1488-1494)
Antiphospholipid syndrome in patients with systemic lupus erythematosus treated by autologous hematopoietic stem cell transplantation
Authors: Statkute Laisvyde , Traynor Ann , Oyama Yu , Yaung Kim , Verda Larissa , Krosnjar Nela , Burt Richard K. 
Published: May 2005

AbstractSystemic lupus erythematosus (SLE) is the most common disease associated with antiphospholipid syndrome (APS). We, therefore, evaluated 46 patients with refractory SLE treated by autologous hematopoietic stem cell transplantation (HSCT) for a history of APS prior to transplantation. The prevalence of SLE-related APS in our patient population was 61% (28 of 46 patients with refractory SLE). Nineteen of 28 patients with APS had lupus anticoagulant (LA) or high titers of anticardiolipin antibodies (ACLAs), either immunoglobulin (Ig)G or IgM, when evaluated at study entry. Six of 8 evaluable LA+ patients became and remained LA–; 5 of 7 initially ACLA IgG+ patients and 9 of 11 ACLA IgM+ patients demonstrated normalization of ACLA titers when followed after HSCT. Eighteen of 22 patients refractory to chronic anticoagulation discontinued anticoagulation therapy a median of 4 months after transplantation; 78% of them remained free of thrombotic events and in complete SLE remission for up to 78 months (median, 15 months) after HSCT. There was no treatment-related mortality. Autologous HSCT may be performed safely in patients with APS and appears to be effective therapy for eliminating ALPAs and preventing thrombotic complications in patients with SLE.
2B4 (CD244)-CD48 interactions provide a novel MHC class I-independent system for NK-cell self-tolerance in mice
Authors: McNerney Megan E. , Guzior Dustin , Kumar Vinay 
Published: May 2005

AbstractNatural killer (NK) cells must be able to eliminate infected and transformed cells while remaining tolerant of normal cells. NK-cell self-tolerance is thought to be maintained by self-major histocompatibility complex (MHC) class I recognition; however, there are examples where NK cells are not regulated by MHC class I and yet remain self-tolerant. Here, we show that 2B4 (CD244) and CD48 represent a second system for murine NK-cell self-recognition. 2B4 and MHC class I receptors act nonredundantly to inhibit NK lysis of syngeneic tumor cells. NK cells from β2 microglobulin (β2m)-deficient mice and NK cells that lack expression of self-MHC-binding inhibitory receptors are inhibited by 2B4. Moreover, we provide the first in vivo evidence for MHC-independent NK self-recognition in a bone marrow rejection assay. These data suggest that NK-cell self-tolerance can be mediated by molecules other than MHC. (Blood. 2005;106:1337-1340)
Nucleophosmin mutations in childhood acute myelogenous leukemia with normal karyotype
Authors: Cazzaniga Giovanni , Dell'Oro Maria Grazia , Mecucci Cristina , Giarin Emanuela , Masetti Riccardo , Rossi Vincenzo , Locatelli Franco , Martelli Massimo F. , Basso Giuseppe , Pession Andrea , Biondi Andrea , Falini Brunangelo 
Published: May 2005

AbstractNucleophosmin (NPM) is a nucleocytoplasmic shuttling protein involved in leukemia-associated chromosomal translocations, and it regulates the alternate reading frame (ARF)-p53 tumorsuppressor pathway. Recently, it has been demonstrated that mutations of the NPM1 gene alter the protein at its C-terminal, causing its cytoplasmic localization. Cytoplasmic NPM was detected in 35% of adult patients with primary non-French-American-British (FAB) classification M3 acute myeloid leukemia (AML), associated mainly with normal karyotype. We evaluated the prevalence of the NPM1 gene mutation in non-M3 childhood AML patients enrolled in the ongoing Associazione Italiana di Ematologia e Oncologia Pediatrica (AIEOP-AML02) protocol in Italy. NPM1 mutations were found in 7 (6.5%) of 107 successfully analyzed patients. NPM1- mutated patients carried a normal karyotype (7/26, 27.1%) and were older in age. Thus, the NPM1 mutation is a frequent abnormality in AML patients without known genetic marker; the mutation may represent a new target to monitor minimal residual disease in AML and a potential candidate for alternative and targeted treatments. (Blood. 2005;106:1419-1422)
Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays
Authors: Wadenbäck Johan , Clapham David H , Craig Deborah , Sederoff Ronald , Peter Gary F , von Arnold Sara , Egertsdotter Ulrika 
Published: May 2005

Abstract
Background
The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments.

Results
Here we compare expression data from Pinus taeda cDNA microarrays using transcripts amplified either exponentially by PCR or linearly by T7 transcription. The amplified transcripts vary significantly in estimated length, GC content and expression depending on amplification technique. Amplification by T7 RNA polymerase gives transcripts with a greater range of lengths, greater estimated mean length, and greater variation of expression levels, but lower average GC content, than those from PCR amplification. For genes with significantly higher expression after T7 transcription than after PCR, the transcripts were 27% longer and had about 2 percentage units lower GC content. The correlation of expression intensities between technical repeats was high for both methods (R2 = 0.98) whereas the correlation of expression intensities using the different methods was considerably lower (R2 = 0.52). Correlation of expression intensities between amplified and unamplified transcripts were intermediate (R2 = 0.68–0.77).

Conclusion
Amplification with T7 transcription better reflects the variation of the unamplified transcriptome than PCR based methods owing to the better representation of long transcripts. If transcripts of particular interest are known to have high GC content and are of limited length, however, PCR-based methods may be preferable.
Brief cognitive assessment in a UK population sample – distributional properties and the relationship between the MMSE and an extended mental state examination
Authors: Huppert Felicia A , Cabelli Sara T , Matthews Fiona E ,   the MRC Cognitive Function and Ageing Study (MRC CFAS)
Published: May 2005

Abstract
Background
Despite the MMSE's known flaws, it is still used extensively as both a screening instrument for dementia and a population measure of cognitive ability. The aim of this paper is to provide data on the distribution of MMSE scores in a representative sample from the UK population and to compare it with an extended cognitive assessment (EMSE) which covers a wider range of cognitive domains and provides a wider range of difficulty levels.

Methods
The MMSE and the EMSE were administered to over 12,000 participants at the screening stage of the MRC Cognitive Function and Ageing Study (MRC CFAS). MRC CFAS is a multi-centre population-based study in England and Wales with respondents aged 65 years and older.

Results
Normative values on the MMSE and EMSE are presented by age group, sex and level of education. There are very large differences between age groups, with smaller differences seen between the sexes and by level of education. The EMSE extends the scores at the high end of the ability range, but is no better than the MMSE at differentiating between dementia and non-dementia.

Conclusion
Population-derived norms are valuable for comparing an individual's score to the score that would be expected among the general population, given the individual's specific demographic characteristics.