bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Predominant and Virulent
Legionella pneumophila
Serogroup 1 Strain Detected in Isolates from Patients and Water in Queensland, Australia, by an Amplified Fragment Length Polymorphism Protocol and Virulence Gene-Based PCR Assays
Authors: Huang Bixing , Heron Brett A. , Gray Bruce R. , Eglezos Sofroni , Bates John R. , Savill John 
Published: September 2004

ABSTRACT

In epidemiological investigations of community legionellosis outbreaks, knowledge of the prevalence, distribution, and clinical significance (virulence) of environmental
Legionella
isolates is crucial for interpretation of the molecular subtyping results. To obtain such information for
Legionella pneumophila
serogroup 1 isolates, we used the standardized amplified fragment length polymorphism (AFLP) protocol of the European Working Group on Legionella Infection to subtype
L. pneumophila
SG1 isolates obtained from patients and water sources in Queensland, Australia. An AFLP genotype, termed AF1, was predominant in isolates from both patients (40.5%) and water (49.0%). The second most common AFLP genotype found in water isolates was AF16 (36.5%), but this genotype was not identified in the patient isolates. When virulence gene-based PCR assays for
lvh
and
rtxA
genes were applied to the isolates from patients and water, nearly all (65 of 66) AF1 strains had both virulence genes,
lvh
and
rtxA
. In contrast, neither the
lvh
nor the
rtxA
gene was found in the AF16 strains, except for one isolate with the
rtxA
gene. It appears that this may explain the failure to find this genotype in the isolates from patients even though it may be common in the environment. In view of the evidence that the AF1 genotype is the most common genotype among strains found in patients and water sources in this region, any suggested epidemiological link derived from comparing the AF1 genotype from patient isolates with the AF1 genotype from environmental isolates must be interpreted and acted on with caution. The use of virulence gene-based PCR assays applied to environmental samples may be helpful in determining the infection potential of the isolates involved.
Phenotypic and Molecular Characteristics of
Streptococcus agalactiae
Isolates Recovered from Milk of Dairy Cows in Brazil
Authors: Duarte Rafael S. , Miranda Otávio P. , Bellei Bruna C. , Brito Maria Aparecida V. P. , Teixeira Lúcia M. 
Published: September 2004

ABSTRACT

Information on the characteristics of
Streptococcus agalactiae
obtained from bovine sources in Brazil is still very limited. The aim of this study was to assess the phenotypic and genotypic diversity among
S. agalactiae
isolates from milk of dairy cows presenting clinical or subclinical mastitis in the southeast region of Brazil. Phenotypic characterization was based on physiological and serological tests. Antimicrobial susceptibility tests were carried out by the disk method. Genetic diversity was evaluated by using random amplified polymorphic DNA-PCR (RAPD-PCR) (by using the primer 1254) and pulsed-field gel electrophoresis (PFGE) (by using SmaI as the restriction enzyme) and by PCRs for detection of genes associated with resistance to erythromycin and tetracycline as well as PCRs for detection of genes coding for cell surface-associated proteins. According to the results of physiologic tests, 45 (52.9%) isolates showed beta-hemolysis and 44 (51.7%) were susceptible to bacitracin. Fourteen different biotypes were detected. The two most frequent biotypes comprised strains that were non-beta-hemolytic; fermented galactose, lactose, and salicin; produced protease; and were negative for DNase production. Serotype III was predominant (66 isolates [77.6%]), followed by serotypes II, Ia, Ib, and VI. Resistance to tetracycline and erythromycin was found in 38 (44.7%) and 9 (10.5%) isolates, respectively, with
tet
(O) (31.7%) and
erm
(B) (100%) being the most frequently occurring resistance genes. Three genes coding for surface proteins,
bca
,
lmb
, and
scpB
, were detected in 55 (64.7%), 7 (8.2%), and 43 (50.5%) isolates, respectively. In most cases, isolates from animals in the same herd presented closely related genetic profiles (determined by either RAPD-PCR or PFGE), which were distinct from those of isolates from different herds.
Whole-Blood Counting Immunoassay as a Short-Turnaround Test for Detection of Hepatitis B Surface Antigen, Anti-Hepatitis C Virus Antibodies, and Anti-Treponema pallidumAntibodies
Authors: Kudo Toyoichiro , Kido Aiko , Nishiyama Yukiko , Koganeya Hiroshi , Okuda Takako , Nabeshima Motoshige , Iinuma Yoshitsugu , Ichiyama Satoshi 
Published: September 2004

ABSTRACTWhole-blood samples were used for a counting immunoassay (CIA) with the aim of developing a short- turnaround test. After optimization of the CIA, hepatitis B surface antigen (HBsAg), anti-hepatitis C virus antibodies (anti-HCV), and anti-Treponema pallidumantibodies (anti-TP) were detected as efficiently as by an enzyme immunoassay (EIA) with serum samples. The correlations between whole-blood CIA and serum EIA were 99.8, 97.1, and 99.4% for HBsAg, anti-HCV, and anti-TP, respectively. Whole-blood CIA may be of value when rapid screening of many samples is required.
Uses of
Staphylococcus aureus
GeneChips in Genotyping and Genetic Composition Analysis
Authors: Dunman P. M. , Mounts W. , McAleese F. , Immermann F. , Macapagal D. , Marsilio E. , McDougal L. , Tenover F. C. , Bradford P. A. , Petersen P. J. , Projan S. J. , Murphy E. 
Published: September 2004

ABSTRACT

Understanding the relatedness of strains within a bacterial species is essential for monitoring reservoirs of antimicrobial resistance and for epidemiological studies. Pulsed-field gel electrophoresis (PFGE), ribotyping, and multilocus sequence typing are commonly used for this purpose. However, these techniques are either nonquantitative or provide only a limited estimation of strain relatedness. Moreover, they cannot extensively define the genes that constitute an organism. In the present study, 21 oxacillin-resistant
Staphylococcus aureus
(ORSA) isolates, representing eight major ORSA lineages, and each of the seven strains for which the complete genomic sequence is publicly available were genotyped using a novel GeneChip-based approach. Strains were also subjected to PFGE and ribotyping analysis. GeneChip results provided a higher level of discrimination among isolates than either ribotyping or PFGE, although strain clustering was similar among the three techniques. In addition, GeneChip signal intensity cutoff values were empirically determined to provide extensive data on the genetic composition of each isolate analyzed. Using this technology it was shown that strains could be examined for each element represented on the GeneChip, including virulence factors, antimicrobial resistance determinants, and
agr
type. These results were validated by PCR, growth on selective media, and detailed in silico analysis of each of the sequenced genomes. Collectively, this work demonstrates that GeneChips provide extensive genotyping information for
S. aureus
strains and may play a major role in epidemiological studies in the future where correlating genes with particular disease phenotypes is critical.
Potential Screening Assay for Undetectable Viruses on the Basis of Their Capacity To Induce Alpha Interferon Production
Authors: Schmidt Barbara , Ashlock Brittany , Neipel Frank , Levy Jay A. 
Published: September 2004

ABSTRACT

High interferon production by plasmacytoid dendritic cells (PDC) was unexpectedly noted after their coculture with CD4
+
cells from a healthy donor whose cells subsequently showed human herpesvirus type 6 and 7 infections. This release of interferon was not observed with uninfected normal CD4
+
cells. Induction of PDC interferon production could help screen for covert virus infections.
Multiplex PCR Method for Identifying Recombinant Vaccine-Related Polioviruses
Authors: Kilpatrick David R. , Ching Karen , Iber Jane , Campagnoli Ray , Freeman Christopher J. , Mishrik Nada , Liu Hong-Mei , Pallansch Mark A. , Kew Olen M. 
Published: September 2004

ABSTRACT
The recent discovery of recombinant circulating vaccine-derived poliovirus (recombinant cVDPV) has highlighted the need for enhanced global poliovirus surveillance to assure timely detection of any future cVDPV outbreaks. Six pairs of Sabin strain-specific recombinant primers were designed to permit rapid screening for VDPV recombinants by PCR.
Detection and Identification of
Actinobacillus pleuropneumoniae
Serotypes 1, 2, and 8 by Multiplex PCR
Authors: Schuchert Jennifer A. , Inzana T. J. , Angen Ø. , Jessing S. 
Published: September 2004

ABSTRACT

Multiplex PCR assays were developed to identify
Actinobacillus pleuropneumoniae
serotypes 1, 2, and 8. Primers designed for the conserved capsular polysaccharide (CP) export region amplified a 489-bp DNA fragment from all serotypes. Primers specific to the CP biosynthesis regions of serotypes 1, 2, and 8 amplified fragments of 1.6 kb, 1.7 kb, and 970 bp from only their respective serotypes.
TREATMENT OF BASAL JOINT ARTHRITIS OF THE THUMB: TRAPEZIECTOMY WITH OR WITHOUT TENDON INTERPOSITION/LIGAMENT RECONSTRUCTION
Authors: De Smet L. , Sioen W. , Spaepen D. , van Ransbeeck H. 
Published: September 2004

This prospective study compared the outcome — subjective, objective and radiographic — of two surgical techniques for treating basal joint arthritis of the thumb: a "simple" trapeziectomy (group I) and a ligament reconstruction/tendon (group II) interposition technique. There were respectively 22 patients in group I and 34 in group II, all women with primary osteoarthritis. Both techniques gave favourable results and there were no significant differences for pain relief, patient satisfaction, mobility, DASH-score, key pinch force and gripping force. However in group II, the trapezial height was better preserved indicating that the proximal migration of the thumb was prevented or limited. There was also a significant correlation between the remaining trapezial space and key pinch force.
SKIN CLOSURE IN CARPAL TUNNEL SURGERY: A PROSPECTIVE COMPARATIVE STUDY BETWEEN NYLON, POLYGLACTIN 910 AND STAINLESS STEEL SUTURES
Authors: Menovsky Tomas , Bartels Ronald H. M. A. , van Lindert Erik L. , André Grotenhuis J. 
Published: September 2004

Objective: To compare the cosmetic outcome, pain and tenderness around the operation scar of carpal tunnel syndrome surgery using either nylon, polyglactin 910 or stainless steel sutures for skin closure. Methods: A randomised clinical trial comparing nylon, polyglactin 910 or stainless steel sutures for skin closure in 61 patients undergoing carpal tunnel syndrome surgery was performed. Pain, tenderness, scar hypertrophy, redness and the presence of granulomas were assessed in all patients at ten days and six weeks after surgery and compared by non-parametric statistical tests. Results: Adequate surgical decompression of the median nerve could be achieved in all patients. All but two patients experienced significant relief of tingling of the fingers. Nearly all patients reported some degree of discomfort around the scar. At ten days, the mean pain score was 1.7 (±2.2), 3.1 (±2.3) and 1.9 (±2.3) for the nylon, vicryl and steel groups, respectively. At six weeks, the pain score was 3.6 (±3.1), 3.4 (±2.6) and 2.7 (±2.1) for the nylon, vicryl and steel groups, respectively. The infection rate was 0%, 8% and 0% for the nylon, vicryl and steel groups, respectively. Suture granulomas were significantly more present in the vicryl group (p<0.05). There were no statistical differences in redness or hypertrophy of the wound between the three groups. Conclusions: Nylon and stainless steel sutures are both suitable for skin closure after carpal tunnel surgery. Based on this study, absorbable vicryl sutures should not be used, since the incidence of infections and the presence of suture granulomas was much higher than in the nylon and steel suture groups.
SURGICAL PROCESS RE-ENGINEERING: CARPAL TUNNEL DECOMPRESSION — A MODEL
Authors: Casaletto J. A. , Rajaratnam V. 
Published: September 2004

Surgical process re-engineering is a methodology where the entire surgical process is systematically analysed and re-designed. The process starts with mapping of the current process followed by in-depth analysis of the existing process. A new process is drafted with the aim of making the whole procedure more efficient. The new process is then discussed with all the staff involved in the operating room. Following implementation of the process, surgical process re-engineering should ideally be routinely carried out to continuously improve the procedure. We present an example of surgical process re-engineering which we carried out on the procedure of carpal tunnel release. We used carpal tunnel release as a model as it is a very common operation, with predictable intra-operative findings, and the patient is likely to benefit directly from procedure time reduction. A preliminary mapping of three procedures was done followed by a detailed timed mapping of five routine carpal tunnel decompression procedures. The mapped process was analysed in detail and a number of changes were made in the process. After implementing the new process, a further five procedures were mapped and timed again. In comparison to the original process, we achieved a reduction of 20% in the mean procedure time and a reduction of 42% in the number of steps from 66 to 37.
Speciation of Lipids and Humus-Like Colloidal Compounds in a Forest Soil Reclaimed with Municipal Solid Waste Compost
Authors: Zancada M. Cristina , Almendros Gonzalo , Sanz Jesús , Román Román 
Published: September 2004

The progressive transformations of lipid and humus-like fractions in soil after massive input (400 Mg ha-1) of urban waste have been studied during an 87-week experiment in field plots of a degraded Calcic Regosol in Central Spain. Structural changes in the macromolecular fractions were small when compared with the qualitative and quantitative changes in lipid composition. The intense depletion of the lipid fraction with time and the decrease of the humic acid to fulvic acid ratio were the most significant quantitative indices of the compost transformation in soil. Changes in soil lipid fractions were especially noted in relation to their speciation status and distribution patterns (carbon preference index and relative chain length). Three subfractions were considered: (I) direct extraction with petroleum ether, (II) liquid-liquid extraction after soil treatment with 2 M H3PO4 and (III) after soil treatment with 0.1 M NaOH. Although lipid concentration tends to decrease with time, lipids in the fraction tightly bonded to soil (III) remained qualitatively and quantitatively constant in the course of the field experiment. Gas chromatographic-mass spectrometric analyses showed that the more stable the association of lipid to the soil matrix, the fewer the changes observed in the distribution pattern of the fatty acids during the progressive transformation stages.
Vascular leukocytes contribute to tumor vascularization
Authors: Conejo-Garcia Jose R. , Buckanovich Ronald J. , Benencia Fabian , Courreges Maria C. , Rubin Stephen C. , Carroll Richard G. , Coukos George 
Published: September 2004

Abstract
There is no proof that hematopoietic cells contribute significantly to vasculogenesis in postnatal life. Here we report a novel leukocyte subset within ovarian carcinoma that coexpresses endothelial and dendritic cell markers. Fluorescence-activated cell sorter (FACS) analysis identified a high frequency of VE-cadherin+ CD45+ leukocytes (39% of host cells) in 10 of 10 solid tumors evaluated. This population represented less than 1% of nontumor cells in ascites and peripheral blood. At the protein level, more than 86% of these cells expressed the endothelial markers P1H12, CD34, and CD31 and leukocyte markers CD11c and major histocompatibility complex (MHC) class II. At the mRNA level, we detected TEM1, TEM7, and Thy-1, specific markers of angiogenic endothelium. Finally, this population has the capacity to generate functional blood vessels in vivo. Because of its mixed phenotype, we named this population vascular leukocytes (VLCs). Our data provide an important link between hematopoietic endothelial precursors and vascular development in postnatal life and a possible novel therapeutic target.
Enhancer trapping in zebrafish using the Sleeping Beauty transposon
Authors: Balciunas Darius , Davidson Ann E , Sivasubbu Sridhar , Hermanson Spencer B , Welle Zachary , Ekker Stephen C 
Published: September 2004

Abstract
Background
Among functional elements of a metazoan gene, enhancers are particularly difficult to find and annotate. Pioneering experiments in Drosophila have demonstrated the value of enhancer "trapping" using an invertebrate to address this functional genomics problem.

Results
We modulated a Sleeping Beauty transposon-based transgenesis cassette to establish an enhancer trapping technique for use in a vertebrate model system, zebrafish Danio rerio. We established 9 lines of zebrafish with distinct tissue- or organ-specific GFP expression patterns from 90 founders that produced GFP-expressing progeny. We have molecularly characterized these lines and show that in each line, a specific GFP expression pattern is due to a single transposition event. Many of the insertions are into introns of zebrafish genes predicted in the current genome assembly. We have identified both previously characterized as well as novel expression patterns from this screen. For example, the ET7 line harbors a transposon insertion near the mkp3 locus and expresses GFP in the midbrain-hindbrain boundary, forebrain and the ventricle, matching a subset of the known FGF8-dependent mkp3 expression domain. The ET2 line, in contrast, expresses GFP specifically in caudal primary motoneurons due to an insertion into the poly(ADP-ribose) glycohydrolase (PARG) locus. This surprising expression pattern was confirmed using in situ hybridization techniques for the endogenous PARG mRNA, indicating the enhancer trap has replicated this unexpected and highly localized PARG expression with good fidelity. Finally, we show that it is possible to excise a Sleeping Beauty transposon from a genomic location in the zebrafish germline.

Conclusions
This genomics tool offers the opportunity for large-scale biological approaches combining both expression and genomic-level sequence analysis using as a template an entire vertebrate genome.
Exonuclease activity and P nucleotide addition in the generation of the expressed immunoglobulin repertoire
Authors: Jackson Katherine JL , Gaeta Bruno , Sewell William , Collins Andrew M 
Published: September 2004

Abstract
Background
Immunoglobulin rearrangement involves random and imprecise processes that act to both create and constrain diversity. Two such processes are the loss of nucleotides through the action of unknown exonuclease(s) and the addition of P nucleotides. The study of such processes has been compromised by difficulties in reliably aligning immunoglobulin genes and in the partitioning of nucleotides between segment ends, and between N and P nucleotides.

Results
A dataset of 294 human IgM sequences was created and partitioned with the aid of a probabilistic model. Non-random removal of nucleotides is seen between the three IGH gene types with the IGHV gene averaging removals of 1.2 nucleotides compared to 4.7 for the other gene ends (p < 0.001). Individual IGHV, IGHD and IGHJ gene subgroups also display statistical differences in the level of nucleotide loss. For example, within the IGHJ group, IGHJ3 has average removals of 1.3 nucleotides compared to 6.4 nucleotides for IGHJ6 genes (p < 0.002). Analysis of putative P nucleotides within the IgM and pooled datasets revealed only a single putative P nucleotide motif (GTT at the 3' D-REGION end) to occur at a frequency significantly higher then would be expected from random N nucleotide addition.

Conclusions
The loss of nucleotides due to the action of exonucleases is not random, but is influenced by the nucleotide composition of the genes. P nucleotides do not make a significant contribution to diversity of immunoglobulin sequences. Although palindromic sequences are present in 10% of immunologlobulin rearrangements, most of the 'palindromic' nucleotides are likely to have been inserted into the junction during the process of N nucleotide addition. P nucleotides can only be stated with confidence to contribute to diversity of less than 1% of sequences. Any attempt to identify P nucleotides in immunoglobulins is therefore likely to introduce errors into the partitioning of such sequences.
Glycogen Synthase Kinase-3 regulates IGFBP-1 gene transcription through the Thymine-rich Insulin Response Element
Authors: Finlay David , Patel Satish , Dickson Lorna M , Shpiro Natalia , Marquez Rodolfo , Rhodes Chris J , Sutherland Calum 
Published: September 2004

Abstract
Background
Hepatic expression of several gene products involved in glucose metabolism, including phosphoenolpyruvate carboxykinase (PEPCK), glucose-6-phosphatase (G6Pase) and insulin-like growth factor binding protein-1 (IGFBP-1), is rapidly and completely inhibited by insulin. This inhibition is mediated through the regulation of a DNA element present in each of these gene promoters, that we call the T hymine-rich I nsulin R esponse E lement (TIRE). The insulin signalling pathway that results in the inhibition of these gene promoters requires the activation of phosphatidylinositol 3-kinase (PI 3-kinase). However, the molecules that connect PI 3-kinase to these gene promoters are not yet fully defined. Glycogen Synthase Kinase 3 (GSK-3) is inhibited following activation of PI 3-kinase. We have shown previously that inhibitors of GSK-3 reduce the activity of two TIRE-containing gene promoters (PEPCK and G6Pase), whose products are required for gluconeogenesis.

Results
In this report we demonstrate that in H4IIE-C3 cells, four distinct classes of GSK-3 inhibitor mimic the effect of insulin on a third TIRE-containing gene, IGFBP-1. We identify the TIRE as the minimum requirement for inhibition by these agents, and demonstrate that the target of GSK-3 is unlikely to be the postulated TIRE-binding protein FOXO-1. Importantly, overexpression of GSK-3 in cells reduces the insulin regulation of TIRE activity as well as endogenous IGFBP-1 expression.

Conclusions
These results implicate GSK-3 as an intermediate in the pathway from the insulin receptor to the TIRE. Indeed, this is the first demonstration of an absolute requirement for GSK-3 inhibition in insulin regulation of gene transcription. These data support the potential use of GSK-3 inhibitors in the treatment of insulin resistant states such as Type 2 diabetes mellitus, but suggest that it will be important to identify all TIRE-containing genes to assess potential side effects of these agents.