bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus aureus
Genotyping Using Novel Real-Time PCR Formats
Authors: Huygens Flavia , Inman-Bamber John , Nimmo Graeme R. , Munckhof Wendy , Schooneveldt Jacqueline , Harrison Bruce , McMahon Jennifer A. , Giffard Philip M. 
Published: October 2006

ABSTRACT

One approach to microbial genotyping is to make use of sets of single-nucleotide polymorphisms (SNPs) in combination with binary markers. Here we report the modification and automation of a SNP-plus-binary-marker-based approach to the genotyping of
Staphylococcus aureus
and its application to 391
S. aureus
isolates from southeast Queensland, Australia. The SNPs used were
arcC
210,
tpi
243,
arcC
162,
gmk
318,
pta
294,
tpi
36,
tpi
241, and
pta
383. These provide a Simpson's index of diversity (
D
) of 0.95 with respect to the
S. aureus
multilocus sequence typing database and define 61 genotypes and the major clonal complexes. The binary markers used were
pvl
,
cna
,
sdrE
, pT181, and pUB110. Two novel real-time PCR formats for interrogating these markers were compared. One of these makes use of “light upon extension” (LUX) primers and biplexed reactions, while the other is a streamlined modification of kinetic PCR using SYBR green. The latter format proved to be more robust. In addition, automated methods for DNA template preparation, reaction setup, and data analysis were developed. A single SNP-based method for ST-93 (Queensland clone) identification was also devised. The genotyping revealed the numerical importance of the “South West Pacific” and “Queensland” community-acquired methicillin-resistant
S. aureus
(MRSA) clones and the clonal complex 239 “Aus-1/Aus-2” hospital-associated MRSA. There was a strong association between the community-acquired clones and
pvl
.
Design, Construction, and Evaluation of a Specific Chimeric Antigen To Diagnose Chagasic Infection
Authors: Aguirre Sebastián , Silber Ariel M. , Brito Maria Edileuza F. , Ribone María E. , Lagier Claudia M. , Marcipar Iván S. 
Published: October 2006

ABSTRACTChagas' disease is routinely diagnosed by detecting specific antibodies (Abs) using serological methods. The methodology has the drawback of potential cross-reactions with Abs raised during other infectious and autoimmune diseases (AID). Fusion of DNA sequences encoding antigenic proteins is a versatile tool to engineer proteins to be used as sensitizing elements in serological tests. A synthetic gene encoding a chimeric protein containing the C-terminal region of C29 and the N-terminal region of TcP2β was constructed. A 236-serum panel, composed of 104 reactive and 132 nonreactive sera to Chagas' disease, was used to evaluate the performance of the chimera. Among the nonreactive sera, 65 were from patients with AID (systemic lupus erythematosus and rheumatoid arthritis) or patients infected withLeishmania brasiliensis,Brucella abortus,Streptococcus pyogenes, orToxoplasma gondii. The diagnostic performances of the complete TcP2β (TcP2βFL) and its N-terminal region (TcP2βN) were evaluated. TcP2βFLshowed unspecific recognition toward leishmaniasis (40%) and AID Abs (58%), while TcP2βNshowed no unspecific recognition. The diagnostic utility of the chimera was evaluated by analyzing reactivity and comparing the results with those obtained with TcP2βN. The chimera reactivity was higher than that of the peptide fractions (0.874 versus 0.564 optical density,P= 0.0017). The detectability and specificity were both 100% for the whole serum panel tested. We conclude that the obtained chimera shows an improved selectivity and sensitivity compared with other ones previously reported, therefore displaying an optimized performance forTrypanosoma cruziinfection diagnosis.
Evaluation of Peptide Nucleic Acid-Fluorescence In Situ Hybridization for Identification of Clinically Relevant Mycobacteria in Clinical Specimens and Tissue Sections
Authors: Lefmann Michael , Schweickert Birgitta , Buchholz Petra , Göbel Ulf B. , Ulrichs Timo , Seiler Peter , Theegarten Dirk , Moter Annette 
Published: October 2006

ABSTRACT

With fluorescently labeled PNA (peptide nucleic acid) probes targeting 16S rRNA, we established a 3-h fluorescence in situ hybridization (FISH) procedure for specific visualization of members of the
Mycobacterium tuberculosis
complex,
M. leprae
,
M. avium
, and
M. kansasii
. Probe specificity was tested against a panel of 25
Mycobacterium
spp. and 10 gram-positive organisms. After validation, probes were used to identify 52 mycobacterial culture isolates. Results were compared to conventional genotypic identification with amplification-based methods. All isolates (
M. tuberculosis
complex,
n
= 24;
M. avium
,
n
= 7;
M. kansasii
,
n
= 1) were correctly identified by FISH. In addition, the technique was used successfully for visualization of mycobacteria in biopsies from infected humans or animals. In conclusion, PNA-FISH is a fast and accurate tool for species-specific identification of culture-grown mycobacteria and for direct visualization of these organisms in tissue sections. It may be used successfully for both research and clinical microbiology.
Distribution of
hsp65
PCR-Restriction Enzyme Analysis Patterns among
Mycobacterium avium
Complex Isolates in Thailand
Authors: Prammananan Therdsak , Phunpruch Saranya , Tingtoy Nipa , Srimuang Somboon , Chaiprasert Angkana 
Published: October 2006

ABSTRACT

A total of 227 clinical
Mycobacterium avium
complex isolates from Thailand were differentiated into species and types by using PCR-restriction enzyme analysis of
hsp65
. The distribution of types showed the predominance of
M. avium
I (77%) in blood specimens, whereas
M. intracellulare
I was more commonly found in pulmonary specimens (44.2%). In addition, infections with
M. avium
were more likely to be found in younger adults (20 to 39 years old), while infections with
M. intracellulare
were more likely to be found in older adults (≥60 years old). Our results provide the useful epidemiological information that some particular types have more invasive and virulent characters than others.
Expression of calcitonin receptor-like receptor in human vascular tumours
Authors: Hagner S , Stahl U , Grimm T , Stürzl M , Lang R E 
Published: October 2006

Background:Vascular tumours such as Kaposi’s sarcoma and capillary haemangioma are characterised by abnormal vascularisation and proliferation of endothelial cells or neoplastic cells. Adrenomedullin, a potent vasodilative peptide, and its receptor, calcitonin receptor-like receptor (CRLR), play an important part in angiogenesis.Aim:To establish whether this system also plays a part in vascular diseases, showing abnormal proliferation such as vascular tumours.Methods:CRLR expression was investigated in several specimens of Kaposi’s sarcoma and other vascular tumours, using immunohistochemical analysis with a previously described CRLR-specific polyclonal antibody and reverse transcriptase-polymerase chain reaction.Results:Intense and specific CRLR-immunoreactive staining of neoplastic cells was observed in all specimens, which was of greater intensity than similar staining of adjacent normal endothelium.Conclusions:CRLR is expressed in vascular tumours and, with adrenomedullin, may have a role in neoplastic vascular growth.
Magnitude of Stromal Hemangiogenesis Correlates with Histologic Subtype of Non–Hodgkin's Lymphoma
Authors: Ruan Jia , Hyjek Elizabeth , Kermani Pouneh , Christos Paul J. , Hooper Andrea T. , Coleman Morton , Hempstead Barbara , Leonard John P. , Chadburn Amy , Rafii Shahin 
Published: October 2006

Abstract
Purpose: Tumor stromal microenvironment promotes neoplastic growth and angiogenesis. We have previously shown that recruitment of marrow-derived vascular endothelial growth factor receptor-1+ (VEGFR-1+) proangiogenic hematopoietic progenitors contributes instructively and structurally to neoangiogenesis in mouse models. Here, we investigated whether stromal incorporation of CD68+ hemangiogenic cells and α-smooth muscle actin+ (α-SMA+) stromal cells correlates with neoangiogenesis and progression in human non–Hodgkin's lymphoma subtypes.
Experimental Design: Spatial localizations of vascular and stromal cells expressing CD34, VEGFR-1, α-SMA, and CD68 were examined by immunohistochemistry in 42 cases of non–Hodgkin's lymphoma, including diffuse large B-cell lymphoma, Burkitt lymphoma, follicular lymphoma, and chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), and compared with benign follicular hyperplasia.
Results: Compared with indolent lymphomas, there was a profound increase in recruitment of CD68+ cells and VEGFR-1+ neovessels in aggressive subtypes (including those transformed from indolent subtypes), where CD68+ cells were localized to the perivascular region of neovessels as well as the stromal compartment. The perivascular CD68+ cells expressed VEGFR-1 and VEGF-A. In contrast, there was a diffuse increase in α-SMA incorporation throughout the stromal compartment of indolent subtype of CLL/SLL compared with the scant perivascular pattern in aggressive subtypes. Overall, there was no correlation between CD34+ microvessel density and lymphoma histologic subtype.
Conclusions: Heightened stromal hemangiogenesis as marked by infiltration of proangiogenic VEGFR-1+CD68+VEGF-A+ cells and their paracrine cross-talk with neovasculature appears to be a distinct feature of aggressive lymphoma, providing novel targets for antiangiogenic therapy, whereas α-SMA+ stromal vascular network may be differentially targeted in CLL/SLL.
Fuzzy Rule–Based Approach for Detection of Bounded Weak-Echo Regions in Radar Images
Authors: Pal Nikhil R. , Mandal Achintya K. , Pal Srimanta , Das Jyotirmay , Lakshmanan V. 
Published: October 2006

Abstract
A method for the detection of a bounded weak-echo region (BWER) within a storm structure that can help in the prediction of severe weather phenomena is presented. A fuzzy rule–based approach that takes care of the various uncertainties associated with a radar image containing a BWER has been adopted. The proposed technique automatically finds some interpretable (fuzzy) rules for classification of radar data related to BWER. The radar images are preprocessed to find subregions (or segments) that are suspected candidates for BWERs. Each such segment is classified into one of three possible cases: strong BWER, marginal BWER, or no BWER. In this regard, spatial properties of the data are being explored. The method has been tested on a large volume of data that are different from the training set, and the performance is found to be very satisfactory. It is also demonstrated that an interpretation of the linguistic rules extracted by the system described herein can provide important characteristics about the underlying process.
Understanding Farmers’ Forecast Use from Their Beliefs, Values, Social Norms, and Perceived Obstacles*
Authors: Hu Qi , Zillig Lisa M. Pytlik , Lynne Gary D. , Tomkins Alan J. , Waltman William J. , Hayes Michael J. , Hubbard Kenneth G. , Artikov Ikrom , Hoffman Stacey J. , Wilhite Donald A. 
Published: October 2006

Abstract
Although the accuracy of weather and climate forecasts is continuously improving and new information retrieved from climate data is adding to the understanding of climate variation, use of the forecasts and climate information by farmers in farming decisions has changed little. This lack of change may result from knowledge barriers and psychological, social, and economic factors that undermine farmer motivation to use forecasts and climate information. According to the theory of planned behavior (TPB), the motivation to use forecasts may arise from personal attitudes, social norms, and perceived control or ability to use forecasts in specific decisions. These attributes are examined using data from a survey designed around the TPB and conducted among farming communities in the region of eastern Nebraska and the western U.S. Corn Belt. There were three major findings: 1) the utility and value of the forecasts for farming decisions as perceived by farmers are, on average, around 3.0 on a 0–7 scale, indicating much room to improve attitudes toward the forecast value. 2) The use of forecasts by farmers to influence decisions is likely affected by several social groups that can provide “expert viewpoints” on forecast use. 3) A major obstacle, next to forecast accuracy, is the perceived identity and reliability of the forecast makers. Given the rapidly increasing number of forecasts in this growing service business, the ambiguous identity of forecast providers may have left farmers confused and may have prevented them from developing both trust in forecasts and skills to use them. These findings shed light on productive avenues for increasing the influence of forecasts, which may lead to greater farming productivity. In addition, this study establishes a set of reference points that can be used for comparisons with future studies to quantify changes in forecast use and influence.
Glucocorticoids induce differentiation of a specifically activated, anti-inflammatory subtype of human monocytes
Authors: Ehrchen Jan , Steinmüller Lars , Barczyk Katarzyna , Tenbrock Klaus , Nacken Wolfgang , Eisenacher Martin , Nordhues Ursula , Sorg Clemens , Sunderkötter Cord , Roth Johannes 
Published: October 2006

AbstractMonocytes and macrophages may either promote or down-regulate inflammatory reactions depending on their state of activation. The effects of glucocorticoids (GCs), the most widely used immunosuppressive drugs, on monocytes are currently not well defined. By analyzing the GC-induced expression pattern in human monocytes by microarray technology, we identified for the first time GC-dependent regulation of 133 genes, including anti-inflammatory molecules such as adenosine A3 receptor, CD1d, and IL-1 receptor II. The results were independently confirmed by real-time polymerase chain reaction (PCR) and flow cytometry. Functional clustering of GC-regulated genes indicated induction of monocytic properties such as phagocytosis and motility as well as repression of adhesion, apoptosis, and oxidative burst. These predictions were confirmed by independent functional assays. GCs up-regulate fMLP receptors and specifically promote chemotaxis to this chemoattractant. Furthermore, GCs promote survival of an anti-inflammatory monocytic phenotype in inflammatory reactions, probably by inhibition of apoptosis because of oxidative stress. GCs limit tissue damage because of induction of antioxidative properties and high capacity for phagocytosis of proinflammatory agents. Thus, GC treatment did not cause a global suppression of monocytic effector functions but results in differentiation of a specific anti-inflammatory phenotype which seems to be actively involved in resolution of inflammatory reactions.
Fusion of the BCL9 HD2 domain to E1A increases the cytopathic effect of an oncolytic adenovirus that targets colon cancer cells
Authors: Fuerer Christophe , Homicsko Krisztian , Lukashev Alexander N , Pittet Anne-Laure , Iggo Richard D 
Published: October 2006

Abstract

Background
The Wnt signaling pathway is activated by mutations in the APC and β-catenin genes in many types of human cancer. β-catenin is stabilized by these mutations and activates transcription in part by acting as a bridge between Tcf/LEF proteins and the HD2 domain of the BCL9 coactivator. We have previously described oncolytic adenoviruses with binding sites for Tcf/LEF transcription factors inserted into the early viral promoters. These viruses replicate selectively in cells with activation of the Wnt pathway. To increase the activity of these viruses we have fused the viral transactivator E1A to the BCL9 HD2 domain.

Methods
Luciferase assays, co-immunoprecipitation and Western blotting, immunofluorescent cell staining and cytopathic effect assays were used to characterize the E1A-HD2 fusion protein and virus in vitro. Growth curves of subcutaneous SW620 colon cancer xenografts were used to characterize the virus in vivo.

Results
The E1A-HD2 fusion protein binds to β-catenin in vivo and activates a Tcf-regulated luciferase reporter better than wild-type E1A in cells with activated Wnt signaling. Expression of the E1A-HD2 protein promotes nuclear import of β-catenin, mediated by the strong nuclear localization signal in E1A. Tcf-regulated viruses expressing the fusion protein show increased expression of viral proteins and a five-fold increase in cytopathic effect (CPE) in colorectal cancer cell lines. There was no change in viral protein expression or CPE in HeLa cells, indicating that E1A-HD2 viruses retain selectivity for cells with activation of the Wnt signaling pathway. Despite increasing the cytopathic effect of the virus in vitro, fusion of the HD2 domain to E1A did not increase the burst size of the virus in vitro or the anti-tumor effect of the virus in an SW620 xenograft model in vivo.

Conclusion
Despite an increase in the nuclear pool of β-catenin, the effects on viral activity in colon cancer cells were small, suggesting that factors acting downstream of β-catenin are limiting for viral replication and toxicity in these cells. The approach of fusing E1A to a protein domain implicated in oncogenic signaling could be used to selectively increase the activity of oncolytic viruses targeting several other pathways defective in cancer.
Exercise-Induced Improvement in Vasodilatory Function Accompanies Increased Insulin Sensitivity in Obesity and Type 2 Diabetes Mellitus
Authors: De Filippis Elena , Cusi Kenneth , Ocampo Gloria , Berria Rachele , Buck Susan , Consoli Agostino , Mandarino Lawrence J. 
Published: October 2006

AbstractObjective: The present study was undertaken to determine whether improved vasodilatory function accompanies increased insulin sensitivity in overweight, insulin-resistant subjects (OW) and type 2 diabetic patients (T2DM) who participated in an 8-wk exercise training regimen.Design: Before and after training, subjects had euglycemic clamps to determine insulin sensitivity. Brachial artery catheterization was done on another occasion for measurement of vasodilatory function. A lean, healthy, untrained group was studied as nonexercised controls.Results: Training increased oxygen consumption (VO2) peak [OW, 29 ± 1 to 37 ± 4 ml/kg fat-free mass (FFM)·min; T2DM, 33 ± 2 to 43 ± 3 ml/kg FFM·min; P &lt; 0.05] and improved insulin-stimulated glucose disposal (OW, 6.5 ± 0.5 to 7.2 ± 0.4 mg/kg FFM·min; T2DM, 3.8 ± 0.3 to 4.2 ± 0.3 mg/kg FFM·min; P &lt; 0.05) in insulin resistance. OW and T2DM, before training, had decreased acetylcholine chloride (ACh)- and sodium nitroprusside-mediated vasodilation and decreased reactive hyperemia compared with lean controls. Training increased the vasodilatory response to ACh [OW (30 μg ACh/min), 12.2 ± 3.4 to 19 ± 4.2 ml/100 g·min; T2DM (30 μg ACh/min), 10.1 ± 1.5 to 14.2 ± 2.1 ml/100 g·min; P &lt; 0.05] in both groups without affecting nitroprusside response.Conclusion: Because vasodilatory dysfunction has been postulated to contribute to insulin resistance, the exercise-induced improvement in vasodilatory function may signify changes in the endothelium that could contribute to the improvement in insulin sensitivity observed after aerobic exercise training.
A Randomized Controlled Study of Effects of Dietary Magnesium Oxide Supplementation on Bone Mineral Content in Healthy Girls
Authors: Carpenter Thomas O. , DeLucia Maria C. , Zhang Jane Hongyuan , Bejnerowicz Gina , Tartamella Lisa , Dziura James , Petersen Kitt Falk , Befroy Douglas , Cohen Dorothy 
Published: October 2006

Abstract
Context: The role of magnesium (Mg) as a determinant of bone mass has not been extensively explored. Limited studies suggest that dietary Mg intake and bone mineral density are correlated in adults, but no data from interventional studies in children and adolescents are available.
Objective: We sought to determine whether Mg supplementation in periadolescent girls enhances accrual of bone mass.
Design: We carried out a prospective, placebo-controlled, randomized, one-year double-blind trial of Mg supplementation.
Setting: The study was conducted in the Clinical Research Centers at Yale University School of Medicine.
Patients or Other Participants: Healthy 8- to 14-yr-old Caucasian girls were recruited from community pediatricians’ offices. Dietary diaries from over 120 volunteers were analyzed, and those with dietary Mg intake of less than 220 mg/d were invited to participate in the intervention.
Intervention: Magnesium (300 mg elemental Mg per day in two divided doses) or placebo was given orally for 12 months.
Main Outcome Measure: The primary outcome measure was interval change in bone mineral content (BMC) of the total hip, femoral neck, Ward’s area, and lumbar spine (L1–L4) after 12 months of Mg supplementation.
Results: Significantly increased accrual (P = 0.05) in integrated hip BMC occurred in the Mg-supplemented vs. placebo group. Trends for a positive Mg effect were evident in the pre- and early puberty and in mid-late puberty. Lumbar spinal BMC accrual was slightly (but not significantly) greater in the Mg-treated group. Compliance was excellent; 73% of capsules were ingested as inferred by pill counts. Serum mineral levels, calciotropic hormones, and bone markers were similar between groups.
Conclusions: Oral Mg oxide capsules are safe and well tolerated. A positive effect of Mg supplementation on integrated hip BMC was evident in this small cohort.
Otitic hydrocephalus
Authors: Lenz Richard P. , Mcdonald Graeme A. 
Published: October 2006

AbstractOtitic hydrocephalus is one of the less common intrncraninl complications of infectious ear disease, consisting of elevated intracranial pressure without focal neurologic abnormalities other than those due to the elevated pressure. A representative case is discussed in this report, followed by a review of the literature. The clinical course, diagnosis, treatment, and prognosis arc outlined. The etiology and the association with lateral sinus thrombosis remains obscure.
Laryngismus fugax: Transient laryngeal spasm secondary to brain stem ischemia
Authors: Pender Daniel J. 
Published: October 2006

AbstractBilateral vocal cord immobility in adduction is an uncommon, yet potentially life threatening, disorder. Endolaryngeal and neuromuscular causes are well known and for the most part readily diagnosed by the otolaryngologist. Central neurologic etiologies are more unusual. A case of transient spastic laryngeal paralysis secondary to cardiac emboli and brain stem ischemia is presented. A mechanistic analysis suggests that this entity occurs in the setting of pseudobulbar paralysis, and that the ultimate ischemic event may be loss of glycine mediated inhibition of laryngeal motoneurons.
Transmission Network Analysis to Complement Routine Tuberculosis Contact Investigations
Authors: Andre McKenzie , Ijaz Kashef , Tillinghast Jon D. , Krebs Valdis E. , Diem Lois A. , Metchock Beverly , Crisp Theresa , McElroy Peter D. 
Published: October 2006

Objective. We examined the feasibility and value of network analysis to complement routine tuberculosis (TB) contact investigation procedures during an outbreak. Methods. We reviewed hospital, health department, and jail records and interviewed TB patients. Mycobacterium tuberculosis isolates were genotyped. We evaluated contacts of TB patients for latent TB infection (LTBI) and TB, and analyzed routine contact investigation data, including tuberculin skin test (TST) results. Outcomes included number of contacts identified, number of contacts evaluated, and their TST status. We used network analysis visualizations and metrics (reach, degree, betweenness) to characterize the outbreak. Results.secondary TB patients and more than 1200 contacts. Genotyping detected a 21-band pattern of a strain W variant. No HIV-infected patients were diagnosed. Contacts prioritized by network analysis were more likely to have LTBI than nonprioritized contacts (odds ratio=7.8; 95% confidence interval=1.6, 36.6). Network visualizations and metrics highlighted patients central to sustaining the outbreak and helped prioritize contacts for evaluation. Conclusions. A network-informed approach to TB contact investigations provided a novel means to examine large quantities of data and helped focus TB control.