bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical Composition and Antioxidant, Antimicrobial Activities of the Essential Oils of Thymus marschallianus Will. and Thymus proximus Serg.
Authors: Jia H.L. , Ji Q.L. , Xing S.L. , Zhang P.H. , Zhu G.L. , Wang X.H. 
Published: December 2009

ABSTRACT:  Chemical composition and antioxidant, antimicrobial activities of the essential oils from Thymus marschallianus Will. and Thymus proximus Serg. growing in the wild in Xinjiang were studied. Samples were collected from the aerial parts of the plants with simultaneous distillation‐extraction apparatus. The yields ranged between 1.22%± 0.01 and 0.16%± 0.01 (weight/dry weight), respectively, 53 and 60 kinds of volatiles, representing 99.6% and 99.7% of the essential oils, respectively, were identified in extracts from T. marschallianus and T. proximus by GC/MS analysis. The main components were Thymol (28.0% to 32.9%), p‐Cymene (7.7% to 25.4%), and γ‐Terpinene (18.0% to 22.4%). Antioxidant activities of the oils were evaluated using metal chelating, reductive potential, 2,2‐diphenyl‐1‐picrylhydrazyl, hydroxyl radical, and modified thiobarbituric acid reactive substances assay. Antimicrobial activities of the oils were investigated on Escherichia coli, Staphylococcus aureus, Bacillus subtilis, yeast, Rhizopus, and Penicillium. The inhibition zones (IZ) and minimum inhibitory concentration (MIC) values were 5.0 to 35.7 mm in diameter and 1.81 to 4.52 μL/mL, respectively.Practical Application: Due to the economical impacts of spoiled foods and the consumer's concerns over the safety of foods, a lot of attention has been paid to naturally derived compounds. Fresh and dried Thymus species as well as their processed products have been widely used as flavorings since ancient times; however, during the last few decades, they also have become a subject for a search of natural antioxidants and antimicrobial agents. Biological activities of Thymus essential oils depend on their chemical composition, which is determined by the genotype and influenced by environmental conditions. Recent studies have showed that Thymus species have strong antimicrobial and antioxidant activities. To the best of our knowledge, the properties of Thymus species growing wild in the Xinjiang have not been reported before.
Clinical experience of varenicline for smoking cessation
Authors: Jung Jae Woo , Jeon Eun Ju , Kim Jae Gyu , Yang Suh‐Yoon , Choi Jae Chol , Shin Jong Wook , Park In Won , Choi Byoung Whui , Kim Don‐Kyu , Kim Jae Yeol 
Published: December 2009

AbstractIntroduction: Varenicline, a partial agonist/antagonist of the alpha4beta2 nicotinic acetylcholine receptors, is effective in smoking cessation, which was demonstrated by several randomized, controlled clinical trials.Objectives: In the present study, we evaluated the practical efficacy of varenicline for smoking cessation in patients who visited a pulmonary clinic at a university‐affiliated hospital in South Korea.Materials and Methods: Varenicline was prescribed to smokers after brief, standardized, individual counseling from June 2007 to January 2009. Their medical records were reviewed retrospectively. Their smoking status was assessed by telephone interview from October 2007, and final, confirmative telephone inquiry was performed in April 2009. The primary question was 4‐week continuous abstinence from smoking between 9 and 12 weeks.Results: Overall, 217 current smokers (200 men and 17 women) who were prescribed varenicline were enrolled. On average, participants were 52 years old and had 35 pack‐year of smoking history. Nineteen participants (8.8%) did not purchase the drug, and nine (4.1%) who purchased did not take the medicine. Contact was impossible for 32 (14.7%). Fifty participants (23.0%) succeeded, while 107 (49.3%) failed in abstaining from smoking from 9 to 12 weeks. Only 32 (14.7%) had a prescription of varenicline for 12 weeks or more. Most participants (80%) reported their desire for smoking reduced after taking varenicline. Common adverse events were gastrointestinal symptoms and neuropsychiatric symptoms.Conclusion: Although varenicline was effective in reducing the desire to smoke, poor dosing compliance needs to be overcome in clinical practice.Please cite this paper as: Jung JW, Jeon EJ, Kim JG, Yang S‐Y, Choi JC, Shin JW, Park IW, Choi BW, Kim D‐K and Kim JY. Clinical experience of varenicline for smoking cessation.The Clinical Respiratory Journal2010; 4: 215–221.
Optimized construction of microsatellite‐enriched libraries
Authors: TECHEN NATASCHA , ARIAS RENÉE S. , GLYNN NEIL C. , PAN ZHIQIANG , KHAN IKHLAS A. , SCHEFFLER BRIAN E. 
Published: December 2009

AbstractThe construction of microsatellite‐enriched libraries is an indispensable tool to search for molecular markers as complete genome sequences are still not available for the majority of species of interest. Numerous protocols are available in the literature for the construction of these libraries; however, sometimes their low efficiency or lack of optimization in the protocols can restrict their efficacy. We have designed and tested various adapters and ligation methods; we also tested oligo‐repeat combinations and hybridization temperatures, and created libraries with this new protocol for four organisms: Ipomoea batatas (L.) Lam, Chionanthus retusus Lindley & Paxton, Rotylenchulus reniformis Linford & Olivera and Puccinia kuehnii W. Krüger. The number of microsatellites detected for these species ranged from 2494 to 3919 per Mb of nonredundant sequence, that was 0.86 and 1.53 microsatellites per contig, with 37–66% of di‐nucleotide motifs and 21–49% of tri‐ to octa‐nucleotide repeats combined. A simplified protocol is provided for the successful generation of SSR‐enriched libraries.
Combined effects of two stressors on Kenyan coral reefs are additive or antagonistic, not synergistic
Authors: Darling Emily S. , McClanahan Timothy R. , Côté Isabelle M. 
Published: December 2009

AbstractA challenge for conservation science is predicting the impacts of co‐occurring human activities on ecological systems. Multiple anthropogenic and natural stressors impact ecosystems globally and are expected to jeopardize their ecological functions and the success of conservation and management initiatives. The possibility that two or more stressors interact synergistically is of particular concern, but such nonadditive effects remain largely unidentified in nature. A long‐term data set of hard coral cover from Kenyan reefs was used to examine the independent and interactive effects of two stressors: fishing and a temperature anomaly in 1998 that caused mass coral bleaching and mortality. While both stressors decreased coral cover, fishing by 51% and bleaching by 74%, they did not interact synergistically. Instead, their combined effect was antagonistic or weakly additive. The observed nonsynergistic response may be caused by the presence of one dominant stressor, bleaching, and cotolerance of coral taxa to both bleaching and fishing stressors. Consequently, coral bleaching has been the dominant driver of coral loss on Kenyan reefs and while marine reserves offer many benefits to reef ecosystems, they may not provide corals with a refuge from climate change.
Rapid in situ detection of virulent Vibrio vulnificus strains in raw oyster matrices using real‐time PCR
Authors: Baker‐Austin Craig , Gore Anthony , Oliver James D. , Rangdale Rachel , McArthur J Vaun , Lees David N. 
Published: December 2009

Summary Vibrio vulnificus is a Gram‐negative bacterial pathogen responsible for the vast majority of bacterially mediated fatalities from the consumption of raw or undercooked seafood in the USA. Vibrio vulnificus‐associated septicaemia can occur rapidly (< 24 h); however, methods for the isolation and confirmation of V. vulnificus from seafood samples typically require several days. A real‐time PCR assay was developed for V. vulnificus biotype 1 that provides a rapid means of identifying a gene fragment (vcgC) previously indicated as a strong predictor of potential virulence. PCR probe specificity was confirmed by amplification of 17 clinical V. vulnificus strains and by the lack of amplification with seven non‐pathogenic V. vulnificus isolates and a wide range of closely related bacteria. Oyster and seawater samples were amended with a range of environmentally realistic concentrations of C‐genotype V. vulnificus cells, which were quantitatively and unambiguously identified according to biotype. Of some significance, we utilized a sample processing and nucleic acid extraction procedure that allowed identification of pathogenic strains of V. vulnificus from oyster matrices without prior enrichment or culturing of strains. This outlined approach allowed the detection of as little as 50 cfu of V. vulnificus in less than 5 h, which compares favourably with culture‐based approaches. The results indicate the applicability of this approach for monitoring purposes or as a potential diagnostic tool in clinical settings.
Evaluation of Three Multiplex Flow Immunoassays Compared to an Enzyme Immunoassay for the Detection and Differentiation of IgG Class Antibodies to Herpes Simplex Virus Types 1 and 2
Authors: Binnicker M. J. , Jespersen D. J. , Harring J. A. 
Published: December 2009

ABSTRACT

The diagnosis of herpes simplex virus (HSV) infections is routinely made based on clinical findings and supported by laboratory testing using PCR or viral culture. However, in instances of subclinical or unrecognized HSV infection, serologic testing for IgG class antibodies to type-specific HSV glycoprotein G (gG) may be useful. This study evaluated and compared the performances of three multiplex flow immunoassays (AtheNA Multi-Lyte [Zeus Scientific], BioPlex 2200 [Bio-Rad Laboratories], and Plexus HerpeSelect [Focus Diagnostics]) for the simultaneous detection of gG type-specific IgG antibodies to HSV types 1 and 2 (HSV-1 and HSV-2). Serum specimens (
n
= 505) submitted for routine gG type-specific HSV IgG testing by enzyme immunoassay (EIA) (HerpeSelect; Focus Diagnostics) were also tested by the three multiplex flow immunoassays. Specimens showing discordant results were tested by HSV type-specific Western blotting (WB). For HSV-1 IgG, the AtheNA, BioPlex, and Plexus assays demonstrated agreements of 94.9% (479/505 specimens), 97.8% (494/505 specimens), and 97.4% (492/505 specimens), respectively, with the results of EIA. For HSV-2 IgG, the AtheNA, BioPlex, and Plexus assays showed agreements of 87.9% (444/505 specimens), 97.2% (491/505 specimens), and 96.8% (489/505 specimens), respectively, with EIA results. Timing studies showed that the AtheNA, BioPlex, and Plexus assays could provide complete analysis of 90 serum specimens in 3.1, 1.5, and 2.9 h, respectively, versus 3.1 h by EIA. These findings suggest that the gG type-specific HSV IgG multiplex immunoassays may be beneficial to high-volume clinical laboratories experiencing significant increases in the number of specimens submitted for HSV serologic testing. The evaluated systems provide comparable results to those of EIA, while reducing hands-on time and eliminating the necessity to aliquot specimens prior to testing.
A Live Oral Recombinant
Salmonella enterica
Serovar Typhimurium Vaccine Expressing
Clostridium perfringens
Antigens Confers Protection against Necrotic Enteritis in Broiler Chickens
Authors: Kulkarni R. R. , Parreira V. R. , Jiang Y.-F. , Prescott J. F. 
Published: December 2009

ABSTRACT

Necrotic enteritis (NE) in broiler chickens is caused by
Clostridium perfringens
, and there is currently no effective vaccine for NE. We previously showed that in broiler chickens protection against NE can be achieved through intramuscular immunization with alpha toxin (AT) and hypothetical protein (HP), and we subsequently identified B-cell epitopes in HP. In the present study, we identified B-cell epitopes in AT recognized by chickens immune to NE. The gene fragments encoding immunodominant epitopes of AT as well as those of HP were codon optimized for
Salmonella
and cloned into pYA3493, and the resultant plasmid constructs were introduced into an attenuated
Salmonella enterica
serovar Typhimurium χ9352 vaccine vehicle. The expression of these
C
lostridium perfringens
proteins, alpha toxoid (ATd) and truncated HP (HPt), was confirmed by immunoblotting. The protection of broiler chickens against experimentally induced NE was assessed at both the moderate and the severe levels of challenge. Birds immunized orally with
Salmonella
expressing ATd were significantly protected against moderate NE, and there was a nonsignificant trend for protection against severe challenge, whereas HPt-immunized birds were significantly protected against both severities of challenge. Immunized birds developed serum IgY and mucosal IgA and IgY antibody responses against
Clostridium
and
Salmonella
antigens. In conclusion, this study identified, for the first time, the B-cell epitopes in AT from an NE isolate recognized by chickens and showed the partial protective ability of codon-optimized ATd and HPt against NE in broiler chickens when they were delivered orally by using a
Salmonella
vaccine vehicle.
Optimal Threshold for a Positive Hybrid Capture 2 Test for Detection of Human Papillomavirus: Data from the ARTISTIC Trial
Authors: Sargent A. , Bailey A. , Turner A. , Almonte M. , Gilham C. , Baysson H. , Peto J. , Roberts C. , Thomson C. , Desai M. , Mather J. , Kitchener H. 
Published: December 2009

ABSTRACT
We present data on the use of the Hybrid Capture 2 (HC2) test for the detection of high-risk human papillomavirus (HR HPV) with different thresholds for positivity within a primary screening setting and as a method of triage for low-grade cytology. In the ARTISTIC population-based trial, 18,386 women were screened by cytology and for HPV. Cervical intraepithelial neoplasia lesions of grade two and higher (CIN2+ lesions) were identified for 453 women within 30 months of an abnormal baseline sample. When a relative light unit/cutoff (RLU/Co) ratio of ≥1 was used as the threshold for considering an HC2 result positive, 15.6% of results were positive, and the proportion of CIN2+ lesions in this group was 14.7%. The relative sensitivity for CIN2+ lesion detection was 93.4%. When an RLU/Co ratio of ≥2 was used as the threshold, there was a 2.5% reduction in positivity, with an increase in the proportion of CIN2+ lesions detected. The relative sensitivity decreased slightly, to 90.3%. Among women with low-grade cytology, HPV prevalences were 43.7% and 40.3% at RLU/Co ratios of ≥1 and ≥2, respectively. The proportions of CIN2+ lesions detected were 17.3% and 18.0%, with relative sensitivities of 87.7% at an RLU/Co ratio of ≥1 and 84.2% at an RLU/Co ratio of ≥2. At an RLU/Co ratio of ≥1, 68.3% of HC2-positive results were confirmed by the Roche line blot assay, compared to 77.2% of those at an RLU/Co ratio of ≥2. Fewer HC2-positive results were confirmed for 35- to 64-year-olds (50.3% at an RLU/Co ratio of ≥1 and 63.2% at an RLU/Co ratio of >2) than for 20- to 34-year-olds (78.7% at an RLU/Co ratio of ≥1 and 83.7% at an RLU/Co ratio of >2). If the HC2 test is used for routine screening as an initial test or as a method of triage for low-grade cytology, we would suggest increasing the threshold for positivity from the RLU/Co ratio of ≥1, recommended by the manufacturer, to an RLU/Co ratio of ≥2, since this study has shown that a beneficial balance between relative sensitivity and the proportion of CIN2+ lesions detected is achieved at this threshold.
Wound Botulism Complicating Internal Fixation of a Complex Radial Fracture
Authors: Taylor Steve M. , Wolfe Cameron R. , Dixon Terry C. , Ruch David S. , Cox Gary M. 
Published: December 2009

ABSTRACT

Botulism developed in a patient following surgical repair of an open radial fracture. Symptoms resolved after treatment with antitoxin and antibiotics, and hardware excision was deferred. Subsequent osteomyelitis necessitated hardware exchange, and wound cultures grew
Clostridium argentinense
. This case highlights the management of botulism associated with orthopedic hardware.
Serotyping Pneumococcal Meningitis Cases in the African Meningitis Belt by Use of Multiplex PCR with Cerebrospinal Fluid
Authors: Njanpop Lafourcade Berthe-Marie , Sanou Oumarou , van der Linden Mark , Levina Natalia , Karanfil Meryem , Yaro Seydou , Tamekloe Tsidi A. , Mueller Judith E. 
Published: December 2009

ABSTRACT
We reformulated a multiplex PCR algorithm for serotyping of pneumococcal meningitis directly on cerebrospinal fluid (CSF). Compared to established methods on isolates, CSF-based PCR had at least 80% sensitivity and 100% specificity. In regional meningitis surveillance, CSF-based PCR increased the serotype information yield from 40% of cases (isolate testing) to 90%.
Comparison of the Abbott RealTi
m
e CT New Formulation Assay with Two Other Commercial Assays for Detection of Wild-Type and New Variant Strains of
Chlamydia trachomatis
Authors: Møller Jens Kjølseth , Pedersen Lisbeth Nørum , Persson Kenneth 
Published: December 2009

ABSTRACT

In an analytical-method comparison study of clinical samples, the Abbott RealTi
m
e CT new formulation assay (
m
2000 real-time PCR), consisting of a duplex PCR targeting different parts of the cryptic plasmid in
Chlamydia trachomatis
, was compared both with version 2 of the Roche Cobas TaqMan CT assay, comprising a duplex PCR for a target in the cryptic plasmid and the
omp1
gene, and with the Gen-Probe Aptima Combo 2 assay (AC2) targeting the
C. trachomatis
23S rRNA molecule. First-catch urine samples from Sweden were tested in Malmö, Sweden, for
C. trachomatis
with the
m
2000 real-time PCR assay and with an in-house PCR for the new variant
C. trachomatis
strain with a deletion in the cryptic plasmid. Aliquots of the urine samples were sent to Aarhus, Denmark, where they were further examined with the TaqMan CT and AC2 assays. A positive prevalence of 9.1% (148/1,632 urine samples examined) was detected according to the combined reference standard. The sensitivities and specificities of the three assays were as follows: for the Abbott
m
2000 assay, 95.3% (141/148) and 99.9% (1,483/1,485), respectively; for the Roche TaqMan assay, 82.4% (122/148) and 100.0% (1,485/1,485); and for the Gen-Probe AC2 assay, 99.3% (147/148) and 99.9% (1,484/1,485). The plasmid mutant strain was detected in 24% (36/148) of the
C. trachomatis
-positive samples. There is a difference in sensitivity between the new formulations of the Abbott and the Roche assays, but both assays detected the wild-type and new variant
C. trachomatis
strains equally well.
Correlation of Genotype and
In Vitro
Susceptibilities of
Cryptococcus gattii
Strains from the Pacific Northwest of the United States
Authors: Iqbal Naureen , DeBess Emilio E. , Wohrle Ron , Sun Ben , Nett Randall J. , Ahlquist Angela M. , Chiller Tom , Lockhart Shawn R. 
Published: December 2009

ABSTRACT

Cryptococcus gattii
emerged in North America in 1999 as a human and veterinary pathogen on Vancouver Island, British Columbia. The emergent subtype, VGIIa, and the closely related subtype VGIIb can now be found in the United States in Washington, Oregon, and California. We performed multilocus sequence typing and antifungal susceptibility testing on 43 isolates of
C. gattii
from human patients in Oregon, Washington, California, and Idaho. In contrast to Vancouver Island, VGIIa was the most frequent but not the predominant subtype in the northwest United States. Antifungal susceptibility testing showed statistically significant differences in MICs between the subtypes. This is the first study to apply antifungal susceptibility testing to
C. gattii
isolates from the Pacific Northwest and the first to make direct comparisons between subtypes.
PCR Using Blood for Diagnosis of Invasive Pneumococcal Disease: Systematic Review and Meta-Analysis
Authors: Avni Tomer , Mansur Nariman , Leibovici Leonard , Paul Mical 
Published: December 2009

ABSTRACT
The use of molecular-based methods for the diagnosis of bacterial infections in blood is appealing, but they have not yet passed the threshold for clinical practice. A systematic review of prospective and case-control studies assessing the diagnostic utility of PCR directly with blood samples for the diagnosis of invasive pneumococcal disease (IPD) was performed. A broad search was conducted to identify published and unpublished studies. Two reviewers independently extracted the data. Summary estimates for sensitivity and specificity with 95% confidence intervals (CIs) were calculated by using the hierarchical summary receiver operating characteristic method. The effects of sample processing, PCR type, the gene-specific primer, study design, the participants' age, and the source of infection on the diagnostic odds ratios were assessed through meta-regression. Twenty-nine studies published between 1993 and 2009 were included. By using pneumococcal bacteremia for case definition and healthy people or patients with bacteremia caused by other bacteria as controls (22 studies), the summary estimates for sensitivity and specificity were 57.1% (95% CI, 45.7 to 67.8%) and 98.6% (95% CI, 96.4 to 99.5%), respectively. When the controls were patients suspected of having IPD without pneumococcal bacteremia (26 studies), the respective values were 66.4% (95% CI, 55.9 to 75.6%) and 87.8% (95% CI, 79.5 to 93.1%). With lower degrees of proof for IPD (any culture or serology result and the clinical impression), the sensitivity of PCR decreased and the specificity increased. All analyses were highly heterogeneous. The use of nested PCR and being a child were associated with low specificity, while the use of a cohort study design was associated with a low sensitivity. The lack of an appropriate reference standard might have caused underestimation of the performance of the PCR. Currently available methods for PCR with blood samples for the diagnosis of IPD lack the sensitivity and specificity necessary for clinical practice.
Direct Serogrouping of
Streptococcus pneumoniae
Strains in Clinical Samples by Use of a Latex Agglutination Test
Authors: Sanz Juan Carlos , Culebras Esther , Ríos Esther , Rodríguez-Avial Iciar , Wilhelmi Isabel , Ramos Belén , Ordobás María , Picazo Juan José 
Published: December 2009

ABSTRACT

Pneumotest-Latex (Statens Seruminstitut) was evaluated for direct serogrouping of
Streptococcus pneumoniae
strains in clinical samples from patients with invasive disease. The technique was accurate to its level of discrimination for 62 of 67 clinical samples (92.5%). Pneumotest-Latex would be a useful alternative for direct serogrouping of pneumococci in clinical samples.
K2 Serotype
Klebsiella pneumoniae
Causing a Liver Abscess Associated with Infective Endocarditis
Authors: Rivero Andres , Gomez Eric , Alland David , Huang David B. , Chiang Tom 
Published: December 2009

ABSTRACT

Klebsiella pneumoniae
primary liver abscess (KPLA) is an emerging disease that is associated with distant septic complications. We report the first case of KPLA associated with infective endocarditis. The
K. pneumoniae
strain was a hypermucoid K2 serotype carrying the
rmpA
virulence-associated gene.
First Autochthonous Case of
Rhinocladiella mackenziei
Cerebral Abscess Outside the Middle East
Authors: Badali Hamid , Chander Jagdish , Bansal Shaifali , Aher Atul , Borkar Surendra S. , Meis Jacques F. , De Hoog G. Sybren 
Published: December 2009

ABSTRACT

Cerebral phaeohyphomycosis due to
Rhinocladiella mackenziei
is a severe infection in the middle east, resulting in nearly 100% mortality despite the application of combined surgical and antifungal therapy and occurring occasionally in otherwise healthy patients. We report the first case of brain infection in a middle-aged male in India, where
R. mackenziei
is not endemic.