bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dye shift: a neglected source of genotyping error in molecular ecology
Authors: SUTTON JOLENE T. , ROBERTSON BRUCE C. , JAMIESON IAN G. 
Published: January 2011

AbstractMolecular ecologists must be vigilant in detecting and accounting for genotyping error, yet potential errors stemming from dye‐induced mobility shift (dye shift) may be frequently neglected and largely unknown to researchers who employ 3‐primer systems with automated genotyping. When left uncorrected, dye shift can lead to mis‐scoring alleles and even to falsely calling new alleles if different dyes are used to genotype the same locus in subsequent reactions. When we used four different fluorophore labels from a standard dye set to genotype the same set of loci, differences in the resulting size estimates for a single allele ranged from 2.07 bp to 3.68 bp. The strongest effects were associated with the fluorophore PET, and relative degree of dye shift was inversely related to locus size. We found little evidence in the literature that dye shift is regularly accounted for in 3‐primer studies, despite knowledge of this phenomenon existing for over a decade. However, we did find some references to erroneous standard correction factors for the same set of dyes that we tested. We thus reiterate the need for strict quality control when attempting to reduce possible sources of genotyping error, and in cases where different dyes are applied to a single locus, perhaps mistakenly, we strongly discourage researchers from assuming generic correction patterns.
Clinical value of polymerase chain reaction in the diagnosis of joint tuberculosis by detecting the DNA ofMycobacterium tuberculosis
Authors: Sun Yong‐sheng , Lou Si‐quan , Wen Jian‐min , Lv Wei‐xin , Jiao Chang‐geng , Yang Su‐min , Xu Hai‐bin 
Published: January 2011

Objective: To assess the clinical value of polymerase chain reaction (PCR) in the diagnosis and differential diagnosis of joint tuberculosis (TB).Methods: PCR was used blindly to detect the DNA ofMycobacterium tuberculosis(M.TB) in five specimens of M.TB, 5 of BCG, and 10 of other bacteria. Then, M. TB in 98 samples from patients with joint TB and 100 samples from patients with non‐tubercular joint disorders were detected by PCR, acid‐fast staining and culture,. The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of PCR were calculated. The χ2 test was used for statistical analysis of the frequency of various factors. At the same time, some problems with PCR were also systematically analyzed.Results: (1) In the “standard samples”, both M. TB and BCG showed positive while other bacteria were negative. (2) In 98 cases from patients with joint TB, 81 were positive by PCR, 6 by acid‐fast staining, and 17 by culture. In 100 cases from patients with non‐tuberculous joint disorders, 9 were positive by PCR, and none by either acid‐fast staining or culture. Sensitivity, specificity, accuracy, positive and negative predictive value of PCR were 82.65% (81/98), 91.00% (91/100), 86.87% (172/198), 90.00% (81/90) and 84.26% (91/108), respectively. (3) The positive rates for PCR, acid‐fast staining and culture in detection of M. TB were 82.65% (81/98), 6.12% (6/98), and 17.34% (17/98), respectively. There were statistically significant differences between the three methods (P < 0.001). (4) The process of PCR is automatic, and can be completed within 3 to 6 hours, whereas 4 to 8 weeks are required for the conventional culture of M. TB.Conclusion: PCR is a sensitive, specific, rapid, simple and minimally invasive method for detection of M. TB in samples from joint TB, and can play an important role in early and rapid diagnosis and differential diagnosis of joint TB. But it also has some limitations, such as false positivity and false negativity.
Comparison of proximal femoral nail antirotation blade and reverse less invasive stabilization system‐distal femur systems in the treatment of proximal femoral fractures
Authors: Han Ning , Sun Gui‐xin , Li Zeng‐chun , Li Guo‐feng , Lu Qing‐you , Han Qing‐hui , Wei Xin 
Published: January 2011

Objective:  To compare the effects of proximal femoral nail antirotation blade (PFNA) and reverse less invasive stabilization system‐distal femur (Liss‐DF) systems in the treatment of proximal femoral fractures.Methods:  Between June 2007 and October 2009, 41 proximal femoral fractures were treated, 22 with PFNA (group A) and 19 with reverse LISS‐DF plates (group B). The time to starting full weight‐bearing, fracture healing time, functional recovery (Parker and Palmer mobility score), neck‐shaft angle discrepancies with the intact contralateral hip, preoperative American Society of Anesthesiologists (ASA) scores, the operation durations and amount of intraoperative bleeding were recorded and compared.Results:  The mean follow‐up period was 11.2 months (range, 10–12 months). Compared with Group A, Group B showed a statistically longer mean time to bear full body weight and heal their fractures, but a smaller neck‐shaft angle discrepancy (all P < 0.05). The groups were similar in ASA score, operation duration, amount of intraoperative bleeding and Parker and Palmer mobility score.Conclusion:  Both PFNA and reverse Liss‐DF were satisfactory for the treatment of proximal femoral fractures, but had different advantages. PFNA allowed earlier weight‐bearing and accelerated fracture healing. Reverse Liss‐DF more effectively avoided coxa vara and may be indicated for patients with very severe osteoporosis.
Autoimmune fulminant liver failure in adults: Experience in a Japanese center
Authors: Fujiwara Keiichi , Yasui Shin , Tawada Akinobu , Okitsu Koichiro , Yonemitsu Yutaka , Chiba Tetsuhiro , Arai Makoto , Kanda Tatsuo , Imazeki Fumio , Nakano Masayuki , Oda Shigeto , Yokosuka Osamu 
Published: January 2011

Aim:  After the establishment of the international criteria of autoimmune hepatitis (AIH) in 1999 and the recognition of acute onset AIH, the diagnosis of patients with fulminant type of AIH came to be made. We diagnosed autoimmune fulminant liver failure based on the criteria, and discussed the etiology of fulminant hepatitis (FH) and late onset hepatic failure (LOHF), and the characteristics of autoimmune fulminant liver failure.Methods:  We investigated the etiology of 95 consecutive adult patients with FH or LOHF admitted to our liver unit between 1990 and 2009. Clinical and biochemical features, therapies and outcomes were examined in patients with AIH after 2000.Results:  Of 95 patients, 85 were FH and 10 LOHF. The etiology was due to viral infections in 51.6% (hepatitis A virus in 7.4%, hepatitis B virus in 43.2% and hepatitis E virus in 1.1%), AIH in 15.8%, drug allergy‐induced in 12.6%, and unknown causes in 20.0%. The rate of patients with AIH increased significantly between 2000 and 2009 compared to the rate between 1990 and 1999 (P = 0.002). In recovered patients with AIH without transplantation after 2000, coma grade was lower, alanine aminotransferase level, prothrombin time activity and alfa‐fetoprotein level were higher than in the others with statistical significance.Conclusion:  AIH is not a rare cause of FH and LOHF, and the number of patients with unknown causes would surely decrease in concert with the precise diagnosis of AIH.
+49A/G polymorphism of cytotoxic T‐lymphocyte antigen 4 gene in type 1 autoimmune hepatitis and primary biliary cirrhosis: A meta‐analysis
Authors: Miyake Yasuhiro , Ikeda Fusao , Takaki Akinobu , Nouso Kazuhiro , Yamamoto Kazuhide 
Published: January 2011

Aim:  Recently, the associations of +49A/G polymorphisms of cytotoxic T‐lymphocyte antigen 4 (CTLA‐4) gene with the susceptibility to type 1 autoimmune hepatitis (AIH) and primary biliary cirrhosis (PBC) have been reported; however these associations are yet to be fully elucidated. This study aimed to identify the associations of CTLA‐4 gene +49A/G polymorphisms with the susceptibility to type 1 AIH and PBC by using a meta‐analysis.Methods:  PubMed was searched by using the following keywords: “autoimmune hepatitis AND (polymorphism OR polymorphisms)” or “primary biliary cirrhosis AND (polymorphism OR polymorphisms)”. Meta‐analyses of five studies including 526 patients with type 1 AIH and 631 controls and seven studies including 1500 patients with PBC and 2345 controls were performed.Results:  For type 1 AIH, the odds ratio (OR) of G allele was 1.26 [95% confidence interval (CI) 1.06–1.51] although G/G homozygosity was not associated with the susceptibility to type 1 AIH. On the other hand, the OR of A/A homozygosity for type 1 AIH was 0.66 (95% CI 0.50–0.86). For PBC, the OR of G allele was 1.20 (95% CI 1.06–1.34). Furthermore, G/G homozygosity was significantly associated with the susceptibility to PBC (OR 1.29, 95% CI 1.01–1.66). The OR of A/A homozygosity for PBC was 0.81 (95% CI 0.70–0.94).Conclusions:  This study suggests that CTLA‐4 gene +49A/G polymorphisms may be associated with the susceptibility to type 1 AIH and PBC. Especially, while G/G genotype may be associated with the susceptibility to PBC, A/A genotype may be protective against type 1 AIH and PBC.
Caries experience in 15‐year‐old school children in Bangalore with inherited taste sensitivity levels to 6‐n‐propylthiouracil: an observational study
Authors: Jyothirmai Jaddu , Naganandini Sampathkumar , Aradhya Shankar 
Published: January 2011

AbstractAim: The relationship between sugar consumption and caries has been researched extensively for many years. The individual drive for the consumption of sweet food is controlled by a variety of biologic, psychologic, and sociologic factors. Sweet preference has been linked to bitter taste sensitivity to 6‐n‐propylthiouracil, a heritable trait. The present study investigates the association between inherited taste sensitivity to 6‐n‐popylthiouracil and dental caries experience in 15‐year‐old school children.Methods: Two hundred 15‐year‐old school children from randomly selected schools in Bangalore, India, participated in the study. Data were collected regarding demographic factors and socioeconomic status by personal interviews with the children. Sensitivity to 6‐n‐propylthiouracil was determined using Tepper filter paper method, and the responses were recorded on the labeled magnitude scale. Each child was examined thoroughly for oral hygiene status and caries experience. Appropriate statistical tests, such as chi‐squared test, Fisher’s exact test, and Kruskal–Wallis test, were used to analyze the data.Results: Non‐tasters were significantly associated with caries experience (P < 0.001). The decayed component in non‐tasters (3.43 ± 2.18) was statistically significant when compared to tasters (2.86 ± 1.58 medium tasters, 1.50 ± 0.55 supertasters).Conclusions: After all associated factors were controlled, 6‐n‐propylthiouracil taste status was the only independent variable significantly related to overall caries experience.
In Vitro
Susceptibility of
Madurella mycetomatis
to Posaconazole and Terbinafine
Authors: van Belkum Alex , Fahal Ahmed H. , van de Sande Wendy W. J. 
Published: January 2011

ABSTRACT

Presently, therapy of eumycetoma in Sudan is still based on surgery combined with prolonged ketoconazole therapy. This usually results in a poor clinical outcome. To determine if posaconazole and terbinafine could offer better therapeutic alternatives, the
in vitro
susceptibilities of 34
Madurella mycetomatis
strains were determined. It appeared that posaconazole was highly active against
M. mycetomatis
but terbinafine was only moderately active. Since posaconazole has an excellent safety profile, it might provide an important alternative in mycetoma therapy.
Heterogeneity of Tn
5253
-Like Composite Elements in Clinical
Streptococcus pneumoniae
Isolates
Authors: Mingoia Marina , Tili Emily , Manso Esther , Varaldo Pietro E. , Montanari Maria Pia 
Published: January 2011

ABSTRACT

Several drug resistances in
Streptococcus pneumoniae
are associated with mobile genetic elements, which are loosely subdivided into a group of smaller (18- to 27-kb) and a group of larger (>50-kb) elements. While the elements of the former group, which typically carry the tetracycline resistance determinant
tet
(M) and whose prototype is Tn
916
(18 kb), have been studied extensively, the larger elements, whose prototype is Tn
5253
(∼65.5 kb), are not as well explored. Tn
5253
is a composite structure consisting of two independent conjugative transposons, Tn
5251
(which is virtually identical to Tn
916
) and Tn
5252
(∼47.5 kb), with the former inserted into the latter. Tn
5252
, which so far has only partially been sequenced, carries an integrase gene, driving its site-specific insertion into the host cell genome, and the chloramphenicol resistance
cat
pC194
determinant. This study investigated 20 clinical isolates of
S. pneumoniae
, which were selected on the basis of
cat
pC194
-mediated chloramphenicol resistance. All 20 isolates harbored a Tn
5253
-like element. The composite elements (some of which have been completely sequenced) demonstrated considerable heterogeneity that stemmed from a dual variability: in the Tn
5252
-like element, due primarily to differences in the integrase gene but also to differences in cargo genes and in the overall genetic organization, and in the Tn
916
-like element, with the possible involvement, besides Tn
916
, of a number of Tn
916
family pneumococcal elements carrying different erythromycin resistance genes. In mating experiments, only one composite element, containing a less typical Tn
916
family element, appeared to be nonmobile. Being part of a Tn
5253
-like composite element may confer on some Tn
916
-like transposons, which are apparently nontransferable as independent genetic elements, the ability to be mobilized.
Zanamivir, at 600 Milligrams Twice Daily, Inhibits Oseltamivir-Resistant 2009 Pandemic H1N1 Influenza Virus in anIn VitroHollow-Fiber Infection Model System
Authors: Brown Ashley N. , McSharry James J. , Weng Qingmei , Adams Jonathan R. , Kulawy Robert , Drusano George L. 
Published: January 2011

ABSTRACTIn 2009, a novel H1N1 influenza A virus emerged and spread worldwide, initiating a pandemic. Various isolates obtained from disparate parts of the world were shown to be uniformly resistant to the adamantanes but sensitive to the neuraminidase inhibitors oseltamivir and zanamivir. Over time, resistance to oseltamivir became more prevalent among pandemic H1N1 virus isolates, while most remained susceptible to zanamivir. The government has proposed the use of intravenous (i.v.) zanamivir to treat serious influenza virus infections among hospitalized patients. To use zanamivir effectively for patients with severe influenza, it is necessary to know the optimal dose and schedule of administration of zanamivir that will inhibit the replication of oseltamivir-sensitive and -resistant influenza viruses. Therefore, we performed studies using thein vitrohollow-fiber infection model system to predict optimal dosing regimens for zanamivir against an oseltamivir-sensitive and an oseltamivir-resistant virus. Our results demonstrated that zanamivir, at a dose of 600 mg given twice a day (Q12h), inhibited the replication of oseltamivir-sensitive and oseltamivir-resistant influenza viruses throughout the course of the experiment. Thus, our findings suggest that intravenous zanamivir, at a dose of 600 mg Q12h, could be used to treat hospitalized patients suffering from serious infections with oseltamivir-sensitive or -resistant influenza viruses.
Antibiotics Cure Anthrax in Animal Models
Authors: Weiss Shay , Kobiler David , Levy Haim , Pass Avi , Ophir Yakir , Rothschild Nili , Tal Arnon , Schlomovitz Josef , Altboum Zeev 
Published: January 2011

ABSTRACTRespiratory anthrax, in the absence of early antibiotic treatment, is a fatal disease. This study aimed to test the efficiency of antibiotic therapy in curing infected animals and those sick with anthrax. Postexposure prophylaxis (24 h postinfection [p.i.]) of guinea pigs infected intranasally withBacillus anthracisVollum spores with doxycycline, ofloxacin, imipenem, and gentamicin conferred protection. However, upon termination of treatment, the animals died from respiratory anthrax. Combined treatment with antibiotics and active vaccination with a protective antigen-based vaccine leads to full protection even after cessation of treatment. Delaying the initiation of antibiotic administration to over 24 h p.i. resulted in treatment of animals with anthrax exhibiting various degrees of bacteremia and toxemia. Treatment with doxycycline or ciprofloxacin cured sick guinea pigs and rabbits exhibiting bacteremia levels up to 105CFU/ml. Addition of anti-protective antigen (PA) antibodies augmented the efficiency of protection, allowing the cure of guinea pigs and rabbits with 10- to 20-fold-higher bacteremia levels, up to 7 × 105CFU/ml and 2 × 106CFU/ml, respectively. Treatment with ciprofloxacin and a monoclonal anti-PA antibody rescued rabbits with bacteremia levels up to 4 × 106CFU/ml. During antibiotic administration, all surviving animals developed a protective immune response against development of a fatal disease and subcutaneous challenge with Vollum spores. In conclusion, these results demonstrate that antibiotic treatment can prevent the development of fatal disease in respiratory-anthrax-infected animals and can cure animals after disease establishment. A therapeutic time window of 40 h to 48 h from infection to initiation of efficient antibiotic-mediated cure was observed.
NOD-Like Receptor Activation by Outer Membrane Vesicles from
Vibrio cholerae
Non-O1 Non-O139 Strains Is Modulated by the Quorum-Sensing Regulator HapR
Authors: Bielig H. , Rompikuntal P. K. , Dongre M. , Zurek B. , Lindmark B. , Ramstedt M. , Wai S. N. , Kufer T. A. 
Published: January 2011

ABSTRACT

Vibrio cholerae
is an inhabitant of aquatic systems and one of the causative agents of severe dehydrating diarrhea in humans. It has also emerged as an important cause of different kinds of inflammatory responses, and in particular,
V. cholerae
strains of the non-O1 non-O139 serogroups (NOVC) have been associated with such infections in human. We analyzed the potential of outer membrane vesicles (OMVs) derived from the NOVC strain V:5/04 to induce inflammatory responses in human host cells. V:5/04 OMVs were taken up by human epithelial cells and induced inflammatory responses. Small interfering RNA (siRNA)-mediated gene knockdown revealed that the inflammatory potential of NOVC OMVs was partially mediated by the nucleotide-binding domain-, leucine-rich repeat-containing family member NOD1. Physiochemical analysis of the content of these OMVs, in conjunction with NOD1 and NOD2 reporter assays in HEK293T cells, confirmed the presence of both NOD1 and NOD2 active peptidoglycan in the OMVs. Furthermore, we show that deletion of the quorum-sensing regulator HapR, which mimics an infective life style, specifically reduced the inflammatory potential of the V:5/04 OMVs and their ability to activate NOD1 and NOD2. In conclusion, our study shows that NOVC OMVs elicit immune responses mediated by NOD1 and NOD2 in mammalian host cells. Moreover, we provide evidence that the quorum-sensing machinery plays an important regulatory role in this process by attenuating the inflammatory potential of OMVs under infective conditions. This work thus identifies a new facet of how
Vibrio
affects host immune responses and defines a role for the quorum-sensing machinery in this process.
Polymicrobial Infection with Periodontal Pathogens Specifically Enhances MicroRNA miR-146a in ApoE
−/−
Mice during Experimental Periodontal Disease
Authors: Nahid Md A. , Rivera Mercedes , Lucas Alexandra , Chan Edward K. L. , Kesavalu L. 
Published: January 2011

ABSTRACT

Porphyromonas gingivalis
,
Treponema denticola
, and
Tannerella forsythia
are periodontal pathogens associated with the etiology of adult periodontitis as polymicrobial infections. Recent studies demonstrated that oral infection with
P. gingivalis
induces both periodontal disease and atherosclerosis in hyperlipidemic and proatherogenic ApoE
−/−
mice. In this study, we explored the expression of microRNAs (miRNAs) in maxillas (periodontium) and spleens isolated from ApoE
−/−
mice infected with
P. gingivalis
,
T. denticola
, and
T. forsythia
as a polymicrobial infection. miRNA expression levels, including miRNA miR-146a, and associated mRNA expression levels of the inflammatory cytokines tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β) were measured in the maxillas and spleens from mice infected with periodontal pathogens and compared to those in the maxillas and spleens from sham-infected controls. Furthermore, in response to these periodontal pathogens (as mono- and polymicrobial heat-killed and live bacteria), human THP-1 monocytes demonstrated similar miRNA expression patterns, including that of miR-146a,
in vitro
. Strikingly, miR-146a had a negative correlation with TNF-α secretion
in vitro
, reducing levels of the adaptor kinases IL-1 receptor-associated kinase 1 (IRAK-1) and TNF receptor-associated factor 6 (TRAF6). Thus, our studies revealed a persistent association of miR-146a expression with these periodontal pathogens, suggesting that miR-146a may directly or indirectly modulate or alter the chronic periodontal pathology induced by these microorganisms.
Performance of Various Testing Methodologies for Detection of Heteroresistant Vancomycin-Intermediate Staphylococcus aureus in Bloodstream Isolates
Authors: van Hal Sebastian J. , Wehrhahn Michael C. , Barbagiannakos Thelma , Mercer Joanne , Chen Dehua , Paterson David L. , Gosbell Iain B. 
Published: January 2011

ABSTRACT

The best screening method for detecting heteroresistant vancomycin-intermediate
Staphylococcus aureus
(hVISA) remains unclear. Using population analysis profiling utilizing the area under the concentration-time curve (PAP-AUC) as the gold standard, we screened 458 consecutive methicillin-resistant
S. aureus
(MRSA) bloodstream isolates to determine the most accurate and cost-effective testing strategy to detect the presence of heteroresistance. All isolates were also tested using the macromethod Etest (MET) and glycopeptide resistance detection (GRD) Etest. The MIC was determined by several methods, including standard vancomycin Etest, vancomycin broth microdilution (BMD), and Vitek2 testing. Fifty-five (12%) hVISA and 4 (1%) VISA isolates were detected by PAP-AUC. Compared to PAP-AUC, the sensitivities and specificities of MET, GRD Etest, BMD (using a MIC cutoff of ≥2 mg/liter), and standard vancomycin Etest (using a MIC cutoff of ≥2 mg/liter) were 89 and 55%, 71 and 94%, 82 and 97%, and 71 and 94%, respectively. Combination testing increased the overall testing accuracy by reducing the number of false-positive results. Cost was determined predominately by the number of PAP-AUC runs required following a screening assay. The most cost-effective strategy was BMD (using a MIC cutoff of ≥2 μg/ml) as a standalone assay or in combination with PAP-AUC, provided that BMD testing was batched. GRD Etest remained an alternative, with 71% of hVISA isolates detected. Prevalence influenced both cost and test accuracy, with results remaining unchanged for hVISA prevalences of up to 25%. Implementation of any testing strategy would therefore be dependent on balancing cost with accuracy in a given population and clinical context.
Performance and Cost Analysis of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Routine Identification of Yeast
Authors: Dhiman Neelam , Hall Leslie , Wohlfiel Sherri L. , Buckwalter Seanne P. , Wengenack Nancy L. 
Published: January 2011

ABSTRACT
Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ≥1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory.