Depth in Coxeter groups of type BB

The depth statistic was defined for every Coxeter group in terms of factorizations of its elements into product of reflections. Essentially, the depth gives the minimal path cost in the Bruaht graph, where the edges have prescribed weights. We present an algorithm for calculating the depth of a signed permutation which yields a simple formula for this statistic. We use our algorithm to characterize signed permutations having depth equal to length. These are the fully commutative top-and-bottom elements defined by Stembridge. We finally give a characterization of the signed permutations in which the reflection length coincides with both the depth and the length

Detection of Candida species in vaginal samples in a clinical laboratory setting.

OBJECTIVE: To present the detection rates of Candida species in vaginal samples from patients visiting physicians. METHODS: The presence of C. albicans, C. glabrata, C. parapsilosis and C. tropicalis in 3978 vaginal swabs from patients in six US states was detected by PCR amplification. RESULTS: Candida DNA was detected in 33.1% of the population studied. Of the 1316 positive samples, 80.2% contained C. albicans, 14.3% contained C. glabrata, 5.9% contained C. parapsilosis and 8.0% contained C. tropicalis. Comparing samples by patients' state of residence revealed an association with the detection of C. glabrata (p = 0.029). Comparing samples by patients' age revealed a decrease in the overall detection of Candida (p < 0.001) and C. albicans (p < 0.001), concomitant with an increase in the detection of C. glabrata (p < 0.001) and C. parapsilosis (p = 0.025). CONCLUSIONS: These results provide geographic- and age-specific data on four Candida species associated with vaginitis

Prevalence of Bordetella pertussis and Bordetella parapertussis in Samples Submitted for RSV Screening

Background: The clinical presentation of Bordetella pertussis can overlap with that of respiratory syncytial virus (RSV); however, management differs.Hypothesis: First, the prevalence of B. pertussis is less than 2% among patients screened for RSV, and second the prevalence of B. parapertussis is also less than 2% among these patients.Methods: Nasal washings submitted to a clinical laboratory for RSV screening were tested for B. pertussis and B. parapertussis, using species-specific real-time polymerase chain reaction (PCR) assays. These were optimized to target conserved regions within a complement gene and the CarB gene, respectively. A Bordetella spp. genus-specific real-time PCR assay was designed to detect the Bhur gene of B. pertussis, B. parapertussis, and B. bronchiseptica. RSV A and B subtypes were tested by reverse transcription-PCR.Results: Four hundred and eighty-nine clinical samples were tested. There was insufficient material to complete testing for one B. pertussis, 10 RSV subtype A, and four RSV subtype B assays. Bordetella pertussis was detected in 3/488 (0.6%) (95% CI 0.1% to 1.8%), while B. parapertussis was detected in 5/489 (1.0%) (95% CI 0.3% to 2.4%). Dual infection of B. pertussis with RSV and of B. parapertussis with RSV occurred in two and in three cases respectively. RSV was detected by PCR in 127 (26.5%).Conclusion: The prevalence of B. pertussis in nasal washings submitted for RSV screening was less than 2%. The prevalence of parapertussis may be higher than 2%. RSV with B. pertussis and RSV with B. parapertussis coinfection do occur.[WestJEM. 2008;9:135-140.

Molecular characterization of vaginal microbiota using a new 22-species qRT-PCR test to achieve a relative-abundance and species-based diagnosis of bacterial vaginosis

BackgroundNumerous bacteria are involved in the etiology of bacterial vaginosis (BV). Yet, current tests only focus on a select few. We therefore designed a new test targeting 22 BV-relevant species.MethodsUsing 946 stored vaginal samples, a new qPCR test that quantitatively identifies 22 bacterial species was designed. The distribution and relative abundance of each species, α- and β-diversities, correlation, and species co-existence were determined per sample. A diagnostic index was modeled from the data, trained, and tested to classify samples into BV-positive, BV-negative, or transitional BV.ResultsThe qPCR test identified all 22 targeted species with 95 – 100% sensitivity and specificity within 8 hours (from sample reception). Across most samples, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensenii, Gardnerella vaginalis, Fannyhessea (Atopobium) vaginae, Prevotella bivia, and Megasphaera sp. type 1 were relatively abundant. BVAB-1 was more abundant and distributed than BVAB-2 and BVAB-3. No Mycoplasma genitalium was found. The inter-sample similarity was very low, and correlations existed between key species, which were used to model, train, and test a diagnostic index: MDL-BV index. The MDL-BV index, using both species and relative abundance markers, classified samples into three vaginal microbiome states. Testing this index on our samples, 491 were BV-positive, 318 were BV-negative, and 137 were transitional BV. Although important differences in BV status were observed between different age groups, races, and pregnancy status, they were statistically insignificant.ConclusionUsing a diverse and large number of vaginal samples from different races and age groups, including pregnant women, the new qRT-PCR test and MDL-BV index efficiently diagnosed BV within 8 hours (from sample reception), using 22 BV-associated species

Oncoprotein DEK as a tissue and urinary biomarker for bladder cancer

<p>Abstract</p> <p>Background</p> <p>Bladder cancer is a significant healthcare problem in the United States of America with a high recurrence rate. Early detection of bladder cancer is essential for removing the tumor with preservation of the bladder, avoiding metastasis and hence improving prognosis and long-term survival. The objective of this study was to analyze the presence of DEK protein in voided urine of bladder cancer patients as a urine-based bladder cancer diagnostic test.</p> <p>Methods</p> <p>We examined the expression of DEK protein by western blot in 38 paired transitional cell carcinoma (TCC) bladder tumor tissues and adjacent normal tissue. The presence of DEK protein in voided urine was analyzed by western blot in 42 urine samples collected from patients with active TCC, other malignant urogenital disease and healthy individuals.</p> <p>Results</p> <p>The DEK protein is expressed in 33 of 38 bladder tumor tissues with no expression in adjacent normal tissue. Based on our sample size, DEK protein is expressed in 100% of tumors of low malignant potential, 92% of tumors of low grade and in 71% of tumors of high grade. Next, we analyzed 42 urine samples from patients with active TCC, other malignant urogenital disease, non-malignant urogenital disease and healthy individuals for DEK protein expression by western blot analysis. We are the first to show that the DEK protein is present in the urine of bladder cancer patients. Approximately 84% of TCC patient urine specimens were positive for urine DEK.</p> <p>Conclusion</p> <p>Based on our pilot study of 38 bladder tumor tissue and 42 urine samples from patients with active TCC, other malignant urogenital disease, non-malignant urogenital disease and healthy individuals; DEK protein is expressed in bladder tumor tissue and voided urine of bladder cancer patients. The presence of DEK protein in voided urine is potentially a suitable biomarker for bladder cancer and that the screening for the presence of DEK protein in urine can be explored as a noninvasive diagnostic test for bladder cancer.</p