PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays

MOTIVATION: Detection and identification of microbes using diagnostic arrays is still subject of ongoing research. Existing significance-based algorithms consider an organism detected even if a significant number of the microarray probes that match the organism are called absent in a hybridization. Further, they do generate redundant results if the target organisms show high sequence similarity and the microarray probes cannot discriminate all of them. RESULTS: We propose a new analysis strategy that considers organism similarities and calls organisms only present if the probes that match the organism but are absent in a hybridization can be explained by random events. In our strategy, we.rst identify the groups of target organisms that are actually distinguishable by the array. Subsequently, these organism groups are placed in a hierarchical tree such that groups matching only less specific probes are closer to the tree root, and groups that are discriminated only by few probes are close to each other. Finally, we compute for each group a likelihood score that is based on a hypothesis test with the null hypothesis that the group was actually present in the hybridized sample. We have validated our strategy using datasets from two different array types and implemented it as an easy-to-use web application. AVAILABILITY: http://www.fgcz.ethz.ch/PhyloDetect. SUPPLEMENTARY INFORMATION: Example data is available at http://www.fgcz.ethz.ch/PhyloDetect

Ein Fall von akuter disseminierter Mucor-Enzephalitis bei einem Rind

The case of a 2 1/2 year old Swiss Braunvieh heifer suffering from an acute disseminated mycotic encephalitis caused by a Mucorales spp. infection is presented. Clinical signs and analysis of cerebrospinal fluid (increased protein concentration and pleocytosis) were typical for an acute encephalitis, probably due to a listeriosis. The histological examination of the brain revealed an acute disseminated thrombo-embolic encephalomyelitis due to a fungi infection, morphologically consistent with Mucorales spp. The occurrence of bovine cerebral mucormycosis is rare and therefore the veterinarian should become aware of a case which was clinically not distinguishable from a listeriosis

Comparison of sampling and culture methods for the diagnosis of Tritrichomonas foetus infection in bulls

abstract: Sampling methods for preputial secretions and culture methods for T. foetus were compared in a 2-by-2 factorial experiment. 14 bulls were confirmed as infected by repeated weekly sampling and culture on Diamond's medium over the course of 10 months. In a 6-week test of alternative methods of diagnosis, the bulls were randomly assigned to have their preputial contents sampled weekly either by washing or by scraping of the preputial membrane. The samples were cultured on Claussen's medium and in InPouch packets at 37°C in air for 7 days. The results were compared by McNemar's χ² test for symmetry. Washing yielded 69 positive cultures from 84 samples whereas scraping yielded 65 from 83. These differences were not statistically significant. InPouch culture detected 73 of 83 samples from positive bulls, whereas Claussen's medium detected 61 of 83. The difference in sensitivity between the two culture methods was highly significant, with the InPouch method 'missing' 2 positive samples that were detected by Claussen's medium and Claussen's medium missing 14 positive samples that were detected by InPouch culture

Physical activity and the frequency of acute exacerbations in patients with chronic obstructive pulmonary disease

PURPOSE: Acute exacerbations (AE) in patients with COPD are associated with a decline in lung function, increased risk of hospitalization, and mortality. In this cross-sectional study we tested whether the level of objectively measured daily physical activity and exercise capacity are associated with the number of COPD exacerbations. METHODS: In 210 patients with COPD (67 % men; mean (SD) age: 63 (8) years) enrolled in The Obstructive Pulmonary Disease Outcomes Cohort of Switzerland (TOPDOCS) physical activity (PA) (steps per day, physical activity level, (PAL)), exercise capacity (6-min walking distance, (6MWD)), comorbidities, lung function, and medication were assessed. Differences between COPD patients with frequent (≥2 year) and infrequent (0-1 year) exacerbations were assessed. Univariate and multivariate analyses were performed to investigate whether the level of objectively measured daily physical activity and exercise capacity are associated with the number of COPD exacerbations. RESULTS: Patients with frequent AE had a significantly lower FEV1 and 6MWD compared to patients with infrequent AE. In univariate analysis, the number of exacerbations was inversely associated with FEV1, 6MWD, BMI, and smoking status while there was a positive association with RV/TLC and combined inhaled medication. However, there was no significant association with PAL and steps per day. In multivariate analysis, FEV1 and the use of combined inhaled medication were independently associated with the number of AE, after correction for covariates. CONCLUSIONS: The findings of this study imply that FEV1, independent of inhaled medication, is significantly associated with COPD exacerbations. Neither physical activity nor exercise capacity was independently associated with COPD exacerbations

Single crystal growth of CeTAl₃ (T = Cu, Ag, Au, Pd and Pt)

Abstract We report single crystal growth of the series of CeTAl3 compounds with T = Cu, Ag, Au, Pd and Pt by means of optical float zoning, where high crystal quality was confirmed in a thorough characterization process. With the exception of CeAgAl3, all compounds crystallize in the non-centrosymmetric tetragonal BaNiSn3 structure (space group: I4mm, No. 107), whereas CeAgAl3 adopts the related orthorhombic PbSbO2Cl structure (Cmcm, No. 63). An attempt to grow CeNiAl3 resulted in the composition CeNi2Al5. Low temperature resistivity measurements down to ∼ 0.1 K did not reveal evidence suggestive of magnetic order in CePtAl3 and CePdAl3. In contrast, CeAuAl3, CeCuAl3 and CeAgAl3 display signatures of magnetic transitions at 1.3 K, 2.1 K and 3.2 K, respectively. This is consistent with previous reports of antiferromagnetic order in CeAuAl3 and CeCuAl3 as well as ferromagnetism in CeAgAl3, respectively

Physical Activity and the Frequency of Acute Exacerbations in Patients with Chronic Obstructive Pulmonary Disease

Purpose: Acute exacerbations (AE) in patients with COPD are associated with a decline in lung function, increased risk of hospitalization, and mortality. In this cross-sectional study we tested whether the level of objectively measured daily physical activity and exercise capacity are associated with the number of COPD exacerbations. Methods: In 210 patients with COPD (67% men; mean (SD) age: 63 (8)years) enrolled in The Obstructive Pulmonary Disease Outcomes Cohort of Switzerland (TOPDOCS) physical activity (PA) (steps per day, physical activity level, (PAL)), exercise capacity (6-min walking distance, (6MWD)), comorbidities, lung function, and medication were assessed. Differences between COPD patients with frequent (≥2year) and infrequent (0-1year) exacerbations were assessed. Univariate and multivariate analyses were performed to investigate whether the level of objectively measured daily physical activity and exercise capacity are associated with the number of COPD exacerbations. Results: Patients with frequent AE had a significantly lower FEV1 and 6MWD compared to patients with infrequent AE. In univariate analysis, the number of exacerbations was inversely associated with FEV1, 6MWD, BMI, and smoking status while there was a positive association with RV/TLC and combined inhaled medication. However, there was no significant association with PAL and steps per day. In multivariate analysis, FEV1 and the use of combined inhaled medication were independently associated with the number of AE, after correction for covariates. Conclusions: The findings of this study imply that FEV1, independent of inhaled medication, is significantly associated with COPD exacerbations. Neither physical activity nor exercise capacity was independently associated with COPD exacerbations