Information-theoretic principle entails orthomodularity of a lattice

Quantum logical axiomatic systems for quantum theory usually include a postulate that a lattice under consideration is orthomodular. We propose a derivation of orthomodularity from an information-theoretic axiom. This provides conceptual clarity and removes a long-standing puzzle about the meaning of orthomodularity.Comment: Version prior to published, with slight modification

Combined Inflammatory and Metabolic Defects Reflected by Reduced Serum Protein Levels in Patients with Buruli Ulcer Disease

Buruli ulcer is a skin disease caused by Mycobacterium ulcerans that is spreading in tropical countries, with major public health and economic implications in West Africa. Multi-analyte profiling of serum proteins in patients and endemic controls revealed that Buruli ulcer disease down-regulates the circulating levels of a large array of inflammatory mediators, without impacting on the leukocyte composition of peripheral blood. Notably, several proteins contributing to acute phase reaction, lipid metabolism, coagulation and tissue remodelling were also impacted. Their down-regulation was selective and persisted after the elimination of bacteria with antibiotic therapy. It involved proteins with various functions and origins, suggesting that M. ulcerans infection causes global and chronic defects in the host’s protein metabolism. Accordingly, patients had reduced levels of total serum proteins and blood urea, in the absence of signs of malnutrition, or functional failure of liver or kidney. Interestingly, slow healers had deeper metabolic and coagulation defects at the start of antibiotic therapy. In addition to providing novel insight into Buruli ulcer pathogenesis, our study therefore identifies a unique proteomic signature for this disease

Tazarotene 0.045% Lotion for Moderate-to-Severe Acne in Male and Female Participants: A Phase II Post-hoc Analysis

BACKGROUND: In a Phase II study, tazarotene 0.045% lotion was statistically superior to vehicle and comparable to tazarotene 0.1% cream in reducing acne lesions, with fewer treatment-related adverse events (TEAEs) than the cream. OBJECTIVE: We analyzed data from the aforementioned study post-hoc to evaluate the effects of sex on treatment outcomes. METHODS: Participants aged 12 years or older with moderate-to-severe acne were randomized to tazarotene (0.045% lotion or 0.1% cream) or vehicle (lotion or cream) for 12 weeks of double-blind treatment. Outcomes analyzed in male and female subgroups included changes from baseline in inflammatory/noninflammatory lesions and TEAEs. RESULTS: In the intent-to-treat population (94 males and 116 females), reductions in lesion count were greater with tazarotene (lotion or cream) than with vehicle. In participants receiving tazarotene 0.045% lotion, the least-squares mean percent changes from baseline to Week 12 were greater in females than males, but the differences were not statistically significant (inflammatory [-70.3% vs. -56.2%]; noninflammatory [-60.0% vs. -53.2%]). In both females and males, the TEAE incidence was lower with tazarotene 0.045% lotion than 0.1% cream. CONCLUSION: Tazarotene 0.045% lotion substantially reduced acne lesions in both female and male participants. This newest tazarotene formulation might benefit patients who cannot tolerate older formulations or other topical retinoids. Given the relatively small size of this study, however, the results of this post-hoc analysis are intended to be exploratory in nature

Idealness of k-wise intersecting families

A clutter is k-wise intersecting if every k members have a common element, yet no element belongs to all members. We conjecture that, for some integer k ≥ 4, every k-wise intersecting clutter is non-ideal. As evidence for our conjecture, we prove it for k = 4 for the class of binary clutters. Two key ingredients for our proof are Jaeger’s 8-flow theorem for graphs, and Seymour’s characterization of the binary matroids with the sums of circuits property. As further evidence for our conjecture, we also note that it follows from an unpublished conjecture of Seymour from 1975. We also discuss connections to the chromatic number of a clutter, projective geometries over the two-element field, uniform cycle covers in graphs, and quarter-integral packings of value two in ideal clutters

In-Situ Nuclear Magnetic Resonance Investigation of Strain, Temperature, and Strain-Rate Variations of Deformation-Induced Vacancy Concentration in Aluminum

Critical strain to serrated flow in solid solution alloys exhibiting dynamic strain aging (DSA) or Portevin–LeChatelier effect is due to the strain-induced vacancy production. Nuclear magnetic resonance (NMR) techniques can be used to monitor in situ the dynamical behavior of point and line defects in materials during deformation, and these techniques are nondestructive and noninvasive. The new CUT-sequence pulse method allowed an accurate evaluation of the strain-enhanced vacancy diffusion and, thus, the excess vacancy concentration during deformation as a function of strain, strain rate, and temperature. Due to skin effect problems in metals at high frequencies, thin foils of Al were used and experimental results correlated with models based on vacancy production through mechanical work (vs thermal jogs), while in situ annealing of excess vacancies is noted at high temperatures. These correlations made it feasible to obtain explicit dependencies of the strain-induced vacancy concentration on test variables such as the strain, strain rate, and temperature. These studies clearly reveal the power and utility of these NMR techniques in the determination of deformation-induced vacancies in situ in a noninvasive fashion.

Mycolactone-dependent depletion of endothelial cell thrombomodulin is strongly associated with fibrin deposition in Buruli ulcer lesions

A well-known histopathological feature of diseased skin in Buruli ulcer (BU) is coagulative necrosis caused by the Mycobacterium ulcerans macrolide exotoxin mycolactone. Since the underlying mechanism is not known, we have investigated the effect of mycolactone on endothelial cells, focussing on the expression of surface anticoagulant molecules involved in the protein C anticoagulant pathway. Congenital deficiencies in this natural anticoagulant pathway are known to induce thrombotic complications such as purpura fulimans and spontaneous necrosis. Mycolactone profoundly decreased thrombomodulin (TM) expression on the surface of human dermal microvascular endothelial cells (HDMVEC) at doses as low as 2ng/ml and as early as 8hrs after exposure. TM activates protein C by altering thrombin's substrate specificity, and exposure of HDMVEC to mycolactone for 24 hours resulted in an almost complete loss of the cells' ability to produce activated protein C. Loss of TM was shown to be due to a previously described mechanism involving mycolactone-dependent blockade of Sec61 translocation that results in proteasome-dependent degradation of newly synthesised ER-transiting proteins. Indeed, depletion from cells determined by live-cell imaging of cells stably expressing a recombinant TM-GFP fusion protein occurred at the known turnover rate. In order to determine the relevance of these findings to BU disease, immunohistochemistry of punch biopsies from 40 BU lesions (31 ulcers, nine plaques) was performed. TM abundance was profoundly reduced in the subcutis of 78% of biopsies. Furthermore, it was confirmed that fibrin deposition is a common feature of BU lesions, particularly in the necrotic areas. These findings indicate that there is decreased ability to control thrombin generation in BU skin. Mycolactone's effects on normal endothelial cell function, including its ability to activate the protein C anticoagulant pathway are strongly associated with this. Fibrin-driven tisischemia could contribute to the development of the tissue necrosis seen in BU lesions

Conversion of a molecular classifier obtained by gene expression profiling into a classifier based on real-time PCR: a prognosis predictor for gliomas

<p>Abstract</p> <p>Background</p> <p>The advent of gene expression profiling was expected to dramatically improve cancer diagnosis. However, despite intensive efforts and several successful examples, the development of profile-based diagnostic systems remains a difficult task. In the present work, we established a method to convert molecular classifiers based on adaptor-tagged competitive PCR (ATAC-PCR) (with a data format that is similar to that of microarrays) into classifiers based on real-time PCR.</p> <p>Methods</p> <p>Previously, we constructed a prognosis predictor for glioma using gene expression data obtained by ATAC-PCR, a high-throughput reverse-transcription PCR technique. The analysis of gene expression data obtained by ATAC-PCR is similar to the analysis of data from two-colour microarrays. The prognosis predictor was a linear classifier based on the first principal component (PC1) score, a weighted summation of the expression values of 58 genes. In the present study, we employed the delta-delta Ct method for measurement by real-time PCR. The predictor was converted to a Ct value-based predictor using linear regression.</p> <p>Results</p> <p>We selected <it>UBL5 </it>as the reference gene from the group of genes with expression patterns that were most similar to the median expression level from the previous profiling study. The number of diagnostic genes was reduced to 27 without affecting the performance of the prognosis predictor. PC1 scores calculated from the data obtained by real-time PCR showed a high linear correlation (r = 0.94) with those obtained by ATAC-PCR. The correlation for individual gene expression patterns (r = 0.43 to 0.91) was smaller than for PC1 scores, suggesting that errors of measurement were likely cancelled out during the weighted summation of the expression values. The classification of a test set (n = 36) by the new predictor was more accurate than histopathological diagnosis (log rank p-values, 0.023 and 0.137, respectively) for predicting prognosis.</p> <p>Conclusion</p> <p>We successfully converted a molecular classifier obtained by ATAC-PCR into a Ct value-based predictor. Our conversion procedure should also be applicable to linear classifiers obtained from microarray data. Because errors in measurement are likely to be cancelled out during the calculation, the conversion of individual gene expression is not an appropriate procedure. The predictor for gliomas is still in the preliminary stages of development and needs analytical clinical validation and clinical utility studies.</p

RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization

Background RT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls. There is increasing evidence, however, that the expression of commonly used reference genes can vary significantly in certain contexts. Results Using the Genevestigator database of normalized and well-annotated microarray experiments, we describe the expression stability characteristics of the transciptomes of several organisms. The results show that a) no genes are universally stable, b) most commonly used reference genes yield very high transcript abundances as compared to the entire transcriptome, and c) for each biological context a subset of stable genes exists that has smaller variance than commonly used reference genes or genes that were selected for their stability across all conditions. Conclusion We therefore propose the normalization of RT-qPCR data using reference genes that are specifically chosen for the conditions under study. RefGenes is a community tool developed for that purpose. Validation RT-qPCR experiments across several organisms showed that the candidates proposed by RefGenes generally outperformed commonly used reference genes. RefGenes is available within Genevestigator at http://www.genevestigator.com

Evaluation of Candidate Reference Genes for Gene Expression Normalization in Brassica juncea Using Real Time Quantitative RT-PCR

The real time quantitative reverse transcription PCR (qRT-PCR) is becoming increasingly important to gain insight into function of genes. Given the increased sensitivity, ease and reproducibility of qRT-PCR, the requirement of suitable reference genes for normalization has become important and stringent. It is now known that the expression of internal control genes in living organism vary considerably during developmental stages and under different experimental conditions. For economically important Brassica crops, only a couple of reference genes are reported till date. In this study, expression stability of 12 candidate reference genes including ACT2, ELFA, GAPDH, TUA, UBQ9 (traditional housekeeping genes), ACP, CAC, SNF, TIPS-41, TMD, TSB and ZNF (new candidate reference genes), in a diverse set of 49 tissue samples representing different developmental stages, stress and hormone treated conditions and cultivars of Brassica juncea has been validated. For the normalization of vegetative stages the ELFA, ACT2, CAC and TIPS-41 combination would be appropriate whereas TIPS-41 along with CAC would be suitable for normalization of reproductive stages. A combination of GAPDH, TUA, TIPS-41 and CAC were identified as the most suitable reference genes for total developmental stages. In various stress and hormone treated samples, UBQ9 and TIPS-41 had the most stable expression. Across five cultivars of B. juncea, the expression of CAC and TIPS-41 did not vary significantly and were identified as the most stably expressed reference genes. This study provides comprehensive information that the new reference genes selected herein performed better than the traditional housekeeping genes. The selection of most suitable reference genes depends on the experimental conditions, and is tissue and cultivar-specific. Further, to attain accuracy in the results more than one reference genes are necessary for normalization