Dependence Logic with Generalized Quantifiers: Axiomatizations

We prove two completeness results, one for the extension of dependence logic by a monotone generalized quantifier Q with weak interpretation, weak in the meaning that the interpretation of Q varies with the structures. The second result considers the extension of dependence logic where Q is interpreted as "there exists uncountable many." Both of the axiomatizations are shown to be sound and complete for FO(Q) consequences.Comment: 17 page

Homogenization of random degenerated nonlinear monotone operators

This paper deals with homogenization of random nonlinear monotone operators in divergence form. We assume that the structure conditions (strict monotonicity and continuity conditions) degenerate and are given in terms of a weight function. Under proper integrability assumptions on the weight function we construct the effective operator and prove the homogenization result

Insulin resistance in non-diabetic subjects is associated with increased incidence of myocardial infarction and death.

AIMS: To compare the incidence of myocardial infarction and death in non-diabetic subjects with and without insulin resistance. METHODS: Population-based prospective cohort study, in Malmö, Sweden, of 4748 non-diabetic subjects (60% women), aged 46-68 years, with no history of myocardial infarction or stroke. The prevalence of insulin resistance was established by the homeostasis model assessment (HOMA) and defined as values above the sex-specific 75th percentile (1.80 for women and 2.12 for men). Incidence of myocardial infarction and death is based on record linkage with local and national registers. Cox's proportional hazards model was used to assess the influence of insulin resistance after adjustment for age, sex, hyperglycaemia, raised arterial blood pressure, dyslipidaemia, central obesity, smoking and leisure-time physical activity. RESULTS: Sixty-two subjects suffered a coronary event, and 93 subjects died during the 6-year follow-up period. Insulin resistance was after adjustment for other factors included in the insulin resistance syndrome and other potential confounders, associated with an increased incidence of coronary events (relative risk (RR) 2.18; 95% confidence interval (CI) 1.22-3.87; P = 0.008) and deaths (RR 1.62; 1.03-2.55; P = 0.038). CONCLUSIONS: Insulin resistance, as assessed by the HOMA method, was in this cohort of middle-aged non-diabetic subjects associated with an increased incidence of myocardial infarction and death. This risk remained when smoking, low physical activity and factors included in the insulin resistance syndrome were taken into account in a stepwise regression model. Diabet. Med. 19, 470-475 (2002

Considering Polymorphism in Change-Based Test Suite Reduction

With the increasing popularity of continuous integration, algorithms for selecting the minimal test-suite to cover a given set of changes are in order. This paper reports on how polymorphism can handle false negatives in a previous algorithm which uses method-level changes in the base-code to deduce which tests need to be rerun. We compare the approach with and without polymorphism on two distinct cases ---PMD and CruiseControl--- and discovered an interesting trade-off: incorporating polymorphism results in more relevant tests to be included in the test suite (hence improves accuracy), however comes at the cost of a larger test suite (hence increases the time to run the minimal test-suite).Comment: The final publication is available at link.springer.co

Evasion of autophagy mediated by Rickettsia surface protein OmpB is critical for virulence.

Rickettsia are obligate intracellular bacteria that evade antimicrobial autophagy in the host cell cytosol by unknown mechanisms. Other cytosolic pathogens block different steps of autophagy targeting, including the initial step of polyubiquitin-coat formation. One mechanism of evasion is to mobilize actin to the bacterial surface. Here, we show that actin mobilization is insufficient to block autophagy recognition of the pathogen Rickettsia parkeri. Instead, R. parkeri employs outer membrane protein B (OmpB) to block ubiquitylation of the bacterial surface proteins, including OmpA, and subsequent recognition by autophagy receptors. OmpB is also required for the formation of a capsule-like layer. Although OmpB is dispensable for bacterial growth in endothelial cells, it is essential for R. parkeri to block autophagy in macrophages and to colonize mice because of its ability to promote autophagy evasion in immune cells. Our results indicate that OmpB acts as a protective shield to obstruct autophagy recognition, thereby revealing a distinctive bacterial mechanism to evade antimicrobial autophagy

Experimental and theoretical lifetimes and transition probabilities in Sb I

We present experimental atomic lifetimes for 12 levels in Sb I, out of which seven are reported for the first time. The levels belong to the 5p$^2$($^3$P)6s $^{2}$P, $^{4}$P and 5p$^2$($^3$P)5d $^{4}$P, $^{4}$F and $^{2}$F terms. The lifetimes were measured using time-resolved laser-induced fluorescence. In addition, we report new calculations of transition probabilities in Sb I using a Multiconfigurational Dirac-Hartree-Fock method. The physical model being tested through comparisons between theoretical and experimental lifetimes for 5d and 6s levels. The lifetimes of the 5d $^4$F$_{3/2, 5/2, 7/2}$ levels (19.5, 7.8 and 54 ns, respectively) depend strongly on the $J$-value. This is explained by different degrees of level mixing for the different levels in the $^4$F term.Comment: 10 page

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells

BACKGROUND: Pluripotency is characterized by a unique transcriptional state, in which lineage-specification genes are poised for transcription upon exposure to appropriate stimuli, via a bivalency mechanism involving the simultaneous presence of activating and repressive methylation marks at promoter-associated histones. Recent evidence suggests that other mechanisms, such as RNA polymerase II pausing, might be operational in this process, but their regulation remains poorly understood. RESULTS: Here we identify the non-coding snRNA 7SK as a multifaceted regulator of transcription in embryonic stem cells. We find that 7SK represses a specific cohort of transcriptionally poised genes with bivalent or activating chromatin marks in these cells, suggesting a novel poising mechanism independent of Polycomb activity. Genome-wide analysis shows that 7SK also prevents transcription downstream of polyadenylation sites at several active genes, indicating that 7SK is required for normal transcriptional termination or control of 3′-UTR length. In addition, 7SK suppresses divergent upstream antisense transcription at more than 2,600 loci, including many that encode divergent long non-coding RNAs, a finding that implicates the 7SK snRNA in the control of transcriptional bidirectionality. CONCLUSIONS: Our study indicates that a single non-coding RNA, the snRNA 7SK, is a gatekeeper of transcriptional termination and bidirectional transcription in embryonic stem cells and mediates transcriptional poising through a mechanism independent of chromatin bivalency.GCB was funded by an EMBO Long-Term Post-Doctoral Fellowship and a Marie Curie Intra-European Fellowship for Career Development. PA was supported by a Royal Society Newton International Fellowship and a Corpus Christi College research fellowship. This work was supported by Cancer Research UK, European Research Council (Advanced Grant, TK), EMBL (PB) and Swedish Research Council (GCB)

Impulse oscillometry may be of value in detecting early manifestations of COPD

SummaryBackgroundSpirometry is used to diagnose chronic obstructive pulmonary disease (COPD). The Impulse oscillometry system (IOS) allows determination of respiratory impedance indices, which might be of potential value in early COPD, although previous experience is limited. We examined pulmonary resistance and reactance measured by IOS in subjects with or without self-reported chronic bronchitis or emphysema or COPD (Q+ or Q−) and subjects with or without COPD diagnosed according to the Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria (G+ or G−).MethodsFrom a previous population-based study 450 subjects were examined with spirometry and IOS and answered a questionnaire on respiratory symptoms and diseases.ResultsSeventy-seven subjects were Q+, of whom 34 also were G+. Q+/G− subjects (n = 43) reported respiratory symptoms more frequently (35–40% vs 8–14%) but had higher FEV1 (100% vs 87%) than Q−/G+ subjects (n = 90), p < 0.05 for both comparisons. Q+ subjects had higher pulmonary resistance and lower pulmonary reactance than Q− subjects (p < 0.01 for all comparisons). The same pattern was seen both in G+ subjects ((Q+/Q−) R5 0.39/0.32, R5–R20 0.10/0.07, X5 0.13/0.09, AX 0.55/0.27, p < 0.05 for all) and G− subjects ((Q+/Q−) R5 0.35/0.29, R5–R20 0.08/0.06, X5 0.10/0.08, AX 0.31/0.19 p < 0.05 for all) except for R20 (adjusted for gender and age).ConclusionsSelf-reported chronic bronchitis or emphysema or COPD was associated with higher pulmonary resistance and lower pulmonary reactance measured by IOS, both among subjects with and without COPD according to GOLD criteria. IOS may have the potential to detect pathology associated with COPD earlier than spirometry