Detection of RTX toxin genes in gram-negative bacteria with a set of specific probes

The family of RTX (RTX representing repeats in the structural toxin) toxins is composed of several protein toxins with a characteristic nonapeptide glycine-rich repeat motif. Most of its members were shown to have cytolytic activity. By comparing the genetic relationships of the RTX toxin genes we established a set of 10 gene probes to be used for screening as-yet-unknown RTX toxin genes in bacterial species. The probes include parts of apxIA, apxIIA, and apxIIIA from Actinobacillus pleuropneumoniae, cyaA from Bordetella pertusis, frpA from Neisseria meningitidis, prtC from Erwinia chrysanthemi, hlyA and elyA from Escherichia coli, aaltA from Actinobacillus actinomycetemcomitans and lktA from Pasteurella haemolytica. A panel of pathogenic and nonpathogenic gram-negative bacteria were investigated for the presence of RTX toxin genes. The probes detected all known genes for RTX toxins. Moreover, we found potential RTX toxin genes in several pathogenic bacterial species for which no such toxins are known yet. This indicates that RTX or RTX-like toxins are widely distributed among pathogenic gram-negative bacteria. The probes generated by PCR and the hybridization method were optimized to allow broad-range screening for RTX toxin genes in one step. This included the binding of unlabelled probes to a nylon filter and subsequent hybridization of the filter with labelled genomic DNA of the strain to be tested. The method constitutes a powerful tool for the assessment of the potential pathogenicity of poorly characterized strains intended to be used in biotechnological applications. Moreover, it is useful for the detection of already-known or new RTX toxin genes in bacteria of medical importance.

Fast parallel kriging-based stepwise uncertainty reduction with application to the identification of an excursion set

Stepwise uncertainty reduction (SUR) strategies aim at constructing a sequence of points for evaluating a function  f in such a way that the residual uncertainty about a quantity of interest progressively decreases to zero. Using such strategies in the framework of Gaussian process modeling has been shown to be efficient for estimating the volume of excursion of f above a fixed threshold. However, SUR strategies remain cumbersome to use in practice because of their high computational complexity, and the fact that they deliver a single point at each iteration. In this article we introduce several multipoint sampling criteria, allowing the selection of batches of points at which f can be evaluated in parallel. Such criteria are of particular interest when f is costly to evaluate and several CPUs are simultaneously available. We also manage to drastically reduce the computational cost of these strategies through the use of closed form formulas. We illustrate their performances in various numerical experiments, including a nuclear safety test case. Basic notions about kriging, auxiliary problems, complexity calculations, R code, and data are available online as supplementary materials.

Bet ha-kĕnĕset ... oder Die Mayerische Synagoga in Greiffswalde : zum Nutzen der studirenden Jugend aufgerichtet ...

aus denen Rabbinen deutlich vorgestellet und mit einer Vorrede Brandani Henr. Gebhardi. Mit einem curieusen Anhang vermehret, zum 3. mahl aufgel. und hrsg. von Christoph Wallich

Tree size and fecundity influence ballistic seed dispersal of two dominant mast-fruiting species in a tropical rain forest

Seed production, seed dispersal, and seedling recruitment are integral to forest dynamics, especially in masting species. Often these are studied separately, yet scarcely ever for species with ballistic dispersal even though this mode of dispersal is common in legume trees of tropical African rain forests. Here, we studied two dominant main-canopy tree species, Microberlinia bisulcata and Tetraberlinia bifoliolata (Caesalpinioideae), in 25 ha of primary rain forest at Korup, Cameroon, during two successive masting events (2007/2010). In the vicinity of c. 100 and 130 trees of each species, 476/580 traps caught dispersed seeds and beneath their crowns c. 57,000 pod valves per species were inspected to estimate tree-level fecundity. Seed production of trees increased non-linearly and asymptotically with increasing stem diameters. It was unequal within the two species’ populations, and differed strongly between years to foster both spatial and temporal patchiness in seed rain. The M. bisulcata trees could begin seeding at 42–44 cm diameter: at a much larger size than could T. bifoliolata (25 cm). Nevertheless, per capita life-time reproductive capacity was c. five times greater in M. bisulcata than T. bifoliolata owing to former’s larger adult stature, lower mortality rate (despite a shorter life-time) and smaller seed mass. The two species displayed strong differences in their dispersal capabilities. Inverse modelling (IM) revealed that dispersal of M. bisulcata was best described by a lognormal kernel. Most seeds landed at 10–15 m from stems, with 1% of them going beyond 80 m (<100 m). The direct estimates of fecundity significantly improved the models fitted. The lognormal also described well the seedling recruitment distribution of this species in 121 ground plots. By contrast, the lower intensity of masting and more limited dispersal of the heavier-seeded T. bifoliolata prevented reliable IM. For this species, seed density as function of distance to traps suggested a maximum dispersal distance of 40–50 m, and a correspondingly more aggregated seedling recruitment pattern ensued than for M. bisulcata. From this integrated field study, we conclude that the reproductive traits of M. bisulcata give it a considerable advantage over T. bifoliolata by better dispersing more seeds per capita to reach more suitable establishment sites, and combined with other key traits they explain its local dominance in the forest. Understanding the linkages between size at onset of maturity, individual fecundity, and dispersal capability can better inform the life-history strategies, and hence management, of co-occurring tree species in tropical forests.

Relative Predicativity and dependent recursion in second-order set theory and higher-orders theories

This article reports that some robustness of the notions of predicativity and of autonomous progression is broken down if as the given infinite total entity we choose some mathematical entities other than the traditional ω. Namely, the equivalence between normal transfinite recursion scheme and new dependent transfinite recursion scheme, which does hold in the context of subsystems of second order number theory, does not hold in the context of subsystems of second order set theory where the universe V of sets is treated as the given totality (nor in the contexts of those of n+3-th order number or set theories, where the class of all n+2-th order objects is treated as the given totality).

Explicit mathematics and operational set theory: some ontological comparisons

We discuss several ontological properties of explicit mathematics and operational set theory: global choice, decidable classes, totality and extensionality of operations, function spaces, class and set formation via formulas that contain the definedness predicate and applications.

Lake surface water temperatures of European Alpine lakes (1989–2013) based on the Advanced Very High Resolution Radiometer (AVHRR) 1 km data set

Lake water temperature (LWT) is an important driver of lake ecosystems and it has been identified as an indicator of climate change. Consequently, the Global Climate Observing System (GCOS) lists LWT as an essential climate variable. Although for some European lakes long in situ time series of LWT do exist, many lakes are not observed or only on a non-regular basis making these observations insufficient for climate monitoring. Satellite data can provide the information needed. However, only few satellite sensors offer the possibility to analyse time series which cover 25 years or more. The Advanced Very High Resolution Radiometer (AVHRR) is among these and has been flown as a heritage instrument for almost 35 years. It will be carried on for at least ten more years, offering a unique opportunity for satellite-based climate studies. Herein we present a satellite-based lake surface water temperature (LSWT) data set for European water bodies in or near the Alps based on the extensive AVHRR 1 km data record (1989–2013) of the Remote Sensing Research Group at the University of Bern. It has been compiled out of AVHRR/2 (NOAA-07, -09, -11, -14) and AVHRR/3 (NOAA-16, -17, -18, -19 and MetOp-A) data. The high accuracy needed for climate related studies requires careful pre-processing and consideration of the atmospheric state. The LSWT retrieval is based on a simulation-based scheme making use of the Radiative Transfer for TOVS (RTTOV) Version 10 together with ERA-interim reanalysis data from the European Centre for Medium-range Weather Forecasts. The resulting LSWTs were extensively compared with in situ measurements from lakes with various sizes between 14 and 580 km2 and the resulting biases and RMSEs were found to be within the range of −0.5 to 0.6 K and 1.0 to 1.6 K, respectively. The upper limits of the reported errors could be rather attributed to uncertainties in the data comparison between in situ and satellite observations than inaccuracies of the satellite retrieval. An inter-comparison with the standard Moderate-resolution Imaging Spectroradiometer (MODIS) Land Surface Temperature product exhibits RMSEs and biases in the range of 0.6 to 0.9 and −0.5 to 0.2 K, respectively. The cross-platform consistency of the retrieval was found to be within ~ 0.3 K. For one lake, the satellite-derived trend was compared with the trend of in situ measurements and both were found to be similar. Thus, orbital drift is not causing artificial temperature trends in the data set. A comparison with LSWT derived through global sea surface temperature (SST) algorithms shows lower RMSEs and biases for the simulation-based approach. A running project will apply the developed method to retrieve LSWT for all of Europe to derive the climate signal of the last 30 years. The data are available at doi:10.1594/PANGAEA.831007.

A new model construction by making a detour via intuitionistic theories I: Operational set theory without choice is Π1-equivalent to KP

We introduce a version of operational set theory, OST−, without a choice operation, which has a machinery for Δ0Δ0 separation based on truth functions and the separation operator, and a new kind of applicative set theory, so-called weak explicit set theory WEST, based on Gödel operations. We show that both the theories and Kripke–Platek set theory KPKP with infinity are pairwise Π1Π1 equivalent. We also show analogous assertions for subtheories with ∈-induction restricted in various ways and for supertheories extended by powerset, beta, limit and Mahlo operations. Whereas the upper bound is given by a refinement of inductive definition in KPKP, the lower bound is by a combination, in a specific way, of realisability, (intuitionistic) forcing and negative interpretations. Thus, despite interpretability between classical theories, we make “a detour via intuitionistic theories”. The combined interpretation, seen as a model construction in the sense of Visser's miniature model theory, is a new way of construction for classical theories and could be said the third kind of model construction ever used which is non-trivial on the logical connective level, after generic extension à la Cohen and Krivine's classical realisability model.

Invisible social control as predictor of daily negative affect and smoking after a self-set quit date

The dual-effects model of social control proposes that social control leads to increased psychological distress but also to better health practices. However, findings are inconsistent, and recent research suggests that the most effective control is unnoticed by the receiver (i. e., invisible). Yet, investigations of the influence of invisible control on daily negative affect and smoking have been limited. Using daily diaries, we investigated how invisible social control was associated with negative affect and smoking. Overall, 100 smokers (72.0 % men, age M = 40.48, SD = 9.82) and their nonsmoking partners completed electronic diaries from a self-set quit date for 22 consecutive days, reporting received and provided social control, negative affect, and daily smoking. We found in multilevel analyses of the within-person process that on days with higher-than-average invisible control, smokers reported more negative affect and fewer cigarettes smoked. Findings are in line with the assumptions of the dual-effects model of social control: Invisible social control increased daily negative affect and simultaneously reduced smoking at the within-person level.

Daily negative affect and smoking after a self-set quit attempt: The role of dyadic invisible social support in a daily diary study

Objectives Social support receipt from one's partner is assumed to be beneficial for successful smoking cessation. However, support receipt can have costs. Recent research suggests that the most effective support is unnoticed by the receiver (i.e., invisible). Therefore, this study examined the association between everyday levels of dyadic invisible emotional and instrumental support, daily negative affect, and daily smoking after a self-set quit attempt in smoker–non-smoker couples. Methods Overall, 100 smokers (72.0% men, mean age M = 40.48, SD = 9.82) and their non-smoking partners completed electronic diaries from a self-set quit date on for 22 consecutive days, reporting daily invisible emotional and instrumental social support, daily negative affect, and daily smoking. Results Same-day multilevel analyses showed that at the between-person level, higher individual mean levels of invisible emotional and instrumental support were associated with less daily negative affect. In contrast to our assumption, more receipt of invisible emotional and instrumental support was related to more daily cigarettes smoked. Conclusions The findings are in line with previous results, indicating invisible support to have beneficial relations with affect. However, results emphasize the need for further prospective daily diary approaches for understanding the dynamics of invisible support on smoking cessation.

Examining invisible social control as predictor of daily smoking and negative affect after a self-set quit date

Objectives: The dual-effects model of social control proposes that social control leads to better health practices, but also arouses psychological distress. However, findings are inconsistent in relation to health behavior and psychological distress. Recent research suggests that the most effective control is unnoticed by the receiver (i.e., invisible). There is some evidence that invisible social control is beneficial for positive and negative affective reactions. Yet, investigations of the influence of invisible social control on daily smoking and distress have been limited. In daily diaries, we investigated how invisible social control is associated with number of cigarettes smoked and negative affect on a daily basis. Methods: Overall, 99 smokers (72.0% men, mean age M = 40.48, SD = 9.82) and their non-smoking partners completed electronic diaries from a self-set quit date for 22 consecutive days within the hour before going to bed, reporting received and provided social control, daily number of cigarettes smoked, and negative affect. Results: Multilevel analyses indicated that between-person levels of invisible social control were associated with lower negative affect, whereas they were unrelated to number of cigarettes smoked. On days with higher-than-average invisible social control, smokers reported less cigarettes smoked and more negative affect. Conclusions: Between-person level findings indicate that invisible social control can be beneficial for negative affect. However, findings on the within-person level are in line with the assumptions of the dual-effects model of social control: Invisible social control reduced daily smoking and simultaneously increased daily negative affect within person.

Institutions and coalitions in policy processes: a cross-sectoral comparison

Actors with joint beliefs in a decision-making process form coalitions in order to translate their goals into policy. Yet, coalitions are not formed in an institutional void, but rather institutions confer opportunities and constraints to actors. This paper studies the institutional conditions under which either coalition structures with a dominant coalition or with competing coalitions emerge. It takes into account three conditions, i.e. the degree of federalism of a project, its degree of Europeanisation and the openness of the pre-parliamentary phase of the decision-making process. The cross-sectoral comparison includes the 11 most important decision-making processes in Switzerland between 2001 and 2006 with a fuzzy-set Qualitative Comparative Analysis. Results suggest that Europeanisation or an open pre-parliamentary phase lead to a dominant coalition, whereas only a specific combination of all three conditions is able to explain a structure with competing coalitions.

Two variants in the KIT gene as candidate causative mutations for a dominant white and a white spotting phenotype in the donkey.

White spotting phenotypes have been intensively studied in horses, and although similar phenotypes occur in the donkey, little is known about the molecular genetics underlying these patterns in donkeys. White spotting in donkeys can range from only a few white areas to almost complete depigmentation and is characterised by a loss of pigmentation usually progressing from a white spot in the hip area. Completely white-born donkeys are rare, and the phenotype is characterised by the complete absence of pigment resulting in pink skin and a white coat. A dominant mode of inheritance has been demonstrated for spotting in donkeys. Although the mode of inheritance for the completely white phenotype in donkeys is not clear, the phenotype shows similarities to dominant white in horses. As variants in the KIT gene are known to cause a range of white phenotypes in the horse, we investigated the KIT gene as a potential candidate gene for two phenotypes in the donkey, white spotting and white. A mutation analysis of all 21 KIT exons identified a missense variant in exon 4 (c.662A>C; p.Tyr221Ser) present only in a white-born donkey. A second variant affecting a splice donor site (c.1978+2T>A) was found exclusively in donkeys with white spotting. Both variants were absent in 24 solid-coloured controls. To the authors' knowledge, this is the first study investigating genetic mechanisms underlying white phenotypes in donkeys. Our results suggest that two independent KIT alleles are probably responsible for white spotting and white in donkeys.

Study of heavy-flavor quarks produced in association with top-quark pairs at s √ =7 TeV using the ATLAS detector

Using a sample of dilepton top-quark pair (tt ¯ ) candidate events, a study is performed of the production of top-quark pairs together with heavy-flavor (HF) quarks, the sum of tt ¯ +b+X and tt ¯ +c+X , collectively referred to as tt ¯  + HF . The data set used corresponds to an integrated luminosity of 4.7  fb −1 of proton-proton collisions at a center-of-mass energy of 7 TeV recorded by the ATLAS detector at the CERN Large Hadron Collider. The presence of additional HF (b or c ) quarks in the tt ¯ sample is inferred by looking for events with at least three b -tagged jets, where two are attributed to the b quarks from the tt ¯ decays and the third to additional HF production. The dominant background to tt ¯  + HF in this sample is tt ¯ +jet events in which a light-flavor jet is misidentified as a heavy-flavor jet. To determine the heavy- and light-flavor content of the additional b -tagged jets, a fit to the vertex mass distribution of b -tagged jets in the sample is performed. The result of the fit shows that 79 ± 14 (stat) ± 22 (syst) of the 105 selected extra b -tagged jets originate from HF quarks, 3 standard deviations away from the hypothesis of zero tt ¯  + HF production. The result for extra HF production is quoted as a ratio (R HF ) of the cross section for tt ¯  + HF production to the cross section for tt ¯ production with at least one additional jet. Both cross sections are measured in a fiducial kinematic region within the ATLAS acceptance. R HF is measured to be [6.2±1.1(stat)±1.8(syst)]% for jets with p T >25  GeV and |η|<2.5 , in agreement with the expectations from Monte Carlo generators.