Program transformations using temporal logic side conditions

This paper describes an approach to program optimisation based on transformations, where temporal logic is used to specify side conditions, and strategies are created which expand the repertoire of transformations and provide a suitable level of abstraction. We demonstrate the power of this approach by developing a set of optimisations using our transformation language and showing how the transformations can be converted into a form which makes it easier to apply them, while maintaining trust in the resulting optimising steps. The approach is illustrated through a transformational case study where we apply several optimisations to a small program

Inducible and constitutive promoters for genetic systems in Sulfolobus acidocaldarius

Central to genetic work in any organism are the availability of a range of inducible and constitutive promoters. In this work we studied several promoters for use in the hyperthermophilic archaeon Sulfolobus acidocaldarius. The promoters were tested with the aid of an E. coli–Sulfolobus shuttle vector in reporter gene experiments. As the most suitable inducible promoter a maltose inducible promoter was identified. It comprises 266 bp of the sequence upstream of the gene coding for the maltose/maltotriose binding protein (mbp, Saci_1165). Induction is feasible with either maltose or dextrin at concentrations of 0.2–0.4%. The highest increase in expression (up to 17-fold) was observed in late exponential and stationary phase around 30–50 h after addition of dextrin. Whereas in the presence of glucose and xylose higher basal activity and reduced inducibility with maltose is observed, sucrose can be used in the growth medium additionally without affecting the basal activity or the inducibility. The minimal promoter region necessary could be narrowed down to 169 bp of the upstream sequence. The ABCE1 protein from S. solfataricus was successfully expressed under control of the inducible promoter with the shuttle vector pC and purified from the S. acidocaldarius culture with a yield of about 1 mg L−1 culture. In addition we also determined the promoter strength of several constitutive promoters

How to survey displaced workers in Switzerland ? Sources of bias and ways around them

Studying career outcomes after job loss is challenging because individually displaced worker form a self-selected group. Indeed, the same factors causing the workers to lose their jobs, such as lack of motivation, may also reduce their re-employment prospects. Using data from plant closures where all workers were displaced irrespective of their individual characteristics offers a way around this selection bias. There is no systematic data collection on workers displaced by plant closure in Switzerland. Accordingly, we conducted our own survey on 1200 manufacturing workers who had lost their job 2 years earlier. The analysis of observational data gives rise to a set of methodological challenges, in particular nonresponse bias. Our survey addressed this issue by mixing data collection modes and repeating contact attempts. In addition, we combined the survey data with data from the public unemployment register to examine the extent of nonresponse bias. Our analysis suggests that some of our adjustments helped to reduce bias. Repeated contact attempts increased the response rate, but did not reduce nonresponse bias. In contrast, using telephone interviews in addition to paper questionnaires helped to substantially improve the participation of typically underrepresented subgroups. However, the survey respondents still differ from nonrespondents in terms of age, education and occupation. Interestingly, these differences have no significant impact on the substantial conclusion about displaced workers' re-employment prospects

Magnetic properties and revisited exchange integrals of the frustrated chain cuprate PbCuSO4_4(OH)2_2 - linarite

We present a detailed study in the paramagnetic regime of the frustrated $s$ = 1/2 spin-compound linarite, PbCuSO$_4$(OH)$_2$, with competing ferromagnetic nearest-neighbor and antiferromagnetic next-nearest-neighbor exchange interactions. Our data reveal highly anisotropic values for the saturation field along the crystallographic main directions, with $\sim$ 7.6, $\sim$ 10.5 and $\sim$ 8.5\,T for the $a$, $b$, and $c$ axes, respectively. In the paramagnetic regime, this behavior is explained mainly by the anisotropy of the \textit{g}-factor but leaving room for an easy-axis exchange anisotropy. Within the isotropic $J_1$-$J_2$ spin model our experimental data are described by various theoretical approaches yielding values for the exchange interactions $J_1$ $\sim$ -100\,K and $J_2$ $\sim$ 36\,K. These main intrachain exchange integrals are significantly larger as compared to the values derived in two previous studies in the literature and shift the frustration ratio $\alpha = J_2/|J_1|$ $\approx$ 0.36 of linarite closer to the 1D critical point at 0.25. Electron spin resonance (ESR) and nuclear magnetic resonance (NMR) measurements further prove that the static susceptibility is dominated by the intrinsic spin susceptibility. The Knight shift as well as the broadening of the linewidth in ESR and NMR at elevated temperatures indicate a highly frustrated system with the onset of magnetic correlations far above the magnetic ordering temperature $T_\mathrm{N}$ = 2.75(5)\,K, in agreement with the calculated exchange constants.Comment: 18 pages, 18 figure

Climate Change and invasibility of the Antarctic benthos

Benthic communities living in shallow-shelf habitats in Antarctica (<100-m depth) are archaic in their structure and function. Modern predators, including fast-moving, durophagous (skeleton-crushing) bony fish, sharks, and crabs, are rare or absent; slow-moving invertebrates are the top predators; and epifaunal suspension feeders dominate many soft substratum communities. Cooling temperatures beginning in the late Eocene excluded durophagous predators, ultimately resulting in the endemic living fauna and its unique food-web structure. Although the Southern Ocean is oceanographically isolated, the barriers to biological invasion are primarily physiological rather than geographic. Cold temperatures impose limits to performance that exclude modern predators. Global warming is now removing those physiological barriers, and crabs are reinvading Antarctica. As sea temperatures continue to rise, the invasion of durophagous predators will modernize the shelf benthos and erode the indigenous character of marine life in Antarctica

Upgraded photon calorimeter with integrating readout for Hall A Compton Polarimeter at Jefferson Lab

The photon arm of the Compton polarimeter in Hall A of Jefferson Lab has been upgraded to allow for electron beam polarization measurements with better than 1% accuracy. The data acquisition system (DAQ) now includes an integrating mode, which eliminates several systematic uncertainties inherent in the original counting-DAQ setup. The photon calorimeter has been replaced with a Ce-doped GSO crystal, which has a bright output and fast response, and works well for measurements using the new integrating method at electron beam energies from 1 to 6 GeV.Comment: 16 pages, 15 figure

Isothermal folding of G-quadruplexes

Thermodynamic studies of G-quadruplex stability are an essential complement to structures obtained by NMR or x-ray crystallography. An understanding of the energetics of quadruplex folding provides a necessary foundation for the physical interpretation of quadruplex formation and reactivity. While thermal denaturation methods are most commonly used to evaluate quadruplex stability, it is also possible to study folding using isothermal titration methods. G-quadruplex folding is tightly coupled to specific cation binding. We describe here protocols for monitoring the cation-driven quadruplex folding transition using circular dichroism or absorbance, and for determination of the distribution of free and bound cation using a fluorescence indicator. Together these approaches provide insight into quadruplex folding at constant temperature, and characterize the linkage between cation binding and folding

Software for continuous game experiments

ConG is software for conducting economic experiments in continuous and discrete time. It allows experimenters with limited programming experience to create a variety of strategic environments featuring rich visual feedback in continuous time and over continuous action spaces, as well as in discrete time or over discrete action spaces. Simple, easily edited input files give the experimenter considerable flexibility in specifying the strategic environment and visual feedback. Source code is modular and allows researchers with programming skills to create novel strategic environments and displays

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution