"Boring formal methods" or "Sherlock Holmes deduction methods"?

This paper provides an overview of common challenges in teaching of logic and formal methods to Computer Science and IT students. We discuss our experiences from the course IN3050: Applied Logic in Engineering, introduced as a "logic for everybody" elective course at at TU Munich, Germany, to engage pupils studying Computer Science, IT and engineering subjects on Bachelor and Master levels. Our goal was to overcome the bias that logic and formal methods are not only very complicated but also very boring to study and to apply. In this paper, we present the core structure of the course, provide examples of exercises and evaluate the course based on the students' surveys.Comment: Preprint. Accepted to the Software Technologies: Applications and Foundations (STAF 2016). Final version published by Springer International Publishing AG. arXiv admin note: substantial text overlap with arXiv:1602.0517

The effectiveness of public health interventions to reduce the health impact of climate change:a systematic review of systematic reviews

Climate change is likely to be one of the most important threats to public health in the coming years. Yet despite the large number of papers considering the health impact of climate change, few have considered what public health interventions may be of most value in reducing the disease burden. We aimed to evaluate the effectiveness of public health interventions to reduce the disease burden of high priority climate sensitive diseases

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Membranes by the Numbers

Many of the most important processes in cells take place on and across membranes. With the rise of an impressive array of powerful quantitative methods for characterizing these membranes, it is an opportune time to reflect on the structure and function of membranes from the point of view of biological numeracy. To that end, in this article, I review the quantitative parameters that characterize the mechanical, electrical and transport properties of membranes and carry out a number of corresponding order of magnitude estimates that help us understand the values of those parameters.Comment: 27 pages, 12 figure

Are attitudes towards medication adherence associated with medication adherence behaviours among patients with psychosis? A systematic review and meta analysis

Background Studies have shown patient attitudes to be an important predictor for health related behaviours including medication adherence. It is less clear whether patient attitudes are also associated with medication adherence among patients with psychoses. Method We conducted a systematic review and meta analysis of the data of studies that tested the association of attitude measures with medication adherence among patients with psychoses. 14 studies conducted between 1980 and 2010 were included. Results Results show a small to moderate mean weighted effect size (r + = 0.25 and 0.26 for Pearson and Spearman correlations, respectively). Conclusions Theory based interventions that target potentially modifiable attitude components are needed to assess the relationship between positive patient attitudes and adherence behaviours among patients with psychoses

Light interception principally drives the understory response to boxelder invasion in riparian forests

Since several decades, American boxelder (Acer negundo) is replacing white willow (Salix alba) riparian forests along southern European rivers. This study aims to evaluate the consequences of boxelder invasion on understory community in riparian areas. We determined the understory species richness, composition and biomass in boxelder and white willow stands located in three riparian forests, representative of three rivers with distinct hydrological regimes. We investigated correlation of these variables to soil moisture and particle size, main soil nutrient stocks, potential nitrification and denitrification, tree canopy cover and photosynthetic active radiation (PAR) at the ground level. A greenhouse experiment was then conducted to identify the causal factors responsible for changes in the understory. The effect of soil type, PAR level and water level on the growth and the biomass production of Urtica dioica were examined. A lower plant species richness and biomass, and a modification of community composition were observed for boxelder understory in all sites, regardless of their environmental characteristics. The strongest modification that follows boxelder invasion was the decline in U. dioica, the dominant species of the white willow forest understory. These differences were mainly correlated with a lower incident PAR under boxelder canopy. The greenhouse experiment identified PAR level as the main factor responsible for the changes in U. dioica stem number and biomass. Our results indicate that adult boxelder acts as an ecosystem engineer that decreases light availability. The opportunistic invasion by boxelder leads to important understory changes, which could alter riparian ecosystem functioning

Fibre Distribution and the Process-Property Dilemma

The options for the fibre reinforcement of polymer matrix composites cover a range from short-fibre chopped strand mat, through woven fabric to unidirectional pre-impregnated (prepreg) reinforcements. The modelling of such materials may be simplified by assumptions such as perfect regular packing of fibres and the total absence of fibre waviness. However, these and other features such as the crimp or waviness in woven fabrics make real materials more complex than the simplified models. Clustering of fibres creates fibre-rich and resin-rich volumes (FRV and RRV respectively) in the composites. Prior to impregnation, large RRV will be pore-space that can expedite the flow of resin in liquid composite moulding processes (especially resin transfer moulding (RTM) and resin infusion under flexible tooling (RIFT). In the composite, the clustering of fibres tends to reduce the mechanical properties. The use of image processing and analysis can permit micro-/meso-structural characterisation which may correlate to the respective properties. This chapter considers the quantification of microstructure images in the context of the process-property dilemma for woven carbon-fibre reinforced composites with the aim of increasing understanding of the balance between processability and mechanical performance

How and when plume zonation appeared during the 132 Myr evolution of the Tristan Hotspot

Increasingly, spatial geochemical zonation, present as geographically distinct, subparallel trends, is observed along hotspot tracks, such as Hawaii and the Galapagos. The origin of this zonation is currently unclear. Recently zonation was found along the last B70 Myr of the Tristan-Gough hotspot track. Here we present new Sr–Nd–Pb–Hf isotope data from the older parts of this hotspot track (Walvis Ridge and Rio Grande Rise) and re-evaluate published data from the Etendeka and Parana flood basalts erupted at the initiation of the hotspot track. We show that only the enriched Gough, but not the less-enriched Tristan, component is present in the earlier (70–132 Ma) history of the hotspot. Here we present a model that can explain the temporal evolution and origin of plume zonation for both the Tristan-Gough and Hawaiian hotspots, two end member types of zoned plumes, through processes taking place in the plume sources at the base of the lower mantle

Total synthesis of Escherichia coli with a recoded genome

Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA