Predictions from a stochastic polymer model for the MinDE dynamics in E.coli

The spatiotemporal oscillations of the Min proteins in the bacterium Escherichia coli play an important role in cell division. A number of different models have been proposed to explain the dynamics from the underlying biochemistry. Here, we extend a previously described discrete polymer model from a deterministic to a stochastic formulation. We express the stochastic evolution of the oscillatory system as a map from the probability distribution of maximum polymer length in one period of the oscillation to the probability distribution of maximum polymer length half a period later and solve for the fixed point of the map with a combined analytical and numerical technique. This solution gives a theoretical prediction of the distributions of both lengths of the polar MinD zones and periods of oscillations -- both of which are experimentally measurable. The model provides an interesting example of a stochastic hybrid system that is, in some limits, analytically tractable.Comment: 16 page

Robust safety of timed automata

Timed automata are governed by an idealized semantics that assumes a perfectly precise behavior of the clocks. The traditional semantics is not robust because the slightest perturbation in the timing of actions may lead to completely different behaviors of the automaton. Following several recent works, we consider a relaxation of this semantics, in which guards on transitions are widened byΔ>0 and clocks can drift byε>0. The relaxed semantics encompasses the imprecisions that are inevitably present in an implementation of a timed automaton, due to the finite precision of digital clocks. We solve the safety verification problem for this robust semantics: given a timed automaton and a set of bad states, our algorithm decides if there exist positive values for the parametersΔ andε such that the timed automaton never enters the bad states under the relaxed semantic

Analysis of Probabilistic Basic Parallel Processes

Basic Parallel Processes (BPPs) are a well-known subclass of Petri Nets. They are the simplest common model of concurrent programs that allows unbounded spawning of processes. In the probabilistic version of BPPs, every process generates other processes according to a probability distribution. We study the decidability and complexity of fundamental qualitative problems over probabilistic BPPs -- in particular reachability with probability 1 of different classes of target sets (e.g. upward-closed sets). Our results concern both the Markov-chain model, where processes are scheduled randomly, and the MDP model, where processes are picked by a scheduler.Comment: This is the technical report for a FoSSaCS'14 pape

Current use and legal status of crop protection inputs

This deliverable presents the results of the survey carried out in the frame of Tasks 3.1. and Task 5.1 in the Horizon 2020 Project Organic PLUS. A common table/questionnaire for both tasks was used in order to map the use of contentious inputs linked to plant protection (mainly Cu, S and mineral oils), and the use of peat, plastic and fertilisers used in growing, in 10 countries participating in Organic-PLUS (Denmark, France, Germany, Greece, Italy, Norway, Poland, Spain, Turkey and UK). The survey was carried out mainly by interviewing one to three experienced advisors per crop, asking them to fill in a table describing a typical organic production of the relevant crop, emphasising the use of various inputs. In some cases the survey was based on already available data of the Organic-PLUS partner while an online questionnaire was also developed and used (e.g. CUT for Poland). The collected raw material is presented in a separeate report, the D3.1 Annex I. Statistical data concerning the organic farming in the countries under study are also presented. The deliverable includes also documentation of current policies and legal status of the use of contentious plant protection products in organic farming with emphasis on potato, tomato, citrus and olive crops. Copper-based products are used in plant protection as bactericides and fungicides. Copper is the only active ingredient with a strong antimicrobial effect and a wide range of action that is approved for use in organic farming particularly for grape, potato and apple crops. Recently, the demonstrated adverse effects on the environment (on soil organisms and auxiliary species) have led to a reduction in its use in several European countries. The current regulation in EU related to the use of copper in organic production sets the limit of up to 6 kg copper per ha per year. For perennial crops, Member States may, by derogation, provide that the 6 kg copper limit can be exceeded in a given year provided that the average quantity actually used over a 5-year period consisting of that year and of the four preceding years does not exceed 6 kg. Among the investigated crops (mainly citrus, olive, tomato, potato, strawberry), large amounts of copper are used mainly by Mediterranean growers in citrus, olive and potato. For crops like citrus and olives the limit of 6 kg per ha and per year may not be always respected. Tomato producers apply high amounts of copper in winter crops (greenhouses). In the case of Norway, the use of copper and mineral oil were not permitted for organic growing until March 2017, when the EC regulations were implemented. However, the national limit for copper in Norway is 4 kg per ha and year, thus it is easier for these growers to comply with lower limits of copper use than those in EU. In Denmark, copper is not used in organic agriculture at all because national authorities have not (yet) been asked to approve any commercial product containing copper, or they have not approved it. Many alternatives to copper are under development, but few are already available on the market, and fewer still are currently used by growers to a substantial extent. Alternatives with a low concentration of copper ion are demonstrating good levels of efficacy. Possibly, a reduction of the concentration of copper, together with more efficient formulations, could reduce the presence of copper in the crops (and soils). Nevertheless, abandoning copper cannot be easily achieved through a simple substitution strategy (for instance, replacing copper by biocontrol products); it requires a more or less profound reconstruction of the crop production system, including changing cultivars (in favour of resistant ones), developing prophylaxis and sanitation measures, adjusting fertilisation, etc. This requires an integrative approach, which is still under-developed. Regarding sulphur, this substance is very common for organic vegetable growers, especially for greenhouse growers. The uses of sulphur can move from 10 to 100 kg/ha/year depending on the production system and the incidence of pests. However, it is seldom considered that the use of sulphur is problematic, except as a main component of sulphites in wine production. It is a sort of universal phytosanitary product: repellent to pests, killer of mites, and effective against powdery mildews. However, it is not selective, and it has harmful effects on beneficial arthropods. So, the use of sulphur can limit biological control. Alternatives to sulphur are not currently applied mainly for economic reasons since sulphur is cheap compared to other compounds. Moreover, since sulphur can be an alternative to mineral oil, its use is not easily reduced. Mineral oils are applied to exclusively control insects and mites in citrus and olive orchards and occasionally in tomato. There are not many data available for the use of mineral oils but from the data presented it was found that in some cases (e.g. in citrus) they are considered as the main contentious input. The wide spectrum of this substance makes it more versatile than other alternatives. In other cases, mineral oils are of minor use, and can easily be replaced by organic oils

Dynamic compartmentalization of bacteria: accurate division in E. coli

Positioning of the midcell division plane within the bacterium E. coli is controlled by the min system of proteins: MinC, MinD and MinE. These proteins coherently oscillate from end to end of the bacterium. We present a reaction--diffusion model describing the diffusion of min proteins along the bacterium and their transfer between the cytoplasmic membrane and cytoplasm. Our model spontaneously generates protein oscillations in good agreement with experiments. We explore the oscillation stability, frequency and wavelength as a function of protein concentration and bacterial length.Comment: 4 pages, 4 figures, Latex2e, Revtex

Learning Probabilistic Temporal Safety Properties from Examples in Relational Domains

We propose a framework for learning a fragment of probabilistic computation tree logic (pCTL) formulae from a set of states that are labeled as safe or unsafe. We work in a relational setting and combine ideas from relational Markov Decision Processes with pCTL model-checking. More specifically, we assume that there is an unknown relational pCTL target formula that is satisfied by only safe states, and has a horizon of maximum $k$ steps and a threshold probability $\alpha$. The task then consists of learning this unknown formula from states that are labeled as safe or unsafe by a domain expert. We apply principles of relational learning to induce a pCTL formula that is satisfied by all safe states and none of the unsafe ones. This formula can then be used as a safety specification for this domain, so that the system can avoid getting into dangerous situations in future. Following relational learning principles, we introduce a candidate formula generation process, as well as a method for deciding which candidate formula is a satisfactory specification for the given labeled states. The cases where the expert knows and does not know the system policy are treated, however, much of the learning process is the same for both cases. We evaluate our approach on a synthetic relational domain.Comment: 25 pages, 3 figures, 5 tables, 2 algorithms, preprin

Current use of peat, plastic and fertiliser inputs in organic horticultural and arable crops across Europe

The use of contentious inputs linked to plant protection, and the use of peat, plastic and fertilisers used in growing have been mapped in selected organically produced crops in 10 countries across Europe. This report refers the output of this mapping. It shows that organic production has not come very far to phase out peat or plastic. The consumption of these materials seems to be quite comparable to non-organic production systems.The main utilisation of peat is for production of young plants (transplants). Most organic growers purchase plants e.g. for citrus, olives and grafted tomatoes and the growing media has usually a high content of peat. Vegetable transplants are also commonly produced by special growers. Peat is also used for casing layers for organic mushrooms, and as a potting media for aromatic plants. For plastic, the use is extensive for mulching and to protect crops against frost, less often for insect protection. The use of plastic materials to attach young plants to sticks etc., and to protect grafting wounds in young trees, was also observed. While not big in volume, this use may contribute to micro-plastic waste. Plastic is also very common for solarisation and for tunnels and greenhouses, especially in southern countries. In northern countries,greenhouses are usually made of other materials than plastic. Further research within the Organic PLUS project will reveal farmers and growers who have worked with promising alternatives and develop these further. For applied fertilisers, which in our context need to be approved for use in certified organic production, the application of commercial products seems to be higher in some countries, e.g. Greece, whereas other countries seem to use much less. This may be explained by economic conditions of the growers, cultural differences, by the extent of organic production and development of a market for such products, by the availability of national fertiliser Companies and by other factors. Information about raw materials used to produce these fertilisers is commonly not readily available but may sometimes be found under information about the company’s history. These website sections also reveal that fusions of fertiliser Companies occur rapidly. Many fertiliser products seem to be derived from residuals from sugar or starch production. Horn grid, meat and bone meal, blood meal and feather meals are well known organic fertilisers but were not so much observed in this study. Instead, we observed that animal hides are an important raw material for organic N fertilisers. Seaweed products are quite common, whereas fish-based products were only mentioned from UK. Non-organic manure (from conventional farms) is used in all countries, commonly as pelletised dry poultry manure

Parity-Violating Electron Scattering from the Pion-Correlated Relativistic Fermi Gas

Parity-violating quasielastic electron scattering is studied within the context of the relativistic Fermi gas and its extensions to include the effects of pionic correlations and meson-exchange currents. The work builds on previous studies using the same model; here the part of the parity-violating asymmetry that contains axial-vector hadronic currents is developed in detail using those previous studies and a link is provided to the transverse vector-isovector response. Various integrated observables are constructed from the differential asymmetry. These include an asymmetry averaged over the quasielastic peak, as well as the difference of the asymmetry integrated to the left and right of the peak -- the latter is shown to be optimal for bringing out the nature of the pionic correlations. Special weighted integrals involving the differential asymmetry and electromagnetic cross section, based on the concepts of y-scaling and sum rules, are constructed and shown to be suited to studies of the single-nucleon form factor content in the problem, in particular, to determinations of the isovector/axial-vector and electric strangeness form factors. Comparisons are also made with recent predictions made on the basis of relativistic mean-field theory.Comment: 28 pages, LATeX, 13 figures (tar-compressed postscript files, available from the authors), MIT preprint CTP#222

A novel technique to characterize the spatial intra-pixel sensitivity variations in a CMOS image sensor

To understand the scientific imaging capability, one must characterize the intra-pixel sensitivity variation (IPSV) of the CMOS image sensor. Extracting an IPSV map contributes to an improved detector calibration that allows to eliminate some of the uncertainty in the spatial response of the system. This paper reports the measurement of the sub-pixel sensitivity variation and the extraction of the 2D IPSV map of a front-side illuminated CMOS image sensor with a pixel pitch of 6 {\mu}m. Our optical measurement setup focuses a collimated beam onto the imaging surface with a microscope objective. The spot was scanned in a raster over a single pixel and its immediate neighbors in order to probe its response at selected (sub-pixel) positions. In this work we introduced a novel technique to extract the IPSV map by fitting (forward modeling) the measured data to a mathematical model of the image, generated in a single pixel that allows for a spatially varying sensitivity