Parameter Optimisation of a Virtual Synchronous Machine in a Microgrid

Parameters of a virtual synchronous machine in a small microgrid are optimised. The dynamical behaviour of the system is simulated after a perturbation, where the system needs to return to its steady state. The cost functional evaluates the system behaviour for different parameters. This functional is minimised by Parallel Tempering. Two perturbation scenarios are investigated and the resulting optimal parameters agree with analytical predictions. Dependent on the focus of the optimisation different optima are obtained for each perturbation scenario. During the transient the system leaves the allowed voltage and frequency bands only for a short time if the perturbation is within a certain range.Comment: 17 pages, 5 figure

PeTTSy: a computational tool for perturbation analysis of complex systems biology models

Abstract Background Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Results Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. Conclusions PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and signalling systems. It allows for simulation and analysis of models under a variety of environmental conditions and for experimental optimisation of complex combined experiments. With its unique set of tools it makes a valuable addition to the current library of sensitivity analysis toolboxes. We believe that this software will be of great use to the wider biological, systems biology and modelling communities

PeTTSy : a computational tool for perturbation analysis of complex systems biology models

Background Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Results Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. Conclusions PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and signalling systems. It allows for simulation and analysis of models under a variety of environmental conditions and for experimental optimisation of complex combined experiments. With its unique set of tools it makes a valuable addition to the current library of sensitivity analysis toolboxes. We believe that this software will be of great use to the wider biological, systems biology and modelling communities

Phytochromes function as thermosensors in Arabidopsis

Plants are responsive to temperature, and can distinguish differences of 1ºC. In Arabidopsis, warmer temperature accelerates flowering and increases elongation growth hermomorphogenesis). The mechanisms of temperature perception are however largely unknown. We describe a major thermosensory role for the phytochromes (red light receptors) during the night. Phytochrome null plants display a constitutive warm temperature response, and consistent with this, we show in this background that the warm temperature transcriptome becomes de-repressed at low temperatures. We have discovered phytochrome B (phyB) directly associates with the promoters of key target genes in a temperature dependent manner. The rate of phyB inactivation is proportional to temperature in the dark, enabling phytochromes to function as thermal timers, integrating temperature information over the course of the night

Temperature-sensitive version of P2010 Arabidopsis clock model by Mirela Domijan, from Gould et al. 2013.

Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms. Molecular Systems Biology 9 Article number: 650 doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperaturesGould, Ugarte, Domijan et al.10.1038/msb.2013.

Okratoksin A i omjer sfinganina i sfingozina u urinu stanovnika s područja endemske nefropatije u Hrvatskoj

The most plausible theory of the aetiology of endemic nephropathy links it with exposure to nephrotoxic mycotoxin ochratoxin A (OTA). In this study, the concentration of OTA and sphinganine/sphingosine (Sa/So) ratio, the biomarker of another nephrotoxic mycotoxin fumonisin B1 exposure, were analysed in 45 human urine samples collected in the endemic village of Kaniža in Croatia and in 18 samples from control village. Samples were collected twice from the same persons in 2000 and 2005. In both years the frequency of OTA-positive samples was higher in Kaniža (43 % and 18 %, respectively) than in the control village (28 % and 6 %, respectively). OTA concentrations in samples collected in Kaniža were higher in 2000 than in 2005 (p1 at the same time, while in Kaniža four such samples were collected in 2000 and one in 2005.Najprihvatljivija teorija o etiologiji endemske nefropatije povezuje njezin nastanak s izloženošću nefrotoksičnim mikotoksinima. Dok se izloženost mikotoksinu okratoksinu A (OTA) može dokazati njegovim nalazom u biološkim uzorcima kao što su krv i urin, vrlo kratko zadržavanje fumonizina B1 (FB1) u organizmu to onemogućava. Na pokusnim je životinjama nađeno da je porast omjera koncentracija sfi ngolipida sfi nganina i sfi ngozina (Sa/So) biološki pokazatelj izloženosti tom mikotoksinu. U ovom istraživanju mjerena je koncentracija OTA i omjer koncentracija Sa/So u urinu 45 stanovnika u endemskom selu Kaniža i 18 stanovnika u kontrolnom selu. Uzorci urina skupljeni su od istih osoba 2000. i 2005. godine. U obje godine učestalost uzoraka koji su sadržavali OTA bila je veća u Kaniži (43 % i 18 %) negoli u kontrolnom selu (28 % i 6 %). Koncentracija OTA također je bila viša u urinima skupljenim u Kaniži negoli u kontrolnom selu. Koncentracija OTA u uzorcima skupljenim u Kaniži 2000. bila je viša nego u uzorcima iz 2005. (p<0.005). Iako je u urinima iz obje godine omjer koncentracija Sa/So bio viši u Kaniži negoli u kontrolnom selu, razlika nije bila statistički značajna. Nije nađen nijedan uzorak skupljen u kontrolnom selu koji bi istodobno sadržavao mjerljivu koncentraciju OTA i omjer Sa/So veći od jedan. Za razliku od uzoraka iz kontrolnog sela, četiri uzorka skupljena u Kaniži u 2000. godini i jedan uzorak u 2005. godini upućivali su na istodobnu izloženost ovim mikotoksinima

Određivanje aflatoksina, okratoksina A, fumonizina i zearalenona u žitaricama i krmivu primjenom kompetetivnoga direktnog imunoenzimatskog testa (CD-ELISA) i tankoslojne kromatografije (TLC)

Aspergillus, Penicillium, and Fusarium species frequently contaminate crops. For this reason mycotoxins such as afl atoxins (AFs), ochratoxin A (OTA), fumonisins (FBs), and zearalenone (ZEA) are found in food and feed in a wide range of concentrations, depending on environmental and storage conditions. Consumption of mycotoxin-contaminated food and feed has been associated with acute and chronic poisoning and carcinoma. The aim of this study was to determine the incidence and co-occurrence of AFs (B1+B2+G1+G2), OTA, FBs (B1+B2+B3), and ZEA in 37 samples of cereals and feed randomly collected in 2007 from households of an endemic nephropathy (EN) area in Croatia. The mycotoxins were determined using the competitive direct ELISA test (CD-ELISA) in combination with thin-layer chromatography (TLC). The most frequent mycotoxin was ZEA (92 %, mean 318.3 μg kg-1), followed by FBs (27 %, 3690 μg kg-1), AFs (24.3 %, 4.6 μg kg-1), and OTA (16.2 %, 9.8 μg kg-1). Levels of AFs, ZEA, and FBs detected by CD-ELISA signifi cantly correlated with the TLC results. However, only one OTA-positive sample was confi rmed by TLC due to its high limit of detection. The levels of these mycotoxins were below the permissible limit for animal feed. Twenty-nine percent of cereals were contaminated with FBs, OTA, or ZEA in mass fractions above the permissible limit for humans. Co-occurrence of two toxins varied between 4.2 % and 54 % and of three between 4.2 % and 7.6 %. Prolonged co-exposure to AFs, OTA, FBs, and ZEA might increase the risk of various chronic diseases.Vrste plijesni iz rodova Aspergillus, Penicillium i Fusarium česti su kontaminanti usjeva te na takvim supstratima tvore mikotoksine. Stoga su žitarice i krmiva često kontaminirana afl atoksinima (AFs), okratoksinom A (OTA), fumonizinima (FBs) i zearalenonom (ZEA) u različitim koncentracijama ovisno o mikroklimatskim uvjetima na polju i u skladištu. Konzumiranje hrane kontaminirane mikotoksinima često je povezano s akutnim ili kroničnim trovanjima, ali i s razvojem karcinoma. Cilj ovog rada bio je odrediti istodobnu pojavnost AFs (B1+B2+G1+G2), OTA, FBs (B1+B2+B3) i ZEA u uzorcima žitarica i krme (N=37) koji su nasumično skupljeni u individualnim domaćinstvima na području endemske nefropatije (EN) u Hrvatskoj (2007). Za određivanje navedenih mikotoksina korišten je kompetitivni direktni ELISA-test (CD-ELISA) u kombinaciji s tankoslojnom kromatografi jom (TLC). Najzastupljeniji mikotoksin bio je ZEA (92 %, srednja koncentracija 318.3 μg kg-1), nakon čega slijede FBs (27 %, 3690 μg kg-1), AFs (24.3 %, 4.6 μg kg-1) te OTA (16.2 %, 9.8 μg kg-1). Koncentracije AFs, FBs i ZEA određene CD-ELISA-testom statistički značajno koreliraju s rezultatima dobivenim s TLC. OTA je potvrđen metodom TLC samo u jednom uzorku zbog visokog limita detekcije. Dokazane koncentracije su ispod razina dopuštenih za krmiva, dok je 29 % uzoraka žitarica sadržavalo FBs, OTA ili ZEA u koncentracijama iznad dopuštenih u hrani za ljude. Kokontaminacija s dvama odnosno trima toksinima varirala je između 4.2 % i 54 % odnosno između 4.2 % i 7.6 %. Dugotrajni unos AFs, OTA, FBs i ZEA putem hrane može povećati rizik od razvoja različitih kroničnih bolesti zbog njihova mogućega sinergističkog djelovanja

Kontaminacija zrna pšenice, kukuruza, soje i graška vrstama Fusariuma u Hrvatskoj

From 2002 to 2008, 203 samples of wheat, maize, soybean, and pea were analysed for the presence of Fusarium species. Contamination with Fusarium spp., expressed as the percentage of seeds with Fusarium colonies, ranged from 5 % to 69 % for wheat, from 25 % to 100 % for maize, from 4 % to 17 % for soybean, and from 3 % to 17 % for pea. 187 isolates were collected and the following 19 species determined: F. graminearum, F. poae, F. avenaceum, F. verticillioides, F. sporotrichioides, F. heterosporum, F. crookwellense, F. tricinctum, F. semitectum, F. oxysporum, F. proliferatum, F. solani, F. equiseti, F. pseudograminearum, F. chlamydosporum, F. sambucinum, F. compactum, F. scirpi, and F. culmorum. Dominant species were F. graminearum on wheat (27 % of isolates), F. verticillioides on maize (83 % of isolates), F. sporotrichioides on soybean (34 % of isolates), and F. proliferatum on pea (29 % of isolates). Among species identifi ed, F. heterosporum, F. crookwellense, F. pseudograminearum, F. sambucinum, and F. compactum have been reported for the fi rst time in Croatia.U periodu od 2002. do 2008. g. analizirana je prisutnost vrsta Fusariuma na 208 uzoraka zrna pšenice, kukuruza, soje i graška. Kontaminacija vrstama Fusariuma, izražena kao postotak sjemenki s kolonijama Fusarium spp., kretala se od 5 % do 69 % na pšenici, od 25 % do 100 % na kukuruzu, od 4 % do 17 % na soji te od 3 % do 17 % na grašku. Prosječna kontaminacija vrstama Fusariuma u različitim godinama varirala je od 10 % do 46 % na pšenici, od 50 % do 91 % na kukuruzu, od 5 % do 9 % na soji te od 7 % do 10 % na grašku. Vrste Fusariuma koje se javljaju na zrnu izolirane su i determinirane s odabranih uzoraka pšenice, kukuruza, soje i graška. Skupljeno je 187 izolata, a utvrđeno je 19 vrsta: F. graminearum, F. poae, F. avenaceum, F. verticillioides, F. sporotrichioides, F. heterosporum, F. crookwellense, F. tricinctum, F. semitectum, F. oxysporum, F. proliferatum, F. solani, F. equiseti, F. pseudograminearum, F. chlamydosporum, F. sambucinum, F. compactum, F. scirpi i F. culmorum. Dominantne vrste bile su F. graminearum na pšenici (27 % izolata), F. verticillioides na kukuruzu (83 % izolata), F. sporotrichioides na soji (34 % izolata) te F. proliferatum na grašku (29 % izolata). U Hrvatskoj su prvi put utvrđene vrste F. heterosporum, F. crookwellense, F. pseudograminearum, F. sambucinum i F. compactum

Feedback Enhances Feedforward Figure-Ground Segmentation by Changing Firing Mode

In the visual cortex, feedback projections are conjectured to be crucial in figure-ground segregation. However, the precise function of feedback herein is unclear. Here we tested a hypothetical model of reentrant feedback. We used a previous developed 2-layered feedforwardspiking network that is able to segregate figure from ground and included feedback connections. Our computer model data show that without feedback, neurons respond with regular low-frequency (∼9 Hz) bursting to a figure-ground stimulus. After including feedback the firing pattern changed into a regular (tonic) spiking pattern. In this state, we found an extra enhancement of figure responses and a further suppression of background responses resulting in a stronger figure-ground signal. Such push-pull effect was confirmed by comparing the figure-ground responses withthe responses to a homogenous texture. We propose that feedback controlsfigure-ground segregation by influencing the neural firing patterns of feedforward projecting neurons