120 research outputs found

    Structure and parameter estimation for cell systems biology models

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    In this work we present a new methodology for structure and parameter estimation in cell systems biology modelling. Our modelling framework is based on P systems, an unconventional computational paradigm that abstracts from the structure and functioning of the living cell. The process of designing models, consisting of both the optimisation of the modular structure and of the stochastic kinetic parameters, is performed using a memetic algorithm. Specically, we use a nested evolutionary algorithm where the first layer evolves rule structures while the inner layer, implemented also as a genetic algorithm (GA), fine tunes the parameters of the model. Our approach consists of an incremental methodology. Starting from very simple P system modules specifying basic molecular interactions, more complicated modules are produced to model more complex molecular systems. These newly found modules are in turn added to the library of available P systems modules so as to be used subsequently to develop more intricate and circuitous cellular models. The effectiveness of the algorithm was tested on three case studies, namely, molecular complexation, enzymatic reactions and autoregulation in transcriptional networks.Kingdom's Engineering and Physical Sciences Research Council EP/ E017215/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/F01855X/

    A Multiscale Modeling Framework Based on P Systems

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    Cellular systems present a highly complex organization at different scales including the molecular, cellular and colony levels. The complexity at each one of these levels is tightly interrelated. Integrative systems biology aims to obtain a deeper understanding of cellular systems by focusing on the systemic and systematic integration of the different levels of organization in cellular systems. The different approaches in cellular modeling within systems biology have been classified into mathematical and computational frameworks. Specifically, the methodology to develop computational models has been recently called executable biology since it produces executable algorithms whose computations resemble the evolution of cellular systems. In this work we present P systems as a multiscale modeling framework within executable biology. P system models explicitly specify the molecular, cellular and colony levels in cellular systems in a relevant and understandable manner. Molecular species and their structure are represented by objects or strings, compartmentalization is described using membrane structures and finally cellular colonies and tissues are modeled as a collection of interacting individual P systems. The interactions between the components of cellular systems are described using rewriting rules. These rules can in turn be grouped together into modules to characterize specific cellular processes. One of our current research lines focuses on the design of cell systems biology models exhibiting a prefixed behavior through the automatic assembly of these cellular modules. Our approach is equally applicable to synthetic as well as systems biology.Kingdom's Engineering and Physical Sciences Research Council EP/ E017215/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/F01855X/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/D019613/

    Optical polarization rogue waves from supercontinuum generation in zero dispersion fiber pumped by dissipative soliton

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    Optical rogue waves emerge in nonlinear optical systems with extremely large amplitudes, and leave without a trace. In this work, we reveal the emergence of optical polarization rogue waves in supercontinuum generation from a zero-dispersion fiber, pumped by a dissipative soliton laser. Flat spectral broadening is achieved by modulation instability, followed by cascaded four-wave-mixing. In this process, we identify the emergence of optical polarization rogue waves, based on the probability density function of the relative distance among polarization states. Experimental results show that optical polarization rogue waves originate from vector multi-wave-mixing. Besides, we observe double peaks, and even triple peaks in the histogram of the state of polarization. This is a new and intriguing property, never observed so far in optical rogue waves, for example those emerging in the statistics of pulse intensities. Our polarization domain statistical analysis provides a new insight into the still debated topic of the mechanism for rogue wave generation in optical supercontinuum

    Experimental revealing of asynchronous transient-soliton buildup dynamics

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    The buildup process of coherent structures and patterns from the composite balance between conservative and dissipative effects is a universal phenomenon that occurs in various areas of physics, ranging from quantum mechanics to astrophysics. Dissipative solitons are highly coherent solutions of nonlinear wave equations, and provide an excellent research platform for ultrafast transient phenomena. Herein, by taking advantage of the fast detection technique provided by the dispersive Fourier transform, we experimentally observe the spectral broadening and breathing behavior of transient dissipative structures produced asynchronously during the buildup process of dissipative solitons. These observations unveil a novel dynamics of dissipative soliton generation, which is accompanied by energy quantization, self-phase modulation induced spectral broadening, structural dissipative soliton formation, and Raman soliton self-frequency shifting, thus providing a new insight in transient ultrafast laser dynamics

    A method of attitude measurement and level assessment for skiers based on wearable inertial measurement

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    Quantitative analysis of sports is an important development direction of scientific skiing training, and the digital expression of human movement patterns during skiing is the basis for scientific quantitative analysis. A human motion capture and attitude reconstruction system based on a wearable BSBD inertial measurement unit was designed and built, combined with the human multi-rigid body motion model to realize the human body reconstruction during the skiing, and applied to the auxiliary training of slewing movements in alpine skiing. At the same time, for the indoor training scene based on the multi-degree-of-freedom simulated ski training platform, a digital evaluation method suitable for ski slalom is proposed. The method uses motion capture system and posture reconstruction system to extract five kinds of sliding characteristic data of skiers, and realizes the evaluation of skiers’ technical parameters through similarity measurement and linear fitting with high-level athletes’ motion parameters, so as to assist scientific training. Finally, experiments are carried out on the indoor Olymp simulated ski training bench to verify the effectiveness of the method

    AAV2/8-hSMAD3 gene delivery attenuates aortic atherogenesis, enhances Th2 response without fibrosis, in LDLR-KO mice on high cholesterol diet

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    BACKGROUND: Inflammation is a key etiologic component in atherogenesis and transforming growth factor beta 1 (TGFβ1) is a well known anti-inflammatory cytokine which potentially might be used to limit it. Yet TGFβ1 is pleiomorphic, causing fibrosis, cell taxis, and under certain circumstances, can even worsen inflammation. SMAD3 is an important member of TGFβ1′s signal transduction pathway, but is a fully intracellular protein. OBJECTIVES: With the hope of attenuating TGFβ1′s adverse systemic effects (eg. fibrosis) and accentuating its anti-inflammatory activity, we proposed the use of human (h)SMAD3 as an intracellular substitute for TGFβ1. STUDY DESIGN: To test this hypothesis adeno-associated virus type 2/8 (AAV)/hSMAD3 or AAV/Neo (control) was tail vein injected into the low density lipoprotein receptor knockout (LDLR-KO) mice, then placed on a high-cholesterol diet (HCD). RESULTS: The hSMAD3 delivery was associated with significantly lower atherogenesis as measured by larger aortic cross sectional area, thinner aortic wall thickness, and lower aortic systolic blood velocity compared with Neo gene-treated controls. HSMAD3 delivery also resulted in fewer aortic macrophages by immunohistochemistry for CD68 and ITGAM, and quantitative reverse transcriptase polymerase chain reaction analysis of EMR and ITGAM. Overall, aortic cytokine expression showed an enhancement of Th2 response (higher IL-4 and IL-10); while Th1 response (IL-12) was lower with hSMAD3 delivery. While TGFβ1 is often associated with increased fibrosis, AAV/hSMAD3 delivery exhibited no increase of collagen 1A2 or significantly lower 2A1 expression in the aorta compared with Neo-delivery. Connective tissue growth factor (CTGF), a mediator of TGFβ1/SMAD3-induced fibrosis, was unchanged in hSMAD3-delivered aortas. In the liver, all three of these genes were down-regulated by hSMAD3 gene delivery. CONCLUSION: These data strongly suggest that AAV/hSMAD3 delivery gave anti-atherosclerosis therapeutic effect without the expected undesirable effect of TGFβ1-associated fibrosis

    The impact of two drying methods on the quality of high-moisture rice: Poster

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    In this experiment, freshly harvested rice was dried by natural and mechanical methods. For natural drying, paddy rice was spread on a cement floor under a shelter at a thickness of 4cm, and it was turned twice a day. At a temperature of 19.3°C and a relative humidity of 58.8%, a total of 28 days was needed to reduce the water content from 23.11 to 14.38%. For mechanical drying, the Guwang 5HXG-15B circulating dryer was used, drying temperature was set to 42°C, and it took a total of 5 hours to reduce the water content from 23.1 to 11.8%. The changes in spore count, fatty acid value, germination rate, waist burst rate, whole polished rice rate, and taste value of rice mold after drying were studied. The results showed that compared with mechanical drying, the drying rate of air-dried rice was slower, and the number of mold spores increased from 0.65×105/g to 3.05×105/g, a 3.7 times increase. The number of mold spores in dried rice was not significant. Dried rice fatty acid value of 25.1mg/100g for natural drying was higher than the value of 19.9mg/100g for mechanical drying. High temperature affected rice seed vigor: mechanically dried rice germination rate was 58.0%, far lower than the 87.5% for natural drying. The blasting rate, polished rice rate, and taste value of mechanically dried rice were 5.33%, 57.9%, and 83.7, respectively, which was 2.33%, 58.9%, and 89.3 for naturally-dried rice. The processing quality and taste quality were even worse. Therefore, the drying process of the optimized circulation dryer should be further adjusted to reduce its impact on rice processing quality and taste quality.In this experiment, freshly harvested rice was dried by natural and mechanical methods. For natural drying, paddy rice was spread on a cement floor under a shelter at a thickness of 4cm, and it was turned twice a day. At a temperature of 19.3°C and a relative humidity of 58.8%, a total of 28 days was needed to reduce the water content from 23.11 to 14.38%. For mechanical drying, the Guwang 5HXG-15B circulating dryer was used, drying temperature was set to 42°C, and it took a total of 5 hours to reduce the water content from 23.1 to 11.8%. The changes in spore count, fatty acid value, germination rate, waist burst rate, whole polished rice rate, and taste value of rice mold after drying were studied. The results showed that compared with mechanical drying, the drying rate of air-dried rice was slower, and the number of mold spores increased from 0.65×105/g to 3.05×105/g, a 3.7 times increase. The number of mold spores in dried rice was not significant. Dried rice fatty acid value of 25.1mg/100g for natural drying was higher than the value of 19.9mg/100g for mechanical drying. High temperature affected rice seed vigor: mechanically dried rice germination rate was 58.0%, far lower than the 87.5% for natural drying. The blasting rate, polished rice rate, and taste value of mechanically dried rice were 5.33%, 57.9%, and 83.7, respectively, which was 2.33%, 58.9%, and 89.3 for naturally-dried rice. The processing quality and taste quality were even worse. Therefore, the drying process of the optimized circulation dryer should be further adjusted to reduce its impact on rice processing quality and taste quality
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