Data-Driven Modeling of Partially Observed Biological Systems

We present a numerical approach for modeling unknown dynamical systems using partially observed data,with a focus on biological systems with(relatively)complex dynamical behavior.As an extension of the recently developed deep neural network(DNN)learning methods,our approach is particularly suitable for practical situations when(i)measurement data are available for only a subset of the state variables,and(ii)the system parameters cannot be observed or measured at all.We demonstrate that,with a properly designed DNN structure with memory terms,effective DNN models can be learned from such partially observed data containing hidden parameters.The learned DNN model serves as an accurate predictive tool for system analysis.Through a few representative biological problems,we demonstrate that such DNN models can capture qualitative dynamical behavior changes in the system,such as bifurcations,even when the parameters controlling such behavior changes are completely unknown throughout not only the model learning process but also the system prediction process.The learned DNN model effectively creates a“closed”model involving only the observables when such a closed-form model does not exist mathematically.

Suppression of Chaotic Behaviors in a Complex Biological System by Disturbance Observer-based Derivative-Integral Terminal Sliding Mode

Coronary artery systems are a kind of complex biological systems. Their chaotic phenomena can lead to serious health problems and illness development. From the perspective of engineering, this paper investigates the chaos suppression problem. At first, nonlinear dynamics of coronary artery systems are presented. To suppress the chaotic phenomena, the method of derivative-integral terminal sliding mode control is adopted. Since coronary artery systems suffer from uncertainties, the technique of disturbance observer is taken into consideration. The stability of such a control system that integrates the derivative-integral terminal sliding mode controller and the disturbance observer is proven in the sense of Lyapunov. To verify the feasibility and effectiveness of the proposed strategy, simulation results are illustrated in comparison with a benchmark.

3D Modelling of Biological Systems for Biomimetics

With the advanced development of computer-based enabling technologies, many engineering, medical, biology, chemistry, physics and food science etc have developed to the unprecedented levels, which lead to many research and development interests in various multi-discipline areas. Among them, biomimetics is one of the most promising and attractive branches of study. Biomimetics is a branch of study that uses biological systems as a model to develop synthetic systems. To learn from nature, one of the fundamental issues is to understand the natural systems such animals, insects, plants and human beings etc. The geometrical characterization and representation of natural systems is an important fundamental work for biomimetics research. 3D modeling plays a key role in the geometrical characterization and representation, especially in computer graphical visualization. This paper firstly presents the typical procedure of 3D modelling methods and then reviews the previous work of 3D geometrical modelling techniques and systems developed for industrial, medical and animation applications. Especially the paper discusses the problems associated with the existing techniques and systems when they are applied to 3D modelling of biological systems. Based upon the discussions, the paper proposes some areas of research interests in 3D modelling of biological systems and for Biomimetics.

The Construction and Practice of Ecological Villages and Aquatic Biological Systems

This paper selects Xiaowangliu Village,Banquan Town,Junan County,Linyi City as the test point to explore the construction of he ecological village. The ecological village is divided into two sub-systems: land and waters. The water resource of the ecological village is divided into the village water source,village water system,village pond wetland and water resource output sub-systems. The organic waste in villages is related to the industrialization of insect resources.

Evolution and Development of the Information Concept in Biological Systems: From Empirical Description to Informational Modeling of the Living Structures

With the purpose to smooth the way of a correct understanding of information concepts and their evolution,in this paper,is discussed the evolution and development of the concept of information in biological systems,showing that this concept was intuitively perceived even since ancient times by our predecessors,and described according to their language level of that times,but the crystallization of the real meaning of information is an achievement of our nowadays,by successive contribution of various scientific branches and personalities of the scientific community of the world,leading to a modern description/modeling of reality,in which information plays a fundamental role.It is shown that our reality can be understood as a contribution of matter/energy/information and represented/discussed as the model of the Universal Triangle of Reality(UTR),where various previous models can be suggestively inserted,as a function of their basic concern.The modern concepts on information starting from a theoretic experiment which would infringe the thermodynamics laws and reaching the theory of information and modern philosophic concepts on the world structuration allow us to show that information is a fundamental component of the material world and of the biological structures,in correlation with the structuration/destructuration processes of matter,involving absorption/release of information.Based on these concepts,is discussed the functionality of the biologic structures and is presented the informational model of the human body and living structures,as a general model of info-organization on the entire biological scale,showing that a rudimentary proto-consciousness should be operative even at the low-scale biological systems,because they work on the same principles,like the most developed bio-systems.The operability of biologic structures as informational devices is also pointed out.

Analysis and FDTD Modeling of the Influences of Microwave Electromagnetic Waves on Human Biological Systems

The interactions of electromagnetic waves with the human body are complex and depend on several factors related to the characteristics of the incident wave, including its frequency, its intensity, the polarization of the tissue encountered, the geometry of the tissue and its electromagnetic properties. That’s to say, the dielectric permittivity, the conductivity and the type of coupling between the field and the exposed body. A biological system irradiated by an electromagnetic wave is traversed by induced currents of non-negligible density;the water molecules present in the biological tissues exposed to the electromagnetic field will begin to oscillate at the frequency of the incident wave, thus creating internal friction responsible for the heating of the irradiated tissues. This heating will be all the more important as the tissues are rich in water. This article presents the establishment from a mathematical and numerical analysis explaining the phenomena of interaction and consequences between electromagnetic waves and health. Since the total electric field in the biological system is unknown, that is why it can be determined by the Finite Difference Time Domain FDTD method to assess the electromagnetic power distribution in the biological system under study. For this purpose, the detailed on the mechanisms of interaction of microwave electromagnetic waves with the human body have been presented. Mathematical analysis using Maxwell’s equations as well as bio-heat equations is the basis of this study for a consistent result. Therefore, a thermal model of biological tissues based on an electrical analogy has been developed. By the principle of duality, an electrical model in the dielectric form of a multilayered human tissue was used in order to obtain a corresponding thermal model. This thermal model made it possible to evaluate the temperature profile of biological tissues during exposure to electromagnetic waves. The simulation results obtained from computer tools show that the temperature in the biological tissue is a linear function of the duration of exposure to microwave electromagnetic waves.

Optimal Size for Maximal Energy Efficiency in Information Processing of Biological Systems Due to Bistability

Energy efficiency is closely related to the evolution of biological systems and is important to their information processing. In this work, we calculate the excitation probability of a simple model of a bistable biological unit in response to pulsatile inputs, and its spontaneous excitation rate due to noise perturbation. Then we analytically calculate the mutual information, energy cost, and energy efficiency of an array of these bistable units. We find that the optimal number of units could maximize this array＇s energy efficiency in encoding pulse inputs, which depends on the fixed energy cost. We conclude that demand for energy efficiency in biological systems may strongly influence the size of these systems under the pressure of natural selection.

FROM MOLECULAR RESPONSE TO CELL RESPONSE-Approaching the complexity of biological systems

I. THE COMPLEXITY OFBIOLOGICAL RESPONSESFor an organism, to be living or notdepends on its response to foreign matters.Facing the increasing amount and diversi-ty of chemicals, natural and synthetic, tounderstand the principles of the biologicalresponses becomes extremely importantin pursuing the way of rational utiliza-tion and governing the foreign matters.However, most biological responses aretoo complex to explore their nature. Forinstance, the risk to human beings andorganisms related to the application ofrare earths in agriculture, forestation, fish-ery and husbandry has been argued

Recent advances in zwitterionic nanoscale drug delivery systems to overcome biological barriers

Nanoscale drug delivery systems(nDDS)have been employed widely in enhancing the therapeutic efficacy of drugs against diseases with reduced side effects.Although several nDDS have been successfully approved for clinical use up to now,biological barriers between the administration site and the target site hinder the wider clinical adoption of nDDS in disease treatment.Polyethylene glycol(PEG)-modification(or PEGylation)has been regarded as the gold standard for stabilising nDDS in complex biological environment.However,the accelerated blood clearance(ABC)of PEGylated nDDS after repeated injections becomes great challenges for their clinical applications.Zwitterionic polymer,a novel family of antifouling materials,have evolved as an alternative to PEG due to their super-hydrophilicity and biocompatibility.Zwitterionic nDDS could avoid the generation of ABC phenomenon and exhibit longer blood circulation time than the PEGylated analogues.More impressively,zwitterionic nDDS have recently been shown to overcome multiple biological barriers such as nonspecific organ distribution,pressure gradients,impermeable cell membranes and lysosomal degradation without the need of any complex chemical modifications.The realization of overcoming multiple biological barriers by zwitterionic nDDS may simplify the current overly complex design of nDDS,which could facilitate their better clinical translation.Herein,we summarise the recent progress of zwitterionic nDDS at overcoming various biological barriers and analyse their underlyingmechanisms.Finally,prospects and challenges are introduced to guide the rational design of zwitterionic nDDS for disease treatment.

Construction of Biological Experiment Curriculum System in the Context of Innovation and Entrepreneurship Education

Innovation and entrepreneurship education is an important direction for the current reform of higher education and should be included in the professional talent training plan and the construction of the biological experiment curriculum system.Specific measures include in-depth excavation of the connotation of biological experiment teaching courses from the perspective of talent training,building an innovation and entrepreneurship biological experiment curriculum system guided by the needs of social development,establishing a comprehensive and diversified platform for practice and innovation,and constructing a teaching team that integrates innovation and entrepreneurship education and professional education.

Optical applications of quantum dots in biological system

This review presents a simple introduction on the unique properties and general synthesis of quantum dots (QDs) in which we lay emphasis on the optical applications in the biological system. The detection of biological molecules such as DNA, protein and enzyme, the cell-based analysis and in vivo animal imaging are mainly discussed.

A survey of some tensor analysis techniques for biological systems

Background:Since biological systems are complex and often involve multiple types of genomic relationships,tensor analysis methods can be utilized to elucidate these hidden complex relationships.There is a pressing need for this,as the interpretation of the results of high-throughput experiments has advanced at a much slower pace than the accumulation of data.Results:In this review we provide an overview of some tensor analysis methods for biological systems.Conclusions:Tensors are natural and powerful generalizations of vectors and matrices to higher dimensions and play a fundamental role in physics,mathematics and many other areas.Tensor analysis methods can be used to provide the foundations of systematic approaches to distinguish significant higher order correlations among the elements of a complex systems via finding ensembles of a small number of reduced systems that provide a concise and representative summary of these correlations.

Biological Systems:Reliable Functions out of Randomness

What makes biological systems different from man-made systems?One distinction is explored in this paper:Biological systems achieve reliable functions through randomness,i.e.,by both mitigating and exploiting the effects of randomness.The fundamental reason for biological systems to take such a random approach is the randomness of the microscopic world,which is dramatically different from the macroscopic world we are familiar with.To substantiate the idea,bacterial chemotaxis is used as an example.

Synbiological systems for complex natural products biosynthesis

Natural products(NPs)continue to play a pivotal role in drug discovery programs.The rapid development of synthetic biology has conferred the strategies of NPs production.Synthetic biology is a new engineering discipline that aims to produce desirable products by rationally programming the biological parts and manipulating the pathways.However,there is still a challenge for integrating a heterologous pathway in chassis cells for overproduction purpose due to the limited characterized parts,modules incompatibility,and cell tolerance towards product.Enormous endeavors have been taken for mentioned issues.Herein,in this review,the progresses in naturally discovering novel biological parts and rational design of synthetic biological parts are reviewed,combining with the advanced assembly technologies,pathway engineering,and pathway optimization in global network guidance.The future perspectives are also presented.

A mini-review on rare-earth down-conversion nanoparticles for NIR-II imaging of biological systems

Rare-earth(RE)based luminescent probes exhibit rich optical properties including upconversion and down-conversion luminescence spanning a broad spectral range from 300 to 3,000 nm,and have generated great scientific and practical interest from telecommunication to biological imaging.While upconversion nanoparticles have been investigated for decades,down-conversion luminescence of RE-based probes in the second near-infrared(NIR-II,1,000-1,700 nm)window for in vivo biological imaging with sub-centimeter tissue penetration and micrometer image resolution has come into light only recently.In this review,we present recent progress on RE-based NIR-II probes for in vivo vasculature and molecular imaging with a focus on Er3+-based nanoparticles due to the down-conversion luminescence at the long-wavelength end of the NIR-II window(NIR-IIb,1,500-1,700 nm).Imaging in NIR-IIb is superior to imaging with organic probes such as ICG and IRDye800 in the^800 nm NIR range and the 1,000-1,300 nm short end of NIR-II range,owing to minimized light scattering and autofluorescence background.Doping by cerium and other ions and phase engineering of Er^3+-based nanoparticles,combined with surface hydrophilic coating optimization can afford ultrabright,biocompatible NIR-IIb probe towards clinical translation for human use.The Nd^3+-based probes with NIR-II emission at 1,050 and 1,330 nm are also discussed,including Nd^3+doped nanocrystals and Nd^3+-organic ligand complexes.This review also points out future directions for further development of multi-functional RE NIR-II probes for biological imaging.

Biological Mode of Action of Dimethomorph on Pseudoperonospora cubensis and Its Systemic Activity in Cucumber

Dimethomorph is a fungicide with high activity against Peronosporomycetes plant pathogens. The present study showed that dimethomorph is effective on controlling the oomycete fungal pathogen Pseudoperonospora cubensis causing downy mildew on cucumber. The fungicide did not affect zoospores discharge from sporangia of P. cubensis, but it strongly inhibited mycelial growth and sporangial production in vitro and increased lysis of zoospores. Dose of 2 mg L^-1 of dimethomorph was sufficient to inhibit mycelial growth and sporangial production of P. cubensis on leaf disks, 5 mg L^-1 was enough to lyse zoospores of P. cubensis, and 25 mg L^-1 was required to inhibit sporangial production on detached leaves. In whole plant tests, dimethomorph exhibited strong protective and curative activity. Dimethomorph when applied at a dose of 300 mg L^-1 for 1, 3, 5, 7 days before inoculation exhibited 100% efficacy on disease control. On the other hand, efficacies of 67.1 and 31.5% were obtained when the same dose of dimethomorph was applied for 1 and 3 days after inoculation, respectively. So dimethomorph had persistence effect on leaves for 7 days at least and exhibited strong protective and curative activity. Bioassay analyses showed that dimethomorph could be translocated in the xylem system, redistributed in the leaf, and penetrated from the upper surface to the lower surface of the leaf but could not be translocated in phloem system or transferred from the roots to leaves of cucumber plants in sufficient amounts for disease control. The biocharacteristics of dimethomorph make it well suitable for integration of a control programme against downy mildew disease on cucumber and as a component to delay other peronosporomycetes fungicide-resistance development.

Optimization of Two-species Whole-cell Immobilization System Constructed with Marine-derived Fungi and Its Biological Degradation Ability

Mycelia pellet formed spontaneously in the process of cultivation was exploited as a biological carrier for whole-cell immobilization due to its unique structural characteristic. An innovative two-species whole-cell im- mobilization system was achieved by inoculating the marine-derived fungus Pestalotiopsis sp. J63 spores into cul- ture medium containing another fungus Penicillium janthinellum P1 pre-grown mycelia pellets for 2 days without any pretreatment. In order to evaluate the biological degradation capacity of this novel constructed immobilization system, the immobilized pellets were applied to treat paper mill effluent and decolorize dye Azure B. The use of the constructed immobilization system in the effluent resulted in successful and rapid biodegradation of numerous in- soluble fine fibers. The optimum conditions of immobilized procedure for maximum biodegradation capacity were determined using orthogonal design with biomass of P1 pellets 10 g （wet mass）, concentration of J63 spore 2x109 mlq, and immobilization time 2 d. The results demonstrate that immobilized pellets have more than 99% biodegradation capacity in a ten-hour treatment process. The kinetics of biodegradation fits the Michaelis-Menten equation well. Besides, the decolorization capability of immobilized pellets is more superior than that of P1 mycelia pellets. Overall, the present study offers a simple and reproducible way to construct a two-species whole-cell immobiliza- tion system for sewage treatment.

Biological Early Warning and Emergency Management Support System for Water Pollution Accident

Water pollution accidents such as chemical spill and toxicants leach have become a serious issue in the world, which brings great threats to the aquatic ecosystem and drinking water safety. To detect unknown pollutions in time and take proper emergency actions, this study developed a system which integrated an online intelligent water quality monitoring device with a high efficient water quality model. The device is based on water quality probes and biological sensors which use fish motion as indicator. The numerical model is a combination of Euler and Lagrangian approaches. Finite element method is applied to simulate the flow field in an unstructured grid, and the pollutant be- haviours are traced through particle tracking. Oracle is used to manage the basic and monitoring data, and ArcSDE as well as ArclMS technologies are applied to make the system WebGIS-based so as to improve the data receiving and dispatching efficiency. The developed system has been successfully operated in Douhe Reservoir and Taihu Lake, China, where drinking water intakes are installed. It is seen from the applications that the online intelligent water qual- ity monitoring and emergency support system can be of great support to emergency management.

Biological improvement of saline alkali soil reference system:A review

This work presents a reference system overview to improve the efficiency of biological improvement of saline-alkali soil developed during the last thirty years, ranging from connotation, general methods and species, soil desalination, soil structure, soil organic content, microbial flora, enzyme activity, yield and economic benefits. The reference system presented is divided into three main groups: suitable varieties, suitable cultivation measures, and a comprehensive evaluation system.There has been a lot of research on biological improvement of saline alkali soil, but these studies are very fragmented and lack a comprehensive standard system. Also, there is a lack of practical significance, particularly with regard to optimal species, densities and times of sowing for particular regions. On the other hand, the corresponding cultivation measure is very important. Therefore, a reference system plays an important role to the effect of biological improvement of saline alkali soil.

Analysis on Biological Stability and Influencing Factors of Northern Living District Water Distribution System

A northern living strict water network was employed to investigate interaction among biological stability and classical water quality indexes. Key water quality indexes on water quality were determined by the static test,then the correlations between biological stability and traditional water quality parameters were analyzed. Traditional water quality parameters and limited factors on bacteria were measured in summer and winter respectively. The results show that BDOC concentration change differently in summer and winter.Among classical parameters turbidity has a positive relation with BDOC but pH has a negative relation with BDOC. Total bacteria number shows a positive correlation with BDOC in the water distribution system.Residual chlorine shows a negative relation with total bacteria number. Fe content increasing will induce turbidity rising in water. To guarantee water safety,BDOC and chlorine content control must be incorporated together to restrict bacteria regrowth.