Taking the example of computer systems engineering for the analysis of biological cell systems

In this paper, we discuss the potential for the use of engineering methods that were originally developed for the design of embedded computer systems, to analyse biological cell systems. For embedded systems as well as for biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. In contrast to the biology domain, the computer engineering domain has the opportunity to quickly evaluate design options and consequences of its systems by methods for computer aided design and in particular design space exploration. We argue that there are enough concrete similarities between the two systems to assume that the engineering methodology from the computer systems domain, and in particular that related to embedded systems, can be applied to the domain of cellular systems. This will help to understand the myriad of different design options cellular systems have. First we compare computer systems with cellular systems. Then, we discuss exactly what features of engineering methods could aid researchers with the analysis of cellular systems, and what benefits could be gained.     

Taking the example of computer systems engineering for the analysis of biological cell systems

In this paper, we discuss the potential for the use of engineering methods that were originally developed for the design of embedded computer systems, to analyse biological cell systems. For embedded systems as well as for biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. In contrast to the biology domain, the computer engineering domain has the opportunity to quickly evaluate design options and consequences of its systems by methods for computer aided design and in particular design space exploration. We argue that there are enough concrete similarities between the two systems to assume that the engineering methodology from the computer systems domain, and in particular that related to embedded systems, can be applied to the domain of cellular systems. This will help to understand the myriad of different design options cellular systems have. First we compare computer systems with cellular systems. Then, we discuss exactly what features of engineering methods could aid researchers with the analysis of cellular systems, and what benefits could be gained.     

Evaluation of the sustainability of contrasted pig farming systems: breeding programmes

The sustainability of breeding activities in 15 pig farming systems in five European countries was evaluated. One conventional and two differentiated systems per country were studied. The Conventional systems were the standard systems in their countries. The differentiated systems were of three categories: Adapted Conventional with focus on animal welfare, meat quality or environment (five systems); Traditional with local breeds in small-scale production (three systems) and Organic (two systems). Data were collected with a questionnaire from nine breeding organisations providing animals and semen to the studied farming systems and from, on average, five farmers per farming system. The sustainability assessment of breeding activities was performed in four dimensions. The first dimension described whether the market for the product was well defined, and whether the breeding goal reflected the farming system and the farmers’ demands. The second dimension described recording and selection procedures, together with genetic change in traits that were important in the system. The third dimension described genetic variation, both within and between pig breeds. The fourth dimension described the management of the breeding organisation, including communication, transparency, and technical and human resources. The results show substantial differences in the sustainability of breeding activities, both between farming systems within the same category and between different categories of farming systems. The breeding activities are assessed to be more sustainable for conventional systems than for differentiated systems in three of the four dimensions. In most differentiated farming systems, breeding goals are not related to the system, as these systems use the same genetic material as conventional systems. The breeds used in Traditional farming systems are important for genetic biodiversity, but the small scale of these systems renders them vulnerable. It is hoped that, by reflecting on different aspects of sustainability, this study will encourage sustainable developments in pig production.     

生产疫苗的植物表达系统

综述了近些年来转基因植物作为疫苗表达系统的新进展,比较了植物表达系统相对其他表达系统的优点,介绍了不同介导方式的植物表达系统,包括农杆菌介导的转化和重组植物病毒表达疫苗,讨论了提高表达效率的载体构建策略,对其应用前景提出了展望。     

Dynamical aspects of P systems

A dynamical analysis of P systems is given that is focused on basic phenomena of biological relevance. After a short presentation of a new kind of P systems (PB systems), membrane systems with environment, called PBE systems, are introduced that are more suitable for modeling complex membrane interactions. Some types of periodicity and non-periodicity are considered for PBE systems by showing some "minimal" examples of systems that exhibit these properties. In particular, a discrete formulation of the Belousov-Zhabotinsky (BZ) reaction is given in terms of PBE systems. Some questions and open problems for future research are indicated.     

Supporting upper-level undergraduate students in building a systems perspective in a botany course

Undergraduate biology majors require biological literacy about the critical and dynamic relationships between plants and ecosystems and the effect human-made processes have on these systems. To support students in understanding systems relationships, we redesigned an undergraduate botany course using an ecological framework and embedded systems modelling to support students in understanding the criticality of plant processes to the global carbon cycle. The class meetings included lectures, opportunities to develop systems models identifying the relationships between plant processes and other systems, reflections on their systems understanding and open-floor discussions about assigned primary and secondary readings that explored the relationships between plant systems, abiotic and biotic processes and global carbon cycling in their systems models. We used the systems models students developed at the beginning and end of the course to examine how their systems understanding grew. Our results suggest that at the beginning of term, students’ ideas about plants were egocentric identifying the purpose of plants was to support human life and they did not consider relationships between plants and global carbon systems. By the end of the term, their models and reflections identified elements of a systems perspective and the students considered human impact on this delicate balance.     

Requirements engineering: the key to designing complex medical systems

A variety of business systems, clinical work systems, instrumentation systems, information systems, infrastructure systems, and management systems interact to make the modern healthcare facility work. The key to designing for such a system is systems engineering, a skill often little appreciated among clinical engineers. At the heart of systems engineering is requirements engineering and management (REAM), which is defined as "the process of discovering, documenting and managing systems requirements." The principal activities of REAM include eliciting, understanding, negotiating, describing, validating, and managing system requirements. When REAM is done improperly, the resulting system will be satisfactory only if chance intervenes. Well-done REAM is likely to bring the project in on time, under budget, and at full performance.     

Qualitative theory of compartmental systems with lags

Dynamic models of many processes in the biological and physical sciences give systems of ordinary differential equations called compartmental systems. Often, these systems include time lags; in this context, continuous probability density functions (pdfs) of lags are far more important than discrete lags. There is a relatively complete theory of compartmental systems without lags, both linear and non-linear [SIAM Rev. 35 (1993) 43]. The authors extend their previous work on compartmental systems without lags to show that, for discrete lags and for a very large class of pdfs of continuous lags, compartmental systems with lags are equivalent to larger compartmental systems without lags. Consequently, the properties of compartmental systems with lags are the same as those of compartmental systems without lags. For a very large class of compartmental systems with time lags, one can show that the time lags themselves can be generated by compartmental systems without lags. Thus, such systems can be partitioned into a main system, which is the original system without the lags, plus compartmental subsystems without lags that generate the lags. The latter may be linear or non-linear and may be inserted into main systems that are linear or non-linear. The state variables of the compartmental lag subsystems are hidden variables in the formulation with explicit lags.     

Relations between substrate feeding pattern and development of filamentous bacteria in activated sludge processes

Summary Laboratory scale activated sludge systems were operated under regimes of continuous or intermittent feeding of substrate. It was found that continuously fed systems repeatedly resulted in the development of filamentous bacteria and bulking of the sludge. Intermittently fed systems did form good settling sludges, without filamentous bacteria. The same results were found using different sludge loadings and different concentrations of mixed liquor suspended solids. High dissolved oxygen concentration did not prevent bulking in continuous systems while low dissolved oxygen concentration resulted in bulking with intermittently fed systems. It was found that the substrate removal rate of intermittently operated systems was always higher than for continuously fed systems. The hypothesis is formulated that intermittent feeding leads to higher substrate removal rates by floc forming bacteria and their predominance in intermittently fed systems, which can be compared to plug flow systems.     

Calculating life? Duelling discourses in interdisciplinary systems biology

A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences.     

Doctors' use of electronic medical records systems in hospitals: cross sectional survey

ObjectivesTo compare the use of three electronic medical records systems by doctors in Norwegian hospitals for general clinical tasks.DesignCross sectional questionnaire survey. Semistructured telephone interviews with key staff in information technology in each hospital for details of local implementation of the systems.Setting32 hospital units in 19 Norwegian hospitals with electronic medical records systems.Participants227 (72%) of 314 hospital doctors responded, equally distributed between the three electronic medical records systems.ResultsMost tasks listed in the questionnaire (15/23) were generally covered with implemented functions in the electronic medical records systems. However, the systems were used for only 2-7 of the tasks, mainly associated with reading patient data. Respondents showed significant differences in frequency of use of the different systems for four tasks for which the systems offered equivalent functionality. The respondents scored highly in computer literacy (72.2/100), and computer use showed no correlation with respondents'' age, sex, or work position. User satisfaction scores were generally positive (67.2/100), with some difference between the systems.ConclusionsDoctors used electronic medical records systems for far fewer tasks than the systems supported.

What is already known on this topic

Electronic information systems in health care have not undergone systematic evaluation, and few comparisons between electronic medical records systems have been madeGiven the information intensive nature of clinical work, electronic medical records systems should be of help to doctors for most clinical tasks

What this study adds

Doctors in Norwegian hospitals reported a low level of use of all electronic medical records systemsThe systems were mainly used for reading patient data, and doctors used the systems for less than half of the tasks for which the systems were functionalAnalyses of actual use of electronic medical records provide more information than user satisfaction or functionality of such records systems     

Collective Motion in a Network of Self-Propelled Agent Systems

Collective motions of animals that move towards the same direction is a conspicuous feature in nature. Such groups of animals are called a self-propelled agent (SPA) systems. Many studies have been focused on the synchronization of isolated SPA systems. In real scenarios, different SPA systems are coupled with each other forming a network of SPA systems. For example, a flock of birds and a school of fish show predator-prey relationships and different groups of birds may compete for food. In this work, we propose a general framework to study the collective motion of coupled self-propelled agent systems. Especially, we study how three different connections between SPA systems: symbiosis, predator-prey, and competition influence the synchronization of the network of SPA systems. We find that a network of SPA systems coupled with symbiosis relationship arrive at a complete synchronization as all its subsystems showing a complete synchronization; a network of SPA systems coupled by predator-prey relationship can not reach a complete synchronization and its subsystems converges to different synchronized directions; and the competitive relationship between SPA systems could increase the synchronization of each SPA systems, while the network of SPA systems coupled by competitive relationships shows an optimal synchronization for small coupling strength, indicating that small competition promotes the synchronization of the entire system.     

Parasitic systems of Microsporidia: descriptions and terminology questions

Three parasitic systems of Microsporidia are described: the system of monoxenic Vairimorpha mesnili with paraxenic hosts presented lepidopteran and hymenopteran species; the system of dixenic Amblyospora sp. with metaxenic hosts presented bloodsucking mosquitoes and crustaceans and the system of Metchnikovella sp. as parasite of other obligate parasite. The last case is characterized by very intimate interrelations between hyperparasite (microsporidian species), obligate parasite--host of Microsporidia (gregarine) and hyperhost--host of gregarine (polychaeta). This hyperparasite system is exclusive case of parasitic systems. Parasitic and hyperparasitic systems reflects a population level of host-parasite interactions. On biocenotic level many other organisms such as predators, vectors and reservators of invasion stages of Microsporidia affect parasitic systems giving a chance to one of the members of the system (to the host or to the parasite). These organisms form epiparasitic system. In all cases of the parasitic systems there are two-way communications between parasites and their hosts. In systems on biocenotic level--parasitic consortium--members of epiparasitic systems acts on parasitic systems, but members of parasitic systems don't affect epiparasitic systems.     

Entity grammar systems: A grammatical tool for studying the hierarchal structures of biological systems

The hierarchal structures of biological systems are the typical complex hierarchal dynamical structures in the physical world, the effective investigations on which could not be performed with the existing formal grammar systems. To meet the needs of the investigation on these kinds of systems, especially the emerging field of system biology, a grammatical tool was proposed in the present article. Because the grammatical toolmainly deals with the systems composed of structured entities, they are called entity grammar systems (EGSs). The structure of entities in EGSs have the general form of the objects in the physical world, which means EGSs could be used as a tool to study the complex system composed of many objects with different structures, just like the biological systems. The article contains the formal definition of EGSs and the hierarchy of EGSs, which is congruent with the Chomsky hierarchy. The relationship between EGSs and array grammar systems, graph grammar systems, tree grammar systems, multi-set grammar systems are discussed to show the generative power of EGSs. At the end of the present article, the steps to define new grammar systems with the form of EGS are provided and the possible applicable fields of EGSs are discussed.     

Individual-and population-based diversity in restriction-modification systems

Restriction-modification (RM) systems are cognate gene complexes that code for an endonuclease and a methylase. They are often thought to have developed in bacteria as protection against invading genetic material, e.g., phage DNA. The high diversity of RM systems, as observed in nature, is often ascribed to the coevolution of RM systems (which ‘invent’ novel types) and phages. However, the extent to which phages are insensitive to RM systems casts doubts on the effectiveness of RM systems as protection against infection and thereby on the reason for the diversity of RM systems. We present an eco-evolutionary model in order to study the evolution of the diversity of RM systems. The model predicts that in general diversity of RM systems is high. More importantly, the diversity of the RM systems is expressed either at the individual level or at the population level. In the first case all individuals carry RM systems of all sequence specificities, whereas in the second case they carry only one RM system or no RM systems at all. Nevertheless, in the second case the same number of sequence specificities are present in the population.     

Systems biology,emergence and antireductionism

This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed.Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist–antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.     

Synchronous and asynchronous systems of threshold elements

The role of synchronism in systems of threshold elements (such as neural networks) is examined. Some important differences between synchronous and asynchronous systems are outlined. In particular, important restrictions on limit cycles are found in asynchronous systems along with multi-frequency oscillations which do not appear in synchronous systems. The possible role of deterministic chaos in these systems is discussed.     

Beyond the Food Web Connections to a Deeper Industrial Ecology

Industrial ecology is a school of thought based, in part, upon a simple analogy between industrial systems and ecological systems in terms of their material and energy flows. This article argues for a more sophisticated connection between these diverse systems based on the fact that they are all complex self-organizing systems, operating far from thermodynamic equilibrium. As such, industrial and ecological systems have in common certain constraints and dynamic properties that move beyond the central metaphor of industrial ecology and could align these systems under a more comprehensive analytical framework. If incorporated at a fundamental level, the complex systems framework could add depth and sophistication to the field of industrial ecology.     

固体载体支承的双层膜系统

固态载体支承的双层膜的各种制备过程都简便易行,较脂质体等系统有重复性好、其物化性质可严格控制等优越性,并可将膜蛋白质分子镶嵌其中,是研究生物膜的良好模型．由于其研究方法日益成熟,固态载体支承的双层膜系统越来越成为研究生物膜与膜蛋白的有利工具之一．对固态载体支承的双层膜的制备技术和研究方法进行了系统的综述,并列举了一些在膜生物物理化学领域的应用．