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.     

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.     

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.     

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     

Evaluation of biomedical text-mining systems: lessons learned from information retrieval

Biomedical text-mining systems have great promise for improving the efficiency and productivity of biomedical researchers. However, such systems are still not in routine use. One impediment to their development is the lack of systematic and rigorous evaluation, comparable to the approaches developed for information retrieval systems. The developers of text-mining systems need to improve both test collections for system-oriented evaluation and undertake user-oriented evaluations to determine the most effective use of their systems for their intended audience.     

An analysis of theoretical systems of differentiating nervous tissue

Theoretical systems of neuroblasts differentiating according to various postulates are studied. The analysis determines the most likely patterns of connections implied by the differentiating systems. The exact expressions for the various parameters characterizing the resulting neural networks are approximated by simple analytic expressions which hold for systems having large numbers of neurons. The study is presented as a suggested approach to the more general problem of differentiating nervous systems.     

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.     

Possible involvement of acyltransferase systems in the formation of pulmonary surfactant lipid in rat

Dithiobis (2-nitrobenzoic acid)-resistant and -sensitive glycerophosphate acyltransferase systems were present in rat lung as in liver. The former was specific for palmitate while the latter could incorporate saturated and unsaturated acyl-CoAs comparably. The former has higher affinity for palmitate than the latter indicating that the 1-position of glycerophosphate can be acylated selectively with palmitate under certain conditions. The specificities of 1-acylglycerophosphate and 1-acylglycerophosphocholine acyltransferase systems were similar in lung and liver; both systems showed higher specificities for unsaturated acyl-CoAs. However, the selectivities observed at lower concentrations of phospholipid acceptors in the presence of equimolar mixtures of saturated and unsaturated acyl-CoAs were much different; the lung systems showed relatively higher selectivities for palmitate than the liver systems in the formation of both diacylglycerophosphate and phosphatidylcholine. On the other hand, palmitate was excluded almost completely from the 2-position in the 1-acylglycerophosphoethanolamine acyltransferase systems in lung and liver. These observations provide an enzymatic basis for describing the formation of pulmonary surfactant lipids in rat via acyltransferase systems.     

三种群合作系统的全局渐近性态

考虑三种群合作系统:dχi/dt=χi(b-∑j3=1αijχj),χi(0)>0,b>0,αij<0,i≠j,i,j=1,2,3,完整地分析了其全局渐近性态:证明了该系统不存在闭轨,给出了正平衡点存在且全局渐近稳定的充要条件,证明了若系统不存在正平衡点,则所有解均趋于无穷.     

Comparison of ultrafiltration systems for concentration of biologicals

Ultrafiltration has been used with increasing frequency in recent years in biological laboratories for concentration, separation or purification of biological material. No data have been available on the comparison of the characteristics of Ultrafiltration systems currently in use. This study compares the filtration characteristics of four systems using commercially available membranes on suspensions and solutions: suspension of protein micelles (casein), cell debris (E. coli) and catalase solution. None of the four systems considered is found to be generally superior for all the suspensions and solutions. Vibration systems were most effective when relatively large particles were involved, while laminar flow recycling systems with high wall shear rates were best for dilute suspensions and proteins in solution. It was found that shearing inactivates enzymes in both recycle and vibration systems. It was also observed that vibration actually reduces flux in dilute solutions.     

无细胞蛋白表达体系研究进展及在生物制药领域中的应用

作为一种快速高效的体外蛋白合成手段,无细胞蛋白表达体系(Cell-free Protein Synthesis,CFPS)一直以来就被广泛应用于基础生物学领域的研究。与传统的基于细胞的体内表达体系相比,CFPS突破了细胞的生理限制,其可调控性强、对毒性蛋白的耐受力高,使得许多很难在体内合成的复杂蛋白在体外顺利表达。近年来随着研究人员不断对CFPS进行优化,通过简化制备工艺、开发价格低廉的能量再生系统、稳定底物供应、促进蛋白正确折叠等方式,成功研发出生产效率高、成本低廉、反应体积大的表达体系。凭借其高通量和大规模的蛋白表达优势,CFPS为解决生物制药领域中面临的难题提供了新的解决思路,并成功地应用于高通量药物筛选、大规模生产重组蛋白药物、个体化定制肿瘤疫苗等领域,显示出其在生物制药领域的重要应用潜力。     

Biological information processing: the use of information for the support of function

In biological systems, the processing and use of information has evolved out of the need for survival in the face of an uncertain environment. As a consequence, the information-function relationship in these systems is shaped by their adaptability characteristics. In contrast, the information-function relationship in man-designed, goal-oriented organizational systems depends on the ability of the information processing system to support the achievement of the organization's goals. In this paper we use results from adaptability theory in the analysis of control-related aspects of the information-function relationship in man-designed organizational systems. In particular, we use a conceptual model of organizational control to characterize features of functional and control structures and their effect on the adaptability of these systems. The concept of implicit control and a design principle for adaptability-enhancing information systems are derived for this analysis.     

The role of multiscale computational approaches for rational design of conventional and nanoparticle oral drug delivery systems

Multiscale computational modeling of drug delivery systems (DDS) is poised to provide predictive capabilities for the rational design of targeted drug delivery systems, including multi-functional nanoparticles. Realistic, mechanistic models can provide a framework for understanding the fundamental physico-chemical interactions between drug, delivery system, and patient. Multiscale computational modeling, however, is in its infancy even for conventional drug delivery. The wide range of emerging nanotechnology systems for targeted delivery further increases the need for reliable in silico predictions. This review will present existing computational approaches at different scales in the design of traditional oral drug delivery systems. Subsequently, a multiscale framework for integrating continuum, stochastic, and computational chemistry models will be proposed and a case study will be presented for conventional DDS. The extension of this framework to emerging nanotechnology delivery systems will be discussed along with future directions. While oral delivery is the focus of the review, the outlined computational approaches can be applied to other drug delivery systems as well.     

Population study of electrophoretic polymorphisms of red cell enzymes and plasma proteins in Caucasian Canadians

Blood samples from a random series of Canadian Caucasians were phenotyped for 28 red cell enzyme systems and eight plasma protein systems. Polymorphism was found in 17 and rare variants in 11 of the systems. Allele frequencies are presented for these; distribution of phenotypes is in accordance with the Hardy--Weinberg equilibrium theory. In a complementary study of families there was no evidence of de novo mutation in any of the 36 systems and they allowed a minimum estimate of the frequency of null alleles in the ADA, C2, and GPT systems.     

The dynamic systems approach to control and regulation of intracellular networks

Systems theory and cell biology have enjoyed a long relationship that has received renewed interest in recent years in the context of systems biology. The term 'systems' in systems biology comes from systems theory or dynamic systems theory: systems biology is defined through the application of systems- and signal-oriented approaches for an understanding of inter- and intra-cellular dynamic processes. The aim of the present text is to review the systems and control perspective of dynamic systems. The biologist's conceptual framework for representing the variables of a biochemical reaction network, and for describing their relationships, are pathway maps. A principal goal of systems biology is to turn these static maps into dynamic models, which can provide insight into the temporal evolution of biochemical reaction networks. Towards this end, we review the case for differential equation models as a 'natural' representation of causal entailment in pathways. Block-diagrams, commonly used in the engineering sciences, are introduced and compared to pathway maps. The stimulus-response representation of a molecular system is a necessary condition for an understanding of dynamic interactions among the components that make up a pathway. Using simple examples, we show how biochemical reactions are modelled in the dynamic systems framework and visualized using block-diagrams.     

Current status of transcriptional regulation systems

Many attempts have been undertaken to control transgene activity in mammalian cells. This is of importance for both applied biotechnology and basic research activities. State of the art regulatory systems use elements for transgene regulation which are unrelated to host regulatory networks and thus do not interfere with endogenous activities. Most of these regulation systems consist of transregulators and transregulator responding promoter elements that are derived from non mammalian origin. Apart from the tetracycline (Tet) regulated system which is most widely used for conditional gene expression at the moment, a number of new systems were created. These systems have been significantly refined and their performance makes them suitable for regulating transgenes not only in cellular systems but also in transgenic animals and for human therapeutic use.     

Density functions of residence times for deterministic and stochastic compartmental systems

A significant consideration in modeling systems with stages is to obtain models for the individual stages that have probability density functions (pdfs) of residence times that are close to those of the real system. Consequently, the theory of residence time distributions is important for modeling. Here I show first that linear deterministic compartmental systems with constant coefficients and their corresponding stochastic analogs (stochastic compartmental systems with linear rate laws) have the same pdfs of residence times for the same initial distributions of inputs. Furthermore, these are independent of inflows. Then I show that does not hold for non-linear deterministic systems and their stochastic analogs (stochastic compartmental systems with non-linear rate laws). In fact, for given initial distributions of inputs, the pdfs of non-linear determistic systems without inflows and of their stochastic analogs, are functions of the initial amounts injected. For systems with inflows, the pdfs change as the inflows influence the occupancies of the compartments of the system; they are state-dependent pdfs.     

Enzyme purification with aqueous two-phase systems: comparison between systems composed of pure polymers and systems composed of crude polymers

The main drawback when using aqueous two-phase systems for macromolecule purification is the high cost of most polymers used. The purification of an enzyme, alcohol dehydrogenase, from a crude extract of Saccharomyces cerevisiae was tested in systems composed of poly(ethylene glycol) and a crude hydroxypropyl starch or Reppal PES 100, a purified fraction of hydroxypropyl starch. Purification factors measured for the enzyme were very similar in both systems (between 0.8 and 1.4 for both systems in the upper phase). However, systems composed of Reppal PES present a greater recovery of enzyme, between 77% and 100% versus 60% and 100%, while systems composed of crude hydroxypropyl starch exhibit a larger Δlog K for the tested ligand, 1.26 versus 0.81.     

Music teachers' perceptions of high stakes teacher evaluation

Recent corporate education reform policies have replaced relatively informal systems of principal observations that had been familiar to many teachers for much of their professional careers with high-stakes teacher evaluation (HSTE) systems that now determine who is allowed to remain in the profession and who gets terminated. Many education scholars have found current teacher evaluation systems to be lacking in validity and reliability. This article examines the perspectives of music teachers working within HSTE systems through a policy lens, identifying the major challenges these systems pose for music educators and offering policy recommendations for improving the evaluation of music teachers.