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.     

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.     

Adaptation as a manifestation of informational connections in living systems

The problem of adaptation of living systems in terms of the concept of informational communications is considered. The informational communication means the qualitative evaluation of information and determines correspondence of living systems to concrete conditions of life during interaction of these living systems to the source of the information. The system of the wholeorganism regulatory chemical communication is the main functional basis for the informational communication. Due to it, the transformation of the information signal in biological systems is performed, which results in their adequate response according to this information. The existence of living systems and their adaptation are determined by peculiarities of functioning of elements of their regulatory systems according to the character of the informational communication.     

Do green neighbourhood ratings cover sustainability?

Neighbourhoods are the building blocks of cities, which have their own architectural, cultural and economic systems. To improve neighbourhood sustainability, a consideration of their buildings, public spaces, infrastructure, and cooperation between their parts is necessary. Neighbourhoods are an integral part of urban planning activity, yet the development of neighbourhood assessment tools has just begun to spread.In the scope of this study, five assessment systems, CASBEE-UD, the 2009 and 2012 versions of the BREEAM Communities, LEED-ND, and DGNB-UD were compared. This paper presents the methodology and results of their comparative investigation. These systems categorise, measure, and rate their indexes and indicators differently, therefore it was necessary to integrate their processes to make them comparable. By means of a 3-level comparison and the indicator evaluation, the different neighbourhood sustainability assessment systems were compared in general as well as in detail.An evaluation based on the method provides information about the similarities, differences, and working methods of the systems, and this study can provide guidance in choosing a proper assessment system for a specific development, based on its detailedness, adaptability, and efficiency. It was also important to determine ways to improve the assessment systems.The study states that the DGNB neighbourhood sustainability system provided the best results in a comparison of their sustainability integration issues, the detailedness of their indicators, and their coverage of the pillars of sustainability. The newest systems synthesise the best qualities of each sustainability assessment tool. Meanwhile, the CASBEE tool differs from the others in the most aspects due to its different background. Finally, the LEED and BREEAM systems showed average results in main aspects.     

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.     

Lipid based particulate formulations for the delivery of antigen

Particulate adjuvant systems are largely classified according to their functional characteristics, such as the nature of the typical immune response they induce, or their perceived mode of action. From a formulation science perspective, it is practical to classify antigen delivery systems according to the physical nature of the formulations. This article discusses lipid based particulate systems, grouped according to the nature of their predominant lipid constituent.     

Autopoietic and (M,R) systems

From the many attempts to produce a conceptual framework for the organization of living systems, the notions of (M,R) systems and Autopoiesis stand out for their rigor, their presupposition of the circularity of metabolism, and the new epistemologies that they imply. From their inceptions, these two notions have been essentially disconnected because each has defined its own language and tools. Here we demonstrate the existence of a deep conceptual link between (M,R) systems and Autopoietic systems. This relationship permits us to posit that Autopoietic systems, which have been advanced as capturing the central aspects of living systems, are a subset of (M,R) systems. This result, in conjunction with previous theorems proved by Rosen, can be used to outline a demonstration that the operation of Autopoietic systems cannot be simulated by Turing machines. This powerful result shows the potential of linking these two models. Finally, we suggest that the formalism of (M,R) systems could be used to model the circularity of metabolism.     

Home-Range Dynamics in a Solitary Subterranean Rodent

Despite an important role of subterranean rodents as ecosystem engineers, their belowground mobility is poorly documented. It is supposed that their underground burrow systems, once established, are relatively stable because of high-energy costs of digging. We chose the silvery mole-rat, Heliophobius argenteocinereus (Bathyergidae, Rodentia) from mesic Afrotropics as a representative of solitary subterranean rodents to investigate how, and how fast these rodents process their established burrow systems. We combined radio-tracking of individual animals with subsequent mapping of their burrow systems, and we developed a new method for assessing the rate of burrowing. Mole-rats continuously rebuilt their burrow systems; they excavated approx. 0.7 m of new tunnels per day and backfilled on average 64% of all tunnels. On average, every 32 d they established a new nest. They often completely backfilled newly excavated peripheral burrows, while other parts of their burrow systems were more permanent. Their home-ranges were dynamic and continuously shifted in space. Burrow system processing continued even in the advanced dry season, when soil is difficult to work.     

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.     

Evaluation of Tools for Modeling Manufacturing Systems Design with Multiple Levels of Detail

This paper presents an investigation of simulation packages regarding their ability to model business processes related to manufacturing systems. Three simulation packages are investigated: VS7, SIMAN/CINEMA IV, and SIMFACTORY II.5. These packages are evaluated with regard to their capabily of modeling problems related to the manufacturing systems design (MSD) framework, which involves different levels of detail: the conceptual modeling level and the detailed design level. The investigation is based on a case study related to manufacturing systems. The main objective of this investigation is to examine the manufacturing simulation packages and their ability to offer variable detail modeling. Research findings suggest that no simulation environment offers sufficiently flexible facilities for the variable detailed modeling of manufacturing systems design. The paper proposes a method for systems entity classification to increase the levels of detail in an effective manner without duplication of data collection and model building efforts.     

Putative Nitrogen Sensing Systems in Higher Plants

Nitrogen （N） metabolism is essential for the biosynthesis of vital biomolecules. N status thus exerts profound effects on plant growth and development, and must be closely monitored. In bacteria and fungi, a few sophisticated N sensing systems have been extensively studied. In animals, the ability to receive amino acid signals has evolved to become an integral part of the nervous coordination system. In this review, we will summarize recent developments in the search for putative N sensing systems in higher plants based on homologous systems in bacteria, fungi, and animals. Apparently, although plants have separated and diversified from other organisms during the evolution process, striking similarities can be found in their N sensing systems compared with those of their counterparts; however, our understanding of these systems is still incomplete. Significant modifications of the N sensing systems （including cross-talk with other signal transduction pathways） in higher plants may be a strategy of adaptation to their unique mode of life.     

The Repertoire and Evolution of ATP-Binding Cassette Systems in <Emphasis Type="Italic">Synechococcus</Emphasis> and <Emphasis Type="Italic">Prochlorococcus</Emphasis>

Synechococcus and Prochlorococcus have made great contributions to earth’s photosynthetic biomass. ATP-binding cassette (ABC) protein systems have been characterized to play important roles in various physiological functions, including carbon fixation, phosphate assimilation, and vitamin B₁₂ metabolism. In this study, the repertoire and domain architectures of ABC systems in Synechococcus and Prochlorococcus, as well as their potential evolutionary mechanism, have been surveyed extensively. Comparative analysis revealed an uneven phylogenetic distribution of the ABC systems in these organisms, and in particular that fresh-water Synechococcus strains contain more ABC systems than those of marine ones. Phylogenetic analysis indicated that lineage-specific gene expansion and duplication may be the important forces driving the variability of ABC systems in fresh-water Synechococcus and such an expansion was likely to be relevant to their ecological tolerance. At the domain level, ATP-binding domains in several ABC systems were found to fuse with many additional domains after the divergence from their common ancestor, indicating the versatile functions of ABC systems in cyanobacteria. Subsequently, 19 ABC system families were deduced to be the core set of ABC systems conserved in all marine-living Synechococcus and Prochlorococcus. In conclusion, the comprehensive survey of ABC systems in Synechococcus and Prochlorococcus provides novel insights into their potential evolutionary mechanism and the basis for further investigation of their physiological roles.     

Simulating autonomous anticipation: the importance of Dubois' conjecture

Anticipation allows a system to adapt to conditions that have not yet come to be, either externally to the system or internally. Autonomous systems actively control their own conditions so as to increase their functionality (they self-regulate). Living systems self-regulate in order to increase their own viability. These increasingly stronger conditions, anticipation, autonomy and viability, can give an insight into progressively stronger classes of models of autonomy. I will argue that stronger forms are the relevant ones for Artificial Life. This has consequences for the design of and accurate simulation of living systems.     

Expert systems in histopathology. I. Introduction and overview

An introduction to, and overview of, expert systems is presented, along with some preliminary comments on their application in diagnostic and analytical histopathology and cytopathology. The terminology common to expert systems is defined, and the nature of expert systems is discussed. In particular, the differences between expert systems and other types of computer programs (e.g., algorithms) or means of solving problems are explored. The rationale for their use and the types of tasks for which they are appropriate are also discussed.     

Cooperative nanosystems

Multivalent systems are well known for their enhanced ability to bind multivalent counterparts. This contribution addresses the question whether they can also behave as cooperative catalysts. Analyzing examples from our own laboratory we show that self-assembled systems obtained by covering gold nanoclusters with thiol-terminated amino acids and peptides behave indeed as cooperative catalysts. By comparing their activity profiles with those of discrete, multivalent systems we show what are minimal conditions to elicit cooperativity in multivalent systems. Reactions taken into considerations for our analysis are the hydrolyses of carboxylate- and phosphate esters.     

A Framework for Information Systems in Life-Cycle-Oriented Environmental Management

Although business firms have improved their environmental performance, a variety of forces are pushing businesses toward adopting environmental management throughout the entire life cycle of their products and processes. In this article we discuss the information systems elements of an environmental management approach we call "life-cycle-oriented environmental management" (LCOEM).This approach requires the firm to manage the effects of its processes from the creation of inputs to the final disposal of outputs, that is, from cradle to grave. We present a framework of the classes of information systems needed, describe their use in an LCOEM setting and define their inter relationships. We conclude with a discussion of the implications of LCOEM information systems.     

Designed and real working situations in machine systems operation.

New work situations designed at the stage when new machine systems are introduced are realized on the assumption that the new systems can maintain their designed functions consistently, generally eliminating previous work habits and without sufficient knowledge about real working processes and skills. This may produce differences between designed and real working situations. Some examples are presented from observations on influence of modern design of cargo ships on their crews. It was difficult for crews to maintain stable working conditions, especially when machine systems deviated from their designed functions. Often the crew had to work in off-duty hours giving up private freetime activities. Among various factors contributing to the discrepancies between designed and real work, lack of availability of the new systems is the most important factor. Also important is lack of back-up systems which would function either when the machine systems are out of order or when previous working skills and habits must be applied. A need for developing methods of evaluation of these two factors from ergonomic points of view is pointed out.     

Fluorescent lipid probes: properties and application

This review is devoted to fluorescent lipid probes: the characteristics of their fluorophores; the main methods of their synthesis; and the potentialities, scope, and limitations of their use in studies of biological systems (cells, membranes and their models, enzymes of lipid metabolism, etc.). Particular attention is paid to the lipid specificity of the probes, i.e., the correspondence of their physicochemical characteristics and behavior in biological systems to those of natural lipids.