Data Integration and Mining for Synthetic Biology Design.

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Mısırlı, Göksel; Hallinan, Jennifer; Pocock, Matthew; Lord, Phillip; McLaughlin, James Alastair; Sauro, Herbert; Wipat, Anil

2016-10-21

One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

Synthetic biology between technoscience and thing knowledge.

Science.gov (United States)

Gelfert, Axel

2013-06-01

Synthetic biology presents a challenge to traditional accounts of biology: Whereas traditional biology emphasizes the evolvability, variability, and heterogeneity of living organisms, synthetic biology envisions a future of homogeneous, humanly engineered biological systems that may be combined in modular fashion. The present paper approaches this challenge from the perspective of the epistemology of technoscience. In particular, it is argued that synthetic-biological artifacts lend themselves to an analysis in terms of what has been called 'thing knowledge'. As such, they should neither be regarded as the simple outcome of applying theoretical knowledge and engineering principles to specific technological problems, nor should they be treated as mere sources of new evidence in the general pursuit of scientific understanding. Instead, synthetic-biological artifacts should be viewed as partly autonomous research objects which, qua their material-biological constitution, embody knowledge about the natural world-knowledge that, in turn, can be accessed via continuous experimental interrogation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Integrating data to acquire new knowledge: Three modes of integration in plant science.

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Leonelli, Sabina

2013-12-01

This paper discusses what it means and what it takes to integrate data in order to acquire new knowledge about biological entities and processes. Maureen O'Malley and Orkun Soyer have pointed to the scientific work involved in data integration as important and distinct from the work required by other forms of integration, such as methodological and explanatory integration, which have been more successful in captivating the attention of philosophers of science. Here I explore what data integration involves in more detail and with a focus on the role of data-sharing tools, like online databases, in facilitating this process; and I point to the philosophical implications of focusing on data as a unit of analysis. I then analyse three cases of data integration in the field of plant science, each of which highlights a different mode of integration: (1) inter-level integration, which involves data documenting different features of the same species, aims to acquire an interdisciplinary understanding of organisms as complex wholes and is exemplified by research on Arabidopsis thaliana; (2) cross-species integration, which involves data acquired on different species, aims to understand plant biology in all its different manifestations and is exemplified by research on Miscanthus giganteus; and (3) translational integration, which involves data acquired from sources within as well as outside academia, aims at the provision of interventions to improve human health (e.g. by sustaining the environment in which humans thrive) and is exemplified by research on Phytophtora ramorum. Recognising the differences between these efforts sheds light on the dynamics and diverse outcomes of data dissemination and integrative research; and the relations between the social and institutional roles of science, the development of data-sharing infrastructures and the production of scientific knowledge. Copyright © 2013 Elsevier Ltd. All rights reserved.

Semantic Data Integration and Knowledge Management to Represent Biological Network Associations.

Science.gov (United States)

Losko, Sascha; Heumann, Klaus

2017-01-01

The vast quantities of information generated by academic and industrial research groups are reflected in a rapidly growing body of scientific literature and exponentially expanding resources of formalized data, including experimental data, originating from a multitude of "-omics" platforms, phenotype information, and clinical data. For bioinformatics, the challenge remains to structure this information so that scientists can identify relevant information, to integrate this information as specific "knowledge bases," and to formalize this knowledge across multiple scientific domains to facilitate hypothesis generation and validation. Here we report on progress made in building a generic knowledge management environment capable of representing and mining both explicit and implicit knowledge and, thus, generating new knowledge. Risk management in drug discovery and clinical research is used as a typical example to illustrate this approach. In this chapter we introduce techniques and concepts (such as ontologies, semantic objects, typed relationships, contexts, graphs, and information layers) that are used to represent complex biomedical networks. The BioXM™ Knowledge Management Environment is used as an example to demonstrate how a domain such as oncology is represented and how this representation is utilized for research.

Extensive gaps and biases in our knowledge of a well-known fauna: Implications for integrating biological traits into macroecology

KAUST Repository

Tyler, Elizabeth

2011-12-09

Aim Ecologists seeking to describe patterns at ever larger scales require compilations of data on the global abundance and distribution of species. Comparable compilations of biological data are needed to elucidate the mechanisms behind these patterns, but have received far less attention. We assess the availability of biological data across an entire assemblage: the well-documented demersal marine fauna of the United Kingdom. We also test whether data availability for a species depends on its taxonomic group, maximum body size, the number of times it has been recorded in a global biogeographic database, or its commercial and conservation importance. Location Seas of the United Kingdom. Methods We defined a demersal marine fauna of 973 species from 15 phyla and 40 classes using five extensive surveys around the British Isles. We then quantified the availability of data on eight key biological traits (termed biological knowledge) for each species from online databases. Relationships between biological knowledge and our predictors were tested with generalized linear models. Results Full data on eight fundamental biological traits exist for only 9% (n= 88) of the UK demersal marine fauna, and 20% of species completely lack data. Clear trends in our knowledge exist: fish (median biological knowledge score = six traits) are much better known than invertebrates (one trait). Biological knowledge increases with biogeographic knowledge and (to a lesser extent) with body size, and is greater in species that are commercially exploited or of conservation concern. Main conclusions Our analysis reveals deep ignorance of the basic biology of a well-studied fauna, highlighting the need for far greater efforts to compile biological trait data. Clear biases in our knowledge, relating to how well sampled or \\'important\\' species are suggests that caution is required in extrapolating small subsets of biologically well-known species to ecosystem-level studies. © 2011 Blackwell

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome

Science.gov (United States)

Schoof, Heiko; Zaccaria, Paolo; Gundlach, Heidrun; Lemcke, Kai; Rudd, Stephen; Kolesov, Grigory; Arnold, Roland; Mewes, H. W.; Mayer, Klaus F. X.

2002-01-01

Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published. Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence. Besides completing the list of genes, we need to discover their cellular roles, their regulation and their interactions in order to understand the workings of the whole plant. The MIPS Arabidopsis thaliana Database (MAtDB; http://mips.gsf.de/proj/thal/db) started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project and the Arabidopsis Genome Initiative. Our aim is to transform MAtDB into an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities and by creating a comprehensive resource for Arabidopsis as a reference model for other species, including crop plants. PMID:11752263

Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks.

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Tian, Ye; Zhang, Bai; Hoffman, Eric P; Clarke, Robert; Zhang, Zhen; Shih, Ie-Ming; Xuan, Jianhua; Herrington, David M; Wang, Yue

2014-07-24

Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific and dynamic in nature. To systematically characterize the selectively activated regulatory components and mechanisms, modeling tools must be able to effectively distinguish significant rewiring from random background fluctuations. While differential networks cannot be constructed by existing knowledge alone, novel incorporation of prior knowledge into data-driven approaches can improve the robustness and biological relevance of network inference. However, the major unresolved roadblocks include: big solution space but a small sample size; highly complex networks; imperfect prior knowledge; missing significance assessment; and heuristic structural parameter learning. To address these challenges, we formulated the inference of differential dependency networks that incorporate both conditional data and prior knowledge as a convex optimization problem, and developed an efficient learning algorithm to jointly infer the conserved biological network and the significant rewiring across different conditions. We used a novel sampling scheme to estimate the expected error rate due to "random" knowledge. Based on that scheme, we developed a strategy that fully exploits the benefit of this data-knowledge integrated approach. We demonstrated and validated the principle and performance of our method using synthetic datasets. We then applied our method to yeast cell line and breast cancer microarray data and obtained biologically plausible results. The open-source R software package and the experimental data are freely available at http://www.cbil.ece.vt.edu/software.htm. Experiments on both synthetic and real data demonstrate the effectiveness of the knowledge-fused differential dependency network in revealing the statistically significant rewiring in biological

West-Life, Tools for Integrative Structural Biology

CERN Multimedia

CERN. Geneva

2018-01-01

Structural biology is part of molecular biology focusing on determining structure of macromolecules inside living cells and cell membranes. As macromolecules determines most of the functions of cells the structural knowledge is very useful for further research in metabolism, physiology to application in pharmacology etc. As macromolecules are too small to be observed directly by light microscope, there are other methods used to determine the structure including nuclear magnetic resonance (NMR), X-Ray crystalography, cryo electron microscopy and others. Each method has it's advantages and disadvantages in the terms of availability, sample preparation, resolution. West-Life project has ambition to facilitate integrative approach using multiple techniques mentioned above. As there are already lot of software tools to process data produced by the techniques above, the challenge is to integrate them together in a way they can be used by experts in one technique but not experts in other techniques. One product ...

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics

Science.gov (United States)

Schoof, Heiko; Ernst, Rebecca; Nazarov, Vladimir; Pfeifer, Lukas; Mewes, Hans-Werner; Mayer, Klaus F. X.

2004-01-01

Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db. PMID:14681437

Local Ecological Knowledge and Biological Conservation: Post-normal Science as an Intercultural Field

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Jorje Ignacio Zalles

2017-09-01

Full Text Available From a natural sciences perspective, efforts directed at the conservation of biodiversity are based upon what is known as conservation biology. Given its epistemological assumptions, conservation biology faces obstacles in the incorporation of wisdom originating in local ecological knowledge, that which a local population has gained about the local environment which it is surrounded by and due to its direct contact with this local environment, instead of the result of a product of a positivist scientific inquiry. Post-normal science has emerged in recent decades as an alternative for public management that aims to complement the search for knowledge by means of empirical approaches through the inclusion of understandings based on the everyday experiences and the subjective interpretation of natural phenomena, transcending the compartmentalization associated with scientific traditions born out of modernity. This article discusses the integration of local ecological knowledge and conservation biology from the perspective of post normal science, illustrating different forms of intercultural communication that would make the requisite dialogue of knowledges possible.

Managing heterogeneous knowledge: A Theory of External Knowledge Integration

NARCIS (Netherlands)

Kraaijenbrink, Jeroen; Wijnhoven, Alphonsus B.J.M.

2008-01-01

Knowledge integration has been theorised at the levels of organisations and inter-organisational dyads. However, no theory exists yet of the integration of knowledge from an organisation's environment. This paper addresses this void in the literature by presenting a theory of external knowledge

Integrating cell biology and proteomic approaches in plants.

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Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

2017-10-03

representative studies combining proteomic and cell biology methods for various purposes. Integrating cell biology approaches with proteomic ones allow validation and better interpretation of proteomic data. Moreover, cell biology methods remarkably extend the knowledge provided by proteomic studies and might be fundamental for the functional complementation of proteomic data. This review article summarizes current literature linking proteomics with cell biology. Copyright © 2017 Elsevier B.V. All rights reserved.

The Effect of Knowledge Linking Levels in Biology Lessons upon Students' Knowledge Structure

Science.gov (United States)

Wadouh, Julia; Liu, Ning; Sandmann, Angela; Neuhaus, Birgit J.

2014-01-01

Knowledge structure is an important aspect for defining students' competency in biology learning, but how knowledge structure is influenced by the teaching process in naturalistic biology classroom settings has scarcely been empirically investigated. In this study, 49 biology lessons in the teaching unit "blood and circulatory system" in…

Knowledge integration by thinking along

NARCIS (Netherlands)

Berends, J.J.; Debackere, K.; Garud, R.; Weggeman, M.C.D.P.

2004-01-01

Organizing depends on the integration of specialized knowledge that lies distributed across individuals. There are benefits from specialization, and, yet, the integration of knowledge across boundaries is critical for organizational vitality. How do organizations benefit from knowledge that lies in

Biosocial Conservation: Integrating Biological and Ethnographic Methods to Study Human-Primate Interactions.

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Setchell, Joanna M; Fairet, Emilie; Shutt, Kathryn; Waters, Siân; Bell, Sandra

2017-01-01

Biodiversity conservation is one of the grand challenges facing society. Many people interested in biodiversity conservation have a background in wildlife biology. However, the diverse social, cultural, political, and historical factors that influence the lives of people and wildlife can be investigated fully only by incorporating social science methods, ideally within an interdisciplinary framework. Cultural hierarchies of knowledge and the hegemony of the natural sciences create a barrier to interdisciplinary understandings. Here, we review three different projects that confront this difficulty, integrating biological and ethnographic methods to study conservation problems. The first project involved wildlife foraging on crops around a newly established national park in Gabon. Biological methods revealed the extent of crop loss, the species responsible, and an effect of field isolation, while ethnography revealed institutional and social vulnerability to foraging wildlife. The second project concerned great ape tourism in the Central African Republic. Biological methods revealed that gorilla tourism poses risks to gorillas, while ethnography revealed why people seek close proximity to gorillas. The third project focused on humans and other primates living alongside one another in Morocco. Incorporating shepherds in the coproduction of ecological knowledge about primates built trust and altered attitudes to the primates. These three case studies demonstrate how the integration of biological and social methods can help us to understand the sustainability of human-wildlife interactions, and thus promote coexistence. In each case, an integrated biosocial approach incorporating ethnographic data produced results that would not otherwise have come to light. Research that transcends conventional academic boundaries requires the openness and flexibility to move beyond one's comfort zone to understand and acknowledge the legitimacy of "other" kinds of knowledge. It is

Transdisciplinary knowledge integration : cases from integrated assessment and vulnerability assessment

NARCIS (Netherlands)

Hinkel, J.

2008-01-01

Keywords: climate change, integrated assessment, knowledge integration, transdisciplinary research, vulnerability, vulnerability assessment.
This thesis explores how transdisciplinary knowledge integration can be facilitated in the context of integrated assessments and vulnerability

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes.

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Hassani-Pak, Keywan; Rawlings, Christopher

2017-06-13

Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects. Here we review several bioinformatics tools and databases that play an important role in biological knowledge discovery and candidate gene prioritization. We conclude with several key challenges that need to be addressed in order to facilitate biological knowledge discovery in the future.

Towards Integration of Biological and Physiological Functions at Multiple Levels

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Taishin eNomura

2010-12-01

Full Text Available An aim of systems physiology today can be stated as to establish logical and quantitative bridges between phenomenological attributes of physiological entities such as cells and organs and physical attributes of biological entities, i.e., biological molecules, allowing us to describe and better understand physiological functions in terms of underlying biological functions. This article illustrates possible schema that can be used for promoting systems physiology by integrating quantitative knowledge of biological and physiological functions at multiple levels of time and space with the use of information technology infrastructure. Emphasis will be made for systematic, modular, hierarchical, and standardized descriptions of mathematical models of the functions and advantages for the use of them.

The functionality of biological knowledge in the workplace. Integrating school and workplace learning about reproduction

NARCIS (Netherlands)

Mazereeuw, M.

2013-01-01

This thesis reports on a design research project about a learning, supervising and teaching strategy to enable students in agricultural preparatory vocational secondary education (VMBO) to recognize the functionality of biological knowledge of reproduction in work placement sites. Although

Integrated Network Analysis and Effective Tools in Plant Systems Biology

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Atsushi eFukushima

2014-11-01

Full Text Available One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1 network visualization tools, (2 pathway analyses, (3 genome-scale metabolic reconstruction, and (4 the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms.

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

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Chen, Bor-Sen; Wu, Chia-Chou

2013-01-01

Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2013-10-01

Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

Creative design inspired by biological knowledge: Technologies and methods

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Tan, Runhua; Liu, Wei; Cao, Guozhong; Shi, Yuan

2018-05-01

Biological knowledge is becoming an important source of inspiration for developing creative solutions to engineering design problems and even has a huge potential in formulating ideas that can help firms compete successfully in a dynamic market. To identify the technologies and methods that can facilitate the development of biologically inspired creative designs, this research briefly reviews the existing biological-knowledge-based theories and methods and examines the application of biological-knowledge-inspired designs in various fields. Afterward, this research thoroughly examines the four dimensions of key technologies that underlie the biologically inspired design (BID) process. This research then discusses the future development trends of the BID process before presenting the conclusions.

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

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Falciani Francesco

2011-03-01

Full Text Available Abstract Background To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the

Shaping Biological Knowledge: Applications in Proteomics

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R. Appel

2006-04-01

Full Text Available The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa and a hypothesis-driven (focus on whole bacterial proteomes approach. These applications are potentially the source of specialized complements to classical biological ontologies.

Shaping biological knowledge: applications in proteomics.

Science.gov (United States)

Lisacek, F; Chichester, C; Gonnet, P; Jaillet, O; Kappus, S; Nikitin, F; Roland, P; Rossier, G; Truong, L; Appel, R

2004-01-01

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies.

Representation and integration of sociological knowledge using knowledge graphs

NARCIS (Netherlands)

Popping, R; Strijker, [No Value

1997-01-01

The representation and integration of sociological knowledge using knowledge graphs, a specific kind of semantic network, is discussed. Knowledge it systematically searched this reveals. inconsistencies, reducing superfluous research and knowledge, and showing gaps in a theory. This representation

Developing integrated crop knowledge networks to advance candidate gene discovery.

Science.gov (United States)

Hassani-Pak, Keywan; Castellote, Martin; Esch, Maria; Hindle, Matthew; Lysenko, Artem; Taubert, Jan; Rawlings, Christopher

2016-12-01

The chances of raising crop productivity to enhance global food security would be greatly improved if we had a complete understanding of all the biological mechanisms that underpinned traits such as crop yield, disease resistance or nutrient and water use efficiency. With more crop genomes emerging all the time, we are nearer having the basic information, at the gene-level, to begin assembling crop gene catalogues and using data from other plant species to understand how the genes function and how their interactions govern crop development and physiology. Unfortunately, the task of creating such a complete knowledge base of gene functions, interaction networks and trait biology is technically challenging because the relevant data are dispersed in myriad databases in a variety of data formats with variable quality and coverage. In this paper we present a general approach for building genome-scale knowledge networks that provide a unified representation of heterogeneous but interconnected datasets to enable effective knowledge mining and gene discovery. We describe the datasets and outline the methods, workflows and tools that we have developed for creating and visualising these networks for the major crop species, wheat and barley. We present the global characteristics of such knowledge networks and with an example linking a seed size phenotype to a barley WRKY transcription factor orthologous to TTG2 from Arabidopsis, we illustrate the value of integrated data in biological knowledge discovery. The software we have developed (www.ondex.org) and the knowledge resources (http://knetminer.rothamsted.ac.uk) we have created are all open-source and provide a first step towards systematic and evidence-based gene discovery in order to facilitate crop improvement.

Biological sciences teaching undergraduates’ environmental knowledge: a critical analysis

Directory of Open Access Journals (Sweden)

Silvana do Nascimento Silva

2013-12-01

Full Text Available Nowadays, environmental issues have been addressed in a way that goes beyond the natural impacts, embracing socio-economic, political and cultural aspects. This paper makes a description of the types of environmental conceptions, giving special emphasis to the interactions that permeate it, and develops an empirical work by analyzing the conceptions about the environmental knowledge of students majoring in a teacher preparation course on biological sciences of a university in the State of Bahia, Brazil. In a qualitative research, data were collected by application of a questionnaire with open questions with answers in text and drawings. The results revealed a predominance of naturalistic conceptions, while socio-environmental conceptions of systemic or socio-metabolic characteristics were not found. These findings lead to the need for the integration of these critical approaches about the environmental issue in Sciences and Biology teachers’ training, emphasizing the interactions between work, nature and society. Finally, some suggestions also emerge for future research, among which to analyze the biological sciences university teachers’ environmental conceptions and an action-research with these investigated undergraduates concerning environmental critical approaches.

BiologicalNetworks 2.0 - an integrative view of genome biology data

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Ponomarenko Julia

2010-12-01

Full Text Available Abstract Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other and their relations (interactions, co-expression, co-citations, and other. The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.

An Integrated Knowledge Management System

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Vasile Mazilescu

2014-11-01

Full Text Available The aim of this paper is to present a Knowledge Management System based on Fuzzy Logic (FLKMS, a real-time expert system to meet the challenges of the dynamic environment. The main feature of our integrated shell FLKMS is that it models and integrates the temporal relationships between the dynamic of the evolution of an economic process with some fuzzy inferential methods, using a knowledge model for control, embedded within the expert system’s operational knowledge base.

Knowledge Integration Reconceptualized from an Integrationist Perspective

OpenAIRE

Taxén, Lars

2012-01-01

The concept of knowledge integration remains on precarious ontological and epistemological grounds. Hence, the purpose of this contribution is to suggest a reconceptualization of knowledge integration from the integrationist perspective proposed by the English linguist Roy Harris. In this view, all knowledge is internally generated by the human capacity for sign-making and hence, knowledge arises from creative attempts to integrate the various activities of which human are capable of. Integra...

Integrating pedagogical content knowledge and pedagogical/psychological knowledge in mathematics

Science.gov (United States)

Harr, Nora; Eichler, Andreas; Renkl, Alexander

2014-01-01

In teacher education at universities, general pedagogical and psychological principles are often treated separately from subject matter knowledge and therefore run the risk of not being applied in the teaching subject. In an experimental study (N = 60 mathematics student teachers) we investigated the effects of providing aspects of general pedagogical/psychological knowledge (PPK) and pedagogical content knowledge (PCK) in an integrated or separated way. In both conditions (“integrated” vs. “separated”), participants individually worked on computer-based learning environments addressing the same topic: use and handling of multiple external representations, a central issue in mathematics. We experimentally varied whether PPK aspects and PCK aspects were treated integrated or apart from one another. As expected, the integrated condition led to greater application of pedagogical/psychological aspects and an increase in applying both knowledge types simultaneously compared to the separated condition. Overall, our findings indicate beneficial effects of an integrated design in teacher education. PMID:25191300

Challenges of knowledge integration in small and medium enterprises

Directory of Open Access Journals (Sweden)

Kavoos Mohannak

2014-03-01

Full Text Available This study attempts to develop a better understanding of the challenges of knowledge integration (KI within the innovation process in Small and Medium Enterprises (SMEs. Using several case studies, this study investigates how knowledge integration may be managed within the context of innovation in SMEs. The research places particular focus on identifying the challenges of knowledge integration in SMEs in relation to three aspects of knowledge integration activities, namely knowledge identification, knowledge acquisition, and knowledge sharing. Four distinct tasks emerged in the knowledge integration process, namely team building capability, capturing tacit knowledge, role of knowledge management (KM systems, and technological systemic integration. The paper suggests that managing knowledge integration in SMEs can be best managed by focusing on these four tasks, which in turn will lead to innovation.

Knowledge integration, teamwork and performance in health care.

Science.gov (United States)

Körner, Mirjam; Lippenberger, Corinna; Becker, Sonja; Reichler, Lars; Müller, Christian; Zimmermann, Linda; Rundel, Manfred; Baumeister, Harald

2016-01-01

Knowledge integration is the process of building shared mental models. The integration of the diverse knowledge of the health professions in shared mental models is a precondition for effective teamwork and team performance. As it is known that different groups of health care professionals often tend to work in isolation, the authors compared the perceptions of knowledge integration. It can be expected that based on this isolation, knowledge integration is assessed differently. The purpose of this paper is to test these differences in the perception of knowledge integration between the professional groups and to identify to what extent knowledge integration predicts perceptions of teamwork and team performance and to determine if teamwork has a mediating effect. The study is a multi-center cross-sectional study with a descriptive-explorative design. Data were collected by means of a staff questionnaire for all health care professionals working in the rehabilitation clinics. The results showed that there are significant differences in knowledge integration within interprofessional health care teams. Furthermore, it could be shown that knowledge integration is significantly related to patient-centered teamwork as well as to team performance. Mediation analysis revealed partial mediation of the effect of knowledge integration on team performance through teamwork. PRACTICAL/IMPLICATIONS: In practice, the results of the study provide a valuable starting point for team development interventions. This is the first study that explored knowledge integration in medical rehabilitation teams and its relation to patient-centered teamwork and team performance.

Integration of biological, economic and sociological knowledge by Bayesian belief networks: the interdisciplinary evaluation of potential management plans for Baltic salmon

DEFF Research Database (Denmark)

Levontin, Polina; Kulmala, Soile; Haapasaari, Päivi Elisabet

2011-01-01

There is a growing need to evaluate fisheries management plans in a comprehensive interdisciplinary context involving stakeholders. The use of a probabilistic management model to evaluate potential management plans for Baltic salmon fisheries is demonstrated. The analysis draws on several scientific...... studies: a biological stock assessment with integrated economic analysis of the commercial fisheries, an evaluation of recreational fisheries, and a sociological study aimed at understanding stakeholder perspectives and potential commitment to alternative management plans. A Bayesian belief network is used...... is highlighted by modelling the link between commitment and implementation success. Such analyses, relying on prior knowledge, can forewarn of the consequences of management choices before they are implemented...

Knowledge base and functionality of concepts of some Filipino biology teachers in five biology topics

Science.gov (United States)

Barquilla, Manuel B.

2018-01-01

This mixed research, is a snapshot of some Filipino Biology teachers' knowledge structure and how their concepts of the five topics in Biology (Photosynthesis, Cellular Respiration, human reproductive system, Mendelian genetics and NonMendelian genetics) functions and develops inside a biology classroom. The study focuses on the six biology teachers and a total of 222 students in their respective classes. Of the Six (6) teachers, three (3) are under the Science curriculum and the other three (3) are under regular curriculum in both public and private schools in Iligan city and Lanao del Norte, Philippines. The study utilized classroom discourses, concept maps, interpretative case-study method, bracketing method, and concept analysis for qualitative part; the quantitative part uses a nonparametric statistical tool, Kendall's tau Coefficient for determining relationship and congruency while measures of central tendencies and dispersion (mean, and standard deviation) for concept maps scores interpretation. Knowledge Base of Biology teachers were evaluated by experts in field of specialization having a doctorate program (e.g. PhD in Genetics) and PhD Biology candidates. The data collection entailed seven (7) months immersion: one (1) month for preliminary phase for the researcher to gain teachers' and students' confidence and the succeeding six (6) months for main observation and data collection. The evaluation of teachers' knowledge base by experts indicated that teachers' knowledge of (65%) is lower than the minimum (75%) recommended by ABD-el-Khalick and Boujaoude (1997). Thus, the experts believe that content knowledge of the teachers is hardly adequate for their teaching assignment. Moreover, the teachers in this study do not systematically use reallife situation to apply the concepts they teach. They can identify concepts too abstract for their student; however, they seldom use innovative ways to bring the discussion to their students' level of readiness and

COGMIR: A computer model for knowledge integration

Energy Technology Data Exchange (ETDEWEB)

Chen, Z.X.

1988-01-01

This dissertation explores some aspects of knowledge integration, namely, accumulation of scientific knowledge and performing analogical reasoning on the acquired knowledge. Knowledge to be integrated is conveyed by paragraph-like pieces referred to as documents. By incorporating some results from cognitive science, the Deutsch-Kraft model of information retrieval is extended to a model for knowledge engineering, which integrates acquired knowledge and performs intelligent retrieval. The resulting computer model is termed COGMIR, which stands for a COGnitive Model for Intelligent Retrieval. A scheme, named query invoked memory reorganization, is used in COGMIR for knowledge integration. Unlike some other schemes which realize knowledge integration through subjective understanding by representing new knowledge in terms of existing knowledge, the proposed scheme suggests at storage time only recording the possible connection of knowledge acquired from different documents. The actual binding of the knowledge acquired from different documents is deferred to query time. There is only one way to store knowledge and numerous ways to utilize the knowledge. Each document can be represented as a whole as well as its meaning. In addition, since facts are constructed from the documents, document retrieval and fact retrieval are treated in a unified way. When the requested knowledge is not available, query invoked memory reorganization can generate suggestion based on available knowledge through analogical reasoning. This is done by revising the algorithms developed for document retrieval and fact retrieval, and by incorporating Gentner's structure mapping theory. Analogical reasoning is treated as a natural extension of intelligent retrieval, so that two previously separate research areas are combined. A case study is provided. All the components are implemented as list structures similar to relational data-bases.

Knowledge translation in Africa for 21st century integrative biology: the "know-do gap" in family planning with contraceptive use among Somali women.

Science.gov (United States)

Ahmed, Ahmed A; Mohamed, Abdullahi A; Guled, Ibrahim A; Elamin, Hayfa M; Abou-Zeid, Alaa H

2014-11-01

An emerging dimension of 21(st) century integrative biology is knowledge translation in global health. The maternal mortality rate in Somalia is amongst the highest in the world. We set out to study the "know-do" gap in family planning measures in Somalia, with a view to inform future interventions for knowledge integration between theory and practice. We interviewed 360 Somali females of reproductive age and compared university-educated females to women with less or no education, using structured interviews, with a validated questionnaire. The mean age of marriage was 18 years, with 4.5 pregnancies per marriage. The mean for the desired family size was 9.3 and 10.5 children for the university-educated group and the less-educated group, respectively. Importantly, nearly 90% of the university-educated group knew about family planning, compared to 45.6% of the less-educated group. All of the less-educated group indicated that they would never use contraceptives, as compared to 43.5% of the university-educated group. Prevalence of contraceptive use among ever-married women was 4.3%. In the less-educated group, 80.6% indicated that they would not recommend contraceptives to other women as compared to 66.0% of the university-educated group. There is a huge gap between knowledge and practice regarding family planning in Somalia. The attendant reasons for this gap, such as level of education, expressed personal religious beliefs and others, are examined here. For primary health care to gain traction in Africa, we need to address the existing "know-do" gaps that are endemic and adversely impacting on global health. This is the first independent research study examining the knowledge gaps for family planning in Somalia in the last 20 years, with a view to understanding knowledge integration in a global world. The results shall guide policy makers, donors, and implementers to develop a sound family planning policy and program to improve maternal and child health in 21(st

A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification

Energy Technology Data Exchange (ETDEWEB)

Wang, Jing; Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Varnum, Susan M.; Brown, Joseph N.; Riensche, Roderick M.; Adkins, Joshua N.; Jacobs, Jon M.; Hoidal, John R.; Scholand, Mary Beth; Pounds, Joel G.; Blackburn, Michael R.; Rodland, Karin D.; McDermott, Jason E.

2013-10-01

Background. The availability of large complex data sets generated by high throughput technologies has enabled the recent proliferation of disease biomarker studies. However, a recurring problem in deriving biological information from large data sets is how to best incorporate expert knowledge into the biomarker selection process. Objective. To develop a generalizable framework that can incorporate expert knowledge into data-driven processes in a semiautomated way while providing a metric for optimization in a biomarker selection scheme. Methods. The framework was implemented as a pipeline consisting of five components for the identification of signatures from integrated clustering (ISIC). Expert knowledge was integrated into the biomarker identification process using the combination of two distinct approaches; a distance-based clustering approach and an expert knowledge-driven functional selection. Results. The utility of the developed framework ISIC was demonstrated on proteomics data from a study of chronic obstructive pulmonary disease (COPD). Biomarker candidates were identified in a mouse model using ISIC and validated in a study of a human cohort. Conclusions. Expert knowledge can be introduced into a biomarker discovery process in different ways to enhance the robustness of selected marker candidates. Developing strategies for extracting orthogonal and robust features from large data sets increases the chances of success in biomarker identification.

An Integrated Model of Knowledge Acquisition and Innovation: Examining the Mediation Effects of Knowledge Integration and Knowledge Application

Science.gov (United States)

Dahiyat, Samer E.

2015-01-01

The aim of this research is to empirically investigate the relationships among the three vital knowledge management processes of acquisition, integration and application, and their effects on organisational innovation in the pharmaceutical manufacturing industry in Jordan; a knowledge-intensive business service (KIBS) sector. Structural equation…

On the Limitations of Biological Knowledge

Science.gov (United States)

Dougherty, Edward R; Shmulevich, Ilya

2012-01-01

Scientific knowledge is grounded in a particular epistemology and, owing to the requirements of that epistemology, possesses limitations. Some limitations are intrinsic, in the sense that they depend inherently on the nature of scientific knowledge; others are contingent, depending on the present state of knowledge, including technology. Understanding limitations facilitates scientific research because one can then recognize when one is confronted by a limitation, as opposed to simply being unable to solve a problem within the existing bounds of possibility. In the hope that the role of limiting factors can be brought more clearly into focus and discussed, we consider several sources of limitation as they apply to biological knowledge: mathematical complexity, experimental constraints, validation, knowledge discovery, and human intellectual capacity. PMID:23633917

Integrating phosphoproteomics in systems biology

Directory of Open Access Journals (Sweden)

Yu Liu

2014-07-01

Full Text Available Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed.

Data integration in biological research: an overview.

Science.gov (United States)

Lapatas, Vasileios; Stefanidakis, Michalis; Jimenez, Rafael C; Via, Allegra; Schneider, Maria Victoria

2015-12-01

Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

Multi-omic data integration enables discovery of hidden biological regularities

DEFF Research Database (Denmark)

Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin

2016-01-01

Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi- level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration...... of primary omics data reveals regularities that tie cellular processes together in Escherichia coli: the number of protein molecules made per mRNA transcript and the number of ribosomes required per translated protein molecule. Second, we show that genome- scale models, based on genomic and bibliomic data......, enable quantitative synchronization of disparate data types. Integrating omics data with models enabled the discovery of two novel regularities: condition invariant in vivo turnover rates of enzymes and the correlation of protein structural motifs and translational pausing. These regularities can...

Towards an Integrative Model of Knowledge Transfer

DEFF Research Database (Denmark)

Turcan, Romeo V.; Heslop, Ben

This paper aims to contribute towards the advancement of an efficient architecture of a single market for knowledge through the development of an integrative model of knowledge transfer. Within this aim, several points of departure can be singled out. One, the article builds on the call of the Eu......This paper aims to contribute towards the advancement of an efficient architecture of a single market for knowledge through the development of an integrative model of knowledge transfer. Within this aim, several points of departure can be singled out. One, the article builds on the call...... business and academia, and implementing the respective legislature are enduring. The research objectives were to explore (i) the process of knowledge transfer in universities, including the nature of tensions, obstacles and incentives, (ii) the relationships between key stakeholders in the KT market...... of the emergent integrative model of knowledge transfer. In an attempt to bring it to a higher level of generalizability, the integrative model of KT is further conceptualized from a ‘sociology of markets’ perspective resulting in an emergent architecture of a single market for knowledge. Future research...

Systematic Representation of Biology Knowledge.

Science.gov (United States)

Faletti, Joseph

A major goal of science education is to turn novices (students) into experts (scientists or science literates) with a minimum amount of pain, effort, and time. However, transfer of biology knowledge from instructor to student usually results in a loss of the rich interconnections that an expert has. The papers in this set describe efforts to…

Biology as an Integrating Natural Science Domain

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 3. Biology as an Integrating Natural Science Domain: A Proposal for BSc (Hons) in Integrated Biology. Kambadur Muralidhar. Classroom Volume 13 Issue 3 March 2008 pp 272-276 ...

Fuzzy knowledge bases integration based on ontology

OpenAIRE

Ternovoy, Maksym; Shtogrina, Olena

2012-01-01

the paper describes the approach for fuzzy knowledge bases integration with the usage of ontology. This approach is based on metadata-base usage for integration of different knowledge bases with common ontology. The design process of metadata-base is described.

Integrated knowledge translation: digging deeper, moving forward.

Science.gov (United States)

Kothari, Anita; Wathen, C Nadine

2017-06-01

Integrated knowledge translation has risen in popularity as a solution to the underuse of research in policy and practice settings. It engages knowledge users-policymakers, practitioners, patients/consumers or their advocates, and members of the wider public-in mutually beneficial research that can involve the joint development of research questions, data collection, analysis and dissemination of findings. Knowledge that is co-produced has a better chance of being implemented. The purpose of this paper is to update developments in the field of integrated knowledge translation through a deeper analysis of the approach in practice-oriented and policy-oriented health research. We present collaborative models that fall outside the scope of integrated knowledge translation, but then explore consensus-based approaches and networks as alternate sites of knowledge co-production. We discuss the need to advance the field through the development, or use, of data collection and interpretation tools that creatively engage knowledge users in the research process. Most importantly, conceptually relevant outcomes need to be identified, including ones that focus on team transformation through the co-production of knowledge. We explore some of these challenges and benefits in detail to help researchers understand what integrated knowledge translation means, and whether the approach's potential added value is worth the investment of time, energy and other resources. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

Science.gov (United States)

D'Souza, Mark; Sulakhe, Dinanath; Wang, Sheng; Xie, Bing; Hashemifar, Somaye; Taylor, Andrew; Dubchak, Inna; Conrad Gilliam, T; Maltsev, Natalia

2017-01-01

Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.

Biological and Psychosocial Predictors of Postpartum Depression: Systematic Review and Call for Integration

Science.gov (United States)

Tanner Stapleton, Lynlee R.; Guardino, Christine M.; Hahn-Holbrook, Jennifer; Schetter, Christine Dunkel

2017-01-01

Postpartum depression (PPD) adversely affects the health and well being of many new mothers, their infants, and their families. A comprehensive understanding of biopsychosocial precursors to PPD is needed to solidify the current evidence base for best practices in translation. We conducted a systematic review of research published from 2000 through 2013 on biological and psychosocial factors associated with PPD and postpartum depressive symptoms. Two hundred fourteen publications based on 199 investigations of 151,651 women in the first postpartum year met inclusion criteria. The biological and psychosocial literatures are largely distinct, and few studies provide integrative analyses. The strongest PPD risk predictors among biological processes are hypothalamic-pituitary-adrenal dysregulation, inflammatory processes, and genetic vulnerabilities. Among psychosocial factors, the strongest predictors are severe life events, some forms of chronic strain, relationship quality, and support from partner and mother. Fully integrated biopsychosocial investigations with large samples are needed to advance our knowledge of PPD etiology. PMID:25822344

Biological condition gradient: Applying a framework for determining the biological integrity of coral reefs

Science.gov (United States)

The goals of the U.S. Clean Water Act (CWA) are to restore and maintain the chemical, physical and biological integrity of water resources. Although clean water is a goal, another is to safeguard biological communities by defining levels of biological integrity to protect aquatic...

Untangling knowledge creation and knowledge integration in enterprise wikis

DEFF Research Database (Denmark)

Beck, Roman; Rai, Arun; Fischbach, Kai

2015-01-01

A central challenge organizations face is how to build, store, and maintain knowledge over time. Enterprise wikis are community-based knowledge systems situated in an organizational context. These systems have the potential to play an important role in managing knowledge within organizations......, but the motivating factors that drive individuals to contribute their knowledge to these systems is not very well understood. We theorize that enterprise wiki initiatives require two separate and distinct types of knowledge-sharing behaviors to succeed: knowledge creation (KC) and knowledge integration (KI). We...... examine a Wiki initiative at a major German bank to untangle the motivating factors behind KC and KI. Our results suggest KC and KI are indeed two distinct behaviors, reconcile inconsistent findings from past studies on the role of motivational factors for knowledge sharing to establish shared electronic...

Integrating quantitative thinking into an introductory biology course improves students' mathematical reasoning in biological contexts.

Science.gov (United States)

Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

2014-01-01

Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students' apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students' understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students' inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students' biology learning.

Integrating Quantitative Thinking into an Introductory Biology Course Improves Students’ Mathematical Reasoning in Biological Contexts

Science.gov (United States)

Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

2014-01-01

Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students’ apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students’ understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students’ inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students’ biology learning. PMID:24591504

Knowledge-sharing Behavior and Post-acquisition Integration Failure

DEFF Research Database (Denmark)

Gammelgaard, Jens; Husted, Kenneth; Michailova, Snejina

2004-01-01

AbstractNot achieving the anticipated synergy effects in the post-acquisition integration context is a serious causefor the high acquisition failure rate. While existing studies on failures of acquisitions exist fromeconomics, finance, strategy, organization theory, and human resources management......, this paper appliesinsights from the knowledge-sharing literature. The paper establishes a conceptual link between obstaclesin the post-acquisition integration processes and individual knowledge-sharing behavior as related toknowledge transmitters and knowledge receivers. We argue that such an angle offers...... important insights toexplaining the high failure rate in acquisitions.Descriptors: post-acquisition integration, acquisition failure, individual knowledge-sharing behavior...

Integrating indigenous games and knowledge into Physical Education

African Journals Online (AJOL)

Integrating indigenous games and knowledge into Physical Education: Implications for ... The aim of this study was to analyse indigenous Zulu games towards integrating indigenous game skill and knowledge ... AJOL African Journals Online.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

OpenAIRE

Ziegler, Brittany; Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (postte...

Accelerating knowledge discovery through community data sharing and integration.

Science.gov (United States)

Yip, Y L

2009-01-01

To summarize current excellent research in the field of bioinformatics. Synopsis of the articles selected for the IMIA Yearbook 2009. The selection process for this yearbook's section on Bioinformatics results in six excellent articles highlighting several important trends First, it can be noted that Semantic Web technology continues to play an important role in heterogeneous data integration. Novel applications also put more emphasis on its ability to make logical inferences leading to new insights and discoveries. Second, translational research, due to its complex nature, increasingly relies on collective intelligence made available through the adoption of community-defined protocols or software architectures for secure data annotation, sharing and analysis. Advances in systems biology, bio-ontologies and text-ming can also be noted. Current biomedical research gradually evolves towards an environment characterized by intensive collaboration and more sophisticated knowledge processing activities. Enabling technologies, either Semantic Web or other solutions, are expected to play an increasingly important role in generating new knowledge in the foreseeable future.

Integrative Assessment of Evolutionary Theory Acceptance and Knowledge Levels of Biology Undergraduate Students from a Brazilian University

Science.gov (United States)

Tavares, Gustavo Medina; Bobrowski, Vera Lucia

2018-01-01

The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students'…

IS IT POSSIBLE TO INTEGRATE BASIC BIOLOGICAL DISCIPLINES IN A PRIVATE INSTITUTION?

Directory of Open Access Journals (Sweden)

L.A. Azzalis

2008-05-01

Full Text Available Basic biological disciplines as biochemistry, genetic and molecular biology have grown faster than any of other sciences. Moreover, those disciplines contribute to the understanding and treatment of an elevated number of illnesses. On the other hand, teachers cannot assure the graduating students that each particular discipline  is essential.  Furthermore,  those disciplines are often studied separately without any interdisciplinary integration between them.  The new curriculum proposed at Anhembi Morumbi University  - a private institution placed at São Paulo city  - incorporates learning blocks that  have been designed to integrate basic biological disciplines and clinical contents from the beginning in order to provide the stimulation and motivation to guide the  student through his learning.  The educational trend has concentrated on the following steps: 1 Biochemistry, genetic, cellular and molecular biology teachers´ from that institution have elaborated a new discipline  that was named Biologic Process. The aim of this new discipline was integrate basic biological sciences in a single content;  2  Selecting problems that could be discussed in the light of biochemistry, genetic and molecular contents; e.g. sickle cell anemia; 3 Developing  an innovative instructional method that challenges students “learn to learn” different from problem-based learning , economically unavailable at any particular university,  and  4 Assessments that measure knowledge, skills, attitudes and beliefs.  We believe that the future pedagogical system in  private health university will be a combination of “classical”  presentation of contents combined with actively involved students in the educational process and instruction based on either hypothetical  or real clinical cases in order to create  the stimulus for  the student continues to  integrate basic and clinical investigation.

Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

Science.gov (United States)

Himmelstein, Daniel Scott; Lizee, Antoine; Hessler, Christine; Brueggeman, Leo; Chen, Sabrina L; Hadley, Dexter; Green, Ari; Khankhanian, Pouya; Baranzini, Sergio E

2017-09-22

The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data were integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms. Next, we identified network patterns that distinguish treatments from non-treatments. Then, we predicted the probability of treatment for 209,168 compound-disease pairs (het.io/repurpose). Our predictions validated on two external sets of treatment and provided pharmacological insights on epilepsy, suggesting they will help prioritize drug repurposing candidates. This study was entirely open and received realtime feedback from 40 community members.

A data integration approach for cell cycle analysis oriented to model simulation in systems biology

Directory of Open Access Journals (Sweden)

Mosca Ettore

2007-08-01

Full Text Available Abstract Background The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep knowledge of the molecular aspect of this biological process can contribute to making cancer research more accurate and innovative. In this context the mathematical modelling of the cell cycle has a relevant role to quantify the behaviour of each component of the systems. The mathematical modelling of a biological process such as the cell cycle allows a systemic description that helps to highlight some features such as emergent properties which could be hidden when the analysis is performed only from a reductionism point of view. Moreover, in modelling complex systems, a complete annotation of all the components is equally important to understand the interaction mechanism inside the network: for this reason data integration of the model components has high relevance in systems biology studies. Description In this work, we present a resource, the Cell Cycle Database, intended to support systems biology analysis on the Cell Cycle process, based on two organisms, yeast and mammalian. The database integrates information about genes and proteins involved in the cell cycle process, stores complete models of the interaction networks and allows the mathematical simulation over time of the quantitative behaviour of each component. To accomplish this task, we developed, a web interface for browsing information related to cell cycle genes, proteins and mathematical models. In this framework, we have implemented a pipeline which allows users to deal with the mathematical part of the models, in order to solve, using different variables, the ordinary differential equation systems that describe the biological process. Conclusion This integrated system is freely available in order to support systems biology research on the cell cycle and

Reconstruction of biological networks based on life science data integration.

Science.gov (United States)

Kormeier, Benjamin; Hippe, Klaus; Arrigo, Patrizio; Töpel, Thoralf; Janowski, Sebastian; Hofestädt, Ralf

2010-10-27

For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH--an integration toolkit for building life science data warehouses, CardioVINEdb--a information system for biological data in cardiovascular-disease and VANESA--a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

Science.gov (United States)

Ziegler, Brittany; Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students' perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest…

Overcoming Knowledge Gaps in Postmerger Integration

DEFF Research Database (Denmark)

Alaranta, Maria Eliisa; Martela, Eero

2012-01-01

Over 50% of mergers and acquisitions (M&As) fail, mainly because of integration problems. In such integrations, much of the experiential (learning-by-doing) knowledge critical for running the business becomes redundant or is lost. However, we know virtually nothing about what type of mechanisms...

Reconstruction of biological networks based on life science data integration

Directory of Open Access Journals (Sweden)

Kormeier Benjamin

2010-06-01

Full Text Available For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH - an integration toolkit for building life science data warehouses, CardioVINEdb - a information system for biological data in cardiovascular-disease and VANESA- a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

Integrating Traditional and Evolutionary Knowledge in Biodiversity Conservation: a Population Level Case Study

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Dylan J. Fraser

2006-12-01

Full Text Available Despite their dual importance in the assessment of endangered/threatened species, there have been few attempts to integrate traditional ecological knowledge (TEK and evolutionary biology knowledge (EBK at the population level. We contrasted long-term aboriginal TEK with previously obtained EBK in the context of seasonal migratory habits and population biology of a salmonid fish, brook charr, (Salvelinus fontinalis inhabiting a large, remote postglacial lake. Compilation of TEK spanning four decades involved analytical workshops, semidirective interviews, and collaborative fieldwork with local aboriginal informants and fishing guides. We found that TEK complemented EBK of brook charr by providing concordant and additional information about (1 population viability; (2 breeding areas and migration patterns of divergent populations; and (3 the behavioral ecology of populations within feeding areas; all of which may ultimately affect the maintenance of population diversity. Aboriginal concerns related to human pressures on this species, not revealed by EBK, also help to focus future conservation initiatives for divergent populations and to encourage restoration of traditional fishing practices. However, relative to EBK, the relevance of TEK to salmonid biodiversity conservation was evident mainly at a smaller spatial scale, for example, that of individual rivers occupied by populations or certain lake sectors. Nevertheless, EBK was only collected over a 4-yr period, so TEK provided an essential long-term temporal window to evaluate population differences and persistence. We concluded that, despite different conceptual underpinnings, spatially and temporally varying TEK and EBK both contribute to the knowledge base required to achieve sustainability and effective biodiversity conservation planning for a given species. Such integration may be particularly relevant in many isolated regions, where intraspecific diversity can go unrecognized due to sparse

The acquisition of biological knowledge during childhood: Cognitive conflict or tabula rasa?

Science.gov (United States)

Lawson, Anton E.

Clinical interviews were conducted with three elementary school children, who varied in age but not in family or school environment, to determine the extent to which they held naive misconceptions about important biological topics and to determine agewise trends in the development of biological knowledge. Does early biological knowledge acquisition follow a pattern of spontaneous naive theory construction and cognitive conflict or does it follow a pattern of gradual accretion to an initially blank slate? Contrary to findings in the physical sciences, little evidence was found for biological misconceptions as knowledge acquisition appeared to more directly follow the gradual accretion hypothesis with the primary source of that knowledge adult authority rather than personal experience. However, conceptual change teaching is still advocated due to its ability to provoke students to consider and test alternative conceptions (even if they are not their own) as a means of encouraging the development of important general reasoning patterns utilized in the testing of causal hypotheses.

PathSys: integrating molecular interaction graphs for systems biology

Directory of Open Access Journals (Sweden)

Raval Alpan

2006-02-01

Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

Science.gov (United States)

Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

2016-06-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

Directory of Open Access Journals (Sweden)

Andra Waagmeester

2016-06-01

Full Text Available The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

Science.gov (United States)

Waagmeester, Andra; Pico, Alexander R.

2016-01-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

Using Multiple Lenses to Examine the Development of Beginning Biology Teachers' Pedagogical Content Knowledge for Teaching Natural Selection Simulations

Science.gov (United States)

Sickel, Aaron J.; Friedrichsen, Patricia

2018-02-01

Pedagogical content knowledge (PCK) has become a useful construct to examine science teacher learning. Yet, researchers conceptualize PCK development in different ways. The purpose of this longitudinal study was to use three analytic lenses to understand the development of three beginning biology teachers' PCK for teaching natural selection simulations. We observed three early-career biology teachers as they taught natural selection in their respective school contexts over two consecutive years. Data consisted of six interviews with each participant. Using the PCK model developed by Magnusson et al. (1999), we examined topic-specific PCK development utilizing three different lenses: (1) expansion of knowledge within an individual knowledge base, (2) integration of knowledge across knowledge bases, and (3) knowledge that explicitly addressed core concepts of natural selection. We found commonalities across the participants, yet each lens was also useful to understand the influence of different factors (e.g., orientation, subject matter preparation, and the idiosyncratic nature of teacher knowledge) on PCK development. This multi-angle approach provides implications for considering the quality of beginning science teachers' knowledge and future research on PCK development. We conclude with an argument that explicitly communicating lenses used to understand PCK development will help the research community compare analytic approaches and better understand the nature of science teacher learning.

Semantic Health Knowledge Graph: Semantic Integration of Heterogeneous Medical Knowledge and Services

Directory of Open Access Journals (Sweden)

Longxiang Shi

2017-01-01

Full Text Available With the explosion of healthcare information, there has been a tremendous amount of heterogeneous textual medical knowledge (TMK, which plays an essential role in healthcare information systems. Existing works for integrating and utilizing the TMK mainly focus on straightforward connections establishment and pay less attention to make computers interpret and retrieve knowledge correctly and quickly. In this paper, we explore a novel model to organize and integrate the TMK into conceptual graphs. We then employ a framework to automatically retrieve knowledge in knowledge graphs with a high precision. In order to perform reasonable inference on knowledge graphs, we propose a contextual inference pruning algorithm to achieve efficient chain inference. Our algorithm achieves a better inference result with precision and recall of 92% and 96%, respectively, which can avoid most of the meaningless inferences. In addition, we implement two prototypes and provide services, and the results show our approach is practical and effective.

Calculation of integrated biological response in brachytherapy

International Nuclear Information System (INIS)

Dale, Roger G.; Coles, Ian P.; Deehan, Charles; O'Donoghue, Joseph A.

1997-01-01

Purpose: To present analytical methods for calculating or estimating the integrated biological response in brachytherapy applications, and which allow for the presence of dose gradients. Methods and Materials: The approach uses linear-quadratic (LQ) formulations to identify an equivalent biologically effective dose (BED eq ) which, if applied to a specified tissue volume, would produce the same biological effect as that achieved by a given brachytherapy application. For simple geometrical cases, BED multiplying factors have been derived which allow the equivalent BED for tumors to be estimated from a single BED value calculated at a dose reference point. For more complex brachytherapy applications a voxel-by-voxel determination of the equivalent BED will be more accurate. Equations are derived which when incorporated into brachytherapy software would facilitate such a process. Results: At both high and low dose rates, the BEDs calculated at the dose reference point are shown to be lower than the true values by an amount which depends primarily on the magnitude of the prescribed dose; the BED multiplying factors are higher for smaller prescribed doses. The multiplying factors are less dependent on the assumed radiobiological parameters. In most clinical applications involving multiple sources, particularly those in multiplanar arrays, the multiplying factors are likely to be smaller than those derived here for single sources. The overall suggestion is that the radiobiological consequences of dose gradients in well-designed brachytherapy treatments, although important, may be less significant than is sometimes supposed. The modeling exercise also demonstrates that the integrated biological effect associated with fractionated high-dose-rate (FHDR) brachytherapy will usually be different from that for an 'equivalent' continuous low-dose-rate (CLDR) regime. For practical FHDR regimes involving relatively small numbers of fractions, the integrated biological effect to

Integrated learning: Ways of fostering the applicability of teachers’ pedagogical and psychological knowledge

Directory of Open Access Journals (Sweden)

Nora eHarr

2015-06-01

Full Text Available In teacher education, general pedagogical and psychological knowledge is often taught separately from the teaching subject itself, potentially leading to inert knowledge. In an experimental study with 69 mathematics student teachers, we tested the benefits of fostering the integration of pedagogical content knowledge and general pedagogical and psychological knowledge with respect to knowledge application. Integration was fostered either by integrating the contents or by prompting the learners to integrate separately-taught knowledge. Fostering integration, as compared to a separate presentation without integration help, led to more applicable pedagogical and psychological knowledge and greater simultaneous application of pedagogical and psychological knowledge and pedagogical content knowledge. The advantages of fostering knowledge integration were not moderated by the student teachers’ prior knowledge or working memory capacity. A disadvantage of integrating different knowledge types referred to increased learning times.

PathText: a text mining integrator for biological pathway visualizations

Science.gov (United States)

Kemper, Brian; Matsuzaki, Takuya; Matsuoka, Yukiko; Tsuruoka, Yoshimasa; Kitano, Hiroaki; Ananiadou, Sophia; Tsujii, Jun'ichi

2010-01-01

Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations. Contact: brian@monrovian.com. PMID:20529930

The Impact of Organizational Knowledge Integrators on Cooperative R&D Projects

DEFF Research Database (Denmark)

Bulathsinhala, Nadika

2014-01-01

This paper addresses the fact that R&D projects that incorporate external knowledge sources not only depend on the number of sources, but also on integrating the right source. An organizational knowledge integrator has a natural interest due to its position in the value chain and the technology...... phase to pull the knowledge from earlier phases of development closer towards commercialization. The aim of the paper is to examine if organizational knowledge integrators in R&D projects have a positive impact on innovative performance compared to projects that do not involve a knowledge integrator...

Assessment of knowledge of participants on basic molecular biology techniques after 5-day intensive molecular biology training workshops in Nigeria.

Science.gov (United States)

Yisau, J I; Adagbada, A O; Bamidele, T; Fowora, M; Brai, B I C; Adebesin, O; Bamidele, M; Fesobi, T; Nwaokorie, F O; Ajayi, A; Smith, S I

2017-07-08

The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of Medical Research (NIMR), to improve the knowledge and skills of laboratory personnel and academics in health, research, and educational facilities. Five-day molecular biology workshops were conducted annually between 2011 and 2014, with participants drawn from health, research facilities, and the academia. The courses consisted of theoretical and practical sessions. The impact of the workshops on knowledge and skill acquisition was evaluated by pre- and post-tests which consisted of 25 multiple choice and other questions. Sixty-five participants took part in the workshops. The mean knowledge of molecular biology as evaluated by the pre- and post-test assessments were 8.4 (95% CI 7.6-9.1) and 13.0 (95 CI 11.9-14.1), respectively. The mean post-test score was significantly greater than the mean pre-test score (p biology workshop significantly increased the knowledge and skills of participants in molecular biology techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):313-317, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data

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Gao Shouguo

2011-08-01

Full Text Available Abstract Background Bayesian Network (BN is a powerful approach to reconstructing genetic regulatory networks from gene expression data. However, expression data by itself suffers from high noise and lack of power. Incorporating prior biological knowledge can improve the performance. As each type of prior knowledge on its own may be incomplete or limited by quality issues, integrating multiple sources of prior knowledge to utilize their consensus is desirable. Results We introduce a new method to incorporate the quantitative information from multiple sources of prior knowledge. It first uses the Naïve Bayesian classifier to assess the likelihood of functional linkage between gene pairs based on prior knowledge. In this study we included cocitation in PubMed and schematic similarity in Gene Ontology annotation. A candidate network edge reservoir is then created in which the copy number of each edge is proportional to the estimated likelihood of linkage between the two corresponding genes. In network simulation the Markov Chain Monte Carlo sampling algorithm is adopted, and samples from this reservoir at each iteration to generate new candidate networks. We evaluated the new algorithm using both simulated and real gene expression data including that from a yeast cell cycle and a mouse pancreas development/growth study. Incorporating prior knowledge led to a ~2 fold increase in the number of known transcription regulations recovered, without significant change in false positive rate. In contrast, without the prior knowledge BN modeling is not always better than a random selection, demonstrating the necessity in network modeling to supplement the gene expression data with additional information. Conclusion our new development provides a statistical means to utilize the quantitative information in prior biological knowledge in the BN modeling of gene expression data, which significantly improves the performance.

Fostering Students' Conceptual Knowledge in Biology in the Context of German National Education Standards

Science.gov (United States)

Förtsch, Christian; Dorfner, Tobias; Baumgartner, Julia; Werner, Sonja; von Kotzebue, Lena; Neuhaus, Birgit J.

2018-04-01

The German National Education Standards (NES) for biology were introduced in 2005. The content part of the NES emphasizes fostering conceptual knowledge. However, there are hardly any indications of what such an instructional implementation could look like. We introduce a theoretical framework of an instructional approach to foster students' conceptual knowledge as demanded in the NES (Fostering Conceptual Knowledge) including instructional practices derived from research on single core ideas, general psychological theories, and biology-specific features of instructional quality. First, we aimed to develop a rating manual, which is based on this theoretical framework. Second, we wanted to describe current German biology instruction according to this approach and to quantitatively analyze its effectiveness. And third, we aimed to provide qualitative examples of this approach to triangulate our findings. In a first step, we developed a theoretically devised rating manual to measure Fostering Conceptual Knowledge in videotaped lessons. Data for quantitative analysis included 81 videotaped biology lessons of 28 biology teachers from different German secondary schools. Six hundred forty students completed a questionnaire on their situational interest after each lesson and an achievement test. Results from multilevel modeling showed significant positive effects of Fostering Conceptual Knowledge on students' achievement and situational interest. For qualitative analysis, we contrasted instruction of four teachers, two with high and two with low student achievement and situational interest using the qualitative method of thematic analysis. Qualitative analysis revealed five main characteristics describing Fostering Conceptual Knowledge. Therefore, implementing Fostering Conceptual Knowledge in biology instruction seems promising. Examples of how to implement Fostering Conceptual Knowledge in instruction are shown and discussed.

Integr8: enhanced inter-operability of European molecular biology databases.

Science.gov (United States)

Kersey, P J; Morris, L; Hermjakob, H; Apweiler, R

2003-01-01

The increasing production of molecular biology data in the post-genomic era, and the proliferation of databases that store it, require the development of an integrative layer in database services to facilitate the synthesis of related information. The solution of this problem is made more difficult by the absence of universal identifiers for biological entities, and the breadth and variety of available data. Integr8 was modelled using UML (Universal Modelling Language). Integr8 is being implemented as an n-tier system using a modern object-oriented programming language (Java). An object-relational mapping tool, OJB, is being used to specify the interface between the upper layers and an underlying relational database. The European Bioinformatics Institute is launching the Integr8 project. Integr8 will be an automatically populated database in which we will maintain stable identifiers for biological entities, describe their relationships with each other (in accordance with the central dogma of biology), and store equivalences between identified entities in the source databases. Only core data will be stored in Integr8, with web links to the source databases providing further information. Integr8 will provide the integrative layer of the next generation of bioinformatics services from the EBI. Web-based interfaces will be developed to offer gene-centric views of the integrated data, presenting (where known) the links between genome, proteome and phenotype.

Integrating ergonomic knowledge into engineering design processes

DEFF Research Database (Denmark)

Hall-Andersen, Lene Bjerg

Integrating ergonomic knowledge into engineering design processes has been shown to contribute to healthy and effective designs of workplaces. However, it is also well-recognized that, in practice, ergonomists often have difficulties gaining access to and impacting engineering design processes...... employed in the same company, constituted a supporting factor for the possibilities to integrate ergonomic knowledge into the engineering design processes. However, the integration activities remained discrete and only happened in some of the design projects. A major barrier was related to the business...... to the ergonomic ambitions of the clients. The ergonomists’ ability to navigate, act strategically, and compromise on ergonomic inputs is also important in relation to having an impact in the engineering design processes. Familiarity with the engineering design terminology and the setup of design projects seems...

Integrative Radiation Biology

Energy Technology Data Exchange (ETDEWEB)

Barcellos-Hoff, Mary Helen [New York University School of Medicine, NY (United States)

2015-02-27

We plan to study tissue-level mechanisms important to human breast radiation carcinogenesis. We propose that the cell biology of irradiated tissues reveals a coordinated multicellular damage response program in which individual cell contributions are primarily directed towards suppression of carcinogenesis and reestablishment of homeostasis. We identified transforming growth factor β1 (TGFβ) as a pivotal signal. Notably, we have discovered that TGFβ suppresses genomic instability by controlling the intrinsic DNA damage response and centrosome integrity. However, TGFβ also mediates disruption of microenvironment interactions, which drive epithelial to mesenchymal transition in irradiated human mammary epithelial cells. This apparent paradox of positive and negative controls by TGFβ is the topic of the present proposal. First, we postulate that these phenotypes manifest differentially following fractionated or chronic exposures; second, that the interactions of multiple cell types in tissues modify the responses evident in this single cell type culture models. The goals are to: 1) study the effect of low dose rate and fractionated radiation exposure in combination with TGFβ on the irradiated phenotype and genomic instability of non-malignant human epithelial cells; and 2) determine whether stromal-epithelial interactions suppress the irradiated phenotype in cell culture and the humanized mammary mouse model. These data will be used to 3) develop a systems biology model that integrates radiation effects across multiple levels of tissue organization and time. Modeling multicellular radiation responses coordinated via extracellular signaling could have a significant impact on the extrapolation of human health risks from high dose to low dose/rate radiation exposure.

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.

Science.gov (United States)

Tolar, Bradley B; Herrmann, Jonathan; Bargar, John R; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A

2017-10-01

Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

[Physicians' knowledge in Israel on the biology and control of head lice].

Science.gov (United States)

Mumcuoglu, Kosta Y; Mumcuoglu, Michael; Danilevich, Maria; Gilead, Leon

2008-10-01

Health providers such as physicians, nurses and pharmacists should be knowledgeable about the biology of head lice and the ways to control them effectively, in order to reduce the proportion of children infested with head lice. To evaluate the knowledge of physicians in Israel on the biology and epidemiology of lice, as well as their experience with infested individuals and their preferences for diagnosis, prophylaxis and control. An anonymous questionnaire with 37 questions was used. The first 20 questions addressed the general knowledge of physicians on lice biology and control, while the remaining 17 questions were related to their personal experience with lice and louse treatment. Out of 273 physicians interviewed 66.8% had good knowledge of lice, while the remaining 33.2% had some knowledge on lice. The difference between the groups of physicians with medium and good knowledge on lice was borderline significant (P=0.0722), with the dermatologists borderline significantly less knowledgeable than the rest (P=0.0765). Significant differences were found between those physicians with 4-6 or 11-20 years of professional experience and the remaining groups (twice Pbiology and control was higher than male physicians (39.4% and 29.4%, respectively), the differences were borderline significant (P=0.09). Pediatricians and dermatologists examined significantly more children than family physicians and general practitioners (P control of head louse infestations.

Knowledge representation for integrated plant operation and maintenance

DEFF Research Database (Denmark)

Lind, Morten

2010-01-01

Integrated operation and maintenance of process plants has many advantages. One advantage is the improved economy obtained by reducing the number of plant shutdowns. Another is to increase reliability of operation by monitoring of risk levels during on-line maintenance. Integrated plant operation...... and maintenance require knowledge bases which can capture the interactions between the two plant activities. As an example, taking out a component or a subsystem for maintenance during operation will require a knowledge base representing the interactions between plant structure, functions, operating states...... and goals and incorporate knowledge about redundancy and reliability data. Multilevel Flow Modeling can be used build knowledge bases representing plant goals and functions and has been applied for fault diagnosis and supervisory control but currently it does not take into account structural information...

An Integrated Approach to Biology

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 8. An Integrated Approach to Biology. Aniket Bhattacharya. General Article Volume 16 Issue 8 August 2011 pp 742-753. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/016/08/0742-0753 ...

Integrating knowledge and knowledge processes: A critical incident study of product development projects.

NARCIS (Netherlands)

Kraaijenbrink, Jeroen

2012-01-01

Various scholars have argued that knowledge processes in organizations are integrally linked in practice. The extant literature though treats them separately and thereby disregards the interactions and tensions between them. A result of this way of studying knowledge processes is that little is

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework.

Science.gov (United States)

Chen, Yi-An; Tripathi, Lokesh P; Mizuguchi, Kenji

2016-01-01

Data analysis is one of the most critical and challenging steps in drug discovery and disease biology. A user-friendly resource to visualize and analyse high-throughput data provides a powerful medium for both experimental and computational biologists to understand vastly different biological data types and obtain a concise, simplified and meaningful output for better knowledge discovery. We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. Here we describe how upgraded and newly modelled data types in TargetMine can now survey the wider biological and chemical data space, relevant to drug discovery and development. To enhance the scope of TargetMine from target prioritization to broad-based knowledge discovery, we have also developed a new auxiliary toolkit to assist with data analysis and visualization in TargetMine. This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. The enhanced system enables users to discover new hypotheses interactively by performing complicated searches with no programming and obtaining the results in an easy to comprehend output format. Database URL: http://targetmine.mizuguchilab.org. © The Author(s) 2016. Published by Oxford University Press.

GenFlow: generic flow for integration, management and analysis of molecular biology data

Directory of Open Access Journals (Sweden)

Marcio Katsumi Oikawa

2004-01-01

Full Text Available A large number of DNA sequencing projects all over the world have yielded a fantastic amount of data, whose analysis is, currently, a big challenge for computational biology. The limiting step in this task is the integration of large volumes of data stored in highly heterogeneous repositories of genomic and cDNA sequences, as well as gene expression results. Solving this problem requires automated analytical tools to optimize operations and efficiently generate knowledge. This paper presents an information flow model , called GenFlow, that can tackle this analytical task.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

Science.gov (United States)

Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. PMID:26086662

Effects of biology teachers' professional knowledge and cognitive activation on students' achievement

Science.gov (United States)

Förtsch, Christian; Werner, Sonja; von Kotzebue, Lena; Neuhaus, Birgit J.

2016-11-01

This study examined the effects of teachers' biology-specific dimensions of professional knowledge - pedagogical content knowledge (PCK) and content knowledge (CK) - and cognitively activating biology instruction, as a feature of instructional quality, on students' learning. The sample comprised 39 German secondary school teachers whose lessons on the topic neurobiology were videotaped twice. Teachers' instruction was coded with regard to cognitive activation using a rating manual. Multilevel path analysis results showed a positive significant effect of cognitive activation on students' learning and an indirect effect of teachers' PCK on students' learning mediated through cognitive activation. These findings highlight the importance of PCK in preservice biology teachers' education. Items of the rating manual may be used to provide exemplars of concrete teaching situations during university seminars for preservice teacher education or professional development initiatives for in-service teachers.

An exploration of knowledge integration problems in interdisciplinary research teams

NARCIS (Netherlands)

Bayerl, P.S.; Steinheider, B.

2009-01-01

The integration of function-specific expertise into a shared knowledge base is a crucial, but complex process for success in interdisciplinary teams. This paper presents an empirically derived typology of knowledge integration problems and links their occurrence to degree of heterogeneity and

Integrating Indigenous Knowledge in Climate Risk Management in ...

International Development Research Centre (IDRC) Digital Library (Canada)

27 mars 2008 ... Integrating Indigenous Knowledge in Climate Risk Management in support of Community Based Adaptation. Traditionally, African farmers have used indigenous knowledge to understand weather and climate patterns and make decisions about crop and irrigation cycles. However, increased variability ...

Developmental "roots" in mature biological knowledge.

Science.gov (United States)

Goldberg, Robert F; Thompson-Schill, Sharon L

2009-04-01

Young children tend to claim that moving artifacts and nonliving natural kinds are alive, but neglect to ascribe life to plants. This research tested whether adults exhibit similar confusions when verifying life status in a speeded classification task. Experiment 1 showed that undergraduates encounter greater difficulty (reduced accuracy and increased response times) in determining life status for plants, relative to animals, and for natural and moving nonliving things, relative to artifacts and non-moving things. Experiment 2 replicated these effects in university biology professors. The professors showed a significantly reduced effect size for living things, as compared with the students, but still showed greater difficulty for plants than animals, even as no differences from the students were apparent in their responses to nonliving things. These results suggest that mature biological knowledge relies on a developmental foundation that is not radically overwritten or erased with the profound conceptual changes that accompany mastery of the domain.

Integrated knowledge base tool for acquisition and verification of NPP alarm systems

International Nuclear Information System (INIS)

Park, Joo Hyun; Seong, Poong Hyun

1998-01-01

Knowledge acquisition and knowledge base verification are important activities in developing knowledge-based systems such as alarm processing systems. In this work, we developed the integrated tool, for knowledge acquisition and verification of NPP alarm processing systems, by using G2 tool. The tool integrates document analysis method and ECPN matrix analysis method, for knowledge acquisition and knowledge verification, respectively. This tool enables knowledge engineers to perform their tasks from knowledge acquisition to knowledge verification consistently

A Sociology of Knowledge Approach to European Integration

DEFF Research Database (Denmark)

Adler-Nissen, Rebecca; Kropp, Kristoffer

2015-01-01

Scholars are deeply involved in the process of European integration, but we lack systematic understanding of this involvement. On the one hand, scholars, academic ideas and ideologies shape European integration and policies (e.g. the Economic and Monetary Union and the free movement of people......). On the other hand, EU institutions, policies and practitioners produce particular forms of knowledge (e.g. the Eurobarometer and benchmarking of national performances) that inform social scientific choices of theories, methods and research topics. Drawing on the new sociology of knowledge as well as Science...

Physical integrity: the missing link in biological monitoring and TMDLs.

Science.gov (United States)

Asmus, Brenda; Magner, Joseph A; Vondracek, Bruce; Perry, Jim

2009-12-01

The Clean Water Act mandates that the chemical, physical, and biological integrity of our nation's waters be maintained and restored. Physical integrity has often been defined as physical habitat integrity, and as such, data collected during biological monitoring programs focus primarily on habitat quality. However, we argue that channel stability is a more appropriate measure of physical integrity and that channel stability is a foundational element of physical habitat integrity in low-gradient alluvial streams. We highlight assessment tools that could supplement stream assessments and the Total Maximum Daily Load stressor identification process: field surveys of bankfull cross-sections; longitudinal thalweg profiles; particle size distribution; and regionally calibrated, visual, stream stability assessments. Benefits of measuring channel stability include a more informed selection of reference or best attainable stream condition for an Index of Biotic Integrity, establishment of a baseline for monitoring changes in present and future condition, and indication of channel stability for investigations of chemical and biological impairments associated with sediment discontinuity and loss of habitat quality.

Farmers’ Technical Knowledge about Integrated Pest Management (IPM in Olive Production

Directory of Open Access Journals (Sweden)

Mohammad S. Allahyari

2017-12-01

Full Text Available While Integrated Pest Management (IPM is a sustainable approach of pest control, contributing to reduced use of pesticides and risks on human health and the environment, farmers have shown limited interest in practicing this method. The present study explored the levels of technical knowledge about integrated management of the olive fly (Bactrocera oleae among olive growers in Roudbar County of Iran and factors underpinning olive farmers’ technical knowledge of integrated management. Data were collected in a survey of olive farmers, on the basis of a structured questionnaire. Almost half of the farmers (48.4% had good to excellent levels of technical knowledge of integrated management, while almost a third of the farmers (35.4% had a moderate knowledge level. However, a noticeable portion of the farmers (15.9% had poor knowledge of integrated management. Moreover, most farmers showed average knowledge of the adverse effects of pesticides on human health. While most farmers showed good levels of social participation, cooperation with institutes, and participation in extension activities, they showed low levels of community involvement (involvement in a group of people that have and share common interests with each other. Olive imports and the lack of a common action for olive fly control were perceived as the main barriers of IPM adoption among most farmers. Regression analysis revealed that increased community involvement, large area under olive farming, participation in education activities, and high farming experience promoted farmers’ technical knowledge of integrated olive fly control. Strengthening growers’ technical knowledge of IPM through community involvement and extension services among inexperienced small-scale olive farmers is recommended for reducing possible unnecessary insecticide sprays in olive production.

A computational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks

Directory of Open Access Journals (Sweden)

Thomas eEissing

2011-02-01

Full Text Available Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.

Community-based participatory research and integrated knowledge translation: advancing the co-creation of knowledge.

Science.gov (United States)

Jull, Janet; Giles, Audrey; Graham, Ian D

2017-12-19

Better use of research evidence (one form of "knowledge") in health systems requires partnerships between researchers and those who contend with the real-world needs and constraints of health systems. Community-based participatory research (CBPR) and integrated knowledge translation (IKT) are research approaches that emphasize the importance of creating partnerships between researchers and the people for whom the research is ultimately meant to be of use ("knowledge users"). There exist poor understandings of the ways in which these approaches converge and diverge. Better understanding of the similarities and differences between CBPR and IKT will enable researchers to use these approaches appropriately and to leverage best practices and knowledge from each. The co-creation of knowledge conveys promise of significant social impacts, and further understandings of how to engage and involve knowledge users in research are needed. We examine the histories and traditions of CBPR and IKT, as well as their points of convergence and divergence. We critically evaluate the ways in which both have the potential to contribute to the development and integration of knowledge in health systems. As distinct research traditions, the underlying drivers and rationale for CBPR and IKT have similarities and differences across the areas of motivation, social location, and ethics; nevertheless, the practices of CBPR and IKT converge upon a common aim: the co-creation of knowledge that is the result of knowledge user and researcher expertise. We argue that while CBPR and IKT both have the potential to contribute evidence to implementation science and practices for collaborative research, clarity for the purpose of the research-social change or application-is a critical feature in the selection of an appropriate collaborative approach to build knowledge. CBPR and IKT bring distinct strengths to a common aim: to foster democratic processes in the co-creation of knowledge. As research

[Knowledge and power at a molecular level; biological psychiatry in a social context].

Science.gov (United States)

Verhoeff, B

2009-01-01

How do we acquire our knowledge about psychiatric disorders and how did the current biologically way of thinking in psychiatry originate? With the help of the philosophy of Michel Foucault and Nikolas Rose this essay describes the conditions that made possible today's biological approach in psychiatry. It will become clear that research in the life sciences and the psychiatric knowledge arising from this research are shaped and formed in a complex network of social, economic, political and scientific forces. The biological approach to psychiatric disorders is the product of present-day relationships between scientific developments and commercial corporations.

Representations of the Nature of Scientific Knowledge in Turkish Biology Textbooks

Science.gov (United States)

Irez, Serhat

2016-01-01

Considering the impact of textbooks on learning, this study set out to assess representations of the nature of scientific knowledge in Turkish 9th grade biology textbooks. To this end, the ten most commonly used 9th grade biology textbooks were analyzed. A qualitative research approach was utilized and the textbooks were analyzed using…

Integration of genomic information with biological networks using Cytoscape.

Science.gov (United States)

Bauer-Mehren, Anna

2013-01-01

Cytoscape is an open-source software for visualizing, analyzing, and modeling biological networks. This chapter explains how to use Cytoscape to analyze the functional effect of sequence variations in the context of biological networks such as protein-protein interaction networks and signaling pathways. The chapter is divided into five parts: (1) obtaining information about the functional effect of sequence variation in a Cytoscape readable format, (2) loading and displaying different types of biological networks in Cytoscape, (3) integrating the genomic information (SNPs and mutations) with the biological networks, and (4) analyzing the effect of the genomic perturbation onto the network structure using Cytoscape built-in functions. Finally, we briefly outline how the integrated data can help in building mathematical network models for analyzing the effect of the sequence variation onto the dynamics of the biological system. Each part is illustrated by step-by-step instructions on an example use case and visualized by many screenshots and figures.

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

Science.gov (United States)

Zong, Nobel C; Li, Haomin; Li, Hua; Lam, Maggie P Y; Jimenez, Rafael C; Kim, Christina S; Deng, Ning; Kim, Allen K; Choi, Jeong Ho; Zelaya, Ivette; Liem, David; Meyer, David; Odeberg, Jacob; Fang, Caiyun; Lu, Hao-Jie; Xu, Tao; Weiss, James; Duan, Huilong; Uhlen, Mathias; Yates, John R; Apweiler, Rolf; Ge, Junbo; Hermjakob, Henning; Ping, Peipei

2013-10-12

Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

‘Integrative Physiology 2.0’: integration of systems biology into physiology and its application to cardiovascular homeostasis

Science.gov (United States)

Kuster, Diederik W D; Merkus, Daphne; van der Velden, Jolanda; Verhoeven, Adrie J M; Duncker, Dirk J

2011-01-01

Since the completion of the Human Genome Project and the advent of the large scaled unbiased ‘-omics’ techniques, the field of systems biology has emerged. Systems biology aims to move away from the traditional reductionist molecular approach, which focused on understanding the role of single genes or proteins, towards a more holistic approach by studying networks and interactions between individual components of networks. From a conceptual standpoint, systems biology elicits a ‘back to the future’ experience for any integrative physiologist. However, many of the new techniques and modalities employed by systems biologists yield tremendous potential for integrative physiologists to expand their tool arsenal to (quantitatively) study complex biological processes, such as cardiac remodelling and heart failure, in a truly holistic fashion. We therefore advocate that systems biology should not become/stay a separate discipline with ‘-omics’ as its playing field, but should be integrated into physiology to create ‘Integrative Physiology 2.0’. PMID:21224228

Collaborative Knowledge Building and Integral Theory: On Perspectives, Uncertainty, and Mutual Regard

Directory of Open Access Journals (Sweden)

Tom Murray

2006-06-01

Full Text Available Uncertainty in knowing and communicating affect all aspects of modern life. Ubiquitous and inevitable uncertainty, including ambiguity and paradox, is particularly salient and important in knowledge building communities. Because knowledge building communities represent and evolve knowledge explicitly, the causes, effects, and approaches to this “epistemological indeterminacy” can be directly addressed in knowledge building practices. Integral theory’s approach (including “methodological pluralism” involves accepting and integrating diverse perspectives in ways that transcend and include them. This approach accentuates the problems of epistemological indeterminacy and highlights the general need to deal creatively with it. This article begins with a cursory analysis of textual dialogs among integral theorists, showing that, while integral theory itself points to leading-edge ways of dealing with epistemological indeterminacy, the knowledge building practices of integral theorists, by and large, exhibit the same limitations as traditional intellectual discourses. Yet, due to its values and core methods, the integral theory community is in a unique position to develop novel and more adequate modes of inquiry and dialog. This text explores how epistemological indeterminacy impacts the activities and products of groups engaged in collaborative knowledge building. Approaching the issue from three perspectives–mutual understanding, mutual agreement, and mutual regard—I show the interdependence of those perspectives and ground them in relation to integral theory’s concerns. This article proposes three phases of developing constructive alternatives drawn from the knowledge building field: awareness of the phenomena, understanding the phenomena, and offering some tools (and some hope for dealing with it. Though here I focus on the integral theory community (or communities, the conclusions of the article are meant to be applicable to any

Collaborative Knowledge Building and Integral Theory:On Perspectives,Uncertainty, and Mutual Regard

Directory of Open Access Journals (Sweden)

Tom Murray

2006-06-01

Full Text Available Uncertainty in knowing and communicating affect all aspects of modern life. Ubiquitous and inevitable uncertainty, including ambiguity and paradox, is particularly salient and important in knowledge building communities. Because knowledge building communities represent and evolve knowledge explicitly, the causes, effects, and approaches to this “epistemological indeterminacy” can be directly addressed in knowledge building practices. Integral theory's approach (including “methodological pluralism” involves accepting and integrating diverse perspectives in ways that transcend and include them. This approach accentuates the problems of epistemological indeterminacy and highlights the general need to deal creatively with it. This article begins with a cursory analysis of textual dialogs among integral theorists, showing that, while integral theory itself points to leading-edge ways of dealing with epistemological indeterminacy, the knowledge building practices of integral theorists, by and large, exhibit the same limitations as traditional intellectual discourses. Yet, due to its values and core methods, the integral theory community is in a unique position to develop novel and more adequate modes of inquiry and dialog. This text explores how epistemological indeterminacy impacts the activities and products of groups engaged in collaborative knowledge building. Approaching the issue from three perspectives—mutual understanding, mutual agreement, and mutual regard—I show the interdependence of those perspectives and ground them in relation to integral theory’s concerns. This article proposes three phases of developing constructive alternatives drawn from the knowledge building field: awareness of the phenomena, understanding the phenomena, and offering some tools (and some hope for dealing with it. Though here I focus on the integral theory community (or communities, the conclusions of the article are meant to be applicable to any

The observation of biology implemented by integrated religion values in integrated Islamic school (Decriptive Study in X Integrated Senior Hight School Tasikmalaya)

Science.gov (United States)

Nurjanah, E.; Adisendjaja, Y. H.; Kusumastuti, M. N.

2018-05-01

The learning Integrated Religious value is one of the efforts to increase the motivation of learning and building the student character. This study aims to describe the application of Biology learning integrated religion values in Integrated Islamic School. Research methods used in this research is descriptive. Participants in this study involved the headmaster, headmaster of curriculum, biology teachers, boarding school teachers, the lead of boarding schools, and students. The instruments used are interview, observation and the student questionnaire about learning biology. The results showed that learning in X school consists of two curriculums, there was the curriculum of national education and curriculum of boarding school. The curriculum of national education referred to 2013 curriculum and boarding school curriculum referred to the curriculum of Salafi boarding school (Kitab Kuning). However, in its learning process not delivered integrated. The main obstacle to implementing the learning integrated religious values are 1) the background of general teacher education did not know of any connection between biology subject and subject that are studied in boarding school; 2) schools did not form the teaching team; 3) unavailability of materials integrated religious values.

An integrative approach to knowledge transfer and integration: Spanning boundaries through objects, people and processes

NARCIS (Netherlands)

Duijn, M.; Rijnveld, M.

2008-01-01

Knowledge transfer and integration is the main challenge in many knowledge management projects. This challenge follows from the observation that it is difficult to determine how and what knowledge may transfer from one person to another, from one team to another and from one network or organization

Learning knowledge as an integral part of competencies in higher education: Effects on students' knowledge

NARCIS (Netherlands)

Van Bommel, Marijke; Boshuizen, Els; Kwakman, Kitty

2011-01-01

Van Bommel, M., Boshuizen, H. P. A., & Kwakman, K. (2010, 25-27 August). Learning knowledge as an integral part of competencies in higher education: Effects on students' knowledge. Paper presented at the 5th EARLI-SIG14 Learning and Professional Development, Munich, Germany.

Finding gene regulatory network candidates using the gene expression knowledge base.

Science.gov (United States)

Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin

2014-12-10

Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of 'omics' data can be interpreted. The background information required for the construction of such networks is often dispersed across a multitude of knowledge bases in a variety of formats. The seamless integration of this information is one of the main challenges in bioinformatics. The Semantic Web offers powerful technologies for the assembly of integrated knowledge bases that are computationally comprehensible, thereby providing a potentially powerful resource for constructing biological networks and network-based analysis. We have developed the Gene eXpression Knowledge Base (GeXKB), a semantic web technology based resource that contains integrated knowledge about gene expression regulation. To affirm the utility of GeXKB we demonstrate how this resource can be exploited for the identification of candidate regulatory network proteins. We present four use cases that were designed from a biological perspective in order to find candidate members relevant for the gastrin hormone signaling network model. We show how a combination of specific query definitions and additional selection criteria derived from gene expression data and prior knowledge concerning candidate proteins can be used to retrieve a set of proteins that constitute valid candidates for regulatory network extensions. Semantic web technologies provide the means for processing and integrating various heterogeneous information sources. The GeXKB offers biologists such an integrated knowledge resource, allowing them to address complex biological questions pertaining to gene expression. This work illustrates how GeXKB can be used in combination with gene expression results and literature information to identify new potential candidates that may be considered for extending a gene regulatory network.

Semiconductor Devices Inspired By and Integrated With Biology

Energy Technology Data Exchange (ETDEWEB)

Rogers, John [University of Illinois

2012-04-25

Biology is curved, soft and elastic; silicon wafers are not. Semiconductor technologies that can bridge this gap in form and mechanics will create new opportunities in devices that adopt biologically inspired designs or require intimate integration with the human body. This talk describes the development of ideas for electronics that offer the performance of state-of-the-art, wafer- based systems but with the mechanical properties of a rubber band. We explain the underlying materials science and mechanics of these approaches, and illustrate their use in (1) bio- integrated, ‘tissue-like’ electronics with unique capabilities for mapping cardiac and neural electrophysiology, and (2) bio-inspired, ‘eyeball’ cameras with exceptional imaging properties enabled by curvilinear, Petzval designs.

The Role of Integrated Knowledge Translation in Intervention Research.

Science.gov (United States)

Wathen, C Nadine; MacMillan, Harriet L

2018-04-01

There is widespread recognition across the full range of applied research disciplines, including health and social services, about the challenges of integrating scientifically derived research evidence into policy and/or practice decisions. These "disconnects" or "knowledge-practice gaps" between research production and use have spawned a new research field, most commonly known as either "implementation science" or "knowledge translation." The present paper will review key concepts in this area, with a particular focus on "integrated knowledge translation" (IKT)-which focuses on researcher-knowledge user partnership-in the area of mental health and prevention of violence against women and children using case examples from completed and ongoing work. A key distinction is made between the practice of KT (disseminating, communicating, etc.), and the science of KT, i.e., research regarding effective KT approaches. We conclude with a discussion of the relevance of IKT for mental health intervention research with children and adolescents.

Integrating Traditional Ecological Knowledge and Ecological Science: a Question of Scale

Directory of Open Access Journals (Sweden)

Catherine A. Gagnon

2009-12-01

Full Text Available The benefits and challenges of integrating traditional ecological knowledge and scientific knowledge have led to extensive discussions over the past decades, but much work is still needed to facilitate the articulation and co-application of these two types of knowledge. Through two case studies, we examined the integration of traditional ecological knowledge and scientific knowledge by emphasizing their complementarity across spatial and temporal scales. We expected that combining Inuit traditional ecological knowledge and scientific knowledge would expand the spatial and temporal scales of currently documented knowledge on the arctic fox (Vulpes lagopus and the greater snow goose (Chen caerulescens atlantica, two important tundra species. Using participatory approaches in Mittimatalik (also known as Pond Inlet, Nunavut, Canada, we documented traditional ecological knowledge about these species and found that, in fact, it did expand the spatial and temporal scales of current scientific knowledge for local arctic fox ecology. However, the benefits were not as apparent for snow goose ecology, probably because of the similar spatial and temporal observational scales of the two types of knowledge for this species. Comparing sources of knowledge at similar scales allowed us to gain confidence in our conclusions and to identify areas of disagreement that should be studied further. Emphasizing complementarities across scales was more powerful for generating new insights and hypotheses. We conclude that determining the scales of the observations that form the basis for traditional ecological knowledge and scientific knowledge represents a critical step when evaluating the benefits of integrating these two types of knowledge. This is also critical when examining the congruence or contrast between the two types of knowledge for a given subject.

From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells

OpenAIRE

Centola Michael B; Dozmorov Igor; Buethe David D; Saban Ricardo; Hauser Paul J; Kyker Kimberly D; Dozmorov Mikhail G; Culkin Daniel J; Hurst Robert E

2008-01-01

Abstract A statistically robust and biologically-based approach for analysis of microarray data is described that integrates independent biological knowledge and data with a global F-test for finding genes of interest that minimizes the need for replicates when used for hypothesis generation. First, each microarray is normalized to its noise level around zero. The microarray dataset is then globally adjusted by robust linear regression. Second, genes of interest that capture significant respo...

Knowledge and information management for integrated water resource management

Science.gov (United States)

Watershed information systems that integrate data and analytical tools are critical enabling technologies to support Integrated Water Resource Management (IWRM) by converting data into information, and information into knowledge. Many factors bring people to the table to participate in an IWRM fra...

The KNOMAD Methodology for Integration of Multi-Disciplinary Engineering Knowledge within Aerospace Production

NARCIS (Netherlands)

Curran, R.; Verhagen, W.J.C.; Van Tooren, M.J.L.

2010-01-01

The paper is associated with the integration of multi-disciplinary knowledge within a Knowledge Based Engineering (KBE)-enabled design framework. To support this integration effort, the KNOMAD methodology has been devised. KNOMAD stands for Knowledge Optimized Manufacture And Design and is a

Intelligent Assistants for Distributed Knowledge Acquisition, Integration, Validation, and Maintenance

National Research Council Canada - National Science Library

Tecuci, Gheorghe; Boicu, Mihai

2008-01-01

This research has developed an integrated set of tools, called Disciple 2008 learning agent shell, for continuous acquisition of knowledge directly from subject matter experts, and for the integration...

Subject-specific pedagogical content knowledge: Implications for alternatively and traditionally trained biology teachers

Science.gov (United States)

Ravgiala, Rebekah Rae

Theories regarding the development of expertise hold implications for alternative and traditional certification programs and the teachers they train. The literature suggests that when compared to experts in the field of teaching, the behaviors of novices differ in ways that are directly attributed to their pedagogical content knowledge. However, few studies have examined how first and second year biology teachers entering the profession from traditional and alternative training differ in their demonstration of subject-specific pedagogical content knowledge. The research problem in this multicase, naturalistic inquiry investigated how subject-specific pedagogical content knowledge was manifested among first and second year biology teachers in the task of transforming subject matter into forms that are potentially meaningful to students when explicit formal training has been and has not been imparted to them as preservice teachers. Two first year and two second year biology teachers were the subjects of this investigation. Allen and Amber obtained their certification through an alternative summer training institute in consecutive years. Tiffany and Tricia obtained their certification through a traditional, graduate level training program in consecutive years. Both programs were offered at the same northeastern state university. Participants contributed to six data gathering techniques including an initial semi-structured interview, responses to the Conceptions of Teaching Science questionnaire (Hewson & Hewson, 1989), three videotaped biology lessons, evaluation of three corresponding lesson plans, and a final semi-structured interview conducted at the end of the investigation. An informal, end-of-study survey intended to offer participants an opportunity to disclose their thoughts and needs as first year teachers was also employed. Results indicate that while conceptions of teaching science may vary slightly among participants, there is no evidence to suggest that

"We Like to Listen to Stories about Fish": Integrating Indigenous Ecological and Scientific Knowledge to Inform Environmental Flow Assessments

Directory of Open Access Journals (Sweden)

Sue E. Jackson

2014-03-01

Full Text Available Studies that apply indigenous ecological knowledge to contemporary resource management problems are increasing globally; however, few of these studies have contributed to environmental water management. We interviewed three indigenous landowning groups in a tropical Australian catchment subject to increasing water resource development pressure and trialed tools to integrate indigenous and scientific knowledge of the biology and ecology of freshwater fish to assess their water requirements. The differences, similarities, and complementarities between the knowledge of fish held by indigenous people and scientists are discussed in the context of the changing socioeconomic circumstances experienced by indigenous communities of north Australia. In addition to eliciting indigenous knowledge that confirmed field fish survey results, the approach generated knowledge that was new to both science and indigenous participants, respectively. Indigenous knowledge influenced (1 the conceptual models developed by scientists to understand the flow ecology and (2 the structure of risk assessment tools designed to understand the vulnerability of particular fish to low-flow scenarios.

Integrating ICT in Agriculture for Knowledge-Based Economy

African Journals Online (AJOL)

agriculture –based livelihoods, demands the integration of ICT knowledge with agriculture. .... (CGIAR) shows the vital role of Agricultural development in Rwanda's ... Network, Rwanda National Backbone Project, Regional Communication.

Indicators and measurement tools for health system integration: a knowledge synthesis protocol.

Science.gov (United States)

Oelke, Nelly D; Suter, Esther; da Silva Lima, Maria Alice Dias; Van Vliet-Brown, Cheryl

2015-07-29

Health system integration is a key component of health system reform with the goal of improving outcomes for patients, providers, and the health system. Although health systems continue to strive for better integration, current delivery of health services continues to be fragmented. A key gap in the literature is the lack of information on what successful integration looks like and how to measure achievement towards an integrated system. This multi-site study protocol builds on a prior knowledge synthesis completed by two of the primary investigators which identified 10 key principles that collectively support health system integration. The aim is to answer two research questions: What are appropriate indicators for each of the 10 key integration principles developed in our previous knowledge synthesis and what measurement tools are used to measure these indicators? To enhance generalizability of the findings, a partnership between Canada and Brazil was created as health system integration is a priority in both countries and they share similar contexts. This knowledge synthesis will follow an iterative scoping review process with emerging information from knowledge-user engagement leading to the refinement of research questions and study selection. This paper describes the methods for each phase of the study. Research questions were developed with stakeholder input. Indicator identification and prioritization will utilize a modified Delphi method and patient/user focus groups. Based on priority indicators, a search of the literature will be completed and studies screened for inclusion. Quality appraisal of relevant studies will be completed prior to data extraction. Results will be used to develop recommendations and key messages to be presented through integrated and end-of-grant knowledge translation strategies with researchers and knowledge-users from the three jurisdictions. This project will directly benefit policy and decision-makers by providing an easy

A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture.

Science.gov (United States)

Ciaccio, Mark F; Finkle, Justin D; Xue, Albert Y; Bagheri, Neda

2014-07-01

An organism's ability to maintain a desired physiological response relies extensively on how cellular and molecular signaling networks interpret and react to environmental cues. The capacity to quantitatively predict how networks respond to a changing environment by modifying signaling regulation and phenotypic responses will help inform and predict the impact of a changing global enivronment on organisms and ecosystems. Many computational strategies have been developed to resolve cue-signal-response networks. However, selecting a strategy that answers a specific biological question requires knowledge both of the type of data being collected, and of the strengths and weaknesses of different computational regimes. We broadly explore several computational approaches, and we evaluate their accuracy in predicting a given response. Specifically, we describe how statistical algorithms can be used in the context of integrative and comparative biology to elucidate the genomic, proteomic, and/or cellular networks responsible for robust physiological response. As a case study, we apply this strategy to a dataset of quantitative levels of protein abundance from the mussel, Mytilus galloprovincialis, to uncover the temperature-dependent signaling network. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

From Knowledge Theory to Management Practice: Towards an Integrated Approach.

Science.gov (United States)

Shin, Minsoo; Holden, Tony; Schmidt, Ruth A.

2001-01-01

Critically contrasts the three main schools of thought on knowledge and assesses the resulting implications for knowledge management. Presents a conceptual model to integrate theoretical and practical themes to serve as a framework for developing a future research agenda for the development of knowledge management business tools and applications.…

Future of Chemical Engineering: Integrating Biology into the Undergraduate ChE Curriculum

Science.gov (United States)

Mosto, Patricia; Savelski, Mariano; Farrell, Stephanie H.; Hecht, Gregory B.

2007-01-01

Integrating biology in the chemical engineering curriculum seems to be the future for chemical engineering programs nation and worldwide. Rowan University's efforts to address this need include a unique chemical engineering curriculum with an intensive biology component integrated throughout from freshman to senior years. Freshman and Sophomore…

Integrative radiation systems biology

International Nuclear Information System (INIS)

Unger, Kristian

2014-01-01

Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

Investigating Lebanese Grade Seven Biology Teachers Mathematical Knowledge and Skills: A Case Study

Science.gov (United States)

Raad, Nawal Abou; Chatila, Hanadi

2016-01-01

This paper investigates Lebanese grade 7 biology teachers' mathematical knowledge and skills, by exploring how they explain a visual representation in an activity depending on the mathematical concept "Function". Twenty Lebanese in-service biology teachers participated in the study, and were interviewed about their explanation for the…

Integrating ecological knowledge, public perception and urgency of action into invasive species management.

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Caplat, Paul; Coutts, Shaun R

2011-11-01

Recently Prévot-Julliard and colleagues presented a concept paper on biological conservation strategies using exotic species as a case study. They emphasized the difficulty of integrating conservation into a broad picture that accounts for public perception as well as scientific knowledge. We support this general call for better integration of society in conservation research, but we believe that the original framework might misguide conservation practices if wrongly interpreted. Our objective is to complement their paper and correct a few misleading points, by showing that (1) for regions of high endemicity "reservation" may be the best conservation practice, and does not prevent public participation, (2) aiming for broad societal agreement is valuable, but in some cases risky, and always complex, and (3) calling a harmful invasive species harmful shouldn't be an issue. The Australian context provides us with many cases of the labeling of exotic species as harmful or not, using inputs from scientists, industry, and the public. Integration of social and scientific points of view can only improve conservation on the ground if it allows managers to use the ecological, economic and social impacts of exotic species to prioritize conservation actions in an operative way.

An integrative approach to inferring biologically meaningful gene modules

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Wang Kai

2011-07-01

Full Text Available Abstract Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

Negotiating the dynamics of uncomfortable knowledge: The case of dual use and synthetic biology

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Marris, Claire; Jefferson, Catherine; Lentzos, Filippa

2014-01-01

Institutions need to ignore some knowledge in order to function. This is “uncomfortable knowledge” because it undermines the ability of those institutions to pursue their goals (Rayner, 2012). We identify three bodies of knowledge that are relevant to understandings of the dual use threat posed by synthetic biology but are excluded from related policy discussions. We demonstrate how these “unknown knowns” constitute uncomfortable knowledge because they disrupt the simplified worldview that underpins contemporary discourse on the potential misuse of synthetic biology by malign actors. We describe how these inconvenient truths have been systematically ignored and argue that this is because they are perceived as a threat by organisations involved in the promotion of synthetic biology as well as by those involved in managing biosecurity risks. This has led to a situation where concerns about the biosecurity threat posed by synthetic biology are not only exaggerated, but are, more importantly, misplaced. This, in turn, means that related policies are misdirected and unlikely to have much impact. We focus on the dynamics of discussions about synthetic biology and dual use to demonstrate how the same “knowns” that are denied or dismissed as “unknown knowns” in certain circumstances are sometimes mobilised as “known knowns” by the same category of actors in a different context, when this serves to sustain the goals of the individuals and institutions involved. Based on our own experience, we argue that negotiating the dynamics of uncomfortable knowledge is a difficult, but necessary, component of meaningful transdisciplinary collaborations. PMID:25484910

Presentation planning using an integrated knowledge base

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Arens, Yigal; Miller, Lawrence; Sondheimer, Norman

1988-01-01

A description is given of user interface research aimed at bringing together multiple input and output modes in a way that handles mixed mode input (commands, menus, forms, natural language), interacts with a diverse collection of underlying software utilities in a uniform way, and presents the results through a combination of output modes including natural language text, maps, charts and graphs. The system, Integrated Interfaces, derives much of its ability to interact uniformly with the user and the underlying services and to build its presentations, from the information present in a central knowledge base. This knowledge base integrates models of the application domain (Navy ships in the Pacific region, in the current demonstration version); the structure of visual displays and their graphical features; the underlying services (data bases and expert systems); and interface functions. The emphasis is on a presentation planner that uses the knowledge base to produce multi-modal output. There has been a flurry of recent work in user interface management systems. (Several recent examples are listed in the references). Existing work is characterized by an attempt to relieve the software designer of the burden of handcrafting an interface for each application. The work has generally focused on intelligently handling input. This paper deals with the other end of the pipeline - presentations.

Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge.

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Zhang, Yuji

2015-01-01

Molecular networks act as the backbone of molecular activities within cells, offering a unique opportunity to better understand the mechanism of diseases. While network data usually constitute only static network maps, integrating them with time course gene expression information can provide clues to the dynamic features of these networks and unravel the mechanistic driver genes characterizing cellular responses. Time course gene expression data allow us to broadly "watch" the dynamics of the system. However, one challenge in the analysis of such data is to establish and characterize the interplay among genes that are altered at different time points in the context of a biological process or functional category. Integrative analysis of these data sources will lead us a more complete understanding of how biological entities (e.g., genes and proteins) coordinately perform their biological functions in biological systems. In this paper, we introduced a novel network-based approach to extract functional knowledge from time-dependent biological processes at a system level using time course mRNA sequencing data in zebrafish embryo development. The proposed method was applied to investigate 1α, 25(OH)2D3-altered mechanisms in zebrafish embryo development. We applied the proposed method to a public zebrafish time course mRNA-Seq dataset, containing two different treatments along four time points. We constructed networks between gene ontology biological process categories, which were enriched in differential expressed genes between consecutive time points and different conditions. The temporal propagation of 1α, 25-Dihydroxyvitamin D3-altered transcriptional changes started from a few genes that were altered initially at earlier stage, to large groups of biological coherent genes at later stages. The most notable biological processes included neuronal and retinal development and generalized stress response. In addition, we also investigated the relationship among

Occupational biological risk knowledge and perception: results from a large survey in Rome, Italy

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Maria De Giusti

2012-06-01

Full Text Available BACKGROUND: A cross-sectional survey on knowledge and perception of occupational biological risk among workers in several occupations was carried out in the industrial area of Rome. METHODS: The study was carried out in the period of March-April 2010 using a questionnaire with 33 items on the following areas: a socio-demographic data; b perception of the biological risks in ordinary occupational activity; c knowledge about biological risks; d biological risks in the working environment. The questionnaire was submitted to a convenience sample of workers of an industrial area in Southern Rome. RESULTS: 729 participants entered the study from the following work activities: food, catering, service, farming and breeding, healthcare, school and research (males 57.2%; mean age 37.4 years, SD = 10.9. Significant associations were found between different activity areas with respect to the relevance of the biological risk (p = 0.044 and the perception of the biological risk (p < 0.001. With respect to vehicles of infectious agents, the highest percentages of the most common biological risk exposures were: air and physical contact for the catering and food group, 66.7% and 61.90% respectively; air and blood for the health and research group, with 73.50% and 57.00% respectively; and physical contact and blood for the service group, 63.10 % and 48.30%. Significant difference of proportions were found about the prevalent effect caused by the biological agents was the occurrence of infectious diseases (59.90% food group, 91.60% health and research and 79.30% service group (p < 0.001. The perception of knowledge resulted in a good rank (sufficient, many or complete in the food and catering group, 78.3% with significant difference compared to other professions (p < 0.001. CONCLUSIONS: All participants show good knowledge the effects induced by biological agents and it is significant that almost half of the respondents are aware of the risks concerning allergies

Indigenous Knowledge, Science, and Resilience: What Have We Learned from a Decade of International Literature on "Integration"?

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Erin L. Bohensky

2011-12-01

Full Text Available Despite the increasing trend worldwide of integrating indigenous and scientific knowledge in natural resource management, there has been little stock-taking of literature on lessons learned from bringing indigenous knowledge and science together and the implications for maintaining and building social-ecological system resilience. In this paper we investigate: (1 themes, questions, or problems encountered for integration of indigenous knowledge and science; (2 the relationship between knowledge integration and social-ecological system resilience; and (3 critical features of knowledge integration practice needed to foster productive and mutually beneficial relationships between indigenous knowledge and science. We examine these questions through content analyses of three special journal issues and an edited book published in the past decade on indigenous, local, and traditional knowledge and its interface with science. We identified broad themes in the literature related to: (1 similarities and differences between knowledge systems; (2 methods and processes of integration; (3 social contexts of integration; and (4 evaluation of knowledge. A minority of papers discuss a relationship between knowledge integration and social-ecological system resilience, but there remains a lack of clarity and empirical evidence for such a relationship that can help distinguish how indigenous knowledge and knowledge integration contribute most to resilience. Four critical features of knowledge integration are likely to enable a more productive and mutually beneficial relationship between indigenous and scientific knowledge: new frames for integration, greater cognizance of the social contexts of integration, expanded modes of knowledge evaluation, and involvement of inter-cultural "knowledge bridgers."

Discovering Learning Strategy to Increase Metacognitive Knowledge in Biology Learning in Secondary School

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Y. Herlanti

2017-04-01

Full Text Available The study is aimed at finding an effective learning strategy that can increase metacognitive knowledge. Metacognitive knowledge is a standard that based on 2016-revised edition of 2013 curriculum needs to be achieved by every graduate in all level of education in Indonesia. The study is conducted in three different schools and engages 207 students, which then divided into six groups. The groups are students who study under mind mapping strategy, concept mapping, reciprocal teaching using summary notes, reciprocal teaching using mind mapping, problem-based learning, and investigation group. The results showed that those studying under problem-based learning strategy spent a significantly higher numbers in metacognitive knowledge in biology learning and followed by students who study under reciprocal teaching using mind mapping. According to the finding, it is expected that teachers of Biology will practice problem-based learning strategy in their classroom in order to increase the Metacognitive knowledge.

BioInt: an integrative biological object-oriented application framework and interpreter.

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Desai, Sanket; Burra, Prasad

2015-01-01

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

WISB: Warwick Integrative Synthetic Biology Centre.

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McCarthy, John

2016-06-15

Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. © 2016 The Author(s).

Automated quantitative assessment of proteins' biological function in protein knowledge bases.

Science.gov (United States)

Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter

2008-01-01

Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

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Gabriele Mayr

2008-01-01

Full Text Available Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

IntegromeDB: an integrated system and biological search engine.

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Baitaluk, Michael; Kozhenkov, Sergey; Dubinina, Yulia; Ponomarenko, Julia

2012-01-19

With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

Vertical Integration: Teachers' Knowledge and Teachers' Voice.

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Corrie, L.

1995-01-01

Traces the theoretical basis for vertical integration in early school years. Contrasts transmission-based pedagogy with a higher level of teacher control, and acquirer-based pedagogy with a higher level of student control. Suggests that early childhood pedagogy will be maintained when teachers are able to articulate their pedagogical knowledge and…

The impact of ecolabel knowledge to purchase decision of green producton biology students

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Sigit, Diana Vivanti; Fauziah, Rizky; Heryanti, Erna

2017-08-01

The world needs real solutions to reduce the impact of environmental damages. Students as agents of changes have a role to overcome these problems. One of the important solution is to be a critical consumer who has purchase decisions in a green product. To show the quality of an environmental friendly product, it is then required an ecolabel on the green product which indicates that the product has been through the production processed and come from environmental friendly substances. The research aimed at finding out whether there was an impact of ecolabel knowledge with purchase decision of green product on biology students. This research was conducted in Biology Department. This research used a survey descriptive method. The population used was biology students of Universitas Negeri Jakarta while the sampling technique was done through simple random sampling technique with 147 respondents. Instrument used were ecolabel knowledge test and a questionnaire of green product purchase decision. The result of prerequisite test showed that the data was normally distributed and homogenous variance. The regression model obtained was Ŷ=77.083+ 0.370X. Meanwhile, the determinant coefficient (r2) obtained was 0.047 or 4.7% that mean ecolabel knowledge just contributed 4,71% to the green product purchase decision. These implied that many factors contributed in the purchase decision of green product instead of ecolabel knowledge.

Network Reconstruction of Dynamic Biological Systems

OpenAIRE

Asadi, Behrang

2013-01-01

Inference of network topology from experimental data is a central endeavor in biology, since knowledge of the underlying signaling mechanisms a requirement for understanding biological phenomena. As one of the most important tools in bioinformatics area, development of methods to reconstruct biological networks has attracted remarkable attention in the current decade. Integration of different data types can lead to remarkable improvements in our ability to identify the connectivity of differe...

Vertical and horizontal integration of knowledge and skills - a working model.

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Snyman, W D; Kroon, J

2005-02-01

The new integrated outcomes-based curriculum for dentistry was introduced at the University of Pretoria in 1997. The first participants graduated at the end of 2001. Educational principles that underpin the new innovative dental curriculum include vertical and horizontal integration, problem-oriented learning, student-centred learning, a holistic attitude to patient care and the promotion of oral health. The aim of this research project was to develop and assay a model to facilitate vertical integration of knowledge and skills thereby justifying the above mentioned action. The learning methodology proposed for the specific outcome of the Odontology module, namely the diagnosis of dental caries and the design of a primary preventive programme, included problem-solving as the driving force for the facilitation of vertical and horizontal integration, and an instructional design for the integration of the basic knowledge and clinical skills into a single learning programme. The paper describes the methodology of problem-oriented learning as applied in this study together with the detail of the programme. The consensus of those teachers who represent the basic and clinical sciences and who participate in this learning programme is that this model is practical and can assist vertical as well as horizontal integration of knowledge.

Thinking about Digestive System in Early Childhood: A Comparative Study about Biological Knowledge

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AHI, Berat

2017-01-01

The current study aims to explore how children explain the concepts of biology and how biological knowledge develops across ages by focusing on the structure and functions of the digestive system. The study was conducted with 60 children. The data were collected through the interviews conducted within a think-aloud protocol. The interview data…

Integration of asynchronous knowledge sources in a novel speech recognition framework

OpenAIRE

Van hamme, Hugo

2008-01-01

Van hamme H., ''Integration of asynchronous knowledge sources in a novel speech recognition framework'', Proceedings ITRW on speech analysis and processing for knowledge discovery, 4 pp., June 2008, Aalborg, Denmark.

Integrating knowledge based functionality in commercial hospital information systems.

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Müller, M L; Ganslandt, T; Eich, H P; Lang, K; Ohmann, C; Prokosch, H U

2000-01-01

Successful integration of knowledge-based functions in the electronic patient record depends on direct and context-sensitive accessibility and availability to clinicians and must suit their workflow. In this paper we describe an exemplary integration of an existing standalone scoring system for acute abdominal pain into two different commercial hospital information systems using Java/Corba technolgy.

Integrating Biological Perspectives:. a Quantum Leap for Microarray Expression Analysis

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Wanke, Dierk; Kilian, Joachim; Bloss, Ulrich; Mangelsen, Elke; Supper, Jochen; Harter, Klaus; Berendzen, Kenneth W.

2009-02-01

Biologists and bioinformatic scientists cope with the analysis of transcript abundance and the extraction of meaningful information from microarray expression data. By exploiting biological information accessible in public databases, we try to extend our current knowledge over the plant model organism Arabidopsis thaliana. Here, we give two examples of increasing the quality of information gained from large scale expression experiments by the integration of microarray-unrelated biological information: First, we utilize Arabidopsis microarray data to demonstrate that expression profiles are usually conserved between orthologous genes of different organisms. In an initial step of the analysis, orthology has to be inferred unambiguously, which then allows comparison of expression profiles between orthologs. We make use of the publicly available microarray expression data of Arabidopsis and barley, Hordeum vulgare. We found a generally positive correlation in expression trajectories between true orthologs although both organisms are only distantly related in evolutionary time scale. Second, extracting clusters of co-regulated genes implies similarities in transcriptional regulation via similar cis-regulatory elements (CREs). Vice versa approaches, where co-regulated gene clusters are found by investigating on CREs were not successful in general. Nonetheless, in some cases the presence of CREs in a defined position, orientation or CRE-combinations is positively correlated with co-regulated gene clusters. Here, we make use of genes involved in the phenylpropanoid biosynthetic pathway, to give one positive example for this approach.

Fostering synergy between cell biology and systems biology.

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Eddy, James A; Funk, Cory C; Price, Nathan D

2015-08-01

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Match & Manage : The use of knowledge matching and project management to integrate knowledge in collaborative inbound open innovation

OpenAIRE

Lakemond, Nicolette; Bengtsson, Lars; Laursen, Keld; Tell, Fredrik

2016-01-01

Despite mounting evidence on the potential benefits of inbound open innovation, little is known about how firms purposefully manage inflows of knowledge. We investigate the use of two knowledge governance procedures—project management and knowledge matching—in collaborative inbound open innovation. Our findings suggest that, in addition to “knowledge-precursors,” which the literature on open innovation and absorptive capacity has shown to be important for the integration of external knowledge...

Knowledge Enrichment Analysis for Human Tissue- Specific Genes Uncover New Biological Insights

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Gong Xiu-Jun

2012-06-01

Full Text Available The expression and regulation of genes in different tissues are fundamental questions to be answered in biology. Knowledge enrichment analysis for tissue specific (TS and housekeeping (HK genes may help identify their roles in biological process or diseases and gain new biological insights.In this paper, we performed the knowledge enrichment analysis for 17,343 genes in 84 human tissues using Gene Set Enrichment Analysis (GSEA and Hypergeometric Analysis (HA against three biological ontologies: Gene Ontology (GO, KEGG pathways and Disease Ontology (DO respectively.The analyses results demonstrated that the functions of most gene groups are consistent with their tissue origins. Meanwhile three interesting new associations for HK genes and the skeletal muscle tissuegenes are found. Firstly, Hypergeometric analysis against KEGG database for HK genes disclosed that three disease terms (Parkinson’s disease, Huntington’s disease, Alzheimer’s disease are intensively enriched.Secondly, Hypergeometric analysis against the KEGG database for Skeletal Muscle tissue genes shows that two cardiac diseases of “Hypertrophic cardiomyopathy (HCM” and “Arrhythmogenic right ventricular cardiomyopathy (ARVC” are heavily enriched, which are also considered as no relationship with skeletal functions.Thirdly, “Prostate cancer” is intensively enriched in Hypergeometric analysis against the disease ontology (DO for the Skeletal Muscle tissue genes, which is a much unexpected phenomenon.

Integrated Ecological River Health Assessments, Based on Water Chemistry, Physical Habitat Quality and Biological Integrity

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Ji Yoon Kim

2015-11-01

Full Text Available This study evaluated integrative river ecosystem health using stressor-based models of physical habitat health, chemical water health, and biological health of fish and identified multiple-stressor indicators influencing the ecosystem health. Integrated health responses (IHRs, based on star-plot approach, were calculated from qualitative habitat evaluation index (QHEI, nutrient pollution index (NPI, and index of biological integrity (IBI in four different longitudinal regions (Groups I–IV. For the calculations of IHRs values, multi-metric QHEI, NPI, and IBI models were developed and their criteria for the diagnosis of the health were determined. The longitudinal patterns of the river were analyzed by a self-organizing map (SOM model and the key major stressors in the river were identified by principal component analysis (PCA. Our model scores of integrated health responses (IHRs suggested that mid-stream and downstream regions were impaired, and the key stressors were closely associated with nutrient enrichment (N and P and organic matter pollutions from domestic wastewater disposal plants and urban sewage. This modeling approach of IHRs may be used as an effective tool for evaluations of integrative ecological river health..

"Exploring knowledge-user experiences in integrated knowledge translation: a biomedical investigation of the causes and consequences of food allergy".

Science.gov (United States)

Dixon, Jenna; Elliott, Susan J; Clarke, Ann E

2016-01-01

Food allergy is a serious public health problem in Canada and other high-income countries, as it is potentially life threatening and severely impacts the quality of life for individuals and their families. Yet, many questions still remain as to its origins and determinants, and the best practices for treatment. Formed to tackle these very questions, the GET-FACTS research study centers on a novel concept in biomedical research: in order to make this science useful, knowledge creation must include meaningful interactions with knowledge-users. With this, knowledge-users are present at every stage of the research and are crucial, central and equal contributors. This study reflects on the early part of that journey from the perspective of the knowledge-users. We conducted interviews with all non-scientist members of the GET-FACTS steering committee, representing Canadian organizations that deal with patient advocacy and policy with regards to food allergy. Steering committee members had a clear sense that scientists and knowledge-users are equally responsible for putting knowledge into action and the importance of consulting and integrating knowledge-users throughout research. They also have high expectations for the GET-FACTS integrated process; that this model of doing science will create better scientists (e.g. improve communication skills) and make the scientific output more useful and relevant. Our work highlights both the unique contributions that knowledge-users can offer to knowledge creation as well as the challenges of trying to unify members from such different communities (policy/advocacy and biomedical science). There remains a real need to develop more touch points and opportunities for collaboration if true integration is to be achieved. Despite the obstacles, this model can help change the way knowledge is created in the biomedical world. ᅟ. Despite the burden of food allergic disease many questions remain as to its origins, determinants and best

Innovation and Integrity in Intervention Research: Conceptual Issues, Methodology, and Knowledge Translation.

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Malti, Tina; Beelmann, Andreas; Noam, Gil G; Sommer, Simon

2018-04-01

In this article, we introduce the special issue entitled Innovation and Integrity in Intervention Science. Its focus is on essential problems and prospects for intervention research examining two related topics, i.e., methodological issues and research integrity, and challenges in the transfer of research knowledge into practice and policy. The main aims are to identify how to advance methodology in order to improve research quality, examine scientific integrity in the field of intervention science, and discuss future steps to enhance the transfer of knowledge about evidence-based intervention principles into sustained practice, routine activities, and policy decisions. Themes of the special issue are twofold. The first includes questions about research methodology in intervention science, both in terms of research design and methods, as well as data analyses and the reporting of findings. Second, the issue tackles questions surrounding the types of knowledge translation frameworks that might be beneficial to mobilize the transfer of research-based knowledge into practice and public policies. The issue argues that innovations in methodology and thoughtful approaches to knowledge translation can enable transparency, quality, and sustainability of intervention research.

BIOZON: a system for unification, management and analysis of heterogeneous biological data

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Yona Golan

2006-02-01

Full Text Available Abstract Background Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. Description Here we present a system (Biozon that addresses these problems, and offers biologists a new knowledge resource to navigate through and explore. Biozon unifies multiple biological databases consisting of a variety of data types (such as DNA sequences, proteins, interactions and cellular pathways. It is fundamentally different from previous efforts as it uses a single extensive and tightly connected graph schema wrapped with hierarchical ontology of documents and relations. Beyond warehousing existing data, Biozon computes and stores novel derived data, such as similarity relationships and functional predictions. The integration of similarity data allows propagation of knowledge through inference and fuzzy searches. Sophisticated methods of query that span multiple data types were implemented and first-of-a-kind biological ranking systems were explored and integrated. Conclusion The Biozon system is an extensive knowledge resource of heterogeneous biological data. Currently, it holds more than 100 million biological documents and 6.5 billion relations between them. The database is accessible through an advanced web interface that supports complex queries, "fuzzy" searches, data materialization and more, online at http://biozon.org.

Introducing Knowledge Management into the Integrated Management System of Nuclear Organizations

International Nuclear Information System (INIS)

Yanev, Y.; Brandner, A.; Kosilov, A.

2016-01-01

Full text: The analysis for introducing knowledge management into an integrated management system in nuclear organizations, conducted by NKMI, and discussed in a number of meetings in IAEA and other organizations has shown that currently there is no full and comprehensive implementation of KM in IMS. NKMI has suggested and developed a common, systematic approach for introducing Knowledge Management in the IMS of a nuclear regulatory organization, based on the concept of competence, graded approach and continuous improvement. The approach is based on the concept of integrating an initial review of all knowledge and competence needed for effective and efficient process implementation including a gap analysis and provision of compensatory measures. Knowledge resources are represented as a knowledge resource matrix, which are necessary to complete a given process successfully. The “performance” of the available knowledge resources contribute to an efficient regulatory process is also reviewed at the end of process implementation where relevant decision for enhancement of knowledge and competence are taken, including capturing, preserving, sharing and reuse of new knowledge, gained through the process implementation. The “knowledge resource matrix” approach is fully based on IAEA recommendation and has already been applied in a number of regulatory processes. (author

Bayesian integration of position and orientation cues in perception of biological and non-biological dynamic forms

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Steven Matthew Thurman

2014-02-01

Full Text Available Visual form analysis is fundamental to shape perception and likely plays a central role in perception of more complex dynamic shapes, such as moving objects or biological motion. Two primary form-based cues serve to represent the overall shape of an object: the spatial position and the orientation of locations along the boundary of the object. However, it is unclear how the visual system integrates these two sources of information in dynamic form analysis, and in particular how the brain resolves ambiguities due to sensory uncertainty and/or cue conflict. In the current study, we created animations of sparsely-sampled dynamic objects (human walkers or rotating squares comprised of oriented Gabor patches in which orientation could either coincide or conflict with information provided by position cues. When the cues were incongruent, we found a characteristic trade-off between position and orientation information whereby position cues increasingly dominated perception as the relative uncertainty of orientation increased and vice versa. Furthermore, we found no evidence for differences in the visual processing of biological and non-biological objects, casting doubt on the claim that biological motion may be specialized in the human brain, at least in specific terms of form analysis. To explain these behavioral results quantitatively, we adopt a probabilistic template-matching model that uses Bayesian inference within local modules to estimate object shape separately from either spatial position or orientation signals. The outputs of the two modules are integrated with weights that reflect individual estimates of subjective cue reliability, and integrated over time to produce a decision about the perceived dynamics of the input data. Results of this model provided a close fit to the behavioral data, suggesting a mechanism in the human visual system that approximates rational Bayesian inference to integrate position and orientation signals in dynamic

PathJam: a new service for integrating biological pathway information

Directory of Open Access Journals (Sweden)

Glez-Peña Daniel

2010-03-01

Full Text Available Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.

Science Teachers’ Pedagogical Content Knowledge and Integrated Approach

Science.gov (United States)

Adi Putra, M. J.; Widodo, A.; Sopandi, W.

2017-09-01

The integrated approach refers to the stages of pupils’ psychological development. Unfortunately, the competences which are designed into the curriculum is not appropriate with the child development. This Manuscript presents PCK (pedagogical content knowledge) of teachers who teach science content utilizing an integrated approach. The data has been collected by using CoRe, PaP-eR, and interviews from six elementary teachers who teach science. The paper informs that high and stable teacher PCKs have an impact on how teachers present integrated teaching. Because it is influenced by the selection of important content that must be submitted to the students, the depth of the content, the reasons for choosing the teaching procedures and some other things. So for teachers to be able to integrate teaching, they should have a balanced PCK.

Integrating Expert Knowledge into Mapping Ecosystem Services Trade-offs for Sustainable Forest Management

Directory of Open Access Journals (Sweden)

Adrienne Grêt-Regamey

2013-09-01

Full Text Available Mountain ecosystems are highly sensitive to global change. In fact, the continued capacity of mountain regions to provide goods and services to society is threatened by the impact of environmental changes on ecosystems. Although mapping ecosystem services values is known to support sustainable resource management, the integration of spatially explicit local expert knowledge on ecosystem dynamics and social responses to global changes has not yet been integrated in the modeling process. This contribution demonstrates the importance of integrating local knowledge into the spatially explicit valuation of ecosystem services. Knowledge acquired by expert surveys flows into a GIS-based Bayesian Network for valuing forest ecosystem services under a land-use and a climate change scenario in a case study in the Swiss Alps. Results show that including expert knowledge in ecosystem services mapping not only reduces uncertainties considerably, but also has an important effect on the ecosystem services values. Particularly the iterative process between integrating expert knowledge into the modeling process and mapping ecosystem services guarantees a continuous improvement of ecosystem services values maps while opening a new way for mutual learning between scientists and stakeholders which might support adaptive resource management.

Enabling Integrated Decision Making for Electronic-Commerce by Modelling an Enterprise's Sharable Knowledge.

Science.gov (United States)

Kim, Henry M.

2000-01-01

An enterprise model, a computational model of knowledge about an enterprise, is a useful tool for integrated decision-making by e-commerce suppliers and customers. Sharable knowledge, once represented in an enterprise model, can be integrated by the modeled enterprise's e-commerce partners. Presents background on enterprise modeling, followed by…

An integrative model of knowledge management and team work

Directory of Open Access Journals (Sweden)

Juan A. Marin-Garcia

2008-10-01

Full Text Available Human Resource Management relevance in Knowledge Management has been studied in academic literature mostly from the point of view of recruitment, selection, wages and salaries and career development processes. We have found few publications that are focused in the behaviour of the group of people who generate, share and transfer that knowledge while working in a team. The aim of this paper is to propose a framework that describes the relation between knowledge management and team work,, integrating Nonaka and Takeuchi, Leonard- Barton and Heisig framework proposals, as well as to outline some reflexions for further researches.

Economic value of biological control in integrated pest management of managed plant systems.

Science.gov (United States)

Naranjo, Steven E; Ellsworth, Peter C; Frisvold, George B

2015-01-07

Biological control is an underlying pillar of integrated pest management, yet little focus has been placed on assigning economic value to this key ecosystem service. Setting biological control on a firm economic foundation would help to broaden its utility and adoption for sustainable crop protection. Here we discuss approaches and methods available for valuation of biological control of arthropod pests by arthropod natural enemies and summarize economic evaluations in classical, augmentative, and conservation biological control. Emphasis is placed on valuation of conservation biological control, which has received little attention. We identify some of the challenges of and opportunities for applying economics to biological control to advance integrated pest management. Interaction among diverse scientists and stakeholders will be required to measure the direct and indirect costs and benefits of biological control that will allow farmers and others to internalize the benefits that incentivize and accelerate adoption for private and public good.

Exploring the Associations Among Nutrition, Science, and Mathematics Knowledge for an Integrative, Food-Based Curriculum.

Science.gov (United States)

Stage, Virginia C; Kolasa, Kathryn M; Díaz, Sebastián R; Duffrin, Melani W

2018-01-01

Explore associations between nutrition, science, and mathematics knowledge to provide evidence that integrating food/nutrition education in the fourth-grade curriculum may support gains in academic knowledge. Secondary analysis of a quasi-experimental study. Sample included 438 students in 34 fourth-grade classrooms across North Carolina and Ohio; mean age 10 years old; gender (I = 53.2% female; C = 51.6% female). Dependent variable = post-test-nutrition knowledge; independent variables = baseline-nutrition knowledge, and post-test science and mathematics knowledge. Analyses included descriptive statistics and multiple linear regression. The hypothesized model predicted post-nutrition knowledge (F(437) = 149.4, p mathematics knowledge were predictive of nutrition knowledge indicating use of an integrative science and mathematics curriculum to improve academic knowledge may also simultaneously improve nutrition knowledge among fourth-grade students. Teachers can benefit from integration by meeting multiple academic standards, efficiently using limited classroom time, and increasing nutrition education provided in the classroom. © 2018, American School Health Association.

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

Directory of Open Access Journals (Sweden)

Christopher Y Park

Full Text Available A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction. We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics

Integrating experiences from operations into engineering design: modelling knowledge transfer in the offshore oil industry

DEFF Research Database (Denmark)

Souza da Conceição, Carolina; Broberg, Ole; Paravizo, Esdras

2017-01-01

of knowledge registered in the systems without standards to categorise and store this knowledge, to being difficult to access and retrieve the knowledge in the systems. Discussion: Transferring knowledge and experiences from users brings human factors into play and modelling the knowledge transfer process...... and workwise distance between operations and engineering design teams, integrating human factors and transferring knowledge are key aspects when designing for better performance systems. Research Objective: Based on an in-depth empirical investigation in an offshore oil company, this study aims to provide......Summative Statement: Integrating human factors and users’ experiences in design projects is a well-known challenge. This study focus on the specific challenges for transferring these experiences and how using a knowledge transfer model can help this integration on the design of high-risk productive...

An Integrated Biological Control System At Hanford

International Nuclear Information System (INIS)

Johnson, A.R.; Caudill, J.G.; Giddings, R.F.; Rodriguez, J.M.; Roos, R.C.; Wilde, J.W.

2010-01-01

In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimate spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

Energy Technology Data Exchange (ETDEWEB)

JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

2010-02-11

In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

Advancing nursing practice: redefining the theoretical and practical integration of knowledge.

Science.gov (United States)

Christensen, Martin

2011-03-01

The aim of this paper is to offer an alternative knowing-how knowing-that framework of nursing knowledge, which in the past has been accepted as the provenance of advanced practice. The concept of advancing practice is central to the development of nursing practice and has been seen to take on many different forms depending on its use in context. To many it has become synonymous with the work of the advanced or expert practitioner; others have viewed it as a process of continuing professional development and skills acquisition. Moreover, it is becoming closely linked with practice development. However, there is much discussion as to what constitutes the knowledge necessary for advancing and advanced practice, and it has been suggested that theoretical and practical knowledge form the cornerstone of advanced knowledge. The design of this article takes a discursive approach as to the meaning and integration of knowledge within the context of advancing nursing practice. A thematic analysis of the current discourse relating to knowledge integration models in an advancing and advanced practice arena was used to identify concurrent themes relating to the knowing-how knowing-that framework which commonly used to classify the knowledge necessary for advanced nursing practice. There is a dichotomy as to what constitutes knowledge for advanced and advancing practice. Several authors have offered a variety of differing models, yet it is the application and integration of theoretical and practical knowledge that defines and develops the advancement of nursing practice. An alternative framework offered here may allow differences in the way that nursing knowledge important for advancing practice is perceived, developed and coordinated. What has inevitably been neglected is that there are various other variables which when transposed into the existing knowing-how knowing-that framework allows for advanced knowledge to be better defined. One of the more notable variables is

Models, methods and software for distributed knowledge acquisition for the automated construction of integrated expert systems knowledge bases

International Nuclear Information System (INIS)

Dejneko, A.O.

2011-01-01

Based on an analysis of existing models, methods and means of acquiring knowledge, a base method of automated knowledge acquisition has been chosen. On the base of this method, a new approach to integrate information acquired from knowledge sources of different typologies has been proposed, and the concept of a distributed knowledge acquisition with the aim of computerized formation of the most complete and consistent models of problem areas has been introduced. An original algorithm for distributed knowledge acquisition from databases, based on the construction of binary decision trees has been developed [ru

Knowledge-Intensive Gathering and Integration of Statistical Information on European Fisheries

NARCIS (Netherlands)

Klinkert, M.; Treur, J.; Verwaart, T.; Loganantharaj, R.; Palm, G.; Ali, M.

2000-01-01

Gathering, maintenance, integration and presentation of statistics are major activities of the Dutch Agricultural Economics Research Institute LEI. In this paper we explore how knowledge and agent technology can be exploited to support the information gathering and integration process. In

Knowledge Assisted Integrated Design of a Component and Its Manufacturing Process

Science.gov (United States)

Gautham, B. P.; Kulkarni, Nagesh; Khan, Danish; Zagade, Pramod; Reddy, Sreedhar; Uppaluri, Rohith

Integrated design of a product and its manufacturing processes would significantly reduce the total cost of the products as well as the cost of its development. However this would only be possible if we have a platform that allows us to link together simulations tools used for product design, performance evaluation and its manufacturing processes in a closed loop. In addition to that having a comprehensive knowledgebase that provides systematic knowledge guided assistance to product or process designers who may not possess in-depth design knowledge or in-depth knowledge of the simulation tools, would significantly speed up the end-to-end design process. In this paper, we propose a process and illustrate a case for achieving an integrated product and manufacturing process design assisted by knowledge support for the user to make decisions at various stages. We take transmission component design as an example. The example illustrates the design of a gear for its geometry, material selection and its manufacturing processes, particularly, carburizing-quenching and tempering, and feeding the material properties predicted during heat treatment into performance estimation in a closed loop. It also identifies and illustrates various decision stages in the integrated life cycle and discusses the use of knowledge engineering tools such as rule-based guidance, to assist the designer make informed decisions. Simulation tools developed on various commercial, open-source platforms as well as in-house tools along with knowledge engineering tools are linked to build a framework with appropriate navigation through user-friendly interfaces. This is illustrated through examples in this paper.

Integration of knowledge management system for the decommissioning of nuclear facilities

International Nuclear Information System (INIS)

Iguchi, Yukihiro; Yanagihara, Satoshi

2016-01-01

The decommissioning of a nuclear facility is a long term project, handling information which begins from the design, construction and operation. Moreover, the decommissioning project is likely to be extended because of the lack of the waste disposal site especially in Japan. In this situation, because the transfer of knowledge and education to the next generation is a crucial issue, integration and implementation of a system for knowledge management is necessary in order to solve it. For this purpose, the total system of decommissioning knowledge management system (KMS) is proposed. In this system, we have to arrange, organize and systematize the data and information of the plant design, maintenance history, trouble events, waste management records etc. The collected data, information and records should be organized by computer support system e.g. data base system. It becomes a base of the explicit knowledge. Moreover, measures of extracting tacit knowledge from retiring employees are necessary. The experience of the retirees should be documented as much as possible through effective questionnaire or interview process. The integrated knowledge mentioned above should be used for the planning, implementation of dismantlement or education for the future generation. (author)

Integration of object-oriented knowledge representation with the CLIPS rule based system

Science.gov (United States)

Logie, David S.; Kamil, Hasan

1990-01-01

The paper describes a portion of the work aimed at developing an integrated, knowledge based environment for the development of engineering-oriented applications. An Object Representation Language (ORL) was implemented in C++ which is used to build and modify an object-oriented knowledge base. The ORL was designed in such a way so as to be easily integrated with other representation schemes that could effectively reason with the object base. Specifically, the integration of the ORL with the rule based system C Language Production Systems (CLIPS), developed at the NASA Johnson Space Center, will be discussed. The object-oriented knowledge representation provides a natural means of representing problem data as a collection of related objects. Objects are comprised of descriptive properties and interrelationships. The object-oriented model promotes efficient handling of the problem data by allowing knowledge to be encapsulated in objects. Data is inherited through an object network via the relationship links. Together, the two schemes complement each other in that the object-oriented approach efficiently handles problem data while the rule based knowledge is used to simulate the reasoning process. Alone, the object based knowledge is little more than an object-oriented data storage scheme; however, the CLIPS inference engine adds the mechanism to directly and automatically reason with that knowledge. In this hybrid scheme, the expert system dynamically queries for data and can modify the object base with complete access to all the functionality of the ORL from rules.

Integrating biological and social values when prioritizing places for biodiversity conservation.

Science.gov (United States)

Whitehead, Amy L; Kujala, Heini; Ives, Christopher D; Gordon, Ascelin; Lentini, Pia E; Wintle, Brendan A; Nicholson, Emily; Raymond, Christopher M

2014-08-01

The consideration of information on social values in conjunction with biological data is critical for achieving both socially acceptable and scientifically defensible conservation planning outcomes. However, the influence of social values on spatial conservation priorities has received limited attention and is poorly understood. We present an approach that incorporates quantitative data on social values for conservation and social preferences for development into spatial conservation planning. We undertook a public participation GIS survey to spatially represent social values and development preferences and used species distribution models for 7 threatened fauna species to represent biological values. These spatially explicit data were simultaneously included in the conservation planning software Zonation to examine how conservation priorities changed with the inclusion of social data. Integrating spatially explicit information about social values and development preferences with biological data produced prioritizations that differed spatially from the solution based on only biological data. However, the integrated solutions protected a similar proportion of the species' distributions, indicating that Zonation effectively combined the biological and social data to produce socially feasible conservation solutions of approximately equivalent biological value. We were able to identify areas of the landscape where synergies and conflicts between different value sets are likely to occur. Identification of these synergies and conflicts will allow decision makers to target communication strategies to specific areas and ensure effective community engagement and positive conservation outcomes. © 2014 Society for Conservation Biology.

Integrated Biological Control

International Nuclear Information System (INIS)

JOHNSON, A.R.

2002-01-01

Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects; and microorganisms such as molds that adversely affect the quality of the workplace environment). Biological control activities may be either preventive (apriori) or in response to existing contamination spread (aposteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and apriori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, aposteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response

Laevo: A Temporal Desktop Interface for Integrated Knowledge Work

DEFF Research Database (Denmark)

Jeuris, Steven; Houben, Steven; Bardram, Jakob

2014-01-01

Prior studies show that knowledge work is characterized by highly interlinked practices, including task, file and window management. However, existing personal information management tools primarily focus on a limited subset of knowledge work, forcing users to perform additional manual...... states and transitions of an activity. The life cycle is used to inform the design of Laevo, a temporal activity-centric desktop interface for personal knowledge work. Laevo allows users to structure work within dedicated workspaces, managed on a timeline. Through a centralized notification system which...... configuration work to integrate the different tools they use. In order to understand tool usage, we review literature on how users' activities are created and evolve over time as part of knowledge worker practices. From this we derive the activity life cycle, a conceptual framework describing the different...

Quantum biological information theory

CERN Document Server

Djordjevic, Ivan B

2016-01-01

This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

The Knowledge-Integrated Network Biomarkers Discovery for Major Adverse Cardiac Events

Science.gov (United States)

Jin, Guangxu; Zhou, Xiaobo; Wang, Honghui; Zhao, Hong; Cui, Kemi; Zhang, Xiang-Sun; Chen, Luonan; Hazen, Stanley L.; Li, King; Wong, Stephen T. C.

2010-01-01

The mass spectrometry (MS) technology in clinical proteomics is very promising for discovery of new biomarkers for diseases management. To overcome the obstacles of data noises in MS analysis, we proposed a new approach of knowledge-integrated biomarker discovery using data from Major Adverse Cardiac Events (MACE) patients. We first built up a cardiovascular-related network based on protein information coming from protein annotations in Uniprot, protein–protein interaction (PPI), and signal transduction database. Distinct from the previous machine learning methods in MS data processing, we then used statistical methods to discover biomarkers in cardiovascular-related network. Through the tradeoff between known protein information and data noises in mass spectrometry data, we finally could firmly identify those high-confident biomarkers. Most importantly, aided by protein–protein interaction network, that is, cardiovascular-related network, we proposed a new type of biomarkers, that is, network biomarkers, composed of a set of proteins and the interactions among them. The candidate network biomarkers can classify the two groups of patients more accurately than current single ones without consideration of biological molecular interaction. PMID:18665624

Integrating chemical and biological status assessment: Assembling lines of evidence for the evaluation of river ecosystem risk

International Nuclear Information System (INIS)

Munoz Gracia, Isabel; Sabater, Sergi

2014-01-01

This paper describes various approaches to evaluating ecological risk in rivers affected by multiple chemical stressors, with emphasis on biofilm and invertebrate community responses. Metrics should be considered as different lines of evidence that, when weighted, form an advanced weight of evidence approach to establishing the environmental risk on a basin scale. Combination of field surveys to obtain observational data of communities, in situ experiments, toxicological sediment tests and a good chemical description of the medium (water and sediment) helps give an integrative view of the chemical and biological state of a river ecosystem. The greater and more distinct the variables used, the greater is our ability to identify the effects of major stressors impairing communities. Weight of evidence is an integrative methodology for tackling the challenge of determining causal relations and applying this knowledge in the decision-making processes of river management.

Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology.

Science.gov (United States)

Das, Arya A; Ajayakumar Darsana, T; Jacob, Elizabeth

2017-03-01

Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments. A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies. Implemented on the Agent Modelling Framework developed in-house. C ++ code templates available in Supplementary material . liz.csir@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Knowledge Management tools integration within DLR's concurrent engineering facility

Science.gov (United States)

Lopez, R. P.; Soragavi, G.; Deshmukh, M.; Ludtke, D.

The complexity of space endeavors has increased the need for Knowledge Management (KM) tools. The concept of KM involves not only the electronic storage of knowledge, but also the process of making this knowledge available, reusable and traceable. Establishing a KM concept within the Concurrent Engineering Facility (CEF) has been a research topic of the German Aerospace Centre (DLR). This paper presents the current KM tools of the CEF: the Software Platform for Organizing and Capturing Knowledge (S.P.O.C.K.), the data model Virtual Satellite (VirSat), and the Simulation Model Library (SimMoLib), and how their usage improved the Concurrent Engineering (CE) process. This paper also exposes the lessons learned from the introduction of KM practices into the CEF and elaborates a roadmap for the further development of KM in CE activities at DLR. The results of the application of the Knowledge Management tools have shown the potential of merging the three software platforms with their functionalities, as the next step towards the fully integration of KM practices into the CE process. VirSat will stay as the main software platform used within a CE study, and S.P.O.C.K. and SimMoLib will be integrated into VirSat. These tools will support the data model as a reference and documentation source, and as an access to simulation and calculation models. The use of KM tools in the CEF aims to become a basic practice during the CE process. The settlement of this practice will result in a much more extended knowledge and experience exchange within the Concurrent Engineering environment and, consequently, the outcome of the studies will comprise higher quality in the design of space systems.

Integrating Neuroscience Knowledge into Social Work Education: A Case-Based Approach

Science.gov (United States)

Egan, Marcia; Neely-Barnes, Susan L.; Combs-Orme, Terri

2011-01-01

New knowledge from the rapidly growing field of neuroscience has important implications for our understanding of human behavior in the social environment, yet little of this knowledge has made its way into social work education. This article presents a model for integrating neuroscience into instruction on human development, the bio psychosocial…

Integrating ICT in Agriculture for Knowledge-Based Economy | Balraj ...

African Journals Online (AJOL)

... demands the integration of ICT knowledge with agriculture. Already projects such as Agriculture Management Information System (AMIS), and e-Soko (which means electronic marketing) – which provides farmers with the price decision making tools enlightens the path to socio-economic development through agriculture.

Fort Collins Science Center- Policy Analysis and Science Assistance Branch : Integrating social, behavioral, economic and biological sciences

Science.gov (United States)

2010-01-01

The Fort Collins Science Center's Policy Analysis and Science Assistance (PASA) Branch is a team of approximately 22 scientists, technicians, and graduate student researchers. PASA provides unique capabilities in the U.S. Geological Survey by leading projects that integrate social, behavioral, economic, and biological analyses in the context of human-natural resource interactions. Resource planners, managers, and policymakers in the U.S. Departments of the Interior (DOI) and Agriculture (USDA), State and local agencies, as well as international agencies use information from PASA studies to make informed natural resource management and policy decisions. PASA scientists' primary functions are to conduct both theoretical and applied social science research, provide technical assistance, and offer training to advance performance in policy relevant research areas. Management and research issues associated with human-resource interactions typically occur in a unique context, involve difficult to access populations, require knowledge of both natural/biological science in addition to social science, and require the skill to integrate multiple science disciplines. In response to these difficult contexts, PASA researchers apply traditional and state-of-the-art social science methods drawing from the fields of sociology, demography, economics, political science, communications, social-psychology, and applied industrial organization psychology. Social science methods work in concert with our rangeland/agricultural management, wildlife, ecology, and biology capabilities. The goal of PASA's research is to enhance natural resource management, agency functions, policies, and decision-making. Our research is organized into four broad areas of study.

Making evolutionary biology a basic science for medicine

Science.gov (United States)

Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

2010-01-01

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

Integrative pathway knowledge bases as a tool for systems molecular medicine.

Science.gov (United States)

Liang, Mingyu

2007-08-20

There exists a sense of urgency to begin to generate a cohesive assembly of biomedical knowledge as the pace of knowledge accumulation accelerates. The urgency is in part driven by the emergence of systems molecular medicine that emphasizes the combination of systems analysis and molecular dissection in the future of medical practice and research. A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.

An integration architecture for knowledge management system and business process management system

NARCIS (Netherlands)

Jung, J.; Choi, I.; Song, M.S.

2007-01-01

Recently, interests in the notion of process-oriented knowledge management (PKM) from academia and industry have been significantly increased. Comprehensive research and development requirements along with a cogent framework, however, have not been proposed for integrating knowledge management (KM)

Integrating social science knowledge into natural resource management public involvement practice

DEFF Research Database (Denmark)

Stummann, Cathy Brown

This PhD study explores the long-recognized challenge of integrating social science knowledge into NRM public involvement practice theoretically and empirically. Theoretically, the study draws on research from adult learning, continuing rofessional education and professional knowledge development...... to better understand how social science knowledge can benefit NRM public involvement practice. Empirically, the study explores the potential of NRM continuing professional education as a means for introducing social science knowledge to public NRM professionals. The study finds social science knowledge can...... be of value to NRM public involvement prospectively and retrospectively; and that continuing professional education can be an effective means to introducing social science knowledge to public NRM professionals. In the design of NRM continuing professional education focused on social science knowledge...

Systematic integration of experimental data and models in systems biology.

Science.gov (United States)

Li, Peter; Dada, Joseph O; Jameson, Daniel; Spasic, Irena; Swainston, Neil; Carroll, Kathleen; Dunn, Warwick; Khan, Farid; Malys, Naglis; Messiha, Hanan L; Simeonidis, Evangelos; Weichart, Dieter; Winder, Catherine; Wishart, Jill; Broomhead, David S; Goble, Carole A; Gaskell, Simon J; Kell, Douglas B; Westerhoff, Hans V; Mendes, Pedro; Paton, Norman W

2010-11-29

The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

Content-rich biological network constructed by mining PubMed abstracts

Directory of Open Access Journals (Sweden)

Sharp Burt M

2004-10-01

Full Text Available Abstract Background The integration of the rapidly expanding corpus of information about the genome, transcriptome, and proteome, engendered by powerful technological advances, such as microarrays, and the availability of genomic sequence from multiple species, challenges the grasp and comprehension of the scientific community. Despite the existence of text-mining methods that identify biological relationships based on the textual co-occurrence of gene/protein terms or similarities in abstract texts, knowledge of the underlying molecular connections on a large scale, which is prerequisite to understanding novel biological processes, lags far behind the accumulation of data. While computationally efficient, the co-occurrence-based approaches fail to characterize (e.g., inhibition or stimulation, directionality biological interactions. Programs with natural language processing (NLP capability have been created to address these limitations, however, they are in general not readily accessible to the public. Results We present a NLP-based text-mining approach, Chilibot, which constructs content-rich relationship networks among biological concepts, genes, proteins, or drugs. Amongst its features, suggestions for new hypotheses can be generated. Lastly, we provide evidence that the connectivity of molecular networks extracted from the biological literature follows the power-law distribution, indicating scale-free topologies consistent with the results of previous experimental analyses. Conclusions Chilibot distills scientific relationships from knowledge available throughout a wide range of biological domains and presents these in a content-rich graphical format, thus integrating general biomedical knowledge with the specialized knowledge and interests of the user. Chilibot http://www.chilibot.net can be accessed free of charge to academic users.

Knowledge Representation and Management, It's Time to Integrate!

Science.gov (United States)

Dhombres, F; Charlet, J

2017-08-01

Objectives: To select, present, and summarize the best papers published in 2016 in the field of Knowledge Representation and Management (KRM). Methods: A comprehensive and standardized review of the medical informatics literature was performed based on a PubMed query. Results: Among the 1,421 retrieved papers, the review process resulted in the selection of four best papers focused on the integration of heterogeneous data via the development and the alignment of terminological resources. In the first article, the authors provide a curated and standardized version of the publicly available US FDA Adverse Event Reporting System. Such a resource will improve the quality of the underlying data, and enable standardized analyses using common vocabularies. The second article describes a project developed in order to facilitate heterogeneous data integration in the i2b2 framework. The originality is to allow users integrate the data described in different terminologies and to build a new repository, with a unique model able to support the representation of the various data. The third paper is dedicated to model the association between multiple phenotypic traits described within the Human Phenotype Ontology (HPO) and the corresponding genotype in the specific context of rare diseases (rare variants). Finally, the fourth paper presents solutions to annotation-ontology mapping in genome-scale data. Of particular interest in this work is the Experimental Factor Ontology (EFO) and its generic association model, the Ontology of Biomedical AssociatioN (OBAN). Conclusion: Ontologies have started to show their efficiency to integrate medical data for various tasks in medical informatics: electronic health records data management, clinical research, and knowledge-based systems development. Georg Thieme Verlag KG Stuttgart.

Integrating movement in academic classrooms: understanding, applying and advancing the knowledge base.

Science.gov (United States)

Webster, C A; Russ, L; Vazou, S; Goh, T L; Erwin, H

2015-08-01

In the context of comprehensive and coordinated approaches to school health, academic classrooms have gained attention as a promising setting for increasing physical activity and reducing sedentary time among children. The aims of this paper are to review the rationale and knowledge base related to movement integration in academic classrooms, consider the practical applications of current knowledge to interventions and teacher education, and suggest directions for future research. Specifically, this paper (i) situates movement integration amid policy and research related to children's health and the school as a health-promoting environment; (ii) highlights the benefits of movement integration; (iii) summarizes movement integration programs and interventions; (iv) examines factors associated with classroom teachers' movement integration; (v) offers strategies for translating research to practice and (vi) forwards recommendations for future inquiry related to the effectiveness and sustainability of efforts to integrate movement into classroom routines. This paper provides a comprehensive resource for developing state-of-the-art initiatives to maximize children's movement in academic classrooms as a key strategy for important goals in both education and public health. © 2015 World Obesity.

The Virtual Institute for Integrative Biology (VIIB)

International Nuclear Information System (INIS)

Rivera, G.; Gonzalez-Nieto, F.; Perez-Acle, T.; Isea, R.; Holmes, D. S.

2007-01-01

The Virtual Institute for Integrative Biology (VII B) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, Metagenomic, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomic, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services and protein simulations for biotechnological and medical applications. Human resource development has been promoted through co-sponsored students and shared teaching and seminars via video conferencing. E-Science challenges include: inter operability and connectivity concerns, high performance computing limitations, and the development of customized computational frameworks and flexible work flows to efficiently exploit shared resources without causing impediments to the user. Outreach programs include training workshops and classes for high school teachers and students and the new Adopt-a-Gene initiative. The VIIB has proved an effective way for small teams to transcend the critical mass problem, to overcome geographic limitations, to harness the power of large scale, collaborative science and improve the visibility of Latin American science It may provide a useful paradigm for developing further e-Science initiatives in Latin America and other emerging regions. (Author)

Integrating across Episodes: Investigating the Long-term Accessibility of Self-derived Knowledge in 4-Year-Old Children

Science.gov (United States)

Varga, Nicole L.; Stewart, Rebekah A.; Bauer, Patricia J.

2016-01-01

Semantic memory, defined as our store of knowledge about the world, provides representational support for all of our higher order cognitive functions. As such, it is crucial that the contents of semantic memory remain accessible over time. Although memory for knowledge learned through direct observation has been previously investigated, we know very little about the retention of knowledge derived through integration of information acquired across separate learning episodes. The present research investigated cross-episode integration in 4-year-old children. Participants were presented with novel facts via distinct story episodes and tested for knowledge extension through cross-episode integration, as well as for retention of the information over a 1-week delay. In Experiment 1, children retained the self-derived knowledge over the delay, though performance was primarily evidenced in a forced-choice format. In Experiment 2, we sought to facilitate the accessibility and robustness of self-derived knowledge by providing a verbal reminder after the delay. The accessibility of self-derived knowledge increased, irrespective of whether participants successfully demonstrated knowledge of the integration facts during the first visit. The results suggest knowledge extended through integration remains accessible after delays, even in a population in which this learning process is less robust. The findings also demonstrate the facilitative effect of reminders on the accessibility and further extension of knowledge over extended time periods. PMID:26774259

Knowledge integration in One Health policy formulation, implementation and evaluation.

Science.gov (United States)

Hitziger, Martin; Esposito, Roberto; Canali, Massimo; Aragrande, Maurizio; Häsler, Barbara; Rüegg, Simon R

2018-03-01

The One Health concept covers the interrelationship between human, animal and environmental health and requires multistakeholder collaboration across many cultural, disciplinary, institutional and sectoral boundaries. Yet, the implementation of the One Health approach appears hampered by shortcomings in the global framework for health governance. Knowledge integration approaches, at all stages of policy development, could help to address these shortcomings. The identification of key objectives, the resolving of trade-offs and the creation of a common vision and a common direction can be supported by multicriteria analyses. Evidence-based decision-making and transformation of observations into narratives detailing how situations emerge and might unfold in the future can be achieved by systems thinking. Finally, transdisciplinary approaches can be used both to improve the effectiveness of existing systems and to develop novel networks for collective action. To strengthen One Health governance, we propose that knowledge integration becomes a key feature of all stages in the development of related policies. We suggest several ways in which such integration could be promoted.

Exploration and implementation of ontology-based cultural relic knowledge map integration platform

Science.gov (United States)

Yang, Weiqiang; Dong, Yiqiang

2018-05-01

To help designers to better carry out creative design and improve the ability of searching traditional cultural relic information, the ontology-based knowledge map construction method was explored and an integrated platform for cultural relic knowledge map was developed. First of all, the construction method of the ontology of cultural relics was put forward, and the construction of the knowledge map of cultural relics was completed based on the constructed cultural relic otology. Then, a personalized semantic retrieval framework for creative design was proposed. Finally, the integrated platform of the knowledge map of cultural relics was designed and realized. The platform was divided into two parts. One was the foreground display system, which was used for designers to search and browse cultural relics. The other was the background management system, which was for cultural experts to manage cultural relics' knowledge. The research results showed that the platform designed could improve the retrieval ability of cultural relic information. To sum up, the platform can provide a good support for the designer's creative design.

Conscious knowledge of learning: accessing learning strategies in a final year high school biology class

Science.gov (United States)

Conner, Lindsey; Gunstone, Richard

2004-12-01

This paper reports on a qualitative case study investigation of the knowledge and use of learning strategies by 16 students in a final year high school biology class to expand their conscious knowledge of learning. Students were provided with opportunities to engage in purposeful inquiry into the biological, social and ethical aspects of cancer. A constructivist approach was implemented to access prior content and procedural knowledge in various ways. Students were encouraged to develop evaluation of their learning skills independently through activities that promoted metacognition. Those students who planned and monitored their work produced essays of higher quality. The value and difficulties of promoting metacognitive approaches in this context are discussed, as well as the idea that metacognitive processes are difficult to research, because they have to be conscious in order to be identified by the learner, thereby making them accessible to the researcher.

Prior knowledge-based approach for associating contaminants with biological effects: A case study in the St. Croix River basin, MN, WI, USA

Science.gov (United States)

Schroeder, Anthony L.; Martinovic-Weigelt, Dalma; Ankley, Gerald T.; Lee, Kathy E.; Garcia-Reyero, Natalia; Perkins, Edward J.; Schoenfuss, Heiko L.; Villeneuve, Daniel L.

2017-01-01

Evaluating potential adverse effects of complex chemical mixtures in the environment is challenging. One way to address that challenge is through more integrated analysis of chemical monitoring and biological effects data. In the present study, water samples from five locations near two municipal wastewater treatment plants in the St. Croix River basin, on the border of MN and WI, USA, were analyzed for 127 organic contaminants. Known chemical-gene interactions were used to develop site-specific knowledge assembly models (KAMs) and formulate hypotheses concerning possible biological effects associated with chemicals detected in water samples from each location. Additionally, hepatic gene expression data were collected for fathead minnows (Pimephales promelas) exposed in situ, for 12 d, at each location. Expression data from oligonucleotide microarrays were analyzed to identify functional annotation terms enriched among the differentially-expressed probes. The general nature of many of the terms made hypothesis formulation on the basis of the transcriptome-level response alone difficult. However, integrated analysis of the transcriptome data in the context of the site-specific KAMs allowed for evaluation of the likelihood of specific chemicals contributing to observed biological responses. Thirteen chemicals (atrazine, carbamazepine, metformin, thiabendazole, diazepam, cholesterol, p-cresol, phenytoin, omeprazole, ethyromycin, 17β-estradiol, cimetidine, and estrone), for which there was statistically significant concordance between occurrence at a site and expected biological response as represented in the KAM, were identified. While not definitive, the approach provides a line of evidence for evaluating potential cause-effect relationships between components of a complex mixture of contaminants and biological effects data, which can inform subsequent monitoring and investigation.

Knowledge management driven leadership, culture and innovation success – an integrative model

OpenAIRE

Zieba, M.; Schivinski, Bruno

2015-01-01

Purpose - This article examines the relation between knowledge management (KM) driven leadership, culture and innovation success of knowledge-intensive small and medium sized companies. By building on the previously reported research on leadership, culture, innovation , and knowledge management, we synergistically integrate d KM-driven leadership and innovation success while exploring the meditational role of culture in that. Design/methodology/approach - A conceptual model comprising three c...

A functional overview of conservation biological control

DEFF Research Database (Denmark)

Begg, Graham S; Cook, Samantha M; Dye, Richard

2017-01-01

Conservation biological control (CBC) is a sustainable approach to pest management that can contribute to a reduction in pesticide use as part of an Integrated Pest Management (IPM) strategy. CBC is based on the premise that countering habitat loss and environmental disturbance associated...... CBC prescriptions have proved elusive. To tackle this, we consolidate existing knowledge of CBC using a simple conceptual model that organises the functional elements of CBC into a common, unifying framework. We identify and integrate the key biological processes affecting natural enemies...... and their biological control function across local and regional scales, and consider the interactions, interdependencies and constraints that determine the outcome of CBC strategies. Conservation measures are often effective in supporting natural enemy populations but their success cannot be guaranteed; the greatest...

Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science).

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Zeng, Irene Sui Lan; Lumley, Thomas

2018-01-01

Integrated omics is becoming a new channel for investigating the complex molecular system in modern biological science and sets a foundation for systematic learning for precision medicine. The statistical/machine learning methods that have emerged in the past decade for integrated omics are not only innovative but also multidisciplinary with integrated knowledge in biology, medicine, statistics, machine learning, and artificial intelligence. Here, we review the nontrivial classes of learning methods from the statistical aspects and streamline these learning methods within the statistical learning framework. The intriguing findings from the review are that the methods used are generalizable to other disciplines with complex systematic structure, and the integrated omics is part of an integrated information science which has collated and integrated different types of information for inferences and decision making. We review the statistical learning methods of exploratory and supervised learning from 42 publications. We also discuss the strengths and limitations of the extended principal component analysis, cluster analysis, network analysis, and regression methods. Statistical techniques such as penalization for sparsity induction when there are fewer observations than the number of features and using Bayesian approach when there are prior knowledge to be integrated are also included in the commentary. For the completeness of the review, a table of currently available software and packages from 23 publications for omics are summarized in the appendix.

Integration of an OWL-DL knowledge base with an EHR prototype and providing customized information.

Science.gov (United States)

Jing, Xia; Kay, Stephen; Marley, Tom; Hardiker, Nicholas R

2014-09-01

When clinicians use electronic health record (EHR) systems, their ability to obtain general knowledge is often an important contribution to their ability to make more informed decisions. In this paper we describe a method by which an external, formal representation of clinical and molecular genetic knowledge can be integrated into an EHR such that customized knowledge can be delivered to clinicians in a context-appropriate manner.Web Ontology Language-Description Logic (OWL-DL) is a formal knowledge representation language that is widely used for creating, organizing and managing biomedical knowledge through the use of explicit definitions, consistent structure and a computer-processable format, particularly in biomedical fields. In this paper we describe: 1) integration of an OWL-DL knowledge base with a standards-based EHR prototype, 2) presentation of customized information from the knowledge base via the EHR interface, and 3) lessons learned via the process. The integration was achieved through a combination of manual and automatic methods. Our method has advantages for scaling up to and maintaining knowledge bases of any size, with the goal of assisting clinicians and other EHR users in making better informed health care decisions.

Functionalization and microfluidic integration of silicon nanowire biologically gated field effect transistors

DEFF Research Database (Denmark)

Pfreundt, Andrea

This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project...

Functionalization and microfluidic integration of silicon nanowire biologically gated field effect transistors

DEFF Research Database (Denmark)

Pfreundt, Andrea; Svendsen, Winnie Edith; Dimaki, Maria

2016-01-01

This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project...

Data mining and data integration in biology

DEFF Research Database (Denmark)

Ólason, Páll Ísólfur

2008-01-01

. They also necessitate new ways of data preparation as established methods for sequence sets are often useless when dealing with sets of sequence pairs. Therefore careful analysis on the sequence level as well as the integrated network level is needed to benchmark these data prior to use. The networks, which...... between molecules, the essence of systems biology. Internet technologies are very important in this respect as bioinformatics labs around the world generate staggering amounts of novel annotations, increasing the importance of on-line processing and distributed systems. One of the most important new data...... types in proteomics is protein-protein interactions. Interactions between the functional elements in the cell are a natural place to start when integrating protein annotations with the aim of gaining a systems view of the cell. Interaction data, however, are notoriously biased, erroneous and incomplete...

Cyber integrated MEMS microhand for biological applications

Science.gov (United States)

Weissman, Adam; Frazier, Athena; Pepen, Michael; Lu, Yen-Wen; Yang, Shanchieh Jay

2009-05-01

Anthropomorphous robotic hands at microscales have been developed to receive information and perform tasks for biological applications. To emulate a human hand's dexterity, the microhand requires a master-slave interface with a wearable controller, force sensors, and perception displays for tele-manipulation. Recognizing the constraints and complexity imposed in developing feedback interface during miniaturization, this project address the need by creating an integrated cyber environment incorporating sensors with a microhand, haptic/visual display, and object model, to emulates human hands' psychophysical perception at microscale.

Campus Eco Tours: An Integrative & Interactive Field Project for Undergraduate Biology Students

Science.gov (United States)

Boes, Katie E.

2013-01-01

Outdoor areas within or near college campuses offer an opportunity for biology students to observe the natural world and apply concepts from class. Here, I describe an engaging and integrative project where undergraduate non-major biology students work in teams to develop and present professional "eco tours." This project takes place over multiple…

Graduate Curriculum for Biological Information Specialists: A Key to Integration of Scale in Biology

Directory of Open Access Journals (Sweden)

Carole L. Palmer

2007-12-01

Full Text Available Scientific data problems do not stand in isolation. They are part of a larger set of challenges associated with the escalation of scientific information and changes in scholarly communication in the digital environment. Biologists in particular are generating enormous sets of data at a high rate, and new discoveries in the biological sciences will increasingly depend on the integration of data across multiple scales. This work will require new kinds of information expertise in key areas. To build this professional capacity we have developed two complementary educational programs: a Biological Information Specialist (BIS masters degree and a concentration in Data Curation (DC. We believe that BISs will be central in the development of cyberinfrastructure and information services needed to facilitate interdisciplinary and multi-scale science. Here we present three sample cases from our current research projects to illustrate areas in which we expect information specialists to make important contributions to biological research practice.

BIOLOGY STUDENTS’ TEACHER OPINIONS ABOUT THE INTEGRATION OF ICT INTO THE LEARNING AND TEACHING PROCESS

Directory of Open Access Journals (Sweden)

Andreja Špernjak

2014-05-01

Full Text Available Biology laboratory work can be performed in various ways, even using information and communication technologies (ICT. Whether a teacher incorporates it into laboratory work is related to different factors, but educators can influence students’ beliefs about the value of ICT through their pedagogical practice. In our study, student teachers of biology gave opinions on how successfully university professors use ICT in the classroom, where they acquired most knowledge about ICT and their attitude towards using of ICT in laboratory work. Student teachers were critical about the knowledge and usage of ICT of university professors in class. During their student teachers mostly failed to acquire knowledge about ICT and practice in incorporating it into daily routines. These results will be presented to our university professors, at which time we will suggest how they could use ICT more effectively in daily practice because, on the one hand, they are responsible for students teacher attitudes and for the level of student teacher knowledge, while, on the others, they precipitate indirectly in forming the pupils’ attitudes and determining the level of the pupils’ knowledge of ICT. The study was done on 85 student teachers of biology. Attitudes toward ICT are statistically significant by gender.

"A mission-driven discipline": the growth of conservation biology.

Science.gov (United States)

Meine, Curt; Soulé, Michael; Noss, Reed E

2006-06-01

Conservation biology emerged in the mid-1980s, drawing on established disciplines and integrating them in pursuit of a coherent goal: the protection and perpetuation of the Earth's biological diversity. Opportunistic in its borrowing and application of knowledge, conservation biology had its roots within the established biological sciences and resource management disciplines but has continually incorporated insights from the empirical experience of resource managers, from the social sciences and humanities, and from diverse cultural sources. The Society for Conservation Biology (SCB) has represented the field's core constituency, while expanding that constituency in keeping with the field's integrative spirit. Conservation Biology has served as SCB's flagship publication, promoting research, dialog, debate, and application of the field's essential concepts. Over the last 20 years the field, SCB, and the journal have evolved to meet changing conservation needs, to explore gaps in our knowledge base, to incorporate new information from related fields, to build professional capacity, and to provide expanded opportunities for international participation. In turn, the field, SCB, and journal have prompted change in related fields, organizations, and publications. In its dedication to advancing the scientific foundations of biodiversity conservation and placing that science at the service of society in a world whose variety, wildness, and beauty we care for conservation biology represents both a continuation and radical reconfiguration of the traditional relationship between science and conservation.

Knowledge mobilization in bridging patient-practitioner-researcher boundaries: A systematic integrative review protocol.

Science.gov (United States)

Cowdell, Fiona; Booth, Andrew; Appleby, Ben

2017-11-01

To review published literature to identify when and how patients and healthcare practitioners have been involved in knowledge mobilization activity and the impact this may have had on their care. Improving patient outcomes, satisfaction and quality of care is increasingly reliant on shared decision-making between health professionals and patients. Knowledge mobilization, at its simplest: "moving knowledge to where it can be most useful" is a growing field of academic study. To date, it appears that much effort has focused on moving knowledge from researchers to healthcare practitioners. Knowledge mobilization to patients is currently under-researched. Integrative review. Methods of integrative review will be used to address the review problem. PRISMA guidelines were used as a general framework to guide structuring and reporting the review. Elements of method-specific reporting guidelines for specific streams of evidence will be used as required. This review will aim to provide a broad and deep understanding of patient-practitioner-researcher engagement in knowledge mobilization activity. This synthesis of the extant literature should offer insights into the optimum characteristics of methods for bridging patient-practitioner-researcher boundaries in knowledge mobilization action. © 2017 John Wiley & Sons Ltd.

Integrative Sparse K-Means With Overlapping Group Lasso in Genomic Applications for Disease Subtype Discovery.

Science.gov (United States)

Huo, Zhiguang; Tseng, George

2017-06-01

Cancer subtypes discovery is the first step to deliver personalized medicine to cancer patients. With the accumulation of massive multi-level omics datasets and established biological knowledge databases, omics data integration with incorporation of rich existing biological knowledge is essential for deciphering a biological mechanism behind the complex diseases. In this manuscript, we propose an integrative sparse K -means (is- K means) approach to discover disease subtypes with the guidance of prior biological knowledge via sparse overlapping group lasso. An algorithm using an alternating direction method of multiplier (ADMM) will be applied for fast optimization. Simulation and three real applications in breast cancer and leukemia will be used to compare is- K means with existing methods and demonstrate its superior clustering accuracy, feature selection, functional annotation of detected molecular features and computing efficiency.

Integrative biology approach identifies cytokine targeting strategies for psoriasis.

Science.gov (United States)

Perera, Gayathri K; Ainali, Chrysanthi; Semenova, Ekaterina; Hundhausen, Christian; Barinaga, Guillermo; Kassen, Deepika; Williams, Andrew E; Mirza, Muddassar M; Balazs, Mercedesz; Wang, Xiaoting; Rodriguez, Robert Sanchez; Alendar, Andrej; Barker, Jonathan; Tsoka, Sophia; Ouyang, Wenjun; Nestle, Frank O

2014-02-12

Cytokines are critical checkpoints of inflammation. The treatment of human autoimmune disease has been revolutionized by targeting inflammatory cytokines as key drivers of disease pathogenesis. Despite this, there exist numerous pitfalls when translating preclinical data into the clinic. We developed an integrative biology approach combining human disease transcriptome data sets with clinically relevant in vivo models in an attempt to bridge this translational gap. We chose interleukin-22 (IL-22) as a model cytokine because of its potentially important proinflammatory role in epithelial tissues. Injection of IL-22 into normal human skin grafts produced marked inflammatory skin changes resembling human psoriasis. Injection of anti-IL-22 monoclonal antibody in a human xenotransplant model of psoriasis, developed specifically to test potential therapeutic candidates, efficiently blocked skin inflammation. Bioinformatic analysis integrating both the IL-22 and anti-IL-22 cytokine transcriptomes and mapping them onto a psoriasis disease gene coexpression network identified key cytokine-dependent hub genes. Using knockout mice and small-molecule blockade, we show that one of these hub genes, the so far unexplored serine/threonine kinase PIM1, is a critical checkpoint for human skin inflammation and potential future therapeutic target in psoriasis. Using in silico integration of human data sets and biological models, we were able to identify a new target in the treatment of psoriasis.

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

Science.gov (United States)

2013-01-01

Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

Integrating local pastoral knowledge, participatory mapping, and species distribution modeling for risk assessment of invasive rubber vine (Cryptostegia grandiflora in Ethiopia's Afar region

Directory of Open Access Journals (Sweden)

Matthew W. Luizza

2016-03-01

Full Text Available The threats posed by invasive plants span ecosystems and economies worldwide. Local knowledge of biological invasions has proven beneficial for invasive species research, but to date no work has integrated this knowledge with species distribution modeling for invasion risk assessments. In this study, we integrated pastoral knowledge with Maxent modeling to assess the suitable habitat and potential impacts of invasive Cryptostegia grandiflora Robx. Ex R.Br. (rubber vine in Ethiopia's Afar region. We conducted focus groups with seven villages across the Amibara and Awash-Fentale districts. Pastoral knowledge revealed the growing threat of rubber vine, which to date has received limited attention in Ethiopia, and whose presence in Afar was previously unknown to our team. Rubber vine occurrence points were collected in the field with pastoralists and processed in Maxent with MODIS-derived vegetation indices, topographic data, and anthropogenic variables. We tested model fit using a jackknife procedure and validated the final model with an independent occurrence data set collected through participatory mapping activities with pastoralists. A Multivariate Environmental Similarity Surface analysis revealed areas with novel environmental conditions for future targeted surveys. Model performance was evaluated using area under the receiver-operating characteristic curve (AUC and showed good fit across the jackknife models (average AUC = 0.80 and the final model (test AUC = 0.96. Our results reveal the growing threat rubber vine poses to Afar, with suitable habitat extending downstream of its current known location in the middle Awash River basin. Local pastoral knowledge provided important context for its rapid expansion due to acute changes in seasonality and habitat alteration, in addition to threats posed to numerous endemic tree species that provide critical provisioning ecosystem services. This work demonstrates the utility of integrating local

Topical Knowledge in L2 Speaking Assessment: Comparing Independent and Integrated Speaking Test Tasks

Science.gov (United States)

Huang, Heng-Tsung Danny; Hung, Shao-Ting Alan; Plakans, Lia

2018-01-01

Integrated speaking test tasks (integrated tasks) provide reading and/or listening input to serve as the basis for test-takers to formulate their oral responses. This study examined the influence of topical knowledge on integrated speaking test performance and compared independent speaking test performance and integrated speaking test performance…

Making United States Integrated Ocean Observing System (U.S. IOOS) inclusive of marine biological resources

Science.gov (United States)

Moustahfid, H.; Potemra, J.; Goldstein, P.; Mendelssohn, R.; Desrochers, A.

2011-01-01

An important Data Management and Communication (DMAC) goal is to enable a multi-disciplinary view of the ocean environment by facilitating discovery and integration of data from various sources, projects and scientific domains. United States Integrated Ocean Observing System (U.S. IOOS) DMAC functional requirements are based upon guidelines for standardized data access services, data formats, metadata, controlled vocabularies, and other conventions. So far, the data integration effort has focused on geophysical U.S. IOOS core variables such as temperature, salinity, ocean currents, etc. The IOOS Biological Observations Project is addressing the DMAC requirements that pertain to biological observations standards and interoperability applicable to U.S. IOOS and to various observing systems. Biological observations are highly heterogeneous and the variety of formats, logical structures, and sampling methods create significant challenges. Here we describe an informatics framework for biological observing data (e.g. species presence/absence and abundance data) that will expand information content and reconcile standards for the representation and integration of these biological observations for users to maximize the value of these observing data. We further propose that the approach described can be applied to other datasets generated in scientific observing surveys and will provide a vehicle for wider dissemination of biological observing data. We propose to employ data definition conventions that are well understood in U.S. IOOS and to combine these with ratified terminologies, policies and guidelines. ?? 2011 MTS.

Integrating Neuroscience Knowledge and Neuropsychiatric Skills Into Psychiatry: The Way Forward.

Science.gov (United States)

Schildkrout, Barbara; Benjamin, Sheldon; Lauterbach, Margo D

2016-05-01

Increasing the integration of neuroscience knowledge and neuropsychiatric skills into general psychiatric practice would facilitate expanded approaches to diagnosis, formulation, and treatment while positioning practitioners to utilize findings from emerging brain research. There is growing consensus that the field of psychiatry would benefit from more familiarity with neuroscience and neuropsychiatry. Yet there remain numerous factors impeding the integration of these domains of knowledge into general psychiatry.The authors make recommendations to move the field forward, focusing on the need for advocacy by psychiatry and medical organizations and changes in psychiatry education at all levels. For individual psychiatrists, the recommendations target obstacles to attaining expanded neuroscience and neuropsychiatry education and barriers stemming from widely held, often unspoken beliefs. For the system of psychiatric care, recommendations address the conceptual and physical separation of psychiatry from medicine, overemphasis on the Diagnostic and Statistical Manual of Mental Disorders and on psychopharmacology, and different systems in medicine and psychiatry for handling reimbursement and patient records. For psychiatry residency training, recommendations focus on expanding neuroscience/neuropsychiatry faculty and integrating neuroscience education throughout the curriculum.Psychiatry traditionally concerns itself with helping individuals construct meaningful life narratives. Brain function is one of the fundamental determinants of individuality. It is now possible for psychiatrists to integrate knowledge of neuroscience into understanding the whole person by asking, What person has this brain? How does this brain make this person unique? How does this brain make this disorder unique? What treatment will help this disorder in this person with this brain?

Memory integration in amnesia: prior knowledge supports verbal short-term memory.

Science.gov (United States)

Race, Elizabeth; Palombo, Daniela J; Cadden, Margaret; Burke, Keely; Verfaellie, Mieke

2015-04-01

Short-term memory (STM) and long-term memory (LTM) have traditionally been considered cognitively distinct. However, it is known that STM can improve when to-be-remembered information appears in contexts that make contact with prior knowledge, suggesting a more interactive relationship between STM and LTM. The current study investigated whether the ability to leverage LTM in support of STM critically depends on the integrity of the hippocampus. Specifically, we investigated whether the hippocampus differentially supports between-domain versus within-domain STM-LTM integration given prior evidence that the representational domain of the elements being integrated in memory is a critical determinant of whether memory performance depends on the hippocampus. In Experiment 1, we investigated hippocampal contributions to within-domain STM-LTM integration by testing whether immediate verbal recall of words improves in MTL amnesic patients when words are presented in familiar verbal contexts (meaningful sentences) compared to unfamiliar verbal contexts (random word lists). Patients demonstrated a robust sentence superiority effect, whereby verbal STM performance improved in familiar compared to unfamiliar verbal contexts, and the magnitude of this effect did not differ from that in controls. In Experiment 2, we investigated hippocampal contributions to between-domain STM-LTM integration by testing whether immediate verbal recall of digits improves in MTL amnesic patients when digits are presented in a familiar visuospatial context (a typical keypad layout) compared to an unfamiliar visuospatial context (a random keypad layout). Immediate verbal recall improved in both patients and controls when digits were presented in the familiar compared to the unfamiliar keypad array, indicating a preserved ability to integrate activated verbal information with stored visuospatial knowledge. Together, these results demonstrate that immediate verbal recall in amnesia can benefit from two

Revised Bloom's Taxonomy and Integral Calculus: Unpacking the Knowledge Dimension

Science.gov (United States)

Radmehr, Farzad; Drake, Michael

2017-01-01

In this paper, the knowledge dimension for Revised Bloom's taxonomy (RBT) is unpacked for integral calculus. As part of this work, the 11 subtypes of the knowledge dimension are introduced, and through document analysis of chapter 4 of the RBT handbook, these subtypes are defined. Then, by consulting materials frequently used for teaching integral…

Cognition and Knowledge Sharing in Post-acquisition Integration

DEFF Research Database (Denmark)

Jaura, Manya; Michailova, Snejina

2014-01-01

conducted with ten respondents in four Indian IT companies that have acquired firms abroad. Findings: The authors find evidence for supporting the negative effect of in- and out-groups differentiation and the positive effect of interpersonal interaction on knowledge sharing among employees of the acquired...... of organisational objectives in a post-acquisition context. Managers should understand that the knowledge their employees possess is a strategic asset, and therefore how they use it is influential in attaining organisational goals in general, and acquisition integration objectives in particular. The creation...... of task- and project-related communities or groups can help in establishing a shared organisational identity, especially after the turbulent event of one company acquiring another one. The creation of communities or groups where socialisation is encouraged can lead to employees interacting with one...

Milkweed Seed Dispersal: A Means for Integrating Biology and Physics.

Science.gov (United States)

Bisbee, Gregory D.; Kaiser, Cheryl A.

1997-01-01

Describes an activity that integrates biology and physics concepts by experimenting with the seed dispersal of common milkweed or similar wind-dispersed seeds. Student teams collect seeds and measure several parameters, review principles of trajectory motion, perform experiments, and graph data. Students examine the ideas of…

The Integrated Knowledge Space - the Foundation for Enhancing the Effectiveness of the University’s Innovative Activity

Directory of Open Access Journals (Sweden)

Yury TELNOV

2009-01-01

Full Text Available The paper examines the implementation of Integrated Knowledge Space as an effective method for knowledge management in a global university network which will integrate all interested parties of the educational space: the faculty, scholars and business people within the framework of distributed departments on the basis of Information Centre of Disciplines (ICD. ICD enables higher education institutions to accumulate and make on-line renewal of knowledge for teaching and learning processes and for enhancing innovation potential. ICD facilitates the development of human and relational capital of integrated and interconnected educational, research and business communities.

An experiential approach to improving the integration of knowledge during EIA in transport planning

Energy Technology Data Exchange (ETDEWEB)

Soria-Lara, Julio A., E-mail: julio.soria-lara@ouce.ox.ac.uk [Transport Research Unit, School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY (United Kingdom); Bertolini, Luca, E-mail: l.bertolini@uva.nl [Centre for Urban Studies, University of Amsterdam, Nieuwe Achtergracht 166 1018 WV Amsterdam (Netherlands); Brömmelstroet, Marco te, E-mail: M.C.G.teBrommelstroet@uva.nl [Centre for Urban Studies, University of Amsterdam, Nieuwe Achtergracht 166 1018 WV Amsterdam (Netherlands)

2016-01-15

The integration of knowledge from stakeholders and the public at large is seen as one of the biggest process-related barriers during the scoping phase of EIA application in transport planning. While the academic literature offers abundant analyses, discussions and suggestions how to overcome this problem, the proposed solutions are yet to be adequately tested in practice. In order to address this gap, we test the effectiveness of a set of interventions and trigger mechanisms for improving different aspects of knowledge integration. The interventions are tested in an experiential study with two sequential cases, representing “close-to-real-life” conditions, in the context of two cities in Andalusia, Spain. In general terms, the participants perceived that the integration of knowledge improved during the simulation of the EIA scoping phase. Certain shortcomings were also discussed, fundamentally related to how the time spent during the scoping phase was crucial to lead an effective learning process between the involved people. The study concludes with a reflection on the effectiveness of the tested interventions according to similarities and differences obtained from the two experiential case studies, as well as with a discussion of the potential to generate new knowledge through the use of experiential studies in EIA practice. - Highlights: • It tests a set of interventions and mechanisms to improve the integration of knowledge. • The scoping phase of EIA is simulated to assess the effectiveness of interventions. • Two sequential case studies are used.

An experiential approach to improving the integration of knowledge during EIA in transport planning

International Nuclear Information System (INIS)

Soria-Lara, Julio A.; Bertolini, Luca; Brömmelstroet, Marco te

2016-01-01

The integration of knowledge from stakeholders and the public at large is seen as one of the biggest process-related barriers during the scoping phase of EIA application in transport planning. While the academic literature offers abundant analyses, discussions and suggestions how to overcome this problem, the proposed solutions are yet to be adequately tested in practice. In order to address this gap, we test the effectiveness of a set of interventions and trigger mechanisms for improving different aspects of knowledge integration. The interventions are tested in an experiential study with two sequential cases, representing “close-to-real-life” conditions, in the context of two cities in Andalusia, Spain. In general terms, the participants perceived that the integration of knowledge improved during the simulation of the EIA scoping phase. Certain shortcomings were also discussed, fundamentally related to how the time spent during the scoping phase was crucial to lead an effective learning process between the involved people. The study concludes with a reflection on the effectiveness of the tested interventions according to similarities and differences obtained from the two experiential case studies, as well as with a discussion of the potential to generate new knowledge through the use of experiential studies in EIA practice. - Highlights: • It tests a set of interventions and mechanisms to improve the integration of knowledge. • The scoping phase of EIA is simulated to assess the effectiveness of interventions. • Two sequential case studies are used.

Biological standards for the Knowledge-Based BioEconomy: What is at stake.

Science.gov (United States)

de Lorenzo, Víctor; Schmidt, Markus

2018-01-25

The contribution of life sciences to the Knowledge-Based Bioeconomy (KBBE) asks for the transition of contemporary, gene-based biotechnology from being a trial-and-error endeavour to becoming an authentic branch of engineering. One requisite to this end is the need for standards to measure and represent accurately biological functions, along with languages for data description and exchange. However, the inherent complexity of biological systems and the lack of quantitative tradition in the field have largely curbed this enterprise. Fortunately, the onset of systems and synthetic biology has emphasized the need for standards not only to manage omics data, but also to increase reproducibility and provide the means of engineering living systems in earnest. Some domains of biotechnology can be easily standardized (e.g. physical composition of DNA sequences, tools for genome editing, languages to encode workflows), while others might be standardized with some dedicated research (e.g. biological metrology, operative systems for bio-programming cells) and finally others will require a considerable effort, e.g. defining the rules that allow functional composition of biological activities. Despite difficulties, these are worthy attempts, as the history of technology shows that those who set/adopt standards gain a competitive advantage over those who do not. Copyright © 2017 Elsevier B.V. All rights reserved.

Tav4SB: integrating tools for analysis of kinetic models of biological systems.

Science.gov (United States)

Rybiński, Mikołaj; Lula, Michał; Banasik, Paweł; Lasota, Sławomir; Gambin, Anna

2012-04-05

Progress in the modeling of biological systems strongly relies on the availability of specialized computer-aided tools. To that end, the Taverna Workbench eases integration of software tools for life science research and provides a common workflow-based framework for computational experiments in Biology. The Taverna services for Systems Biology (Tav4SB) project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Tav4SB operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. As an illustration of possibilities offered by our project we apply the multi-parameter sensitivity analysis. To visualize the results of model analysis a flexible plotting operation is provided as well. Tav4SB operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. The user guide, contact information, full documentation of available Web service operations, workflows and other additional resources can be found at the Tav4SB project's Web page: http://bioputer.mimuw.edu.pl/tav4sb/. The Tav4SB Web service provides a set of integrated tools in the domain for which Web-based applications are still not as widely available as for other areas of computational biology. Moreover, we extend the dedicated hardware base for computationally expensive task of simulating cellular models. Finally, we promote the standardization of models and experiments as well as accessibility and usability of remote services.

DNA barcodes for assessment of the biological integrity of aquatic ecosystems

Science.gov (United States)

Water quality regulations and aquatic ecosystem monitoring increasingly rely on direct assessments of biological integrity. Because these aquatic “bioassessments” evaluate the incidence and abundance of sensitive aquatic species, they are able to measure cumulative ecosystem eff...

Integrating knowledge seeking into knowledge management models and frameworks

Directory of Open Access Journals (Sweden)

Francois Lottering

2012-09-01

Objectives: This article investigates the theoretical status of the knowledge-seeking process in extant KM models and frameworks. It also statistically describes knowledge seeking and knowledge sharing practices in a sample of South African companies. Using this data, it proposes a KM model based on knowledge seeking. Method: Knowledge seeking is traced in a number of KM models and frameworks with a specific focus on Han Lai and Margaret Graham’s adapted KM cycle model, which separates knowledge seeking from knowledge sharing. This empirical investigation used a questionnaire to examine knowledge seeking and knowledge sharing practices in a sample of South African companies. Results: This article critiqued and elaborated on the adapted KM cycle model of Lai and Graham. It identified some of the key features of knowledge seeking practices in the workplace. It showed that knowledge seeking and sharing are human-centric actions and that seeking knowledge uses trust and loyalty as its basis. It also showed that one cannot separate knowledge seeking from knowledge sharing. Conclusion: The knowledge seeking-based KM model elaborates on Lai and Graham’s model. It provides insight into how and where people seek and share knowledge in the workplace. The article concludes that it is necessary to cement the place of knowledge seeking in KM models as well as frameworks and suggests that organisations should apply its findings to improving their knowledge management strategies.

Knowledge of Adverse Drug Reaction Reporting and the Pharmacovigilance of Biological Medicines: A Survey of Healthcare Professionals in Ireland.

Science.gov (United States)

O'Callaghan, J; Griffin, B T; Morris, J M; Bermingham, Margaret

2018-06-01

In Europe, changes to pharmacovigilance legislation, which include additional monitoring of medicines, aim to optimise adverse drug reaction (ADR) reporting systems. The legislation also makes provisions related to the traceability of biological medicines. The objective of this study was to assess (i) knowledge and general experience of ADR reporting, (ii) knowledge, behaviours, and attitudes related to the pharmacovigilance of biologicals, and (iii) awareness of additional monitoring among healthcare professionals (HCPs) in Ireland. Hospital doctors (n = 88), general practitioners (GPs) (n = 197), nurses (n = 104) and pharmacists (n = 309) completed an online questionnaire. There were differences in mean knowledge scores relating to ADR reporting and the pharmacovigilance of biologicals among the HCP groups. The majority of HCPs who use biological medicines in their practice generally record biologicals by brand name but practice behaviours relating to batch number recording differed between some professions. HCPs consider batch number recording to be valuable but also regard it as being more difficult than brand name recording. Most respondents were aware of the concept of additional monitoring but awareness rates differed between some groups. Among those who knew about additional monitoring, there was higher awareness of the inverted black triangle symbol among pharmacists (> 86.4%) compared with hospital doctors (35.1%), GPs (35.6%), and nurses (14.9%). Hospital pharmacists had more experience and knowledge of ADR reporting than other practising HCPs. This study highlights the important role hospital pharmacists play in post-marketing surveillance. There is a need to increase pharmacovigilance awareness of biological medicines and improve systems to support their batch traceability.

Do large-scale assessments measure students' ability to integrate scientific knowledge?

Science.gov (United States)

Lee, Hee-Sun

2010-03-01

Large-scale assessments are used as means to diagnose the current status of student achievement in science and compare students across schools, states, and countries. For efficiency, multiple-choice items and dichotomously-scored open-ended items are pervasively used in large-scale assessments such as Trends in International Math and Science Study (TIMSS). This study investigated how well these items measure secondary school students' ability to integrate scientific knowledge. This study collected responses of 8400 students to 116 multiple-choice and 84 open-ended items and applied an Item Response Theory analysis based on the Rasch Partial Credit Model. Results indicate that most multiple-choice items and dichotomously-scored open-ended items can be used to determine whether students have normative ideas about science topics, but cannot measure whether students integrate multiple pieces of relevant science ideas. Only when the scoring rubric is redesigned to capture subtle nuances of student open-ended responses, open-ended items become a valid and reliable tool to assess students' knowledge integration ability.

Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.

Directory of Open Access Journals (Sweden)

Judith Somekh

2012-12-01

Full Text Available We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM, a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure-the objects that comprise the system, and behavior-how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point-the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model.

The use of theoretical and empirical knowledge in the production of explanations and arguments in an inquiry biology activity

Directory of Open Access Journals (Sweden)

Maíra Batistoni e Silva

2017-08-01

Full Text Available Agreeing with the scientific literacy as the purpose of science education and with the recent propositions that in order to achieve it we should favor the engagement of students in practices of scientific culture, this study intends to analyze the production of explanations and arguments in an inquiry based teaching activity in order to characterize students' mobilization of theoretical and empirical knowledge by engaging in these practices. Analyzing the scientific reports elaborated by the students (14-15 years old after the inquiry activity on population dynamics, we highlight the importance of empirical knowledge about the experimental context as a repertoire for construction of explanations, especially when students deal with anomalous data. This knowledge was also important for production of valid arguments, since most of the justifications were empirical, regardless of whether or not the data were in accordance with the explanatory model already known. These results reinforce the importance of students' engagement in inquiry activities, as already defended by different authors of this research area, and indicate that the inquiry practice allowed the engagement in epistemic practices, since the knowledge about the experimental conditions and the procedures of data collection provided a repertoire for the production of explanations and arguments. Finally, we discuss the relevance of this research to the field of biology teaching, seeking to defend the promotion of inquiry activities with an experimental approach as an opportunity to integrate conceptual and epistemic objectives and overcome the difficulties generated by the specificities of this area of knowledge in relation to the other disciplines in nature sciences.

Integrating knowledge seeking into knowledge management models and frameworks

Directory of Open Access Journals (Sweden)

Francois Lottering

2012-02-01

Full Text Available Background: A striking feature of the knowledge management (KM literature is that the standard list of KM processes either subsumes or overlooks the process of knowledge seeking. Knowledge seeking is manifestly under-theorised, making the need to address this gap in KM theory and practice clear and urgent.Objectives: This article investigates the theoretical status of the knowledge-seeking process in extant KM models and frameworks. It also statistically describes knowledge seeking and knowledge sharing practices in a sample of South African companies. Using this data, it proposes a KM model based on knowledge seeking.Method: Knowledge seeking is traced in a number of KM models and frameworks with a specific focus on Han Lai and Margaret Graham’s adapted KM cycle model, which separates knowledge seeking from knowledge sharing. This empirical investigation used a questionnaire to examine knowledge seeking and knowledge sharing practices in a sample of South African companies.Results: This article critiqued and elaborated on the adapted KM cycle model of Lai and Graham. It identified some of the key features of knowledge seeking practices in the workplace. It showed that knowledge seeking and sharing are human-centric actions and that seeking knowledge uses trust and loyalty as its basis. It also showed that one cannot separate knowledge seeking from knowledge sharing.Conclusion: The knowledge seeking-based KM model elaborates on Lai and Graham’s model. It provides insight into how and where people seek and share knowledge in the workplace. The article concludes that it is necessary to cement the place of knowledge seeking in KM models as well as frameworks and suggests that organisations should apply its findings to improving their knowledge management strategies. 

Academic Preparation in Biology and Advocacy for Teaching Evolution: Biology versus Non-Biology Teachers

Science.gov (United States)

Nehm, Ross H.; Kim, Sun Young; Sheppard, Keith

2009-01-01

Despite considerable focus on evolution knowledge-belief relationships, little research has targeted populations with strong content backgrounds, such as undergraduate degrees in biology. This study (1) measured precertified biology and non-biology teachers' (n = 167) knowledge of evolution and the nature of science; (2) quantified teacher…

Evaluation of gene association methods for coexpression network construction and biological knowledge discovery.

Directory of Open Access Journals (Sweden)

Sapna Kumari

Full Text Available BACKGROUND: Constructing coexpression networks and performing network analysis using large-scale gene expression data sets is an effective way to uncover new biological knowledge; however, the methods used for gene association in constructing these coexpression networks have not been thoroughly evaluated. Since different methods lead to structurally different coexpression networks and provide different information, selecting the optimal gene association method is critical. METHODS AND RESULTS: In this study, we compared eight gene association methods - Spearman rank correlation, Weighted Rank Correlation, Kendall, Hoeffding's D measure, Theil-Sen, Rank Theil-Sen, Distance Covariance, and Pearson - and focused on their true knowledge discovery rates in associating pathway genes and construction coordination networks of regulatory genes. We also examined the behaviors of different methods to microarray data with different properties, and whether the biological processes affect the efficiency of different methods. CONCLUSIONS: We found that the Spearman, Hoeffding and Kendall methods are effective in identifying coexpressed pathway genes, whereas the Theil-sen, Rank Theil-Sen, Spearman, and Weighted Rank methods perform well in identifying coordinated transcription factors that control the same biological processes and traits. Surprisingly, the widely used Pearson method is generally less efficient, and so is the Distance Covariance method that can find gene pairs of multiple relationships. Some analyses we did clearly show Pearson and Distance Covariance methods have distinct behaviors as compared to all other six methods. The efficiencies of different methods vary with the data properties to some degree and are largely contingent upon the biological processes, which necessitates the pre-analysis to identify the best performing method for gene association and coexpression network construction.

Integrated analysis of multiple data sources reveals modular structure of biological networks

International Nuclear Information System (INIS)

Lu Hongchao; Shi Baochen; Wu Gaowei; Zhang Yong; Zhu Xiaopeng; Zhang Zhihua; Liu Changning; Zhao, Yi; Wu Tao; Wang Jie; Chen Runsheng

2006-01-01

It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

An Educational Program of Mechatronics for Multidisciplinary Knowledge Acquisition

Science.gov (United States)

Watanuki, Keiichi; Kojima, Kazuyuki

Recently, as the technologies surrounding mechanical engineering have improved remarkably, the expectations for students who graduate from departments of mechanical engineering have increased. For example, in order to develop a mechatronics system, a student needs to integrate a wide variety of technologies, such as mechanical engineering, electrical and electronics engineering, and information technology. Therefore, from the perspective of educators, the current education system, which stresses expertizing each technology, should be replaced by an education system that stresses integrating multidisciplinary knowledge. In this paper, a trial education program for students of the department of mechanical engineering in our university, in which students are required to integrate multidisciplinary knowledge in order to develop a biologically-based robot, is described. Finally, the efficacy of the program is analyzed.

Integrated pathway clusters with coherent biological themes for target prioritisation.

Directory of Open Access Journals (Sweden)

Yi-An Chen

Full Text Available Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.

An Integrated Model for Effective Knowledge Management in Chinese Organizations

Science.gov (United States)

An, Xiaomi; Deng, Hepu; Wang, Yiwen; Chao, Lemen

2013-01-01

Purpose: The purpose of this paper is to provide organizations in the Chinese cultural context with a conceptual model for an integrated adoption of existing knowledge management (KM) methods and to improve the effectiveness of their KM activities. Design/methodology/approaches: A comparative analysis is conducted between China and the western…

Implications of Big Data for cell biology

OpenAIRE

Dolinski, Kara; Troyanskaya, Olga G.

2015-01-01

“Big Data” has surpassed “systems biology” and “omics” as the hottest buzzword in the biological sciences, but is there any substance behind the hype? Certainly, we have learned about various aspects of cell and molecular biology from the many individual high-throughput data sets that have been published in the past 15–20 years. These data, although useful as individual data sets, can provide much more knowledge when interrogated with Big Data approaches, such as applying integrative methods ...

Teaching the fundamentals of biological data integration using classroom games.

Directory of Open Access Journals (Sweden)

Maria Victoria Schneider

Full Text Available This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems as a method for data integration.

An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology.

Science.gov (United States)

Kohl, Kevin D

2017-10-01

Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Knowledge Sharing, Communities of Practice, and Learning Asset Integration - DAU's Major Initiatives

National Research Council Canada - National Science Library

Hickok, John

2005-01-01

.... What follows is an overview of Knowledge Sharing through the eyes of the Defense Acquisition University, along with some new initiatives called Learning Asset Integration and Workflow Learning...

The integration of expert knowledge in decision support systems for facility location planning

NARCIS (Netherlands)

Arentze, T.A.; Borgers, A.W.J.; Timmermans, H.J.P.

1995-01-01

The integration of expert systems in DSS has led to a new generation of systems commonly referred to as knowledge-based or intelligent DSS. This paper investigates the use of expert system technology for the development of a knowledge-based DSS for the planning of retail and service facilities. The

Challenges and promises of integrating knowledge engineering and qualitative methods

Science.gov (United States)

Lundberg, C. Gustav; Holm, Gunilla

Our goal is to expose some of the close ties that exist between knowledge engineering (KE) and qualitative methodology (QM). Many key concepts of qualitative research, for example meaning, commonsense, understanding, and everyday life, overlap with central research concerns in artificial intelligence. These shared interests constitute a largely unexplored avenue for interdisciplinary cooperation. We compare and take some steps toward integrating two historically diverse methodologies by exploring the commonalities of KE and QM both from a substantive and a methodological/technical perspective. In the second part of this essay, we address knowledge acquisition problems and procedures. Knowledge acquisition within KE has been based primarily on cognitive psychology/science foundations, whereas knowledge acquisition within QM has a broader foundation in phenomenology, symbolic interactionism, and ethnomethodology. Our discussion and examples are interdisciplinary in nature. We do not suggest that there is a clash between the KE and QM frameworks, but rather that the lack of communication potentially may limit each framework's future development.

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

Directory of Open Access Journals (Sweden)

Ogurtsov Aleksey Y

2008-10-01

Full Text Available Abstract Background Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through consideration of amino acid substitutions/modifications as well as information from disease studies. Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies. Description We have integrated from various sources annotated single amino acid polymorphisms, post-translational modifications, and their documented disease associations (if they exist into one enhanced database per organism. We have also augmented our peptide identification software RAId_DbS to take into account this information while analyzing a tandem mass spectrum. In principle, one may choose to respect or ignore the correlation of amino acid polymorphisms/modifications within each protein. The former leads to targeted searches and avoids scoring of unnecessary polymorphism/modification combinations; the latter explores possible polymorphisms in a controlled fashion. To facilitate new discoveries, RAId_DbS also allows users to conduct searches permitting novel polymorphisms as well as to search a knowledge database created by the users. Conclusion We have finished constructing enhanced databases for 17 organisms. The web link to RAId_DbS and the enhanced databases is http://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/RAId_DbS/index.html. The relevant databases and binaries of RAId_DbS for Linux, Windows, and Mac OS X are available for download from the same web page.

Exploration of student's creativity by integrating STEM knowledge into creative products

Science.gov (United States)

Mayasari, Tantri; Kadarohman, Asep; Rusdiana, Dadi; Kaniawati, Ida

2016-02-01

Creativity is an important capability that should be held to competitive standards in the 21st century in entering the era of information and knowledge. It requires a creative generation that is able to innovate to meet the challenges of an increasingly complex future. This study examines the student's creativity level by integrating STEM (Science, Technology, Engineering, and Mathematics) knowledge to make creative products in renewable energy (solar energy). Total respondents in this study were 29 students who take applied science course. This research used qualitative and quantitative method (mixed methods), and used "4P" dimension of creativity to assess student's creativity level. The result showed a creative product is influenced by STEM knowledge that can support student's creativity while collaborating an application of knowledge, skills, and ability to solve daily problems associated with STEM.

Applying fuzzy integral for evaluating intensity of knowledge work in jobs

Directory of Open Access Journals (Sweden)

Jalil Heidary Dahooie

2013-10-01

Full Text Available In this article, a framework is proposed to define and identify knowledge work intensity in jobs, quantitatively. For determining the Knowledge Work Intensity Score (KWIS of a job, it is supposed that the job comprises some tasks and KWIS of the job is determined based on knowledge intensity of these tasks. Functional Job Analysis (FJA method is applied to determine tasks of jobs and then Task’s Knowledge Intensity Score (TKIS is computed by using Fuzzy integral method. Besides, importance weight and time weight of tasks are determined by utilizing appropriate methods. Finally, KWIS is calculated by a formula composed of tasks’ TKISs and the weights. For evaluating applicability of the framework, it is applied to calculate KWISs of two jobs (Deputy of Finance and service, Laboratory technician.

ChemProt: a disease chemical biology database

DEFF Research Database (Denmark)

Taboureau, Olivier; Nielsen, Sonny Kim; Audouze, Karine Marie Laure

2011-01-01

Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network...... biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). We assembled more than 700 000 unique chemicals with biological annotation for 30...... evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram...

Vernacular Knowledge and Water Management – Towards the Integration of Expert Science and Local Knowledge in Ontario, Canada

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Hugh Simpson

2015-10-01

Full Text Available Complex environmental problems cannot be solved using expert science alone. Rather, these kinds of problems benefit from problem-solving processes that draw on 'vernacular' knowledge. Vernacular knowledge integrates expert science and local knowledge with community beliefs and values. Collaborative approaches to water problem-solving can provide forums for bringing together diverse, and often competing, interests to produce vernacular knowledge through deliberation and negotiation of solutions. Organised stakeholder groups are participating increasingly in such forums, often through involvement of networks, but it is unclear what roles these networks play in the creation and sharing of vernacular knowledge. A case-study approach was used to evaluate the involvement of a key stakeholder group, the agricultural community in Ontario, Canada, in creating vernacular knowledge during a prescribed multi-stakeholder problem-solving process for source water protection for municipal supplies. Data sources – including survey questionnaire responses, participant observation, and publicly available documents – illustrate how respondents supported and participated in the creation of vernacular knowledge. The results of the evaluation indicate that the respondents recognised and valued agricultural knowledge as an information source for resolving complex problems. The research also provided insight concerning the complementary roles and effectiveness of the agricultural community in sharing knowledge within a prescribed problem-solving process.

Improving integrative searching of systems chemical biology data using semantic annotation.

Science.gov (United States)

Chen, Bin; Ding, Ying; Wild, David J

2012-03-08

Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

INTEGRATION OF FRACTAL AND NEURAL NETWORK TECHNOLOGIES IN PEDAGOGICAL MONITORING AND ASSESSMENT OF KNOWLEDGE OF TRAINEES

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Svetlana N Dvoryatkina

2017-12-01

Full Text Available The possibility of statement and solution of the problem of searching of theoretical justification and development of efficient didactic mechanisms of the organization of process of pedagogical monitoring and assessment of level of knowledge of trainees can be based on convergence of the leading psychological and pedagogical, mathematical, and informational technologies with accounting of the modern achievements in science. In the article, the pedagogical expediency of realization of opportunities of means of informational technologies in monitoring and assessment of the composite mathematical knowledge, in the management of cognitive activity of students is proved. The ability to integrate fractal methods and neural network technologies in perfecting of a system of pedagogical monitoring of mathematical knowledge of trainees as a part of the automated training systems (ATS is investigated and realized in practice. It is proved that fractal methods increase the accuracy and depth of estimation of the level of proficiency of students and also complexes of intellectual operations of the integrative qualities allowing to master and apply cross-disciplinary knowledge and abilities in professional activity. Neural network technologies solve a problem of realization of the personal focused tutoring from positions of optimum individualization of mathematical education and self-realization of the person. The technology of projection of integrative system of pedagogical monitoring of knowledge of students includes the following stages: establishment of the required tutoring parameters; definition and preparation of input data for realization of integration of fractal and neural network technologies; development of the diagnostic module as a part of the block of an artificial intelligence of ATS, filling of the databases structured by system; start of system for obtaining the forecast. In development of the integrative automated system of pedagogical

Camels, Cormorants, and Kangaroo Rats: Integration and Synthesis in Organismal Biology After World War II.

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Hagen, Joel B

2015-01-01

During the decades following World War II diverse groups of American biologists established a variety of distinctive approaches to organismal biology. Rhetorically, organismal biology could be used defensively to distinguish established research traditions from perceived threats from newly emerging fields such as molecular biology. But, organismal biologists were also interested in integrating biological disciplines and using a focus on organisms to synthesize levels of organization from molecules and cells to populations and communities. Part of this broad movement was the development of an area of research variously referred to as physiological ecology, environmental physiology, or ecophysiology. This area of research was distinctive in its self-conscious blend of field and laboratory practices and its explicit integration with other areas of biology such as ecology, animal behavior, and evolution in order to study adaptation. Comparing the intersecting careers of Knut Schmidt-Nielsen and George Bartholomew highlights two strikingly different approaches to physiological ecology. These alternative approaches to studying the interactions of organisms and environments also differed in important ways from the organismal biology championed by leading figures in the modern synthesis.

Incorporation of Nuclear Knowledge Management to the Integrated System of Quality and Technological Innovation in Cubaenergía

International Nuclear Information System (INIS)

Oviedo Rivero, I.; González García, A.; Amado Picasso, M.; Yera López, B.; Contreras, M.; López Núñez, A.; García Rodríguez, B.; Elías Hardy, L. L.; Rivero Blanco, J. M.; Peña Tornet, A.; Quintana Castillo, N.

2016-01-01

Full text: Technical knowledge management and innovation become important tools for organizations to meet the needs and expectations of the market and society in general; especially those related to the peaceful use of nuclear energy. Since 2011 Cubaenergia, under the model of the UNE 166002, integrated process management Scientific and Technological Innovation to the requirements of NC-ISO 9001, compliance with national regulations applicable to the sector. In September 2015 the new ISO 9001 includes a clause that makes explicit mention knowledge. Although this clause is not a standard for knowledge management nor does it imply its obligatory; Cubaenergia decided to expand its integrated management system to include the Nuclear Knowledge Management system. In this article the conceptual framework for the integration of these three systems, diagnosis in the organization and the proposed design and implementation plan of management knowledge management integrated analyzes R&D and the quality management system in Cubaenergía. (author

Examining portfolio-based assessment in an upper-level biology course

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Ziegler, Brittany Ann

Historically, students have been viewed as empty vessels and passive participants in the learning process but students actually are active forming their own conceptions. One way student learning is impacted is through assessment. Alternative assessment, which contrasts traditional assessment methods, takes into account how students learn by promoting engagement and construction of knowledge This dissertation explores portfolio-based assessment, a method of alternative assessment, which requires students to compose a purposeful collection of work demonstrating their knowledge in an upper-level biology course. The research objectives include characterizing and contributing to the understanding of portfolio-based assessment in higher education, examining reflection and inquiry portfolio components, determining student knowledge of biological concepts, and investigating student integrative thinking through the transformation of reflections into concept webs One main finding includes the majority of reflections categorized as naive or novice in quality. There was no difference in quality of reflections among biological topic. There was a relatively equal amount of high and low cognitive level questions. Students' knowledge of biological concepts significantly increased from the beginning to end of the course. Student written reflections were transformed into concept webs to allow for examination of student integrative thinking. Concepts, relationships, and interconnections in concept webs showed variation but declined by the end of the semester This study is one of the first examining portfolio-based assessment in an upper-level biology course We do not contend that this method of assessment is the only way to promote student learning but portfolio-based assessment may be a tool that can transform science education but currently the role of portfolio-based assessment in science education remains unclear. Additional research needs to be conducted before we will fully

Supporting students' knowledge integration with technology-enhanced inquiry curricula

Science.gov (United States)

Chiu, Jennifer Lopseen

Dynamic visualizations of scientific phenomena have the potential to transform how students learn and understand science. Dynamic visualizations enable interaction and experimentation with unobservable atomic-level phenomena. A series of studies clarify the conditions under which embedding dynamic visualizations in technology-enhanced inquiry instruction can help students develop robust and durable chemistry knowledge. Using the knowledge integration perspective, I designed Chemical Reactions, a technology-enhanced curriculum unit, with a partnership of teachers, educational researchers, and chemists. This unit guides students in an exploration of how energy and chemical reactions relate to climate change. It uses powerful dynamic visualizations to connect atomic level interactions to the accumulation of greenhouse gases. The series of studies were conducted in typical classrooms in eleven high schools across the country. This dissertation describes four studies that contribute to understanding of how visualizations can be used to transform chemistry learning. The efficacy study investigated the impact of the Chemical Reactions unit compared to traditional instruction using pre-, post- and delayed posttest assessments. The self-monitoring study used self-ratings in combination with embedded assessments to explore how explanation prompts help students learn from dynamic visualizations. The self-regulation study used log files of students' interactions with the learning environment to investigate how external feedback and explanation prompts influence students' exploration of dynamic visualizations. The explanation study compared specific and general explanation prompts to explore the processes by which explanations benefit learning with dynamic visualizations. These studies delineate the conditions under which dynamic visualizations embedded in inquiry instruction can enhance student outcomes. The studies reveal that visualizations can be deceptively clear

Tensions in R&D networks : Implications for knowledge search and integration

NARCIS (Netherlands)

Ritala, Paavo; Huizingh, Eelko; Almpanopoulou, Argyro; Wijbenga, Paul

R&D Networks comprise different actors with various goals and motivations. Thus, such networks are filled with tensions that emerge from simultaneously existing, competing or contradictory organizing elements and demands. In this study, we examine the knowledge search and integration behaviour of

Reproductive biology knowledge, and behaviour of teenagers in East, Central and Southern Africa: the Zimbabwe case study.

Science.gov (United States)

Mbizvo, M T; Kasule, J; Gupta, V; Rusakaniko, S; Gumbo, J; Kinoti, S N; Mpanju-Shumbusho, W; Sebina-Zziwa; Mwateba, R; Padayachy, J

1995-11-01

Sexuality in the teenager is often complicated by unplanned/unwanted pregnancy, abortion and the risks of STDs including AIDS. There is therefore a need for improved understanding of factors affecting adolescent sexuality and the implementation of programmes designed to improve their knowledge, risk awareness and subsequent behavioural outcomes. A multicentre study of reproductive health knowledge and behaviour followed by a health education intervention was undertaken amongst teenagers in selected countries of East, Central and Southern Africa. Reported here are findings at baseline derived from the Zimbabwe component on reproductive biology knowledge and behavior. A self-administered questionnaire was used among 1 689 adolescent pupils drawn from rural, urban, co-education, single sex, boarding and day secondary schools in Zimbabwe. Correct knowledge on reproductive biology as measured by the meaning and interpretation of menstruation and wet dreams varied by school from 68 pc to 86 pc, with a significant trend (p < 0,01) based on level of education at baseline. The reported mean age at which menarche took place was 13,5 years +/- 1,3 (mean +/- SD). First coitus was reported to have taken place at the mean age of 12 years for boys and 13,6 years for girls. Seventeen pc of the adolescent pupils reported that they were sexually experienced and 33,2 had relationships. There were misconceptions reported on menstruation with 23 pc reporting that it was an illness. Peers, followed by magazines were the first sources of information on various aspects of reproductive biology, both of which might not provide the correct first information. Among pupils reporting that they were sexually experienced, the largest proportion (56 pc) had unprotected sex. The findings point to the need for targeting the adolescent pupils for information on reproductive biology and increased awareness on the risks of pregnancy, STDs and HIV.

Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.

Directory of Open Access Journals (Sweden)

Nguyen T Nguyen

2014-03-01

Full Text Available Vast research efforts have been devoted to providing clinical diagnostic markers of myocardial infarction (MI, leading to over one million abstracts associated with "MI" and "Cardiovascular Diseases" in PubMed. Accumulation of the research results imposed a challenge to integrate and interpret these results. To address this problem and better understand how the left ventricle (LV remodels post-MI at both the molecular and cellular levels, we propose here an integrative framework that couples computational methods and experimental data. We selected an initial set of MI-related proteins from published human studies and constructed an MI-specific protein-protein-interaction network (MIPIN. Structural and functional analysis of the MIPIN showed that the post-MI LV exhibited increased representation of proteins involved in transcriptional activity, inflammatory response, and extracellular matrix (ECM remodeling. Known plasma or serum expression changes of the MIPIN proteins in patients with MI were acquired by data mining of the PubMed and UniProt knowledgebase, and served as a training set to predict unlabeled MIPIN protein changes post-MI. The predictions were validated with published results in PubMed, suggesting prognosticative capability of the MIPIN. Further, we established the first knowledge map related to the post-MI response, providing a major step towards enhancing our understanding of molecular interactions specific to MI and linking the molecular interaction, cellular responses, and biological processes to quantify LV remodeling.

Imaging and the new biology: What's wrong with this picture?

Science.gov (United States)

Vannier, Michael W.

2004-05-01

The Human Genome has been defined, giving us one part of the equation that stems from the central dogma of molecular biology. Despite this awesome scientific achievement, the correspondence between genomics and imaging is weak, since we cannot predict an organism's phenotype from even perfect knowledge of its genetic complement. Biological knowledge comes in several forms, and the genome is perhaps the best known and most completely understood type. Imaging creates another form of biological information, providing the ability to study morphology, growth and development, metabolic processes, and diseases in vitro and in vivo at many levels of scale. The principal challenge in biomedical imaging for the future lies in the need to reconcile the data provided by one or multiple modalities with other forms of biological knowledge, most importantly the genome, proteome, physiome, and other "-ome's." To date, the imaging science community has not set a high priority on the unification of their results with genomics, proteomics, and physiological functions in most published work. Images are relatively isolated from other forms of biological data, impairing our ability to conceive and address many fundamental questions in research and clinical practice. This presentation will explain the challenge of biological knowledge integration in basic research and clinical applications from the standpoint of imaging and image processing. The impediments to progress, isolation of the imaging community, and mainstream of new and future biological science will be identified, so the critical and immediate need for change can be highlighted.

An integrated framework of knowledge transfer and ICT issues in co-creation value networks

NARCIS (Netherlands)

Bagheri, S.; Kusters, R.J.; Trienekens, J.J.M.; Varajão, J.E.Q.; Cruz-Cunha, M.M.; Martinho, R.; Rijo, R.; Bjørn-Andersen, N.; Turner, R.; Alves, D.

2016-01-01

In dynamic value networks (VNs), knowledge serves as a basis for close collaboration of actors (i.e. firms with their partners and customers) to enhance co-creation of integrated solutions. In order to provide a technical foundation for seamless knowledge transfer among actors, VNs require

Biomarker Gene Signature Discovery Integrating Network Knowledge

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Holger Fröhlich

2012-02-01

Full Text Available Discovery of prognostic and diagnostic biomarker gene signatures for diseases, such as cancer, is seen as a major step towards a better personalized medicine. During the last decade various methods, mainly coming from the machine learning or statistical domain, have been proposed for that purpose. However, one important obstacle for making gene signatures a standard tool in clinical diagnosis is the typical low reproducibility of these signatures combined with the difficulty to achieve a clear biological interpretation. For that purpose in the last years there has been a growing interest in approaches that try to integrate information from molecular interaction networks. Here we review the current state of research in this field by giving an overview about so-far proposed approaches.

Landscape characterization integrating expert and local spatial knowledge of land and forest resources.

Science.gov (United States)

Fagerholm, Nora; Käyhkö, Niina; Van Eetvelde, Veerle

2013-09-01

In many developing countries, political documentation acknowledges the crucial elements of participation and spatiality for effective land use planning. However, operative approaches to spatial data inclusion and representation in participatory land management are often lacking. In this paper, we apply and develop an integrated landscape characterization approach to enhance spatial knowledge generation about the complex human-nature interactions in landscapes in the context of Zanzibar, Tanzania. We apply an integrated landscape conceptualization as a theoretical framework where the expert and local knowledge can meet in spatial context. The characterization is based on combining multiple data sources in GIS, and involves local communities and their local spatial knowledge since the beginning into the process. Focusing on the expected information needs for community forest management, our characterization integrates physical landscape features and retrospective landscape change data with place-specific community knowledge collected through participatory GIS techniques. The characterization is established in a map form consisting of four themes and their synthesis. The characterization maps are designed to support intuitive interpretation, express the inherently uncertain nature of the data, and accompanied by photographs to enhance communication. Visual interpretation of the characterization mediates information about the character of areas and places in the studied local landscape, depicting the role of forest resources as part of the landscape entity. We conclude that landscape characterization applied in GIS is a highly potential tool for participatory land and resource management, where spatial argumentation, stakeholder communication, and empowerment are critical issues.

Interdisciplinarity to Integrate Knowledge in Engineering

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Stella Abreu

2017-06-01

Full Text Available This paper is an extension of work originally presented at the 2nd International Conference of the Portuguese Society for Engineering Education and aims to describe an interdisciplinarity teaching experiment involving three subjects of the scientific area of Mathematics and a fourth one in the area of Management. Using only one project, the students developed skills, in an integrated way, in the fields of the subjects involved. The structure of the project is described in detail. It is shown how the knowledge obtained in the different subjects is needed and how it connects together to answer the proposed challenges. We report the progress of the students’ work, the main difficulties and the skills developed during this process. We conclude with a reflection on the main problems and gains that may arise in similar projects.

Supporting Knowledge Integration in Chemistry with a Visualization-Enhanced Inquiry Unit

Science.gov (United States)

Chiu, Jennifer L.; Linn, Marcia C.

2014-01-01

This paper describes the design and impact of an inquiry-oriented online curriculum that takes advantage of dynamic molecular visualizations to improve students' understanding of chemical reactions. The visualization-enhanced unit uses research-based guidelines following the knowledge integration framework to help students develop coherent…

iTools: a framework for classification, categorization and integration of computational biology resources.

Directory of Open Access Journals (Sweden)

Ivo D Dinov

2008-05-01

Full Text Available The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long

Concise Review: Organ Engineering: Design, Technology, and Integration

NARCIS (Netherlands)

Kaushik, G.; Leijten, Jeroen Christianus Hermanus; Khademhosseini, A.

Engineering complex tissues and whole organs has the potential to dramatically impact translational medicine in several avenues. Organ engineering is a discipline that integrates biological knowledge of embryological development, anatomy, physiology, and cellular interactions with enabling

Integrating declarative knowledge programming styles and tools for building expert systems

Energy Technology Data Exchange (ETDEWEB)

Barbuceanu, M; Trausan-Matu, S; Molnar, B

1987-01-01

The XRL system reported in this paper is an integrated knowledge programming environment whose major research theme is the investigation of declarative knowledge programming styles and features and of the way they can be effectively integrated and used to support AI programming. This investigation is carried out in the context of the structured-object representation paradigm which provides the glue keeping XRL components together. The paper describes several declarative programming styles and associated support tools available in XRL. These include an instantiation system supporting a generalized view of the ubiquous frame installation process, a description based programming system providing a novel declarative programming style which embeds a mathematical oriented description language in the structured object environment and a transformational interpreter for using it, a semantics oriented programming framework which offers a specific semantic construct based approach supporting maintenance and evolution and a self description and self generation tool which applies the latter approach to XRL itself. 29 refs., 16 figs.

Improving integrative searching of systems chemical biology data using semantic annotation

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Chen Bin

2012-03-01

Full Text Available Abstract Background Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. Results We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i simplifies the process of building SPARQL queries, (ii enables useful new kinds of queries on the data and (iii makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Availability Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

Systems biology approach to bioremediation

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

2012-06-01

Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

Methods of integrating Islamic values in teaching biology for shaping attitude and character

Science.gov (United States)

Listyono; Supardi, K. I.; Hindarto, N.; Ridlo, S.

2018-03-01

Learning is expected to develop the potential of learners to have the spiritual attitude: moral strength, self-control, personality, intelligence, noble character, as well as the skills needed by themselves, society, and nation. Implementation of role and morale in learning is an alternative way which is expected to answer the challenge. The solution offered is to inject student with religious material Islamic in learning biology. The content value of materials teaching biology includes terms of practical value, religious values, daily life value, socio-political value, and the value of art. In Islamic religious values (Qur'an and Hadith) various methods can touch human feelings, souls, and generate motivation. Integrating learning with Islamic value can be done by the deductive or inductive approach. The appropriate method of integration is the amtsal (analog) method, hiwar (dialog) method, targhib & tarhib (encouragement & warning) method, and example method (giving a noble role model / good example). The right strategy in integrating Islamic values is outlined in the design of lesson plan. The integration of Islamic values in lesson plan will facilitate teachers to build students' character because Islamic values can be implemented in every learning steps so students will be accustomed to receiving the character value in this integrated learning.

Requirement Volatility, Standardization and Knowledge Integration in Software Projects: An Empirical Analysis on Outsourced IS Development Projects

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Rajesri Govindaraju

2015-08-01

Full Text Available Information systems development (ISD projects are highly complex, with different groups of people having  to collaborate and exchange their knowledge. Considering the intensity of knowledge exchange that takes place in outsourced ISD projects, in this study a conceptual model was developed, aiming to examine the influence of four antecedents, i.e. standardization, requirement volatility, internal integration, and external integration, on two dependent variables, i.e. process performance and product performance. Data  were collected from 46 software companies in four big cities in Indonesia. The collected data were examined to verify the proposed theoretical model using the partial least square structural equation modeling (PLS-SEM technique. The results show that process performance is significantly influenced by internal integration and standardization, while product performance is  significantly influenced by external integration and  requirement volatility. This study contributes  to a better understanding of how knowledge integration can be managed in outsourced ISD projects in view of increasing their success.

The role of boundary organizations in co-management: examining the politics of knowledge integration in a marine protected area in Belize

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Noella J. Gray

2016-08-01

Full Text Available Marine protected areas (MPAs are an increasingly popular tool for management of the marine commons. Effective governance is essential if MPAs are to achieve their objectives, yet many MPAs face conflicts and governance challenges, including lack of trust and knowledge integration between fishers, scientists, and policy makers. This paper considers the role of a boundary organization in facilitating knowledge integration in a co-managed MPA, the Gladden Spit and Silk Cayes Marine Reserve in Belize. Boundary organizations can play an important role in resource management, by bridging the science-policy divide, facilitating knowledge integration, and enabling communication in conditions of uncertainty. Drawing on ethnographic research conducted in Belize, the paper identifies four challenges for knowledge integration. First, actors have divergent perspectives on whether and how knowledge is being integrated. Second, actors disagree on resource conditions within the MPA and how these should be understood. Third, in order to maintain accountability with multiple actors, including fishers, government, and funders, the boundary organization has promoted the importance of different types of knowledge for different purposes (science and fishers’ knowledge, rather than the integration of these. Finally, a lack of trust and uneven power relations make it difficult to separate knowledge claims from political claims. However, even if knowledge integration proves difficult, boundary organizations may still play an important role by maintaining accountability, providing space for conflicting understandings to co-exist, and ultimately for governance institutions to evolve.

Quality controls in integrative approaches to detect errors and inconsistencies in biological databases

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Ghisalberti Giorgio

2010-12-01

Full Text Available Numerous biomolecular data are available, but they are scattered in many databases and only some of them are curated by experts. Most available data are computationally derived and include errors and inconsistencies. Effective use of available data in order to derive new knowledge hence requires data integration and quality improvement. Many approaches for data integration have been proposed. Data warehousing seams to be the most adequate when comprehensive analysis of integrated data is required. This makes it the most suitable also to implement comprehensive quality controls on integrated data. We previously developed GFINDer (http://www.bioinformatics.polimi.it/GFINDer/, a web system that supports scientists in effectively using available information. It allows comprehensive statistical analysis and mining of functional and phenotypic annotations of gene lists, such as those identified by high-throughput biomolecular experiments. GFINDer backend is composed of a multi-organism genomic and proteomic data warehouse (GPDW. Within the GPDW, several controlled terminologies and ontologies, which describe gene and gene product related biomolecular processes, functions and phenotypes, are imported and integrated, together with their associations with genes and proteins of several organisms. In order to ease maintaining updated the GPDW and to ensure the best possible quality of data integrated in subsequent updating of the data warehouse, we developed several automatic procedures. Within them, we implemented numerous data quality control techniques to test the integrated data for a variety of possible errors and inconsistencies. Among other features, the implemented controls check data structure and completeness, ontological data consistency, ID format and evolution, unexpected data quantification values, and consistency of data from single and multiple sources. We use the implemented controls to analyze the quality of data available from several

Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.

Science.gov (United States)

Brohée, Sylvain; Barriot, Roland; Moreau, Yves

2010-09-01

In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis. The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.

Developing Guided Inquiry-Based Student Lab Worksheet for Laboratory Knowledge Course

Science.gov (United States)

Rahmi, Y. L.; Novriyanti, E.; Ardi, A.; Rifandi, R.

2018-04-01

The course of laboratory knowledge is an introductory course for biology students to follow various lectures practicing in the biology laboratory. Learning activities of laboratory knowledge course at this time in the Biology Department, Universitas Negeri Padang has not been completed by supporting learning media such as student lab worksheet. Guided inquiry learning model is one of the learning models that can be integrated into laboratory activity. The study aimed to produce student lab worksheet based on guided inquiry for laboratory knowledge course and to determine the validity of lab worksheet. The research was conducted using research and developmet (R&D) model. The instruments used in data collection in this research were questionnaire for student needed analysis and questionnaire to measure the student lab worksheet validity. The data obtained was quantitative from several validators. The validators consist of three lecturers. The percentage of a student lab worksheet validity was 94.18 which can be categorized was very good.

Integrating Ecological and Social Knowledge: Learning from CHANS Research

Directory of Open Access Journals (Sweden)

Bruce Shindler

2017-03-01

Full Text Available Scientists are increasingly called upon to integrate across ecological and social disciplines to tackle complex coupled human and natural system (CHANS problems. Integration of these disciplines is challenging and many scientists do not have experience with large integrated research projects. However, much can be learned about the complicated process of integration from such efforts. We document some of these lessons from a National Science Foundation-funded CHANS project (Forests, People, Fire and present considerations for developing and engaging in coupled human and natural system projects. Certainly we are not the first to undertake this endeavor, and many of our findings complement those of other research teams. We focus here on the process of coming together, learning to work as an integrated science team, and describe the challenges and opportunities of engaging stakeholders (agency personnel and citizen communities of interests in our efforts. Throughout this project our intention was to foster dialogue among diverse interests and, thus, incorporate this knowledge into uncovering primary social and ecological drivers of change. A primary tool was an agent-based model, Envision, that used this information in landscape simulation, visualization models, and scenario development. Although integration can be an end in itself, the proof of value in the approach can be the degree to which it provides new insights or tools to CHANS, including closer interaction among multiple stakeholders, that could not have been reached without it.

Teaching About "Brain and Learning" in High School Biology Classes: Effects on Teachers' Knowledge and Students' Theory of Intelligence.

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Dekker, Sanne; Jolles, Jelle

2015-01-01

This study evaluated a new teaching module about "Brain and Learning" using a controlled design. The module was implemented in high school biology classes and comprised three lessons: (1) brain processes underlying learning; (2) neuropsychological development during adolescence; and (3) lifestyle factors that influence learning performance. Participants were 32 biology teachers who were interested in "Brain and Learning" and 1241 students in grades 8-9. Teachers' knowledge and students' beliefs about learning potential were examined using online questionnaires. Results indicated that before intervention, biology teachers were significantly less familiar with how the brain functions and develops than with its structure and with basic neuroscientific concepts (46 vs. 75% correct answers). After intervention, teachers' knowledge of "Brain and Learning" had significantly increased (64%), and more students believed that intelligence is malleable (incremental theory). This emphasizes the potential value of a short teaching module, both for improving biology teachers' insights into "Brain and Learning," and for changing students' beliefs about intelligence.

Teaching about ‘Brain & Learning’ in high school biology classes: Effects on teachers’ knowledge and students’ theory of intelligence

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Sanne eDekker

2015-12-01

Full Text Available This study evaluated a new teaching module about ‘Brain&Learning’ using a controlled design. The module was implemented in high school biology classes and comprised three lessons: 1 brain processes underlying learning; 2 neuropsychological development during adolescence; and 3 lifestyle factors that influence learning performance. Participants were 32 biology teachers who were interested in ‘Brain&Learning’ and 1241 students in grades 8-9. Teachers’ knowledge and students’ beliefs about learning potential were examined using online questionnaires. Results indicated that before intervention, biology teachers were significantly less familiar with how the brain functions and develops than with its structure and with basic neuroscientific concepts (46% vs. 75% correct answers. After intervention, teachers’ knowledge of ‘Brain&Learning’ had significantly increased (64%, and more students believed that intelligence is malleable (incremental theory. This emphasizes the potential value of a short teaching module, both for improving biology teachers’ insights into ‘Brain&Learning’, and for changing students’ beliefs about intelligence.

Knowledge-based immunosuppressive therapy for kidney transplant patients--from theoretical model to clinical integration.

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Seeling, Walter; Plischke, Max; de Bruin, Jeroen S; Schuh, Christian

2015-01-01

Immunosuppressive therapy is a risky necessity after a patient received a kidney transplant. To reduce risks, a knowledge-based system was developed that determines the right dosage of the immunosuppresive agent Tacrolimus. A theoretical model, to classify medication blood levels as well as medication adaptions, was created using data from almost 500 patients, and over 13.000 examinations. This model was then translated into an Arden Syntax knowledge base, and integrated directly into the hospital information system of the Vienna General Hospital. In this paper we give an overview of the construction and integration of such a system.

Designing Critique for Knowledge Integration

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Sato, Mie Elissa

Generating explanations is central to science and has the potential to have a powerful impact on students' conceptual understanding in science instruction. However, improving conceptual understanding by generating explanations is a fraught affair: students may struggle with the sense of false clarity that may arise from generating explanations, fail to detect gaps in their understanding, and dismiss salient information that contradict their beliefs. Critiquing explanations has the potential to counteract these pitfalls by exposing students to alternative ideas to contrast with their own. This dissertation seeks to clarify how to design critique in technology-enhanced science instruction to support students in revising their explanations about scientific phenomena, and in doing so, refining their conceptual understanding. Using the Knowledge Integration framework, I revised two technology-enhanced curriculum units, Plate Tectonics and Global Climate Change, in a design partnership between teachers, researchers, and technologists. I conducted a series of studies with sixth-grade students to investigate the conditions under which guided critique of explanations can support revision. The pilot critique study investigated the impact of the revised Plate Tectonics unit on students' understanding of convection, as well as of a preliminary design of critique where students generated and applied their own criteria for what makes a good explanation in science. The guidance study explored how incorporating a complex selection task that features meta-explanatory criteria into critique supports students in distinguishing among different criteria, as well as how students use peer or expert guidance on their initial explanation during revision. The critique study investigated how designing critique with a complex selection task that features plausible alternative ideas and giving guidance on students' critiques support students in distinguishing among a range of relevant ideas

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

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May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

2009-05-04

The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

Broadening Participation in the Society for Integrative and Comparative Biology.

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Wilga, Cheryl A D; Nishiguchi, Michele; Tsukimura, Brian

2017-07-01

The goal of the Society for Integrative and Comparative Biology's Broadening Participation Committee (SICB BPC) is to increase the number of underrepresented group (URG) members within the society and to expand their capabilities as future researchers and leaders within SICB. Our short-term 10-year goal was to increase the recruitment and retention of URG members in the society by 10%. Our long-term 25-year goal is to increase the membership of URG in the society through recruitment and retention until the membership demographic mirrors that of the US Census. Our plans to accomplish this included establishment of a formal standing committee, establishment of a moderate budget to support BPC activities, hosting professional development workshops, hosting diversity and mentor socials, and obtaining grant funds to supplement our budget. This paper documents broadening participation activities in the society, discusses the effectiveness of these activities, and evaluates BPC goals after 5 years of targeted funded activities. Over the past 5 years, the number of URG members rose by 5.2% to a total of 16.2%, members who report ethnicity and gender increased by 25.2% and 18%, respectively, and the number of members attending BPC activities has increased to 33% by 2016. SICB has made significant advances in broadening participation, not only through increased expenditures, but also with a commitment by its members and leadership to increase diversity. Most members realize that increasing diversity will both improve the Society's ability to develop different approaches to tackling problems within integrative biology, and help solve larger global issues that are evident throughout science and technology fields. In addition, having URG members as part of the executive committee would provide other URG members role models within the society, as well as have a voice in the leadership that represents diversity and inclusion for all scientists. © The Author 2017. Published by

[The discussion of the infiltrative model of mathematical knowledge to genetics teaching].

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Liu, Jun; Luo, Pei-Gao

2011-11-01

Genetics, the core course of biological field, is an importance major-basic course in curriculum of many majors related with biology. Due to strong theoretical and practical as well as abstract of genetics, it is too difficult to study on genetics for many students. At the same time, mathematics is one of the basic courses in curriculum of the major related natural science, which has close relationship with the establishment, development and modification of genetics. In this paper, to establish the intrinsic logistic relationship and construct the integral knowledge network and to help students improving the analytic, comprehensive and logistic abilities, we applied some mathematical infiltrative model genetic knowledge in genetics teaching, which could help students more deeply learn and understand genetic knowledge.

Physical properties of biological entities: an introduction to the ontology of physics for biology.

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Daniel L Cook

Full Text Available As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB, a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration.

Physical properties of biological entities: an introduction to the ontology of physics for biology.

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Cook, Daniel L; Bookstein, Fred L; Gennari, John H

2011-01-01

As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration. © 2011 Cook et al.

Integrated Molecular and Cellular Biophysics

CERN Document Server

Raicu, Valerica

2008-01-01

This book integrates concepts and methods from physics, biology, biochemistry and physical chemistry into a standalone, unitary text of biophysics that aims to provide a quantitative description of structures and processes occurring in living matter. The book introduces graduate physics students and physicists interested in biophysics research to 'classical' as well as emerging areas of biophysics. The advanced undergraduate physics students and the life scientists are also invited to join in, by building on their knowledge of basic physics. Essential notions of biochemistry and biology are introduced, as necessary, throughout the book, while the reader's familiarity with basic knowledge of physics is assumed. Topics covered include interactions between biological molecules, physical chemistry of phospholipids association into bilayer membranes, DNA and protein structure and folding, passive and active electrical properties of the cell membrane, classical as well as fractal aspects of reaction kinetics and di...

Biological and psychological rhythms: an integrative approach to rhythm disturbances in autistic disorder.

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Botbol, Michel; Cabon, Philippe; Kermarrec, Solenn; Tordjman, Sylvie

2013-09-01

Biological rhythms are crucial phenomena that are perfect examples of the adaptation of organisms to their environment. A considerable amount of work has described different types of biological rhythms (from circadian to ultradian), individual differences in their patterns and the complexity of their regulation. In particular, the regulation and maturation of the sleep-wake cycle have been thoroughly studied. Its desynchronization, both endogenous and exogenous, is now well understood, as are its consequences for cognitive impairments and health problems. From a completely different perspective, psychoanalysts have shown a growing interest in the rhythms of psychic life. This interest extends beyond the original focus of psychoanalysis on dreams and the sleep-wake cycle, incorporating central theoretical and practical psychoanalytic issues related to the core functioning of the psychic life: the rhythmic structures of drive dynamics, intersubjective developmental processes and psychic containment functions. Psychopathological and biological approaches to the study of infantile autism reveal the importance of specific biological and psychological rhythmic disturbances in this disorder. Considering data and hypotheses from both perspectives, this paper proposes an integrative approach to the study of these rhythmic disturbances and offers an etiopathogenic hypothesis based on this integrative approach. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ultra-Structure database design methodology for managing systems biology data and analyses

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Hemminger Bradley M

2009-08-01

Full Text Available Abstract Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping. Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

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Christley Scott

2010-08-01

Full Text Available Abstract Background Simulation of sophisticated biological models requires considerable computational power. These models typically integrate together numerous biological phenomena such as spatially-explicit heterogeneous cells, cell-cell interactions, cell-environment interactions and intracellular gene networks. The recent advent of programming for graphical processing units (GPU opens up the possibility of developing more integrative, detailed and predictive biological models while at the same time decreasing the computational cost to simulate those models. Results We construct a 3D model of epidermal development and provide a set of GPU algorithms that executes significantly faster than sequential central processing unit (CPU code. We provide a parallel implementation of the subcellular element method for individual cells residing in a lattice-free spatial environment. Each cell in our epidermal model includes an internal gene network, which integrates cellular interaction of Notch signaling together with environmental interaction of basement membrane adhesion, to specify cellular state and behaviors such as growth and division. We take a pedagogical approach to describing how modeling methods are efficiently implemented on the GPU including memory layout of data structures and functional decomposition. We discuss various programmatic issues and provide a set of design guidelines for GPU programming that are instructive to avoid common pitfalls as well as to extract performance from the GPU architecture. Conclusions We demonstrate that GPU algorithms represent a significant technological advance for the simulation of complex biological models. We further demonstrate with our epidermal model that the integration of multiple complex modeling methods for heterogeneous multicellular biological processes is both feasible and computationally tractable using this new technology. We hope that the provided algorithms and source code will be a

The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis.

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Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J; Inzé, Dirk; Van de Peer, Yves

2013-03-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies.

Integration of a zebrafish research project into a molecular biology course to support critical thinking and course content goals.

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Felzien, Lisa K

2016-11-12

Engaging undergraduates in research is essential for teaching them to think like scientists, and it has become a desired component of classroom and laboratory instruction. Research projects that span an entire semester expose students to a variety of concepts and techniques and allow students to use experiments to learn scientific principles, understand why specific techniques are applicable, critically analyze varied data, and examine how experimentation leads to acquiring knowledge. To provide an experience with these features, a semester long research project was integrated into a combined lecture and laboratory course, Molecular Biology. The project utilized the zebrafish model to examine gene expression during embryonic development and required students to develop and test hypotheses about the timing of expression of previously uncharacterized genes. The main goals for the project were to provide opportunities for students to develop critical thinking skills required for conducting research and to support the content goals of the course. To determine whether these goals were met, student performance on the steps of the project and related pre-test and post-test questions was examined. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):565-573, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Measurement of the Ecological Integrity of Cerrado Streams Using Biological Metrics and the Index of Habitat Integrity

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Deusiano Florêncio dos Reis

2017-01-01

Full Text Available Generally, aquatic communities reflect the effects of anthropogenic changes such as deforestation or organic pollution. The Cerrado stands among the most threatened ecosystems by human activities in Brazil. In order to evaluate the ecological integrity of the streams in a preserved watershed in the Northern Cerrado biome corresponding to a mosaic of ecosystems in transition to the Amazonia biome in Brazil, biological metrics related to diversity, structure, and sensitivity of aquatic macroinvertebrates were calculated. Sampling included collections along stretches of 200 m of nine streams and measurements of abiotic variables (temperature, electrical conductivity, pH, total dissolved solids, dissolved oxygen, and discharge and the Index of Habitat Integrity (HII. The values of the abiotic variables and the HII indicated that most of the streams have good ecological integrity, due to high oxygen levels and low concentrations of dissolved solids and electric conductivity. Two streams showed altered HII scores mainly related to small dams for recreational and domestic use, use of Cerrado natural pasture for cattle raising, and spot deforestation in bathing areas. However, this finding is not reflected in the biological metrics that were used. Considering all nine streams, only two showed satisfactory ecological quality (measured by Biological Monitoring Working Party (BMWP, total richness, and EPT (Ephemeroptera, Plecoptera, and Trichoptera richness, only one of which had a low HII score. These results indicate that punctual measures of abiotic parameters do not reveal the long-term impacts of anthropic activities in these streams, including related fire management of pasture that annually alters the vegetation matrix and may act as a disturbance for the macroinvertebrate communities. Due to this, biomonitoring of low order streams in Cerrado ecosystems of the Northern Central Brazil by different biotic metrics and also physical attributes of the

An Integrated Open Approach to Capturing Systematic Knowledge for Manufacturing Process Innovation Based on Collective Intelligence

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Gangfeng Wang

2018-02-01

Full Text Available Process innovation plays a vital role in the manufacture realization of increasingly complex new products, especially in the context of sustainable development and cleaner production. Knowledge-based innovation design can inspire designers’ creative thinking; however, the existing scattered knowledge has not yet been properly captured and organized according to Computer-Aided Process Innovation (CAPI. Therefore, this paper proposes an integrated approach to tackle this non-trivial issue. By analyzing the design process of CAPI and technical features of open innovation, a novel holistic paradigm of process innovation knowledge capture based on collective intelligence (PIKC-CI is constructed from the perspective of the knowledge life cycle. Then, a multi-source innovation knowledge fusion algorithm based on semantic elements reconfiguration is applied to form new public knowledge. To ensure the credibility and orderliness of innovation knowledge refinement, a collaborative editing strategy based on knowledge lock and knowledge–social trust degree is explored. Finally, a knowledge management system MPI-OKCS integrating the proposed techniques is implemented into the pre-built CAPI general platform, and a welding process innovation example is provided to illustrate the feasibility of the proposed approach. It is expected that our work would lay the foundation for the future knowledge-inspired CAPI and smart process planning.

Hybrid integrated biological-solid-state system powered with adenosine triphosphate

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Roseman, Jared M.; Lin, Jianxun; Ramakrishnan, Siddharth; Rosenstein, Jacob K.; Shepard, Kenneth L.

2015-12-01

There is enormous potential in combining the capabilities of the biological and the solid state to create hybrid engineered systems. While there have been recent efforts to harness power from naturally occurring potentials in living systems in plants and animals to power complementary metal-oxide-semiconductor integrated circuits, here we report the first successful effort to isolate the energetics of an electrogenic ion pump in an engineered in vitro environment to power such an artificial system. An integrated circuit is powered by adenosine triphosphate through the action of Na+/K+ adenosine triphosphatases in an integrated in vitro lipid bilayer membrane. The ion pumps (active in the membrane at numbers exceeding 2 × 106 mm-2) are able to sustain a short-circuit current of 32.6 pA mm-2 and an open-circuit voltage of 78 mV, providing for a maximum power transfer of 1.27 pW mm-2 from a single bilayer. Two series-stacked bilayers provide a voltage sufficient to operate an integrated circuit with a conversion efficiency of chemical to electrical energy of 14.9%.

THE ADVERSE OUTCOME PATHWAY (AOP) FRAMEWORK: A FRAMEWORK FOR ORGANIZING BIOLOGICAL KNOWLEDGE LEADING TO HEALTH RISKS.

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An Adverse Outcome Pathway (AOP) represents the organization of current and newly acquired knowledge of biological pathways. These pathways contain a series of nodes (Key Events, KEs) that when sufficiently altered influence the next node on the pathway, beginning from an Molecul...

A Methodology for Multiple Rule System Integration and Resolution Within a Singular Knowledge Base

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Kautzmann, Frank N., III

1988-01-01

Expert Systems which support knowledge representation by qualitative modeling techniques experience problems, when called upon to support integrated views embodying description and explanation, especially when other factors such as multiple causality, competing rule model resolution, and multiple uses of knowledge representation are included. A series of prototypes are being developed to demonstrate the feasibility of automating the process of systems engineering, design and configuration, and diagnosis and fault management. A study involves not only a generic knowledge representation; it must also support multiple views at varying levels of description and interaction between physical elements, systems, and subsystems. Moreover, it will involve models of description and explanation for each level. This multiple model feature requires the development of control methods between rule systems and heuristics on a meta-level for each expert system involved in an integrated and larger class of expert system. The broadest possible category of interacting expert systems is described along with a general methodology for the knowledge representation and control of mutually exclusive rule systems.

Quantifying biological integrity by taxonomic completeness: its utility in regional and global assessments.

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Hawkins, Charles P

2006-08-01

Water resources managers and conservation biologists need reliable, quantitative, and directly comparable methods for assessing the biological integrity of the world's aquatic ecosystems. Large-scale assessments are constrained by the lack of consistency in the indicators used to assess biological integrity and our current inability to translate between indicators. In theory, assessments based on estimates of taxonomic completeness, i.e., the proportion of expected taxa that were observed (observed/expected, O/E) are directly comparable to one another and should therefore allow regionally and globally consistent summaries of the biological integrity of freshwater ecosystems. However, we know little about the true comparability of O/E assessments derived from different data sets or how well O/E assessments perform relative to other indicators in use. I compared the performance (precision, bias, and sensitivity to stressors) of O/E assessments based on five different data sets with the performance of the indicators previously applied to these data (three multimetric indices, a biotic index, and a hybrid method used by the state of Maine). Analyses were based on data collected from U.S. stream ecosystems in North Carolina, the Mid-Atlantic Highlands, Maine, and Ohio. O/E assessments resulted in very similar estimates of mean regional conditions compared with most other indicators once these indicators' values were standardized relative to reference-site means. However, other indicators tended to be biased estimators of O/E, a consequence of differences in their response to natural environmental gradients and sensitivity to stressors. These results imply that, in some cases, it may be possible to compare assessments derived from different indicators by standardizing their values (a statistical approach to data harmonization). In situations where it is difficult to standardize or otherwise harmonize two or more indicators, O/E values can easily be derived from existing

Development of tools for integrated monitoring and assessment of hazardous substances and their biological effects in the Baltic Sea.

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Lehtonen, Kari K; Sundelin, Brita; Lang, Thomas; Strand, Jakob

2014-02-01

The need to develop biological effects monitoring to facilitate a reliable assessment of hazardous substances has been emphasized in the Baltic Sea Action Plan of the Helsinki Commission. An integrated chemical-biological approach is vitally important for the understanding and proper assessment of anthropogenic pressures and their effects on the Baltic Sea. Such an approach is also necessary for prudent management aiming at safeguarding the sustainable use of ecosystem goods and Services. The BEAST project (Biological Effects of Anthropogenic Chemical Stress: Tools for the Assessment of Ecosystem Health) set out to address this topic within the BONUS Programme. BEAST generated a large amount of quality-assured data on several biological effects parameters (biomarkers) in various marine species in different sub-regions of the Baltic Sea. New indicators (biological response measurement methods) and management tools (integrated indices) with regard to the integrated monitoring approach were suggested.

Systems Biology and Stem Cell Pluripotency

DEFF Research Database (Denmark)

Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

2016-01-01

Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

Empirical study using network of semantically related associations in bridging the knowledge gap.

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Abedi, Vida; Yeasin, Mohammed; Zand, Ramin

2014-11-27

The data overload has created a new set of challenges in finding meaningful and relevant information with minimal cognitive effort. However designing robust and scalable knowledge discovery systems remains a challenge. Recent innovations in the (biological) literature mining tools have opened new avenues to understand the confluence of various diseases, genes, risk factors as well as biological processes in bridging the gaps between the massive amounts of scientific data and harvesting useful knowledge. In this paper, we highlight some of the findings using a text analytics tool, called ARIANA--Adaptive Robust and Integrative Analysis for finding Novel Associations. Empirical study using ARIANA reveals knowledge discovery instances that illustrate the efficacy of such tool. For example, ARIANA can capture the connection between the drug hexamethonium and pulmonary inflammation and fibrosis that caused the tragic death of a healthy volunteer in a 2001 John Hopkins asthma study, even though the abstract of the study was not part of the semantic model. An integrated system, such as ARIANA, could assist the human expert in exploratory literature search by bringing forward hidden associations, promoting data reuse and knowledge discovery as well as stimulating interdisciplinary projects by connecting information across the disciplines.

Legislative Regulation of Traditional Medicinal Knowledge in Eritrea vis-à-vis Eritrea's Commitments under the Convention on Biological Diversity: Issues and Alternatives

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Senai Andemariam

2010-09-01

Full Text Available On 21 March 1996, Eritrea acceded to the Convention on Biological Diversity which, among others, obliges states to sustainably conserve and develop customary uses of biological resources. Among the many forms of traditional practices of biological resources is traditional medicinal knowledge. Research has revealed that Eritrea has abundant pool of such knowledge and a high percentage of its population, as it is true with many developing and underdeveloped countries, resorts to traditional medicine for curing numerous ailments. However, no specific policy or legislative framework has yet been developed to sift, preserve and encourage the practice. Analysis of existing Eritrean laws and policies will show that they are neither adequate nor specific enough to be used in the preservation and development of Eritrean traditional medicinal knowledge. This article will, therefore, in view of the rich, yet unregulated, traditional medicinal knowledge resource in Eritrea, highlight the need for the development of a specific legal instrument legislation for Eritrea from the perspective of international and country level experiences. It will be argued that the development of a specific legislation is preferred to the alternative of keeping traditional medicinal knowledge as a component of a legal instrument developed for a larger mass such as health or traditional knowledge.

Development of an integrated knowledge-base and its management tool for computerized alarm processing system

International Nuclear Information System (INIS)

Heo, Gyun Young; Choi, Seong Soo; Kim, Han Gon; Chang, Soon Heung

1997-01-01

For a long time, a number of alarm processing techniques have been researched to reduce the number of actuated alarms for operators to deal with effectively during the abnormal as well as the normal conditions. However, the strategy that the only systems with a few clear technologies should be used as a part of an alarm annunciation system has been adopted considering the effectiveness and the reliability in actual alarm processing systems. Therefore, alarm processing systems have difficult knowledge-base maintenance problems and limited expansion or enhancement defects. To solve these shortcomings, the integrated knowledge-base which can express the general information related to all the alarm processing techniques is proposed and its management tool, Knowledge Input Tool for Alarm (KIT-A) which can handle the data of the knowledge-base efficiently is developed. Since the integrated knowledge-base with KIT-A can manipulate all the alarm information without the modification of alarm processing system itself, it is expected to considerably advance the overall capability of maintenance and enhancement of the alarm processing systems

State of Academic Knowledge on Toxicity and Biological Fate of Quantum Dots

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Pelley, Jennifer L.; Daar, Abdallah S.; Saner, Marc A.

2009-01-01

Quantum dots (QDs), an important class of emerging nanomaterial, are widely anticipated to find application in many consumer and clinical products in the near future. Premarket regulatory scrutiny is, thus, an issue gaining considerable attention. Previous review papers have focused primarily on the toxicity of QDs. From the point of view of product regulation, however, parameters that determine exposure (e.g., dosage, transformation, transportation, and persistence) are just as important as inherent toxicity. We have structured our review paper according to regulatory risk assessment practices, in order to improve the utility of existing knowledge in a regulatory context. Herein, we summarize the state of academic knowledge on QDs pertaining not only to toxicity, but also their physicochemical properties, and their biological and environmental fate. We conclude this review with recommendations on how to tailor future research efforts to address the specific needs of regulators. PMID:19684286

Indicators and Measurement Tools for Health Systems Integration: A Knowledge Synthesis

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Esther Suter

2017-11-01

Full Text Available Background: Despite far reaching support for integrated care, conceptualizing and measuring integrated care remains challenging. This knowledge synthesis aimed to identify indicator domains and tools to measure progress towards integrated care. Methods: We used an established framework and a Delphi survey with integration experts to identify relevant measurement domains. For each domain, we searched and reviewed the literature for relevant tools. Findings: From 7,133 abstracts, we retrieved 114 unique tools. We found many quality tools to measure care coordination, patient engagement and team effectiveness/performance. In contrast, there were few tools in the domains of performance measurement and information systems, alignment of organizational goals and resource allocation. The search yielded 12 tools that measure overall integration or three or more indicator domains. Discussion: Our findings highlight a continued gap in tools to measure foundational components that support integrated care. In the absence of such targeted tools, “overall integration” tools may be useful for a broad assessment of the overall state of a system. Conclusions: Continued progress towards integrated care depends on our ability to evaluate the success of strategies across different levels and context. This study has identified 114 tools that measure integrated care across 16 domains, supporting efforts towards a unified measurement framework.

Indicators and Measurement Tools for Health Systems Integration: A Knowledge Synthesis

Science.gov (United States)

Oelke, Nelly D.; da Silva Lima, Maria Alice Dias; Stiphout, Michelle; Janke, Robert; Witt, Regina Rigatto; Van Vliet-Brown, Cheryl; Schill, Kaela; Rostami, Mahnoush; Hepp, Shelanne; Birney, Arden; Al-Roubaiai, Fatima; Marques, Giselda Quintana

2017-01-01

Background: Despite far reaching support for integrated care, conceptualizing and measuring integrated care remains challenging. This knowledge synthesis aimed to identify indicator domains and tools to measure progress towards integrated care. Methods: We used an established framework and a Delphi survey with integration experts to identify relevant measurement domains. For each domain, we searched and reviewed the literature for relevant tools. Findings: From 7,133 abstracts, we retrieved 114 unique tools. We found many quality tools to measure care coordination, patient engagement and team effectiveness/performance. In contrast, there were few tools in the domains of performance measurement and information systems, alignment of organizational goals and resource allocation. The search yielded 12 tools that measure overall integration or three or more indicator domains. Discussion: Our findings highlight a continued gap in tools to measure foundational components that support integrated care. In the absence of such targeted tools, “overall integration” tools may be useful for a broad assessment of the overall state of a system. Conclusions: Continued progress towards integrated care depends on our ability to evaluate the success of strategies across different levels and context. This study has identified 114 tools that measure integrated care across 16 domains, supporting efforts towards a unified measurement framework. PMID:29588637

Knowledge Integration and Inter-Disciplinary Communication in Action Research

Directory of Open Access Journals (Sweden)

Hahn Heidi Ann

2014-08-01

Full Text Available In a plenary talk at WMSCI 2012 entitled "Planning for Action Research: Looking at Practice through a Different Lens," this author asserted that behavioral science practitioners, often "back into" action research – they start out doing a process improvement or intervention and discover something along the way, i.e., generalizable knowledge, that seems worthwhile to share with their community of practice. It was further asserted that, had the efforts been conceived of as research from the outset, the contributions to the body of knowledge would be more robust and the utility of the projects would improve as well. This paper continues on that theme. Action research and process improvement methods are briefly described and compared. A comparison of two Los Alamos National Laboratory engineering ethics training projects – one developed using a process improvement framework, the other using an action research framework – is put forth to provide evidence that use of a research "lens" can enhance behavioral science interventions and the knowledge that may result from them. The linkage between the Specifying Learning and Diagnosing stages of the Action Research Cycle provides one mechanism for integrating the knowledge gained into the product or process being studied and should provide a reinforcing loop that leads to continual improvement. The collaborative relationships among researchers and the individual, group, or organization that is the subject of the imp rovement op p ortunity (the "client", who are likely from very different backgrounds, and the interpretive epistemology that are among the hallmarks of action research also contribute to the quality of the knowledge gained. This paper closes with a discussion of how Inter-Disciplinary Communication is embedded within the action research paradigm and how this likely also enriches the knowledge gained.

A knowledge integration approach to flood vulnerability

Science.gov (United States)

Mazzorana, Bruno; Fuchs, Sven

2014-05-01

Understanding, qualifying and quantifying vulnerability is an essential need for implementing effective and efficient flood risk mitigation strategies; in particular if possible synergies between different mitigation alternatives, such as active and passive measures, should be achieved. In order to combine different risk management options it is necessary to take an interdisciplinary approach to vulnerability reduction, and as a result the affected society may be willing to accept a certain degree of self-responsibility. However, due to differing mono-disciplinary approaches and regional foci undertaken until now, different aspects of vulnerability to natural hazards in general and to floods in particular remain uncovered and as a result the developed management options remain sub-optimal. Taking an even more fundamental viewpoint, the empirical vulnerability functions used in risk assessment specifically fail to capture physical principles of the damage-generating mechanisms to the build environment. The aim of this paper is to partially close this gap by discussing a balanced knowledge integration approach which can be used to resolve the multidisciplinary disorder in flood vulnerability research. Modelling techniques such as mathematical-physical modelling of the flood hazard impact to and response from the building envelope affected, and formative scenario analyses of possible consequences in terms of damage and loss are used in synergy to provide an enhanced understanding of vulnerability and to render the derived knowledge into interdisciplinary mitigation strategies. The outlined formal procedure allows for a convincing knowledge alignment of quantified, but partial, information about vulnerability as a result of the application of physical and engineering notions and valuable, but often underspecified, qualitative argumentation strings emerging from the adopted socio-economic viewpoint.

Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses.

Science.gov (United States)

Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

2016-01-01

Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning. © 2016 K. Hoffman, S. Leupen, et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Integrating ethnobiological knowledge into biodiversity conservation in the Eastern Himalayas.

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O'Neill, Alexander R; Badola, Hemant K; Dhyani, Pitamber P; Rana, Santosh K

2017-03-29

Biocultural knowledge provides valuable insight into ecological processes, and can guide conservation practitioners in local contexts. In many regions, however, such knowledge is underutilized due to its often-fragmented record in disparate sources. In this article, we review and apply ethnobiological knowledge to biodiversity conservation in the Eastern Himalayas. Using Sikkim, India as a case study, we: (i) traced the history and trends of ethnobiological documentation; (ii) identified priority species and habitat types; and, (iii) analyzed within and among community differences pertaining to species use and management. Our results revealed that Sikkim is a biocultural hotspot, where six ethnic communities and 1128 species engage in biocultural relationships. Since the mid-1800s, the number of ethnobiological publications from Sikkim has exponentially increased; however, our results also indicate that much of this knowledge is both unwritten and partitioned within an aging, gendered, and caste or ethnic group-specific stratum of society. Reviewed species were primarily wild or wild cultivated, native to subtropical and temperate forests, and pend IUCN Red List of Threatened Species assessment. Our results demonstrate the value of engaging local knowledge holders as active participants in conservation, and suggest the need for further ethnobiological research in the Eastern Himalayas. Our interdisciplinary approach, which included rank indices and geospatial modelling, can help integrate diverse datasets into evidence-based policy.

Exploring the Associations among Nutrition, Science, and Mathematics Knowledge for an Integrative, Food-Based Curriculum

Science.gov (United States)

Stage, Virginia C.; Kolasa, Kathryn M.; Díaz, Sebastián R.; Duffrin, Melani W.

2018-01-01

Background: Explore associations between nutrition, science, and mathematics knowledge to provide evidence that integrating food/nutrition education in the fourth-grade curriculum may support gains in academic knowledge. Methods: Secondary analysis of a quasi-experimental study. Sample included 438 students in 34 fourth-grade classrooms across…

Integrating scientific knowledge into large-scale restoration programs: the CALFED Bay-Delta Program experience

Science.gov (United States)

Taylor, K.A.; Short, A.

2009-01-01

Integrating science into resource management activities is a goal of the CALFED Bay-Delta Program, a multi-agency effort to address water supply reliability, ecological condition, drinking water quality, and levees in the Sacramento-San Joaquin Delta of northern California. Under CALFED, many different strategies were used to integrate science, including interaction between the research and management communities, public dialogues about scientific work, and peer review. This paper explores ways science was (and was not) integrated into CALFED's management actions and decision systems through three narratives describing different patterns of scientific integration and application in CALFED. Though a collaborative process and certain organizational conditions may be necessary for developing new understandings of the system of interest, we find that those factors are not sufficient for translating that knowledge into management actions and decision systems. We suggest that the application of knowledge may be facilitated or hindered by (1) differences in the objectives, approaches, and cultures of scientists operating in the research community and those operating in the management community and (2) other factors external to the collaborative process and organization.

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

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Kempa Stefan

2009-05-01

Full Text Available Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

Integrating complex business processes for knowledge-driven clinical decision support systems.

Science.gov (United States)

Kamaleswaran, Rishikesan; McGregor, Carolyn

2012-01-01

This paper presents in detail the component of the Complex Business Process for Stream Processing framework that is responsible for integrating complex business processes to enable knowledge-driven Clinical Decision Support System (CDSS) recommendations. CDSSs aid the clinician in supporting the care of patients by providing accurate data analysis and evidence-based recommendations. However, the incorporation of a dynamic knowledge-management system that supports the definition and enactment of complex business processes and real-time data streams has not been researched. In this paper we discuss the process web service as an innovative method of providing contextual information to a real-time data stream processing CDSS.

PANDORA: keyword-based analysis of protein sets by integration of annotation sources.

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Kaplan, Noam; Vaaknin, Avishay; Linial, Michal

2003-10-01

Recent advances in high-throughput methods and the application of computational tools for automatic classification of proteins have made it possible to carry out large-scale proteomic analyses. Biological analysis and interpretation of sets of proteins is a time-consuming undertaking carried out manually by experts. We have developed PANDORA (Protein ANnotation Diagram ORiented Analysis), a web-based tool that provides an automatic representation of the biological knowledge associated with any set of proteins. PANDORA uses a unique approach of keyword-based graphical analysis that focuses on detecting subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA currently supports SwissProt keywords, NCBI Taxonomy, InterPro entries and the hierarchical classification terms from ENZYME, SCOP and GO databases. The integrated study of several annotation sources simultaneously allows a representation of biological relations of structure, function, cellular location, taxonomy, domains and motifs. PANDORA is also integrated into the ProtoNet system, thus allowing testing thousands of automatically generated clusters. We illustrate how PANDORA enhances the biological understanding of large, non-uniform sets of proteins originating from experimental and computational sources, without the need for prior biological knowledge on individual proteins.

Informing biological design by integration of systems and synthetic biology.

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Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

On challenges and opportunities of designing integrated IT platforms for supporting knowledge works in organizations

OpenAIRE

Laha, Arijit

2009-01-01

Designing and implementing comprehensive IT-based support environments for KM in organizations is fraught with many problems. Solving them requires intimate knowledge about the information usage in knowledge works and the scopes of technology intervention. In this paper, the Task-oriented Organizational Knowledge Management or TOKM, a design theory for building integrated IT platforms for supporting organizational KM, is proposed. TOKM brings together two apparently mutually exclusive practic...

Knowledge Gaps in Rodent Pancreas Biology: Taking Human Pluripotent Stem Cell-Derived Pancreatic Beta Cells into Our Own Hands.

Science.gov (United States)

Santosa, Munirah Mohamad; Low, Blaise Su Jun; Pek, Nicole Min Qian; Teo, Adrian Kee Keong

2015-01-01

In the field of stem cell biology and diabetes, we and others seek to derive mature and functional human pancreatic β cells for disease modeling and cell replacement therapy. Traditionally, knowledge gathered from rodents is extended to human pancreas developmental biology research involving human pluripotent stem cells (hPSCs). While much has been learnt from rodent pancreas biology in the early steps toward Pdx1(+) pancreatic progenitors, much less is known about the transition toward Ngn3(+) pancreatic endocrine progenitors. Essentially, the later steps of pancreatic β cell development and maturation remain elusive to date. As a result, the most recent advances in the stem cell and diabetes field have relied upon combinatorial testing of numerous growth factors and chemical compounds in an arbitrary trial-and-error fashion to derive mature and functional human pancreatic β cells from hPSCs. Although this hit-or-miss approach appears to have made some headway in maturing human pancreatic β cells in vitro, its underlying biology is vaguely understood. Therefore, in this mini-review, we discuss some of these late-stage signaling pathways that are involved in human pancreatic β cell differentiation and highlight our current understanding of their relevance in rodent pancreas biology. Our efforts here unravel several novel signaling pathways that can be further studied to shed light on unexplored aspects of rodent pancreas biology. New investigations into these signaling pathways are expected to advance our knowledge in human pancreas developmental biology and to aid in the translation of stem cell biology in the context of diabetes treatments.

A review on machine learning principles for multi-view biological data integration.

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Li, Yifeng; Wu, Fang-Xiang; Ngom, Alioune

2018-03-01

Driven by high-throughput sequencing techniques, modern genomic and clinical studies are in a strong need of integrative machine learning models for better use of vast volumes of heterogeneous information in the deep understanding of biological systems and the development of predictive models. How data from multiple sources (called multi-view data) are incorporated in a learning system is a key step for successful analysis. In this article, we provide a comprehensive review on omics and clinical data integration techniques, from a machine learning perspective, for various analyses such as prediction, clustering, dimension reduction and association. We shall show that Bayesian models are able to use prior information and model measurements with various distributions; tree-based methods can either build a tree with all features or collectively make a final decision based on trees learned from each view; kernel methods fuse the similarity matrices learned from individual views together for a final similarity matrix or learning model; network-based fusion methods are capable of inferring direct and indirect associations in a heterogeneous network; matrix factorization models have potential to learn interactions among features from different views; and a range of deep neural networks can be integrated in multi-modal learning for capturing the complex mechanism of biological systems.

Integrated MEMS/NEMS Resonant Cantilevers for Ultrasensitive Biological Detection

Directory of Open Access Journals (Sweden)

Xinxin Li

2009-01-01

Full Text Available The paper reviews the recent researches implemented in Chinese Academy of Sciences, with achievements on integrated resonant microcantilever sensors. In the resonant cantilevers, the self-sensing elements and resonance exciting elements are both top-down integrated with silicon micromachining techniques. Quite a lot of effort is focused on optimization of the resonance mode and sensing structure for improvement of sensitivity. On the other hand, to enable the micro-cantilevers specifically sensitive to bio/chemical molecules, sensing materials are developed and modified on the cantilever surface with a self-assembled monolayer (SAM based bottom-up construction and surface functionalization. To improve the selectivity of the sensors and depress environmental noise, multiple and localized surface modifications are developed. The achieved volume production capability and satisfactory detecting resolution to trace-level biological antigen of alpha-fetoprotein (AFP give the micro-cantilever sensors a great promise for rapid and high-resoluble detection.

Human Processing of Knowledge from Texts: Acquisition, Integration, and Reasoning

Science.gov (United States)

1979-06-01

comprehension. Norwood, N.J.: Ablex, 1977. Craik , F.I.M., and Lockhart , R. S. Levels of processing : for memory research. Journal of Verbal Learning A...Table 5.9 presents summary data regarding the performance levels and memory and search processes of individual subjects. The first row in Table 5.9...R-2256-ARP A June 1979 ARPA Order No.: 189-1 9020 Cybernetics Technology Human Processing of Knowledge from Texts: Acquisition, Integration, and

Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics.

Science.gov (United States)

Nottale, Laurent; Auffray, Charles

2008-05-01

In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, which aims at describing the effects of a non-differentiable and fractal (i.e., explicitly scale dependent) geometry of space-time. The first paper of this series was devoted, in this new framework, to the construction from first principles of scale laws of increasing complexity, and to the discussion of some tentative applications of these laws to biological systems. In this second review and perspective paper, we describe the effects induced by the internal fractal structures of trajectories on motion in standard space. Their main consequence is the transformation of classical dynamics into a generalized, quantum-like self-organized dynamics. A Schrödinger-type equation is derived as an integral of the geodesic equation in a fractal space. We then indicate how gauge fields can be constructed from a geometric re-interpretation of gauge transformations as scale transformations in fractal space-time. Finally, we introduce a new tentative development of the theory, in which quantum laws would hold also in scale space, introducing complexergy as a measure of organizational complexity. Initial possible applications of this extended framework to the processes of morphogenesis and the emergence of prokaryotic and eukaryotic cellular structures are discussed. Having founded elements of the evolutionary, developmental, biochemical and cellular theories on the first principles of scale relativity theory, we introduce proposals for the construction of an integrative theory of life and for the design and implementation of novel macroscopic quantum-type experiments and devices, and discuss their potential

Hybrid integrated biological-solid-state system powered with adenosine triphosphate.

Science.gov (United States)

Roseman, Jared M; Lin, Jianxun; Ramakrishnan, Siddharth; Rosenstein, Jacob K; Shepard, Kenneth L

2015-12-07

There is enormous potential in combining the capabilities of the biological and the solid state to create hybrid engineered systems. While there have been recent efforts to harness power from naturally occurring potentials in living systems in plants and animals to power complementary metal-oxide-semiconductor integrated circuits, here we report the first successful effort to isolate the energetics of an electrogenic ion pump in an engineered in vitro environment to power such an artificial system. An integrated circuit is powered by adenosine triphosphate through the action of Na(+)/K(+) adenosine triphosphatases in an integrated in vitro lipid bilayer membrane. The ion pumps (active in the membrane at numbers exceeding 2 × 10(6) mm(-2)) are able to sustain a short-circuit current of 32.6 pA mm(-2) and an open-circuit voltage of 78 mV, providing for a maximum power transfer of 1.27 pW mm(-2) from a single bilayer. Two series-stacked bilayers provide a voltage sufficient to operate an integrated circuit with a conversion efficiency of chemical to electrical energy of 14.9%.

Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle

DEFF Research Database (Denmark)

Mazzoni, Gianluca; Pedersen, Hanne S.; de Oliveira Junior, Gerson A.

2017-01-01

by both conventional and ARTs such as OPU-IVP. The integration of systems biology information across different biological layers generates a complete view of the different molecular networks that control complex traits and can provide a strong contribution to the understanding of traits related to ARTs....

Using the Biodatamation(TM) strategy to learn introductory college biology: Value-added effects on selected students' conceptual understanding and conceptual integration of the processes of photosynthesis and cellular respiration

Science.gov (United States)

Reuter, Jewel Jurovich

The purpose of this exploratory research was to study how students learn photosynthesis and cellular respiration and to determine the value added to the student's learning by each of the three technology-scaffolded learning strategy components (animated concept presentations and WebQuest-style activities, data collection, and student-constructed animations) of the BioDatamation(TM) (BDM) Program. BDM learning strategies utilized the Theory of Interacting Visual Fields(TM) (TIVF) (Reuter & Wandersee, 2002a, 2002b; 2003a, 2003b) which holds that meaningful knowledge is hierarchically constructed using the past, present, and future visual fields, with visual metacognitive components that are derived from the principles of Visual Behavior (Jones, 1995), Human Constructivist Theory (Mintzes & Wandersee, 1998a), and Visual Information Design Theory (Tufte, 1990, 1997, 2001). Student alternative conceptions of photosynthesis and cellular respiration were determined by the item analysis of 263,267 Biology Advanced Placement Examinations and were used to develop the BDM instructional strategy and interview questions. The subjects were 24 undergraduate students of high and low biology prior knowledge enrolled in an introductory-level General Biology course at a major research university in the Deep South. Fifteen participants received BDM instruction which included original and innovative learning materials and laboratories in 6 phases; 8 of the 15 participants were the subject of in depth, extended individual analysis. The other 9 participants received traditional, non-BDM instruction. Interviews which included participants' creation of concept maps and visual field diagrams were conducted after each phase. Various content analyses, including Chi's Verbal Analysis and quantitizing/qualitizing were used for data analysis. The total value added to integrative knowledge during BDM instruction with the three visual fields was an average increase of 56% for cellular respiration

BioTCM-SE: a semantic search engine for the information retrieval of modern biology and traditional Chinese medicine.

Science.gov (United States)

Chen, Xi; Chen, Huajun; Bi, Xuan; Gu, Peiqin; Chen, Jiaoyan; Wu, Zhaohui

2014-01-01

Understanding the functional mechanisms of the complex biological system as a whole is drawing more and more attention in global health care management. Traditional Chinese Medicine (TCM), essentially different from Western Medicine (WM), is gaining increasing attention due to its emphasis on individual wellness and natural herbal medicine, which satisfies the goal of integrative medicine. However, with the explosive growth of biomedical data on the Web, biomedical researchers are now confronted with the problem of large-scale data analysis and data query. Besides that, biomedical data also has a wide coverage which usually comes from multiple heterogeneous data sources and has different taxonomies, making it hard to integrate and query the big biomedical data. Embedded with domain knowledge from different disciplines all regarding human biological systems, the heterogeneous data repositories are implicitly connected by human expert knowledge. Traditional search engines cannot provide accurate and comprehensive search results for the semantically associated knowledge since they only support keywords-based searches. In this paper, we present BioTCM-SE, a semantic search engine for the information retrieval of modern biology and TCM, which provides biologists with a comprehensive and accurate associated knowledge query platform to greatly facilitate the implicit knowledge discovery between WM and TCM.

BioTCM-SE: A Semantic Search Engine for the Information Retrieval of Modern Biology and Traditional Chinese Medicine

Directory of Open Access Journals (Sweden)

Xi Chen

2014-01-01

Full Text Available Understanding the functional mechanisms of the complex biological system as a whole is drawing more and more attention in global health care management. Traditional Chinese Medicine (TCM, essentially different from Western Medicine (WM, is gaining increasing attention due to its emphasis on individual wellness and natural herbal medicine, which satisfies the goal of integrative medicine. However, with the explosive growth of biomedical data on the Web, biomedical researchers are now confronted with the problem of large-scale data analysis and data query. Besides that, biomedical data also has a wide coverage which usually comes from multiple heterogeneous data sources and has different taxonomies, making it hard to integrate and query the big biomedical data. Embedded with domain knowledge from different disciplines all regarding human biological systems, the heterogeneous data repositories are implicitly connected by human expert knowledge. Traditional search engines cannot provide accurate and comprehensive search results for the semantically associated knowledge since they only support keywords-based searches. In this paper, we present BioTCM-SE, a semantic search engine for the information retrieval of modern biology and TCM, which provides biologists with a comprehensive and accurate associated knowledge query platform to greatly facilitate the implicit knowledge discovery between WM and TCM.

Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

Science.gov (United States)

Nesse, Randolph M; Bergstrom, Carl T; Ellison, Peter T; Flier, Jeffrey S; Gluckman, Peter; Govindaraju, Diddahally R; Niethammer, Dietrich; Omenn, Gilbert S; Perlman, Robert L; Schwartz, Mark D; Thomas, Mark G; Stearns, Stephen C; Valle, David

2010-01-26

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

The role of bacillus-based biological control agents in integrated pest management systems: plant diseases.

Science.gov (United States)

Jacobsen, B J; Zidack, N K; Larson, B J

2004-11-01

ABSTRACT Bacillus-based biological control agents (BCAs) have great potential in integrated pest management (IPM) systems; however, relatively little work has been published on integration with other IPM management tools. Unfortunately, most research has focused on BCAs as alternatives to synthetic chemical fungicides or bactericides and not as part of an integrated management system. IPM has had many definitions and this review will use the national coalition for IPM definition: "A sustainable approach to managing pests by combining biological, cultural, physical and chemical tools in a way that minimizes economic, health and environmental risks." This review will examine the integrated use of Bacillus-based BCAs with disease management tools, including resistant cultivars, fungicides or bactericides, or other BCAs. This integration is important because the consistency and degree of disease control by Bacillus-based BCAs is rarely equal to the control afforded by the best fungicides or bactericides. In theory, integration of several tools brings stability to disease management programs. Integration of BCAs with other disease management tools often provides broader crop adaptation and both more efficacious and consistent levels of disease control. This review will also discuss the use of Bacillus-based BCAs in fungicide resistance management. Work with Bacillus thuringiensis and insect pest management is the exception to the relative paucity of reports but will not be the focus of this review.

Modeling Cancer Metastasis using Global, Quantitative and Integrative Network Biology

DEFF Research Database (Denmark)

Schoof, Erwin; Erler, Janine

understanding of molecular processes which are fundamental to tumorigenesis. In Article 1, we propose a novel framework for how cancer mutations can be studied by taking into account their effect at the protein network level. In Article 2, we demonstrate how global, quantitative data on phosphorylation dynamics...... can be generated using MS, and how this can be modeled using a computational framework for deciphering kinase-substrate dynamics. This framework is described in depth in Article 3, and covers the design of KinomeXplorer, which allows the prediction of kinases responsible for modulating observed...... phosphorylation dynamics in a given biological sample. In Chapter III, we move into Integrative Network Biology, where, by combining two fundamental technologies (MS & NGS), we can obtain more in-depth insights into the links between cellular phenotype and genotype. Article 4 describes the proof...

Joining Forces: The Chemical Biology-Medicinal Chemistry Continuum.

Science.gov (United States)

Plowright, Alleyn T; Ottmann, Christian; Arkin, Michelle; Auberson, Yves P; Timmerman, Henk; Waldmann, Herbert

2017-09-21

The scientific advances being made across all disciplines are creating ever-increasing opportunities to enhance our knowledge of biological systems and how they relate to human disease. One of the central driving forces in discovering new medicines is medicinal chemistry, where the design and synthesis of novel compounds has led to multiple drugs. Chemical biology, sitting at the interface of many disciplines, has now emerged as a major contributor to the understanding of biological systems and is becoming an integral part of drug discovery. Bringing chemistry and biology much closer and blurring the boundaries between disciplines is creating new opportunities to probe and understand biology; both disciplines play key roles and need to join forces and work together effectively to synergize their impact. The power of chemical biology will then reach its full potential and drive innovation, leading to the discovery of transformative medicines to treat patients. Advances in cancer biology and drug discovery highlight this potential. Copyright © 2017 Elsevier Ltd. All rights reserved.

Enabling collaboration on semiformal mathematical knowledge by semantic web integration

CERN Document Server

Lange, C

2011-01-01

Mathematics is becoming increasingly collaborative, but software does not sufficiently support that: Social Web applications do not currently make mathematical knowledge accessible to automated agents that have a deeper understanding of mathematical structures. Such agents exist but focus on individual research tasks, such as authoring, publishing, peer-review, or verification, instead of complex collaboration workflows. This work effectively enables their integration by bridging the document-oriented perspective of mathematical authoring and publishing, and the network perspective of threaded

A Bayesian network approach to knowledge integration and representation of farm irrigation: 1. Model development

Science.gov (United States)

Wang, Q. J.; Robertson, D. E.; Haines, C. L.

2009-02-01

Irrigation is important to many agricultural businesses but also has implications for catchment health. A considerable body of knowledge exists on how irrigation management affects farm business and catchment health. However, this knowledge is fragmentary; is available in many forms such as qualitative and quantitative; is dispersed in scientific literature, technical reports, and the minds of individuals; and is of varying degrees of certainty. Bayesian networks allow the integration of dispersed knowledge into quantitative systems models. This study describes the development, validation, and application of a Bayesian network model of farm irrigation in the Shepparton Irrigation Region of northern Victoria, Australia. In this first paper we describe the process used to integrate a range of sources of knowledge to develop a model of farm irrigation. We describe the principal model components and summarize the reaction to the model and its development process by local stakeholders. Subsequent papers in this series describe model validation and the application of the model to assess the regional impact of historical and future management intervention.

Lean Big Data integration in systems biology and systems pharmacology.

Science.gov (United States)

Ma'ayan, Avi; Rouillard, Andrew D; Clark, Neil R; Wang, Zichen; Duan, Qiaonan; Kou, Yan

2014-09-01

Data sets from recent large-scale projects can be integrated into one unified puzzle that can provide new insights into how drugs and genetic perturbations applied to human cells are linked to whole-organism phenotypes. Data that report how drugs affect the phenotype of human cell lines and how drugs induce changes in gene and protein expression in human cell lines can be combined with knowledge about human disease, side effects induced by drugs, and mouse phenotypes. Such data integration efforts can be achieved through the conversion of data from the various resources into single-node-type networks, gene-set libraries, or multipartite graphs. This approach can lead us to the identification of more relationships between genes, drugs, and phenotypes as well as benchmark computational and experimental methods. Overall, this lean 'Big Data' integration strategy will bring us closer toward the goal of realizing personalized medicine. Copyright © 2014 Elsevier Ltd. All rights reserved.

Exploring Alternatives for Representing and Accessing Design Knowledge About Enterprise Integration

Science.gov (United States)

Umapathy, Karthikeyan; Purao, Sandeep

Enterprise integration refers to solutions that facilitate meaningful interactions among heterogeneous legacy applications. The scale, complexity and specificity of most enterprise integration efforts mean that design knowledge for enterprise integration has resisted codification. Important exceptions to this include: use of Business Process Models (BPM) to understand integration requirements; and Enterprise Integration Patterns (EIP), which present designers with abstract descriptions of recurring design tactics for integrating applications. The two, however, can be at odds. BPM encourages the control flow perspective; whereas EIP codifies an operational perspective. Mapping between the two to develop coherent solutions, therefore, tends to be problematic. To bridge the gap, we suggest an approach that builds on the theory of speech acts. We develop essential components of such an approach, including a re-representation of EIP as structures of speech acts, a characterization of tasks in BPM with action types, and a mapping between speech acts and action types. These components are accompanied by inference rules that produce a mapping between sets of tasks in a business process and structures of speech acts to allow reasoning on identification of appropriate EIPs for given set of tasks. We demonstrate usefulness of the proposed approach by application to industry cases.

Development and application of knowledge-based subject group integration platforms:A case study of Shanghai Institute of Ceramics,CAS

Institute of Scientific and Technical Information of China (English)

Yu; LIU; Jian; FU; Huijun; ZHENG; Hao; CHEN; Zhiping; YANG

2014-01-01

Purpose:According to the different requirements of research group users,we established the knowledge-based subject group integration platforms of Shanghai Institute of Ceramics,the Chinese Academy of Sciences(abbreviated as SIC CAS hereinafter),which were designed and constructed to better meet the needs of CAS research groups for their development,collaboration and communication.Design/methodology/approach:We first identified the requirements of users via preliminary investigation,and then chose CASI1 P,iLibrary and XKE technology,respectively as the building tools compatible with the major demands of users.These steps helped us complete the layout design of SIC CAS integration platforms,as well as its knowledge organization and integration.Findings:According to the need of users,we applied three types of platform construction technologies to five SIC integration platforms,and formulated standard norms for the further construction process,which could provide useful reference for a sustainable development for the extensive construction in CAS institutes.Research limitations:In order to make the SIC integration platforms more intelligent and have more functions,we need to enlarge the scale of the Platforms and upgrade the building tools for the platform construction.Practical implications:The nature of SIC sub-project integration platforms is to construct a content-sensitive environment which can embed knowledge services and knowledge applications seamlessly into scientific activities,so the Platform is expected to be a useful tool to help researchers better understand the recent development of the research field and form collaborations with their peers.Originality/value:SIC integration platforms are the only pilot construction that used 3different platform technologies in the first batch of knowledge-based subject group integration platforms of the Chinese Academy of Sciences.The construction is user-centered throughout the whole process,namely,from the technology

A critical review of the current knowledge regarding the biological impact of nanocellulose.

Science.gov (United States)

Endes, C; Camarero-Espinosa, S; Mueller, S; Foster, E J; Petri-Fink, A; Rothen-Rutishauser, B; Weder, C; Clift, M J D

2016-12-01

Several forms of nanocellulose, notably cellulose nanocrystals and nanofibrillated cellulose, exhibit attractive property matrices and are potentially useful for a large number of industrial applications. These include the paper and cardboard industry, use as reinforcing filler in polymer composites, basis for low-density foams, additive in adhesives and paints, as well as a wide variety of food, hygiene, cosmetic, and medical products. Although the commercial exploitation of nanocellulose has already commenced, little is known as to the potential biological impact of nanocellulose, particularly in its raw form. This review provides a comprehensive and critical review of the current state of knowledge of nanocellulose in this format. Overall, the data seems to suggest that when investigated under realistic doses and exposure scenarios, nanocellulose has a limited associated toxic potential, albeit certain forms of nanocellulose can be associated with more hazardous biological behavior due to their specific physical characteristics.

On the origin of biological construction, with a focus on multicellularity.

Science.gov (United States)

van Gestel, Jordi; Tarnita, Corina E

2017-10-17

Biology is marked by a hierarchical organization: all life consists of cells; in some cases, these cells assemble into groups, such as endosymbionts or multicellular organisms; in turn, multicellular organisms sometimes assemble into yet other groups, such as primate societies or ant colonies. The construction of new organizational layers results from hierarchical evolutionary transitions, in which biological units (e.g., cells) form groups that evolve into new units of biological organization (e.g., multicellular organisms). Despite considerable advances, there is no bottom-up, dynamical account of how, starting from the solitary ancestor, the first groups originate and subsequently evolve the organizing principles that qualify them as new units. Guided by six central questions, we propose an integrative bottom-up approach for studying the dynamics underlying hierarchical evolutionary transitions, which builds on and synthesizes existing knowledge. This approach highlights the crucial role of the ecology and development of the solitary ancestor in the emergence and subsequent evolution of groups, and it stresses the paramount importance of the life cycle: only by evaluating groups in the context of their life cycle can we unravel the evolutionary trajectory of hierarchical transitions. These insights also provide a starting point for understanding the types of subsequent organizational complexity. The central research questions outlined here naturally link existing research programs on biological construction (e.g., on cooperation, multilevel selection, self-organization, and development) and thereby help integrate knowledge stemming from diverse fields of biology.

New ways of integrating material knowledge into the design process

DEFF Research Database (Denmark)

Højris, Anders; Nielsen, Louise Møller

2013-01-01

– based on technical performance, no longer apply. Accordingly the approach in this paper is to view information and knowledge about materials through the perspective of organizational memory and technology brokering. This paper is build upon two cases from the German based design studio: designaffairs...... libraries and thereby access to information on new material possibilities has also changed the way designers integrate knowledge about materials into the design process. This means that the traditional design process model, where the selection of materials takes place after the design of form and function...... in order to help clients to find the right material among hundreds of samples. Furthermore a number of material libraries have also been developed into online database, which provides detailed information about new material and makes the information accessible from almost everywhere. The access to material...

Polymer micro-grippers with an integrated force sensor for biological manipulation

International Nuclear Information System (INIS)

Mackay, R E; Le, H R; Clark, S; Williams, J A

2013-01-01

The development of a novel micro-system integrating SU-8 polymer micro-grippers with a tensile force sensor for handling and characterizing the mechanical properties of delicate biological materials, such as fibrils, is presented. The micro-grippers are actuated by the electro-thermal effect and have gripping forces comparable to the common ‘hot-and-cold-arm’ grippers. A robust finite element model was developed to investigate system performance and validated experimentally. A new micro-mechanical calibration method using a piezoelectric manipulator with a micro-force measurement system was successfully applied to test the structure. Both FEA simulation and micro-mechanical testing results indicated that the system could fulfil the requirements for micro-object manipulation within a biological environment. (paper)

An integrated system for interactive continuous learning of categorical knowledge

Science.gov (United States)

Skočaj, Danijel; Vrečko, Alen; Mahnič, Marko; Janíček, Miroslav; Kruijff, Geert-Jan M.; Hanheide, Marc; Hawes, Nick; Wyatt, Jeremy L.; Keller, Thomas; Zhou, Kai; Zillich, Michael; Kristan, Matej

2016-09-01

This article presents an integrated robot system capable of interactive learning in dialogue with a human. Such a system needs to have several competencies and must be able to process different types of representations. In this article, we describe a collection of mechanisms that enable integration of heterogeneous competencies in a principled way. Central to our design is the creation of beliefs from visual and linguistic information, and the use of these beliefs for planning system behaviour to satisfy internal drives. The system is able to detect gaps in its knowledge and to plan and execute actions that provide information needed to fill these gaps. We propose a hierarchy of mechanisms which are capable of engaging in different kinds of learning interactions, e.g. those initiated by a tutor or by the system itself. We present the theory these mechanisms are build upon and an instantiation of this theory in the form of an integrated robot system. We demonstrate the operation of the system in the case of learning conceptual models of objects and their visual properties.

A Neural Systems-Based Neurobiology and Neuropsychiatry Course: Integrating Biology, Psychodynamics, and Psychology in the Psychiatric Curriculum

Science.gov (United States)

Lacy, Timothy; Hughes, John D.

2006-01-01

Objective: Psychotherapy and biological psychiatry remain divided in psychiatry residency curricula. Behavioral neurobiology and neuropsychiatry provide a systems-level framework that allows teachers to integrate biology, psychodynamics, and psychology. Method: The authors detail the underlying assumptions and outline of a neural systems-based…

Biological data - Integrated acoustic and trawl survey of Pacific hake off the Pacific Coast

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Integrated acoustic and trawl surveys are used to assess the distribution, biomass, and biology of Pacific hake along the Pacific coasts of the United States and...

Integrating design and production planning with knowledge-based inspection planning system

International Nuclear Information System (INIS)

Abbasi, Ghaleb Y.; Ketan, Hussein S.; Adil, Mazen B.

2005-01-01

In this paper an intelligent environment to integrate design and inspection earlier to the design stage. A hybrid knowledge-based approach integrating computer-aided design (CAD) and computer-aided inspection planning (CAIP) was developed, thereafter called computer-aided design and inspection planning (CADIP). CADIP was adopted for automated dimensional inspection planning. Critical functional features were screened based on certain attributes for part features for inspection planning application. Testing the model resulted in minimizing the number of probing vectors associated with the most important features in the inspected prismatic part, significant reduction in inspection costs and release of human labor. In totality, this tends to increase customer satisfaction as a final goal of the developed system. (author)

The Role of Research Coordination in Enhancing Integrative Research: the Co-production of Knowledge Agenda of the Global Land Programme

Science.gov (United States)

Scarpa, F. M.; Boillat, S. P.; Grove, J. M.

2015-12-01

The search for sustainability and resilience requires the integration of natural science with social science, as well as the joint production of knowledge and solutions by science and society. In this context, international science coordination initiatives, like Future Earth, have increasingly stressed the need to perform more integrated and more socially relevant research. This contribution has the objective to highlight the potential role of a research coordination initiative, the Global Land Programme (GLP), to provide guidance for more integrative research. The need to perform integrative research is particularly true for land systems, which include dynamic interactions among social and natural drivers that are often multifunctional. Thus, their governance and management is particularity complex and involve highly diverse stakeholders. A key aspect of integrative research is co-production of knowledge, understood as the interactive production of knowledge by both academics and non-academics, that leads to new forms of solutions-oriented knowledge. We relied on experiences of co-production of knowledge on land systems from the GLP network, and drove seven lessons learnt: 1) the importance of including several learning loops in the process, 2) the importance of long-term relationships, 3) the need to overcome the distinction between basic and applied science, 4) the opportunities offered by new communication technologies, 5) the need to train professionals in both breadth and depth, 6) the access to knowledge, and 7) the need to understand better the roles of scientists and decision-makers. These lessons were used to define action-research priorities for enhancing co-production of knowledge on land systems in GLP projects and working groups. As a conclusion, we argue that research coordination initiatives have the potential to provide analysis and guidance for more integrative research. This can be done by performing synthesis and self-reflection activities that

Capturing knowledge integration through collaborations: measures of the diversity and coherence in multiple proximity dimensions

Energy Technology Data Exchange (ETDEWEB)

Lang, F.; Rafols, I.; Hopkins, M.

2016-07-01

This paper proposes a novel approach to determine changes that occur as a result of collaborations that is intended to support knowledge integration. The approach combines and applies indicators of proximity, diversity, coherence and has potential applications in the study and evaluation of research collaborations. The scientometric literature has been exploring the topic of knowledge integration and interdisciplinarity for more than a decade (Bordons, 2004; Zitt, 2005; Rafols, 2014). The paper builds on the line of research that seeks to develop measures of knowledge integration, namely diversity and coherence (Rafols, 2014). Successful exchange and integration of knowledge through collaboration not only requires disciplinary or cognitive diversity, as previously studied in the scientometric literature (Rafols & Meyer, 2009; Rafols, 2014) but also other dimensions linked to the social, cultural background of the individuals involved. Economic geographers have developed a framework, the proximity framework (Boschma, 2005), identifying five features that may be important for collaborative learning which are: cognitive, social, geographical, institutional, and organisational proximities. The paper therefore proposes to use the diversity and coherence measures to not only look at diversity from a cognitive standpoint, but also apply it to the other proximities proposed in the Boschma framework. These indicators will capture the relationship occurring betweenindividuals taking part in the research and the categories (proximity dimensions) that they are associated to. This paper reviews and integrates concepts from economic geography with the scientometric literature on interdisciplinarity to form a conceptual framework that the paper applies to an illustrative case study. In order to apply the framework, the paper develops indicators for diversity and coherence that can be applied to each of Boschma’s five proximities. The illustrative case study looks at

The mammary gland in domestic ruminants: a systems biology perspective.

Science.gov (United States)

Ferreira, Ana M; Bislev, Stine L; Bendixen, Emøke; Almeida, André M

2013-12-06

Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main species used worldwide. An adequate management of dairy farming cannot be achieved without the knowledge on the biological mechanisms behind lactation in ruminants. Thus, understanding the morphology, development and regulation of the mammary gland in health, disease and production is crucial. Presently, innovative and high-throughput technologies such as genomics, transcriptomics, proteomics and metabolomics allow a much broader and detailed knowledge on such issues. Additionally, the application of a systems biology approach to animal science is vastly growing, as new advances in one field of specialization or animal species lead to new lines of research in other areas or/and are expanded to other species. This article addresses how modern research approaches may help us understand long-known issues in mammary development, lactation biology and dairy production. Dairy production depends upon the knowledge of the morphology and regulation of the mammary gland and lactation. High-throughput technologies allow a much broader and detailed knowledge on the biology of the mammary gland. This paper reviews the major contributions that genomics, transcriptomics, metabolomics and proteomics approaches have provided to understand the regulation of the mammary gland in health, disease and production. In the context of mammary gland "omics"-based research, the integration of results using a Systems Biology Approach is of key importance. © 2013.

Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

Science.gov (United States)

Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

2015-01-01

Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.

The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis[C][W

Science.gov (United States)

Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J.; Inzé, Dirk; Van de Peer, Yves

2013-01-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein–protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies. PMID:23532071

Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

Science.gov (United States)

Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

2016-02-01

The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

The biological knowledge discovery by PCCF measure and PCA-F projection.

Science.gov (United States)

Jia, Xingang; Zhu, Guanqun; Han, Qiuhong; Lu, Zuhong

2017-01-01

In the process of biological knowledge discovery, PCA is commonly used to complement the clustering analysis, but PCA typically gives the poor visualizations for most gene expression data sets. Here, we propose a PCCF measure, and use PCA-F to display clusters of PCCF, where PCCF and PCA-F are modeled from the modified cumulative probabilities of genes. From the analysis of simulated and experimental data sets, we demonstrate that PCCF is more appropriate and reliable for analyzing gene expression data compared to other commonly used distances or similarity measures, and PCA-F is a good visualization technique for identifying clusters of PCCF, where we aim at such data sets that the expression values of genes are collected at different time points.

Do Zoo Visitors Need Zoology Knowledge to Understand Conservation Messages? An Exploration of the Public Understanding of Animal Biology and of the Conservation of Biodiversity in a Zoo Setting

Science.gov (United States)

Dove, Tracy; Byrne, Jenny

2014-01-01

This study explores the current knowledge and understanding about animal biology of zoo visitors and investigates whether knowledge of animal biology influences the ability of people to understand how human activity affects biodiversity. Zoos can play a role in the development of scientific literacy in the fields of animal biology and biodiversity…

Endodontic radiology, practice, and knowledge of radiation biology, hazard, and protection among clinical dental students and interns

Directory of Open Access Journals (Sweden)

Joan Emien Enabulele

2015-01-01

Full Text Available Objective: To evaluate the practice and knowledge of endodontic radiology as well as assess the knowledge of radiation biology, hazard, and protection among clinical dental students and interns. Materials and Methods: Cross-sectional study of clinical dental students and interns at University of Benin and University of Benin Teaching hospital respectively. Data was collected using a questionnaire which covered practice and knowledge of endodontic radiography, knowledge of radiation biology, hazard, and protection. Data was analyzed using Statistical Package for Social Sciences (SPSS version 17.0. Result: Seventy participants were included in the study, 40% were final year students and 24.3% house officers. Majority (95.7% agreed that they exposed radiographs as part of endodontic treatment. Only 18.6% knew that the apices of teeth should be 3mm from the border of the X-ray film, while 24.3% knew that 3mm of periapical bone should be visible on X-ray. Less than half (31.4% knew that paralleling technique was the technique of choice for endodontic radiography and this was statistically Significant in relationship to the status of the of the respondents. A few (4.3% of the respondents had knowledge of new horizons in endodontic imaging. Half of the respondents knew that damage by X-rays is mainly due to formation of free radicals. The most frequently reported radiation hazards was reduced salivary flow, while the least reported was rampant caries. Most knew how to protect patients, themselves, and other persons while exposing radiographs. Conclusion: There is need for inclusion of endodontic radiography in the undergraduate curriculum to ensure proper and correct radiographs during endodontic procedure.

Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

Science.gov (United States)

He, Yongqun

2014-07-01

While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ('OneNet') Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach

DEFF Research Database (Denmark)

Pan, Xiaoyong; Shen, Hong Bin

2017-01-01

, their domain specific features and formats have posed significant computational challenges. One of current difficulties is that the cross-source shared common knowledge is at a higher abstraction level beyond the observed data, resulting in a low efficiency of direct integration of observed data across domains...... space using multiple layers of learning blocks, where the shared representations across different domains are integrated. To validate our iDeep method, we performed experiments on 31 large-scale CLIP-seq datasets, and our results show that by integrating multiple sources of data, the average AUC can...... be improved by 8% compared to the best single-source-based predictor; and through cross-domain knowledge integration at an abstraction level, it outperforms the state-of-the-art predictors by 6%. Besides the overall enhanced prediction performance, the convolutional neural network module embedded in i...

Integrating the Use of Interdisciplinary Learning Activity Task in Creating Students' Mathematical Knowledge

Science.gov (United States)

Mahanin, Hajah Umisuzimah Haji; Shahrill, Masitah; Tan, Abby; Mahadi, Mar Aswandi

2017-01-01

This study investigated the use of interdisciplinary learning activity task to construct students' knowledge in Mathematics, specifically on the topic of scale drawing application. The learning activity task involved more than one academic discipline, which is Mathematics, English Language, Art, Geography and integrating the Brunei Darussalam…

Using two classification schemes to develop vegetation indices of biological integrity for wetlands in West Virginia, USA.

Science.gov (United States)

Veselka, Walter; Rentch, James S; Grafton, William N; Kordek, Walter S; Anderson, James T

2010-11-01

Bioassessment methods for wetlands, and other bodies of water, have been developed worldwide to measure and quantify changes in "biological integrity." These assessments are based on a classification system, meant to ensure appropriate comparisons between wetland types. Using a local site-specific disturbance gradient, we built vegetation indices of biological integrity (Veg-IBIs) based on two commonly used wetland classification systems in the USA: One based on vegetative structure and the other based on a wetland's position in a landscape and sources of water. The resulting class-specific Veg-IBIs were comprised of 1-5 metrics that varied in their sensitivity to the disturbance gradient (R2=0.14-0.65). Moreover, the sensitivity to the disturbance gradient increased as metrics from each of the two classification schemes were combined (added). Using this information to monitor natural and created wetlands will help natural resource managers track changes in biological integrity of wetlands in response to anthropogenic disturbance and allows the use of vegetative communities to set ecological performance standards for mitigation banks.

Integrating knowledge and control into hypermedia-based training environments: Experiments with HyperCLIPS

Science.gov (United States)

Hill, Randall W., Jr.

1990-01-01

The issues of knowledge representation and control in hypermedia-based training environments are discussed. The main objective is to integrate the flexible presentation capability of hypermedia with a knowledge-based approach to lesson discourse management. The instructional goals and their associated concepts are represented in a knowledge representation structure called a 'concept network'. Its functional usages are many: it is used to control the navigation through a presentation space, generate tests for student evaluation, and model the student. This architecture was implemented in HyperCLIPS, a hybrid system that creates a bridge between HyperCard, a popular hypertext-like system used for building user interfaces to data bases and other applications, and CLIPS, a highly portable government-owned expert system shell.

Discovery informatics in biological and biomedical sciences: research challenges and opportunities.

Science.gov (United States)

Honavar, Vasant

2015-01-01

New discoveries in biological, biomedical and health sciences are increasingly being driven by our ability to acquire, share, integrate and analyze, and construct and simulate predictive models of biological systems. While much attention has focused on automating routine aspects of management and analysis of "big data", realizing the full potential of "big data" to accelerate discovery calls for automating many other aspects of the scientific process that have so far largely resisted automation: identifying gaps in the current state of knowledge; generating and prioritizing questions; designing studies; designing, prioritizing, planning, and executing experiments; interpreting results; forming hypotheses; drawing conclusions; replicating studies; validating claims; documenting studies; communicating results; reviewing results; and integrating results into the larger body of knowledge in a discipline. Against this background, the PSB workshop on Discovery Informatics in Biological and Biomedical Sciences explores the opportunities and challenges of automating discovery or assisting humans in discovery through advances (i) Understanding, formalization, and information processing accounts of, the entire scientific process; (ii) Design, development, and evaluation of the computational artifacts (representations, processes) that embody such understanding; and (iii) Application of the resulting artifacts and systems to advance science (by augmenting individual or collective human efforts, or by fully automating science).

Assembly and integration of geo-scientific knowledge and arguments

International Nuclear Information System (INIS)

Gierszewki, P.; Gautschi, A.; Nguyen, T.S.; Laaksohaju, M.; Rohlig, K.J.; Peake, T.; Peltier, R.; Pitkanen, P.; Skagius Elert, K.; Sykes, J.F.

2007-01-01

The purpose of this working group was to consider the assembly and integration of geo-scientific knowledge and arguments. In an introductory presentation, K. Skagius Elert presented 'Assessment of Uncertainty and Confidence in Site Descriptive Models Experience from the On-going Site Investigation Programme in Sweden'. The detailed description of concepts and procedures established at SKB for the development of a Site Descriptive Model (SDM) provided a starting point for the discussion of the working group. The SDM components and the procedures to achieve them were used as 'references' for the discussion of comparable elements in other national programmes. The observations have been placed into two broad themes: 1. How to manage the integration? 2. How to handle uncertainties? No specific prescription was identified for either of these questions; rather a range of suggestions were noted based on experience. The appropriate solution will depend on the organisation, the site, the state of the programme, and other factors. A final observation from the working group was on the handling of evolution of the site with time. This topic incorporates aspects of both site integration and uncertainty management. Specifically, the integrated site description model (SDM) noted above represents a description of the site as it presently exists. This description takes into account the site history, but does not describe its evolution. The latter involves a number of uncertainties. This time evolution of the site can be described through Scenarios. The definition of scenarios, similar to the definition of the SDM, is an integrated and multidisciplinary process in order to ensure a self-consistent description. It will involve use of common assumptions. Since it involves the future and the associated uncertainties, it can be useful to draw on expert panels to help define the key assumptions and outlines for scenarios. (authors)

Integration of ecological-biological thresholds in conservation decision making.

Science.gov (United States)

Mavrommati, Georgia; Bithas, Kostas; Borsuk, Mark E; Howarth, Richard B

2016-12-01

In the Anthropocene, coupled human and natural systems dominate and only a few natural systems remain relatively unaffected by human influence. On the one hand, conservation criteria based on areas of minimal human impact are not relevant to much of the biosphere. On the other hand, conservation criteria based on economic factors are problematic with respect to their ability to arrive at operational indicators of well-being that can be applied in practice over multiple generations. Coupled human and natural systems are subject to economic development which, under current management structures, tends to affect natural systems and cross planetary boundaries. Hence, designing and applying conservation criteria applicable in real-world systems where human and natural systems need to interact and sustainably coexist is essential. By recognizing the criticality of satisfying basic needs as well as the great uncertainty over the needs and preferences of future generations, we sought to incorporate conservation criteria based on minimal human impact into economic evaluation. These criteria require the conservation of environmental conditions such that the opportunity for intergenerational welfare optimization is maintained. Toward this end, we propose the integration of ecological-biological thresholds into decision making and use as an example the planetary-boundaries approach. Both conservation scientists and economists must be involved in defining operational ecological-biological thresholds that can be incorporated into economic thinking and reflect the objectives of conservation, sustainability, and intergenerational welfare optimization. © 2016 Society for Conservation Biology.

A national comparison of biochemistry and molecular biology capstone experiences.

Science.gov (United States)

Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

2015-01-01

Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices. © 2015 The International Union of Biochemistry and Molecular Biology.

Integration of Heterogeneous Information Sources into a Knowledge Resource Management System for Lifelong Learning

NARCIS (Netherlands)

Demidova, Elena; Ternier, Stefaan; Olmedilla, Daniel; Duval, Erik; Dicerto, Michele; Stefanov, Krassen; Sacristán, Naiara

2007-01-01

Demidova, E., Ternier, S., Olmedilla, D., Duval, E., Dicerto, M., Stefanov, K., et al. (2007). Integration of Heterogeneous Information Sources into a Knowledge Resource Management System for Lifelong. TENCompetence Workshop on Service Oriented Approaches and Lifelong Competence Development

Bridging Professional Teacher Knowledge for Science and Literary Integration via Design-Based Research

Science.gov (United States)

Fazio, Xavier; Gallagher, Tiffany L.

2018-01-01

We offer insights for using design-based research (DBR) as a model for constructing professional development that supports curriculum and instructional knowledge regarding science and literacy integration. We spotlight experiences in the DBR process from data collected from a sample of four elementary teachers. Findings from interviews, focus…

Paradigms for biologically inspired design

DEFF Research Database (Denmark)

Lenau, T. A.; Metzea, A.-L.; Hesselberg, T.

2018-01-01

engineering, medical engineering, nanotechnology, photonics,environmental protection and agriculture. However, a major obstacle for the wider use of biologically inspired design isthe knowledge barrier that exist between the application engineers that have insight into how to design suitable productsand......Biologically inspired design is attracting increasing interest since it offers access to a huge biological repository of wellproven design principles that can be used for developing new and innovative products. Biological phenomena can inspireproduct innovation in as diverse areas as mechanical...... the biologists with detailed knowledge and experience in understanding how biological organisms function in theirenvironment. The biologically inspired design process can therefore be approached using different design paradigmsdepending on the dominant opportunities, challenges and knowledge characteristics...

Verbal Final Exam in Introductory Biology Yields Gains in Student Content Knowledge and Longitudinal Performance

Science.gov (United States)

Luckie, Douglas B.; Rivkin, Aaron M.; Aubry, Jacob R.; Marengo, Benjamin J.; Creech, Leah R.; Sweeder, Ryan D.

2013-01-01

We studied gains in student learning over eight semesters in which an introductory biology course curriculum was changed to include optional verbal final exams (VFs). Students could opt to demonstrate their mastery of course material via structured oral exams with the professor. In a quantitative assessment of cell biology content knowledge, students who passed the VF outscored their peers on the medical assessment test (MAT), an exam built with 40 Medical College Admissions Test (MCAT) questions (66.4% [n = 160] and 62% [n = 285], respectively; p students performed better on MCAT questions in all topic categories tested; the greatest gain occurred on the topic of cellular respiration. Because the VF focused on a conceptually parallel topic, photosynthesis, there may have been authentic knowledge transfer. In longitudinal tracking studies, passing the VF also correlated with higher performance in a range of upper-level science courses, with greatest significance in physiology, biochemistry, and organic chemistry. Participation had a wide range but not equal representation in academic standing, gender, and ethnicity. Yet students nearly unanimously (92%) valued the option. Our findings suggest oral exams at the introductory level may allow instructors to assess and aid students striving to achieve higher-level learning. PMID:24006399

The Relationships Between Epistemic Beliefs in Biology and Approaches to Learning Biology Among Biology-Major University Students in Taiwan

Science.gov (United States)

Lin, Yi-Chun; Liang, Jyh-Chong; Tsai, Chin-Chung

2012-12-01

The aim of this study was to investigate the relationships between students' epistemic beliefs in biology and their approaches to learning biology. To this end, two instruments, the epistemic beliefs in biology and the approaches to learning biology surveys, were developed and administered to 520 university biology students, respectively. By and large, it was found that the students reflected "mixed" motives in biology learning, while those who had more sophisticated epistemic beliefs tended to employ deep strategies. In addition, the results of paired t tests revealed that the female students were more likely to possess beliefs about biological knowledge residing in external authorities, to believe in a right answer, and to utilize rote learning as a learning strategy. Moreover, compared to juniors and seniors, freshmen and sophomores tended to hold less mature views on all factors of epistemic beliefs regarding biology. Another comparison indicated that theoretical biology students (e.g. students majoring in the Department of Biology) tended to have more mature beliefs in learning biology and more advanced strategies for biology learning than those students studying applied biology (e.g. in the Department of Biotechnology). Stepwise regression analysis, in general, indicated that students who valued the role of experiments and justify epistemic assumptions and knowledge claims based on evidence were more oriented towards having mixed motives and utilizing deep strategies to learn biology. In contrast, students who believed in the certainty of biological knowledge were more likely to adopt rote learning strategies and to aim to qualify in biology.

Key characteristics of knowledge transfer and exchange in healthcare: integrative literature review.

Science.gov (United States)

Pentland, Duncan; Forsyth, Kirsty; Maciver, Donald; Walsh, Mike; Murray, Richard; Irvine, Linda; Sikora, Simon

2011-07-01

This paper presents the results of a review of literature relating to knowledge transfer and exchange in healthcare. Treatment, planning and policy decisions in contemporary nursing and healthcare should be based on sound evidence wherever possible, but research knowledge remains generally underused. Knowledge transfer and exchange initiatives aim to facilitate the accessibility, application and production of evidence and may provide solutions to this challenge. This review was conducted to help inform the design and implementation of knowledge transfer and exchange activities for a large healthcare organization. Databases: ASSIA, Business Source Premier, CINAHL, PsychInfo, Medline and the Cochrane Database of Systematic Reviews. An integrative literature review was carried out including an extensive literature search. English language systematic reviews, literature reviews, primary quantitative and qualitative papers and grey literature of high relevance evaluating, describing or discussing knowledge transfer or exchange activities in healthcare were included for review (January 1990-September 2009). Thirty-three papers were reviewed (four systematic reviews, nine literature reviews, one environmental scan, nine empirical studies and ten case studies). Robust research into knowledge transfer and exchange in healthcare is limited. Analysis of a wide range of evidence indicates a number of commonly featured characteristics but further evaluation of these activities would benefit their application in facilitating evidence-based practice in nursing. © 2011 The Authors. Journal of Advanced Nursing © 2011 Blackwell Publishing Ltd.

Practice as source of learning and knowledge that comes from experience: what science and biology teachers say about it

Directory of Open Access Journals (Sweden)

Luciana M. Lunardi Campos

2001-01-01

Full Text Available This paper is about the possible knowledge that Science and Biology teachers may acquire form their daily work. Fourth three teachers were considered in this research and all belong to the Public School of the city of Botucatu, S.P. All of them were unanimous in stressing the importance of their professional activity as a meaningful aspect. They learned more about themselves, their methods, their employed resources and their pupils through it. Three dimensions can be pointed out here: personal, professional and pedagogical and it can be named nine aspects of the knowledge from experience. An organized and active knowledge may be achieved by reckoning the teacher as the main producer of knowledge about his occupation and assuming as well how important his practice and knowledge from experience are.

Sustainable Design Re-Examined: Integrated Approach to Knowledge Creation for Sustainable Interior Design

Science.gov (United States)

Lee, Young S.

2014-01-01

The article focuses on a systematic approach to the instructional framework to incorporate three aspects of sustainable design. It also aims to provide an instruction model for sustainable design stressing a collective effort to advance knowledge creation as a community. It develops a framework conjoining the concept of integrated process in…

An Integrative Model of Organizational Learning and Social Capital on Effective Knowledge Transfer and Perceived Organizational Performance

Science.gov (United States)

Rhodes, Jo; Lok, Peter; Hung, Richard Yu-Yuan; Fang, Shih-Chieh

2008-01-01

Purpose: The purpose of this paper is to set out to examine the relationships of organizational learning, social capital and the effectiveness of knowledge transfer and perceived organisational performance. Integrating organizational learning capability with social capital networks to shape a holistic knowledge sharing and management enterprise…

Interactive Knowledge Co-Production and Integration for Healthy Urban Development