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Sample records for incorporate biological knowledge

  1. Incorporating Biological Knowledge into Evaluation of Casual Regulatory Hypothesis

    NASA Technical Reports Server (NTRS)

    Chrisman, Lonnie; Langley, Pat; Bay, Stephen; Pohorille, Andrew; DeVincenzi, D. (Technical Monitor)

    2002-01-01

    Biological data can be scarce and costly to obtain. The small number of samples available typically limits statistical power and makes reliable inference of causal relations extremely difficult. However, we argue that statistical power can be increased substantially by incorporating prior knowledge and data from diverse sources. We present a Bayesian framework that combines information from different sources and we show empirically that this lets one make correct causal inferences with small sample sizes that otherwise would be impossible.

  2. The Incorporation and Abjection of Official Knowledge

    ERIC Educational Resources Information Center

    Kearl, Benjamin Kelsey

    2012-01-01

    In this essay, the author analyzes two theoretical perspectives--incorporation and abjection--that inform official knowledge generally and high school American history textbooks specifically. While contemporary textbooks increasingly depict the experiences of historically marginalized groups such as women, African Americans, Latinos, American…

  3. Information and Knowledge in Biology

    PubMed Central

    2007-01-01

    The second law of thermodynamics accounts for irreversibility of processes in the universe. As a statement about increasing disorder, it also plays a central role in creating order. Structuring is a way of how to increase the rate of dissipation of matter and energy. This is the reason why chemical reactions on Earth have produced a profusion of structures. Chemical structures with particularly high stability, maintained by continual dissipation, are designated, somewhat arbitrarily, as living systems. To preserve stability, organisms are unceasingly performing ontic work, assisted by epistemic work. Biological evolution is a progressing process of knowledge acquisition (cognition) and, correspondingly, of growth of complexity. The acquired knowledge represents epistemic complexity. Biological species are the main “bookkeepers” of acquired knowledge, with individual members of the species functioning as “explorers” of novelty. Science, a human species-specific mode of acquiring knowledge, abounds in metaphors no less than art. In the postgenomic era, the metaphor of information, along with the related metaphor of selfish genes, may need reconsideration and/or complementation. The world of great complexity, which is becoming the focus of studies of contemporary biology, may require—similarly as is the case of quantum physics—descriptions based on the principle of complementarity. Embodied knowledge, molecular engine, ontic and epistemic work, and triggering may become parts of a new conceptual armory. PMID:19516970

  4. Classifier Design Given an Uncertainty Class of Feature Distributions via Regularized Maximum Likelihood and the Incorporation of Biological Pathway Knowledge in Steady-State Phenotype Classification.

    PubMed

    Esfahani, Mohammad Shahrokh; Knight, Jason; Zollanvari, Amin; Yoon, Byung-Jun; Dougherty, Edward R

    2013-10-01

    Contemporary high-throughput technologies provide measurements of very large numbers of variables but often with very small sample sizes. This paper proposes an optimization-based paradigm for utilizing prior knowledge to design better performing classifiers when sample sizes are limited. We derive approximate expressions for the first and second moments of the true error rate of the proposed classifier under the assumption of two widely-used models for the uncertainty classes; ε-contamination and p-point classes. The applicability of the approximate expressions is discussed by defining the problem of finding optimal regularization parameters through minimizing the expected true error. Simulation results using the Zipf model show that the proposed paradigm yields improved classifiers that outperform traditional classifiers that use only training data. Our application of interest involves discrete gene regulatory networks possessing labeled steady-state distributions. Given prior operational knowledge of the process, our goal is to build a classifier that can accurately label future observations obtained in the steady state by utilizing both the available prior knowledge and the training data. We examine the proposed paradigm on networks containing NF-κB pathways, where it shows significant improvement in classifier performance over the classical data-only approach to classifier design. Companion website: http://gsp.tamu.edu/Publications/supplementary/shahrokh12a.

  5. Incorporating knowledge into commercially available systems.

    PubMed

    Roberts, J

    2000-01-01

    The ways in which a potential commercial 'user' treats different knowledge types are explored in this paper. The issues are dealt with by the pragmatism with which a marketing manager might evaluate an opportunity. Academics are typically motivated by drivers that are different from a commercial 'push'. Thus partnership is needed for a productive compromise; addressing questions such as why should academic institutions let commercial organizations have their intellectual capital. The paper considers issues of hand-over, product maintenance and a continued development partnership, especially in a volatile [Inter] net-based age.

  6. Incorporating World Knowledge to Document Clustering via Heterogeneous Information Networks.

    PubMed

    Wang, Chenguang; Song, Yangqiu; El-Kishky, Ahmed; Roth, Dan; Zhang, Ming; Han, Jiawei

    2015-08-01

    One of the key obstacles in making learning protocols realistic in applications is the need to supervise them, a costly process that often requires hiring domain experts. We consider the framework to use the world knowledge as indirect supervision. World knowledge is general-purpose knowledge, which is not designed for any specific domain. Then the key challenges are how to adapt the world knowledge to domains and how to represent it for learning. In this paper, we provide an example of using world knowledge for domain dependent document clustering. We provide three ways to specify the world knowledge to domains by resolving the ambiguity of the entities and their types, and represent the data with world knowledge as a heterogeneous information network. Then we propose a clustering algorithm that can cluster multiple types and incorporate the sub-type information as constraints. In the experiments, we use two existing knowledge bases as our sources of world knowledge. One is Freebase, which is collaboratively collected knowledge about entities and their organizations. The other is YAGO2, a knowledge base automatically extracted from Wikipedia and maps knowledge to the linguistic knowledge base, Word-Net. Experimental results on two text benchmark datasets (20newsgroups and RCV1) show that incorporating world knowledge as indirect supervision can significantly outperform the state-of-the-art clustering algorithms as well as clustering algorithms enhanced with world knowledge features.

  7. Incorporating World Knowledge to Document Clustering via Heterogeneous Information Networks

    PubMed Central

    Wang, Chenguang; Song, Yangqiu; El-Kishky, Ahmed; Roth, Dan; Zhang, Ming; Han, Jiawei

    2015-01-01

    One of the key obstacles in making learning protocols realistic in applications is the need to supervise them, a costly process that often requires hiring domain experts. We consider the framework to use the world knowledge as indirect supervision. World knowledge is general-purpose knowledge, which is not designed for any specific domain. Then the key challenges are how to adapt the world knowledge to domains and how to represent it for learning. In this paper, we provide an example of using world knowledge for domain dependent document clustering. We provide three ways to specify the world knowledge to domains by resolving the ambiguity of the entities and their types, and represent the data with world knowledge as a heterogeneous information network. Then we propose a clustering algorithm that can cluster multiple types and incorporate the sub-type information as constraints. In the experiments, we use two existing knowledge bases as our sources of world knowledge. One is Freebase, which is collaboratively collected knowledge about entities and their organizations. The other is YAGO2, a knowledge base automatically extracted from Wikipedia and maps knowledge to the linguistic knowledge base, Word-Net. Experimental results on two text benchmark datasets (20newsgroups and RCV1) show that incorporating world knowledge as indirect supervision can significantly outperform the state-of-the-art clustering algorithms as well as clustering algorithms enhanced with world knowledge features. PMID:26705504

  8. Incorporating Linguistic Knowledge for Learning Distributed Word Representations

    PubMed Central

    Wang, Yan; Liu, Zhiyuan; Sun, Maosong

    2015-01-01

    Combined with neural language models, distributed word representations achieve significant advantages in computational linguistics and text mining. Most existing models estimate distributed word vectors from large-scale data in an unsupervised fashion, which, however, do not take rich linguistic knowledge into consideration. Linguistic knowledge can be represented as either link-based knowledge or preference-based knowledge, and we propose knowledge regularized word representation models (KRWR) to incorporate these prior knowledge for learning distributed word representations. Experiment results demonstrate that our estimated word representation achieves better performance in task of semantic relatedness ranking. This indicates that our methods can efficiently encode both prior knowledge from knowledge bases and statistical knowledge from large-scale text corpora into a unified word representation model, which will benefit many tasks in text mining. PMID:25874581

  9. Incorporating linguistic knowledge for learning distributed word representations.

    PubMed

    Wang, Yan; Liu, Zhiyuan; Sun, Maosong

    2015-01-01

    Combined with neural language models, distributed word representations achieve significant advantages in computational linguistics and text mining. Most existing models estimate distributed word vectors from large-scale data in an unsupervised fashion, which, however, do not take rich linguistic knowledge into consideration. Linguistic knowledge can be represented as either link-based knowledge or preference-based knowledge, and we propose knowledge regularized word representation models (KRWR) to incorporate these prior knowledge for learning distributed word representations. Experiment results demonstrate that our estimated word representation achieves better performance in task of semantic relatedness ranking. This indicates that our methods can efficiently encode both prior knowledge from knowledge bases and statistical knowledge from large-scale text corpora into a unified word representation model, which will benefit many tasks in text mining.

  10. Synthetic biology between technoscience and thing knowledge.

    PubMed

    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.

  11. "Violent Intent Modeling: Incorporating Cultural Knowledge into the Analytical Process

    SciTech Connect

    Sanfilippo, Antonio P.; Nibbs, Faith G.

    2007-08-24

    While culture has a significant effect on the appropriate interpretation of textual data, the incorporation of cultural considerations into data transformations has not been systematic. Recognizing that the successful prevention of terrorist activities could hinge on the knowledge of the subcultures, Anthropologist and DHS intern Faith Nibbs has been addressing the need to incorporate cultural knowledge into the analytical process. In this Brown Bag she will present how cultural ideology is being used to understand how the rhetoric of group leaders influences the likelihood of their constituents to engage in violent or radicalized behavior, and how violent intent modeling can benefit from understanding that process.

  12. Synthetic biology and the ethics of knowledge

    PubMed Central

    Douglas, Thomas; Savulescu, Julian

    2011-01-01

    Synthetic biologists aim to generate biological organisms according to rational design principles. Their work may have many beneficial applications, but it also raises potentially serious ethical concerns. In this article, we consider what attention the discipline demands from bioethicists. We argue that the most important issue for ethicists to examine is the risk that knowledge from synthetic biology will be misused, for example, in biological terrorism or warfare. To adequately address this concern, bioethics will need to broaden its scope, contemplating not just the means by which scientific knowledge is produced, but also what kinds of knowledge should be sought and disseminated. PMID:20935316

  13. Advancing landscape change research through the incorporation of Inupiaq knowledge

    USGS Publications Warehouse

    Eisner, Wendy R.; Cuomo, Chris J.; Hinkel, Kenneth M.; Jones, Benjamin M.; Brower, Ronald H.

    2009-01-01

    Indigenous knowledge is a valuable but under-used source of information relevant to landscape change research. We interviewed Iñupiat elders, hunters, and other knowledge-holders in the villages of Barrow and Atqasuk on the western Arctic Coastal Plain of northern Alaska to gain further insight into the processes governing the ubiquitous lakes and the dynamics of landscape change in this region of continuous permafrost. The interviews provided a suite of information related to lakes and associated drained lake basins, as well as knowledge on landforms, environmental change, human events, and other phenomena. We were able to corroborate many observations independently and verify the timing of several large and significant lake drainage events using either aerial photography or remotely sensed time series. Data collected have been incorporated into a geodatabase to develop a multi-layer Geographic Information System that will be useful for local and scientific communities. This research demonstrates that indigenous knowledge can reveal a new understanding of landscape changes on the Arctic Coastal Plain in general and on lake processes in particular. We advocate ongoing, community-oriented research throughout the Arctic as a means of assessing and responding to the consequences of rapid environmental change.

  14. On the Limitations of Biological Knowledge

    PubMed Central

    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

  15. Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

    NASA Astrophysics Data System (ADS)

    Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

    2006-12-01

    Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

  16. The Notion of Scientific Knowledge in Biology

    NASA Astrophysics Data System (ADS)

    Morante, Silvia; Rossi, Giancarlo

    2016-03-01

    The purpose of this work is to reconsider and critically discuss the conceptual foundations of modern biology and bio-sciences in general, and provide an epistemological guideline to help framing the teaching of these disciplines and enhancing the quality of their presentation in High School, Master and Ph.D. courses. After discussing the methodological problems that arise in trying to construct a sensible and useful scientific approach applicable to the study of living systems, we illustrate what are the general requirements that a workable scheme of investigation should meet to comply with the principles of the Galilean method. The amazing success of basic physics, the Galilean science of election, can be traced back to the development of a radically " reductionistic" approach in the interpretation of experiments and a systematic procedure tailored on the paradigm of " falsifiability" aimed at consistently incorporating new information into extended models/theories. The development of bio-sciences seems to fit with neither reductionism (the deeper is the level of description of a biological phenomenon the more difficult looks finding general and simple laws), nor falsifiability (not always experiments provide a yes-or-no answer). Should we conclude that biology is not a science in the Galilean sense? We want to show that this is not so. Rather in the study of living systems, the novel interpretative paradigm of " complexity" has been developed that, without ever conflicting with the basic principles of physics, allows organizing ideas, conceiving new models and understanding the puzzling lack of reproducibility that seems to affect experiments in biology and in other modern areas of investigation. In the delicate task of conveying scientific concepts and principles to students as well as in popularising bio-sciences to a wider audience, it is of the utmost importance for the success of the process of learning to highlight the internal logical consistency of

  17. Ontological knowledge structure of intuitive biology

    NASA Astrophysics Data System (ADS)

    Martin, Suzanne Michele

    It has become increasingly important for individuals to understand infections disease, as there has been a tremendous rise in viral and bacterial disease. This research examines systematic misconceptions regarding the characteristics of viruses and bacteria present in individuals previously educated in biological sciences at a college level. 90 pre-nursing students were administered the Knowledge Acquisition Device (KAD) which consists of 100 True/False items that included statements about the possible attributes of four entities: bacteria, virus, amoeba, and protein. Thirty pre-nursing students, who incorrectly stated that viruses were alive, were randomly assigned to three conditions. (1) exposed to information about the ontological nature of viruses, (2) Information about viruses, (3) control. In the condition that addressed the ontological nature of a virus, all of those participants were able to classify viruses correctly as not alive; however any items that required inferences, such as viruses come in male and female forms or viruses breed with each other to make baby viruses were still incorrectly answered by all conditions in the posttest. It appears that functional knowledge, ex. If a virus is alive or dead, or how it is structured, is not enough for an individual to have a full and accurate understanding of viruses. Ontological knowledge information may alter the functional knowledge but underlying inferences remain systematically incorrect.

  18. Biological evaluation of nanosilver incorporated cellulose pulp for hygiene products.

    PubMed

    Kavitha Sankar, P C; Ramakrishnan, Reshmi; Rosemary, M J

    2016-04-01

    Cellulose pulp has a visible market share in personal hygiene products such as sanitary napkins and baby diapers. However it offers good surface for growth of microorganisms. Huge amount of research is going on in developing hygiene products that do not initiate microbial growth. The objective of the present work is to produce antibacterial cellulose pulp by depositing silver nanopowder on the cellulose fiber. The silver nanoparticles used were of less than 100 nm in size and were characterised using transmission electron microscopy and X-ray powder diffraction studies. Antibacterial activity of the functionalized cellulose pulp was proved by JIS L 1902 method. The in-vitro cytotoxicity, in-vivo vaginal irritation and intracutaneous reactivity studies were done with silver nanopowder incorporated cellulose pulp for introducing a new value added product to the market. Cytotoxicity evaluation suggested that the silver nanoparticle incorporated cellulose pulp is non-cytotoxic. No irritation and skin sensitization were identified in animals tested with specific extracts prepared from the test material in the in-vivo experiments. The results indicated that the silver nanopowder incorporated cellulose pulp meets the requirements of the standard practices recommended for evaluating the biological reactivity and has good biocompatibility, hence can be classified as a safe hygiene product.

  19. Incorporating New Information Into One's Existing World Knowledge.

    ERIC Educational Resources Information Center

    Potts, George R.

    It is reasonable to assume that information such as the fact that "a beaver is larger than a mouse" is part of the average college student's generalized world knowledge. The present experiments examine the processes whereby new information is integrated with this type of generalized world knowledge. During the study phase of these experiments,…

  20. Product Aspect Clustering by Incorporating Background Knowledge for Opinion Mining

    PubMed Central

    Chen, Yiheng; Zhao, Yanyan; Qin, Bing; Liu, Ting

    2016-01-01

    Product aspect recognition is a key task in fine-grained opinion mining. Current methods primarily focus on the extraction of aspects from the product reviews. However, it is also important to cluster synonymous extracted aspects into the same category. In this paper, we focus on the problem of product aspect clustering. The primary challenge is to properly cluster and generalize aspects that have similar meanings but different representations. To address this problem, we learn two types of background knowledge for each extracted aspect based on two types of effective aspect relations: relevant aspect relations and irrelevant aspect relations, which describe two different types of relationships between two aspects. Based on these two types of relationships, we can assign many relevant and irrelevant aspects into two different sets as the background knowledge to describe each product aspect. To obtain abundant background knowledge for each product aspect, we can enrich the available information with background knowledge from the Web. Then, we design a hierarchical clustering algorithm to cluster these aspects into different groups, in which aspect similarity is computed using the relevant and irrelevant aspect sets for each product aspect. Experimental results obtained in both camera and mobile phone domains demonstrate that the proposed product aspect clustering method based on two types of background knowledge performs better than the baseline approach without the use of background knowledge. Moreover, the experimental results also indicate that expanding the available background knowledge using the Web is feasible. PMID:27561001

  1. The Cultural and Social Incorporation of Sociological Knowledge.

    ERIC Educational Resources Information Center

    Merton, Robert K.; Wolfe, Alan

    1995-01-01

    Explores the extent that sociological concepts have been incorporated into the vernacular of U.S. society and the impact of sociological techniques on politics and society. Study tracked frequency of selected sociological terms in the popular press. Identifies a danger of sociology becoming too popular and losing its credibility. (MJP)

  2. Creating a knowledge base of biological research papers

    SciTech Connect

    Hafner, C.D.; Baclawski, K.; Futrelle, R.P.; Fridman, N.

    1994-12-31

    Intelligent text-oriented tools for representing and searching the biological research literature are being developed, which combine object-oriented databases with artificial intelligence techniques to create a richly structured knowledge base of Materials and Methods sections of biological research papers. A knowledge model of experimental processes, biological and chemical substances, and analytical techniques is described, based on the representation techniques of taxonomic semantic nets and knowledge frames. Two approaches to populating the knowledge base with the contents of biological research papers are described: natural language processing and an interactive knowledge definition tool.

  3. Development of a Knowledge Base for Incorporating Technology into Courses

    ERIC Educational Resources Information Center

    Rath, Logan

    2013-01-01

    This article discusses a project resulting from the request of a group of faculty at The College at Brockport to create a website for best practices in teaching and technology. The project evolved into a knowledge base powered by WordPress. Installation and configuration of WordPress resulted in the creation of custom taxonomies and post types,…

  4. Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic.

    PubMed

    Lee, B; Yen, J; Yang, L; Liao, J C

    1999-03-20

    Modeling of metabolic pathway dynamics requires detailed kinetic equations at the enzyme level. In particular, the kinetic equations must account for metabolite effectors that contribute significantly to the pathway regulation in vivo. Unfortunately, most kinetic rate laws available in the literature do not consider all the effectors simultaneously, and much kinetic information exists in a qualitative or semiquantitative form. In this article, we present a strategy to incorporate such information into the kinetic equation. This strategy uses fuzzy logic-based factors to modify algebraic rate laws that account for partial kinetic characteristics. The parameters introduced by the fuzzy factors are then optimized by use of a hybrid of simplex and genetic algorithms. The resulting model provides a flexible form that can simulate various kinetic behaviors. Such kinetic models are suitable for pathway modeling without complete enzyme mechanisms. Three enzymes in Escherichia coli central metabolism are used as examples: phosphoenolpyruvate carboxylase; phosphoenolpyruvate carboxykinase; and pyruvate kinase I. Results show that, with fuzzy logic-augmented models, the kinetic data can be much better described. In particular, complex behavior, such as allosteric inhibition, can be captured using fuzzy rules. The resulting models, even though they do not provide additional physical meaning in enzyme mechanisms, allow the model to incorporate semiquantitative information in metabolic pathway models.

  5. Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources.

    PubMed

    Praveen, Paurush; Fröhlich, Holger

    2013-01-01

    Inferring regulatory networks from experimental data via probabilistic graphical models is a popular framework to gain insights into biological systems. However, the inherent noise in experimental data coupled with a limited sample size reduces the performance of network reverse engineering. Prior knowledge from existing sources of biological information can address this low signal to noise problem by biasing the network inference towards biologically plausible network structures. Although integrating various sources of information is desirable, their heterogeneous nature makes this task challenging. We propose two computational methods to incorporate various information sources into a probabilistic consensus structure prior to be used in graphical model inference. Our first model, called Latent Factor Model (LFM), assumes a high degree of correlation among external information sources and reconstructs a hidden variable as a common source in a Bayesian manner. The second model, a Noisy-OR, picks up the strongest support for an interaction among information sources in a probabilistic fashion. Our extensive computational studies on KEGG signaling pathways as well as on gene expression data from breast cancer and yeast heat shock response reveal that both approaches can significantly enhance the reconstruction accuracy of Bayesian Networks compared to other competing methods as well as to the situation without any prior. Our framework allows for using diverse information sources, like pathway databases, GO terms and protein domain data, etc. and is flexible enough to integrate new sources, if available.

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

    ERIC Educational Resources Information Center

    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…

  7. Preservice Biology Teachers' Professional Knowledge: Structure and Learning Opportunities

    ERIC Educational Resources Information Center

    Großschedl, Jörg; Harms, Ute; Kleickmann, Thilo; Glowinski, Ingrid

    2015-01-01

    What learning opportunities in higher education promote the development of content knowledge (CK), pedagogical content knowledge (PCK), and pedagogical knowledge (PK)? In order to investigate this question, a cross-sectional study with a total of 274 German preservice biology teachers (21.5% male, average age 22.8 years) was conducted in German…

  8. An environment for knowledge discovery in biology.

    PubMed

    Barrera, Junior; Cesar, Roberto M; Ferreira, João E; Gubitoso, Marco D

    2004-07-01

    This paper describes a data mining environment for knowledge discovery in bioinformatics applications. The system has a generic kernel that implements the mining functions to be applied to input primary databases, with a warehouse architecture, of biomedical information. Both supervised and unsupervised classification can be implemented within the kernel and applied to data extracted from the primary database, with the results being suitably stored in a complex object database for knowledge discovery. The kernel also includes a specific high-performance library that allows designing and applying the mining functions in parallel machines. The experimental results obtained by the application of the kernel functions are reported.

  9. The Notion of Scientific Knowledge in Biology

    ERIC Educational Resources Information Center

    Morante, Silvia; Rossi, Giancarlo

    2016-01-01

    The purpose of this work is to reconsider and critically discuss the conceptual foundations of modern biology and bio-sciences in general, and provide an epistemological guideline to help framing the teaching of these disciplines and enhancing the quality of their presentation in High School, Master and Ph.D. courses. After discussing the…

  10. Biologically Plausible, Human-Scale Knowledge Representation.

    PubMed

    Crawford, Eric; Gingerich, Matthew; Eliasmith, Chris

    2016-05-01

    Several approaches to implementing symbol-like representations in neurally plausible models have been proposed. These approaches include binding through synchrony (Shastri & Ajjanagadde, ), "mesh" binding (van der Velde & de Kamps, ), and conjunctive binding (Smolensky, ). Recent theoretical work has suggested that most of these methods will not scale well, that is, that they cannot encode structured representations using any of the tens of thousands of terms in the adult lexicon without making implausible resource assumptions. Here, we empirically demonstrate that the biologically plausible structured representations employed in the Semantic Pointer Architecture (SPA) approach to modeling cognition (Eliasmith, ) do scale appropriately. Specifically, we construct a spiking neural network of about 2.5 million neurons that employs semantic pointers to successfully encode and decode the main lexical relations in WordNet, which has over 100,000 terms. In addition, we show that the same representations can be employed to construct recursively structured sentences consisting of arbitrary WordNet concepts, while preserving the original lexical structure. We argue that these results suggest that semantic pointers are uniquely well-suited to providing a biologically plausible account of the structured representations that underwrite human cognition.

  11. Direct Experience with Nature and the Development of Biological Knowledge

    ERIC Educational Resources Information Center

    Longbottom, Sarah E.; Slaughter, Virginia

    2016-01-01

    Research Findings: An emerging consensus is that casual, direct contact with nature influences the development of children's biological knowledge. Here we review the existing literature on this topic, focusing on the effects of (a) rural versus urban rearing environments and (b) pet ownership and care on children's biological concepts and…

  12. Visualising Knowledge Structures in Biology: Discipline, Curriculum and Student Understanding

    ERIC Educational Resources Information Center

    Kinchin, Ian M.

    2011-01-01

    Concept mapping is discussed as a tool for the visualisation of knowledge structures that can be exploited within biological education. Application of this tool makes it possible to relate the structure of the curriculum to the structure of the discipline, in order to support the development of robust student knowledge structures in ways that…

  13. Visualization Skills and Their Incorporation in Biology Curriculum

    ERIC Educational Resources Information Center

    Osodo, J.; Amory, A.; Graham-Jolly, M.; Indoshi, F. C.

    2010-01-01

    Many graduates of various levels and disciplines appear unable to practically apply their knowledge in problem solving situations. However, few education systems are adopting modern education practices such as visualization skills that intrinsically motivate and engage learners and are at the same time flexible enough to consider students'…

  14. Silicon Incorporated Morpholine Antifungals: Design, Synthesis, and Biological Evaluation

    PubMed Central

    2015-01-01

    Known morpholine class antifungals (fenpropimorph, fenpropidin, and amorolfine) were synthetically modified through silicon incorporation to have 15 sila-analogues. Twelve sila-analogues exhibited potent antifungal activity against different human fungal pathogens such as Candida albicans, Candida glabrata, Candida tropicalis, Cryptococcus neoformans, and Aspergillus niger. Sila-analogue 24 (fenpropimorph analogue) was the best in our hands, which showed superior fungicidal potential than fenpropidin, fenpropimorph, and amorolfine. The mode of action of sila-analogues was similar to morpholines, i.e., inhibition of sterol reductase and sterol isomerase enzymes of ergosterol synthesis pathway. PMID:26617963

  15. Integrative Systems Biology for Data Driven Knowledge Discovery

    PubMed Central

    Greene, Casey S.; Troyanskaya, Olga G.

    2015-01-01

    Integrative systems biology is an approach that brings together diverse high throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost effective manner. Using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of yet unknown components of a system of interest and how its malfunction leads to disease. PMID:21044756

  16. College biology students' conceptions related to the nature of biological knowledge: Implications for conceptual change

    NASA Astrophysics Data System (ADS)

    Ameny, Gloria Millie Apio

    Adequate understanding of the nature of science is a major goal of science education. Understanding of the evolutionary nature of biological knowledge is a means of reinforcing biology students' understanding of the nature of science. It provides students with the philosophical basis, explanatory ideals, and subject matter-specific views of what counts as a scientifically-acceptable biological explanation. This study examined 121 college introductory biology and advanced zoology students for their conceptions related to the nature of biological knowledge. A 60-item Likert-scale questionnaire called the Nature of Biological Knowledge Scale and student interviews were used as complementary research instruments. Firstly, the study showed that 80--100% of college biology students have an adequate understanding of scientific methods, and that a similar percentage of students had learned the theory of evolution by natural selection in their biology courses. Secondly, the study showed that at least 60--80% of the students do not understand the importance of evolution in biological knowledge. Yet the study revealed that a statistically significant positive correlation exist among students' understanding of natural selection, divergent, and convergent evolutionary models. Thirdly, the study showed that about 20--58% of college students hold prescientific conceptions which, in part, are responsible for students' lack of understanding of the nature of biological knowledge. A statistically significant negative correlation was found among students' prescientific conceptions about basis of biological knowledge and nature of change in biological processes, and their understanding of natural selection and evolutionary models. However, the study showed that students' characteristics such as gender, age, major, or years in college have no statistically significant influence on students' conceptions related to the nature of biological knowledge. Only students' depth of biological

  17. Preservice Biology Teachers' Professional Knowledge: Structure and Learning Opportunities

    NASA Astrophysics Data System (ADS)

    Großschedl, Jörg; Harms, Ute; Kleickmann, Thilo; Glowinski, Ingrid

    2015-04-01

    What learning opportunities in higher education promote the development of content knowledge (CK), pedagogical content knowledge (PCK), and pedagogical knowledge (PK)? In order to investigate this question, a cross-sectional study with a total of 274 German preservice biology teachers (21.5 % male, average age 22.8 years) was conducted in German universities. Preservice teachers were recruited via announcements in teacher education courses. The participation rate amounted to 45 %. Results indicate that CK, PCK, and PK are three unique and separable, but correlated domains of knowledge. Regression analyses show how particular learning opportunities are related to preservice biology teachers' CK, PCK, and PK. Both (a) the type of teacher education program and (b) the period of university studies are related to CK and PCK. Moreover, (c) additional subjects studied and (d) teaching experience seem relevant for PCK development. Conclusions for teacher education are drawn.

  18. Persulfides: Current Knowledge and Challenges in Chemistry and Chemical Biology

    PubMed Central

    Park, Chung-Min; Weerasinghe, Laksiri; Day, Jacob J.; Fukuto, Jon M.; Xian, Ming

    2015-01-01

    Recent studies conducted in hydrogen sulfide (H2S) signaling have revealed potential importance of persulfides (RSSH) in redox biology. The inherent instability of RSSH makes these species difficult to study and sometimes controversial results are reported. In this review article we summarize known knowledge about both small molecule persulfides and protein persulfides. Their fundamental physical and chemical properties such as preparation/formation and reactivity are discussed. The biological implications of persulfides and their detection methods are also discussed. PMID:25969163

  19. Incorporating Molecular and Cellular Biology into a Chemical Engineering Degree Program

    ERIC Educational Resources Information Center

    O'Connor, Kim C.

    2005-01-01

    There is a growing need for a workforce that can apply engineering principles to molecular based discovery and product development in the biological sciences. To this end, Tulane University established a degree program that incorporates molecular and cellular biology into the chemical engineering curriculum. In celebration of the tenth anniversary…

  20. The Regional Advisory Councils: what is their potential to incorporate stakeholder knowledge into fisheries governance?

    PubMed

    Linke, Sebastian; Dreyer, Marion; Sellke, Piet

    2011-03-01

    The protection of the Baltic Sea ecosystem is exacerbated by the social, environmental and economic complexities of governing European fisheries. Increased stakeholder participation and knowledge integration are suggested to improve the EU's Common Fisheries Policy (CFP), suffering from legitimacy, credibility and compliance problems. As a result, the CFP was revised in 2002 to involve fisheries representatives, NGOs and other stakeholders through so called Regional Advisory Councils (RACs) in the policy process. We address the RAC's task to incorporate stakeholder knowledge into the EU's fisheries governance system in empirical and theoretical perspectives. Drawing on a four-stage governance concept we subsequently suggest that a basic problem is a mismatch between participation purpose (knowledge inclusion) and the governance stage at which RACs are formally positioned (evaluation of management proposals). We conclude that, if the aim is to broaden the knowledge base of fisheries management, stakeholders need to be included earlier in the governance process.

  1. Knowledge representation and data mining for biological imaging.

    PubMed

    Ahmed, Wamiq M

    2008-01-01

    Biological and pharmaceutical research relies heavily on microscopically imaging cell populations for understanding their structure and function. Much work has been done on automated analysis of biological images, but image analysis tools are generally focused only on extracting quantitative information for validating a particular hypothesis. Images contain much more information than is normally required for testing individual hypotheses. The lack of symbolic knowledge representation schemes for representing semantic image information and the absence of knowledge mining tools are the biggest obstacles in utilizing the full information content of these images. In this paper we first present a graph-based scheme for integrated representation of semantic biological knowledge contained in cellular images acquired in spatial, spectral, and temporal dimensions. We then present a spatio-temporal knowledge mining framework for extracting non-trivial and previously unknown association rules from image data sets. This mechanism can change the role of biological imaging from a tool used to validate hypotheses to one used for automatically generating new hypotheses. Results for an apoptosis screen are also presented.

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

    ERIC Educational Resources Information Center

    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…

  3. Using a Module-Based Laboratory to Incorporate Inquiry into a Large Cell Biology Course

    ERIC Educational Resources Information Center

    Howard, David R.; Miskowski, Jennifer A.

    2005-01-01

    Because cell biology has rapidly increased in breadth and depth, instructors are challenged not only to provide undergraduate science students with a strong, up-to-date foundation of knowledge, but also to engage them in the scientific process. To these ends, revision of the Cell Biology Lab course at the University of Wisconsin-La Crosse was…

  4. Nature or Nurture? A Lesson Incorporating Students' Interests in a High-School Biology Class

    ERIC Educational Resources Information Center

    Hagay, Galit; Peleg, Ran; Laslo, Esti; Baram-Tsabari, Ayelet

    2013-01-01

    We present a case study of a lesson that incorporates high school students' interests in heredity alongside the requirements of the curriculum. This was done by collecting students' questions in advance and inserting them in strategic places in the biology curriculum, thus creating a "shadow curriculum". The idea underlying the lesson…

  5. Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 2: Peptide Identification via Molecular Mass Determination

    ERIC Educational Resources Information Center

    Arnquist, Isaac J.; Beussman, Douglas J.

    2009-01-01

    Mass spectrometry has become a routine analytical tool in the undergraduate curriculum in the form of GC-MS. While relatively few undergraduate programs have incorporated biological mass spectrometry into their programs, the importance of these techniques, as demonstrated by their recognition with the 2002 Nobel Prize, will hopefully lead to…

  6. Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology (Final Report)

    EPA Science Inventory

    EPA announced the release of the final report, Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology. This report describes new approaches that are faster, less resource intensive, and more robust that can help ...

  7. A Shadow Curriculum: Incorporating Students' Interests into the Formal Biology Curriculum

    ERIC Educational Resources Information Center

    Hagay, Galit; Baram-Tsabari, Ayelet

    2011-01-01

    Students have been largely ignored in discussions about how best to teach science, and many students feel the curriculum is detached from their lives and interests. This article presents a strategy for incorporating students' interests into the formal Biology curriculum, by drawing on the political meaning of "shadow government" as alternative…

  8. Improving protein-protein interaction article classification using biological domain knowledge.

    PubMed

    Chen, Yifei; Guo, Hongjian; Liu, Feng; Manderick, Bernard

    2015-01-01

    Interaction Article Classification (IAC) is a specific text classification application in biological domain that tries to find out which articles describe Protein-Protein Interactions (PPIs) to help extract PPIs from biological literature more efficiently. However, the existing text representation and feature weighting schemes commonly used for text classification are not well suited for IAC. We capture and utilise biological domain knowledge, i.e. gene mentions also known as protein or gene names in the articles, to address the problem. We put forward a new gene mention order-based approach that highlights the important role of gene mentions to represent the texts. Furthermore, we also incorporate the information concerning gene mentions into a novel feature weighting scheme called Gene Mention-based Term Frequency (GMTF). By conducting experiments, we show that using the proposed representation and weighting schemes, our Interaction Article Classifier (IACer) performs better than other leading systems for the moment.

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

    PubMed Central

    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

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

    PubMed

    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 (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.

  11. Evolving Strategies for the Incorporation of Bioinformatics Within the Undergraduate Cell Biology Curriculum

    PubMed Central

    Honts, Jerry E.

    2003-01-01

    Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in three courses, beginning with an introductory course in cell biology. The exercises and projects that were used to help students develop literacy in bioinformatics are described. In a recently offered course in bioinformatics, students developed their own simple sequence analysis tool using the Perl programming language. These experiences are described from the point of view of the instructor as well as the students. A preliminary assessment has been made of the degree to which students had developed a working knowledge of bioinformatics concepts and methods. Finally, some conclusions have been drawn from these courses that may be helpful to instructors wishing to introduce bioinformatics within the undergraduate biology curriculum. PMID:14673489

  12. Efficient fuzzy Bayesian inference algorithms for incorporating expert knowledge in parameter estimation

    NASA Astrophysics Data System (ADS)

    Rajabi, Mohammad Mahdi; Ataie-Ashtiani, Behzad

    2016-05-01

    Bayesian inference has traditionally been conceived as the proper framework for the formal incorporation of expert knowledge in parameter estimation of groundwater models. However, conventional Bayesian inference is incapable of taking into account the imprecision essentially embedded in expert provided information. In order to solve this problem, a number of extensions to conventional Bayesian inference have been introduced in recent years. One of these extensions is 'fuzzy Bayesian inference' which is the result of integrating fuzzy techniques into Bayesian statistics. Fuzzy Bayesian inference has a number of desirable features which makes it an attractive approach for incorporating expert knowledge in the parameter estimation process of groundwater models: (1) it is well adapted to the nature of expert provided information, (2) it allows to distinguishably model both uncertainty and imprecision, and (3) it presents a framework for fusing expert provided information regarding the various inputs of the Bayesian inference algorithm. However an important obstacle in employing fuzzy Bayesian inference in groundwater numerical modeling applications is the computational burden, as the required number of numerical model simulations often becomes extremely exhaustive and often computationally infeasible. In this paper, a novel approach of accelerating the fuzzy Bayesian inference algorithm is proposed which is based on using approximate posterior distributions derived from surrogate modeling, as a screening tool in the computations. The proposed approach is first applied to a synthetic test case of seawater intrusion (SWI) in a coastal aquifer. It is shown that for this synthetic test case, the proposed approach decreases the number of required numerical simulations by an order of magnitude. Then the proposed approach is applied to a real-world test case involving three-dimensional numerical modeling of SWI in Kish Island, located in the Persian Gulf. An expert

  13. Bayesian network prior: network analysis of biological data using external knowledge

    PubMed Central

    Isci, Senol; Dogan, Haluk; Ozturk, Cengizhan; Otu, Hasan H.

    2014-01-01

    Motivation: Reverse engineering GI networks from experimental data is a challenging task due to the complex nature of the networks and the noise inherent in the data. One way to overcome these hurdles would be incorporating the vast amounts of external biological knowledge when building interaction networks. We propose a framework where GI networks are learned from experimental data using Bayesian networks (BNs) and the incorporation of external knowledge is also done via a BN that we call Bayesian Network Prior (BNP). BNP depicts the relation between various evidence types that contribute to the event ‘gene interaction’ and is used to calculate the probability of a candidate graph (G) in the structure learning process. Results: Our simulation results on synthetic, simulated and real biological data show that the proposed approach can identify the underlying interaction network with high accuracy even when the prior information is distorted and outperforms existing methods. Availability: Accompanying BNP software package is freely available for academic use at http://bioe.bilgi.edu.tr/BNP. Contact: hasan.otu@bilgi.edu.tr Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:24215027

  14. New biological reference materials - in vivo incorporated toxic metals in water hyacinth tissues

    SciTech Connect

    Austin, J.R.; Simon, S.J.; Williams, L.R.; Beckert, W.F.

    1985-06-01

    The purpose of this study was to demonstrate that high-quality reference materials, containing high levels of multiple toxic elements, can be produced with in vivo incorporation procedures. The approach taken was to produce water hyacinth tissue materials - leaves and stems containing high levels of arsenic, cadmium, lead, and mercury - as follows: apply a hydroponic feeding procedure for the in vivo incorporation of toxic elements into water hyacinths; dry, blend, and homogenize the plant materials and determine the levels of the incorporated elements and the homogeneity of the generated plant material; demonstrate that low-level control materials can be successfully blended with high-level materials to yield a homogeneous material with intermediate toxicant levels; evaluate the precision of the analytical methods used to determine toxic element levels in the materials; and evaluate the stability of the resulting materials. Sufficient quantities of the parent materials were produced so that characterized reference materials can now be made available on request. Levels of the toxic elements incorporated in water hyacinth leaves were 100, 300, 60, and 27 times the levels present in the control leaves for arsenic, cadmium, lead, and mercury, respectively. Overall precision of sampling, subsampling, and digestion, and chemical analysis of the treated materials, ranged from 3 to 10% relative standard deviation and was generally comparable to that of three NBS biological reference materials tested. 3 references, 1 figure, 4 tables.

  15. Ways of incorporating photographic images in learning and assessing high school biology: A study of visual perception and visual cognition

    NASA Astrophysics Data System (ADS)

    Nixon, Brenda Chaumont

    This study evaluated the cognitive benefits and costs of incorporating biology-textbook and student-generated photographic images into the learning and assessment processes within a 10th grade biology classroom. The study implemented Wandersee's (2000) 20-Q Model of Image-Based Biology Test-Item Design (20-Q Model) to explore the use of photographic images to assess students' understanding of complex biological processes. A thorough review of the students' textbook using ScaleMaster R with PC Interface was also conducted. The photographs, diagrams, and other representations found in the textbook were measured to determine the percentage of each graphic depicted in the book and comparisons were made to the text. The theoretical framework that guided the research included Human Constructivist tenets espoused by Mintzes, Wandersee and Novak (2000). Physiological and cognitive factors of images and image-based learning as described by Robin (1992), Solso (1997) and Wandersee (2000) were examined. Qualitative case study design presented by Yin (1994), Denzin and Lincoln (1994) was applied and data were collected through interviews, observations, student activities, student and school artifacts and Scale Master IIRTM measurements. The results of the study indicate that although 24% of the high school biology textbook is devoted to photographic images which contribute significantly to textbook cost, the teacher and students paid little attention to photographic images other than as aesthetic elements for creating biological ambiance, wasting valuable opportunities for learning. The analysis of the photographs corroborated findings published by the Association American Association for the Advancement of Science that indicated "While most of the books are lavishly illustrated, these representations are rarely helpful, because they are too abstract, needlessly complicated, or inadequately explained" (Roseman, 2000, p. 2). The findings also indicate that applying the 20-Q

  16. Exploring Biology Teachers' Pedagogical Content Knowledge in the Teaching of Genetics in Swaziland Science Classrooms

    ERIC Educational Resources Information Center

    Mthethwa-Kunene, Eunice; Onwu, Gilbert Oke; de Villiers, Rian

    2015-01-01

    This study explored the pedagogical content knowledge (PCK) and its development of four experienced biology teachers in the context of teaching school genetics. PCK was defined in terms of teacher content knowledge, pedagogical knowledge and knowledge of students' preconceptions and learning difficulties. Data sources of teacher knowledge base…

  17. A Computationally Efficient, Exploratory Approach to Brain Connectivity Incorporating False Discovery Rate Control, A Priori Knowledge, and Group Inference

    PubMed Central

    Liu, Aiping; Li, Junning; Wang, Z. Jane; McKeown, Martin J.

    2012-01-01

    Graphical models appear well suited for inferring brain connectivity from fMRI data, as they can distinguish between direct and indirect brain connectivity. Nevertheless, biological interpretation requires not only that the multivariate time series are adequately modeled, but also that there is accurate error-control of the inferred edges. The PCfdr algorithm, which was developed by Li and Wang, was to provide a computationally efficient means to control the false discovery rate (FDR) of computed edges asymptotically. The original PCfdr algorithm was unable to accommodate a priori information about connectivity and was designed to infer connectivity from a single subject rather than a group of subjects. Here we extend the original PCfdr algorithm and propose a multisubject, error-rate-controlled brain connectivity modeling approach that allows incorporation of prior knowledge of connectivity. In simulations, we show that the two proposed extensions can still control the FDR around or below a specified threshold. When the proposed approach is applied to fMRI data in a Parkinson's disease study, we find robust group evidence of the disease-related changes, the compensatory changes, and the normalizing effect of L-dopa medication. The proposed method provides a robust, accurate, and practical method for the assessment of brain connectivity patterns from functional neuroimaging data. PMID:23251232

  18. Tissue lead distribution and hematologic effects in American kestrels (Falco sparverius) fed biologically incorporated lead

    USGS Publications Warehouse

    Custer, T.W.; Franson, J.C.; Pattee, O.H.

    1984-01-01

    American kestrels were fed a diet containing 0.5, 120, 212, and 448 ppm (dry wt) biologically incorporated lead (Pb) for 60 days. The diet consisted of homogenized 4-wk-old cockerels raised on feed mixed with and without lead. No kestrels died and weights did not differ among treatment groups. The control group (0.5 ppm Pb) had the lowest mean concentration of lead and the high dietary group had the highest for the following tissues: Kidney, liver, femur, brain, and blood. Concentrations of lead were significantly correlated among tissues. There were no differences among treatment groups for packed cell volume, hemoglobin concentration, or erythrocyte count.

  19. Effects of Biology Teachers' Professional Knowledge and Cognitive Activation on Students' Achievement

    ERIC Educational Resources Information Center

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

    2016-01-01

    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…

  20. Strontium incorporation to optimize the antibacterial and biological characteristics of silver-substituted hydroxyapatite coating.

    PubMed

    Geng, Zhen; Cui, Zhenduo; Li, Zhaoyang; Zhu, Shengli; Liang, Yanqin; Liu, Yunde; Li, Xue; He, Xin; Yu, Xiaoxu; Wang, Renfeng; Yang, Xianjin

    2016-01-01

    Infection in primary total joint prostheses is attracting considerable attention. In this study, silver (Ag) was incorporated into hydroxyapatite (HA) using a hydrothermal method in order to improve its antimicrobial properties. Strontium (Sr) was added as a second binary element to improve the biocompatibility. The substituted HA samples were fixed on titanium (Ti) substrates by dopamine-assisted immobilization in order to evaluate their antibacterial and biological properties. The results showed that Ag and Sr were successfully incorporated into HA without affecting their crystallinity. Further, the antibacterial tests showed that all the Ag-substituted samples had good anti-bacterial properties against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). Despite their good antibacterial ability, the Ag-substituted samples showed evidence of cytotoxicity on MG63 cells, characterized by low cell density and poor spreadability. The addition of Sr to the Ag-substituted samples considerably reduced the cytotoxicity of Ag. Although the viability of the cells grown on the surfaces of co-substituted HA was not as high as that of the cells grown on the HA surfaces, it is believed that excellent antibacterial properties and good biological activity can be achieved by balancing the dosage of Sr and Ag.

  1. Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2′-deoxyadenosine mimic

    PubMed Central

    Berthet, Nathalie; Crey-Desbiolles, Caroline; Kotera, Mitsuharu; Dumy, Pascal

    2009-01-01

    The phototriggered cleavage of chemical bonds has found numerous applications in biology, particularly in the field of gene sequencing through photoinduced DNA strand scission. However, only a small number of modified nucleosides that are able to cleave DNA at selected positions have been reported in the literature. Herein, we show that a new photoactivable deoxyadenosine analogue, 3-nitro-3-deaza-2′-deoxyadenosine (d(3-NiA)), was able to induce DNA backbone breakage upon irradiation (λ > 320 nm). The d(3-NiA) nucleoside was chemically incorporated at desired positions into 40-mer oligonucleotides as a phosphoramidite monomer and subsequent hybridization studies confirmed that the resulting modified duplexes display a behaviour that is close to that of the related natural sequence. Enzymatic action of the Klenow fragment exonuclease free revealed the preferential incorporation of dAMP opposite the 3-NiA base. On the other hand, incorporation of the analogous 3-NiA triphosphate to a primer revealed high enzyme efficiency and selectivity for insertion opposite thymine. Furthermore, only the enzymatically synthesized base pair 3-NiA:T was a substrate for further extension by the enzyme. All the hybridization and enzymatic data indicate that this new photoactivable 3-NiA triphosphate can be considered as a photochemically cleavable dATP analogue. PMID:19586934

  2. Incorporating personalized gene sequence variants, molecular genetics knowledge, and health knowledge into an EHR prototype based on the Continuity of Care Record standard

    PubMed Central

    Jing, Xia; Kay, Stephen; Marley, Tom; Hardiker, Nicholas R.; Cimino, James J.

    2011-01-01

    Summary Objectives The current volume and complexity of genetic tests, and the molecular genetics knowledge and health knowledge related to interpretation of the results of those tests, are rapidly outstripping the ability of individual clinicians to recall, understand and convey to their patients information relevant to their care. The tailoring of molecular genetics knowledge and health knowledge in clinical settings is important both for the provision of personalized medicine and to reduce clinician information overload. In this paper we describe the incorporation, customization and demonstration of molecular genetic data (mainly sequence variants), molecular genetics knowledge and health knowledge into a standards-based electronic health record (EHR) prototype developed specifically for this study. Methods We extended the CCR (Continuity of Care Record), an existing EHR standard for representing clinical data, to include molecular genetic data. An EHR prototype was built based on the extended CCR and designed to display relevant molecular genetics knowledge and health knowledge from an existing knowledge base for cystic fibrosis (OntoKBCF). We reconstructed test records from published case reports and represented them in the CCR schema. We then used the EHR to dynamically filter molecular genetics knowledge and health knowledge from OntoKBCF using molecular genetic data and clinical data from the test cases. Results The molecular genetic data were successfully incorporated in the CCR by creating a category of laboratory results called “Molecular Genetics ” and specifying a particular class of test (“Gene Mutation Test”) in this category. Unlike other laboratory tests reported in the CCR, results of tests in this class required additional attributes (“Molecular Structure” and “Molecular Position”) to support interpretation by clinicians. These results, along with clinical data (age, sex, ethnicity, diagnostic procedures, and therapies) were used

  3. Content-Related Knowledge of Biology Teachers from Secondary Schools: Structure and learning opportunities

    NASA Astrophysics Data System (ADS)

    Großschedl, Jörg; Mahler, Daniela; Kleickmann, Thilo; Harms, Ute

    2014-09-01

    Teachers' content-related knowledge is a key factor influencing the learning progress of students. Different models of content-related knowledge have been proposed by educational researchers; most of them take into account three categories: content knowledge, pedagogical content knowledge, and curricular knowledge. As there is no consensus about the empirical separability (i.e. empirical structure) of content-related knowledge yet, a total of 134 biology teachers from secondary schools completed three tests which were to capture each of the three categories of content-related knowledge. The empirical structure of content-related knowledge was analyzed by Rasch analysis, which suggests content-related knowledge to be composed of (1) content knowledge, (2) pedagogical content knowledge, and (3) curricular knowledge. Pedagogical content knowledge and curricular knowledge are highly related (rlatent = .70). The latent correlations between content knowledge and pedagogical content knowledge (rlatent = .48)-and curricular knowledge, respectively (rlatent = .35)-are moderate to low (all ps < .001). Beyond the empirical structure of content-related knowledge, different learning opportunities for teachers were investigated with regard to their relationship to content knowledge, pedagogical content knowledge, and curricular knowledge acquisition. Our results show that an in-depth training in teacher education, professional development, and teacher self-study are positively related to particular categories of content-related knowledge. Furthermore, our results indicate that teaching experience is negatively related to curricular knowledge, compared to no significant relationship with content knowledge and pedagogical content knowledge.

  4. Microarray missing data imputation based on a set theoretic framework and biological knowledge

    PubMed Central

    Gan, Xiangchao; Liew, Alan Wee-Chung; Yan, Hong

    2006-01-01

    Gene expressions measured using microarrays usually suffer from the missing value problem. However, in many data analysis methods, a complete data matrix is required. Although existing missing value imputation algorithms have shown good performance to deal with missing values, they also have their limitations. For example, some algorithms have good performance only when strong local correlation exists in data while some provide the best estimate when data is dominated by global structure. In addition, these algorithms do not take into account any biological constraint in their imputation. In this paper, we propose a set theoretic framework based on projection onto convex sets (POCS) for missing data imputation. POCS allows us to incorporate different types of a priori knowledge about missing values into the estimation process. The main idea of POCS is to formulate every piece of prior knowledge into a corresponding convex set and then use a convergence-guaranteed iterative procedure to obtain a solution in the intersection of all these sets. In this work, we design several convex sets, taking into consideration the biological characteristic of the data: the first set mainly exploit the local correlation structure among genes in microarray data, while the second set captures the global correlation structure among arrays. The third set (actually a series of sets) exploits the biological phenomenon of synchronization loss in microarray experiments. In cyclic systems, synchronization loss is a common phenomenon and we construct a series of sets based on this phenomenon for our POCS imputation algorithm. Experiments show that our algorithm can achieve a significant reduction of error compared to the KNNimpute, SVDimpute and LSimpute methods. PMID:16549873

  5. A moving target--incorporating knowledge of the spatial ecology of fish into the assessment and management of freshwater fish populations.

    PubMed

    Cooke, Steven J; Martins, Eduardo G; Struthers, Daniel P; Gutowsky, Lee F G; Power, Michael; Doka, Susan E; Dettmers, John M; Crook, David A; Lucas, Martyn C; Holbrook, Christopher M; Krueger, Charles C

    2016-04-01

    Freshwater fish move vertically and horizontally through the aquatic landscape for a variety of reasons, such as to find and exploit patchy resources or to locate essential habitats (e.g., for spawning). Inherent challenges exist with the assessment of fish populations because they are moving targets. We submit that quantifying and describing the spatial ecology of fish and their habitat is an important component of freshwater fishery assessment and management. With a growing number of tools available for studying the spatial ecology of fishes (e.g., telemetry, population genetics, hydroacoustics, otolith microchemistry, stable isotope analysis), new knowledge can now be generated and incorporated into biological assessment and fishery management. For example, knowing when, where, and how to deploy assessment gears is essential to inform, refine, or calibrate assessment protocols. Such information is also useful for quantifying or avoiding bycatch of imperiled species. Knowledge of habitat connectivity and usage can identify critically important migration corridors and habitats and can be used to improve our understanding of variables that influence spatial structuring of fish populations. Similarly, demographic processes are partly driven by the behavior of fish and mediated by environmental drivers. Information on these processes is critical to the development and application of realistic population dynamics models. Collectively, biological assessment, when informed by knowledge of spatial ecology, can provide managers with the ability to understand how and when fish and their habitats may be exposed to different threats. Naturally, this knowledge helps to better evaluate or develop strategies to protect the long-term viability of fishery production. Failure to understand the spatial ecology of fishes and to incorporate spatiotemporal data can bias population assessments and forecasts and potentially lead to ineffective or counterproductive management actions.

  6. A moving target—incorporating knowledge of the spatial ecology of fish into the assessment and management of freshwater fish populations

    USGS Publications Warehouse

    Cooke, Steven J.; Martins, Eduardo G; Struthers, Daniel P; Gutowsky, Lee F G; Powers, Michael H.; Doka, Susan E; Dettmers, John M.; Crook, David A; Lucas, Martyn C.; Holbrook, Christopher; Krueger, Charles C.

    2016-01-01

    Freshwater fish move vertically and horizontally through the aquatic landscape for a variety of reasons, such as to find and exploit patchy resources or to locate essential habitats (e.g., for spawning). Inherent challenges exist with the assessment of fish populations because they are moving targets. We submit that quantifying and describing the spatial ecology of fish and their habitat is an important component of freshwater fishery assessment and management. With a growing number of tools available for studying the spatial ecology of fishes (e.g., telemetry, population genetics, hydroacoustics, otolith microchemistry, stable isotope analysis), new knowledge can now be generated and incorporated into biological assessment and fishery management. For example, knowing when, where, and how to deploy assessment gears is essential to inform, refine, or calibrate assessment protocols. Such information is also useful for quantifying or avoiding bycatch of imperiled species. Knowledge of habitat connectivity and usage can identify critically important migration corridors and habitats and can be used to improve our understanding of variables that influence spatial structuring of fish populations. Similarly, demographic processes are partly driven by the behavior of fish and mediated by environmental drivers. Information on these processes is critical to the development and application of realistic population dynamics models. Collectively, biological assessment, when informed by knowledge of spatial ecology, can provide managers with the ability to understand how and when fish and their habitats may be exposed to different threats. Naturally, this knowledge helps to better evaluate or develop strategies to protect the long-term viability of fishery production. Failure to understand the spatial ecology of fishes and to incorporate spatiotemporal data can bias population assessments and forecasts and potentially lead to ineffective or counterproductive management actions.

  7. Incorporating tree-thinking and evolutionary time scale into developmental biology.

    PubMed

    Kuraku, Shigehiro; Feiner, Nathalie; Keeley, Sean D; Hara, Yuichiro

    2016-01-01

    Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples.

  8. A Shadow Curriculum: Incorporating Students' Interests into the Formal Biology Curriculum

    NASA Astrophysics Data System (ADS)

    Hagay, Galit; Baram-Tsabari, Ayelet

    2011-11-01

    Students have been largely ignored in discussions about how best to teach science, and many students feel the curriculum is detached from their lives and interests. This article presents a strategy for incorporating students' interests into the formal Biology curriculum, by drawing on the political meaning of "shadow government" as alternative policies developed by parties not in office. A "shadow curriculum" thus reflects the interests and information needs of those who have no voice in deciding what the formal curriculum should include, although they are the ones who are most influenced by it. High school students' interests in three Biology topics were identified ( n = 343) and retested on another student sample ( n = 375), based on their solicited questions as indicators for interests. The results of this exploratory case study showed that half of the questions asked by students in the areas of genetics, the cardiovascular system and the reproductive system are not addressed by the national curriculum. Students' questions were then expressed in the curricular language of principles, phenomena and concepts in order to create a shadow curriculum. A procedure that could be used by other researchers and practitioners to guide the development of a curriculum that is more aligned with student interests is suggested.

  9. REE incorporation and behaviour in aquatic turtles as a consequence of environmental exposure and biological processes

    NASA Astrophysics Data System (ADS)

    Censi, P.; Randazzo, L. A.; D'Angelo, S.; Cuttitta, A.; Saiano, F.

    2012-04-01

    Rare Earth Elements (REE) contents in Emys trinacris have been investigated for the first time in order to recognise effects of the chemistry of the environment on the composition of biological fluids. Representing radionuclides a potential health risk for living organisms in case of incorporation in tissues and being REE geochemical analogues of actinides in hydrosphere, this study was focused on investigation of REE behaviour in whole blood and esoskeleton of selected individuals of Emys trinacris. The choice of this species is related to its amphibian character that allowed us to evidence environmental stress in terms of composition of environmental freshwaters whose REE compositions were investigated and compared with blood samples. Moreover effects induced by different environmental conditions were investigated collecting samples in two sites characterised by absence of an anthropogenic signature (GT site) and subjected to strong anthropogenic pressure in terms of wastewater input (SIC site), respectively. In both sites REE contents in whole blood samples of studied turtles are quite similar even if in GT site the highest REE contents have been recognised. Shale-normalised REE patterns show very similar REE behaviour with light REE (LREE) enrichments with respect to heavier REE (HREE), mainly in samples from anthropized site. If REE concentrations in whole blood are normalised to the composition of environmental waters, calculated REE patterns show upward concave shapes centred on Gd that are more pronounced in samples from GT site because their patterns are more enriched in LREE. The last features observed in blood samples from GT can be related to larger REE contents occurred in environmental water from this site with respect to waters collected in SIC site, suggesting that a relationship occurs between REE contents in environmental and biological fluids. Since MREE depletions were observed in waters experiencing phosphate crystallization, observed REE

  10. Synthetic Biology: Knowledge Accessed by Everyone (Open Sources)

    ERIC Educational Resources Information Center

    Sánchez Reyes, Patricia Margarita

    2016-01-01

    Using the principles of biology, along with engineering and with the help of computer, scientists manage to copy. DNA sequences from nature and use them to create new organisms. DNA is created through engineering and computer science managing to create life inside a laboratory. We cannot dismiss the role that synthetic biology could lead in…

  11. Professional Development for Biology Teachers in the Knowledge Economy

    ERIC Educational Resources Information Center

    Eiser, Simone; Knight, Bruce Allen

    2008-01-01

    Increasingly, the general media cover new advancements and research in the field of biology. Stem cell research, emerging diseases and bioethics are some of the issues gaining public attention. The rate of increase of these new developments creates additional challenges to teachers of biology as they try to remain abreast of new information and…

  12. High School Biology Students' Knowledge and Certainty about Diffusion and Osmosis Concepts

    ERIC Educational Resources Information Center

    Odom, Arthur L.; Barrow, Lloyd H.

    2007-01-01

    The purpose of this study was to investigate students' understanding about scientifically acceptable content knowledge by exploring the relationship between knowledge of diffusion and osmosis and the students' certainty in their content knowledge. Data was collected from a high school biology class with the Diffusion and Osmosis Diagnostic Test…

  13. College Re-Culturing, Marketisation and Knowledge: The Meaning of Incorporation

    ERIC Educational Resources Information Center

    Smith, Rob

    2015-01-01

    The further education (FE) sector in England has experienced two decades of marketisation. This article takes as its focus the first five years of incorporation (1993-1998) for one case study college in a city ("Coppleton") in the West Midlands of England, five years that were dominated by a contract dispute. Data from interviews with…

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

    PubMed

    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

    2017-02-01

    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 < 0.0001). The five-day molecular biology workshop significantly increased the knowledge and skills of participants in molecular biology techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017.

  15. HIV/AIDS Content Knowledge and Presentation Strategies in Biology for Effective Use in Everyday Life

    ERIC Educational Resources Information Center

    Mnguni, Lindelani; Abrie, Mia

    2012-01-01

    HIV/AIDS education should empower students to create knowledge using everyday life experiences. Such knowledge should then be used to construe experience and resolve social problems such as risk behaviour that leads to infection. In South Africa, attempts to reduce the spread of HIV include incorporating HIV/AIDS education in the biology…

  16. Biological Nature of Knowledge in the Learning Organisation

    ERIC Educational Resources Information Center

    Hall, William P.

    2005-01-01

    Purpose: To develop a biological approach to the analysis of learning organisations based on complexity theory, autopoiesis, and evolutionary epistemology. Design/methodology/approach: This paper synthesises ideas from disciplines ranging from physics, epistemology and philosophy of science to military affairs, to sketch a scientific framework in…

  17. INCORPORATING PRIOR KNOWLEDGE IN ENVIRONMENTAL SAMPLING: RANKED SET SAMPLING AND OTHER DOUBLE SAMPLING PROCEDURES

    EPA Science Inventory

    Environmental sampling can be difficult and expensive to carry out. Those taking the samples would like to integrate their knowledge of the system of study or their judgment about the system into the sample selection process to decrease the number of necessary samples. However,...

  18. Improved ant colony optimization for optimal crop and irrigation water allocation by incorporating domain knowledge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An improved ant colony optimization (ACO) formulation for the allocation of crops and water to different irrigation areas is developed. The formulation enables dynamic adjustment of decision variable options and makes use of visibility factors (VFs, the domain knowledge that can be used to identify ...

  19. C[superscript 2] = BOK: Two Apparel Studies' Capstone Courses Incorporating the Body of Knowledge

    ERIC Educational Resources Information Center

    Smith, Kathleen R.; Apple, Laurie; Souhtward, Leigh

    2014-01-01

    Guided by the five cross-cutting themes of the American Association of Family & Consumer Sciences (AAFCS) Body of Knowledge (BOK) two capstone courses (C[superscript 2]) in Apparel Studies were designed to help prepare students for careers, further study, or both.

  20. A Framework for Incorporating General Domain Knowledge into Latent Dirichlet Allocation using First-Order Logic

    SciTech Connect

    Andrzejewski, D; Zhu, X; Craven, M; Recht, B

    2011-01-18

    Topic models have been used successfully for a variety of problems, often in the form of application-specific extensions of the basic Latent Dirichlet Allocation (LDA) model. Because deriving these new models in order to encode domain knowledge can be difficult and time-consuming, we propose the Fold-all model, which allows the user to specify general domain knowledge in First-Order Logic (FOL). However, combining topic modeling with FOL can result in inference problems beyond the capabilities of existing techniques. We have therefore developed a scalable inference technique using stochastic gradient descent which may also be useful to the Markov Logic Network (MLN) research community. Experiments demonstrate the expressive power of Fold-all, as well as the scalability of our proposed inference method.

  1. Incorporating Semantic Knowledge into Dynamic Data Processing for Smart Power Grids

    SciTech Connect

    Zhou, Qunzhi; Simmhan, Yogesh; Prasanna, Viktor

    2012-11-15

    Semantic Web allows us to model and query time-invariant or slowly evolving knowledge using ontologies. Emerging applications in Cyber Physical Systems such as Smart Power Grids that require continuous information monitoring and integration present novel opportunities and challenges for Semantic Web technologies. Semantic Web is promising to model diverse Smart Grid domain knowledge for enhanced situation awareness and response by multi-disciplinary participants. However, current technology does pose a performance overhead for dynamic analysis of sensor measurements. In this paper, we combine semantic web and complex event processing for stream based semantic querying. We illustrate its adoption in the USC Campus Micro-Grid for detecting and enacting dynamic response strategies to peak power situations by diverse user roles. We also describe the semantic ontology and event query model that supports this. Further, we introduce and evaluate caching techniques to improve the response time for semantic event queries to meet our application needs and enable sustainable energy management.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    ERIC Educational Resources Information Center

    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…

  4. Representations of the Nature of Scientific Knowledge in Turkish Biology Textbooks

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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,…

  6. A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

    ERIC Educational Resources Information Center

    van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

    2011-01-01

    Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge…

  7. Features of Knowledge Building in Biology: Understanding Undergraduate Students' Ideas about Molecular Mechanisms

    ERIC Educational Resources Information Center

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S.

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections…

  8. [Practical knowledge in fungal diagnosis in some biological materials].

    PubMed

    Mencl, Karel

    2012-08-01

    The article deals with certain problematic issues associated with routine laboratory diagnosis of mycoses from secretions and samples taken from the respiratory tract and maxillary sinuses as well as samples of skin and skin appendages. The text is based on both the author's own long-term experience and experience gained from cooperation with other laboratories. To improve the detection of filamentous fungi in lower respiratory tract secretions, it is recommended to use 0.5 mL of the material for individual culture media. In both secretions and other biological material, the role of microscopic examination is stressed. In many cases, this may also be the only reliable laboratory procedure. Detection of filamentous fungi should be interpreted in close cooperation with clinicians, especially in order to obtain history data. These are particularly important in the diagnosis of endemic mycoses. Equivocal or unusual findings should be verified by repeated laboratory tests.

  9. Mapping biological ideas: Concept maps as knowledge integration tools for evolution education

    NASA Astrophysics Data System (ADS)

    Schwendimann, Beat Adrian

    Many students leave school with a fragmented understanding of biology that does not allow them to connect their ideas to their everyday lives (Wandersee, 1989; Mintzes, Wandersee, & Novak, 1998; Mintzes, Wandersee, & Novak, 2000a). Understanding evolution ideas is seen as central to building an integrated knowledge of biology (Blackwell, Powell, & Dukes, 2003; Thagard & Findlay, 2010). However, the theory of evolution has been found difficult to understand as it incorporates a wide range of ideas from different areas (Bahar et al., 1999; Tsui & Treagust, 2003) and multiple interacting levels (Wilensky & Resnick, 1999; Duncan & Reiser, 2007; Hmelo-Silver et al., 2007). Research suggests that learners can hold a rich repertoire of co-existing alternative ideas of evolution (for example, Bishop & Anderson, 1990; Demastes, Good, & Peebles, 1996; Evans, 2008), especially of human evolution (for example, Nelson, 1986; Sinatra et al., 2003; Poling & Evans, 2004). Evolution ideas are difficult to understand because they often contradict existing alternative ideas (Mayr, 1982; Wolpert, 1994; Evans, 2008). Research suggests that understanding human evolution is a key to evolution education (for example, Blackwell et al., 2003; Besterman & Baggott la Velle, 2007). This dissertation research investigates how different concept mapping forms embedded in a collaborative technology-enhanced learning environment can support students' integration of evolution ideas using case studies of human evolution. Knowledge Integration (KI) (Linn et al., 2000; Linn et al., 2004) is used as the operational framework to explore concept maps as knowledge integration tools to elicit, add, critically distinguish, group, connect, and sort out alternative evolution ideas. Concept maps are a form of node-link diagram for organizing and representing connections between ideas as a semantic network (Novak & Gowin, 1984). This dissertation research describes the iterative development of a novel biology

  10. Evolving Strategies for the Incorporation of Bioinformatics within the Undergraduate Cell Biology Curriculum

    ERIC Educational Resources Information Center

    Honts, Jerry E.

    2003-01-01

    Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in…

  11. Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 1: Identifying Proteins Based on Molecular Mass

    ERIC Educational Resources Information Center

    Arnquist, Isaac J.; Beussman, Douglas J.

    2007-01-01

    Biological mass spectrometry is an important analytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. Currently, few hands-on opportunities exist for undergraduate students to learn about this technique. With the 2002 Nobel Prize being awarded, in part, for the development of biological mass…

  12. Incorporating Biological, Chemical and Toxicological Knowledge into Predictive Models of Toxicity: Letter to the Editor

    EPA Science Inventory

    Thomas et al. (2012) recently published an evaluation of statistical models for classifying in vivo toxicity endpoints from ToxRefDB (Knudsen et al. 2009; Martin et al. 2009a and 2009b) using ToxCast in vitro bioactivity data (Judson et al. 2010) and chemical structure descriptor...

  13. A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

    NASA Astrophysics Data System (ADS)

    van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

    2011-10-01

    Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge concerning genetic testing and the related consequences for decision-making indicate the societal relevance of such a situated learning approach. What content knowledge do biology teachers need for teaching genetics in the personal health context of genetic testing? This study describes the required content knowledge by exploring the educational practice and clinical genetic practices. Nine experienced teachers and 12 respondents representing the clinical genetic practices (clients, medical professionals, and medical ethicists) were interviewed about the biological concepts and ethical, legal, and social aspects (ELSA) of testing they considered relevant to empowering students as future health care clients. The ELSA suggested by the respondents were complemented by suggestions found in the literature on genetic counselling. The findings revealed that the required teacher knowledge consists of multiple layers that are embedded in specific genetic test situations: on the one hand, the knowledge of concepts represented by the curricular framework and some additional concepts (e.g. multifactorial and polygenic disorder) and, on the other hand, more knowledge of ELSA and generic characteristics of genetic test practice (uncertainty, complexity, probability, and morality). Suggestions regarding how to translate these characteristics, concepts, and ELSA into context-based genetics education are discussed.

  14. Biological nomenclatures: a source of lexical knowledge and ambiguity.

    PubMed

    Tuason, O; Chen, L; Liu, H; Blake, J A; Friedman, C

    2004-01-01

    There has been increased work in developing automated systems that involve natural language processing (NLP) to recognize and extract genomic information from the literature. Recognition and identification of biological entities is a critical step in this process. NLP systems generally rely on nomenclatures and ontological specifications as resources for determining the names of the entities, assigning semantic categories that are consistent with the corresponding ontology, and assignment of identifiers that map to well-defined entities within a particular nomenclature. Although nomenclatures and ontologies are valuable for text processing systems, they were developed to aid researchers and are heterogeneous in structure and semantics. A uniform resource that is automatically generated from diverse resources, and that is designed for NLP purposes would be a useful tool for the field, and would further database interoperability. This paper presents work towards this goal. We have automatically created lexical resources from four model organism nomenclature systems (mouse, fly, worm, and yeast), and have studied performance of the resources within an existing NLP system, GENIES. Using nomenclatures is not straightforward because issues concerning ambiguity, synonymy, and name variations are quite challenging. In this paper we focus mainly on ambiguity. We determined that the number of ambiguous gene names within the individual nomenclatures, across the four nomenclatures, and with general English ranged from 0%-10.18%, 1.187%-20.30%, and 0%-2.49% respectively. When actually processing text, we found the rate of ambiguous occurrences (not counting ambiguities stemming from English words) to range from 2.4%-32.9% depending on the organisms considered.

  15. Exploring Biology Teachers' Pedagogical Content Knowledge in the Teaching of Genetics in Swaziland Science Classrooms

    NASA Astrophysics Data System (ADS)

    Mthethwa-Kunene, Eunice; Oke Onwu, Gilbert; de Villiers, Rian

    2015-05-01

    This study explored the pedagogical content knowledge (PCK) and its development of four experienced biology teachers in the context of teaching school genetics. PCK was defined in terms of teacher content knowledge, pedagogical knowledge and knowledge of students' preconceptions and learning difficulties. Data sources of teacher knowledge base included teacher-constructed concept maps, pre- and post-lesson teacher interviews, video-recorded genetics lessons, post-lesson teacher questionnaire and document analysis of teacher's reflective journals and students' work samples. The results showed that the teachers' individual PCK profiles consisted predominantly of declarative and procedural content knowledge in teaching basic genetics concepts. Conditional knowledge, which is a type of meta-knowledge for blending together declarative and procedural knowledge, was also demonstrated by some teachers. Furthermore, the teachers used topic-specific instructional strategies such as context-based teaching, illustrations, peer teaching, and analogies in diverse forms but failed to use physical models and individual or group student experimental activities to assist students' internalization of the concepts. The finding that all four teachers lacked knowledge of students' genetics-related preconceptions was equally significant. Formal university education, school context, journal reflection and professional development programmes were considered as contributing to the teachers' continuing PCK development. Implications of the findings for biology teacher education are briefly discussed.

  16. Resisting Official Knowledge: The Incorporation and Abjection of Race and Poverty in High School American History Textbooks, 1960s-2000s

    ERIC Educational Resources Information Center

    Kearl, Benjamin Kelsey

    2014-01-01

    Through an interpretive analysis of how high school American history textbooks depict the urban-riots of the late-1960s, in this article the author discusses how textbooks incorporate and abject official knowledge related to the intersections of race and poverty. Incorporation is related with Raymond Williams' theory of the selective tradition and…

  17. Barbers' knowledge and practice about occupational biological hazards was low in Gondar town, North West Ethiopia

    PubMed Central

    2012-01-01

    Background Several health hazards including communicable diseases and skin conditions are associated with Barbers’ profession to which their visitors are exposed. Thus, knowledge and practice of Barbers would play a vital part in prevention and control of these health hazards. So, the aim of this study is to assess knowledge and practice, and associated factors among barbers about biological hazards associated with their profession in Gondar town, North West Ethiopia. Methods To assess knowledge and practice, and associated factors among barbers about biological hazards associated with their profession in Gondar town, North West Ethiopia, A work place based cross-sectional study was conducted from March 28 to April 6, 2012. The total numbers of Barbers in the town were 960 of which 400 Barbers were participated in the study. Sample size was determined using the formula for single population proportion by considering, 51% proportion, knowledgeable Barbers from Jimma, Ethiopia, 95% level of confidence, 5% margin of error and 15% none response rate. The numbers of barbers included in the study were selected by using systematic random sampling. Data was collected by face to face interview using a structured and pre-tested questionnaire. Binary and multivariate logistic regression analyses were conducted to identify factors associated with knowledge and practice of barbers. Results Of 400 barbers, only 72 (18%) had good knowledge about biological hazards associated to their profession, While only 61 (15.3%) were practicing safely during barbering. Knowledge of the barbers was associated significantly with educational level, owner of the business, working hour and work experience, while practice was associated only with availability of UV sterilizers in the room and working hour. Conclusion Barbers’ practice and knowledge to prevent biological hazards associated with their profession is very poor. Thus, giving training for the Barbers is required toward prevention of

  18. A convenient dichotomy: critical eyes on the limits to biological knowledge

    NASA Astrophysics Data System (ADS)

    Milne, Catherine

    2011-06-01

    In The Secret Identity of a Biology Textbook: straight and naturally sexed, Jesse Bazzul and Heather Sykes conduct a case study of a biology textbook as an oppressive instructional material. Using queer theory they explore how the text of the biology textbook produces "truths" about sex, gender, and sexuality. Their analysis is complemented by the Forum papers by Jay Lemke and Francis Broadway who broaden the analysis examining the way that what counts as knowledge in science is a political decision while also encouraging authors, including Bazzul and Sykes, to also look critically at their own theoretical lenses. In this paper I pull together their ideas while exploring cultural contexts for a more nuanced representation of biological knowledge and the politics of what it means to know science.

  19. Biology Faculty at Large Research Institutions: The Nature of their Pedagogical Content Knowledge

    NASA Astrophysics Data System (ADS)

    Hill, Kathleen M.

    To address the need of scientists and engineers in the United States workforce and ensure that students in higher education become scientifically literate, research and policy has called for improvements in undergraduate education in the sciences. One particular pathway for improving undergraduate education in the science fields is to reform undergraduate teaching. Only a limited number of studies have explored the pedagogical content knowledge of postsecondary level teachers. This study was conducted to characterize the PCK of biology faculty and explore the factors influencing their PCK. Data included semi-structured interviews, classroom observations, documents, and instructional artifacts. A qualitative inquiry was designed to conduct an in-depth investigation focusing on the PCK of six biology instructors, particularly the types of knowledge they used for teaching biology, their perceptions of teaching, and the social interactions and experiences that influenced their PCK. The findings of this study reveal that the PCK of the biology faculty included eight domains of knowledge: (1) content, (2) context, (3) learners and learning, (4) curriculum, (5) instructional strategies, (6) representations of biology, (7) assessment, and (8) building rapport with students. Three categories of faculty PCK emerged: (1) PCK as an expert explainer, (2) PCK as an instructional architect, and (3) a transitional PCK, which fell between the two prior categories. Based on the interpretations of the data, four social interactions and experiences were found to influence biology faculty PCK: (1) teaching experience, (2) models and mentors, (3) collaborations about teaching, and (4) science education research. The varying teaching perspectives of the faculty also influenced their PCK. This study shows that the PCK of biology faculty for teaching large introductory courses at large research institutions is heavily influenced by factors beyond simply years of teaching experience and

  20. The Experience of Addiction as Told by the Addicted: Incorporating Biological Understandings into Self-Story

    PubMed Central

    Hammer, Rachel R; Dingel, Molly J; Ostergren, Jenny E; Nowakowski, Katherine E; Koenig, Barbara A

    2012-01-01

    How do the addicted view addiction against the framework of formal theories that attempt to explain the condition? In this empirical paper, we report on the lived experience of addiction based on 63 semi-structured, open-ended interviews with individuals in treatment for alcohol and nicotine abuse at five sites in Minnesota. Using qualitative analysis, we identified four themes that provide insights into understanding how people who are addicted view their addiction, with particular emphasis on the biological model. More than half of our sample articulated a biological understanding of addiction as a disease. Themes did not cluster by addictive substance used; however, biological understandings of addiction did cluster by treatment center. Biological understandings have the potential to become dominant narratives of addiction in the current era. Though the desire for a “unified theory” of addiction seems curiously seductive to scholars, it lacks utility. Conceptual “disarray” may actually reflect a more accurate representation of the illness as told by those who live with it. For practitioners in the field of addiction, we suggest the practice of narrative medicine with its ethic of negative capability as a useful approach for interpreting and relating to diverse experiences of disease and illness. PMID:23081782

  1. Experiencing Our Anatomy: Incorporating Human Biology into Dance Class via Imagery, Imagination, and Somatics

    ERIC Educational Resources Information Center

    Kirk, Johanna

    2014-01-01

    This article proposes a model for introducing biological perspectives into teaching dance as a means to encourage students toward deeper, healthier, and more personal relationships with their art form as well as appreciation for their physical and cognitive abilities, both inside and outside of the dance studio. It recommends that dance teachers…

  2. Cloning, Stem Cells, and the Current National Debate: Incorporating Ethics into a Large Introductory Biology Course

    ERIC Educational Resources Information Center

    Fink, Rachel D.

    2002-01-01

    Discussing the ethical issues involved in topics such as cloning and stem cell research in a large introductory biology course is often difficult. Teachers may be wary of presenting material biased by personal beliefs, and students often feel inhibited speaking about moral issues in a large group. Yet, to ignore what is happening "out there"…

  3. Pre-Service Science Teachers' Pedagogical Content Knowledge in the Physics, Chemistry, and Biology Topics

    ERIC Educational Resources Information Center

    Bektas, Oktay

    2015-01-01

    This study investigated pre-service science teachers' pedagogical content knowledge in the physics, chemistry, and biology topics. These topics were the light and sound, the physical and chemical changes, and reproduction, growth, and evolution. Qualitative research design was utilized. Data were collected from 33 pre-service science teachers…

  4. CONCEPTUAL FRAMEWORK FOR THE CHEMICAL EFFECTS IN BIOLOGICAL SYSTEMS (CEBS) TOXICOGENOMICS KNOWLEDGE BASE

    EPA Science Inventory

    Conceptual Framework for the Chemical Effects in Biological Systems (CEBS) T oxicogenomics Knowledge Base

    Abstract
    Toxicogenomics studies how the genome is involved in responses to environmental stressors or toxicants. It combines genetics, genome-scale mRNA expressio...

  5. Measuring the Disparities between Biology Undergraduates' Perceptions and Their Actual Knowledge of Scientific Literature with Clickers

    ERIC Educational Resources Information Center

    Bandyopadhyay, Aditi

    2013-01-01

    This article demonstrates an innovative method used to determine the need for information literacy among science undergraduate students at Adelphi University. Using clickers technology, this study measured the disconnect between biology undergraduates' perceived and actual knowledge of scientific literature. The quantitative data collected in the…

  6. Nursing and the new biology: towards a realist, anti-reductionist approach to nursing knowledge.

    PubMed

    Nairn, Stuart

    2014-10-01

    As a system of knowledge, nursing has utilized a range of subjects and reconstituted them to reflect the thinking and practice of health care. Often drawn to a holistic model, nursing finds it difficult to resist the reductionist tendencies in biological and medical thinking. In this paper I will propose a relational approach to knowledge that is able to address this issue. The paper argues that biology is not characterized by one stable theory but is often a contentious topic and employs philosophically diverse models in its scientific research. Biology need not be seen as a reductionist science, but reductionism is nonetheless an important current within biological thinking. These reductionist currents can undermine nursing knowledge in four main ways. Firstly, that the conclusions drawn from reductionism go far beyond their data based on an approach that prioritizes biological explanations and eliminates others. Secondly, that the methods employed by biologists are sometimes weak, and the limitations are insufficiently acknowledged. Thirdly, that the assumptions that drive the research agenda are problematic, and finally that uncritical application of these ideas can be potentially disastrous for nursing practice. These issues are explored through an examination of the problems reductionism poses for the issue of gender, mental health, and altruism. I then propose an approach based on critical realism that adopts an anti-reductionist philosophy that utilizes the conceptual tools of emergence and a relational ontology.

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

    NASA Astrophysics Data System (ADS)

    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.

  8. Protecting Traditional Knowledge Related to Biological Resources: Is Scientific Research Going to Become More Bureaucratized?

    PubMed

    Reddy, Prashant; Lakshmikumaran, Malathi

    2015-06-22

    For the past several decades, there has been a world debate on the need for protecting traditional knowledge. A global treaty appears to be a distant reality. Of more immediate concern are the steps taken by the global community to protect access to biological resources in the name of protecting traditional knowledge. The Indian experience with implementing the Convention on Biological Diversity has created substantial legal uncertainty in collaborative scientific research between Indians and foreigners apart from bureaucratizing the entire process of scientific research, especially with regard to filing of applications for intellectual property rights. The issue therefore is whether the world needs to better balance the needs of the scientific community with the rights of those who have access to traditional knowledge.

  9. Incorporating biologically based models into assessments of risk from chemical contaminants

    NASA Technical Reports Server (NTRS)

    Bull, R. J.; Conolly, R. B.; De Marini, D. M.; MacPhail, R. C.; Ohanian, E. V.; Swenberg, J. A.

    1993-01-01

    The general approach to assessment of risk from chemical contaminants in drinking water involves three steps: hazard identification, exposure assessment, and dose-response assessment. Traditionally, the risks to humans associated with different levels of a chemical have been derived from the toxic responses observed in animals. It is becoming increasingly clear, however, that further information is needed if risks to humans are to be assessed accurately. Biologically based models help clarify the dose-response relationship and reduce uncertainty.

  10. Incorporating Community Knowledge to Lahar Hazard Maps: Canton Buenos Aires Case Study, at Santa Ana (Ilamatepec) Volcano

    NASA Astrophysics Data System (ADS)

    Bajo, J. V.; Martinez-Hackert, B.; Polio, C.; Gutierrez, E.

    2015-12-01

    Santa Ana (Ilamatepec) Volcano is an active composite volcano located in the Apaneca Volcanic Field located in western part of El Salvador, Central America. The volcano is surrounded by rural communities in its proximal areas and the second (Santa Ana, 13 km) and fourth (Sonsosante, 15 km) largest cities of the country. On October 1st, 2005, the volcano erupted after months of increased activity. Following the eruption, volcanic mitigation projects were conducted in the region, but the communities had little or no input on them. This project consisted in the creation of lahar volcanic hazard map for the Canton Buanos Aires on the northern part of the volcano by incorporating the community's knowledge from prior events to model parameters and results. The work with the community consisted in several meetings where the community members recounted past events. They were asked to map the outcomes of those events using either a topographic map of the area, a Google Earth image, or a blank paper poster size. These maps have been used to identify hazard and vulnerable areas, and for model validation. These maps were presented to the communities and they accepted their results and the maps.

  11. Incorporating bioinformatics into biological science education in Nigeria: prospects and challenges.

    PubMed

    Ojo, O O; Omabe, M

    2011-06-01

    The urgency to process and analyze the deluge of data created by proteomics and genomics studies worldwide has caused bioinformatics to gain prominence and importance. However, its multidisciplinary nature has created a unique demand for specialist trained in both biology and computing. Several countries, in response to this challenge, have developed a number of manpower training programmes. This review presents a description of the meaning, scope, history and development of bioinformatics with focus on prospects and challenges facing bioinformatics education worldwide. The paper also provides an overview of attempts at the introduction of bioinformatics in Nigeria; describes the existing bioinformatics scenario in Nigeria and suggests strategies for effective bioinformatics education in Nigeria.

  12. Development and anti-listerial activity of PE-based biological preservative films incorporating plantaricin BM-1.

    PubMed

    Zhang, Min; Gao, Xiuzhi; Zhang, Hongxing; Liu, Hui; Jin, Junhua; Yang, Wenge; Xie, Yuanhong

    2016-12-18

    In recent years, bacteriocin as a natural antimicrobial compound, provides enormous promise to be used in food safety preservation. In this work, the polyethylene(PE)-based biological preservative films incorporating plantaricin BM-1, a typical IIa bacteriocin produced by Lactobacillus plantarum BM-1, were developed and characterized. The results showed that polyethylene (PE), low-density polyethylene (LDPE) and high-density polyethylene (HDPE) films soaked in plantaricin BM-1 solution had obvious antimicrobial activities aganist Listeria monocytogenes And the volume of plantaricin BM-1 solution absorbed by PE, LDPE and HDPE films continued to increase and reached the maximum during exposure for up to 10, 6 and 16 hours, respectively. And the maximum absorption volumes of plantaricin BM-1 solution had no significant difference (p>0.05) between the PE, LDPE and HDPE films. When soaking in water, the release amount of plantaricin BM-1 from active PE, LDPE and HDPE films reached the maximum potency at 16, 12 and 20 hours respectively. And the maximum release amount of plantaricin BM-1 from PE and LDPE active films were dramatically more than the HDPE active film (p<0.05). Moreover, the inhibitory effect of active films incorporating plantaricin BM-1 maintained stability for at least 120 days against L. monocytogenes stored at 25°C, which suggest a potential application of the biological preservative films on the control of foodborne pathogens L. monocytogenes.

  13. RegenBase: a knowledge base of spinal cord injury biology for translational research

    PubMed Central

    Callahan, Alison; Abeyruwan, Saminda W.; Al-Ali, Hassan; Sakurai, Kunie; Ferguson, Adam R.; Popovich, Phillip G.; Shah, Nigam H.; Visser, Ubbo; Bixby, John L.; Lemmon, Vance P.

    2016-01-01

    Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download. Database URL: http://regenbase.org PMID:27055827

  14. Cloning, stem cells, and the current national debate: incorporating ethics into a large introductory biology course.

    PubMed

    Fink, Rachel D

    2002-01-01

    Discussing the ethical issues involved in topics such as cloning and stem cell research in a large introductory biology course is often difficult. Teachers may be wary of presenting material biased by personal beliefs, and students often feel inhibited speaking about moral issues in a large group. Yet, to ignore what is happening "out there" beyond the textbooks and lab work is to do a disservice to students. This essay describes a semester-long project in which upperclass students presented some of the most complex and controversial ideas imaginable to introductory students by staging a mock debate and acting as members of the then newly appointed President's Council on Bioethics. Because the upperclass students were presenting the ideas of real people who play an important role in shaping national policy, no student's personal beliefs were put on the line, and many ideas were articulated. The introductory audience could accept or reject what they were hearing and learn information important for making up their own minds on these issues. This project is presented as an example of how current events can be used to put basic cell biology into context and of how exciting it can be when students teach students.

  15. Cloning, Stem Cells, and the Current National Debate: Incorporating Ethics into a Large Introductory Biology Course

    PubMed Central

    2002-01-01

    Discussing the ethical issues involved in topics such as cloning and stem cell research in a large introductory biology course is often difficult. Teachers may be wary of presenting material biased by personal beliefs, and students often feel inhibited speaking about moral issues in a large group. Yet, to ignore what is happening “out there” beyond the textbooks and lab work is to do a disservice to students. This essay describes a semester-long project in which upperclass students presented some of the most complex and controversial ideas imaginable to introductory students by staging a mock debate and acting as members of the then newly appointed President's Council on Bioethics. Because the upperclass students were presenting the ideas of real people who play an important role in shaping national policy, no student's personal beliefs were put on the line, and many ideas were articulated. The introductory audience could accept or reject what they were hearing and learn information important for making up their own minds on these issues. This project is presented as an example of how current events can be used to put basic cell biology into context and of how exciting it can be when students teach students. PMID:12669102

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

    PubMed Central

    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

  17. Examining beginning biology teachers' knowledge, beliefs, and practice for teaching natural selection

    NASA Astrophysics Data System (ADS)

    Sickel, Aaron J.

    The teacher is the most important school-based factor in student learning. Thus, in order to improve student learning, we must examine how teachers learn to teach. My overarching research agenda centers upon K-16 science teacher learning and development. Within this agenda, I conduct studies focused on two strands of research: 1) How teachers learn to teach science using constructivist and inquiry-oriented teaching strategies; and 2) How teachers learn to teach biological evolution. This dissertation merges the two strands together, and consists of four related manuscripts that address how beginning biology teachers learn to teach natural selection using constructivist and inquiry-oriented teaching strategies. In the first manuscript, I reviewed the evolution education literature focused on K-12 teachers’ knowledge, beliefs, and practice for teaching evolution. Based upon findings across the studies, I articulated five goals for preparing teachers to teach evolution. The second and third manuscripts are longitudinal empirical studies focused on three beginning biology teachers learning to teach natural selection using the 5E instructional model and interactive classroom simulations. The fourth manuscript is a practitioner article that explains how to teach natural selection simulations using a constructivist, analogy-based teaching strategy. Findings that cut across the four manuscripts are organized into the following themes: (A) The participants developed some common types of knowledge for teaching natural selection, yet also developed in unique ways. All participants developed knowledge of the horizontal curriculum. Yet, participants also developed different types of knowledge. For example, participants who had taken an evolution course developed more integrated pedagogical content knowledge for teaching the core concepts of natural selection. The participant who integrated discipline-level knowledge for teaching science through inquiry with topic

  18. Biological markers in petroleum asphaltenes and coals: Possible mode of incorporation

    SciTech Connect

    Trifilieff, S.; Blanc, P.; Sieskind, O.; Albrecht, P. )

    1989-03-01

    n-Heptane precipitated asphaltenes from several crude oils and several pre-extracted coals of varying ranks were treated by ruthenium tetroxide which is known to selectively oxidize aromatic rings. A study of the branched and cyclic acids formed during this procedure showed that acyclic isoprenoid acids occurred in all asphaltenes and culminated at C{sub 21}, whereas hopanoic acids usually extended up to C{sub 36}. Steroid acids (C{sub 28}-C{sub 30}) were particularly abundant in the asphaltenes of Rozel Point seep oil and were identified by synthesis. They bear one additional carbon as compared with the steranes of the oil. Hopanoic acids and traces of steroid acids were also detected in the oxidation products of the less mature coals. Evidence from the carbon number distribution of the different families indicated that these molecules could at least partially be incorporated into high molecular weight entities via Friedel-Crafts type reactions. Simulation experiments carried out with pure standards confirmed this hypothesis.

  19. Features of Knowledge Building in Biology: Understanding Undergraduate Students’ Ideas about Molecular Mechanisms

    PubMed Central

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S.

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning. PMID:26931398

  20. Features of Knowledge Building in Biology: Understanding Undergraduate Students' Ideas about Molecular Mechanisms.

    PubMed

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning.

  1. Changes in physicochemical and biological properties of porcine bone derived hydroxyapatite induced by the incorporation of fluoride

    PubMed Central

    Qiao, Wei; Liu, Quan; Li, Zhipeng; Zhang, Hanqing; Chen, Zhuofan

    2017-01-01

    Abstract As the main inorganic component of xenogenic bone graft material, bone-derived biological apatite (BAp) has been widely used in implant dentistry, oral and maxillofacial surgery and orthopedics. However, BAp produced via calcination of animal bones still suffers from some drawbacks, such as insufficient mechanical strength and inadequate degradation rate, which impede its application. Fluoride is known to play important roles in both physiological and pathological processes of human hard tissues for its double effects on bones and teeth. In order to understand the effects of fluoride on the properties of BAp, as well as the mechanism behind them, porcine bone derived hydroxyapatite (PHAp) was prepared via thermal treatment, which was then fluoride incorporated at a series concentrations of sodium fluoride, and noted as 0.25-FPHAp, 0.50-FPHAp, and 0.75-FPHAp respectively. The physicochemical characteristics of the materials, including crystal morphology, crystallinity, functional groups, elemental composition, compressive strength, porosity and solubility, were then determined. The biological properties, such as protein adsorption and cell attachment, were also evaluated. It was found that the spheroid-like crystals of PHAp were changed into rod-like after fluoride substitution, resulting in a fluoride concentration-dependent increase in compressive strength, as well as a decreased porosity and solubility of the apatite. However, even though the addition of fluoride was demonstrated to enhance protein adsorption and cell attachment of the materials, the most favorable results were intriguingly achieved in FPHAp with the least fluoride content. Collectively, low level of fluoride incorporation is proposed promising for the modification of clinically used BAp based bone substitute materials, because of its being able to maintain a good balance between physicochemical and biological properties of the apatite. PMID:28243337

  2. Overdose toxicity studies versus threshold: elements of biology must be incorporated into risk assessment.

    PubMed

    Hildebrandt, A G

    1987-01-01

    The estimation of risk and evaluation of risk/benefit are traditionally and by necessity oriented at the current state of science and technology to ensure contemporary rights of safety. This demands a careful development in the methodology of hazard identification and risk assessment and its continuous updating and involvement. Compounds, e.g. erythrosine, 2,4,5-T, TCDD, and antioxidants, have still to be judged case-by-case, taking into account all available information on dosage, effect, kinetics, and mechanism of action, i.e., matters of biology rather than of mathematics alone. Considerations of mechanism of action and kinetics, especially recognition of low-dose/high-affinity assumptions in vitro, are necessary. This might lead to a new view upon thresholds which appears to apply for promoters. As accepted in pharmacology the dose-dependent magnitude of response observed in vivo is often a composite effect. Composite effects in toxicology can be viewed as having similar characteristics in vivo as in vitro in terms of potency, slope, maximal efficay and variability. Composite vectors can be antagonistic, leading to toxic and carcinogenic results, but also to protection. A continuous updating of scientific expertise supported by own experimental work is required for the regulator.

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

    NASA Astrophysics Data System (ADS)

    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

  4. Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits.

    PubMed

    Ma, Li; Keinan, Alon; Clark, Andrew G

    2015-01-01

    While the importance of epistasis is well established, specific gene-gene interactions have rarely been identified in human genome-wide association studies (GWAS), mainly due to low power associated with such interaction tests. In this chapter, we integrate biological knowledge and human GWAS data to reveal epistatic interactions underlying quantitative lipid traits, which are major risk factors for coronary artery disease. To increase power to detect interactions, we only tested pairs of SNPs filtered by prior biological knowledge, including GWAS results, protein-protein interactions (PPIs), and pathway information. Using published GWAS and 9,713 European Americans (EA) from the Atherosclerosis Risk in Communities (ARIC) study, we identified an interaction between HMGCR and LIPC affecting high-density lipoprotein cholesterol (HDL-C) levels. We then validated this interaction in additional multiethnic cohorts from ARIC, the Framingham Heart Study, and the Multi-Ethnic Study of Atherosclerosis. Both HMGCR and LIPC are involved in the metabolism of lipids and lipoproteins, and LIPC itself has been marginally associated with HDL-C. Furthermore, no significant interaction was detected using PPI and pathway information, mainly due to the stringent significance level required after correcting for the large number of tests conducted. These results suggest the potential of biological knowledge-driven approaches to detect epistatic interactions in human GWAS, which may hold the key to exploring the role gene-gene interactions play in connecting genotypes and complex phenotypes in future GWAS.

  5. CT-simulator based brachytherapy planner: seed localization and incorporation of biological considerations.

    PubMed

    Mayer, R; Fong, W; Frankel, T; Simons, S; Kleinberg, L; Lee, D J

    1998-01-01

    Radiation dose prescription, interpretation, and planning can be problematic for brachytherapy due to high spatial heterogeneity, varying and various dose rates, absence of superimposed calculated isodose distributions onto affected tissues, and lack of dose volume histograms. A new treatment planner has been developed to reduce these limitations in brachytherapy planning. The PC-based planning system uses a CT-simulator to sequentially scan the patient to generate orthogonal images (to localize seed positions) and subsequently axially scan the patient. This sequential scanning procedure avoids using multiple independent patient scans, templates, external frames, or fiducial markers to register the reconstructed seed positions with patient contours. Dose is computed after assigning activity to (low dose rate) Ir192, linear Cs137, or I125 seeds or dwell times (high dose rate) to the Ir192 source. The planar isodose distribution is superimposed onto axial, coronal, or sagittal views of the tissues following image reconstruction. The treatment plan computes (1) direct and cumulative volume dose histograms for individual tissues, (2) the average, standard deviation, and coefficient of skewness of the dose distribution within individual tissues, (3) an average (over all tissue pixels) survival probability (S) and average survival dose DASD for a given radiation treatment, (4) normal tissue complication probability (NTCP) delivered to a given tissue. All four computed quantities account for dose heterogeneity. These estimates of the biological response to radiation from laboratory-based studies may help guide the evaluation of the prescribed low- or high-dose rate therapy in retrospective and prospective clinical studies at a number of treatment sites.

  6. Defense Civil Support: DOD Has Made Progress Incorporating the Homeland Response Force into the Chemical, Biological, Radiological, and Nuclear Response Enterprise

    DTIC Science & Technology

    2016-06-01

    DEFENSE CIVIL SUPPORT DOD Has Made Progress Incorporating the Homeland Response Force into the Chemical...Biological, Radiological, and Nuclear Response Enterprise Report to the Committee on Armed Services, House of Representatives June 2016 GAO-16-599... Response Force into the Chemical, Biological, Radiological, and Nuclear Response Enterprise Why GAO Did This Study DOD is expected to play a prominent

  7. The effect of strontium incorporation into CaSiO3 ceramics on their physical and biological properties.

    PubMed

    Wu, Chengtie; Ramaswamy, Yogambha; Kwik, Danielle; Zreiqat, Hala

    2007-07-01

    CaSiO3 ceramics have been regarded as a potential bioactive material for bone regeneration. Strontium (Sr) as a trace element in human body has been found to have beneficial effects on bone formation. The aim of this study was to incorporate Sr into CaSiO3 bioactive ceramics and to investigate their effect(s) on phase transition, sintering property, apatite-formation ability, ionic dissolution, and human bone-derived cells (HBDC) proliferation. Sr containing CaSiO3 (Sr-CaSiO3) ceramics at various concentrations (0-10% Sr) were prepared. The incorporation of Sr into CaSiO3 promoted the phase transition from beta to alpha-CaSiO3 and enhanced ceramic densification but did not alter the mechanism and ability of apatite formation in SBF. The ionic dissolution rate of the Sr-CaSiO3 decreased compared to the CaSiO3. The addition of Sr decreased pH value in SBF. The effect of Sr-CaSiO3 extracts, carried out according to the International Standard Organization, on HBDC proliferation was evaluated. At high extract concentration (100 and 200 mg/mL), CaSiO3 was found to stimulate HBDC proliferation, however, the incorporation of Sr into CaSiO3 stimulated HBDC proliferation even at low extract concentration (ranging from 12.5, 25 to 50 mg/mL). Our results indicate that Sr-CaSiO3 ceramics improved the physical and biological properties of the pure CaSiO3 ceramics.

  8. Integrated Bio-Entity Network: A System for Biological Knowledge Discovery

    PubMed Central

    Bell, Lindsey; Chowdhary, Rajesh; Liu, Jun S.; Niu, Xufeng; Zhang, Jinfeng

    2011-01-01

    A significant part of our biological knowledge is centered on relationships between biological entities (bio-entities) such as proteins, genes, small molecules, pathways, gene ontology (GO) terms and diseases. Accumulated at an increasing speed, the information on bio-entity relationships is archived in different forms at scattered places. Most of such information is buried in scientific literature as unstructured text. Organizing heterogeneous information in a structured form not only facilitates study of biological systems using integrative approaches, but also allows discovery of new knowledge in an automatic and systematic way. In this study, we performed a large scale integration of bio-entity relationship information from both databases containing manually annotated, structured information and automatic information extraction of unstructured text in scientific literature. The relationship information we integrated in this study includes protein–protein interactions, protein/gene regulations, protein–small molecule interactions, protein–GO relationships, protein–pathway relationships, and pathway–disease relationships. The relationship information is organized in a graph data structure, named integrated bio-entity network (IBN), where the vertices are the bio-entities and edges represent their relationships. Under this framework, graph theoretic algorithms can be designed to perform various knowledge discovery tasks. We designed breadth-first search with pruning (BFSP) and most probable path (MPP) algorithms to automatically generate hypotheses—the indirect relationships with high probabilities in the network. We show that IBN can be used to generate plausible hypotheses, which not only help to better understand the complex interactions in biological systems, but also provide guidance for experimental designs. PMID:21738677

  9. Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa.

    PubMed

    Percudani, Riccardo; Carnevali, Davide; Puggioni, Vincenzo

    2013-01-01

    An opaque biochemical definition, an insufficient functional characterization, an interpolated database description, and a beautiful 3D structure with a wrong reaction. All these are elements of an exemplar case of misannotation in biological databases and confusion in the scientific literature concerning genes and enzymes acting on ureidoglycolate, an intermediate of purine catabolism. Here we show biochemical evidence for the relocation of genes assigned to EC 3.5.3.19 (ureidoglycolate hydrolase, releasing ammonia), such as allA of Escherichia coli or DAL3 of Saccharomyces cerevisiae, to EC 4.3.2.3 (ureidoglycolate lyase, releasing urea). The EC 3.5.3.19 should be more appropriately named ureidoglycolate amidohydrolase and include genes equivalent to UAH of Arabidopsis thaliana. The distinction between ammonia- or urea-releasing activities from ureidoglycolate is relevant for the understanding of nitrogen metabolism in various organisms and of virulence factors in certain pathogens rather than a nomenclature problem. We trace the original fault in database annotation and provide a rationale for its incorporation and persistence in the scientific literature. Notwithstanding the technological distance, yet not surprising for the constancy of human nature, error categories and mechanisms established in the study of the work of amanuensis monks still apply to the modern curation of biological databases.

  10. On-line synthesis of pseudopeptide library incorporating a benzodiazepinone turn mimic: biological evaluation on MC1 receptors.

    PubMed

    Verdié, Pascal; Subra, Gilles; Feliu, Lidia; Sanchez, Pierre; Bergé, Gilbert; Garcin, Geneviève; Martinez, Jean

    2007-01-01

    Alpha melanocyte stimulating hormone (alpha-MSH) is a widely distributed hormone. This tridecapeptide exhibits various biological activities mediated through different receptors. alpha-MSH binds to the melanocortin-1 receptor (MC1-R), mainly expressed in keratinocytes and melanocytes, inducing melanogenesis and anti-inflammatory processes. The central His-Phe-Arg-Trp tetrapeptide sequence of alpha-MSH is known to form a turn in the bioactive conformation. To find new potent analogs of alpha-MSH, we decided to introduce non-peptide building blocks in the alpha-MSH sequence. Molecular modeling studies showed that two amino acids of the central core sequence could be replaced by the benzodiazepinone building block without loosing the beta-turn conformation. Benzodiazepines are well-known pharmacophores exhibiting a wide scope of biological activities and are described as constrained dipeptide mimics templates. Although numerous synthetic pathways leading to benzodiazepinones have been described in literature, no methodology has 1,4-benzodiazepine-2,5-diones building blocks bearing a free carboxylic acid function and a protected amino function suitable for incorporation into peptide sequences. In this study, we report the synthesis of peptides with a benzodiazepinone moiety obtained directly during the course of solid-phase peptide synthesis (SPPS). This "on-line" strategy leads to the generation of a 54-member pseudo-peptide library of alpha-MSH analogs. After LC/MS purification, binding assays were performed on the MC1 receptor leading to the discovery of several micromolar ligands.

  11. Effect of different hydroxyapatite incorporation methods on the structural and biological properties of porous collagen scaffolds for bone repair.

    PubMed

    Ryan, Alan J; Gleeson, John P; Matsiko, Amos; Thompson, Emmet M; O'Brien, Fergal J

    2015-12-01

    treatment. Control of scaffold microstructure was examined via alterations in freezing temperature. It was found that the addition of HA prior to freeze-drying generally reduced the pore size and so the CpHA scaffold fabrication method offered increased control over the resulting scaffolds microstructure. These findings will help guide future design considerations for composite biomaterials and demonstrate that the method of HA incorporation can have profound effects on the resulting scaffold structural and biological response.

  12. Local knowledge and perception of biological soil crusts by land users in the Sahel (Niger)

    NASA Astrophysics Data System (ADS)

    J-M Ambouta, K.; Hassan Souley, B.; Malam Issa, O.; Rajot, J. L.; Mohamadou, A.

    2012-04-01

    Local knowledge, i.e. knowledge based on accumulation of observations is of great interest for many scientific fields as it can help for identification, evaluation and selection of relevant indicators and furthermore for progress through conservation goals. This study aimed at gathering and understanding the local knowledge and perception of biological soil crusts (BSC) by users of land, pastoralists that cross the Sahel and sedentary farmers. The methodological approach is based on a semi-direct surveys conducted on a north-south rainfall gradient (350 to 650 mm/year) including agricultural- and pastoral-dominated areas in western Niger. Denomination, formation processes, occurrence, distribution and role of biological soil crusts are among the major issues of the inquiry. The results of the surveys showed that BSC are mainly identified by the names of "Bankwado" and "Korobanda", respectively in hausa and zarma langages, what means "toad back". Other denominations varying according to region, ethnic groups and users are used. They are all related to the aspects, colors and behaviour of BSC with regard wetting and drying cycle. From the point of view of users depressed areas and land lied fallow are favourable places for the occurrence of BSC, while cultivation and observed changes in rainfall regimes represent negative factors. The formation processes of BSC are mainly related to the occurrence and the impact of rain and wind on soil surface. Their roles in protecting soil against degradation or as an indicator of soil fertility were recognised by at least 83% of farmers and breeders. This study reveals significant aspects of BSC already validated by scientific knowledge. Integrating the two forms of knowledge will help to define relevant indicators of soil surface dynamics and to perform practices to minimize farming and grazing impacts on BSCs.

  13. The effect of parents' conversational style and disciplinary knowledge on children's observation of biological phenomena

    NASA Astrophysics Data System (ADS)

    Eberbach, Catherine

    This study was designed to better understand how children begin to make the transition from seeing the natural world to scientifically observing the natural world during shared family activity in an informal learning environment. Specifically, this study addressed research questions: (1) What is the effect of differences in parent conversational style and disciplinary knowledge on children's observations of biological phenomena? (2) What is the relationship between parent disciplinary knowledge and conversational style to children's observations of biological phenomena? and (3) Can parents, regardless of knowledge, be trained to use a teaching strategy with their children that can be implemented in informal learning contexts? To address these questions, 79 parent-child dyads with children 6-10 years old participated in a controlled study in which half of the parents used their natural conversational style and the other half were trained to use particular conversational strategies during family observations of pollination in a botanical garden. Parents were also assigned to high and low knowledge groups according to their disciplinary knowledge of pollination. Data sources included video recordings of parent-child observations in a garden, pre-post child tasks, and parent surveys. Findings revealed that parents who received training used the conversational strategies more than parents who used their natural conversational style. Parents and children who knew more about pollination at the start of the study exhibited higher levels of disciplinary talk in the garden, which is to be expected. However, the use of the conversational strategies also increased the amount of disciplinary talk in the garden, independent of what families knew about pollination. The extent to which families engaged in disciplinary talk in the garden predicted significant variance in children's post-test scores. In addition to these findings, an Observation Framework (Eberbach & Crowley, 2009

  14. Integrating biological knowledge based on functional annotations for biclustering of gene expression data.

    PubMed

    Nepomuceno, Juan A; Troncoso, Alicia; Nepomuceno-Chamorro, Isabel A; Aguilar-Ruiz, Jesús S

    2015-05-01

    Gene expression data analysis is based on the assumption that co-expressed genes imply co-regulated genes. This assumption is being reformulated because the co-expression of a group of genes may be the result of an independent activation with respect to the same experimental condition and not due to the same regulatory regime. For this reason, traditional techniques are recently being improved with the use of prior biological knowledge from open-access repositories together with gene expression data. Biclustering is an unsupervised machine learning technique that searches patterns in gene expression data matrices. A scatter search-based biclustering algorithm that integrates biological information is proposed in this paper. In addition to the gene expression data matrix, the input of the algorithm is only a direct annotation file that relates each gene to a set of terms from a biological repository where genes are annotated. Two different biological measures, FracGO and SimNTO, are proposed to integrate this information by means of its addition to-be-optimized fitness function in the scatter search scheme. The measure FracGO is based on the biological enrichment and SimNTO is based on the overlapping among GO annotations of pairs of genes. Experimental results evaluate the proposed algorithm for two datasets and show the algorithm performs better when biological knowledge is integrated. Moreover, the analysis and comparison between the two different biological measures is presented and it is concluded that the differences depend on both the data source and how the annotation file has been built in the case GO is used. It is also shown that the proposed algorithm obtains a greater number of enriched biclusters than other classical biclustering algorithms typically used as benchmark and an analysis of the overlapping among biclusters reveals that the biclusters obtained present a low overlapping. The proposed methodology is a general-purpose algorithm which allows

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

    PubMed

    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.

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

    PubMed Central

    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

  17. Evaluation of Gene Association Methods for Coexpression Network Construction and Biological Knowledge Discovery

    PubMed Central

    Kumari, Sapna; Nie, Jeff; Chen, Huann-Sheng; Ma, Hao; Stewart, Ron; Li, Xiang; Lu, Meng-Zhu; Taylor, William M.; Wei, Hairong

    2012-01-01

    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. PMID:23226279

  18. BINNING SOMATIC MUTATIONS BASED ON BIOLOGICAL KNOWLEDGE FOR PREDICTING SURVIVAL: AN APPLICATION IN RENAL CELL CARCINOMA

    PubMed Central

    Kim, Dokyoon; Li, Ruowang; Dudek, Scott M.; Wallace, John R.; Ritchie, Marylyn D.

    2014-01-01

    Enormous efforts of whole exome and genome sequencing from hundreds to thousands of patients have provided the landscape of somatic genomic alterations in many cancer types to distinguish between driver mutations and passenger mutations. Driver mutations show strong associations with cancer clinical outcomes such as survival. However, due to the heterogeneity of tumors, somatic mutation profiles are exceptionally sparse whereas other types of genomic data such as miRNA or gene expression contain much more complete data for all genomic features with quantitative values measured in each patient. To overcome the extreme sparseness of somatic mutation profiles and allow for the discovery of combinations of somatic mutations that may predict cancer clinical outcomes, here we propose a new approach for binning somatic mutations based on existing biological knowledge. Through the analysis using renal cell carcinoma dataset from The Cancer Genome Atlas (TCGA), we identified combinations of somatic mutation burden based on pathways, protein families, evolutionary conversed regions, and regulatory regions associated with survival. Due to the nature of heterogeneity in cancer, using a binning strategy for somatic mutation profiles based on biological knowledge will be valuable for improved prognostic biomarkers and potentially for tailoring therapeutic strategies by identifying combinations of driver mutations. PMID:25592572

  19. Verbal final exam in introductory biology yields gains in student content knowledge and longitudinal performance.

    PubMed

    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 < 0.001);. The higher-achieving 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.

  20. Improvement of physical, chemical, and biological properties of aridisol from Botswana by the incorporation of torrefied biomass

    PubMed Central

    Ogura, Tatsuki; Date, Yasuhiro; Masukujane, Masego; Coetzee, Tidimalo; Akashi, Kinya; Kikuchi, Jun

    2016-01-01

    Effective use of agricultural residual biomass may be beneficial for both local and global ecosystems. Recently, biochar has received attention as a soil enhancer, and its effects on plant growth and soil microbiota have been investigated. However, there is little information on how the physical, chemical, and biological properties of soil amended with biochar are affected. In this study, we evaluated the effects of the incorporation of torrefied plant biomass on physical and structural properties, elemental profiles, initial plant growth, and metabolic and microbial dynamics in aridisol from Botswana. Hemicellulose in the biomass was degraded while cellulose and lignin were not, owing to the relatively low-temperature treatment in the torrefaction preparation. Water retentivity and mineral availability for plants were improved in soils with torrefied biomass. Furthermore, fertilization with 3% and 5% of torrefied biomass enhanced initial plant growth and elemental uptake. Although the metabolic and microbial dynamics of the control soil were dominantly associated with a C1 metabolism, those of the 3% and 5% torrefied biomass soils were dominantly associated with an organic acid metabolism. Torrefied biomass was shown to be an effective soil amendment by enhancing water retentivity, structural stability, and plant growth and controlling soil metabolites and microbiota. PMID:27313139

  1. Improvement of physical, chemical, and biological properties of aridisol from Botswana by the incorporation of torrefied biomass

    NASA Astrophysics Data System (ADS)

    Ogura, Tatsuki; Date, Yasuhiro; Masukujane, Masego; Coetzee, Tidimalo; Akashi, Kinya; Kikuchi, Jun

    2016-06-01

    Effective use of agricultural residual biomass may be beneficial for both local and global ecosystems. Recently, biochar has received attention as a soil enhancer, and its effects on plant growth and soil microbiota have been investigated. However, there is little information on how the physical, chemical, and biological properties of soil amended with biochar are affected. In this study, we evaluated the effects of the incorporation of torrefied plant biomass on physical and structural properties, elemental profiles, initial plant growth, and metabolic and microbial dynamics in aridisol from Botswana. Hemicellulose in the biomass was degraded while cellulose and lignin were not, owing to the relatively low-temperature treatment in the torrefaction preparation. Water retentivity and mineral availability for plants were improved in soils with torrefied biomass. Furthermore, fertilization with 3% and 5% of torrefied biomass enhanced initial plant growth and elemental uptake. Although the metabolic and microbial dynamics of the control soil were dominantly associated with a C1 metabolism, those of the 3% and 5% torrefied biomass soils were dominantly associated with an organic acid metabolism. Torrefied biomass was shown to be an effective soil amendment by enhancing water retentivity, structural stability, and plant growth and controlling soil metabolites and microbiota.

  2. [A novel biological pathway expansion method based on the knowledge of protein-protein interactions].

    PubMed

    Zhao, Xiaolei; Zuo, Xiaoyu; Qin, Jiheng; Liang, Yan; Zhang, Naizun; Luan, Yizhao; Rao, Shaoqi

    2014-04-01

    Biological pathways have been widely used in gene function studies; however, the current knowledge for biological pathways is per se incomplete and has to be further expanded. Bioinformatics prediction provides us a cheap but effective way for pathway expansion. Here, we proposed a novel method for biological pathway prediction, by intergrating prior knowledge of protein?protein interactions and Gene Ontology (GO) database. First, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to which the interacting neighbors of a targe gene (at the level of protein?protein interaction) belong were chosen as the candidate pathways. Then, the pathways to which the target gene belong were determined by testing whether the genes in the candidate pathways were enriched in the GO terms to which the target gene were annotated. The protein?protein interaction data obtained from the Human Protein Reference Database (HPRD) and Biological General Repository for Interaction Datasets (BioGRID) were respectively used to predict the pathway attribution(s) of the target gene. The results demanstrated that both the average accuracy (the ratio of the correctly predicted pathways to the totally pathways to which all the target genes were annotated) and the relative accuracy (of the genes with at least one annotated pathway being successful predicted, the percentage of the genes with all the annotated pathways being correctly predicted) for pathway predictions were increased with the number of the interacting neighbours. When the number of interacting neighbours reached 22, the average accuracy was 96.2% (HPRD) and 96.3% (BioGRID), respectively, and the relative accuracy was 93.3% (HPRD) and 84.1% (BioGRID), respectively. Further validation analysis of 89 genes whose pathway knowledge was updated in a new database release indicated that 50 genes were correctly predicted for at least one updated pathway, and 43 genes were accurately predicted for all the updated pathways, giving an

  3. The Effect of an Instructional Unit Incorporating Live Animals on Knowledge of Nutrition for Different Age Levels.

    ERIC Educational Resources Information Center

    Roth, Anne I.; Wunderlich, Kenneth W.

    A nutrition education unit, Rat Pak, developed by Dairy Council, Inc., is an attempt to influence students to make wise food choices. It consists of eleven lessons in an instructional sequence which incorporates the use of white rats as a means of illustrating the effect of improper diet while teaching proper diet. The purpose of this…

  4. A semantic web framework to integrate cancer omics data with biological knowledge

    PubMed Central

    2012-01-01

    Background The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. Results For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. Conclusions We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily. PMID:22373303

  5. Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

    PubMed Central

    Rowland, Jessica; Guan, Yuanfang; Bongo, Lars A.; Burdine, Rebecca D.; Troyanskaya, Olga G.

    2013-01-01

    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 techniques and will

  6. Regulatory component analysis: a semi-blind extraction approach to infer gene regulatory networks with imperfect biological knowledge

    PubMed Central

    Wang, Chen; Xuan, Jianhua; Shih, Ie-Ming; Clarke, Robert; Wang, Yue

    2011-01-01

    With the advent of high-throughput biotechnology capable of monitoring genomic signals, it becomes increasingly promising to understand molecular cellular mechanisms through systems biology approaches. One of the active research topics in systems biology is to infer gene transcriptional regulatory networks using various genomic data; this inference problem can be formulated as a linear model with latent signals associated with some regulatory proteins called transcription factors (TFs). As common statistical assumptions may not hold for genomic signals, typical latent variable algorithms such as independent component analysis (ICA) are incapable to reveal underlying true regulatory signals. Liao et al. [1] proposed to perform inference using an approach named network component analysis (NCA), the optimization of which is achieved by a least-squares fitting approach with biological knowledge constraints. However, the incompleteness of biological knowledge and its inconsistency with gene expression data are not considered in the original NCA solution, which could greatly affect the inference accuracy. To overcome these limitations, we propose a linear extraction scheme, namely regulatory component analysis (RCA), to infer underlying regulatory signals even with partial biological knowledge. Numerical simulations show a significant improvement of our proposed RCA over NCA, not only when signal-to-noise-ratio (SNR) is low, but also when the given biological knowledge is incomplete and inconsistent to gene expression data. Furthermore, real biological experiments on E. coli are performed for regulatory network inference in comparison with several typical linear latent variable methods, which again demonstrates the effectiveness and improved performance of the proposed algorithm. PMID:22685363

  7. Development and Use of a Test Instrument to Measure Biology Teachers' Content Knowledge (CK) and Pedagogical Content Knowledge (PCK)

    ERIC Educational Resources Information Center

    Juttner, Melanie; Boone, Williame; Park, Soonhye; Neuhaus, Birgit J.

    2013-01-01

    Research on teachers' professionalism and professional development has increased in the last two decades. A main focus of this line of research has been the cognitive component of teacher professionalism, i.e., professional knowledge. Most of the previous studies on teacher knowledge--such as the Learning Mathematics for Teaching (LMT) (Hill et…

  8. Incorporating Indigenous Knowledge Systems into Agricultural and Extension Education Programs: A Study of the Perceptions of Extension Professionals.

    ERIC Educational Resources Information Center

    Rajasekaran, B.; Martin, Robert A.

    Dissemination of technologies to increase agricultural production using the conventional transfer of technology system has often failed to consider the natural environment, indigenous knowledge systems, and resource endowments around which resource-poor farmers normally operate. A sample of 96 agricultural extension professionals in 2 districts in…

  9. Knowledge.

    ERIC Educational Resources Information Center

    Online-Offline, 1999

    1999-01-01

    This theme issue on knowledge includes annotated listings of Web sites, CD-ROMs and computer software, videos, books, and additional resources that deal with knowledge and differences between how animals and humans learn. Sidebars discuss animal intelligence, learning proper behavior, and getting news from the Internet. (LRW)

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

    PubMed

    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.

  11. Opportunities and strategies to incorporate ecosystem services knowledge and decision support tools into planning and decision making in Hawai'i.

    PubMed

    Bremer, Leah L; Delevaux, Jade M S; Leary, James J K; J Cox, Linda; Oleson, Kirsten L L

    2015-04-01

    Incorporating ecosystem services into management decisions is a promising means to link conservation and human well-being. Nonetheless, planning and management in Hawai'i, a state with highly valued natural capital, has yet to broadly utilize an ecosystem service approach. We conducted a stakeholder assessment, based on semi-structured interviews, with terrestrial (n = 26) and marine (n = 27) natural resource managers across the State of Hawai'i to understand the current use of ecosystem services (ES) knowledge and decision support tools and whether, how, and under what contexts, further development would potentially be useful. We found that ES knowledge and tools customized to Hawai'i could be useful for communication and outreach, justifying management decisions, and spatial planning. Greater incorporation of this approach is clearly desired and has a strong potential to contribute to more sustainable decision making and planning in Hawai'i and other oceanic island systems. However, the unique biophysical, socio-economic, and cultural context of Hawai'i, and other island systems, will require substantial adaptation of existing ES tools. Based on our findings, we identified four key opportunities for the use of ES knowledge and tools in Hawai'i: (1) linking native forest protection to watershed health; (2) supporting sustainable agriculture; (3) facilitating ridge-to-reef management; and (4) supporting statewide terrestrial and marine spatial planning. Given the interest expressed by natural resource managers, we envision broad adoption of ES knowledge and decision support tools if knowledge and tools are tailored to the Hawaiian context and coupled with adequate outreach and training.

  12. Opportunities and Strategies to Incorporate Ecosystem Services Knowledge and Decision Support Tools into Planning and Decision Making in Hawai`i

    NASA Astrophysics Data System (ADS)

    Bremer, Leah L.; Delevaux, Jade M. S.; Leary, James J. K.; J. Cox, Linda; Oleson, Kirsten L. L.

    2015-04-01

    Incorporating ecosystem services into management decisions is a promising means to link conservation and human well-being. Nonetheless, planning and management in Hawai`i, a state with highly valued natural capital, has yet to broadly utilize an ecosystem service approach. We conducted a stakeholder assessment, based on semi-structured interviews, with terrestrial ( n = 26) and marine ( n = 27) natural resource managers across the State of Hawai`i to understand the current use of ecosystem services (ES) knowledge and decision support tools and whether, how, and under what contexts, further development would potentially be useful. We found that ES knowledge and tools customized to Hawai`i could be useful for communication and outreach, justifying management decisions, and spatial planning. Greater incorporation of this approach is clearly desired and has a strong potential to contribute to more sustainable decision making and planning in Hawai`i and other oceanic island systems. However, the unique biophysical, socio-economic, and cultural context of Hawai`i, and other island systems, will require substantial adaptation of existing ES tools. Based on our findings, we identified four key opportunities for the use of ES knowledge and tools in Hawai`i: (1) linking native forest protection to watershed health; (2) supporting sustainable agriculture; (3) facilitating ridge-to-reef management; and (4) supporting statewide terrestrial and marine spatial planning. Given the interest expressed by natural resource managers, we envision broad adoption of ES knowledge and decision support tools if knowledge and tools are tailored to the Hawaiian context and coupled with adequate outreach and training.

  13. Knowledge discovery from high-frequency stream nitrate concentrations: hydrology and biology contributions.

    PubMed

    Aubert, Alice H; Thrun, Michael C; Breuer, Lutz; Ultsch, Alfred

    2016-08-30

    High-frequency, in-situ monitoring provides large environmental datasets. These datasets will likely bring new insights in landscape functioning and process scale understanding. However, tailoring data analysis methods is necessary. Here, we detach our analysis from the usual temporal analysis performed in hydrology to determine if it is possible to infer general rules regarding hydrochemistry from available large datasets. We combined a 2-year in-stream nitrate concentration time series (time resolution of 15 min) with concurrent hydrological, meteorological and soil moisture data. We removed the low-frequency variations through low-pass filtering, which suppressed seasonality. We then analyzed the high-frequency variability component using Pareto Density Estimation, which to our knowledge has not been applied to hydrology. The resulting distribution of nitrate concentrations revealed three normally distributed modes: low, medium and high. Studying the environmental conditions for each mode revealed the main control of nitrate concentration: the saturation state of the riparian zone. We found low nitrate concentrations under conditions of hydrological connectivity and dominant denitrifying biological processes, and we found high nitrate concentrations under hydrological recession conditions and dominant nitrifying biological processes. These results generalize our understanding of hydro-biogeochemical nitrate flux controls and bring useful information to the development of nitrogen process-based models at the landscape scale.

  14. Knowledge discovery from high-frequency stream nitrate concentrations: hydrology and biology contributions

    NASA Astrophysics Data System (ADS)

    Aubert, Alice H.; Thrun, Michael C.; Breuer, Lutz; Ultsch, Alfred

    2016-08-01

    High-frequency, in-situ monitoring provides large environmental datasets. These datasets will likely bring new insights in landscape functioning and process scale understanding. However, tailoring data analysis methods is necessary. Here, we detach our analysis from the usual temporal analysis performed in hydrology to determine if it is possible to infer general rules regarding hydrochemistry from available large datasets. We combined a 2-year in-stream nitrate concentration time series (time resolution of 15 min) with concurrent hydrological, meteorological and soil moisture data. We removed the low-frequency variations through low-pass filtering, which suppressed seasonality. We then analyzed the high-frequency variability component using Pareto Density Estimation, which to our knowledge has not been applied to hydrology. The resulting distribution of nitrate concentrations revealed three normally distributed modes: low, medium and high. Studying the environmental conditions for each mode revealed the main control of nitrate concentration: the saturation state of the riparian zone. We found low nitrate concentrations under conditions of hydrological connectivity and dominant denitrifying biological processes, and we found high nitrate concentrations under hydrological recession conditions and dominant nitrifying biological processes. These results generalize our understanding of hydro-biogeochemical nitrate flux controls and bring useful information to the development of nitrogen process-based models at the landscape scale.

  15. Knowledge discovery from high-frequency stream nitrate concentrations: hydrology and biology contributions

    PubMed Central

    Aubert, Alice H.; Thrun, Michael C.; Breuer, Lutz; Ultsch, Alfred

    2016-01-01

    High-frequency, in-situ monitoring provides large environmental datasets. These datasets will likely bring new insights in landscape functioning and process scale understanding. However, tailoring data analysis methods is necessary. Here, we detach our analysis from the usual temporal analysis performed in hydrology to determine if it is possible to infer general rules regarding hydrochemistry from available large datasets. We combined a 2-year in-stream nitrate concentration time series (time resolution of 15 min) with concurrent hydrological, meteorological and soil moisture data. We removed the low-frequency variations through low-pass filtering, which suppressed seasonality. We then analyzed the high-frequency variability component using Pareto Density Estimation, which to our knowledge has not been applied to hydrology. The resulting distribution of nitrate concentrations revealed three normally distributed modes: low, medium and high. Studying the environmental conditions for each mode revealed the main control of nitrate concentration: the saturation state of the riparian zone. We found low nitrate concentrations under conditions of hydrological connectivity and dominant denitrifying biological processes, and we found high nitrate concentrations under hydrological recession conditions and dominant nitrifying biological processes. These results generalize our understanding of hydro-biogeochemical nitrate flux controls and bring useful information to the development of nitrogen process-based models at the landscape scale. PMID:27572284

  16. Biological determinants linking infant weight gain and child obesity: current knowledge and future directions.

    PubMed

    Young, Bridget E; Johnson, Susan L; Krebs, Nancy F

    2012-09-01

    Childhood obesity rates have reached epidemic proportions. Excessive weight gain in infancy is associated with persistence of elevated weight status and later obesity. In this review, we make the case that weight gain in the first 6 mo is especially predictive of later obesity risk due to the metabolic programming that can occur early postpartum. The current state of knowledge regarding the biological determinants of excess infant weight gain is reviewed, with particular focus on infant feeding choice. Potential mechanisms by which different feeding approaches may program the metabolic profile of the infant, causing the link between early weight gain and later obesity are proposed. These mechanisms are likely highly complex and involve synergistic interactions between endocrine effects and factors that alter the inflammatory and oxidative stress status of the infant. Gaps in current knowledge are highlighted. These include a lack of data describing 1) what type of infant body fat distribution may impart risk and 2) how maternal metabolic dysfunction (obesity and/or diabetes) may affect milk composition and exert downstream effects on infant metabolism. Improved understanding and management of these early postnatal determinants of childhood obesity may have great impact on reducing its prevalence.

  17. Teacher knowledge and discourse control: Quantitative evidence from novice biology teachers' classrooms

    NASA Astrophysics Data System (ADS)

    Carlsen, William S.

    This article describes the effects of science teacher subject-matter knowledge on classroom discourse at the level of individual utterances. It details one of three parallel analyses conducted in a year-long study of language in the classrooms of four new biology teachers. The conceptual framework of the study predicts that when teaching unfamiliar subject matter, teachers use a variety of discourse strategies to constrain student talk to a narrowly circumscribed topic domain. This article includes the results of an utterance-by-utterance analysis of teacher and student talk in a 30-lesson sample of science instruction. Data are broken down by classroom activity (e.g., lecture, laboratory, group work) for several measures, including mean duration of utterances, domination of the speaking floor by the teacher, frequency of teacher questioning, cognitive level of teacher questions, and student verbal participation. When teaching unfamiliar topics, the four teachers in this study tended to talk more often and for longer periods of time, ask questions frequently, and rely heavily on low cognitive level questions. The rate of student questions to the teacher varied with classroom activity. In common classroom communicative settings, student questions were less common when the teacher was teaching unfamiliar subject matter. The implications of these findings include a suggestion that teacher knowledge may be an important unconsidered variable in research on the cognitive level of questions and teacher wait-time.

  18. Knowledge discovery and system biology in molecular medicine: an application on neurodegenerative diseases.

    PubMed

    Fattore, Matteo; Arrigo, Patrizio

    2005-01-01

    The possibility to study an organism in terms of system theory has been proposed in the past, but only the advancement of molecular biology techniques allow us to investigate the dynamical properties of a biological system in a more quantitative and rational way than before . These new techniques can gave only the basic level view of an organisms functionality. The comprehension of its dynamical behaviour depends on the possibility to perform a multiple level analysis. Functional genomics has stimulated the interest in the investigation the dynamical behaviour of an organism as a whole. These activities are commonly known as System Biology, and its interests ranges from molecules to organs. One of the more promising applications is the 'disease modeling'. The use of experimental models is a common procedure in pharmacological and clinical researches; today this approach is supported by 'in silico' predictive methods. This investigation can be improved by a combination of experimental and computational tools. The Machine Learning (ML) tools are able to process different heterogeneous data sources, taking into account this peculiarity, they could be fruitfully applied to support a multilevel data processing (molecular, cellular and morphological) that is the prerequisite for the formal model design; these techniques can allow us to extract the knowledge for mathematical model development. The aim of our work is the development and implementation of a system that combines ML and dynamical models simulations. The program is addressed to the virtual analysis of the pathways involved in neurodegenerative diseases. These pathologies are multifactorial diseases and the relevance of the different factors has not yet been well elucidated. This is a very complex task; in order to test the integrative approach our program has been limited to the analysis of the effects of a specific protein, the Cyclin dependent kinase 5 (CDK5) which relies on the induction of neuronal

  19. The Integration Process for Incorporating Nuclear Explosion Monitoring Research Results into the National Nuclear Security Administration Knowledge Base

    SciTech Connect

    GALLEGOS, DAVID P.; CARR, DORTHE B.; HERRINGTON, PRESTON B.; HARRIS, JAMES M.; EDWARDS, C.L.; TAYLOR, STEVEN R.; WOGMAN, NED A.; ANDERSON, DALE N.; CASEY, LESLIE A.

    2002-09-01

    The process of developing the National Nuclear Security Administration (NNSA) Knowledge Base (KB) must result in high-quality Information Products in order to support activities for monitoring nuclear explosions consistent with United States treaty and testing moratoria monitoring missions. The validation, verification, and management of the Information Products is critical to successful scientific integration, and hence, will enable high-quality deliveries to be made to the United States National Data Center (USNDC) at the Air Force Technical Applications Center (AFTAC). As an Information Product passes through the steps necessary to become part of a delivery to AFTAC, domain experts (including technical KB Working Groups that comprise NNSA and DOE laboratory staff and the customer) will provide coordination and validation, where validation is the determination of relevance and scientific quality. Verification is the check for completeness and correctness, and will be performed by both the Knowledge Base Integrator and the Scientific Integrator with support from the Contributor providing two levels of testing to assure content integrity and performance. The Information Products and their contained data sets will be systematically tracked through the integration portion of their life cycle. The integration process, based on lessons learned during its initial implementations, is presented in this report.

  20. Content-Related Knowledge of Biology Teachers from Secondary Schools: Structure and Learning Opportunities

    ERIC Educational Resources Information Center

    Großschedl, Jörg; Mahler, Daniela; Kleickmann, Thilo; Harms, Ute

    2014-01-01

    Teachers' content-related knowledge is a key factor influencing the learning progress of students. Different models of content-related knowledge have been proposed by educational researchers; most of them take into account three categories: content knowledge, pedagogical content knowledge, and curricular knowledge. As there is no consensus about…

  1. Whose ethics of knowledge? Taking the next step in evaluating knowledge in synthetic biology: a response to Douglas and Savulescu.

    PubMed

    Pierce, Robin L

    2012-10-01

    The recent proposal by Douglas and Savulescu for an ethics of knowledge provokes a renewed consideration of an enduring issue. Yet, the concept raises significant challenges for procedural and substantive justice. Indeed, the operationalisation of 'an ethics of knowledge' could be as alarming as what it seeks to prevent. While we can acknowledge that there is, and surely always will be, potential for misuse of beneficial science and technology, a contemplated conception of what we ought to not know, devise or disseminate sets before us an enormously complex task. This essay challenges an ethics of knowledge to respond to concerns of procedural and substantive justice. While the concept has a certain appeal, it does not appear to adequately address certain fundamental issues as it is currently presented. Here, the author invites consideration of two primary points: (1) who should decide, based on whose interests? and (2) could such an exercise actually be effective in achieving its goal?

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

    NASA Astrophysics Data System (ADS)

    Sickel, Aaron J.; Friedrichsen, Patricia

    2017-03-01

    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.

  3. Influence of using challenging tasks in biology classrooms on students' cognitive knowledge structure: an empirical video study

    NASA Astrophysics Data System (ADS)

    Nawani, Jigna; Rixius, Julia; Neuhaus, Birgit J.

    2016-08-01

    Empirical analysis of secondary biology classrooms revealed that, on average, 68% of teaching time in Germany revolved around processing tasks. Quality of instruction can thus be assessed by analyzing the quality of tasks used in classroom discourse. This quasi-experimental study analyzed how teachers used tasks in 38 videotaped biology lessons pertaining to the topic 'blood and circulatory system'. Two fundamental characteristics used to analyze tasks include: (1) required cognitive level of processing (e.g. low level information processing: repetiition, summary, define, classify and high level information processing: interpret-analyze data, formulate hypothesis, etc.) and (2) complexity of task content (e.g. if tasks require use of factual, linking or concept level content). Additionally, students' cognitive knowledge structure about the topic 'blood and circulatory system' was measured using student-drawn concept maps (N = 970 students). Finally, linear multilevel models were created with high-level cognitive processing tasks and higher content complexity tasks as class-level predictors and students' prior knowledge, students' interest in biology, and students' interest in biology activities as control covariates. Results showed a positive influence of high-level cognitive processing tasks (β = 0.07; p < .01) on students' cognitive knowledge structure. However, there was no observed effect of higher content complexity tasks on students' cognitive knowledge structure. Presented findings encourage the use of high-level cognitive processing tasks in biology instruction.

  4. Preparation, Purification, and Secondary Structure Determination of Bacillus Circulans Xylanase. A Molecular Laboratory Incorporating Aspects of Molecular Biology, Biochemistry, and Biophysical Chemistry

    ERIC Educational Resources Information Center

    Russo, Sal; Gentile, Lisa

    2006-01-01

    A project module designed for biochemistry or cellular and molecular biology student which involves determining the secondary structure of Bacillus circulans xylanase (BCX) by circular dichroism (CD) spectroscopy under conditions that compromise its stabilizing intramolecular forces is described. The lab model enhanced students knowledge of the…

  5. Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction.

    PubMed

    Thiele, Herbert; Glandorf, Jörg; Hufnagel, Peter

    2010-05-27

    With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScape bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists; current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specific questions about the biological condition or disease model of the analyzed sample. In this context, a new tool has been developed at the Spanish Centro Nacional de Biotecnologia Proteomics Facility termed PIKE (Protein information and Knowledge Extractor) that allows researchers to control, filter and access specific information from genomics and proteomic databases, to understand the role and relationships of the proteins identified in the experiments. Additionally, an EU funded project, ProDac, has coordinated systematic data collection in public standards-compliant repositories like PRIDE. This will cover all aspects from generating MS data in the laboratory, assembling the whole annotation information and storing it together with identifications in a standardised format.

  6. Review: Improving our knowledge of male mosquito biology in relation to genetic control programmes.

    PubMed

    Lees, Rosemary Susan; Knols, Bart; Bellini, Romeo; Benedict, Mark Q; Bheecarry, Ambicadutt; Bossin, Hervé Christophe; Chadee, Dave D; Charlwood, Jacques; Dabiré, Roch K; Djogbenou, Luc; Egyir-Yawson, Alexander; Gato, René; Gouagna, Louis Clément; Hassan, Mo'awia Mukhtar; Khan, Shakil Ahmed; Koekemoer, Lizette L; Lemperiere, Guy; Manoukis, Nicholas C; Mozuraitis, Raimondas; Pitts, R Jason; Simard, Frederic; Gilles, Jeremie R L

    2014-04-01

    The enormous burden placed on populations worldwide by mosquito-borne diseases, most notably malaria and dengue, is currently being tackled by the use of insecticides sprayed in residences or applied to bednets, and in the case of dengue vectors through reduction of larval breeding sites or larviciding with insecticides thereof. However, these methods are under threat from, amongst other issues, the development of insecticide resistance and the practical difficulty of maintaining long-term community-wide efforts. The sterile insect technique (SIT), whose success hinges on having a good understanding of the biology and behaviour of the male mosquito, is an additional weapon in the limited arsenal against mosquito vectors. The successful production and release of sterile males, which is the mechanism of population suppression by SIT, relies on the release of mass-reared sterile males able to confer sterility in the target population by mating with wild females. A five year Joint FAO/IAEA Coordinated Research Project brought together researchers from around the world to investigate the pre-mating conditions of male mosquitoes (physiology and behaviour, resource acquisition and allocation, and dispersal), the mosquito mating systems and the contribution of molecular or chemical approaches to the understanding of male mosquito mating behaviour. A summary of the existing knowledge and the main novel findings of this group is reviewed here, and further presented in the reviews and research articles that form this Acta Tropica special issue.

  7. Knowledge of the biological actions of extra virgin olive oil gained from mice lacking apolipoprotein E.

    PubMed

    Guillén, Natalia; Acín, Sergio; Navarro, María A; Surra, Joaquín Carlos; Arnal, Carmen; Lou-Bonafonte, José Manuel; Muniesa, Pedro; Martínez-Gracia, María Victoria; Osada, Jesús

    2009-03-01

    The low incidence of cardiovascular disease in countries bordering the Mediterranean basin, where olive oil is the main source of dietary fat, has stimulated interest in the chemical composition of olive oil and in the production of other oils enriched with its minor components. This review summarizes what has been learned about the effects of different olive oil preparations on the development of atherosclerosis and about the prognostic value of associated plasma variables in the disease from experiments on genetically modified mice that spontaneously develop atherosclerosis. The limitations of this animal model associated with its morphological and physiological differences with humans are minimized by the similarity of the two genomes and by the potential for increased understanding attainable, given that the dietary interventions reported here would have taken 400 years to achieve in humans. As observed in traditional Mediterranean populations, it has been confirmed that extra virgin olive oil is beneficial when consumed judiciously and in a diet that is low in cholesterol due to the relative scarcity of animal products. Furthermore, the use of genomic techniques has led to the identification of new markers of response to olive oil. In conclusion, multidisciplinary research into extra virgin olive oil is expanding our knowledge of the substance's biological properties.

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

    PubMed

    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.

  9. Development of a biologically based fertilizer, incorporating Bacillus megaterium A6, for improved phosphorus nutrition of oilseed rape.

    PubMed

    Hu, Xiaojia; Roberts, Daniel P; Xie, Lihua; Maul, Jude E; Yu, Changbing; Li, Yinshui; Zhang, Shujie; Liao, Xing

    2013-04-01

    Sustainable methods with diminished impact on the environment need to be developed for the production of oilseed rape in China and other regions of the world. A biological fertilizer consisting of Bacillus megaterium A6 cultured on oilseed rape meal improved oilseed rape seed yield (P < 0.0001) relative to the nontreated control in 2 greenhouse pot experiments using natural soil. This treatment resulted in slightly greater yield than oilseed rape meal without strain A6 in 1 of 2 experiments, suggesting a role for strain A6 in improving yield. Strain A6 was capable of solubilizing phosphorus from rock phosphate in liquid culture and produced enzymes capable of mineralizing organic phosphorus (acid phosphatase, phytase) in liquid culture and in the biological fertilizer. The biologically based fertilizer, containing strain A6, improved plant phosphorus nutrition in greenhouse pot experiments resulting in significantly greater available phosphorus in natural soil and in significantly greater plant phosphorus content relative to the nontreated control. Seed yield and available phosphorus in natural soil were significantly greater with a synthetic chemical fertilizer treatment, reduced in phosphorus content, than the biological fertilizer treatment, but a treatment containing the biological fertilizer combined with the synthetic fertilizer provided the significantly greatest seed yield, available phosphorus in natural soil, and plant phosphorus content. These results suggest that the biological fertilizer was capable of improving oilseed rape seed yield, at least in part, through the phosphorus-solubilizing activity of B. megaterium A6.

  10. Removing the center from computing: biology's new mode of digital knowledge production.

    PubMed

    November, Joseph

    2011-06-01

    This article shows how the USA's National Institutes of Health (NIH) helped to bring about a major shift in the way computers are used to produce knowledge and in the design of computers themselves as a consequence of its early 1960s efforts to introduce information technology to biologists. Starting in 1960 the NIH sought to reform the life sciences by encouraging researchers to make use of digital electronic computers, but despite generous federal support biologists generally did not embrace the new technology. Initially the blame fell on biologists' lack of appropriate (i.e. digital) data for computers to process. However, when the NIH consulted MIT computer architect Wesley Clark about this problem, he argued that the computer's quality as a device that was centralized posed an even greater challenge to potential biologist users than did the computer's need for digital data. Clark convinced the NIH that if the agency hoped to effectively computerize biology, it would need to satisfy biologists' experimental and institutional needs by providing them the means to use a computer without going to a computing center. With NIH support, Clark developed the 1963 Laboratory Instrument Computer (LINC), a small, real-time interactive computer intended to be used inside the laboratory and controlled entirely by its biologist users. Once built, the LINC provided a viable alternative to the 1960s norm of large computers housed in computing centers. As such, the LINC not only became popular among biologists, but also served in later decades as an important precursor of today's computing norm in the sciences and far beyond, the personal computer.

  11. A Convenient Dichotomy: Critical Eyes on the Limits to Biological Knowledge

    ERIC Educational Resources Information Center

    Milne, Catherine

    2011-01-01

    In "The Secret Identity of a Biology Textbook: straight and naturally sexed," Jesse Bazzul and Heather Sykes conduct a case study of a biology textbook as an oppressive instructional material. Using queer theory they explore how the text of the biology textbook produces "truths" about sex, gender, and sexuality. Their analysis is complemented by…

  12. Effect of the incorporation of chitosan on the physico-chemical, mechanical properties and biological activity on a mixture of polycaprolactone and polyurethanes obtained from castor oil.

    PubMed

    Arévalo, Fabian; Uscategui, Yomaira L; Diaz, Luis; Cobo, Martha; Valero, Manuel F

    2016-11-01

    In the present study, polyurethane materials were obtained from castor oil, polycaprolactone and isophorone diisocyanate by incorporating different concentrations of chitosan (0.5, 1.0 and 2.0% w/w) as an additive to improve the mechanical properties and the biological activity of polyurethanes. The polyurethanes were characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, stress/strain fracture tests and swelling analysis, and the hydrophilic character of the surface was determined by contact angle trials. The objectives of the study were to evaluate the effect of the incorporation of chitosan on the changes of the physico-chemical and mechanical properties and the in vitro biological activity of the polyurethanes. It was found that the incorporation of chitosan enhances the ultimate tensile strength of the polyurethanes and does not affect the strain at fracture in polyurethanes with 5% w/w of polycaprolactone and concentrations of chitosan ranging from 0 to 2% w/w. In addition, PCL5-Q-PU formulations and their degradation products did not affect cell viability of L929 mouse fibroblast and 3T3, respectively. Polyurethane formulations showed antibacterial activities against Staphylococcus aureus and Escherichia coli bacteria. The results of this study have highlighted the potential biomedical application of this polyurethanes related to soft and cardiovascular tissues.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26834702

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

    PubMed

    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.

  15. Development of a biologically based fertilizer, incorporating Bacillus megaterium A6, for improved phosphorus nutrition of oilseed rape

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sustainable methods with diminished impact on the environment need to be developed for the production of oilseed rape in China and other regions of the world. A biological fertilizer consisting of Bacillus megaterium A6 cultured on oilseed rape meal doubled oilseed rape seed yield (P < 0.0001) rela...

  16. Effects of an Educational Experience Incorporating an Inventory of Factors Potentially Influencing Student Acceptance of Biological Evolution

    ERIC Educational Resources Information Center

    Wiles, Jason R.; Alters, Brian

    2011-01-01

    This investigation provides an extensive review of scientific, religious, and otherwise non-scientific factors that may influence student acceptance of biological evolution. We also measure the extent to which students' levels of acceptance changed following an educational experience designed to address an inclusive inventory of factors identified…

  17. Introducing Bond-Line Organic Structures in High School Biology: An Activity that Incorporates Pleasant-Smelling Molecules

    ERIC Educational Resources Information Center

    Rios, Andro C.; French, Gerald

    2011-01-01

    Chemical education occurs in settings other than just the chemistry classroom. High school biology courses are frequently where students are introduced to organic molecules and their importance to cellular chemistry. However, structural representations are often intimidating because students have not been introduced to the language. As part of a…

  18. Whether 2-aminopurine induces incorporation errors at the DNA replication? A quantum-mechanical answer on the actual biological issue.

    PubMed

    Brovarets', Ol'ha O; Pérez-Sánchez, Horacio

    2016-12-26

    In this paper, we consider the mutagenic properties of the 2-aminopurine (2AP), which has intrigued molecular biologists, biophysicists and physical chemists for a long time and been widely studied by both experimentalists and theorists. We have shown for the first time using QM calculations, that 2AP very effectively produces incorporation errors binding with cytosine (C) into the wobble (w) C·2AP(w) mispair, which is supported by the N4H⋯N1 and N2H⋯N3 H-bonds and is tautomerized into the Watson-Crick (WC)-like base mispair C*·2AP(WC) (asterisk denotes the mutagenic tautomer of the base), that quite easily in the process of the thermal fluctuations acquires enzymatically competent conformation. 2AP less effectively produces transversions forming the wobble mispair with A base - A·2AP(w), stabilized by the participation of the N6H⋯N1 and N2H⋯N1 H-bonds, followed by further tautomerization A·2AP(w) → A*·2AP(WC) and subsequent conformational transition A*·2AP(WC) → A*·2APsyn thus acquiring enzymatically competent structure. In this case, incorporation errors occur only in those case, when 2AP belongs to the incoming nucleotide. Thus, answering the question posed in the title of the article, we affirm for certain that 2AP induces incorporation errors at the DNA replication. Obtained results are consistent well with numerous experimental data.

  19. Chemical and biological properties of wheat soil in response to paddy straw incorporation and its biodegradation by fungal inoculants.

    PubMed

    Gaind, Sunita; Nain, Lata

    2007-08-01

    A field experiment was conducted to evaluate the relative contribution of organic fertilizers (paddy straw, microbial inoculants and vermicompost) and inorganic fertilizers (urea and superphosphate) in improving pH, C, N, humus, microbial biomass, dehydrogenase, phosphatase, cellulase, beta-glucosidase and xylanase activities of soil under wheat crop. Vermicompost fertilization resulted in highest microbial biomass, available phosphorus, and nitrogen content of wheat soil. It was also found effective in minimizing the alkalinity of soil compared to other treatments as indicated by pH change. However incorporation of paddy straw in conjunction with N(60)P(60) and T. reesei inoculation resulted in maximum dehydrogenase, alkaline phosphatase and highest humus content of soil. Mixed inoculation of A. awamori and T. reesei did not prove effective in improving the soil biochemical properties in comparison to single inoculation of T. reesei. Results showed that in situ incorporation of paddy straw in combination with N(60)P(60) and T. reesei inoculation can be used as an effective measure for valuable disposal of paddy straw and to improve the soil health by reducing mineral fertilization.

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

    PubMed

    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.

  1. Essentialist Reasoning and Knowledge Effects on Biological Reasoning in Young Children

    ERIC Educational Resources Information Center

    Herrmann, Patricia A.; French, Jason A.; DeHart, Ganie B.; Rosengren, Karl S.

    2013-01-01

    Biological kinds undergo a variety of changes during their life span, and these changes vary in degree by organism. Understanding that an organism, such as a caterpillar, maintains category identity over its life span despite dramatic changes is a key concept in biological reasoning. At present, we know little about the developmental trajectory of…

  2. Literary Genres and the Construction of Knowledge in Biology: Semantic Shifts and Scientific Change.

    ERIC Educational Resources Information Center

    Sinding, Christiane

    1996-01-01

    Analyzes the literary strategy used by a biologist in order to make a new knowledge claim in a different discipline. Argues that review papers afford the best opportunity for constructing new knowledge claims, because they do not have to conform to a routinely standardized structure, and they allow a wider semantic repertoire than do experimental…

  3. Does Teaching Experience Matter? Examining Biology Teachers' Prior Knowledge for Teaching in an Alternative Certification Program

    ERIC Educational Resources Information Center

    Friedrichsen, Patricia J.; Abell, Sandra K.; Pareja, Enrique M.; Brown, Patrick L.; Lankford, Deanna M.; Volkmann, Mark J.

    2009-01-01

    Alternative certification programs (ACPs) have been proposed as a viable way to address teacher shortages, yet we know little about how teacher knowledge develops within such programs. The purpose of this study was to investigate prior knowledge for teaching among students entering an ACP, comparing individuals with teaching experience to those…

  4. Gene Selection Integrated with Biological Knowledge for Plant Stress Response Using Neighborhood System and Rough Set Theory.

    PubMed

    Meng, Jun; Zhang, Jing; Luan, Yushi

    2015-01-01

    Mining knowledge from gene expression data is a hot research topic and direction of bioinformatics. Gene selection and sample classification are significant research trends, due to the large amount of genes and small size of samples in gene expression data. Rough set theory has been successfully applied to gene selection, as it can select attributes without redundancy. To improve the interpretability of the selected genes, some researchers introduced biological knowledge. In this paper, we first employ neighborhood system to deal directly with the new information table formed by integrating gene expression data with biological knowledge, which can simultaneously present the information in multiple perspectives and do not weaken the information of individual gene for selection and classification. Then, we give a novel framework for gene selection and propose a significant gene selection method based on this framework by employing reduction algorithm in rough set theory. The proposed method is applied to the analysis of plant stress response. Experimental results on three data sets show that the proposed method is effective, as it can select significant gene subsets without redundancy and achieve high classification accuracy. Biological analysis for the results shows that the interpretability is well.

  5. Conceptual Model-Based Systems Biology: Mapping Knowledge and Discovering Gaps in the mRNA Transcription Cycle

    PubMed Central

    Somekh, Judith; Choder, Mordechai; Dori, Dov

    2012-01-01

    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. PMID:23308089

  6. MO-G-304-01: FEATURED PRESENTATION: Expanding the Knowledge Base for Data-Driven Treatment Planning: Incorporating Patient Outcome Models

    SciTech Connect

    Robertson, SP; Quon, H; Cheng, Z; Moore, JA; Bowers, M; McNutt, TR

    2015-06-15

    Purpose: To extend the capabilities of knowledge-based treatment planning beyond simple dose queries by incorporating validated patient outcome models. Methods: From an analytic, relational database of 684 head and neck cancer patients, 372 patients were identified having dose data for both left and right parotid glands as well as baseline and follow-up xerostomia assessments. For each existing patient, knowledge-based treatment planning was simulated for by querying the dose-volume histograms and geometric shape relationships (overlap volume histograms) for all other patients. Dose predictions were captured at normalized volume thresholds (NVT) of 0%, 10%, 20, 30%, 40%, 50%, and 85% and were compared with the actual achieved doses using the Wilcoxon signed-rank test. Next, a logistic regression model was used to predict the maximum severity of xerostomia up to three months following radiotherapy. Baseline xerostomia scores were subtracted from follow-up assessments and were also included in the model. The relative risks from predicted doses and actual doses were computed and compared. Results: The predicted doses for both parotid glands were significantly less than the achieved doses (p < 0.0001), with differences ranging from 830 cGy ± 1270 cGy (0% NVT) to 1673 cGy ± 1197 cGy (30% NVT). The modelled risk of xerostomia ranged from 54% to 64% for achieved doses and from 33% to 51% for the dose predictions. Relative risks varied from 1.24 to 1.87, with maximum relative risk occurring at 85% NVT. Conclusions: Data-driven generation of treatment planning objectives without consideration of the underlying normal tissue complication probability may Result in inferior plans, even if quality metrics indicate otherwise. Inclusion of complication models in knowledge-based treatment planning is necessary in order to close the feedback loop between radiotherapy treatments and patient outcomes. Future work includes advancing and validating complication models in the context

  7. A modified Wright-Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity.

    PubMed

    Zhao, Lei; Gossmann, Toni I; Waxman, David

    2016-03-21

    The Wright-Fisher model is an important model in evolutionary biology and population genetics. It has been applied in numerous analyses of finite populations with discrete generations. It is recognised that real populations can behave, in some key aspects, as though their size that is not the census size, N, but rather a smaller size, namely the effective population size, Ne. However, in the Wright-Fisher model, there is no distinction between the effective and census population sizes. Equivalently, we can say that in this model, Ne coincides with N. The Wright-Fisher model therefore lacks an important aspect of biological realism. Here, we present a method that allows Ne to be directly incorporated into the Wright-Fisher model. The modified model involves matrices whose size is determined by Ne. Thus apart from increased biological realism, the modified model also has reduced computational complexity, particularly so when Ne⪡N. For complex problems, it may be hard or impossible to numerically analyse the most commonly-used approximation of the Wright-Fisher model that incorporates Ne, namely the diffusion approximation. An alternative approach is simulation. However, the simulations need to be sufficiently detailed that they yield an effective size that is different to the census size. Simulations may also be time consuming and have attendant statistical errors. The method presented in this work may then be the only alternative to simulations, when Ne differs from N. We illustrate the straightforward application of the method to some problems involving allele fixation and the determination of the equilibrium site frequency spectrum. We then apply the method to the problem of fixation when three alleles are segregating in a population. This latter problem is significantly more complex than a two allele problem and since the diffusion equation cannot be numerically solved, the only other way Ne can be incorporated into the analysis is by simulation. We have

  8. XML-based data model and architecture for a knowledge-based grid-enabled problem-solving environment for high-throughput biological imaging.

    PubMed

    Ahmed, Wamiq M; Lenz, Dominik; Liu, Jia; Paul Robinson, J; Ghafoor, Arif

    2008-03-01

    High-throughput biological imaging uses automated imaging devices to collect a large number of microscopic images for analysis of biological systems and validation of scientific hypotheses. Efficient manipulation of these datasets for knowledge discovery requires high-performance computational resources, efficient storage, and automated tools for extracting and sharing such knowledge among different research sites. Newly emerging grid technologies provide powerful means for exploiting the full potential of these imaging techniques. Efficient utilization of grid resources requires the development of knowledge-based tools and services that combine domain knowledge with analysis algorithms. In this paper, we first investigate how grid infrastructure can facilitate high-throughput biological imaging research, and present an architecture for providing knowledge-based grid services for this field. We identify two levels of knowledge-based services. The first level provides tools for extracting spatiotemporal knowledge from image sets and the second level provides high-level knowledge management and reasoning services. We then present cellular imaging markup language, an extensible markup language-based language for modeling of biological images and representation of spatiotemporal knowledge. This scheme can be used for spatiotemporal event composition, matching, and automated knowledge extraction and representation for large biological imaging datasets. We demonstrate the expressive power of this formalism by means of different examples and extensive experimental results.

  9. A mathematical model for the interpretation of nuclear bomb test derived 14C incorporation in biological systems

    NASA Astrophysics Data System (ADS)

    Bernard, Samuel; Frisén, Jonas; Spalding, Kirsty L.

    2010-04-01

    Human tissues continually replace dying cells with newborn cells. However, the rate of renewal varies by orders of magnitudes between blood cells, which are renewed every day and neurons, for which renewal is non-existent or limited to specific regions of the brain. Between those extreme are many tissues that turnover on a time scale of years, although no direct measurements have been done. We present here a mathematical method to estimate cell turnover in slowly renewing biological systems. Age distribution of DNA can be estimated from the integration of radiocarbon derived from nuclear bomb-testing during the cold war (1955-1963). For slowly renewing tissues, this method provides a better estimate of the average age of the tissue than direct estimates from the bomb-curve. Moreover, death, birth and turnover rates can be estimated. We highlight this method with data from human fat cells.

  10. Examining the pedagogical content knowledge and practice of experienced secondary biology teachers for teaching diffusion and osmosis

    NASA Astrophysics Data System (ADS)

    Lankford, Deanna

    Teachers are the most important factor in student learning (National Research Council, 1996); yet little is known about the specialized knowledge held by experienced teachers. The purpose of this study was twofold: first, to make explicit the pedagogical content knowledge (PCK) for teaching diffusion and osmosis held by experienced biology teachers and, second, to reveal how topic-specific PCK informs teacher practice. The Magnusson et al. (1999) PCK model served as the theoretical framework for the study. The overarching research question was: When teaching lessons on osmosis and diffusion, how do experienced biology teachers draw upon their topic-specific pedagogical content knowledge? Data sources included observations of two consecutive lessons, three semi-structured interviews, lesson plans, and student handouts. Data analysis indicated five of the six teachers held a constructivist orientation to science teaching and engaged students in explorations of diffusion and osmosis prior to introducing the concepts to students. Explanations for diffusion and osmosis were based upon students' observations and experiences during explorations. All six teachers used representations at the molecular, cellular, and plant organ levels to serve as foci for explorations of diffusion and osmosis. Three potential learning difficulties identified by the teachers included: (a) understanding vocabulary terms, (b) predicting the direction of osmosis, and (c) identifying random molecular motion as the driving force for diffusion and osmosis. Participants used student predictions as formative assessments to reveal misconceptions before instruction and evaluate conceptual understanding during instruction. This study includes implications for teacher preparation, research, and policy.

  11. Effects of an Educational Experience Incorporating an Inventory of Factors Potentially Influencing Student Acceptance of Biological Evolution

    NASA Astrophysics Data System (ADS)

    Wiles, Jason R.; Alters, Brian

    2011-12-01

    This investigation provides an extensive review of scientific, religious, and otherwise non-scientific factors that may influence student acceptance of biological evolution. We also measure the extent to which students' levels of acceptance changed following an educational experience designed to address an inclusive inventory of factors identified as potentially affecting student acceptance of evolution (n = 81, pre-test/post-test) n = 37, one-year longitudinal). Acceptance of evolution was measured using the Measure of Acceptance of the Theory of Evolution (MATE) instrument among participants enrolled in a secondary-level academic programme during the summer prior to their final year of high school and as they transitioned to the post-secondary level. Student acceptance of evolution was measured to be significantly higher than initial levels both immediately following and over one year after the educational experience. Results reported herein carry implications for future quantitative and qualitative research as well as for cross-disciplinary instruction plans related to evolutionary science and non-scientific factors which may influence student understanding of evolution.

  12. Moving Away from Dogmatic Knowledge Dissemination in a Cell Biology Module: Examples from Singapore

    ERIC Educational Resources Information Center

    Yeong, Foong May

    2012-01-01

    A surge in the amount of information in the discipline of Cell Biology presents a problem to the teaching of undergraduates under time constraints. In most textbooks and during lectures, students in Singapore are often taught in a dogmatic manner where concepts and ideas are expounded to them. The students in turn passively receive the materials…

  13. Pre-Service Biology Teachers' and Primary School Students' Attitudes toward and Knowledge about Snakes

    ERIC Educational Resources Information Center

    Tomazic, Iztok

    2011-01-01

    Snakes are controversial animals emblazoned by legends, but also endangered as a result of human prejudice and fear. The author investigated gender and age-related differences in attitudes to and knowledge of snakes comparing samples of school children and pre-service teachers. It was found that although pre-service teachers had better knowledge…

  14. Instructional Effect of Knowledge Mapping on South Australian Matriculation Biology Achievement in Malaysian Students

    ERIC Educational Resources Information Center

    Chong, Cordelia

    2009-01-01

    When students make the transition from one curriculum to another, with significant overlap of content, the challenge is not so much to impart new information but rather to tap into students' existing knowledge base. The purpose of this study was to determine if achievement in an external examination that requires analysis could be enhanced by the…

  15. Knowledge Restructuring in Biology: Testing a Punctuated Model of Conceptual Change

    ERIC Educational Resources Information Center

    Mintzes, Joel; Quinn, Heather J.

    2007-01-01

    Emerging from a human constructivist view of learning and a punctuated model of conceptual change, these studies explored differences in the structural complexity and content validity of knowledge about prehistoric life depicted in concept maps by learners ranging in age from approximately 10 to 20 years. Study 1 (cross-age) explored the…

  16. Educative Mentoring: How a Mentor Supported a Preservice Biology Teacher's Pedagogical Content Knowledge Development

    ERIC Educational Resources Information Center

    Barnett, Ellen; Friedrichsen, Patricia J.

    2015-01-01

    Research suggests discipline-specific, educative mentoring can help preservice teachers develop more sophisticated pedagogical content knowledge (PCK). However, there are few studies examining the nature of mentors' practice and "how" mentors influence preservice teacher's (PST) PCK. The purpose of this case study was to describe the…

  17. Measuring Student Attitude and Knowledge in Technology-Rich Biology Classrooms

    ERIC Educational Resources Information Center

    Incantalupo, Lisa; Treagust, David F.; Koul, Rekha

    2014-01-01

    The use of technology in schools is now ubiquitous, but the effectiveness on the learning environment has mixed results. This paper describes the development and validation of an instrument to measure students' attitudes toward and knowledge of technology with the aim of investigating any differences based on gender after a course where the…

  18. Virtual fetal pig dissection as an agent of knowledge acquisition and attitudinal change in female high school biology students

    NASA Astrophysics Data System (ADS)

    Maloney, Rebecca Scudari

    One way to determine if all students can learn through the use of computers is to introduce a lesson taught completely via computers and compare the results with those gained when the same lesson is taught in a traditional manner. This study attempted to determine if a virtual fetal pig dissection can be used as a viable alternative for an actual dissection for females enrolled in high school biology classes by comparing the knowledge acquisition and attitudinal change between the experimental (virtual dissection) and control (actual dissection) groups. Two hundred and twenty-four students enrolled in biology classes in a suburban all-girl parochial high school participated in this study. Female students in an all-girl high school were chosen because research shows differences in science competency and computer usage between the genders that may mask the performance of females on computer-based tasks in a science laboratory exercise. Students who completed the virtual dissection scored significantly higher on practical test and objective tests that were used to measure knowledge acquisition. Attitudinal change was measured by examining the students' attitudes toward dissections, computer usage in the classroom, and toward biology both before and after the dissections using pre and post surveys. Significant results in positive gain scores were found in the virtual dissection group's attitude toward dissections, and their negative gain score toward virtual dissections. Attitudinal changes toward computers and biology were not significant. A purposefully selected sample of the students were interviewed, in addition to gathering a sample of the students' daily dissection journals, as data highlighting their thoughts and feelings about their dissection experience. Further research is suggested to determine if a virtual laboratory experience can be a substitute for actual dissections, or may serve as an enhancement to an actual dissection.

  19. Tannins: current knowledge of food sources, intake, bioavailability and biological effects.

    PubMed

    Serrano, José; Puupponen-Pimiä, Riitta; Dauer, Andreas; Aura, Anna-Marja; Saura-Calixto, Fulgencio

    2009-09-01

    Tannins are a unique group of phenolic metabolites with molecular weights between 500 and 30 000 Da, which are widely distributed in almost all plant foods and beverages. Proanthocyanidins and hydrolysable tannins are the two major groups of these bioactive compounds, but complex tannins containing structural elements of both groups and specific tannins in marine brown algae have also been described. Most literature data on food tannins refer only to oligomeric compounds that are extracted with aqueous-organic solvents, but a significant number of non-extractable tannins are usually not mentioned in the literature. The biological effects of tannins usually depend on their grade of polymerisation and solubility. Highly polymerised tannins exhibit low bioaccessibility in the small intestine and low fermentability by colonic microflora. This review summarises a new approach to analysis of extractable and non-extractable tannins, major food sources, and effects of storage and processing on tannin content and bioavailability. Biological properties such as antioxidant, antimicrobial and antiviral effects are also described. In addition, the role of tannins in diabetes mellitus has been discussed.

  20. Biological diversity, indigenous knowledge, drug discovery and intellectual property rights: creating reciprocity and maintaining relationships.

    PubMed

    King, S R; Carlson, T J; Moran, K

    1996-04-01

    When new plant-derived therapeutics based on indigenous knowledge are being explored, it is important that the pharmaceutical companies return benefits to the native populations and the local governments from which the research material was obtained. When a potentially marketable plant product is being developed, it is essential that equitable agreements have already been established between the pharmaceutical companies and the people and/or countries from which this indigenous knowledge was acquired. Equally important is the commitment to provide immediate reciprocity that will enhance the welfare, the biocultural diversity and the well-being of the forest peoples. These measures should commence when a research project begins and continue during its duration. The development of these measures must be based upon the expressed needs of the indigenous communities. The relationship between the stability of the rain forest biocultural diversity, the creation and development of agro-forest resources and the long term benefits to the forest people is highlighted. Examples of initiatives taken by Shaman Pharmaceuticals Inc. and the Healing Forest Conservancy are described and discussed in the context of exploring appropriate use of intellectual property law to address the ethical issues facing all business and research groups working in the tropics.

  1. Pubic lice (Pthirus pubis): history, biology and treatment vs. knowledge and beliefs of US college students.

    PubMed

    Anderson, Alice L; Chaney, Elizabeth

    2009-02-01

    Pubic lice (Pthirus pubis) maintain a worldwide parasitic population infesting two to over 10 percent of human populations, continuing a presence that has been constant since early evidence 10,000 years ago. Outbreaks in the 1970s have been recorded, but incomplete records preclude description of a definitive population cycle. Current levels of infestation in a US college student population were investigated in this study. Knowledge and opinions of students were also recorded in an online survey administered to college students taking a basic health course at a mid-sized East Coast University. In a group of 817 students, 35 reported experience with pubic lice or other STD infection. Knowledge, beliefs, and treatment attitudes were examined for the 782 students who did not have experience with either pubic lice or STD infection. These students deemed antibiotics as a viable treatment for pubic lice infestation. They also indicated negative attitudes toward the use of pesticide crèmes, which are the most useful prescription. Symptoms and transmission myths in student answers are described.

  2. Pubic Lice (Pthirus pubis): History, Biology and Treatment vs. Knowledge and Beliefs of US College Students

    PubMed Central

    Anderson, Alice L.; Chaney, Elizabeth

    2009-01-01

    Pubic lice (Pthirus pubis) maintain a worldwide parasitic population infesting two to over 10 percent of human populations, continuing a presence that has been constant since early evidence 10,000 years ago. Outbreaks in the 1970s have been recorded, but incomplete records preclude description of a definitive population cycle. Current levels of infestation in a US college student population were investigated in this study. Knowledge and opinions of students were also recorded in an online survey administered to college students taking a basic health course at a mid-sized East Coast University. In a group of 817 students, 35 reported experience with pubic lice or other STD infection. Knowledge, beliefs, and treatment attitudes were examined for the 782 students who did not have experience with either pubic lice or STD infection. These students deemed antibiotics as a viable treatment for pubic lice infestation. They also indicated negative attitudes toward the use of pesticide crèmes, which are the most useful prescription. Symptoms and transmission myths in student answers are described. PMID:19440402

  3. Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function

    PubMed Central

    Chasman, Daniel I.; Fuchsberger, Christian; Pattaro, Cristian; Teumer, Alexander; Böger, Carsten A.; Endlich, Karlhans; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C.; O'Seaghdha, Conall M.; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V.; O'Connell, Jeffrey R.; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D.; Gierman, Hinco J.; Feitosa, Mary F.; Hwang, Shih-Jen; Atkinson, Elizabeth J.; Lohman, Kurt; Cornelis, Marilyn C.; Johansson, Åsa; Tönjes, Anke; Dehghan, Abbas; Lambert, Jean-Charles; Holliday, Elizabeth G.; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y.; Murgia, Federico; Trompet, Stella; Imboden, Medea; Coassin, Stefan; Pistis, Giorgio; Harris, Tamara B.; Launer, Lenore J.; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D.; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank; Demirkan, Ayse; Oostra, Ben A.; de Andrade, Mariza; Turner, Stephen T.; Ding, Jingzhong; Andrews, Jeanette S.; Freedman, Barry I.; Giulianini, Franco; Koenig, Wolfgang; Illig, Thomas; Meisinger, Christa; Gieger, Christian; Zgaga, Lina; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E.; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H.; Wright, Alan F.; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K.; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; Aulchenko, Yurii S.; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Stengel, Bénédicte; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Krämer, Bernhard K.; Portas, Laura; Ford, Ian; Buckley, Brendan M.; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K.; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J. Wouter; Probst-Hensch, Nicole M.; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R.; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S.; van Duijn, Cornelia M.; Borecki, Ingrid B.; Kardia, Sharon L.R.; Liu, Yongmei; Curhan, Gary C.; Rudan, Igor; Gyllensten, Ulf; Wilson, James F.; Franke, Andre; Pramstaller, Peter P.; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline; Hayward, Caroline; Ridker, Paul M; Parsa, Afshin; Bochud, Murielle; Heid, Iris M.; Kao, W.H. Linda; Fox, Caroline S.; Köttgen, Anna

    2012-01-01

    In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10−9) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10−4–2.2 × 10−7. Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general. PMID:22962313

  4. Current gaps in basic science knowledge of botulinum neurotoxin biological actions.

    PubMed

    Rossetto, Ornella; Pirazzini, Marco; Montecucco, Cesare

    2015-12-01

    Botulinum neurotoxins are produced by anaerobic spore-forming bacteria of the genus Clostridium in several dozens of variants that inactivate neurotransmitter release owing to their metalloprotease activity. This results in a persistent paralysis of peripheral nerve terminals known as botulism. They are the most potent toxins known and are classified as one of the six highest-risk threat agents of bioterrorism. Despite their high toxicity, two of them are used as valuable pharmaceutical for the therapy of many neurological and non-neurological disorders. Notwithstanding the many advances in our understanding of the genetics and structure of botulinum neurotoxins, there are still many gaps in knowledge of toxin mechanism of action that will be discussed here.

  5. Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology

    PubMed Central

    Afendi, Farit M.; Ono, Naoaki; Nakamura, Yukiko; Nakamura, Kensuke; Darusman, Latifah K.; Kibinge, Nelson; Morita, Aki Hirai; Tanaka, Ken; Horai, Hisayuki; Altaf-Ul-Amin, Md.; Kanaya, Shigehiko

    2013-01-01

    Molecular biological data has rapidly increased with the recent progress of the Omics fields, e.g., genomics, transcriptomics, proteomics and metabolomics that necessitates the development of databases and methods for efficient storage, retrieval, integration and analysis of massive data. The present study reviews the usage of KNApSAcK Family DB in metabolomics and related area, discusses several statistical methods for handling multivariate data and shows their application on Indonesian blended herbal medicines (Jamu) as a case study. Exploration using Biplot reveals many plants are rarely utilized while some plants are highly utilized toward specific efficacy. Furthermore, the ingredients of Jamu formulas are modeled using Partial Least Squares Discriminant Analysis (PLS-DA) in order to predict their efficacy. The plants used in each Jamu medicine served as the predictors, whereas the efficacy of each Jamu provided the responses. This model produces 71.6% correct classification in predicting efficacy. Permutation test then is used to determine plants that serve as main ingredients in Jamu formula by evaluating the significance of the PLS-DA coefficients. Next, in order to explain the role of plants that serve as main ingredients in Jamu medicines, information of pharmacological activity of the plants is added to the predictor block. Then N-PLS-DA model, multiway version of PLS-DA, is utilized to handle the three-dimensional array of the predictor block. The resulting N-PLS-DA model reveals that the effects of some pharmacological activities are specific for certain efficacy and the other activities are diverse toward many efficacies. Mathematical modeling introduced in the present study can be utilized in global analysis of big data targeting to reveal the underlying biology. PMID:24688691

  6. Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology.

    PubMed

    Afendi, Farit M; Ono, Naoaki; Nakamura, Yukiko; Nakamura, Kensuke; Darusman, Latifah K; Kibinge, Nelson; Morita, Aki Hirai; Tanaka, Ken; Horai, Hisayuki; Altaf-Ul-Amin, Md; Kanaya, Shigehiko

    2013-01-01

    Molecular biological data has rapidly increased with the recent progress of the Omics fields, e.g., genomics, transcriptomics, proteomics and metabolomics that necessitates the development of databases and methods for efficient storage, retrieval, integration and analysis of massive data. The present study reviews the usage of KNApSAcK Family DB in metabolomics and related area, discusses several statistical methods for handling multivariate data and shows their application on Indonesian blended herbal medicines (Jamu) as a case study. Exploration using Biplot reveals many plants are rarely utilized while some plants are highly utilized toward specific efficacy. Furthermore, the ingredients of Jamu formulas are modeled using Partial Least Squares Discriminant Analysis (PLS-DA) in order to predict their efficacy. The plants used in each Jamu medicine served as the predictors, whereas the efficacy of each Jamu provided the responses. This model produces 71.6% correct classification in predicting efficacy. Permutation test then is used to determine plants that serve as main ingredients in Jamu formula by evaluating the significance of the PLS-DA coefficients. Next, in order to explain the role of plants that serve as main ingredients in Jamu medicines, information of pharmacological activity of the plants is added to the predictor block. Then N-PLS-DA model, multiway version of PLS-DA, is utilized to handle the three-dimensional array of the predictor block. The resulting N-PLS-DA model reveals that the effects of some pharmacological activities are specific for certain efficacy and the other activities are diverse toward many efficacies. Mathematical modeling introduced in the present study can be utilized in global analysis of big data targeting to reveal the underlying biology.

  7. Knowledge-based fuzzy system for diagnosis and control of an integrated biological wastewater treatment process.

    PubMed

    Pires, O C; Palma, C; Costa, J C; Moita, I; Alves, M M; Ferreira, E C

    2006-01-01

    A supervisory expert system based on fuzzy logic rules was developed for diagnosis and control of a laboratory- scale plant comprising anaerobic digestion and anoxic/aerobic modules for combined high rate biological N and C removal. The design and implementation of a computational environment in LabVIEW for data acquisition, plant operation and distributed equipment control is described. A step increase in ammonia concentration from 20 to 60 mg N/L was applied during a trial period of 73 h. Recycle flow rate from the aerobic to the anoxic module and bypass flow rate from the influent directly to the anoxic reactor were the output variables of the fuzzy system. They were automatically changed (from 34 to 111 L/day and from 8 to 13 L/day, respectively), when new plant conditions were recognised by the expert system. Denitrification efficiency higher than 85% was achieved 30 h after the disturbance and 15 h after the system response at an HRT as low as 1.5 h. Nitrification efficiency gradually increased from 12 to 50% at an HRT of 3 h. The system proved to react properly in order to set adequate operating conditions that led to timely and efficient recovery of N and C removal rates.

  8. Sparse ice: Geophysical, biological and Indigenous knowledge perspectives on a habitat for ice-associated fauna

    NASA Astrophysics Data System (ADS)

    Lee, O. A.; Eicken, H.; Weyapuk, W., Jr.; Adams, B.; Mohoney, A. R.

    2015-12-01

    The significance of highly dispersed, remnant Arctic sea ice as a platform for marine mammals and indigenous hunters in spring and summer may have increased disproportionately with changes in the ice cover. As dispersed remnant ice becomes more common in the future it will be increasingly important to understand its ecological role for upper trophic levels such as marine mammals and its role for supporting primary productivity of ice-associated algae. Potential sparse ice habitat at sea ice concentrations below 15% is difficult to detect using remote sensing data alone. A combination of high resolution satellite imagery (including Synthetic Aperture Radar), data from the Barrow sea ice radar, and local observations from indigenous sea ice experts was used to detect sparse sea ice in the Alaska Arctic. Traditional knowledge on sea ice use by marine mammals was used to delimit the scales where sparse ice could still be used as habitat for seals and walrus. Potential sparse ice habitat was quantified with respect to overall spatial extent, size of ice floes, and density of floes. Sparse ice persistence offshore did not prevent the occurrence of large coastal walrus haul outs, but the lack of sparse ice and early sea ice retreat coincided with local observations of ringed seal pup mortality. Observations from indigenous hunters will continue to be an important source of information for validating remote sensing detections of sparse ice, and improving understanding of marine mammal adaptations to sea ice change.

  9. Nature of Science Knowledge and Scientific Argumentation Skills in Taiwanese College Biology Students

    NASA Astrophysics Data System (ADS)

    Lai, Mei-Chun

    Although many believe that students with mature understanding of NOS engage in argumentation more, mixed results were found in empirical studies. In argumentation studies, consensus assessment was lacking and most researchers only evaluated the structural aspects of argumentation. However in the science classroom, an assessment that examines the "content correctness" in addition to the "structural complexity" is necessary because scientific argumentation that is structurally complicated but full of misconceptions cannot be considered strong. Therefore, the goal of this study was first to develop a method to evaluate the quality of students' scientific argumentation in both the content and structure aspects. The second goal was to examine to what extent NOS knowledge and argumentation skills correlate. Furthermore, through semi-structured interview, this study documented students' NOS understandings in the target aspects of NOS. Significant correlation between NOS and argumentation was found in the first year of the study. Although no correlation between NOS and argumentation was found in follow-up study, the score distribution implied that students with mixed views of NOS engaged more in scientific argumentation in which specific scientific data were required to support their claims. The qualitative analysis of students' NOS interview revealed that students with strong argumentation skills view science as an open entity that may be challenged and discussed. Further, all of the interview participants placed high values on empirical support. The majority of the participants held the misconception about theories and laws, and expressed that the theory of evolution is less persuasive than other theories because some parts of the supporting evidence lack empirical support.

  10. TOLKIN – Tree of Life Knowledge and Information Network: Filling a Gap for Collaborative Research in Biological Systematics

    PubMed Central

    Beaman, Reed S.; Traub, Greg H.; Dell, Christopher A.; Santiago, Nestor; Koh, Jin; Cellinese, Nico

    2012-01-01

    The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email. PMID:22724002

  11. Immunotherapy for Alzheimer's disease: harnessing our knowledge of T cell biology using a cholesterol-fed rabbit model.

    PubMed

    Coico, Richard; Woodruff-Pak, Diana S

    2008-12-01

    This timely special issue of the Journal of Alzheimer's Disease provides the opportunity to examine interfaces between basic science and clinical medicine using animal models to develop more effective therapies for the treatment and, ideally, prevention of Alzheimer's disease (AD). That some patients with AD enrolled in a clinical trial to inoculate against amyloid-beta (Abeta) experienced a misdirected polarization of Th cells reminds us that our knowledge of T cell biology, immune regulation, and the precise functional properties of adjuvants is incomplete. We review this knowledge and consider the advantages of the rabbit for immunological studies. The langomorph species is proximate to primates on the phylogenetic scale, its amino acid sequence of Abeta is 97% identical to the human Abeta sequence, and the rabbit model system is extensively characterized on a form of associative learning with parallels in normal aging in rabbits and humans that is severely impaired in human AD. Cholesterol-fed rabbits treated with Abeta immunotherapy generate high titer anti-Abeta responses. The cholesterol-fed rabbit model of AD with its close parallels to human genetics and physiology, along with its validity from molecular to cognitive levels as a model of human AD, provides a promising vehicle for development of immunotherapies.

  12. Mapping out the Integration of the Components of Pedagogical Content Knowledge (PCK): Examples from High School Biology Classrooms

    ERIC Educational Resources Information Center

    Park, Soonhye; Chen, Ying-Chih

    2012-01-01

    This study explored the nature of the integration of the five components of pedagogical content knowledge (PCK): (a) Orientations toward Teaching Science, (b) Knowledge of Student Understanding, (c) Knowledge of Instructional Strategies and Representations, (d) Knowledge of Science Curriculum, and (e) Knowledge of Assessment of Science Learning.…

  13. North Atlantic demersal deep-water fish distribution and biology: present knowledge and challenges for the future.

    PubMed

    Bergstad, O A

    2013-12-01

    This paper summarizes knowledge and knowledge gaps on benthic and benthopelagic deep-water fishes of the North Atlantic Ocean, i.e. species inhabiting deep continental shelf areas, continental and island slopes, seamounts and the Mid-Atlantic Ridge. While several studies demonstrate that distribution patterns are species specific, several also show that assemblages of species can be defined and such assemblages are associated with circulatory features and water mass distributions. In many subareas, sampling has, however, been scattered, restricted to shallow areas or soft substrata, and results from different studies tend to be difficult to compare quantitatively because of sampler differences. Particularly, few studies have been conducted on isolated deep oceanic seamounts and in Arctic deep-water areas. Time series of data are very few and most series are short. Recent studies of population structure of widely distributed demersal species show less than expected present connectivity and considerable spatial genetic heterogeneity and complexity for some species. In other species, genetic homogeneity across wide ranges was discovered. Mechanisms underlying the observed patterns have been proposed, but to test emerging hypotheses more species should be investigated across their entire distribution ranges. Studies of population biology reveal greater diversity in life-history strategies than often assumed, even between co-occurring species of the same family. Some slope and ridge-associated species are rather short-lived, others very long-lived, and growth patterns also show considerable variation. Recent comparative studies suggest variation in life-history strategies along a continuum correlated with depth, ranging from shelf waters to the deep sea where comparatively more species have extended lifetimes, and slow rates of growth and reproduction. Reproductive biology remains too poorly known for most deep-water species, and temporal variation in recruitment has

  14. Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data.

    PubMed

    Moore, Carrie B; Wallace, John R; Wolfe, Daniel J; Frase, Alex T; Pendergrass, Sarah A; Weiss, Kenneth M; Ritchie, Marylyn D

    2013-01-01

    Analyses investigating low frequency variants have the potential for explaining additional genetic heritability of many complex human traits. However, the natural frequencies of rare variation between human populations strongly confound genetic analyses. We have applied a novel collapsing method to identify biological features with low frequency variant burden differences in thirteen populations sequenced by the 1000 Genomes Project. Our flexible collapsing tool utilizes expert biological knowledge from multiple publicly available database sources to direct feature selection. Variants were collapsed according to genetically driven features, such as evolutionary conserved regions, regulatory regions genes, and pathways. We have conducted an extensive comparison of low frequency variant burden differences (MAF<0.03) between populations from 1000 Genomes Project Phase I data. We found that on average 26.87% of gene bins, 35.47% of intergenic bins, 42.85% of pathway bins, 14.86% of ORegAnno regulatory bins, and 5.97% of evolutionary conserved regions show statistically significant differences in low frequency variant burden across populations from the 1000 Genomes Project. The proportion of bins with significant differences in low frequency burden depends on the ancestral similarity of the two populations compared and types of features tested. Even closely related populations had notable differences in low frequency burden, but fewer differences than populations from different continents. Furthermore, conserved or functionally relevant regions had fewer significant differences in low frequency burden than regions under less evolutionary constraint. This degree of low frequency variant differentiation across diverse populations and feature elements highlights the critical importance of considering population stratification in the new era of DNA sequencing and low frequency variant genomic analyses.

  15. The embryonic cell lineage of Caenorhabditis elegans: A modern hieroglyph: The best way to acquire knowledge in Developmental Biology is to learn how this knowledge was derived.

    PubMed

    Sáenz-Narciso, Beatriz; Gómez-Orte, Eva; Zheleva, Angelina; Torres-Pérez, Rafael; Cabello, Juan

    2015-03-01

    Nowadays, in the Internet databases era, certain knowledge is being progressively lost. This knowledge, which we feel is essential and should be acquired through education, is the understanding of how the pioneer researchers faced major questions in their field and made their discoveries.

  16. Novel joint TOA/RSSI-based WCE location tracking method without prior knowledge of biological human body tissues.

    PubMed

    Ito, Takahiro; Anzai, Daisuke; Jianqing Wang

    2014-01-01

    This paper proposes a novel joint time of arrival (TOA)/received signal strength indicator (RSSI)-based wireless capsule endoscope (WCE) location tracking method without prior knowledge of biological human tissues. Generally, TOA-based localization can achieve much higher localization accuracy than other radio frequency-based localization techniques, whereas wireless signals transmitted from a WCE pass through various kinds of human body tissues, as a result, the propagation velocity inside a human body should be different from one in free space. Because the variation of propagation velocity is mainly affected by the relative permittivity of human body tissues, instead of pre-measurement for the relative permittivity in advance, we simultaneously estimate not only the WCE location but also the relative permittivity information. For this purpose, this paper first derives the relative permittivity estimation model with measured RSSI information. Then, we pay attention to a particle filter algorithm with the TOA-based localization and the RSSI-based relative permittivity estimation. Our computer simulation results demonstrates that the proposed tracking methods with the particle filter can accomplish an excellent localization accuracy of around 2 mm without prior information of the relative permittivity of the human body tissues.

  17. A comparison of retention of anatomical knowledge in an introductory college biology course: Traditional dissection vs. virtual dissection

    NASA Astrophysics Data System (ADS)

    Taeger, Kelli Rae

    Dissection has always played a crucial role in biology and anatomy courses at all levels of education. However, in recent years, ethical concerns, as well as improved technology, have brought to the forefront the issue of whether virtual dissection is as effective or whether it is more effective than traditional dissection. Most prior research indicated the two methods produced equal results. However, none of those studies examined retention of information past the initial test of knowledge. Two groups of college students currently enrolled in an introductory level college biology course were given one hour to complete a frog dissection. One group performed a traditional frog dissection, making cuts in an actual preserved frog specimen with scalpels and scissors. The other group performed a virtual frog dissection, using "The Digital Frog 2" software. Immediately after the dissections were completed, each group was given an examination consisting of questions on actual specimens, pictures generated from the computer software, and illustrations that neither group had seen. Two weeks later, unannounced, the groups took the same exam in order to test retention. The traditional dissection group scored significantly higher on two of the three sections, as well as the total score on the initial exam. However, with the exception of specimen questions (on which the traditional group retained significantly more information), there was no significant difference in the retention from exam 1 to exam 2 between the two groups. These results, along with the majority of prior studies, show that the two methods produce, for the most part, the same end results. Therefore, the decision of which method to employ should be based on the goals and preferences of the instructor(s) and the department. If that department's goals include: Being at the forefront of new technology, increasing time management, increasing student: teacher ratio for economic reasons, and/or ethical issues, then

  18. How to Build a Course in Mathematical-Biological Modeling: Content and Processes for Knowledge and Skill

    ERIC Educational Resources Information Center

    Hoskinson, Anne-Marie

    2010-01-01

    Biological problems in the twenty-first century are complex and require mathematical insight, often resulting in mathematical models of biological systems. Building mathematical-biological models requires cooperation among biologists and mathematicians, and mastery of building models. A new course in mathematical modeling presented the opportunity…

  19. Expansion of Biology Teachers' Pedagogical Content Knowledge (PCK) during a Long-Term Professional Development Program

    ERIC Educational Resources Information Center

    Rozenszajn, Ronit; Yarden, Anat

    2014-01-01

    Experienced teachers possess a unique teaching knowledge comprised of an inter-related set of knowledge and beliefs that gives direction and justification to a teacher's actions. This study examined the expansion of two components of pedagogical content knowledge (PCK) of three in-service teachers in the course of a professional development…

  20. Does Increasing Biology Teacher Knowledge of Evolution and the Nature of Science Lead to Greater Preference for the Teaching of Evolution in Schools?

    NASA Astrophysics Data System (ADS)

    Nehm, Ross H.; Schonfeld, Irvin Sam

    2007-10-01

    This study investigated whether or not an increase in secondary science teacher knowledge about evolution and the nature of science gained from completing a graduate-level evolution course was associated with greater preference for the teaching of evolution in schools. Forty-four precertified secondary biology teachers participated in a 14-week intervention designed to address documented misconceptions identified by a precourse instrument. The course produced statistically significant gains in teacher knowledge of evolution and the nature of science and a significant decrease in misconceptions about evolution and natural selection. Nevertheless, teachers’ postcourse preference positions remained unchanged; the majority of science teachers still preferred that antievolutionary ideas be taught in school.

  1. Effects of Cholesterol Incorporation on the Physicochemical, Colloidal, and Biological Characteristics of pH-sensitive AB2 Miktoarm Polymer-Based Polymersomes

    PubMed Central

    Yin, Haiqing; Kang, Han Chang; Huh, Kang Moo; Bae, You Han

    2014-01-01

    In our previous study, a histidine-based AB2 miktoarm polymer, methoxy poly(ethylene glycol)-b-poly(l-histidine)2 (mPEG-b-(PolyHis)2), was designed to construct pH-sensitive polymersomes that transform in acidic pH; the polymer self-assembles into a structure that mimics phospholipids. In this study, the polymersomes further imitated liposomes due to the incorporation of cholesterol (CL). The hydrodynamic radii of the polymersomes increased with increasing CL wt% (e.g., 70 nm for 0 wt% vs. 91 nm for 1 wt%), resulting in an increased capacity for encapsulating hydrophilic drugs (e.g., 0.92 µL/mg for 0 wt% vs. 1.42 µL/mg for 1 wt%). The CL incorporation enhanced the colloidal stability of the polymersomes in the presence of serum protein and retarded their payload release. However, CL-incorporating polymersomes still demonstrated accelerated release of a hydrophilic dye (e.g., 5(6)-carboxyfluorescein (CF)) below pH 6.8 without losing their desirable pH sensitivity. CF-loaded CL-incorporating polymersomes showed better cellular internalization than the hydrophilic CF, whereas doxorubicin (DOX)-loaded CL-incorporating polymersomes presented similar or somewhat lower anti-tumor effects than free hydrophobic DOX. The findings suggest that CL-incorporating mPEG-b-(PolyHis)2-based polymersomes may have potential for intracellular drug delivery of chemical drugs due to their improved colloidal stability, lower drug loss during circulation, acidic pH-induced drug release, and endosomal disruption. PMID:24463148

  2. Use of Antimicrobial Films and Edible Coatings Incorporating Chemical and Biological Preservatives to Control Growth of Listeria monocytogenes on Cold Smoked Salmon

    PubMed Central

    Mahomoodally, Fawzi

    2014-01-01

    The relatively high incidence of Listeria monocytogenes in cold smoked salmon (CSS) is of concern as it is a refrigerated processed food of extended durability (REPFED). The objectives of this study were to compare and optimize the antimicrobial effectiveness of films and coatings incorporating nisin (Nis) and sodium lactate (SL), sodium diacetate (SD), potassium sorbate (PS), and/or sodium benzoate (SB) in binary or ternary combinations on CSS. Surface treatments incorporating Nis (25000 IU/mL) in combination with PS (0.3%) and SB (0.1%) had the highest inhibitory activity, reducing the population of L. monocytogenes by a maximum of 3.3 log CFU/cm2 (films) and 2.9 log CFU/cm2 (coatings) relative to control samples after 10 days of storage at 21°C. During refrigerated storage, coatings were more effective in inhibiting growth of L. monocytogenes than their film counterparts. Cellulose-based coatings incorporating Nis, PS, and SB reduced the population of L. monocytogenes, and anaerobic and aerobic spoilage flora by a maximum of 4.2, 4.8, and 4.9 log CFU/cm2, respectively, after 4 weeks of refrigerated storage. This study highlights the effectiveness of cellulose-based edible coatings incorporating generally regarded as safe (GRAS) natural and chemical antimicrobials to inhibit the development of L. monocytogenes and spoilage microflora thus enhancing the safety and quality of CSS. PMID:25089272

  3. The Influence of Religion and High School Biology Courses on Students' Knowledge of Evolution When They Enter College

    ERIC Educational Resources Information Center

    Moore, Randy; Cotner, Sehoya; Bates, Alex

    2009-01-01

    Students whose high school biology course included evolution but not creationism knew more about evolution when they entered college than did students whose courses included evolution plus creationism or whose courses included neither evolution nor creationism. Similarly, students who believed that their high school biology classes were the…

  4. Influence of Using Challenging Tasks in Biology Classrooms on Students' Cognitive Knowledge Structure: An Empirical Video Study

    ERIC Educational Resources Information Center

    Nawani, Jigna; Rixius, Julia; Neuhaus, Birgit J.

    2016-01-01

    Empirical analysis of secondary biology classrooms revealed that, on average, 68% of teaching time in Germany revolved around processing tasks. Quality of instruction can thus be assessed by analyzing the quality of tasks used in classroom discourse. This quasi-experimental study analyzed how teachers used tasks in 38 videotaped biology lessons…

  5. The Influence of Pedagogical Content Knowledge (PCK) for Teaching Macroevolution on Student Outcomes in a General Education Biology Course

    ERIC Educational Resources Information Center

    Walter, Emily Marie

    2013-01-01

    This study investigated the influence of pedagogical content knowledge (PCK) for teaching macroevolution on non-science majors' knowledge of macroevolution and evolution acceptance. The nature and sources of an experienced faculty member's PCK and instruction as enacted PCK (Park & Oliver, 2008) were examined to consider the influence of these…

  6. Investigating Student Perceptions of Knowledge Acquisition within a Role-Play Simulation of the Convention on Biological Diversity

    ERIC Educational Resources Information Center

    Schnurr, Matthew A.; De Santo, Elizabeth M.; Green, Amanda D.; Taylor, Alanna

    2015-01-01

    This article investigates the particular mechanisms through which a role-play simulation impacts student perceptions of knowledge acquisition. Longitudinal data were mobilized in the form of quantitative and qualitative surveys to examine whether the simulation succeeded in increasing knowledge around both content and skills. It then delves deeper…

  7. Three forms of assessment of prior knowledge, and improved performance following an enrichment programme, of English second language biology students within the context of a marine theme

    NASA Astrophysics Data System (ADS)

    Feltham, Nicola F.; Downs, Colleen T.

    2002-02-01

    The Science Foundation Programme (SFP) was launched in 1991 at the University of Natal, Pietermaritzburg, South Africa in an attempt to equip a selected number of matriculants from historically disadvantaged schools with the skills, resources and self-confidence needed to embark on their tertiary studies. Previous research within the SFP biology component suggests that a major contributor to poor achievement and low retention rates among English second language (ESL) students in the Life Sciences is the inadequate background knowledge in natural history. In this study, SFP student background knowledge was assessed along a continuum of language dependency using a set of three probes. Improved student performance in each of the respective assessments examined the extent to which a sound natural history background facilitated meaningful learning relative to ESL proficiency. Student profiles and attitudes to biology were also examined. Results indicated that students did not perceive language to be a problem in biology. However, analysis of the student performance in the assessment probes indicated that, although the marine course provided the students with the background knowledge that they were initially lacking, they continued to perform better in the drawing and MCQ tools in the post-tests, suggesting that it is their inability to express themselves in the written form that hampers their development. These results have implications for curriculum development within the constructivist framework of the SFP.

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

    PubMed Central

    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. PMID:26648900

  9. Approaches to Cell Biology Teaching: Mapping the Journey--Concept Maps as Signposts of Developing Knowledge Structures

    ERIC Educational Resources Information Center

    Allen, Deborah; Tanner, Kimberly

    2003-01-01

    An instructor contemplating a course transformation to incorporate a student-centered learning environment may feel faced with what seems like a high-wire balancing act--a constantly renegotiated compromise between students' legitimate needs for structure, well-understood expectations, and good grades and instructors' foreknowledge that the path…

  10. Beliefs, Practical Knowledge, and Context: A Longitudinal Study of a Beginning Biology Teacher's 5E Unit

    ERIC Educational Resources Information Center

    Sickel, Aaron J.; Friedrichsen, Patricia

    2015-01-01

    The purpose of this three-year case study was to understand how a beginning biology teacher (Alice) designed and taught a 5E unit on natural selection, how the unit changed when she took a position in a different school district, and why the changes occurred. We examined Alice's developing beliefs about science teaching and learning,…

  11. Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock.

    PubMed

    Tyagi, Rahul; Joachim, Anja; Ruttkowski, Bärbel; Rosa, Bruce A; Martin, John C; Hallsworth-Pepin, Kymberlie; Zhang, Xu; Ozersky, Philip; Wilson, Richard K; Ranganathan, Shoba; Sternberg, Paul W; Gasser, Robin B; Mitreva, Makedonka

    2015-11-01

    Many infectious diseases caused by eukaryotic pathogens have a devastating, long-term impact on animal health and welfare. Hundreds of millions of animals are affected by parasitic nematodes of the order Strongylida. Unlocking the molecular biology of representatives of this order, and understanding nematode-host interactions, drug resistance and disease using advanced technologies could lead to entirely new ways of controlling the diseases that they cause. Oesophagostomum dentatum (nodule worm; superfamily Strongyloidea) is an economically important strongylid nematode parasite of swine worldwide. The present article reports recent advances made in biology and animal biotechnology through the draft genome and developmental transcriptome of O. dentatum, in order to support biological research of this and related parasitic nematodes as well as the search for new and improved interventions. This first genome of any member of the Strongyloidea is 443 Mb in size and predicted to encode 25,291 protein-coding genes. Here, we review the dynamics of transcription throughout the life cycle of O. dentatum, describe double-stranded RNA interference (RNAi) machinery and infer molecules involved in development and reproduction, and in inducing or modulating immune responses or disease. The secretome predicted for O. dentatum is particularly rich in peptidases linked to interactions with host tissues and/or feeding activity, and a diverse array of molecules likely involved in immune responses. This research progress provides an important resource for future comparative genomic and molecular biological investigations as well as for biotechnological research toward new anthelmintics, vaccines and diagnostic tests.

  12. Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock

    PubMed Central

    Tyagi, Rahul; Joachim, Anja; Ruttkowski, Bärbel; Rosa, Bruce A.; Martin, John C.; Hallsworth-Pepin, Kymberlie; Zhang, Xu; Ozersky, Philip; Wilson, Richard K.; Ranganathan, Shoba; Sternberg, Paul W.; Gasser, Robin B.; Mitreva, Makedonka

    2016-01-01

    Many infectious diseases caused by eukaryotic pathogens have a devastating, long-term impact on animal health and welfare. Hundreds of millions of animals are affected by parasitic nematodes of the order Stronglida. Unlocking the molecular biology of representatives of this order, and understanding nematode-host interactions, drug resistance and disease using advanced technologies could lead to entirely new ways of controlling the diseases that they cause. Oesphagostomum dentatum (nodule worm; superfamily Strongyloidea) is an economically important strongylid nematode of swine worldwide. The present article reports recent advances made in biology and animal biotechnology through the draft genome and developmental transcriptome of O. dentatum, in order to support biological research of this and related parasitic nematodes as well as the search for new and improved interventions. This first genome of any member of the Strongyloidea is 443 Mb in size and predicted to encode 25,291 protein-coding genes. Here, we review the dynamics of transcription throughout the life cycle of O. dentatum, describe double-stranded RNA interference (RNAi) machinery and infer molecules involved in development and reproduction, and in inducing or modulating immune responses or disease. The secretome predicted for O. dentatum is particularly rich in peptidases linked to interactions with host tissues and/or feeding activity, and a diverse array of molecules likely involved in immune responses. This research progress provides an important resource for future comparative genomic and molecular biological investigations as well as for biotechnological research toward new anthelmintics, vaccines and diagnostic tests. PMID:26026709

  13. Investigating Greek Biology Teachers' Attitudes towards Evolution Teaching with Respect to Their Pedagogical Content Knowledge: Suggestions for Their Professional Development

    ERIC Educational Resources Information Center

    Stasinakis, Panagiotis K.; Athanasiou, Kyriacos

    2016-01-01

    Evolution Teaching (ET) among in-service teachers in Greece was examined in an attempt to evaluate their Pedagogical Content Knowledge. Evolution teaching is a problematic issue. For this purpose, we constructed a questionnaire that was distributed to the target population and to which 181 teachers responded. We used quantitative method to…

  14. Formative Assessment Pre-Test to Identify College Students' Prior Knowledge, Misconceptions and Learning Difficulties in Biology

    ERIC Educational Resources Information Center

    Lazarowitz, Reuven; Lieb, Carl

    2006-01-01

    A formative assessment pretest was administered to undergraduate students at the beginning of a science course in order to find out their prior knowledge, misconceptions and learning difficulties on the topic of the human respiratory system and energy issues. Those findings could provide their instructors with the valuable information required in…

  15. Biological conservation of a prey-predator system incorporating constant prey refuge through provision of alternative food to predators: a theoretical study.

    PubMed

    Chakraborty, Kunal; Das, Sankha Subhra

    2014-06-01

    We describe a prey-predator system incorporating constant prey refuge through provision of alternative food to predators. The proposed model deals with a problem of non-selective harvesting of a prey-predator system in which both the prey and the predator species obey logistic law of growth. The long-run sustainability of an exploited system is discussed through provision of alternative food to predators. We have analyzed the variability of the system in presence of constant prey refuge and examined the stabilizing effect on predator-prey system. The steady states of the system are derived and dynamical behavior of the system is extensively analyzed around steady states. The optimal harvesting policy is formulated and solved with the help of Pontryagin's maximal principle. Our objective is to maximize the monetary social benefit through protecting the predator species from extinction, keeping the ecological balance. Results finally illustrated with the help of numerical examples.

  16. Biologically active vallesamine, strychnan, and rhazinilam alkaloids from Alstonia: Pneumatophorine, a nor-secovallesamine with unusual incorporation of a 3-ethylpyridine moiety.

    PubMed

    Lim, Jun-Lee; Sim, Kae-Shin; Yong, Kien-Thai; Loong, Bi-Juin; Ting, Kang-Nee; Lim, Siew-Huah; Low, Yun-Yee; Kam, Toh-Seok

    2015-09-01

    Four alkaloids comprising two vallesamine, one strychnan, and one pyranopyridine alkaloid, in addition to 32 other known alkaloids were isolated from two Malayan Alstonia species, Alstonia pneumatophora and Alstonia rostrata. The structures of these alkaloids were determined using NMR and MS analyses, and in one instance, confirmed by X-ray diffraction analysis. The nor-6,7-secovallesamine alkaloid, pneumatophorine, is notable for an unusual incorporation of a 3-ethylpyridine moiety in a monoterpenoid indole. The rhazinilam-type alkaloids (rhazinicine, nor-rhazinicine, rhazinal, and rhazinilam) showed strong cytotoxicity toward human KB, HCT-116, MDA-MB-231, and MRC-5 cells, while pneumatophorine, the uleine alkaloid undulifoline, and the strychnan alkaloids, N4-demethylalstogustine and echitamidine, induced concentration dependent relaxation in phenylephrine-precontracted rat aortic rings.

  17. Using student motivation to design groups in a non-majors biology course for team-based collaborative learning: Impacts on knowledge, views, attitudes, and perceptions

    NASA Astrophysics Data System (ADS)

    Walters, Kristi L.

    The importance of student motivation and its connection to other learning variables (i.e., attitudes, knowledge, persistence, attendance) is well established. Collaborative work at the undergraduate level has been recognized as a valuable tool in large courses. However, motivation and collaborative group work have rarely been combined. This project utilized student motivation to learn biology to place non-major biology undergraduates in collaborative learning groups at East Carolina University, a mid-sized southeastern American university, to determine the effects of this construct on student learning. A pre-test measuring motivation to learn biology, attitudes toward biology, perceptions of biology and biologists, views of science, and content knowledge was administered. A similar post-test followed as part of the final exam. Two sections of the same introductory biology course (n = 312) were used and students were divided into homogeneous and heterogeneous groups (based on their motivation score). The heterogeneous groups (n = 32) consisted of a mixture of different motivation levels, while the homogeneous groups (n = 32) were organized into teams with similar motivation scores using tiers of high-, middle-, and low-level participants. Data analysis determined mixed perceptions of biology and biologists. These include the perceptions biology was less intriguing, less relevant, less practical, less ethical, and less understandable. Biologists were perceived as being neat and slightly intelligent, but not very altruistic, humane, ethical, logical, honest, or moral. Content knowledge scores more than doubled from pre- to post-test. Half of the items measuring views of science were not statistically significantly different from pre- to post-test. Many of the factors for attitudes toward biology became more agreeable from pre- to post-test. Correlations between motivation scores, participation levels, attendance rates, and final course grades were examined at both the

  18. A Review of the Current State of European Research and Knowledge Concerning the Biological Effects of Radiowaves and Microwaves.

    DTIC Science & Technology

    1982-09-15

    within the needle of a hypodermic syrtnge, have been built and tested. Temperature measuring instruments which have been devised include...with the interaction of acoustic waves and electrumagnetic waves with various media . Very recently attention has been turned to the particular problems...posed by biological media and in the course of this research tissue-equivalent materials have been developed by simulating the known dielectric

  19. Online versus face-to-face biology: A comparison of student transactional distance, approach to learning, and knowledge outcomes

    NASA Astrophysics Data System (ADS)

    Riggins, Mary Erin

    Community colleges are among many other institutions increasing course offerings online, but there is still some concern about the quality of online learning. Educator concerns, a lack of empirical evidence on biology courses offered online, and the need for an equal opportunity for education support the need for clarification of the quality of distance education in biology, especially in the community college setting. Student attitudes, approaches to learning, and performance should all be studied in order to formulate a better evaluation of the quality and effectiveness of online courses (Svirko & Mellanby, 2008). The purpose of this study was to determine whether there were differences in student perceptions of transactional distance, approaches to learning, and student learning outcomes in online versus face-to-face community college introductory biology courses. The results of this investigation indicate that some aspects of transactional distance did affect the participants' desires for deep learning approaches. Also, except for perceptions of student interaction and collaboration, the online and face-to-face course experiences and outcomes seemed similar.

  20. How to Build a Course in Mathematical–Biological Modeling: Content and Processes for Knowledge and Skill

    PubMed Central

    2010-01-01

    Biological problems in the twenty-first century are complex and require mathematical insight, often resulting in mathematical models of biological systems. Building mathematical–biological models requires cooperation among biologists and mathematicians, and mastery of building models. A new course in mathematical modeling presented the opportunity to build both content and process learning of mathematical models, the modeling process, and the cooperative process. There was little guidance from the literature on how to build such a course. Here, I describe the iterative process of developing such a course, beginning with objectives and choosing content and process competencies to fulfill the objectives. I include some inductive heuristics for instructors seeking guidance in planning and developing their own courses, and I illustrate with a description of one instructional model cycle. Students completing this class reported gains in learning of modeling content, the modeling process, and cooperative skills. Student content and process mastery increased, as assessed on several objective-driven metrics in many types of assessments. PMID:20810966

  1. How to build a course in mathematical-biological modeling: content and processes for knowledge and skill.

    PubMed

    Hoskinson, Anne-Marie

    2010-01-01

    Biological problems in the twenty-first century are complex and require mathematical insight, often resulting in mathematical models of biological systems. Building mathematical-biological models requires cooperation among biologists and mathematicians, and mastery of building models. A new course in mathematical modeling presented the opportunity to build both content and process learning of mathematical models, the modeling process, and the cooperative process. There was little guidance from the literature on how to build such a course. Here, I describe the iterative process of developing such a course, beginning with objectives and choosing content and process competencies to fulfill the objectives. I include some inductive heuristics for instructors seeking guidance in planning and developing their own courses, and I illustrate with a description of one instructional model cycle. Students completing this class reported gains in learning of modeling content, the modeling process, and cooperative skills. Student content and process mastery increased, as assessed on several objective-driven metrics in many types of assessments.

  2. Homosexuality, biology, and ideology.

    PubMed

    Haumann, G

    1995-01-01

    This paper critically examines the complex relationships and interdependencies between biological theories on homosexuality and sociosexual ideologies. It challenges the privileged status of biology as the ultimate authority on homosexuality. This status is based on the belief that biology is a value-free science. On the contrary, this essay shows how unacknowledged assumptions and culturally bound patterns of thinking about sexuality taint biological research. Sociosexual ideologies are defined as principles that organize the ways we express our sexualities and the way we theorize about them in biology. The following ideologies are identified: (1) sexuality-as-heterosexuality, (2) sexuality-as-reproduction, (3) sexual dualism (male vs. female), and (4) the view the homosexuality is a sexual inversion. The process by which these ideologies are incorporated into biology is two-fold: (1) as a projective act from society onto nature and (2) as a reflective act from nature back into society. It is further argued that biological knowledge of homosexuality resulting from that process can be used for diverse political interests. Finally, it is proposed that since biological theories on homosexuality are inseparable from the context of their paradigmatic origin, it is possible that new theories could be derived from new ideologies.

  3. Subcellular fractionation of Cu exposed oysters, Crassostrea virginica, and Cu accumulation from a biologically incorporated Cu rich oyster diet in Fundulus heteroclitus in fresh and sea water.

    PubMed

    Blanchard, Jonathan; Brix, Kevin; Grosell, Martin

    2009-05-01

    In order to examine the effect of salinity on Cu accumulation from a naturally incorporated diet, oysters (Crassostrea virginica) were exposed in sea water for 96 days to four waterborne [Cu]: 2.9+/-0.7 (control), 4.3+/-0.6, 5.4+/-0.5, and 10.7+/-1.0 microg L(-1). After 96 days, the control whole body [Cu] increased from 2.1+/-0.5 to 9.1+/-1.1 microg g(-1) w.w. and the highest [Cu] was 163.4+/-27.1 microg g(-1) w.w. in the oysters. Despite large differences in tissue [Cu], there was no effect on the fraction of trophically available metal in the oyster suggesting that trophic transfer will correlate well with tissue [Cu]. The control and highest [Cu] oysters became diet for killifish (Fundulus heteroclitus) in fresh and seawater for 40 days. The two diets contained 84.7+/-5.1 and 850.5+/-8.8 microg Cu g(-1) d.w. Fish were fed a combined diet of oyster and a pellet supplement (20.5+/-1.0 microg Cu g(-1) d.w.) both at 5% body mass day(-1). In killifish, Cu increased approximately 7% in gills and 100% in intestines after 6 weeks of exposure to the high Cu diet. No other tissues accumulated Cu above control levels. An 11-fold difference free Cu(2+) concentrations was predicted in intestinal fluid between fresh and sea water, but there was no corresponding effect of salinity on intestinal Cu accumulation suggesting that Cu is not accumulated as the free ion.

  4. Executive summary of NIH workshop on the Use and Biology of Energy Drinks: Current Knowledge and Critical Gaps

    PubMed Central

    Sorkin, Barbara C; Camp, Kathryn M; Haggans, Carol J; Deuster, Patricia A; Haverkos, Lynne; Maruvada, Padma; Witt, Ellen; Coates, Paul M

    2014-01-01

    Sales of energy drinks in the United States reached $12.5 billion in 2012. Emergency department visits related to consumption of these products have increased sharply, and while these numbers remain small relative to product sales, they raise important questions regarding biological and behavioral effects. Although some common ingredients of energy drinks have been extensively studied (e.g., caffeine, B vitamins, sugars, inositol), data on other ingredients (e.g., taurine) are limited. Summarized here are data presented elsewhere in this issue on the prevalence and patterns of caffeine-containing energy drink use, the effects of these products on alertness, fatigue, cognitive functions, sleep, mood, homeostasis, as well as on exercise physiology and metabolism, and the biological mechanisms mediating the observed effects. There are substantial data on the effects of some energy drink ingredients, such as caffeine and sugars, on many of these outcomes; however, even for these ingredients many controversies and gaps remain, and data on other ingredients in caffeine-containing energy drinks, and on ingredient interactions, are sparse. This summary concludes with a discussion of critical gaps in the data and potential next steps. PMID:25293538

  5. Executive summary of NIH workshop on the Use and Biology of Energy Drinks: Current Knowledge and Critical Gaps.

    PubMed

    Sorkin, Barbara C; Camp, Kathryn M; Haggans, Carol J; Deuster, Patricia A; Haverkos, Lynne; Maruvada, Padma; Witt, Ellen; Coates, Paul M

    2014-10-01

    Sales of energy drinks in the United States reached $12.5 billion in 2012. Emergency department visits related to consumption of these products have increased sharply, and while these numbers remain small relative to product sales, they raise important questions regarding biological and behavioral effects. Although some common ingredients of energy drinks have been extensively studied (e.g., caffeine, B vitamins, sugars, inositol), data on other ingredients (e.g., taurine) are limited. Summarized here are data presented elsewhere in this issue on the prevalence and patterns of caffeine-containing energy drink use, the effects of these products on alertness, fatigue, cognitive functions, sleep, mood, homeostasis, as well as on exercise physiology and metabolism, and the biological mechanisms mediating the observed effects. There are substantial data on the effects of some energy drink ingredients, such as caffeine and sugars, on many of these outcomes; however, even for these ingredients many controversies and gaps remain, and data on other ingredients in caffeine-containing energy drinks, and on ingredient interactions, are sparse. This summary concludes with a discussion of critical gaps in the data and potential next steps.

  6. Biological and Chemical Characterization of a New Larvicide Ovitrap Made of Plastic With Pyriproxyfen Incorporated for Aedes aegypti (Diptera: Culicidae) Control.

    PubMed

    Harburguer, Laura; Licastro, Susana; Masuh, Héctor; Zerba, Eduardo

    2016-05-01

    Aedes aegypti (L.) is a species of international concern because of its ability to transmit serious human arboviral diseases including yellow fever, dengue, and chikungunya, which have spread to all continents. Ovitraps are containers constructed to imitate Aedes' natural breeding sites and have been used for many decades as a sensitive and inexpensive surveillance tool for detecting the presence of container-inhabiting mosquitoes. In addition to their value for vector surveillance, various ovitrap devices have been evaluated as tools for suppressing Ae. aegypti populations. In this study, we performed a biological and chemical characterization of a new ovitrap prototype manufactured by injection molding of low-density polyethylene (LDPE) with the larvicide pyriproxyfen. Our research shows that pyriproxyfen was immediately released from the LDPE into the water of the ovitrap and led to an emergence inhibition of 100% for over 30 weeks. In addition, ovitraps continued to show a high larvicidal activity after over 20 washes. Pyriproxyfen was detectable in the water after 20 s and reached a peak after 24 h. Our results show that this ovitrap can be an effective, inexpensive, and low-maintenance tool for Ae. aegypti surveillance and control.

  7. Incorporating Informatics for Integrating Biology and the Bedside (i2b2) into Predoctoral Trainee Curriculum to Evaluate Student-Generated Hypotheses.

    PubMed

    Schieffer, Kathleen M; Peters, Douglas G; Richter, Chesney K; Loc, Welley S; Pawelczyk, James A

    2015-12-01

    As part of the Clinical and Translational Science Institute predoctoral TL1 training program at the Pennsylvania State University, a multidisciplinary team of predoctoral trainees representing the Chemistry, Neurosurgery, Nutritional Sciences, and Public Health Sciences departments were introduced to the NIH-sponsored Informatics for Integrating Biology and the Bedside (i2b2) database to test the following student-generated hypothesis: children with iron deficiency anemia (IDA) are at increased risk of attention deficit-hyperactivity disorder (ADHD). Children aged 4-12 and 4-17 years were categorized into IDA and control groups. De-identified medical records from the Penn State Milton S. Hershey Medical Center (HMC) and the Virginia Commonwealth University Medical Center (VCUMC) were used for the analysis. Overall, ADHD prevalence at each institution was lower than 2011 state estimates. There was a significant association between IDA and ADHD in the 4-17-year-old age group for all children (OR: 1.902 [95% CI: 1.363-2.656]), Caucasian children (OR: 1.802 [95% CI: 1.133-2.864]), and African American children (OR: 1.865 [95% CI: 1.152-3.021]). Clinical and Translational Science Award (CTSA) infrastructure is particularly useful for trainees to answer de novo scientific questions with minimal additional training and technical expertise. Moreover, projects can be expanded by collaborating within the CTSA network.

  8. A novel biological role for nsLTP2 from Oriza sativa: Potential incorporation with anticancer agents, nucleosides and their analogues.

    PubMed

    Tousheh, Mojtaba; Darvishi, Fatemeh Zahra; Miroliaei, Mehran

    2015-10-01

    Development of a protein-based drug delivery system has major impact on the efficacy and bioavailability of unstable and water insoluble drugs. In the present study, the binding modes of a nonspecific lipid transfer protein (nsLTP2) from Oryza sativa with various nucleosides and analogous molecules were identified. The 3-D structure of the protein was designed and validated using modeler 9.13, Molegro virtual docker and procheck tool, respectively. The binding affinity and strength of interactions, key contributing residues and specificity toward the substrates were accomplished by computational docking and model prediction. The protein presented high affinity to acyclovir and vidarabine as purine-analogous drugs. Binding affinity is influenced by the core template and functional groups of the ligands which are structurally different cause the variation of interaction energies with nsLTP2. Nonetheless, all the evaluated analogous drugs occupy the proximity space at the nsLTP active site with high similarity in their binding modes. Our findings hold great promise for the future applications of nsLTPs in various aspects of pharmaceutical science and molecular biology.

  9. Virtually the Same: A Comparison of STEM Students' Content Knowledge, Course Performance, and Motivation to Learn in Virtual and Face-to-Face Introductory Biology Laboratories. Research and Teaching

    ERIC Educational Resources Information Center

    Reece, Amber J.; Butler, Malcolm B.

    2017-01-01

    Biology I is a required course for many science, technology, engineering, and mathematics (STEM) majors and is often their first college-level laboratory experience. The replacement of the traditional face-to-face laboratory experience with virtual laboratories could influence students' content knowledge, motivation to learn biology, and overall…

  10. Herpetofauna of the Beni Biological Station Biosphere Reserve, Amazonian Bolivia: Additional information, and current knowledge in context

    USGS Publications Warehouse

    Middendorf, G.; Reynolds, R.; Herrera-MacBryde, Olga; Dallmeier, Francisco; MacBryde, Bruce; Cominskey, James A.; Miranda, Carmen

    2000-01-01

    Previous collections in the Departamento del Beni in tropical Bolivia only hinted at high levels of herpetological biodiversity (Fugler 1986, 1988; de la Riva 1990a; Fugler and de la Riva 1990). Fieldwork (totaling 48 days) in July-August 1988 and September 1987 (dry seasons) and November-December 1990 (wet season) has resulted in collection and identification of 401 amphibian and reptilian specimens from the general area of the Beni Biological Station's (EBB) headquarters at El Porvenir. These collections represent 33 amphibian and 17 reptilian species in 29 genera (14 amphibian, 15 reptilian). The inventory of herpetofauna scientifically documented to occur in the Departamento del Beni is considered to have been increased by 6 amphibian and 10 reptilian species. Specimens that could not be definitively identified (reflecting taxonomic uncertainty and/or probably species new to science) include 3 amphibian species (anurans) and 2 reptilian species (snakes). The EBB harbors the richest savanna for anuran species known in South America.

  11. Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

    PubMed Central

    Baskauf, Steve; Blum, Stanley; Bowers, Shawn; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Tuama, Éamonn Ó.; Schildhauer, Mark; Smith, Barry; Stucky, Brian J.; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers

  12. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

    PubMed

    Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Ó Tuama, Éamonn; Schildhauer, Mark; Smith, Barry; Stucky, Brian J; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

  13. Averaged Propulsive Body Acceleration (APBA) Can Be Calculated from Biologging Tags That Incorporate Gyroscopes and Accelerometers to Estimate Swimming Speed, Hydrodynamic Drag and Energy Expenditure for Steller Sea Lions

    PubMed Central

    Trites, Andrew W.; Rosen, David A. S.; Potvin, Jean

    2016-01-01

    Forces due to propulsion should approximate forces due to hydrodynamic drag for animals horizontally swimming at a constant speed with negligible buoyancy forces. Propulsive forces should also correlate with energy expenditures associated with locomotion—an important cost of foraging. As such, biologging tags containing accelerometers are being used to generate proxies for animal energy expenditures despite being unable to distinguish rotational movements from linear movements. However, recent miniaturizations of gyroscopes offer the possibility of resolving this shortcoming and obtaining better estimates of body accelerations of swimming animals. We derived accelerations using gyroscope data for swimming Steller sea lions (Eumetopias jubatus), and determined how well the measured accelerations correlated with actual swimming speeds and with theoretical drag. We also compared dive averaged dynamic body acceleration estimates that incorporate gyroscope data, with the widely used Overall Dynamic Body Acceleration (ODBA) metric, which does not use gyroscope data. Four Steller sea lions equipped with biologging tags were trained to swim alongside a boat cruising at steady speeds in the range of 4 to 10 kph. At each speed, and for each dive, we computed a measure called Gyro-Informed Dynamic Acceleration (GIDA) using a method incorporating gyroscope data with accelerometer data. We derived a new metric—Averaged Propulsive Body Acceleration (APBA), which is the average gain in speed per flipper stroke divided by mean stroke cycle duration. Our results show that the gyro-based measure (APBA) is a better predictor of speed than ODBA. We also found that APBA can estimate average thrust production during a single stroke-glide cycle, and can be used to estimate energy expended during swimming. The gyroscope-derived methods we describe should be generally applicable in swimming animals where propulsive accelerations can be clearly identified in the signal—and they should

  14. Averaged Propulsive Body Acceleration (APBA) Can Be Calculated from Biologging Tags That Incorporate Gyroscopes and Accelerometers to Estimate Swimming Speed, Hydrodynamic Drag and Energy Expenditure for Steller Sea Lions.

    PubMed

    Ware, Colin; Trites, Andrew W; Rosen, David A S; Potvin, Jean

    2016-01-01

    Forces due to propulsion should approximate forces due to hydrodynamic drag for animals horizontally swimming at a constant speed with negligible buoyancy forces. Propulsive forces should also correlate with energy expenditures associated with locomotion-an important cost of foraging. As such, biologging tags containing accelerometers are being used to generate proxies for animal energy expenditures despite being unable to distinguish rotational movements from linear movements. However, recent miniaturizations of gyroscopes offer the possibility of resolving this shortcoming and obtaining better estimates of body accelerations of swimming animals. We derived accelerations using gyroscope data for swimming Steller sea lions (Eumetopias jubatus), and determined how well the measured accelerations correlated with actual swimming speeds and with theoretical drag. We also compared dive averaged dynamic body acceleration estimates that incorporate gyroscope data, with the widely used Overall Dynamic Body Acceleration (ODBA) metric, which does not use gyroscope data. Four Steller sea lions equipped with biologging tags were trained to swim alongside a boat cruising at steady speeds in the range of 4 to 10 kph. At each speed, and for each dive, we computed a measure called Gyro-Informed Dynamic Acceleration (GIDA) using a method incorporating gyroscope data with accelerometer data. We derived a new metric-Averaged Propulsive Body Acceleration (APBA), which is the average gain in speed per flipper stroke divided by mean stroke cycle duration. Our results show that the gyro-based measure (APBA) is a better predictor of speed than ODBA. We also found that APBA can estimate average thrust production during a single stroke-glide cycle, and can be used to estimate energy expended during swimming. The gyroscope-derived methods we describe should be generally applicable in swimming animals where propulsive accelerations can be clearly identified in the signal-and they should also

  15. Knowledge and Theme Discovery across Very Large Biological Data Sets Using Distributed Queries: A Prototype Combining Unstructured and Structured Data

    PubMed Central

    Repetski, Stephen; Venkataraman, Girish; Che, Anney; Luke, Brian T.; Girard, F. Pascal; Stephens, Robert M.

    2013-01-01

    As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not keeping pace. In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively. As we move towards personalized medicine, the need to combine unstructured data, such as medical literature, with large amounts of highly structured and high-throughput data such as human variation or expression data from very large cohorts, is especially urgent. For our study, we investigated a likely biomedical query using the Hadoop framework. We ran queries using native MapReduce tools we developed as well as other open source and proprietary tools. Our results suggest that the available technologies within the Big Data domain can reduce the time and effort needed to utilize and apply distributed queries over large datasets in practical clinical applications in the life sciences domain. The methodologies and technologies discussed in this paper set the stage for a more detailed evaluation that investigates how various data structures and data models are best mapped to the proper computational framework. PMID:24312478

  16. Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data.

    PubMed

    Mudunuri, Uma S; Khouja, Mohamad; Repetski, Stephen; Venkataraman, Girish; Che, Anney; Luke, Brian T; Girard, F Pascal; Stephens, Robert M

    2013-01-01

    As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not keeping pace. In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively. As we move towards personalized medicine, the need to combine unstructured data, such as medical literature, with large amounts of highly structured and high-throughput data such as human variation or expression data from very large cohorts, is especially urgent. For our study, we investigated a likely biomedical query using the Hadoop framework. We ran queries using native MapReduce tools we developed as well as other open source and proprietary tools. Our results suggest that the available technologies within the Big Data domain can reduce the time and effort needed to utilize and apply distributed queries over large datasets in practical clinical applications in the life sciences domain. The methodologies and technologies discussed in this paper set the stage for a more detailed evaluation that investigates how various data structures and data models are best mapped to the proper computational framework.

  17. On Crowd-verification of Biological Networks

    PubMed Central

    Ansari, Sam; Binder, Jean; Boue, Stephanie; Di Fabio, Anselmo; Hayes, William; Hoeng, Julia; Iskandar, Anita; Kleiman, Robin; Norel, Raquel; O’Neel, Bruce; Peitsch, Manuel C.; Poussin, Carine; Pratt, Dexter; Rhrissorrakrai, Kahn; Schlage, Walter K.; Stolovitzky, Gustavo; Talikka, Marja

    2013-01-01

    Biological networks with a structured syntax are a powerful way of representing biological information generated from high density data; however, they can become unwieldy to manage as their size and complexity increase. This article presents a crowd-verification approach for the visualization and expansion of biological networks. Web-based graphical interfaces allow visualization of causal and correlative biological relationships represented using Biological Expression Language (BEL). Crowdsourcing principles enable participants to communally annotate these relationships based on literature evidences. Gamification principles are incorporated to further engage domain experts throughout biology to gather robust peer-reviewed information from which relationships can be identified and verified. The resulting network models will represent the current status of biological knowledge within the defined boundaries, here processes related to human lung disease. These models are amenable to computational analysis. For some period following conclusion of the challenge, the published models will remain available for continuous use and expansion by the scientific community. PMID:24151423

  18. Fostering synergy between cell biology and systems biology.

    PubMed

    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.

  19. Fostering synergy between cell biology and systems biology

    PubMed Central

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

    2015-01-01

    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 critical 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. PMID:26013981

  20. Novelty or knowledge? A study of using a student response system in non-major biology courses at a community college

    NASA Astrophysics Data System (ADS)

    Thames, Tasha Herrington

    The advancement in technology integration is laying the groundwork of a paradigm shift in the higher education system (Noonoo, 2011). The National Dropout Prevention Center (n.d.) claims that technology offers some of the best opportunities for presenting instruction to engage students in meaningful education, addressing multiple intelligences, and adjusting to students' various learning styles. The purpose of this study was to investigate if implementing clicker technology would have a statistically significant difference on student retention and student achievement, while controlling for learning styles, for students in non-major biology courses who were and were not subjected to the technology. This study also sought to identify if students perceived the use of clickers as beneficial to their learning. A quantitative quasi-experimental research design was utilized to determine the significance of differences in pre/posttest achievement scores between students who participated during the fall semester in 2014. Overall, 118 students (n = 118) voluntarily enrolled in the researcher's fall non-major Biology course at a southern community college. A total of 71 students were assigned to the experimental group who participated in instruction incorporating the ConcepTest Process with clicker technology along with traditional lecture. The remaining 51 students were assigned to the control group who participated in a traditional lecture format with peer instruction embedded. Statistical analysis revealed the experimental clicker courses did have higher posttest scores than the non-clicker control courses, but this was not significant (p >.05). Results also implied that clickers did not statistically help retain students to complete the course. Lastly, the results indicated that there were no significant statistical difference in student's clicker perception scores between the different learning style preferences.

  1. The `What is a system' reflection interview as a knowledge integration activity for high school students' understanding of complex systems in human biology

    NASA Astrophysics Data System (ADS)

    Tripto, Jaklin; Ben-Zvi Assaraf, Orit; Snapir, Zohar; Amit, Miriam

    2016-03-01

    This study examined the reflection interview as a tool for assessing and facilitating the use of 'systems language' amongst 11th grade students who have recently completed their first year of high school biology. Eighty-three students composed two concept maps in the 10th grade-one at the beginning of the school year and one at its end. The first part of the interview is dedicated to guiding the students through comparing their two concept maps and by means of both explicit and non-explicit teaching. Our study showed that the explicit guidance in comparing the two concept maps was more effective than the non-explicit, eliciting a variety of different, more specific, types of interactions and patterns (e.g. 'hierarchy', 'dynamism', 'homeostasis') in the students' descriptions of the human body system. The reflection interview as a knowledge integration activity was found to be an effective tool for assessing the subjects' conceptual models of 'system complexity', and for identifying those aspects of a system that are most commonly misunderstood.

  2. Development and Evaluation of the Tigriopus Course-Based Undergraduate Research Experience: Impacts on Students' Content Knowledge, Attitudes, and Motivation in a Majors Introductory Biology Course.

    PubMed

    Olimpo, Jeffrey T; Fisher, Ginger R; DeChenne-Peters, Sue Ellen

    2016-01-01

    Within the past decade, course-based undergraduate research experiences (CUREs) have emerged as a viable mechanism to enhance novices' development of scientific reasoning and process skills in the science, technology, engineering, and mathematics disciplines. Recent evidence within the bioeducation literature suggests that student engagement in such experiences not only increases their appreciation for and interest in scientific research but also enhances their ability to "think like a scientist." Despite these critical outcomes, few studies have objectively explored CURE versus non-CURE students' development of content knowledge, attitudes, and motivation in the discipline, particularly among nonvolunteer samples. To address these concerns, we adopted a mixed-methods approach to evaluate the aforementioned outcomes following implementation of a novel CURE in an introductory cell/molecular biology course. Results indicate that CURE participants exhibited more expert-like outcomes on these constructs relative to their non-CURE counterparts, including in those areas related to self-efficacy, self-determination, and problem-solving strategies. Furthermore, analysis of end-of-term survey data suggests that select features of the CURE, such as increased student autonomy and collaboration, mediate student learning and enjoyment. Collectively, this research provides novel insights into the benefits achieved as a result of CURE participation and can be used to guide future development and evaluation of authentic research opportunities.

  3. Development and Evaluation of the Tigriopus Course-Based Undergraduate Research Experience: Impacts on Students’ Content Knowledge, Attitudes, and Motivation in a Majors Introductory Biology Course

    PubMed Central

    Olimpo, Jeffrey T.; Fisher, Ginger R.; DeChenne-Peters, Sue Ellen

    2016-01-01

    Within the past decade, course-based undergraduate research experiences (CUREs) have emerged as a viable mechanism to enhance novices’ development of scientific reasoning and process skills in the science, technology, engineering, and mathematics disciplines. Recent evidence within the bioeducation literature suggests that student engagement in such experiences not only increases their appreciation for and interest in scientific research but also enhances their ability to “think like a scientist.” Despite these critical outcomes, few studies have objectively explored CURE versus non-CURE students’ development of content knowledge, attitudes, and motivation in the discipline, particularly among nonvolunteer samples. To address these concerns, we adopted a mixed-methods approach to evaluate the aforementioned outcomes following implementation of a novel CURE in an introductory cell/molecular biology course. Results indicate that CURE participants exhibited more expert-like outcomes on these constructs relative to their non-CURE counterparts, including in those areas related to self-efficacy, self-determination, and problem-solving strategies. Furthermore, analysis of end-of-term survey data suggests that select features of the CURE, such as increased student autonomy and collaboration, mediate student learning and enjoyment. Collectively, this research provides novel insights into the benefits achieved as a result of CURE participation and can be used to guide future development and evaluation of authentic research opportunities. PMID:27909022

  4. Learning To Use Scientific Knowledge in Education and Practice Settings: An Evaluation of the Contribution of the Biological Behavioural and Social Sciences to Pre-Registration Nursing and Midwifery Programmes. Researching Professional Education. Research Reports Series Number 3.

    ERIC Educational Resources Information Center

    Eraut, Michael; And Others

    A research project evaluated the contribution of biological, behavioral, and social sciences to nursing and midwifery education programs in Britain. The study of scientific knowledge relevant to recently qualified nurses and midwives was confined to six topics: fluids, electrolytes, and renal systems; nutrition; acute pain; shock; stress; and…

  5. The Effects of the SUN Project on Teacher Knowledge and Self-Efficacy Regarding Biological Energy Transfer Are Significant and Long-Lasting: Results of a Randomized Controlled Trial

    PubMed Central

    Batiza, Ann Finney; Gruhl, Mary; Zhang, Bo; Harrington, Tom; Roberts, Marisa; LaFlamme, Donna; Haasch, Mary Anne; Knopp, Jonathan; Vogt, Gina; Goodsell, David; Hagedorn, Eric; Marcey, David; Hoelzer, Mark; Nelson, Dave

    2013-01-01

    Biological energy flow has been notoriously difficult to teach. Our approach to this topic relies on abiotic and biotic examples of the energy released by moving electrons in thermodynamically spontaneous reactions. A series of analogical model-building experiences was supported with common language and representations including manipulatives. These materials were designed to help learners understand why electrons move in a hydrogen explosion and hydrogen fuel cell, so they could ultimately understand the rationale for energy transfer in the mitochondrion and the chloroplast. High school biology teachers attended a 2-wk Students Understanding eNergy (SUN) workshop during a randomized controlled trial. These treatment group teachers then took hydrogen fuel cells, manipulatives, and other materials into their regular biology classrooms. In this paper, we report significant gains in teacher knowledge and self-efficacy regarding biological energy transfer in the treatment group versus randomized controls. Significant effects on treatment group teacher knowledge and self-efficacy were found not only post–SUN workshop but even 1 yr later. Teacher knowledge was measured with both a multiple-choice exam and a drawing with a written explanation. Teacher confidence in their ability to teach biological energy transfer was measured by a modified form of the Science Teaching Efficacy Belief Instrument, In-Service A. Professional development implications regarding this topic are discussed. PMID:23737635

  6. The effects of the SUN project on teacher knowledge and self-efficacy regarding biological energy transfer are significant and long-lasting: results of a randomized controlled trial.

    PubMed

    Batiza, Ann Finney; Gruhl, Mary; Zhang, Bo; Harrington, Tom; Roberts, Marisa; LaFlamme, Donna; Haasch, Mary Anne; Knopp, Jonathan; Vogt, Gina; Goodsell, David; Hagedorn, Eric; Marcey, David; Hoelzer, Mark; Nelson, Dave

    2013-06-01

    Biological energy flow has been notoriously difficult to teach. Our approach to this topic relies on abiotic and biotic examples of the energy released by moving electrons in thermodynamically spontaneous reactions. A series of analogical model-building experiences was supported with common language and representations including manipulatives. These materials were designed to help learners understand why electrons move in a hydrogen explosion and hydrogen fuel cell, so they could ultimately understand the rationale for energy transfer in the mitochondrion and the chloroplast. High school biology teachers attended a 2-wk Students Understanding eNergy (SUN) workshop during a randomized controlled trial. These treatment group teachers then took hydrogen fuel cells, manipulatives, and other materials into their regular biology classrooms. In this paper, we report significant gains in teacher knowledge and self-efficacy regarding biological energy transfer in the treatment group versus randomized controls. Significant effects on treatment group teacher knowledge and self-efficacy were found not only post-SUN workshop but even 1 yr later. Teacher knowledge was measured with both a multiple-choice exam and a drawing with a written explanation. Teacher confidence in their ability to teach biological energy transfer was measured by a modified form of the Science Teaching Efficacy Belief Instrument, In-Service A. Professional development implications regarding this topic are discussed.

  7. Creating Illusions of Knowledge: Learning Errors that Contradict Prior Knowledge

    ERIC Educational Resources Information Center

    Fazio, Lisa K.; Barber, Sarah J.; Rajaram, Suparna; Ornstein, Peter A.; Marsh, Elizabeth J.

    2013-01-01

    Most people know that the Pacific is the largest ocean on Earth and that Edison invented the light bulb. Our question is whether this knowledge is stable, or if people will incorporate errors into their knowledge bases, even if they have the correct knowledge stored in memory. To test this, we asked participants general-knowledge questions 2 weeks…

  8. The PlaNet Consortium: A Network of European Plant Databases Connecting Plant Genome Data in an Integrated Biological Knowledge Resource

    PubMed Central

    Ernst, R.; Mayer, K. F. X.

    2004-01-01

    The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project. PMID:18629059

  9. The PlaNet Consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource.

    PubMed

    Schoof, H; Ernst, R; Mayer, K F X

    2004-01-01

    The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project.

  10. Adding Confidence to Knowledge

    ERIC Educational Resources Information Center

    Goodson, Ludwika Aniela; Slater, Don; Zubovic, Yvonne

    2015-01-01

    A "knowledge survey" and a formative evaluation process led to major changes in an instructor's course and teaching methods over a 5-year period. Design of the survey incorporated several innovations, including: a) using "confidence survey" rather than "knowledge survey" as the title; b) completing an instructional…

  11. Incorporation of multiple cloud layers for ultraviolet radiation modeling studies

    NASA Technical Reports Server (NTRS)

    Charache, Darryl H.; Abreu, Vincent J.; Kuhn, William R.; Skinner, Wilbert R.

    1994-01-01

    Cloud data sets compiled from surface observations were used to develop an algorithm for incorporating multiple cloud layers into a multiple-scattering radiative transfer model. Aerosol extinction and ozone data sets were also incorporated to estimate the seasonally averaged ultraviolet (UV) flux reaching the surface of the Earth in the Detroit, Michigan, region for the years 1979-1991, corresponding to Total Ozone Mapping Spectrometer (TOMS) version 6 ozone observations. The calculated UV spectrum was convolved with an erythema action spectrum to estimate the effective biological exposure for erythema. Calculations show that decreasing the total column density of ozone by 1% leads to an increase in erythemal exposure by approximately 1.1-1.3%, in good agreement with previous studies. A comparison of the UV radiation budget at the surface between a single cloud layer method and a multiple cloud layer method presented here is discussed, along with limitations of each technique. With improved parameterization of cloud properties, and as knowledge of biological effects of UV exposure increase, inclusion of multiple cloud layers may be important in accurately determining the biologically effective UV budget at the surface of the Earth.

  12. Knowledge Mobilization across Boundaries with the Use of Novel Organizational Structures, Conferencing Strategies, and Technological Tools: The Ontario Consortium of Undergraduate Biology Educators (oCUBE) Model

    ERIC Educational Resources Information Center

    Kajiura, Lovaye; Smit, Julie; Montpetit, Colin; Kelly, Tamara; Waugh, Jennifer; Rawle, Fiona; Clark, Julie; Neumann, Melody; French, Michelle

    2014-01-01

    The Ontario Consortium of Undergraduate Biology Educators (oCUBE) brings together over 50 biology educators from 18 Ontario universities with the common goal to improve the biology undergraduate experience for both students and educators. This goal is achieved through an innovative mix of highly interactive face-to-face meetings, online…

  13. Biology and the Government

    ERIC Educational Resources Information Center

    Reid, Roger D.

    1969-01-01

    Emphasizes the social implications of biological knowledge and discusses two main government roles in biology: (1) a creative and supportive role, including support of education and research, (2) control, regulation and protection related to the applications of biological knowledge. Public control is considered necessary in areas such as food and…

  14. Creating biological nanomaterials using synthetic biology

    NASA Astrophysics Data System (ADS)

    Rice, MaryJoe K.; Ruder, Warren C.

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  15. Creating biological nanomaterials using synthetic biology.

    PubMed

    Rice, MaryJoe K; Ruder, Warren C

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  16. Why the Current Insistence on Open Access to Scientific Data? Big Data, Knowledge Production, and the Political Economy of Contemporary Biology

    ERIC Educational Resources Information Center

    Leonelli, Sabina

    2013-01-01

    The collection and dissemination of data on human and nonhuman organisms has become a central feature of 21st-century biology and has been endorsed by funding agencies in the United States and Europe as crucial to translating biological research into therapeutic and agricultural innovation. Large molecular data sets, often referred to as "big…

  17. Biological warfare agents.

    PubMed

    Pohanka, Miroslav; Kuca, Kamil

    2010-01-01

    Biological warfare agents are a group of pathogens and toxins of biological origin that can be potentially misused for military or criminal purposes. The present review attempts to summarize necessary knowledge about biological warfare agents. The historical aspects, examples of applications of these agents such as anthrax letters, biological weapons impact, a summary of biological warfare agents and epidemiology of infections are described. The last section tries to estimate future trends in research on biological warfare agents.

  18. Learning Biology by Designing

    ERIC Educational Resources Information Center

    Janssen, Fred; Waarlo, Arend Jan

    2010-01-01

    According to a century-old tradition in biological thinking, organisms can be considered as being optimally designed. In modern biology this idea still has great heuristic value. In evolutionary biology a so-called design heuristic has been formulated which provides guidance to researchers in the generation of knowledge about biological systems.…

  19. Marine Education Knowledge Inventory.

    ERIC Educational Resources Information Center

    Hounshell, Paul B.; Hampton, Carolyn

    This 35-item, multiple-choice Marine Education Knowledge Inventory was developed for use in upper elementary/middle schools to measure a student's knowledge of marine science. Content of test items is drawn from oceanography, ecology, earth science, navigation, and the biological sciences (focusing on marine animals). Steps in the construction of…

  20. Women care about local knowledge, experiences from ethnomycology.

    PubMed

    Garibay-Orijel, Roberto; Ramírez-Terrazo, Amaranta; Ordaz-Velázquez, Marisa

    2012-07-18

    Gender is one of the main variables that influence the distribution of local knowledge. We carried out a literature review concerning local mycological knowledge, paying special attention to data concerning women's knowledge and comparative gender data. We found that unique features of local mycological knowledge allow people to successfully manage mushrooms. Women are involved in every stage of mushroom utilization from collection to processing and marketing. Local mycological knowledge includes the use mushrooms as food, medicine, and recreational objects as well as an aid to seasonal household economies. In many regions of the world, women are often the main mushroom collectors and possess a vast knowledge about mushroom taxonomy, biology, and ecology. Local experts play a vital role in the transmission of local mycological knowledge. Women participate in the diffusion of this knowledge as well as in its enrichment through innovation. Female mushroom collectors appreciate their mycological knowledge and pursue strategies and organization to reproduce it in their communities. Women mushroom gatherers are conscious of their knowledge, value its contribution in their subsistence systems, and proudly incorporate it in their cultural identity.

  1. Women care about local knowledge, experiences from ethnomycology

    PubMed Central

    2012-01-01

    Gender is one of the main variables that influence the distribution of local knowledge. We carried out a literature review concerning local mycological knowledge, paying special attention to data concerning women’s knowledge and comparative gender data. We found that unique features of local mycological knowledge allow people to successfully manage mushrooms. Women are involved in every stage of mushroom utilization from collection to processing and marketing. Local mycological knowledge includes the use mushrooms as food, medicine, and recreational objects as well as an aid to seasonal household economies. In many regions of the world, women are often the main mushroom collectors and possess a vast knowledge about mushroom taxonomy, biology, and ecology. Local experts play a vital role in the transmission of local mycological knowledge. Women participate in the diffusion of this knowledge as well as in its enrichment through innovation. Female mushroom collectors appreciate their mycological knowledge and pursue strategies and organization to reproduce it in their communities. Women mushroom gatherers are conscious of their knowledge, value its contribution in their subsistence systems, and proudly incorporate it in their cultural identity. PMID:22809491

  2. The "What Is a System" Reflection Interview as a Knowledge Integration Activity for High School Students' Understanding of Complex Systems in Human Biology

    ERIC Educational Resources Information Center

    Tripto, Jaklin; Ben-Zvi Assaraf, Orit; Snapir, Zohar; Amit, Miriam

    2016-01-01

    This study examined the reflection interview as a tool for assessing and facilitating the use of "systems language" amongst 11th grade students who have recently completed their first year of high school biology. Eighty-three students composed two concept maps in the 10th grade--one at the beginning of the school year and one at its end.…

  3. The Development of Biology Teaching Material Based on the Local Wisdom of Timorese to Improve Students Knowledge and Attitude of Environment in Caring the Preservation of Environment

    ERIC Educational Resources Information Center

    Ardan, Andam S.

    2016-01-01

    The purposes of this study were (1) to describe the biology learning such as lesson plans, teaching materials, media and worksheets for the tenth grade of High School on the topic of Biodiversity and Basic Classification, Ecosystems and Environment Issues based on local wisdom of Timorese; (2) to analyze the improvement of the environmental…

  4. Three Forms of Assessment of Prior Knowledge, and Improved Performance Following an Enrichment Programme, of English Second Language Biology Students within the Context of a Marine Theme.

    ERIC Educational Resources Information Center

    Feltham, Nicola F.; Downs, Colleen T.

    2002-01-01

    Reports on the assessment of student background knowledge along a continuum of language dependency using a set of three probes. Examines improved student performance in each of the respective assessments on the extent to which a sound natural history background facilitated meaningful learning relative to English as Second Language (ESL)…

  5. Knowledge of, Attitudes toward, and Acceptance of Genetically Modified Organisms among Prospective Teachers of Biology, Home Economics, and Grade School in Slovenia

    ERIC Educational Resources Information Center

    Sorgo, Andrej; Ambrozic-Dolinsek, Jana

    2010-01-01

    The objective of this study was to investigate knowledge, opinions, and attitudes toward, as well as readiness to accept genetically modified organisms (GMOs) among prospective primary and secondary Slovene teachers. Our findings are that prospective teachers want to take an active role in rejecting or supporting individual GMOs and are aware of…

  6. Development, Evaluation, and Validation of a Paper-and-Pencil Test for Measuring Two Components of Biology Teachers' Pedagogical Content Knowledge Concerning the "Cardiovascular System"

    ERIC Educational Resources Information Center

    Schmelzing, Stephan; van Driel, Jan H.; Jüttner, Melanie; Brandenbusch, Stefanie; Sandmann, Angela; Neuhaus, Birgit J.

    2013-01-01

    One main focus of teacher education research concentrates on teachers' pedagogical content knowledge (PCK). It has been shown that teachers' PCK correlates with teaching effectiveness as well as with students' achievement gains. Teachers' PCK should be analyzed as one of the main important components to evaluate professional…

  7. Incorporating Social Media in the Classroom

    ERIC Educational Resources Information Center

    McMeans, April

    2015-01-01

    Incorporating social media into the classroom will provide a positive, upbeat learning environment that students are engaged in on a regular basis. In doing this, educators will be ensuring discussion, collaboration, critical thinking, and creativity amongst their students. Social media is a knowledgeable topic for our students, and it is an…

  8. Reasoning from Incomplete Knowledge.

    ERIC Educational Resources Information Center

    Collins, Allan M.; And Others

    People use a variety of plausible, but uncertain inferences to answer questions about which their knowledge is incomplete. Such inferential thinking and reasoning is being incorporated into the SCHOLAR computer-assisted instruction (CAI) system. Socratic tutorial techniques in CAI systems such as SCHOLAR are described, and examples of their…

  9. Teaching and Learning Biology.

    ERIC Educational Resources Information Center

    Dowdeswell, W. H.

    Provided in this book is a critical review of modern biology curricula and teaching methods with particular reference to the advance of knowledge and changes in society. The book consists of an introduction (discussing biology as a subject, attitudes to learning, and values in biology teaching), 12 chapters, and 4 appendices. Teaching/learning…

  10. Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies

    SciTech Connect

    Ghosh, Arun; Gemma, Sandra; Takayama, Jun; Baldridge, Abigail; Leshchenko-Yashchuk, Sofiya; Miller, Heather; Wang, Yuan-Fang; Kovalevsky, Andrey; Koh, Yashiro; Weber, Irene; Mitsuya, Hiroaki

    2008-12-05

    Recently, we designed a series of novel HIV-1 protease inhibitors incorporating a stereochemically defined bicyclic fused cyclopentyl (Cp-THF) urethane as the high affinity P2-ligand. Inhibitor 1 with this P2-ligand has shown very impressive potency against multi-drug-resistant clinical isolates. Based upon the 1-bound HIV-1 protease X-ray structure, we have now designed and synthesized a number of meso-bicyclic ligands which can conceivably interact similarly to the Cp-THF ligand. The design of meso-ligands is quite attractive as they do not contain any stereocenters. Inhibitors incorporating urethanes of bicyclic-1,3-dioxolane and bicyclic-1,4-dioxane have shown potent enzyme inhibitory and antiviral activities. Inhibitor 2 (K{sub i} = 0.11 nM; IC{sub 50} = 3.8 nM) displayed very potent antiviral activity in this series. While inhibitor 3 showed comparable enzyme inhibitory activity (K{sub i} = 0.18 nM) its antiviral activity (IC{sub 50} = 170 nM) was significantly weaker than inhibitor 2. Inhibitor 2 maintained an antiviral potency against a series of multi-drug resistant clinical isolates comparable to amprenavir. A protein-ligand X-ray structure of 3-bound HIV-1 protease revealed a number of key hydrogen bonding interactions at the S2-subsite. We have created an active model of inhibitor 2 based upon this X-ray structure.

  11. Creating illusions of knowledge: learning errors that contradict prior knowledge.

    PubMed

    Fazio, Lisa K; Barber, Sarah J; Rajaram, Suparna; Ornstein, Peter A; Marsh, Elizabeth J

    2013-02-01

    Most people know that the Pacific is the largest ocean on Earth and that Edison invented the light bulb. Our question is whether this knowledge is stable, or if people will incorporate errors into their knowledge bases, even if they have the correct knowledge stored in memory. To test this, we asked participants general-knowledge questions 2 weeks before they read stories that contained errors (e.g., "Franklin invented the light bulb"). On a later general-knowledge test, participants reproduced story errors despite previously answering the questions correctly. This misinformation effect was found even for questions that were answered correctly on the initial test with the highest level of confidence. Furthermore, prior knowledge offered no protection against errors entering the knowledge base; the misinformation effect was equivalent for previously known and unknown facts. Errors can enter the knowledge base even when learners have the knowledge necessary to catch the errors.

  12. Bearings Incorporating Deadband Rollers

    NASA Technical Reports Server (NTRS)

    Gualtieri, Guy V.

    1996-01-01

    Bearings in high-pressure turbopump redesigned to incorporate rollers allowing limited axial motion within small deadband. Does not permit radial deadband motion. Axial deadband motion used for rotor-thrust-balance control. Design eliminates some nonlinearities in dynamics of pump rotor and assists in suppressing vibrations at harmonics of frequency of rotation.

  13. Incorporating nitrogen fixing cyanobacteria in the global biogeochemical model HAMOCC

    NASA Astrophysics Data System (ADS)

    Paulsen, Hanna; Ilyina, Tatiana; Six, Katharina

    2015-04-01

    Nitrogen fixation by marine diazotrophs plays a fundamental role in the oceanic nitrogen and carbon cycle as it provides a major source of 'new' nitrogen to the euphotic zone that supports biological carbon export and sequestration. Since most global biogeochemical models include nitrogen fixation only diagnostically, they are not able to capture its spatial pattern sufficiently. Here we present the incorporation of an explicit, dynamic representation of diazotrophic cyanobacteria and the corresponding nitrogen fixation in the global ocean biogeochemical model HAMOCC (Hamburg Ocean Carbon Cycle model), which is part of the Max Planck Institute for Meteorology Earth system model (MPI-ESM). The parameterization of the diazotrophic growth is thereby based on available knowledge about the cyanobacterium Trichodesmium spp., which is considered as the most significant pelagic nitrogen fixer. Evaluation against observations shows that the model successfully reproduces the main spatial distribution of cyanobacteria and nitrogen fixation, covering large parts of the tropical and subtropical oceans. Besides the role of cyanobacteria in marine biogeochemical cycles, their capacity to form extensive surface blooms induces a number of bio-physical feedback mechanisms in the Earth system. The processes driving these interactions, which are related to the alteration of heat absorption, surface albedo and momentum input by wind, are incorporated in the biogeochemical and physical model of the MPI-ESM in order to investigate their impacts on a global scale. First preliminary results will be shown.

  14. Unequal Knowledge.

    ERIC Educational Resources Information Center

    Tilly, Charles

    2003-01-01

    Discusses how the persistence of knowledge inequalities influences higher education. Explores how the control of and access to knowledge affects human well being (i.e., control over production of knowledge, control over its distribution, and access to knowledge by people whose well being it will or could affect). (EV)

  15. Knowledge Management.

    ERIC Educational Resources Information Center

    1999

    The first of the four papers in this symposium, "Knowledge Management and Knowledge Dissemination" (Wim J. Nijhof), presents two case studies exploring the strategies companies use in sharing and disseminating knowledge and expertise among employees. "A Theory of Knowledge Management" (Richard J. Torraco), develops a conceptual…

  16. The Medawar Lecture 2001 Knowledge for vision: vision for knowledge

    PubMed Central

    Gregory, Richard L

    2005-01-01

    An evolutionary development of perception is suggested—from passive reception to active perception to explicit conception—earlier stages being largely retained and incorporated in later species. A key is innate and then individually learned knowledge, giving meaning to sensory signals. Inappropriate or misapplied knowledge produces rich cognitive phenomena of illusions, revealing normally hidden processes of vision, tentatively classified here in a ‘peeriodic table’. Phenomena of physiology are distinguished from phenomena of general rules and specific object knowledge. It is concluded that vision uses implicit knowledge, and provides knowledge for intelligent behaviour and for explicit conceptual understanding including science. PMID:16147519

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

    ERIC Educational Resources Information Center

    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…

  18. Zinc Incorporation Into Hydroxylapatite

    SciTech Connect

    Tang, Y.; Chappell, H; Dove, M; Reeder, R; Lee, Y

    2009-01-01

    By theoretical modeling and X-ray absorption spectroscopy, the local coordination structure of Zn incorporated into hydroxylapatite was examined. Density function theory (DFT) calculations show that Zn favors the Ca2 site over the Ca1 site, and favors tetrahedral coordination. X-ray absorption near edge structure (XANES) spectroscopy results suggest one dominant coordination environment for the incorporated Zn, and no evidence was observed for other Zn-containing phases. Extended X-ray absorption fine structure (EXAFS) fitting of the synthetic samples confirms that Zn occurs in tetrahedral coordination, with two P shells at 2.85-3.07 {angstrom}, and two higher Ca shells at 3.71-4.02 {angstrom}. These fit results are consistent with the most favored DFT model for Zn substitution in the Ca2 site.

  19. Blended Learning for Faculty Professional Development Incorporating Knowledge Management Principles

    ERIC Educational Resources Information Center

    Hewitt, Julie E.

    2016-01-01

    Adjunct faculty comprise a large percentage of part-time faculty for many colleges and universities today. Adjunct faculty are hired because they are experts in their content areas; however, this does not guarantee that they are skilled in effective classroom management. These instructors can become bewildered and frustrated because they lack the…

  20. Incorporating Domain Knowledge in Matching Problems via Harmonic Analysis.

    PubMed

    Pachauri, Deepti; Collins, Maxwell; Kondor, Risi; Singh, Vikas

    2012-01-01

    Matching one set of objects to another is a ubiquitous task in machine learning and computer vision that often reduces to some form of the quadratic assignment problem (QAP). The QAP is known to be notoriously hard, both in theory and in practice. Here, we investigate if this difficulty can be mitigated when some additional piece of information is available: (a) that all QAP instances of interest come from the same application, and (b) the correct solution for a set of such QAP instances is given. We propose a new approach to accelerate the solution of QAPs based on learning parameters for a modified objective function from prior QAP instances. A key feature of our approach is that it takes advantage of the algebraic structure of permutations, in conjunction with special methods for optimizing functions over the symmetric group n in Fourier space. Experiments show that in practical domains the new method can outperform existing approaches.

  1. Incorporating Domain Knowledge in Matching Problems via Harmonic Analysis

    PubMed Central

    Pachauri, Deepti; Collins, Maxwell; Kondor, Risi; Singh, Vikas

    2012-01-01

    Matching one set of objects to another is a ubiquitous task in machine learning and computer vision that often reduces to some form of the quadratic assignment problem (QAP). The QAP is known to be notoriously hard, both in theory and in practice. Here, we investigate if this difficulty can be mitigated when some additional piece of information is available: (a) that all QAP instances of interest come from the same application, and (b) the correct solution for a set of such QAP instances is given. We propose a new approach to accelerate the solution of QAPs based on learning parameters for a modified objective function from prior QAP instances. A key feature of our approach is that it takes advantage of the algebraic structure of permutations, in conjunction with special methods for optimizing functions over the symmetric group 𝕊n in Fourier space. Experiments show that in practical domains the new method can outperform existing approaches. PMID:25309968

  2. Scaffolded biology.

    PubMed

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  3. Data Integration and Mining for Synthetic Biology Design.

    PubMed

    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.

  4. Biological Effects of Ionizing Radiation

    DOE R&D Accomplishments Database

    Ingram, M.; Mason, W. B.; Whipple, G. H.; Howland, J. W.

    1952-04-07

    This report presents a review of present knowledge and concepts of the biological effects of ionizing radiations. Among the topics discussed are the physical and chemical effects of ionizing radiation on biological systems, morphological and physiological changes observed in biological systems subjected to ionizing radiations, physiological changes in the intact animal, latent changes following exposure of biological systems to ionizing radiations, factors influencing the biological response to ionizing radiation, relative effects of various ionizing radiations, and biological dosimetry.

  5. Molecular Biology of Nitrogen Fixation

    ERIC Educational Resources Information Center

    Shanmugam, K. T.; Valentine, Raymond C.

    1975-01-01

    Reports that as a result of our increasing knowledge of the molecular biology of nitrogen fixation it might eventually be possible to increase the biological production of nitrogenous fertilizer from atmospheric nitrogen. (GS)

  6. Visual Knowledge.

    ERIC Educational Resources Information Center

    Chipman, Susan F.

    Visual knowledge is an enormously important part of our total knowledge. The psychological study of learning and knowledge has focused almost exclusively on verbal materials. Today, the advance of technology is making the use of visual communication increasingly feasible and popular. However, this enthusiasm involves the illusion that visual…

  7. Preserving Knowledge

    ERIC Educational Resources Information Center

    Taintor, Spence

    2008-01-01

    Every year, teachers leave the profession and take valuable experience and knowledge with them. An increasing retirement rate makes schools vulnerable to a significant loss of knowledge. This article describes how implementing a knowledge management process will ensure that valuable assets are captured and shared. (Contains 3 online resources.)

  8. Plant proteomics update (2007-2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge.

    PubMed

    Jorrín-Novo, Jesús V; Maldonado, Ana M; Echevarría-Zomeño, Sira; Valledor, Luis; Castillejo, Mari A; Curto, Miguel; Valero, José; Sghaier, Besma; Donoso, Gabriel; Redondo, Inmaculada

    2009-04-13

    This review is the continuation of three previously published articles [Jorrin JV, Maldonado AM, Castillejo MA. Plant proteome analysis: a 2006 update. Proteomics 2007; 7: 2947-2962; Rossignol M, Peltier JB, Mock HP, Matros A, Maldonado AM, Jorrin JV. Plant proteome analysis: a 2004-2006 update. Proteomics 2006; 6: 5529-5548; Canovas FM, Dumas-Gaudot E, Recorbet G, Jorrin J, Mock HP, Rossignol M. Plant proteome analysis. Proteomics 2004; 4: 285-298] and aims to update the contribution of Proteomics to plant research between 2007 and September 2008 by reviewing most of the papers, which number approximately 250, that appeared in the Plant Proteomics field during that period. Most of the papers published deal with the proteome of Arabidopsis thaliana and rice (Oryza sativa), and focus on profiling organs, tissues, cells or subcellular proteomes, and studying developmental processes and responses to biotic and abiotic stresses using a differential expression strategy. Although the platform based on 2-DE is still the most commonly used, the use of gel-free and second-generation Quantitative Proteomic techniques has increased. Proteomic data are beginning to be validated using complementary -omics or classical biochemical or cellular biology techniques. In addition, appropriate experimental design and statistical analysis are being carried out in accordance with the required Minimal Information about a Proteomic Experiment (MIAPE) standards. As a result, the coverage of the plant cell proteome and the plant biology knowledge is increasing. Compared to human and yeast systems, however, plant biology research has yet to exploit fully the potential of proteomics, in particular its applications to PTMs and Interactomics.

  9. Dealing with the Biological Challenge

    NASA Astrophysics Data System (ADS)

    Schultz, Emeric

    1996-05-01

    The bio-technological revolution presents a real challenge to the chemical education community. This challenge is two-fold: 1) the necessity of teaching students the underlying chemical principles and other skills necessary for sucess in the expanding biotechnological workplace and 2) ensuring and enhancing respect from the biological community for the first two years of the chemistry curriculum. In the opinion of the author, we are not doing a particularly good job of meeting this challenge, although progress is being made. As the "doing" of chemistry becomes easier for biologists, there is the real danger that the knowledge of a significant portion of the underlying chemistry will increasingly be viewed as less valuable, and perhaps even superfluous. The three "Trojan Horses" are: synthetic, analytical, and "process" kits; instrumentation coupled with computer "interpretation"; and molecular modeling. The author believes that in order to address the biological challenge head on, we should give serious consideration to the following: 1) reversing the "learning arrow"; 2) embedding molecular and other modeling; 3) incorporating instrumental analysis and chemistry-by-kit. Reversing the learning arrow approaches the chemistry curriculum by starting with large biomolecules first and working toward smaller fundamental units. The author believes that this approach and a more proactive stance on establishing what is in the domain of chemistry is the means by which the biological challenge, spawned by the bio-technological revolution, can most forcefully be addressed.

  10. A Challenge to Biology

    ERIC Educational Resources Information Center

    Trumbull, Richard

    1975-01-01

    Cautions biology instructors to be aware of the possible overproduction of life science scholars whose future may include unemployment or underemployment. Urges that these instructors provide their students with knowledge for employment outside the traditional educational and research fields. (MLH)

  11. Knowledge Management

    NASA Technical Reports Server (NTRS)

    Shariq, Syed Z.; Kutler, Paul (Technical Monitor)

    1997-01-01

    The emergence of rapidly expanding technologies for distribution and dissemination of information and knowledge has brought to focus the opportunities for development of knowledge-based networks, knowledge dissemination and knowledge management technologies and their potential applications for enhancing productivity of knowledge work. The challenging and complex problems of the future can be best addressed by developing the knowledge management as a new discipline based on an integrative synthesis of hard and soft sciences. A knowledge management professional society can provide a framework for catalyzing the development of proposed synthesis as well as serve as a focal point for coordination of professional activities in the strategic areas of education, research and technology development. Preliminary concepts for the development of the knowledge management discipline and the professional society are explored. Within this context of knowledge management discipline and the professional society, potential opportunities for application of information technologies for more effectively delivering or transferring information and knowledge (i.e., resulting from the NASA's Mission to Planet Earth) for the development of policy options in critical areas of national and global importance (i.e., policy decisions in economic and environmental areas) can be explored, particularly for those policy areas where a global collaborative knowledge network is likely to be critical to the acceptance of the policies.

  12. New approaches in data integration for systems chemical biology.

    PubMed

    Seoane, Jose A; López-Campos, Guillermo; Dorado, Julian; Martin-Sanchez, Fernando

    2013-01-01

    Advances done in "-Omics" technologies in the last 20 years have made available to the researches huge amounts of data spanning a wide variety of biological processes from gene sequences to the metabolites present in a cell at a particular time. The management, analysis and representation of these data have been facilitated by mean of the advances made by biomedical informatics in areas such as data architecture and integration systems. However, despite the efforts done by biologists in this area, research in drug design adds a new level of information by incorporating data related with small molecules, which increases the complexity of these integration systems. Current knowledge in molecular biology has shown that it is possible to use comprehensive and integrative approaches to understand the biological processes from a systems perspective and that pathological processes can be mapped into biological networks. Therefore, current strategies for drug design are focusing on how to interact with or modify those networks to achieve the desired effects on what is called systems chemical biology. In this review several approaches for data integration in systems chemical biology will be analysed and described. Furthermore, because of the increasing relevance of the development and use of nanomaterials and their expected impact in the near future, the requirements of integration systems that incorporate these new data types associated with nanomaterials will also be analysed.

  13. DISTRIBUTED AMPLIFIER INCORPORATING FEEDBACK

    DOEpatents

    Bell, P.R. Jr.

    1958-10-21

    An improved distributed amplifier system employing feedback for stabilization is presented. In accordance with the disclosed invention, a signal to be amplified is applled to one end of a suitable terminated grid transmission line. At intervals along the transmission line, the signal is fed to stable, resistance-capacitance coupled amplifiers incorporating feedback loops therein. The output current from each amplifier is passed through an additional tube to minimize the electrostatic capacitance between the tube elements of the last stage of the amplifier, and fed to appropriate points on an output transmission line, similar to the grid line, but terminated at the opposite (input) end. The output taken from the unterminated end of the plate transmission line is proportional to the input voltage impressed upon the grid line.

  14. Knowledge-driven genomic interactions: an application in ovarian cancer

    PubMed Central

    2014-01-01

    Background Effective cancer clinical outcome prediction for understanding of the mechanism of various types of cancer has been pursued using molecular-based data such as gene expression profiles, an approach that has promise for providing better diagnostics and supporting further therapies. However, clinical outcome prediction based on gene expression profiles varies between independent data sets. Further, single-gene expression outcome prediction is limited for cancer evaluation since genes do not act in isolation, but rather interact with other genes in complex signaling or regulatory networks. In addition, since pathways are more likely to co-operate together, it would be desirable to incorporate expert knowledge to combine pathways in a useful and informative manner. Methods Thus, we propose a novel approach for identifying knowledge-driven genomic interactions and applying it to discover models associated with cancer clinical phenotypes using grammatical evolution neural networks (GENN). In order to demonstrate the utility of the proposed approach, an ovarian cancer data from the Cancer Genome Atlas (TCGA) was used for predicting clinical stage as a pilot project. Results We identified knowledge-driven genomic interactions associated with cancer stage from single knowledge bases such as sources of pathway-pathway interaction, but also knowledge-driven genomic interactions across different sets of knowledge bases such as pathway-protein family interactions by integrating different types of information. Notably, an integration model from different sources of biological knowledge achieved 78.82% balanced accuracy and outperformed the top models with gene expression or single knowledge-based data types alone. Furthermore, the results from the models are more interpretable because they are framed in the context of specific biological pathways or other expert knowledge. Conclusions The success of the pilot study we have presented herein will allow us to pursue

  15. Extracting biological knowledge from DNA sequences

    SciTech Connect

    De La Vega, F.M.; Thieffry, D. |; Collado-Vides, J.

    1996-12-31

    This session describes the elucidation of information from dna sequences and what challenges computational biologists face in their task of summarizing and deciphering the human genome. Techniques discussed include methods from statistics, information theory, artificial intelligence and linguistics. 1 ref.

  16. Biologically Plausible, Human-scale Knowledge Representation

    ERIC Educational Resources Information Center

    Crawford, Eric; Gingerich, Matthew; Eliasmith, Chris

    2016-01-01

    Several approaches to implementing symbol-like representations in neurally plausible models have been proposed. These approaches include binding through synchrony (Shastri & Ajjanagadde, 1993), "mesh" binding (van der Velde & de Kamps, 2006), and conjunctive binding (Smolensky, 1990). Recent theoretical work has suggested that…

  17. Teachers' incorporation of nanoscale science and engineering lessons into the classroom and factors that influence this incorporation

    NASA Astrophysics Data System (ADS)

    Hutchinson, Kelly M.

    Previous research has shown that teachers face a number of challenges when incorporating innovative science content into their curricula. These challenges include: lack of science equipment; lack of support from a professional development team; lack of time to plan and teach the lessons; weak teacher content knowledge; and problems created by teachers' beliefs about teaching and learning including, their beliefs about reform efforts (Peers, Diezmann, & Watters, 2003; Roehrig, Kruse, & Kern, 2007). One innovative and interdisciplinary science field currently under investigation is nanoscale science and engineering (NSE) due to its emerging prominence in society, the need to help students gain entry into the job market, and the need to educate informed citizens. As teachers and science educators begin to incorporate nanoscale science and engineering concepts into existing science curricula, many factors will influence the incorporation of the NSE concepts. This study was specifically designed to examine how middle- and high-school teachers incorporated NSE lessons into their current curricula and the factors that influenced how these lessons were incorporated. Interviews were the primary data source for this study, with teachers' reflective narratives and classroom observations contributing to the data. The constant comparative method (Glaser & Strauss, 1967; Patton, 2002) was used in analyzing the data to determine the themes that emerged. The results of this study demonstrated that although teachers indicated many factors that influenced their decision to incorporate NSE into the curriculum. Teachers' content knowledge, teachers' beliefs about student abilities, and teachers' beliefs about the fit of NSE lessons to the current science curriculum were the most influential factors in determining the way teachers' incorporated NSE lessons. If teachers did not have the content knowledge nor were confident in their content knowledge, NSE incorporation did not occur

  18. Nepal CRS project incorporates.

    PubMed

    1983-01-01

    The Nepal Contraceptive Retail Sales (CRS) Project, 5 years after lauching product sales in June 1978, incorporated as a private, nonprofit company under Nepalese management. The transition was finalized in August 1983. The Company will work through a cooperative agreement with USAID/Kathmandu to complement the national family planning goals as the program continues to provide comtraceptives through retail channels at subsidized prices. Company objectives include: increase contraceptive sales by at least 15% per year; make CRS cost effective and move towards self sufficiency; and explore the possibility of marketing noncontraceptive health products to improve primary health care. After only5 years the program can point to some impressive successes. The number of retial shops selling family planning products increased from 100 in 1978 to over 8000, extending CRS product availability to 66 of the country's 75 districts. Retail sales have climbed dramatically in the 5-year period, from Rs 46,817 in 1978 to Rs 271,039 in 1982. Sales in terms of couple year protection CYP) have grown to 24,451 CYP(1982), a 36% increase over 1980 CYP. Since the beginning of the CRS marketing program, total distribution of contraceptives--through both CRS and the Family Planning Maternal and Child Haelth (FP/MCH) Project--has been increasing. While the FP/MCH program remains the largest distributor,contribution of CRS Products is increasing, indicating that CRS is creating new product acceptors. CRS market share in 1982 was 43% for condoms and 16% for oral contraceptives (OCs). CRS markets 5 products which are subsidized in order to be affordable to consumers as well as attractive to sellers. The initial products launched in June 1978 were Gulaf standard dose OCs and Dhaal lubricated colored condoms. A less expensive lubricates, plain Suki-Dhaal condom was introduced in June 1980 in an attempt to reach poorer rural populations, but rural distribution costs are excessive and Suki

  19. Automatic acquisition of domain and procedural knowledge

    NASA Technical Reports Server (NTRS)

    Ferber, H. J.; Ali, M.

    1988-01-01

    The design concept and performance of AKAS, an automated knowledge-acquisition system for the development of expert systems, are discussed. AKAS was developed using the FLES knowledge base for the electrical system of the B-737 aircraft and employs a 'learn by being told' strategy. The system comprises four basic modules, a system administration module, a natural-language concept-comprehension module, a knowledge-classification/extraction module, and a knowledge-incorporation module; details of the module architectures are explored.

  20. Teachers' Journal Club: Bridging between the Dynamics of Biological Discoveries and Biology Teachers

    ERIC Educational Resources Information Center

    Brill, Gilat; Falk, Hedda; Yarden, Anat

    2003-01-01

    Since biology is one of the most dynamic research fields within the natural sciences, the gap between the accumulated knowledge in biology and the knowledge that is taught in schools, increases rapidly with time. Our long-term objective is to develop means to bridge between the dynamics of biological discoveries and the biology teachers and…

  1. Synthesis and Biological Evaluation of Aminonaphthols Incorporated Indole Derivatives

    PubMed Central

    Anand Raghunath, Saundane; Nandibeoor Mathada, Kirankumar

    2014-01-01

    An efficient one pot condensation of naphthols (1), 2,5-disubstituted indole-3-carboxaldehydes (2), and secondary amines (3) has been achieved using dichloromethane as a solvent, stirring at room temperature. Some of the new [(disubstituted amino)(5-substituted 2-phenyl-1H-indol-3-yl)methyl]naphthalene-ols (4) derivatives were prepared in good yields. The significant features of this method are simple work-up procedure, inexpensive nontoxic solvent, shorter reaction times, and excellent product yields. The structures of newly synthesized compounds (4a–r) are confirmed by their elemental analysis, FTIR, 1H and 13C NMR, and mass spectral data. These compounds were screened for their in vitro antioxidant, antimicrobial, antitubercular, and anticancer activities. Among the synthesized compounds (4a–r), the compound 4e exhibited highest activity for radical scavenging and ferric ions reducing antioxidant power activities; compounds 4b, 4h, and 4k showed good metal chelating activity. Compounds 4n and 4q showed excellent antimicrobial activities with MIC value 08 µg/mL against tested strains. Compounds 4h, 4k, 4n, and 4q exhibited promising antitubercular activity with MIC value 12.5 µg/mL. Compounds 4k and 4q exhibited 100% cell lysis at concentration 10 µg/mL against MDA-MB-231 (human adenocarcinoma mammary gland) cell lines. PMID:25383220

  2. Biological isolation garment

    NASA Technical Reports Server (NTRS)

    Spross, F. R.

    1968-01-01

    Biological Isolation Garment /BIG/ is a one-piece loose fitting garment fabricated from a tightly woven, permeable, 100 percent-cotton fabric. Its headpiece, incorporates an integral oronsal respirator with 0.3-micron-particle filters, and a full width visor. All fabrication seams are sealed on the inside of the garment.

  3. Building Preservation Knowledge in Brazil.

    ERIC Educational Resources Information Center

    Beck, Ingrid

    The project to translate into Portuguese and disseminate preservation knowledge was part of a broader partnership between the Council on Library and Information Resources, which incorporates the former Commission on Preservation and Access, and a consortium of Brazilian archival, library, and museum institutions. The partnership was intended to…

  4. Evaluating the effectiveness of integrating food science lessons in high school Biology curriculum in comparison to high school Chemistry curriculum

    NASA Astrophysics Data System (ADS)

    Ivey, Lauren Elizabeth

    Historically, high school chemistry has been the predominate venue for introducing food science curriculum to students. The purpose of this research was to determine if high school students in a biology class without a chemistry background could comprehend eight basic food science principles equally as well as students in a chemistry class that were taught the same principles. This study assessed baseline knowledge of high school students, determined the effect of food science-based lessons on baseline knowledge and level of understanding, and determined the effect of food science-based lessons on students' awareness of and interest in food science. Baseline knowledge and awareness of food science was low. Food science-based instruction resulted in higher post-test scores. Results indicated no differences between biology and chemistry and supported the idea of further incorporating a food science curriculum into high school biology.

  5. Introducing Knowledge into Differential Expression Analysis

    PubMed Central

    Biecek, Przemysław; Tiuryn, Jerzy; Vingron, Martin

    2010-01-01

    Abstract Gene expression measurements allow determining sets of up- or down-regulated, or unchanged genes in a particular experimental condition. Additional biological knowledge can suggest examples of genes from one of these sets. For instance, known target genes of a transcriptional activator are expected, but are not certain to go down after this activator is knocked out. Available differential expression analysis tools do not take such imprecise examples into account. Here we put forward a novel partially supervised mixture modeling methodology for differential expression analysis. Our approach, guided by imprecise examples, clusters expression data into differentially expressed and unchanged genes. The partially supervised methodology is implemented by two methods: a newly introduced belief-based mixture modeling, and soft-label mixture modeling, a method proved efficient in other applications. We investigate on synthetic data the input example settings favorable for each method. In our tests, both belief-based and soft-label methods prove their advantage over semi-supervised mixture modeling in correcting for erroneous examples. We also compare them to alternative differential expression analysis approaches, showing that incorporation of knowledge yields better performance. We present a broad range of knowledge sources and data to which our partially supervised methodology can be applied. First, we determine targets of Ste12 based on yeast knockout data, guided by a Ste12 DNA-binding experiment. Second, we distinguish miR-1 from miR-124 targets in human by clustering expression data under transfection experiments of both microRNAs, using their computationally predicted targets as examples. Finally, we utilize literature knowledge to improve clustering of time-course expression profiles. PMID:20726790

  6. Synthetic Biology - The Synthesis of Biology.

    PubMed

    Ausländer, Simon; Ausländer, David; Fussenegger, Martin

    2016-12-11

    Synthetic biology envisages the engineering of man-made living biomachines from standardized components that can perform pre-defined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic or signalling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials and fine chemicals and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis and transfer of complete genomes into host cells and the application of efficient genome-wide intervention techniques point to the future of synthetic biology: the creation of living designer cells with tailored desirable properties for biomedicine and biotechnology.

  7. Procedural knowledge

    NASA Technical Reports Server (NTRS)

    Georgeff, Michael P.; Lansky, Amy L.

    1986-01-01

    Much of commonsense knowledge about the real world is in the form of procedures or sequences of actions for achieving particular goals. In this paper, a formalism is presented for representing such knowledge using the notion of process. A declarative semantics for the representation is given, which allows a user to state facts about the effects of doing things in the problem domain of interest. An operational semantics is also provided, which shows how this knowledge can be used to achieve particular goals or to form intentions regarding their achievement. Given both semantics, the formalism additionally serves as an executable specification language suitable for constructing complex systems. A system based on this formalism is described, and examples involving control of an autonomous robot and fault diagnosis for NASA's Space Shuttle are provided.

  8. Ranked retrieval of Computational Biology models

    PubMed Central

    2010-01-01

    Background The study of biological systems demands computational support. If targeting a biological problem, the reuse of existing computational models can save time and effort. Deciding for potentially suitable models, however, becomes more challenging with the increasing number of computational models available, and even more when considering the models' growing complexity. Firstly, among a set of potential model candidates it is difficult to decide for the model that best suits ones needs. Secondly, it is hard to grasp the nature of an unknown model listed in a search result set, and to judge how well it fits for the particular problem one has in mind. Results Here we present an improved search approach for computational models of biological processes. It is based on existing retrieval and ranking methods from Information Retrieval. The approach incorporates annotations suggested by MIRIAM, and additional meta-information. It is now part of the search engine of BioModels Database, a standard repository for computational models. Conclusions The introduced concept and implementation are, to our knowledge, the first application of Information Retrieval techniques on model search in Computational Systems Biology. Using the example of BioModels Database, it was shown that the approach is feasible and extends the current possibilities to search for relevant models. The advantages of our system over existing solutions are that we incorporate a rich set of meta-information, and that we provide the user with a relevance ranking of the models found for a query. Better search capabilities in model databases are expected to have a positive effect on the reuse of existing models. PMID:20701772

  9. Working Knowledge.

    ERIC Educational Resources Information Center

    Beckett, David

    The resurgence of "lifelong learning" has renewed consideration of the nature of "working knowledge." Lifelong learning has many aspects, including construction and distribution of individuals' very self-hood, educational institutions' role in capturing informal experiences, and the juggling required between family and…

  10. Data warehousing in molecular biology.

    PubMed

    Schönbach, C; Kowalski-Saunders, P; Brusic, V

    2000-05-01

    In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data represent a major challenge in data warehousing for molecular biology. By combining experiences in other domains with our findings from building a model database, we have defined the requirements for data warehousing in molecular biology.

  11. Field Computation and Nonpropositional Knowledge.

    DTIC Science & Technology

    1987-09-01

    embodied practical knowledge. Biologial evidence shows that animals use this knowledge in a way very different from digital computation. This suggests...Biological evi- dence shows that animals use this kno ledge in a way very ifferent from digital corn I tation. This sug- gests that if these problems are to...Indeed, most of these recalcitrant tasks are performed skillfully by animals endowed with much simpler nervous systems than our own. How is this possible

  12. Overview of Plant Incorporated Protectants

    EPA Pesticide Factsheets

    When assessing the potential risks of genetically engineered plant-incorporated protectants, EPA requires extensive studies examining numerous factors. Learn more about the history and process for regulating PIPs.

  13. A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification

    SciTech Connect

    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.

  14. A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification

    DOE PAGES

    Wang, Jing; Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; ...

    2013-01-01

    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).more » 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.« less

  15. Incorporating Learning Outcomes into an Introductory Geotechnical Engineering Course

    ERIC Educational Resources Information Center

    Fiegel, Gregg L.

    2013-01-01

    The article describes the process of incorporating a set of learning outcomes into a geotechnical engineering course. The outcomes were developed using Bloom's taxonomy and define the knowledge, skills, and abilities the students are expected to achieve upon completion of the course. Each outcome begins with an action-oriented verb corresponding…

  16. Influence of Content Knowledge on Pedagogical Content Knowledge: The Case of Teaching Photosynthesis and Plant Growth

    ERIC Educational Resources Information Center

    Kapyla, Markku; Heikkinen, Jussi-Pekka; Asunta, Tuula

    2009-01-01

    The aim of the research was to investigate the effect of the amount and quality of content knowledge on pedagogical content knowledge (PCK). The biological content photosynthesis and plant growth was used as an example. The research sample consisted of 10 primary and 10 secondary (biology) teacher students. Questionnaires, lesson preparation task…

  17. All biology is computational biology

    PubMed Central

    2017-01-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science. PMID:28278152

  18. All biology is computational biology.

    PubMed

    Markowetz, Florian

    2017-03-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science.

  19. Biological Resource Centers and Systems Biology.

    PubMed

    Wang, Yufeng; Lilburn, Timothy G

    2009-02-11

    There are hundreds of Biological Resource Centers (BRCs) around the world, holding many little-studied microorganism. The proportion of bacterial strains that is well represented in the sequence and literature databases may be as low as 1%. This body of unexplored diversity represents an untapped source of useful strains and derived products. However, a modicum of phenotypic data is available for almost all the bacterial strains held by BRCs around the world. It is at the phenotypic level that our knowledge of the well-studied strains of bacteria and the many yet-to-be studied strains intersects. This suggests we might leverage the phenotypic data from the data-poor bacteria with the omics data from the data-rich bacteria, using our knowledge of their evolutionary relationships, to map the metabolic networks of the little-known bacteria. This systems biology-based approach is a new way to explore the diversity harbored in BRCs.

  20. Host thin films incorporating nanoparticles

    NASA Astrophysics Data System (ADS)

    Qureshi, Uzma

    The focus of this research project was the investigation of the functional properties of thin films that incorporate a secondary nanoparticulate phase. In particular to assess if the secondary nanoparticulate material enhanced a functional property of the coating on glass. In order to achieve this, new thin film deposition methods were developed, namely use of nanopowder precursors, an aerosol assisted transport technique and an aerosol into atmospheric pressure chemical vapour deposition system. Aerosol assisted chemical vapour deposition (AACVD) was used to deposit 8 series of thin films on glass. Five different nanoparticles silver, gold, ceria, tungsten oxide and zinc oxide were tested and shown to successfully deposit thin films incorporating nanoparticles within a host matrix. Silver nanoparticles were synthesised and doped within a titania film by AACVD. This improved solar control properties. A unique aerosol assisted chemical vapour deposition (AACVD) into atmospheric pressure chemical vapour deposition (APCVD) system was used to deposit films of Au nanoparticles and thin films of gold nanoparticles incorporated within a host titania matrix. Incorporation of high refractive index contrast metal oxide particles within a host film altered the film colour. The key goal was to test the potential of nanopowder forms and transfer the suspended nanopowder via an aerosol to a substrate in order to deposit a thin film. Discrete tungsten oxide nanoparticles or ceria nanoparticles within a titanium dioxide thin film enhanced the self-cleaning and photo-induced super-hydrophilicity. The nanopowder precursor study was extended by deposition of zinc oxide thin films incorporating Au nanoparticles and also ZnO films deposited from a ZnO nanopowder precursor. Incorporation of Au nanoparticles within a VO: host matrix improved the thermochromic response, optical and colour properties. Composite VC/TiC and Au nanoparticle/V02/Ti02 thin films displayed three useful

  1. Incorporating global components into ethics education.

    PubMed

    Wang, George; Thompson, Russell G

    2013-03-01

    Ethics is central to science and engineering. Young engineers need to be grounded in how corporate social responsibility principles can be applied to engineering organizations to better serve the broader community. This is crucial in times of climate change and ecological challenges where the vulnerable can be impacted by engineering activities. Taking a global perspective in ethics education will help ensure that scientists and engineers can make a more substantial contribution to development throughout the world. This paper presents the importance of incorporating the global and cross culture components in the ethic education. The authors bring up a question to educators on ethics education in science and engineering in the globalized world, and its importance, necessity, and impendency. The paper presents several methods for discussion that can be used to identify the differences in ethics standards and practices in different countries; enhance the student's knowledge of ethics in a global arena.

  2. Selenium incorporation using recombinant techniques

    SciTech Connect

    Walden, Helen

    2010-04-01

    An overview of techniques for recombinant incorporation of selenium and subsequent purification and crystallization of the resulting labelled protein. Using selenomethionine to phase macromolecular structures is common practice in structure determination, along with the use of selenocysteine. Selenium is consequently the most commonly used heavy atom for MAD. In addition to the well established recombinant techniques for the incorporation of selenium in prokaryal expression systems, there have been recent advances in selenium labelling in eukaryal expression, which will be discussed. Tips and things to consider for the purification and crystallization of seleno-labelled proteins are also included.

  3. 17 CFR 260.7a-30 - Identification of material incorporated; form of incorporation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... incorporated; form of incorporation. 260.7a-30 Section 260.7a-30 Commodity and Securities Exchanges SECURITIES... Incorporation by Reference § 260.7a-30 Identification of material incorporated; form of incorporation. In each case of incorporation by reference, the matter incorporated shall be clearly identified in...

  4. Constructing Knowledge

    NASA Astrophysics Data System (ADS)

    Blanton, Patricia

    2003-02-01

    Schools are expected to lay the foundation upon which knowledge can be built and equip students with the tools necessary to accomplish the construction. The role of the teacher in this building process is crucial to the type of structure the student can build. Whether you call it constructivism, discussion teaching, project-based learning, inquiry learning, or any of the other names given to the instructional strategies being suggested by education researchers, the key is getting students to become active participants in the process. While some students may be able to learn from eloquently delivered lectures and dynamic demonstrations, the majority of students cannot effectively retain and apply ideas communicated in this manner.

  5. Biological Technicians

    MedlinePlus

    ... Biological technicians typically need a bachelor’s degree in biology or a closely related field. It is important ... Biological technicians typically need a bachelor’s degree in biology or a closely related field. It is important ...

  6. Incorporating Argumentation through Forensic Science

    ERIC Educational Resources Information Center

    Wheeler, Lindsay B.; Maeng, Jennifer L.; Smetana, Lara K.

    2014-01-01

    This article outlines how to incorporate argumentation into a forensic science unit using a mock trial. Practical details of the mock trial include: (1) a method of scaffolding students' development of their argument for the trial, (2) a clearly outlined set of expectations for students during the planning and implementation of the mock…

  7. Subclonal variant calling with multiple samples and prior knowledge

    PubMed Central

    Gerstung, Moritz; Papaemmanuil, Elli; Campbell, Peter J.

    2014-01-01

    Motivation: Targeted resequencing of cancer genes in large cohorts of patients is important to understand the biological and clinical consequences of mutations. Cancers are often clonally heterogeneous, and the detection of subclonal mutations is important from a diagnostic point of view, but presents strong statistical challenges. Results: Here we present a novel statistical approach for calling mutations from large cohorts of deeply resequenced cancer genes. These data allow for precisely estimating local error profiles and enable detecting mutations with high sensitivity and specificity. Our probabilistic method incorporates knowledge about the distribution of variants in terms of a prior probability. We show that our algorithm has a high accuracy of calling cancer mutations and demonstrate that the detected clonal and subclonal variants have important prognostic consequences. Availability: Code is available as part of the Bioconductor package deepSNV. Contact: mg14@sanger.ac.uk; pc8@sanger.ac.uk PMID:24443148

  8. [Infectious complications of biological therapy].

    PubMed

    Holub, M; Rozsypal, H; Chalupa, P

    2011-02-01

    Biological treatment represents a significant progress in the therapy of many serious diseases. Together with the growing knowledge of pathophysiology and subsequent development of new therapeutic agents, this progress will definitely lead to further expansion of biologics. Since biologics interfere with many mechanisms of host defence, which may sometimes be compromised by them, increased risk of infectious complications must be taken into account. Patients treated with biologics are prone to classical virulent infections (e.g. listeriosis, legionellosis and tuberculosis) and opportunistic infections such as progressive multifocal leukoencephalopathy. Furthermore, suppression of the immune response that is caused by biologics may lead to reactivation of latent infections such as tuberculosis or viral hepatitis B. Therefore, the knowledge of basic mechanisms by which biologics modify the immune response is important for a rapid clinical diagnosis of possible aetiology of infectious complications.

  9. Space Biology: Patterns of Life

    ERIC Educational Resources Information Center

    Salisbury, Frank B.

    1971-01-01

    Present knowledge about Mars is compared with past beliefs about the planet. Biological experiments that indicate life may exist on Mars are interpreted. Life patterns or biological features that might be postulated for extraterrestrial life are presented at the molecular, cellular, organism, and ecosystem levels. (DS)

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

    NASA Astrophysics Data System (ADS)

    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.

  11. On the optimal design of molecular sensing interfaces with lipid bilayer assemblies - A knowledge based approach

    NASA Astrophysics Data System (ADS)

    Siontorou, Christina G.

    2012-12-01

    Biosensors are analytic devices that incorporate a biochemical recognition system (biological, biologicalderived or biomimic: enzyme, antibody, DNA, receptor, etc.) in close contact with a physicochemical transducer (electrochemical, optical, piezoelectric, conductimetric, etc.) that converts the biochemical information, produced by the specific biological recognition reaction (analyte-biomolecule binding), into a chemical or physical output signal, related to the concentration of the analyte in the measuring sample. The biosensing concept is based on natural chemoreception mechanisms, which are feasible over/within/by means of a biological membrane, i.e., a structured lipid bilayer, incorporating or attached to proteinaceous moieties that regulate molecular recognition events which trigger ion flux changes (facilitated or passive) through the bilayer. The creation of functional structures that are similar to natural signal transduction systems, correlating and interrelating compatibly and successfully the physicochemical transducer with the lipid film that is self-assembled on its surface while embedding the reconstituted biological recognition system, and at the same time manage to satisfy the basic conditions for measuring device development (simplicity, easy handling, ease of fabrication) is far from trivial. The aim of the present work is to present a methodological framework for designing such molecular sensing interfaces, functioning within a knowledge-based system built on an ontological platform for supplying sub-systems options, compatibilities, and optimization parameters.

  12. Western Hemisphere Knowledge Partnerships

    NASA Astrophysics Data System (ADS)

    Malone, T. F.

    2001-05-01

    Society in general, and geophysicists in particular, are challenged by problems and opportunities in the prospects for an additional three billion people on finite planet Earth by 2050 in a global economy four to six times larger than it is at present. A problem was identified by the Pilot Assessment of Global Ecosystems (PAGE): "If we choose to continue our current patterns of use, we face almost certain decline in the ability of ecosystems to yield their broad spectrum of benefits - from clean water to stable climate, fuel wood to food crops, timber to wildlife habitat." This is the issue of environmental sustainability. Another problem is the widening gap in wealth and health between affluent nations and impoverished countries. Every day each of the more than a billion people in the industrial nations produces goods and services worth nearly 60 dollars to meet their basic needs and "wants." This figure increases by about 85 cents annually. Every day each of the 600 million people in the least developed countries produces goods and services worth about 75 cents to meet their basic needs and limited wants. That number grows by less that a penny a day annually. This is the issue of economic prosperity and equity. By harnessing revolutionary technologies in communications to distribute expanding knowledge in the physical, chemical, and geophysical sciences and exploding knowledge in the biological and health sciences, a new vision for world society is brought within reach in The Knowledge Age. It is a society in which all of the basic human needs and an equitable share of human wants can be met while maintaining healthy, attractive, and biologically productive ecosystems. This society is environmentally sustainable, economically prosperous and equitable, and therefore likely to be politically stable. The time has arrived to fashion a strategy to pursue that vision. A knowledge-based and human-centered strategy will involve the discovery, integration, dissemination

  13. Synthetic Biology: A Unifying View and Review Using Analog Circuits.

    PubMed

    Teo, Jonathan J Y; Woo, Sung Sik; Sarpeshkar, Rahul

    2015-08-01

    We review the field of synthetic biology from an analog circuits and analog computation perspective, focusing on circuits that have been built in living cells. This perspective is well suited to pictorially, symbolically, and quantitatively representing the nonlinear, dynamic, and stochastic (noisy) ordinary and partial differential equations that rigorously describe the molecular circuits of synthetic biology. This perspective enables us to construct a canonical analog circuit schematic that helps unify and review the operation of many fundamental circuits that have been built in synthetic biology at the DNA, RNA, protein, and small-molecule levels over nearly two decades. We review 17 circuits in the literature as particular examples of feedforward and feedback analog circuits that arise from special topological cases of the canonical analog circuit schematic. Digital circuit operation of these circuits represents a special case of saturated analog circuit behavior and is automatically incorporated as well. Many issues that have prevented synthetic biology from scaling are naturally represented in analog circuit schematics. Furthermore, the deep similarity between the Boltzmann thermodynamic equations that describe noisy electronic current flow in subthreshold transistors and noisy molecular flux in biochemical reactions has helped map analog circuit motifs in electronics to analog circuit motifs in cells and vice versa via a `cytomorphic' approach. Thus, a body of knowledge in analog electronic circuit design, analysis, simulation, and implementation may also be useful in the robust and efficient design of molecular circuits in synthetic biology, helping it to scale to more complex circuits in the future.

  14. Teachers' instructional goals for science practice: Identifying knowledge gaps using cultural-historical activity theory (CHAT)

    NASA Astrophysics Data System (ADS)

    Farrar, Cynthia Hamen

    In AP Biology, the course goal, with respect to scientific acts and reasoning, has recently shifted toward a reform goal of science practice, where the goal is for students to have a scientific perspective that views science as a practice of a community rather than a body of knowledge. Given this recent shift, this study is interested in the gaps that may exist between an individual teacher's instructional goal and the goals of the AP Biology course. A Cultural-Historical Activity Theory (CHAT) methodology and perspective is used to analyze four teachers' knowledge, practice, and learning. Teachers have content knowledge for teaching, a form of knowledge that is unique for teaching called specialized content knowledge. This specialized content knowledge (SCK) defines their instructional goals, the student outcomes they ultimately aim to achieve with their students. The study employs a cultural-historical continuum of scientific acts and reasoning, which represents the development of the AP Biology goal over time, to study gaps in their instructional goal. The study also analyzes the contradictions within their teaching practice and how teachers address those contradictions to shift their instructional practice and learn. The findings suggest that teachers have different interpretations of the AP Biology goals of science practice, placing their instructional goal at different points along the continuum. Based on the location of their instructional goal, different micro-communities of teachers exist along the continuum, comprised of teachers with a shared goal, language, and culture of their AP Biology teaching. The in-depth study of one teacher's AP Biology teaching, using a CHAT perspective, provides a means for studying the mechanisms that connect SCK to classroom actions and ultimately to instructional practice. CHAT also reveals the nature and importance of contradictions or cognitive dissonance in teacher learning and the types of support teachers need to

  15. Incorporating Student Activities into Climate Change Education

    NASA Astrophysics Data System (ADS)

    Steele, H.; Kelly, K.; Klein, D.; Cadavid, A. C.

    2013-12-01

    Under a NASA grant, Mathematical and Geospatial Pathways to Climate Change Education, students at California State University, Northridge integrated Geographic Information Systems (GIS), remote sensing, satellite data technologies, and climate modelling into the study of global climate change under a Pathway for studying the Mathematics of Climate Change (PMCC). The PMCC, which is an interdisciplinary option within the BS in Applied Mathematical Sciences, consists of courses offered by the departments of Mathematics, Physics, and Geography and is designed to prepare students for careers and Ph.D. programs in technical fields relevant to global climate change. Under this option students are exposed to the science, mathematics, and applications of climate change science through a variety of methods including hands-on experience with computer modeling and image processing software. In the Geography component of the program, ESRI's ArcGIS and ERDAS Imagine mapping, spatial analysis and image processing software were used to explore NASA satellite data to examine the earth's atmosphere, hydrosphere and biosphere in areas that are affected by climate change or affect climate. These technology tools were incorporated into climate change and remote sensing courses to enhance students' knowledge and understanding of climate change through hands-on application of image processing techniques to NASA data. Several sets of exercises were developed with specific learning objectives in mind. These were (1) to increase student understanding of climate change and climate change processes; (2) to develop student skills in understanding, downloading and processing satellite data; (3) to teach remote sensing technology and GIS through applications to climate change; (4) to expose students to climate data and methods they can apply to solve real world problems and incorporate in future research projects. In the Math and Physics components of the course, students learned about

  16. Commonality analysis as a knowledge acquisition problem

    NASA Technical Reports Server (NTRS)

    Yeager, Dorian P.

    1987-01-01

    Commonality analysis is a systematic attempt to reduce costs in a large scale engineering project by discontinuing development of certain components during the design phase. Each discontinued component is replaced by another component that has sufficient functionality to be considered an appropriate substitute. The replacement strategy is driven by economic considerations. The System Commonality Analysis Tool (SCAT) is based on an oversimplified model of the problem and incorporates no knowledge acquisition component. In fact, the process of arriving at a compromise between functionality and economy is quite complex, with many opportunities for the application of expert knowledge. Such knowledge is of two types: general knowledge expressible as heuristics or mathematical laws potentially applicable to any set of components, and specific knowledge about the way in which elements of a given set of components interrelate. Examples of both types of knowledge are presented, and a framework is proposed for integrating the knowledge into a more general and useable tool.

  17. Background Knowledge in Learning-Based Relation Extraction

    ERIC Educational Resources Information Center

    Do, Quang Xuan

    2012-01-01

    In this thesis, we study the importance of background knowledge in relation extraction systems. We not only demonstrate the benefits of leveraging background knowledge to improve the systems' performance but also propose a principled framework that allows one to effectively incorporate knowledge into statistical machine learning models for…

  18. Central Component Descriptors for Levels of Technological Pedagogical Content Knowledge

    ERIC Educational Resources Information Center

    Niess, Margaret L.

    2013-01-01

    Technological pedagogical content knowledge (TPACK) proposes a theoretical framework that incorporates four central components: an overarching conception of what it means to teach with technology, knowledge of students' thinking and understandings of specific topics with technologies, knowledge of curricular materials that incorporate…

  19. Selenium incorporation using recombinant techniques.

    PubMed

    Walden, Helen

    2010-04-01

    Using selenomethionine to phase macromolecular structures is common practice in structure determination, along with the use of selenocysteine. Selenium is consequently the most commonly used heavy atom for MAD. In addition to the well established recombinant techniques for the incorporation of selenium in prokaryal expression systems, there have been recent advances in selenium labelling in eukaryal expression, which will be discussed. Tips and things to consider for the purification and crystallization of seleno-labelled proteins are also included.

  20. 75 FR 51148 - Notice of Solicitation of Public Comment on Consideration of Incorporating IFRS Into the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-18

    ... representation and communication of investors' perspectives in connection with accounting standard setting? To what extent do investors believe more education or communication about accounting standards or... incorporation on: U.S. investors' current knowledge of IFRS and preparedness for incorporation of IFRS into...

  1. Epigenetics: Biology's Quantum Mechanics.

    PubMed

    Jorgensen, Richard A

    2011-01-01

    The perspective presented here is that modern genetics is at a similar stage of development as were early formulations of quantum mechanics theory in the 1920s and that in 2010 we are at the dawn of a new revolution in genetics that promises to enrich and deepen our understanding of the gene and the genome. The interrelationships and interdependence of two views of the gene - the molecular biological view and the epigenetic view - are explored, and it is argued that the classical molecular biological view is incomplete without incorporation of the epigenetic perspective and that in a sense the molecular biological view has been evolving to include the epigenetic view. Intriguingly, this evolution of the molecular view toward the broader and more inclusive epigenetic view of the gene has an intriguing, if not precise, parallel in the evolution of concepts of atomic physics from Newtonian mechanics to quantum mechanics that are interesting to consider.

  2. How experienced practitioners gain knowledge.

    PubMed

    Vaughan, Barbara

    2014-01-01

    An evolution in nursing in the United Kingdom in the 1970s from rule-bound toward holistic, autonomous practice engendered an examination of nursing's body of knowledge and how it is incorporated into practice. This article describes Barbara Carper's (1978) Fundamental Patterns of Knowing in Nursing (empiric, ethical, aesthetic, and personal knowledge), and links it to three major worldviews of the way in which knowledge is sought (positivism, naturalism, and critical social theory). Carper's model was used in the United Kingdom as the basis for a curriculum of structured reflective practice using workshops, journaling, and clinical supervision. An example from a practitioner's diary demonstrates how Carper's model informs reflection on an interaction with a patient with newly diagnosed cancer.

  3. Teacher Education and the New Biology

    ERIC Educational Resources Information Center

    Reiss, Michael J.

    2006-01-01

    Recent years have seen a growth not only in biological knowledge but also, and more significantly for teacher education, in the types of knowledge manifested in biology. No longer, therefore, is it adequate for teachers to retain a Mertonian or a Popperian conception of science. Today's teachers of science need also to be able to help their…

  4. Biology. Teacher's Guide. Investigations in Natural Science.

    ERIC Educational Resources Information Center

    Renner, John W.; And Others

    Investigations in Natural Science is a program in secondary school biology, chemistry, and physics based upon the description of science as a quest for knowledge, not the knowledge itself. This teaching guide is designed for use with the 18 biology investigations found in the student manual. These investigations focus on concepts related to:…

  5. On the Edge of Mathematics and Biology Integration: Improving Quantitative Skills in Undergraduate Biology Education

    ERIC Educational Resources Information Center

    Feser, Jason; Vasaly, Helen; Herrera, Jose

    2013-01-01

    In this paper, the authors describe how two institutions are helping their undergraduate biology students build quantitative competencies. Incorporation of quantitative skills and reasoning in biology are framed through a discussion of two cases that both concern introductory biology courses, but differ in the complexity of the mathematics and the…

  6. Molecular biology in physiology

    SciTech Connect

    Chien, S.; Gargus, J.J.

    1987-08-01

    The aim of this symposium on molecular biology in physiology was to introduce molecular biology to physiologists who had relatively little exposure to the new developments in this field, so that they can become conversant on this topic and contribute to the advancement of physiology by incorporating molecular biological approaches as a part of their research arsenal. This report is a review of the symposium, which consisted of two four-part sessions. Each session had four papers. After the discussion of the basic concepts, terminology, and methodology used in molecular biology, it was shown how these basic principles have been applied to the study of the genes encoding two membrane proteins that have important transport functions (band 3 and ATPase). The second half of the symposium consisted of papers on the state-of-the-art developments in the application of molecular biology to the studies of the atrial natriuretic factor and renin genes, adenylate cyclase-coupled adrenergic receptors, acetylcholine receptors and sodium channel, and long-term and short-term memories. The ultimate goal is that these examples will provide an impetus for the opening of new frontiers of research in physiology by taking advantage of the tools developed from recent advances in molecular biology.

  7. Biological Filters.

    ERIC Educational Resources Information Center

    Klemetson, S. L.

    1978-01-01

    Presents the 1978 literature review of wastewater treatment. The review is concerned with biological filters, and it covers: (1) trickling filters; (2) rotating biological contractors; and (3) miscellaneous reactors. A list of 14 references is also presented. (HM)

  8. Biology Today: Parasites and Human Ecology.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    1984-01-01

    Offers various reasons why the study of parasites and the diseases they cause should be incorporated into classroom biology discussions. Examples of several parasitic diseases and their ecological significance are provided. (JN)

  9. Methods for virus classification and the challenge of incorporating metagenomic sequence data.

    PubMed

    Simmonds, Peter

    2015-06-01

    The division of viruses into orders, families, genera and species provides a classification framework that seeks to organize and make sense of the diversity of viruses infecting animals, plants and bacteria. Classifications are based on similarities in genome structure and organization, the presence of homologous genes and sequence motifs and at lower levels such as species, host range, nucleotide and antigenic relatedness and epidemiology. Classification below the level of family must also be consistent with phylogeny and virus evolutionary histories. Recently developed methods such as PASC, DEMaRC and NVR offer alternative strategies for genus and species assignments that are based purely on degrees of divergence between genome sequences. They offer the possibility of automating classification of the vast number of novel virus sequences being generated by next-generation metagenomic sequencing. However, distance-based methods struggle to deal with the complex evolutionary history of virus genomes that are shuffled by recombination and reassortment, and where taxonomic lineages evolve at different rates. In biological terms, classifications based on sequence distances alone are also arbitrary whereas the current system of virus taxonomy is of utility precisely because it is primarily based upon phenotypic characteristics. However, a separate system is clearly needed by which virus variants that lack biological information might be incorporated into the ICTV classification even if based solely on sequence relationships to existing taxa. For these, simplified taxonomic proposals and naming conventions represent a practical way to expand the existing virus classification and catalogue our rapidly increasing knowledge of virus diversity.

  10. Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency.

    PubMed

    Wang, Hua; Huang, Heng; Ding, Chris

    2015-06-01

    Conventional computational approaches for protein function prediction usually predict one function at a time, fundamentally. As a result, the protein functions are treated as separate target classes. However, biological processes are highly correlated in reality, which makes multiple functions assigned to a protein not independent. Therefore, it would be beneficial to make use of function category correlations when predicting protein functions. In this article, we propose a novel Maximization of Data-Knowledge Consistency (MDKC) approach to exploit function category correlations for protein function prediction. Our approach banks on the assumption that two proteins are likely to have large overlap in their annotated functions if they are highly similar according to certain experimental data. We first establish a new pairwise protein similarity using protein annotations from knowledge perspective. Then by maximizing the consistency between the established knowledge similarity upon annotations and the data similarity upon biological experiments, putative functions are assigned to unannotated proteins. Most importantly, function category correlations are gracefully incorporated into our learning objective through the knowledge similarity. Comprehensive experimental evaluations on the Saccharomyces cerevisiae species have demonstrated promising results that validate the performance of our methods.

  11. The Effects of the SUN Project on Teacher Knowledge and Self-Efficacy regarding Biological Energy Transfer Are Significant and Long-Lasting: Results of a Randomized Controlled Trial

    ERIC Educational Resources Information Center

    Batiza, Ann Finney; Gruhl, Mary; Zhang, Bo; Harrington, Tom; Roberts, Marisa; LaFlamme, Donna; Haasch, Mary Anne; Knopp, Jonathan; Vogt, Gina; Goodsell, David; Hagedorn, Eric; Marcey, David; Hoelzer, Mark; Nelson, Dave

    2013-01-01

    Biological energy flow has been notoriously difficult to teach. Our approach to this topic relies on abiotic and biotic examples of the energy released by moving electrons in thermodynamically spontaneous reactions. A series of analogical model-building experiences was supported with common language and representations including manipulatives.…

  12. Development of the Neuron Assessment for Measuring Biology Students’ Use of Experimental Design Concepts and Representations

    PubMed Central

    Dasgupta, Annwesa P.; Anderson, Trevor R.; Pelaez, Nancy J.

    2016-01-01

    Researchers, instructors, and funding bodies in biology education are unanimous about the importance of developing students’ competence in experimental design. Despite this, only limited measures are available for assessing such competence development, especially in the areas of molecular and cellular biology. Also, existing assessments do not measure how well students use standard symbolism to visualize biological experiments. We propose an assessment-design process that 1) provides background knowledge and questions for developers of new “experimentation assessments,” 2) elicits practices of representing experiments with conventional symbol systems, 3) determines how well the assessment reveals expert knowledge, and 4) determines how well the instrument exposes student knowledge and difficulties. To illustrate this process, we developed the Neuron Assessment and coded responses from a scientist and four undergraduate students using the Rubric for Experimental Design and the Concept-Reasoning Mode of representation (CRM) model. Some students demonstrated sound knowledge of concepts and representations. Other students demonstrated difficulty with depicting treatment and control group data or variability in experimental outcomes. Our process, which incorporates an authentic research situation that discriminates levels of visualization and experimentation abilities, shows potential for informing assessment design in other disciplines. PMID:27146159

  13. Development of the Neuron Assessment for Measuring Biology Students' Use of Experimental Design Concepts and Representations.

    PubMed

    Dasgupta, Annwesa P; Anderson, Trevor R; Pelaez, Nancy J

    2016-01-01

    Researchers, instructors, and funding bodies in biology education are unanimous about the importance of developing students' competence in experimental design. Despite this, only limited measures are available for assessing such competence development, especially in the areas of molecular and cellular biology. Also, existing assessments do not measure how well students use standard symbolism to visualize biological experiments. We propose an assessment-design process that 1) provides background knowledge and questions for developers of new "experimentation assessments," 2) elicits practices of representing experiments with conventional symbol systems, 3) determines how well the assessment reveals expert knowledge, and 4) determines how well the instrument exposes student knowledge and difficulties. To illustrate this process, we developed the Neuron Assessment and coded responses from a scientist and four undergraduate students using the Rubric for Experimental Design and the Concept-Reasoning Mode of representation (CRM) model. Some students demonstrated sound knowledge of concepts and representations. Other students demonstrated difficulty with depicting treatment and control group data or variability in experimental outcomes. Our process, which incorporates an authentic research situation that discriminates levels of visualization and experimentation abilities, shows potential for informing assessment design in other disciplines.

  14. How to improve the incorporation of massive allografts?

    PubMed

    Delloye, C

    2003-01-01

    The incorporation of a bone graft is the result of creeping and substitutional activities that remove the original grafted bone and replace it by newly formed bone from the host cells. However, this intricate process is very limited in time and space. A bone allograft is poorly remodeled and is almost non viable even after several years of implantation. This lack of vitality accounts for the high rate of complications such as non union and fracture. One way to minimize the allograft complications is to improve its incorporation. The process of incorporation in animals and human beings is reviewed as well as the various avenues for a biologic improvement either through modulation on the host: the immune response, the inhibition of bone resorption, the use of bone morphogenetic proteins, the autogenous cell augmentation or through processing the bone allograft: bisphosphonate adsorption or bone perforations. In 2002, biologic enhancement of the incorporation is still in its infancy but will be in a near future a reality through influence on both the host and the allograft.

  15. Engineering microbes with synthetic biology frameworks.

    PubMed

    Leonard, Effendi; Nielsen, David; Solomon, Kevin; Prather, Kristala Jones

    2008-12-01

    Typically, the outcome of biologically engineered unit operations cannot be controlled a priori due to the incorporation of ad hoc design into complex natural systems. To mitigate this problem, synthetic biology presents a systematic approach to standardizing biological components for the purpose of increasing their programmability and robustness when assembled with the aim to achieve novel biological functions. A complex engineered biological system using only standardized biological components is yet to exist. Nevertheless, current attempts to create and to implement modular, standardized biological components pave the way for the future creation of highly predictable artificial biological systems. Although synthetic biology frameworks can be applied to any biological engineering endeavor, this article will focus on providing a brief overview of advances in the field and its recent utilization for the engineering of microbes.

  16. Incorporating Spirituality in Primary Care.

    PubMed

    Isaac, Kathleen S; Hay, Jennifer L; Lubetkin, Erica I

    2016-06-01

    Addressing cultural competency in health care involves recognizing the diverse characteristics of the patient population and understanding how they impact patient care. Spirituality is an aspect of cultural identity that has become increasingly recognized for its potential to impact health behaviors and healthcare decision-making. We consider the complex relationship between spirituality and health, exploring the role of spirituality in primary care, and consider the inclusion of spirituality in existing models of health promotion. We discuss the feasibility of incorporating spirituality into clinical practice, offering suggestions for physicians.

  17. Incorporation of additives into polymers

    DOEpatents

    McCleskey, T. Mark; Yates, Matthew Z.

    2003-07-29

    There has been invented a method for incorporating additives into polymers comprising: (a) forming an aqueous or alcohol-based colloidal system of the polymer; (b) emulsifying the colloidal system with a compressed fluid; and (c) contacting the colloidal polymer with the additive in the presence of the compressed fluid. The colloidal polymer can be contacted with the additive by having the additive in the compressed fluid used for emulsification or by adding the additive to the colloidal system before or after emulsification with the compressed fluid. The invention process can be carried out either as a batch process or as a continuous on-line process.

  18. The Physics of Marine Biology.

    ERIC Educational Resources Information Center

    Conn, Kathleen

    1992-01-01

    Discusses ways in which marine biology can be integrated into the physics classroom. Topics suggested for incorporation include the harmonic motion of ocean waves, ocean currents, the interaction of visible light with ocean water, pressure, light absorption, and sound transfer in water. (MDH)

  19. Biology Majors' Performance in a Biomathematics Course

    ERIC Educational Resources Information Center

    Mahir, Nevin; Çetin, Nezahat; Üreyen, Mehmet

    2007-01-01

    The recent considerable developments in the field of biology have necessitated the knowledge of mathematics and its applications in biology. Therefore; most of the universities, now, believe that it is essential to include mathematics courses in the curricula of biology departments. Taking this fact into consideration, this study aims at exploring…

  20. When Knowledge Knows No Bounds: Self-Perceived Expertise Predicts Claims of Impossible Knowledge.

    PubMed

    Atir, Stav; Rosenzweig, Emily; Dunning, David

    2015-08-01

    People overestimate their knowledge, at times claiming knowledge of concepts, events, and people that do not exist and cannot be known, a phenomenon called overclaiming. What underlies assertions of such impossible knowledge? We found that people overclaim to the extent that they perceive their personal expertise favorably. Studies 1a and 1b showed that self-perceived financial knowledge positively predicts claiming knowledge of nonexistent financial concepts, independent of actual knowledge. Study 2 demonstrated that self-perceived knowledge within specific domains (e.g., biology) is associated specifically with overclaiming within those domains. In Study 3, warning participants that some of the concepts they saw were fictitious did not reduce the relationship between self-perceived knowledge and overclaiming, which suggests that this relationship is not driven by impression management. In Study 4, boosting self-perceived expertise in geography prompted assertions of familiarity with nonexistent places, which supports a causal role for self-perceived expertise in claiming impossible knowledge.

  1. [Biological markers of alcoholism].

    PubMed

    Marcos Martín, M; Pastor Encinas, I; Laso Guzmán, F J

    2005-09-01

    Diagnosis of alcoholism is very important, given its high prevalence and possibility of influencing the disease course. For this reason, the so-called biological markers of alcoholism are useful. These are analytic parameters that alter in the presence of excessive alcohol consumption. The two most relevant markers are the gamma-glutamyltranspeptidase and carbohydrate deficient transferrin. With this clinical comment, we aim to contribute to the knowledge of these tests and promote its use in the clinical practice.

  2. Alcohol Pharmacology Education Partnership: Using Chemistry and Biology Concepts To Educate High School Students about Alcohol

    PubMed Central

    2015-01-01

    We developed the Alcohol Pharmacology Education Partnership (APEP), a set of modules designed to integrate a topic of interest (alcohol) with concepts in chemistry and biology for high school students. Chemistry and biology teachers (n = 156) were recruited nationally to field-test APEP in a controlled study. Teachers obtained professional development either at a conference-based workshop (NSTA or NCSTA) or via distance learning to learn how to incorporate the APEP modules into their teaching. They field-tested the modules in their classes during the following year. Teacher knowledge of chemistry and biology concepts increased significantly following professional development, and was maintained for at least a year. Their students (n = 14 014) demonstrated significantly higher scores when assessed for knowledge of both basic and advanced chemistry and biology concepts compared to students not using APEP modules in their classes the previous year. Higher scores were achieved as the number of modules used increased. These findings are consistent with our previous studies, demonstrating higher scores in chemistry and biology after students use modules that integrate topics interesting to them, such as drugs (the Pharmacology Education Partnership). PMID:24803686

  3. Alcohol Pharmacology Education Partnership: Using Chemistry and Biology Concepts To Educate High School Students about Alcohol.

    PubMed

    Godin, Elizabeth A; Kwiek, Nicole; Sikes, Suzanne S; Halpin, Myra J; Weinbaum, Carolyn A; Burgette, Lane F; Reiter, Jerome P; Schwartz-Bloom, Rochelle D

    2014-02-11

    We developed the Alcohol Pharmacology Education Partnership (APEP), a set of modules designed to integrate a topic of interest (alcohol) with concepts in chemistry and biology for high school students. Chemistry and biology teachers (n = 156) were recruited nationally to field-test APEP in a controlled study. Teachers obtained professional development either at a conference-based workshop (NSTA or NCSTA) or via distance learning to learn how to incorporate the APEP modules into their teaching. They field-tested the modules in their classes during the following year. Teacher knowledge of chemistry and biology concepts increased significantly following professional development, and was maintained for at least a year. Their students (n = 14 014) demonstrated significantly higher scores when assessed for knowledge of both basic and advanced chemistry and biology concepts compared to students not using APEP modules in their classes the previous year. Higher scores were achieved as the number of modules used increased. These findings are consistent with our previous studies, demonstrating higher scores in chemistry and biology after students use modules that integrate topics interesting to them, such as drugs (the Pharmacology Education Partnership).

  4. Enhancing Scientific Literacy in the Undergraduate Cell Biology Laboratory Classroom†

    PubMed Central

    Woodham, Hadiya; Marbach-Ad, Gili; Downey, Gretchen; Tomei, Erika; Thompson, Katerina

    2016-01-01

    This paper describes the implementation of the Scientific Literacy in Cell Biology (SLCB) curriculum in an undergraduate biology laboratory course. The SLCB curriculum incorporated the reading and discussion of primary literature into hands-on and collaborative practical experiences. It was implemented in five stages over an 11-week period, during which students were also introduced to the theory and practice of common cell biology techniques. We report on the effectiveness of the course, as measured by pre- and post-course survey data probing students’ content knowledge and their level of familiarity, confidence, and experience with different skills pertaining to analyzing (reading, interpreting, and discussing) primary literature. In the spring 2015 semester, 287 (72%) of the 396 students who were enrolled in the laboratory completed both the pre- and post-course survey. The average score on the content questions of the post-course survey was significantly higher (p < 0.0001) than the average score on the pre-course survey. Students reported that they gained greater familiarity, experience, and confidence in the skills that were measured. Our findings may aid in reforming higher-education science laboratory courses to better promote writing, reading, data processing, and presentation skills. Journal of Microbiology & Biology Education PMID:28101274

  5. Biological satellite scientific devices

    NASA Astrophysics Data System (ADS)

    Perepech, B. L.; Rumiantsev, V. P.; Galkin, V. M.; Shakhvorostov, S. V.; Rvachev, S. S.

    1991-02-01

    The paper describes the NA SBS 9 systems developed for the ninth Cosmos-2044 biological test mission. The NA SBS 9 life support systems designed for monkeys and rats follow standard design of BIOS-Vivarium and BIOS-Primate units. The main features of NA SBS 9 include the use of a recently developed HF physiological data recorder Skat-3; the incorporation into BIOS-Primate of two units intended for biorhythmic studies (the BBI-Zh system for studying beetles and the VITALOG developed by NASA for studies on monkeys); and a new version of BIOS-Primate system incorporating a capacitance-link and an inductance-link temperature transmitters and a brain tissue oxygen tension control channel.

  6. The Use of Clinical Interviews to Develop Inservice Secondary Science Teachers' Nature of Science Knowledge and Assessment of Student Nature of Science Knowledge

    ERIC Educational Resources Information Center

    Peters-Burton, Erin E.

    2013-01-01

    To fully incorporate nature of science knowledge into classrooms, teachers must be both proficient in their own nature of science knowledge, but also skillful in translating their knowledge into a learning environment which assesses student knowledge. Twenty-eight inservice teachers enrolled in a graduate course which in part required a clinical…

  7. Incorporation of heparin into biomaterials.

    PubMed

    Sakiyama-Elbert, Shelly E

    2014-04-01

    This review provides an overview of the incorporation of heparin into biomaterials with a focus on drug delivery and the use of heparin-based biomaterials for self-assembly of polymer networks. Heparin conjugation to biomaterials was originally explored to reduce the thrombogenicity of materials in contact with blood. Many of the conjugation strategies that were developed for these applications are still popular today for other applications. More recently heparin has been conjugated to biomaterials for drug delivery applications. Many of the delivery approaches have taken advantage of the ability of heparin to bind to a wide variety of growth factors, protecting them from degradation and potentiating interactions with cell surface receptors. More recently, the use of heparin as a base polymer for scaffold fabrication has also been explored, often utilizing non-covalent binding of heparin with peptides or proteins to promote self-assembly of hydrogel networks. This review will highlight recent advances in each of these areas.

  8. Knowledge management: organizing nursing care knowledge.

    PubMed

    Anderson, Jane A; Willson, Pamela

    2009-01-01

    Almost everything we do in nursing is based on our knowledge. In 1984, Benner (From Novice to Expert: Excellence and Power in Clinical Nursing Practice. Menlo Park, CA: Addison-Wesley; 1984) described nursing knowledge as the culmination of practical experience and evidence from research, which over time becomes the "know-how" of clinical experience. This "know-how" knowledge asset is dynamic and initially develops in the novice critical care nurse, expands within competent and proficient nurses, and is actualized in the expert intensive care nurse. Collectively, practical "know-how" and investigational (evidence-based) knowledge culminate into the "knowledge of caring" that defines the profession of nursing. The purpose of this article is to examine the concept of knowledge management as a framework for identifying, organizing, analyzing, and translating nursing knowledge into daily practice. Knowledge management is described in a model case and implemented in a nursing research project.

  9. Biological Applications in the Mathematics Curriculum

    ERIC Educational Resources Information Center

    Marland, Eric; Palmer, Katrina M.; Salinas, Rene A.

    2008-01-01

    In this article we provide two detailed examples of how we incorporate biological examples into two mathematics courses: Linear Algebra and Ordinary Differential Equations. We use Leslie matrix models to demonstrate the biological properties of eigenvalues and eigenvectors. For Ordinary Differential Equations, we show how using a logistic growth…

  10. Collaborative Instructional Strategies to Enhance Knowledge Convergence

    ERIC Educational Resources Information Center

    Draper, Darryl C.

    2015-01-01

    To promote knowledge convergence through collaborative learning activities in groups, this qualitative case study involved a layered approach for the design and delivery of a highly collaborative learning environment incorporating various instructional technologies grounded in learning theory. In a graduate-level instructional technology course,…

  11. Academic Knowledge Construction and Multimodal Curriculum Development

    ERIC Educational Resources Information Center

    Loveless, Douglas J., Ed.; Griffith, Bryant, Ed.; Bérci, Margaret E., Ed.; Ortlieb, Evan, Ed.; Sullivan, Pamela, Ed.

    2014-01-01

    While incorporating digital technologies into the classroom has offered new ways of teaching and learning into educational processes, it is essential to take a look at how the digital shift impacts teachers, school administration, and curriculum development. "Academic Knowledge Construction and Multimodal Curriculum Development" presents…

  12. Knowledge-intensive software design systems: Can too much knowledge be a burden?

    NASA Technical Reports Server (NTRS)

    Keller, Richard M.

    1992-01-01

    While acknowledging the considerable benefits of domain-specific, knowledge-intensive approaches to automated software engineering, it is prudent to carefully examine the costs of such approaches, as well. In adding domain knowledge to a system, a developer makes a commitment to understanding, representing, maintaining, and communicating that knowledge. This substantial overhead is not generally associated with domain-independent approaches. In this paper, I examine the downside of incorporating additional knowledge, and illustrate with examples based on our experience in building the SIGMA system. I also offer some guidelines for developers building domain-specific systems.

  13. Knowledge-intensive software design systems: Can too much knowledge be a burden?

    NASA Technical Reports Server (NTRS)

    Keller, Richard M.

    1992-01-01

    While acknowledging the considerable benefits of domain-specific, knowledge-intensive approaches to automated software engineering, it is prudent to carefully examine the costs of such approaches, as well. In adding domain knowledge to a system, a developer makes a commitment to understanding, representing, maintaining, and communicating that knowledge. This substantial overhead is not generally associated with domain-independent approaches. In this paper, I examine the downside of incorporating additional knowledge, and illustrate with examples based on our experiences building the SIGMA system. I also offer some guidelines for developers building domain-specific systems.

  14. Designing pedagogy incorporating executive function.

    PubMed

    Wasserman, Theodore

    2013-01-01

    The National Academy of Neuropsychology defines clinical neuropsychology as "a sub-field of psychology concerned with the applied science of brain-behavior relationships. Clinical neuropsychologists use this knowledge in the assessment, diagnosis, treatment, and/or rehabilitation of patients across the lifespan with neurological, medical, neurodevelopmental and psychiatric conditions, as well as other cognitive and learning disorders" (National Academy of Neuropsychology, 2011 ). Pediatric neuropsychologists have long been concerned about another area of functionality, making their recommendations educationally relevant. This article describes accommodated metacognitive instruction, a pedagogy based on cognitive neuropsychological principles of learning and used to instruct college faculty on a methodology for teaching in all-inclusive environments.

  15. Is synthetic biology mechanical biology?

    PubMed

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  16. The Knowledge Warehouse: Reusing Knowledge Components.

    ERIC Educational Resources Information Center

    Yacci, Michael

    1999-01-01

    Currently there is little knowledge reuse across training, documentation, and performance support. Knowledge-based materials developed for one purpose are not shared or reused in others. The Knowledge Warehouse, a conceptual solution to this problem is discussed. Benefits and limitations are outlined and a definition of a standardized…

  17. Knowledge Management, Codification and Tacit Knowledge

    ERIC Educational Resources Information Center

    Kimble, Chris

    2013-01-01

    Introduction: This article returns to a theme addressed in Vol. 8(1) October 2002 of the journal: knowledge management and the problem of managing tacit knowledge. Method: The article is primarily a review and analysis of the literature associated with the management of knowledge. In particular, it focuses on the works of a group of economists who…

  18. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Describes laboratory procedures, demonstrations, and classroom activities/materials, including chi-square tests on a microcomputer, an integrated biology game, microscope slides of leaf stomata, culturing soil nematodes, technique for watering locust egg-laying tubes, hazards of biological chemicals (such as benzene, benzidene, calchicine,…

  19. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Describes laboratory procedures, demonstrations, and classroom activities/materials, including use of dwarf cichlids (fishes) in secondary school biology, teaching edge effects on stomatal diffusion, computer program on effects of selection on gene frequencies, biological oxidation/reduction reactions, short cuts with Drosophila, computer program…

  20. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents procedures, exercises, demonstrations, and information on a variety of biology topics including labeling systems, biological indicators of stream pollution, growth of lichens, reproductive capacity of bulbous buttercups, a straw balance to measure transpiration, interaction of fungi, osmosis, and nitrogen fixation and crop production. (DC)

  1. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1978

    1978-01-01

    Presents experiments, demonstrations, activities and ideas relating to various fields of biology to be used in biology courses in secondary schools. Among those experiments presented are demonstrating the early stages of ferns and mosses and simple culture methods for fern prothalli. (HM)

  2. A new organismal systems biology: how animals walk the tight rope between stability and change.

    PubMed

    Padilla, Dianna K; Tsukimura, Brian

    2014-07-01

    The amount of knowledge in the biological sciences is growing at an exponential rate. Simultaneously, the incorporation of new technologies in gathering scientific information has greatly accelerated our capacity to ask, and answer, new questions. How do we, as organismal biologists, meet these challenges, and develop research strategies that will allow us to address the grand challenge question: how do organisms walk the tightrope between stability and change? Organisms and organismal systems are complex, and multi-scale in both space and time. It is clear that addressing major questions about organismal biology will not come from "business as usual" approaches. Rather, we require the collaboration of a wide range of experts and integration of biological information with more quantitative approaches traditionally found in engineering and applied mathematics. Research programs designed to address grand challenge questions will require deep knowledge and expertise within subfields of organismal biology, collaboration and integration among otherwise disparate areas of research, and consideration of organisms as integrated systems. Our ability to predict which features of complex integrated systems provide the capacity to be robust in changing environments is poorly developed. A predictive organismal biology is needed, but will require more quantitative approaches than are typical in biology, including complex systems-modeling approaches common to engineering. This new organismal systems biology will have reciprocal benefits for biologists, engineers, and mathematicians who address similar questions, including those working on control theory and dynamical systems biology, and will develop the tools we need to address the grand challenge questions of the 21st century.

  3. Doctoring the Knowledge Worker

    ERIC Educational Resources Information Center

    Tennant, Mark

    2004-01-01

    In this paper I examine the impact of the new 'knowledge economy' on contemporary doctoral education. I argue that the knowledge economy promotes a view of knowledge and knowledge workers that fundamentally challenges the idea of a university as a community of autonomous scholars transmitting and adding to society's 'stock of knowledge'. The paper…

  4. Knowledge through a Collaborative Network: A Cross-Cultural Partnership

    ERIC Educational Resources Information Center

    Alcorn, Noeline

    2010-01-01

    A recurring issue for researchers, policy-makers and practitioners is how new knowledge can be disseminated, critiqued, assessed and incorporated into policy development and practice. Campbell and Fulford examined strategies in a Canadian Education Ministry which was striving to incorporate research findings into policy debate. They evolved a…

  5. 49 CFR 572.180 - Incorporated materials.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Incorporated materials. 572.180 Section 572.180... Test Dummy, 50th Percentile Adult Male § 572.180 Incorporated materials. (a) The following materials... approved the materials incorporated by reference in accordance with 5 U.S.C. 552(a) and 1 CFR part...

  6. 49 CFR 572.80 - Incorporated materials.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 7 2014-10-01 2014-10-01 false Incorporated materials. 572.80 Section 572.80... Incorporated materials. The drawings and specifications referred to in § 572.81(a) that are not set forth in full are hereby incorporated in this part by reference. These materials are thereby made part of...

  7. 49 CFR 572.30 - Incorporated materials.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Incorporated materials. 572.30 Section 572.30....30 Incorporated materials. (a) The drawings and specifications referred to in this regulation that... Federal Register has approved the materials incorporated by reference. For materials subject to...

  8. 49 CFR 572.30 - Incorporated materials.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Incorporated materials. 572.30 Section 572.30....30 Incorporated materials. (a) The drawings and specifications referred to in this regulation that... Federal Register has approved the materials incorporated by reference. For materials subject to...

  9. 49 CFR 572.30 - Incorporated materials.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Incorporated materials. 572.30 Section 572.30....30 Incorporated materials. (a) The drawings and specifications referred to in this regulation that... Federal Register has approved the materials incorporated by reference. For materials subject to...

  10. 49 CFR 572.30 - Incorporated materials.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Incorporated materials. 572.30 Section 572.30....30 Incorporated materials. (a) The drawings and specifications referred to in this regulation that... Federal Register has approved the materials incorporated by reference. For materials subject to...

  11. 49 CFR 572.190 - Incorporated materials.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Incorporated materials. 572.190 Section 572.190... Test Dummy, Small Adult Female § 572.190 Incorporated materials. (a) The following materials are hereby... Register approved the materials incorporated by reference in accordance with 5 U.S.C. 552(a) and 1 CFR...

  12. 49 CFR 572.80 - Incorporated materials.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Incorporated materials. 572.80 Section 572.80... Incorporated materials. The drawings and specifications referred to in § 572.81(a) that are not set forth in full are hereby incorporated in this part by reference. These materials are thereby made part of...

  13. 49 CFR 587.5 - Incorporated materials.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Incorporated materials. 587.5 Section 587.5... Barrier § 587.5 Incorporated materials. (a) The drawings and specifications referred to in this regulation that are not set forth in full are hereby incorporated in this part by reference. These materials...

  14. 49 CFR 572.80 - Incorporated materials.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Incorporated materials. 572.80 Section 572.80... Incorporated materials. The drawings and specifications referred to in § 572.81(a) that are not set forth in full are hereby incorporated in this part by reference. These materials are thereby made part of...

  15. 49 CFR 572.80 - Incorporated materials.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Incorporated materials. 572.80 Section 572.80... Incorporated materials. The drawings and specifications referred to in § 572.81(a) that are not set forth in full are hereby incorporated in this part by reference. These materials are thereby made part of...

  16. 49 CFR 587.5 - Incorporated materials.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Incorporated materials. 587.5 Section 587.5... Barrier § 587.5 Incorporated materials. (a) The drawings and specifications referred to in this regulation that are not set forth in full are hereby incorporated in this part by reference. These materials...

  17. 49 CFR 587.5 - Incorporated materials.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Incorporated materials. 587.5 Section 587.5... Barrier § 587.5 Incorporated materials. (a) The drawings and specifications referred to in this regulation that are not set forth in full are hereby incorporated in this part by reference. These materials...

  18. 49 CFR 572.180 - Incorporated materials.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Incorporated materials. 572.180 Section 572.180... Test Dummy, 50th Percentile Adult Male § 572.180 Incorporated materials. (a) The following materials... approved the materials incorporated by reference in accordance with 5 U.S.C. 552(a) and 1 CFR part...

  19. 49 CFR 572.80 - Incorporated materials.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Incorporated materials. 572.80 Section 572.80... Incorporated materials. The drawings and specifications referred to in § 572.81(a) that are not set forth in full are hereby incorporated in this part by reference. These materials are thereby made part of...

  20. Numeral Incorporation in Japanese Sign Language

    ERIC Educational Resources Information Center

    Ktejik, Mish

    2013-01-01

    This article explores the morphological process of numeral incorporation in Japanese Sign Language. Numeral incorporation is defined and the available research on numeral incorporation in signed language is discussed. The numeral signs in Japanese Sign Language are then introduced and followed by an explanation of the numeral morphemes which are…

  1. Developing the science of reintroduction biology.

    PubMed

    Seddon, Philip J; Armstrong, Doug P; Maloney, Richard F

    2007-04-01

    With recent increases in the numbers of species reintroduction projects and reintroduction-related publications, there is now a recognizable field of reintroduction biology. Nevertheless, research thus far has been fragmented and ad hoc, rather than an organized attempt to gain reliable knowledge to improve reintroduction success. We reviewed 454 recent (1990-2005) peer-reviewed papers dealing with wildlife reintroductions from 101 journals. Most research has been retrospective, either opportunistic evaluations of techniques or general project summaries, and most inference is gained from post hoc interpretation of monitoring results on a species-by-species basis. Documentation of reintroduction outcomes has improved, however, and the derivation of more general principles via meta-analyses is expected to increase. The fragmentation of the reintroduction literature remains an obstacle. There is scope to improve reintroduction biology by greater application of the hypothetico-deductive method, particularly through the use of modeling approaches and well-designed experiments. Examples of fruitful approaches in reintroduction research include experimental studies to improve outcomes from the release of captive-bred animals, use of simulation modeling to identify factors affecting the viability of reintroduced populations, and the application of spatially explicit models to plan for and evaluate reintroductions. We recommend that researchers contemplating future reintroductions carefully determine a priori the specific goals, overall ecological purpose, and inherent technical and biological limitations of a given reintroduction and that evaluation processes incorporate both experimental and modeling approaches. We suggest that the best progress will be made when multidisciplinary teams of resource managers and scientists work in close collaboration and when results from comparative analyses, experiments, and modeling are combined within and among studies.

  2. Information Extraction from Unstructured Text for the Biodefense Knowledge Center

    SciTech Connect

    Samatova, N F; Park, B; Krishnamurthy, R; Munavalli, R; Symons, C; Buttler, D J; Cottom, T; Critchlow, T J; Slezak, T

    2005-04-29

    The Bio-Encyclopedia at the Biodefense Knowledge Center (BKC) is being constructed to allow an early detection of emerging biological threats to homeland security. It requires highly structured information extracted from variety of data sources. However, the quantity of new and vital information available from every day sources cannot be assimilated by hand, and therefore reliable high-throughput information extraction techniques are much anticipated. In support of the BKC, Lawrence Livermore National Laboratory and Oak Ridge National Laboratory, together with the University of Utah, are developing an information extraction system built around the bioterrorism domain. This paper reports two important pieces of our effort integrated in the system: key phrase extraction and semantic tagging. Whereas two key phrase extraction technologies developed during the course of project help identify relevant texts, our state-of-the-art semantic tagging system can pinpoint phrases related to emerging biological threats. Also we are enhancing and tailoring the Bio-Encyclopedia by augmenting semantic dictionaries and extracting details of important events, such as suspected disease outbreaks. Some of these technologies have already been applied to large corpora of free text sources vital to the BKC mission, including ProMED-mail, PubMed abstracts, and the DHS's Information Analysis and Infrastructure Protection (IAIP) news clippings. In order to address the challenges involved in incorporating such large amounts of unstructured text, the overall system is focused on precise extraction of the most relevant information for inclusion in the BKC.

  3. Face Recognition Incorporating Ancillary Information

    NASA Astrophysics Data System (ADS)

    Kim, Sang-Ki; Toh, Kar-Ann; Lee, Sangyoun

    2007-12-01

    Due to vast variations of extrinsic and intrinsic imaging conditions, face recognition remained to be a challenging computer vision problem even today. This is particularly true when the passive imaging approach is considered for robust applications. To advance existing recognition systems for face, numerous techniques and methods have been proposed to overcome the almost inevitable performance degradation due to external factors such as pose, expression, occlusion, and illumination. In particular, the recent part-based method has provided noticeable room for verification performance improvement based on the localized features which have good tolerance to variation of external conditions. The part-based method, however, does not really stretch the performance without incorporation of global information from the holistic method. In view of the need to fuse the local information and the global information in an adaptive manner for reliable recognition, in this paper we investigate whether such external factors can be explicitly estimated and be used to boost the verification performance during fusion of the holistic and part-based methods. Our empirical evaluations show noticeable performance improvement adopting the proposed method.

  4. Incorporating transgenerational testing and epigenetic ...

    EPA Pesticide Factsheets

    A number of environmental chemicals have been shown to alter markers of epigenetic change. Some published multi-generation rodent studies have identified effects on F2 and greater generations after chemical exposures solely to F0 dams, but were not focused on chemical safety. We were interested in how outcomes related to epigenetic changes could be identified and incorporated into chemical testing and risk assessment. To address this question, we conducted a systematic literature review to identify transgenerational (TG) epigenetic studies in rodents. These were analyzed to characterize the methods and observed outcomes, and to evaluate strengths, limitations, and biases. Our analysis found that test substances were administered to pregnant F0 dams; endpoints assessed in F1 to F4 generation offspring included growth, puberty timing, steroid hormone levels, abdominal adiposity, organ weights, histopathology, and epigenetic biomarkers. Biases were minimized through, e.g., randomization procedures, avoiding sibling or cousin matings, and independent multiple reviews of histopathology data. However, the numbers of litters assigned to control and test groups were not always transparently reported, nested statistical analyses of data was not always utilized to address litter effects, and “blind” testing was seldom performed. Many of these studies identified chemicals or combinations of chemicals that produced TG effects and/or adult-onset diseases, but there is a

  5. Bridging the gap between systems biology and synthetic biology

    PubMed Central

    Liu, Di; Hoynes-O’Connor, Allison; Zhang, Fuzhong

    2013-01-01

    Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology. PMID:23898328

  6. Biological Oceanography

    NASA Astrophysics Data System (ADS)

    Dyhrman, Sonya

    2004-10-01

    The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

  7. Do Knowledge Arrangements Affect Student Reading Comprehension of Genetics?

    ERIC Educational Resources Information Center

    Wu, Jen-Yi; Tung, Yu-Neng; Hwang, Bi-Chi; Lin, Chen-Yung; Che-Di, Lee; Chang, Yung-Ta

    2014-01-01

    Various sequences for teaching genetics have been proposed. Three seventh-grade biology textbooks in Taiwan share similar key knowledge assemblages but have different knowledge arrangements. To investigate the influence of knowledge arrangements on student understanding of genetics, we compared students' reading comprehension of the three texts…

  8. Valuing Local Knowledge: Indigenous People and Intellectual Property Rights.

    ERIC Educational Resources Information Center

    Brush, Stephen B., Ed.; Stabinsky, Doreen, Ed.

    Intellectual property enables individuals to gain financially from sharing unique and useful knowledge. Compensating indigenous people for sharing their knowledge and resources might both validate and be an equitable reward for indigenous knowledge of biological resources, and might promote the conservation of those resources. This book contains…

  9. Isotopic incorporation rates and discrimination factors in mantis shrimp crustaceans.

    PubMed

    deVries, Maya S; Del Rio, Carlos Martínez; Tunstall, Tate S; Dawson, Todd E

    2015-01-01

    Stable isotope analysis has provided insights into the trophic ecology of a wide diversity of animals. Knowledge about isotopic incorporation rates and isotopic discrimination between the consumer and its diet for different tissue types is essential for interpreting stable isotope data, but these parameters remain understudied in many animal taxa and particularly in aquatic invertebrates. We performed a 292-day diet shift experiment on 92 individuals of the predatory mantis shrimp, Neogonodactylus bredini, to quantify carbon and nitrogen incorporation rates and isotope discrimination factors in muscle and hemolymph tissues. Average isotopic discrimination factors between mantis shrimp muscle and the new diet were 3.0 ± 0.6 ‰ and 0.9 ± 0.3 ‰ for carbon and nitrogen, respectively, which is contrary to what is seen in many other animals (e.g. C and N discrimination is generally 0-1 ‰ and 3-4 ‰, respectively). Surprisingly, the average residence time of nitrogen in hemolymph (28.9 ± 8.3 days) was over 8 times longer than that of carbon (3.4 ± 1.4 days). In muscle, the average residence times of carbon and nitrogen were of the same magnitude (89.3 ± 44.4 and 72.8 ± 18.8 days, respectively). We compared the mantis shrimps' incorporation rates, along with rates from four other invertebrate taxa from the literature, to those predicted by an allometric equation relating carbon incorporation rate to body mass that was developed for teleost fishes and sharks. The rate of carbon incorporation into muscle was consistent with rates predicted by this equation. Our findings provide new insight into isotopic discrimination factors and incorporation rates in invertebrates with the former showing a different trend than what is commonly observed in other animals.

  10. Isotopic Incorporation Rates and Discrimination Factors in Mantis Shrimp Crustaceans

    PubMed Central

    deVries, Maya S.; del Rio, Carlos Martínez; Tunstall, Tate S.; Dawson, Todd E.

    2015-01-01

    Stable isotope analysis has provided insights into the trophic ecology of a wide diversity of animals. Knowledge about isotopic incorporation rates and isotopic discrimination between the consumer and its diet for different tissue types is essential for interpreting stable isotope data, but these parameters remain understudied in many animal taxa and particularly in aquatic invertebrates. We performed a 292-day diet shift experiment on 92 individuals of the predatory mantis shrimp, Neogonodactylus bredini, to quantify carbon and nitrogen incorporation rates and isotope discrimination factors in muscle and hemolymph tissues. Average isotopic discrimination factors between mantis shrimp muscle and the new diet were 3.0 ± 0.6 ‰ and 0.9 ± 0.3 ‰ for carbon and nitrogen, respectively, which is contrary to what is seen in many other animals (e.g. C and N discrimination is generally 0–1 ‰ and 3–4 ‰, respectively). Surprisingly, the average residence time of nitrogen in hemolymph (28.9 ± 8.3 days) was over 8 times longer than that of carbon (3.4 ± 1.4 days). In muscle, the average residence times of carbon and nitrogen were of the same magnitude (89.3 ± 44.4 and 72.8 ± 18.8 days, respectively). We compared the mantis shrimps’ incorporation rates, along with rates from four other invertebrate taxa from the literature, to those predicted by an allometric equation relating carbon incorporation rate to body mass that was developed for teleost fishes and sharks. The rate of carbon incorporation into muscle was consistent with rates predicted by this equation. Our findings provide new insight into isotopic discrimination factors and incorporation rates in invertebrates with the former showing a different trend than what is commonly observed in other animals. PMID:25835953

  11. Biological warfare agents.

    PubMed

    Thavaselvam, Duraipandian; Vijayaraghavan, Rajagopalan

    2010-07-01

    The recent bioterrorist attacks using anthrax spores have emphasized the need to detect and decontaminate critical facilities in the shortest possible time. There has been a remarkable progress in the detection, protection and decontamination of biological warfare agents as many instrumentation platforms and detection methodologies are developed and commissioned. Even then the threat of biological warfare agents and their use in bioterrorist attacks still remain a leading cause of global concern. Furthermore in the past decade there have been threats due to the emerging new diseases and also the re-emergence of old diseases and development of antimicrobial resistance and spread to new geographical regions. The preparedness against these agents need complete knowledge about the disease, better research and training facilities, diagnostic facilities and improved public health system. This review on the biological warfare agents will provide information on the biological warfare agents, their mode of transmission and spread and also the detection systems available to detect them. In addition the current information on the availability of commercially available and developing technologies against biological warfare agents has also been discussed. The risk that arise due to the use of these agents in warfare or bioterrorism related scenario can be mitigated with the availability of improved detection technologies.

  12. BIOLOGICAL WARFARE

    PubMed Central

    Beeston, John

    1953-01-01

    The use of biological agents as controlled weapons of war is practical although uncertain. Three types of agents are feasible, including pathogenic organisms and biological pests, toxins, and synthetic hormones regulating plant growth. These agents may be chosen for selective effects varying from prolonged incipient illness to death of plants, man and domestic animals. For specific preventive and control measures required to combat these situations, there must be careful and detailed planning. The nucleus of such a program is available within the existing framework of public health activities. Additional research and expansion of established activities in time of attack are necessary parts of biological warfare defense. PMID:13059641

  13. Foldit Biology

    DTIC Science & Technology

    2015-07-31

    Report 8/1/2013-7/31/2015 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER Foldit Biology NOOO 14-13-C-0221 Sb. GRANT NUMBER N/A Sc. PROGRAM ELEMENT...Include area code) Unclassified Unclassified Unclassified (206) 616-2660 Zoran Popović Foldit Biology (Task 1, 2, 3, 4) Final Report...Period Covered by the Report August 1, 2013 – July 31, 2015 Date of Report: July 31, 2015 Project Title: Foldit Biology Contract Number: N00014-13

  14. Prior knowledge driven Granger causality analysis on gene regulatory network discovery

    SciTech Connect

    Yao, Shun; Yoo, Shinjae; Yu, Dantong

    2015-08-28

    Our study focuses on discovering gene regulatory networks from time series gene expression data using the Granger causality (GC) model. However, the number of available time points (T) usually is much smaller than the number of target genes (n) in biological datasets. The widely applied pairwise GC model (PGC) and other regularization strategies can lead to a significant number of false identifications when n>>T. In this study, we proposed a new method, viz., CGC-2SPR (CGC using two-step prior Ridge regularization) to resolve the problem by incorporating prior biological knowledge about a target gene data set. In our simulation experiments, the propose new methodology CGC-2SPR showed significant performance improvement in terms of accuracy over other widely used GC modeling (PGC, Ridge and Lasso) and MI-based (MRNET and ARACNE) methods. In addition, we applied CGC-2SPR to a real biological dataset, i.e., the yeast metabolic cycle, and discovered more true positive edges with CGC-2SPR than with the other existing methods. In our research, we noticed a “ 1+1>2” effect when we combined prior knowledge and gene expression data to discover regulatory networks. Based on causality networks, we made a functional prediction that the Abm1 gene (its functions previously were unknown) might be related to the yeast’s responses to different levels of glucose. In conclusion, our research improves causality modeling by combining heterogeneous knowledge, which is well aligned with the future direction in system biology. Furthermore, we proposed a method of Monte Carlo significance estimation (MCSE) to calculate the edge significances which provide statistical meanings to the discovered causality networks. All of our data and source codes will be available under the link https://bitbucket.org/dtyu/granger-causality/wiki/Home.

  15. Prior knowledge driven Granger causality analysis on gene regulatory network discovery

    DOE PAGES

    Yao, Shun; Yoo, Shinjae; Yu, Dantong

    2015-08-28

    Our study focuses on discovering gene regulatory networks from time series gene expression data using the Granger causality (GC) model. However, the number of available time points (T) usually is much smaller than the number of target genes (n) in biological datasets. The widely applied pairwise GC model (PGC) and other regularization strategies can lead to a significant number of false identifications when n>>T. In this study, we proposed a new method, viz., CGC-2SPR (CGC using two-step prior Ridge regularization) to resolve the problem by incorporating prior biological knowledge about a target gene data set. In our simulation experiments, themore » propose new methodology CGC-2SPR showed significant performance improvement in terms of accuracy over other widely used GC modeling (PGC, Ridge and Lasso) and MI-based (MRNET and ARACNE) methods. In addition, we applied CGC-2SPR to a real biological dataset, i.e., the yeast metabolic cycle, and discovered more true positive edges with CGC-2SPR than with the other existing methods. In our research, we noticed a “ 1+1>2” effect when we combined prior knowledge and gene expression data to discover regulatory networks. Based on causality networks, we made a functional prediction that the Abm1 gene (its functions previously were unknown) might be related to the yeast’s responses to different levels of glucose. In conclusion, our research improves causality modeling by combining heterogeneous knowledge, which is well aligned with the future direction in system biology. Furthermore, we proposed a method of Monte Carlo significance estimation (MCSE) to calculate the edge significances which provide statistical meanings to the discovered causality networks. All of our data and source codes will be available under the link https://bitbucket.org/dtyu/granger-causality/wiki/Home.« less

  16. Theoretical discussion for quantum computation in biological systems

    NASA Astrophysics Data System (ADS)

    Baer, Wolfgang

    2010-04-01

    Analysis of the brain as a physical system, that has the capacity of generating a display of every day observed experiences and contains some knowledge of the physical reality which stimulates those experiences, suggests the brain executes a self-measurement process described by quantum theory. Assuming physical reality is a universe of interacting self-measurement loops, we present a model of space as a field of cells executing such self-measurement activities. Empty space is the observable associated with the measurement of this field when the mass and charge density defining the material aspect of the cells satisfy the least action principle. Content is the observable associated with the measurement of the quantum wave function ψ interpreted as mass-charge displacements. The illusion of space and its content incorporated into cognitive biological systems is evidence of self-measurement activity that can be associated with quantum operations.

  17. Biological monitoring

    SciTech Connect

    Ho, M.H.; Dillon, H.K.

    1986-02-01

    Biological monitoring is defined as the measurement and assessment of workplace agents or their metabolites in tissues, secreta, excreta, expired air, or any combination of these to evaluate exposure and health risk compared to an appropriate reference. Biological monitoring offers several advantages: it takes into account individual variability in biological activity resulting from a chemical insult. It takes into account the effects of personal physical activity and individual life styles. It is a valuable adjunct to ambient monitoring and health surveillance. The importance of chemical speciation in the toxicity of pollutants is discussed. Basic protocols for lead, aluminum, cadmium, mercury, selenium, and nickel are presented. Basic criteria for biological monitoring methods are presented. 11 references, 1 table.

  18. Bottle Biology.

    ERIC Educational Resources Information Center

    CSTA Journal, 1995

    1995-01-01

    Provides hands-on biology activities using plastic bottles that allow students to become engaged in asking questions, creating experiments, testing hypotheses, and generating answers. Activities explore terrestrial and aquatic systems. (MKR)

  19. Biology Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Ten ideas that have been tried out by the authors in schools are presented for biology teachers. The areas covered include genetics, dispersal of seeds, habituation in earthworms, respiration, sensory neurons, fats and oils. A reading list is provided. (PS)

  20. Biology Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Twelve new experiments in biology are described by teachers for use in classrooms. Broad areas covered include enzyme action, growth regulation, microscopy, respiration, germination, plant succession, leaf structure and blood structure. Explanations are detailed. (PS)

  1. Biology Notes

    ERIC Educational Resources Information Center

    School Science Review, 1973

    1973-01-01

    Some helpful ideas are proposed for use by biology teachers. Topics included are Food Webs,'' Key to Identification of Families,'' Viruses,'' Sieve Tube,'' Woodlice,'' Ecology of Oak Leaf Roller Moth,'' and Model Making.'' (PS)

  2. Optofluidics incorporating actively controlled micro- and nano-particles

    PubMed Central

    Kayani, Aminuddin A.; Khoshmanesh, Khashayar; Ward, Stephanie A.; Mitchell, Arnan; Kalantar-zadeh, Kourosh

    2012-01-01

    The advent of optofluidic systems incorporating suspended particles has resulted in the emergence of novel applications. Such systems operate based on the fact that suspended particles can be manipulated using well-appointed active forces, and their motions, locations and local concentrations can be controlled. These forces can be exerted on both individual and clusters of particles. Having the capability to manipulate suspended particles gives users the ability for tuning the physical and, to some extent, the chemical properties of the suspension media, which addresses the needs of various advanced optofluidic systems. Additionally, the incorporation of particles results in the realization of novel optofluidic solutions used for creating optical components and sensing platforms. In this review, we present different types of active forces that are used for particle manipulations and the resulting optofluidic systems incorporating them. These systems include optical components, optofluidic detection and analysis platforms, plasmonics and Raman systems, thermal and energy related systems, and platforms specifically incorporating biological particles. We conclude the review with a discussion of future perspectives, which are expected to further advance this rapidly growing field. PMID:23864925

  3. Incorporating computational resources in a cancer research program

    PubMed Central

    Woods, Nicholas T.; Jhuraney, Ankita; Monteiro, Alvaro N.A.

    2015-01-01

    Recent technological advances have transformed cancer genetics research. These advances have served as the basis for the generation of a number of richly annotated datasets relevant to the cancer geneticist. In addition, many of these technologies are now within reach of smaller laboratories to answer specific biological questions. Thus, one of the most pressing issues facing an experimental cancer biology research program in genetics is incorporating data from multiple sources to annotate, visualize, and analyze the system under study. Fortunately, there are several computational resources to aid in this process. However, a significant effort is required to adapt a molecular biology-based research program to take advantage of these datasets. Here, we discuss the lessons learned in our laboratory and share several recommendations to make this transition effectively. This article is not meant to be a comprehensive evaluation of all the available resources, but rather highlight those that we have incorporated into our laboratory and how to choose the most appropriate ones for your research program. PMID:25324189

  4. Knowledge Repository for Fmea Related Knowledge

    NASA Astrophysics Data System (ADS)

    Cândea, Gabriela Simona; Kifor, Claudiu Vasile; Cândea, Ciprian

    2014-11-01

    This paper presents innovative usage of knowledge system into Failure Mode and Effects Analysis (FMEA) process using the ontology to represent the knowledge. Knowledge system is built to serve multi-projects work that nowadays are in place in any manufacturing or services provider, and knowledge must be retained and reused at the company level and not only at project level. The system is following the FMEA methodology and the validation of the concept is compliant with the automotive industry standards published by Automotive Industry Action Group, and not only. Collaboration is assured trough web-based GUI that supports multiple users access at any time

  5. Gelsius: a literature-based workflow for determining quantitative associations between genes and biological processes.

    PubMed

    Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; Piva, Roberto; Macii, Enrico

    2013-01-01

    An effective knowledge extraction and quantification methodology from biomedical literature would allow the researcher to organize and analyze the results of high-throughput experiments on microarrays and next-generation sequencing technologies. Despite the large amount of raw information available on the web, a tool able to extract a measure of the correlation between a list of genes and biological processes is not yet available. In this paper, we present Gelsius, a workflow that incorporates biomedical literature to quantify the correlation between genes and terms describing biological processes. To achieve this target, we build different modules focusing on query expansion and document cononicalization. In this way, we reached to improve the measurement of correlation, performed using a latent semantic analysis approach. To the best of our knowledge, this is the first complete tool able to extract a measure of genes-biological processes correlation from literature. We demonstrate the effectiveness of the proposed workflow on six biological processes and a set of genes, by showing that correlation results for known relationships are in accordance with definitions of gene functions provided by NCI Thesaurus. On the other side, the tool is able to propose new candidate relationships for later experimental validation. The tool is available at >http://bioeda1.polito.it:8080/medSearchServlet/.

  6. Incorporating Web Tracking Into EOSDIS Metrics Collection

    NASA Astrophysics Data System (ADS)

    Murphy, K. J.; Boquist, C. L.; Hines-Watts, T. M.; Moses, J. F.; Sofinowski, E. J.

    2007-12-01

    The Earth Observing System Data and Information System (EOSDIS) and related data centers have been collecting and analyzing information on the archiving, processing and distribution of Earth science data for more than 10 years. Long-standing approaches for evaluating the performance of systems managed by EOSDIS have provided insights into how system engineering requirements are being met, how user communities are being served and the levels of interest across the science data products. However, data and services are increasingly being made available to users via web-based applications that cannot be evaluated with current methodologies. New tools are required to record and analyze how users find, navigate and use the continuously evolving landscape of web-based resources supported by EOSDIS. Without such tools a significant portion of the data and services EOSDIS provides would not be captured. EOSDIS will be able to incorporate metrics collection on new web-based applications across geographically distributed and differently configured systems while not interfering in those systems' operations. A consistent process has been devised for collection and reporting of information on web data usage and the characterization of the community of web service users. To provide a more complete picture of system utilization, knowledge of the web resource usage is coupled with improvements to the current approaches for collection of processing, archival and distribution metrics of Earth science products. This combined information improves evaluation of engineering requirements and understanding of how the new web capabilities are impacting usage and distribution of science data and services provided by EOSDIS. This paper describes the new, non-intrusive methodology EOSDIS is using to capture and analyze information on the usage of web services across all related systems. The paper will discuss initial results demonstrating the benefits of the reengineered system.

  7. Prior knowledge-based approach for associating ...

    EPA Pesticide Factsheets

    Evaluating the potential human health and/or ecological risks associated with exposures to complex chemical mixtures in the ambient environment is one of the central challenges of chemical safety assessment and environmental protection. There is a need for approaches that can help to integrate chemical monitoring and bio-effects data to evaluate risks associated with chemicals present in the environment. We used prior knowledge about chemical-gene interactions to develop a knowledge assembly model for detected chemicals at five locations near two wastewater treatment plants. The assembly model was used to generate hypotheses about the biological impacts of the chemicals at each location. The hypotheses were tested using empirical hepatic gene expression data from fathead minnows exposed for 12 d at each location. Empirical gene expression data was also mapped to the assembly models to statistically evaluate the likelihood of a chemical contributing to the observed biological responses. The prior knowledge approach was able reasonably hypothesize the biological impacts at one site but not the other. Chemicals most likely contributing to the observed biological responses were identified at each location. Despite limitations to the approach, knowledge assembly models have strong potential for associating chemical occurrence with potential biological effects and providing a foundation for hypothesis generation to guide research and/or monitoring efforts relat

  8. Knowledge of Aging and Life Satisfaction among Older Adults

    ERIC Educational Resources Information Center

    Davis, Neil C.; Friedrich, Douglas

    2004-01-01

    Four hundred young-, middle-, and old-old adults responded to a battery of quizzes dealing with life satisfaction and objective aging knowledge in the physical, psychological, and social domains. Analyses incorporated domains of aging knowledge, life satisfaction, age, gender, and demographic variables. Both means difference and regression…

  9. Knowledge-Based Hierarchies: Using Organizations to Understand the Economy

    ERIC Educational Resources Information Center

    Garicano, Luis; Rossi-Hansberg, Esteban

    2015-01-01

    Incorporating the decision of how to organize the acquisition, use, and communication of knowledge into economic models is essential to understand a wide variety of economic phenomena. We survey the literature that has used knowledge-based hierarchies to study issues such as the evolution of wage inequality, the growth and productivity of firms,…

  10. "Shut up and Squat!" Learning Body Knowledge within the Gym

    ERIC Educational Resources Information Center

    Andreasson, Jesper

    2014-01-01

    The aim of this article is to describe and analyse learning processes among bodybuilders in bodybuilding environments, focusing on the ways activities form the basis for incorporation of both physical and cultural knowledge. Emanating from an ethnographic study, the arguments are based on a constructionist approach to knowledge. The result…

  11. The role of low-grade inflammation and metabolic flexibility in aging and nutritional modulation thereof: a systems biology approach.

    PubMed

    Calçada, Dulce; Vianello, Dario; Giampieri, Enrico; Sala, Claudia; Castellani, Gastone; de Graaf, Albert; Kremer, Bas; van Ommen, Ben; Feskens, Edith; Santoro, Aurelia; Franceschi, Claudio; Bouwman, Jildau

    2014-01-01

    Aging is a biological process characterized by the progressive functional decline of many interrelated physiological systems. In particular, aging is associated with the development of a systemic state of low-grade chronic inflammation (inflammaging), and with progressive deterioration of metabolic function. Systems biology has helped in identifying the mediators and pathways involved in these phenomena, mainly through the application of high-throughput screening methods, valued for their molecular comprehensiveness. Nevertheless, inflammation and metabolic regulation are dynamical processes whose behavior must be understood at multiple levels of biological organization (molecular, cellular, organ, and system levels) and on multiple time scales. Mathematical modeling of such behavior, with incorporation of mechanistic knowledge on interactions between inflammatory and metabolic mediators, may help in devising nutritional interventions capable of preventing, or ameliorating, the age-associated functional decline of the corresponding systems.

  12. Commentary: Prerequisite Knowledge

    ERIC Educational Resources Information Center

    Taylor, Ann T. S.

    2013-01-01

    Most biochemistry, genetics, cell biology, and molecular biology classes have extensive prerequisite or co-requisite requirements, often including introductory chemistry, introductory biology, and organic chemistry coursework. But what is the function of these prerequisites? While it seems logical that a basic understanding of biological and…

  13. The Development of Prospective Secondary Biology Teachers PCK

    ERIC Educational Resources Information Center

    Brown, Patrick; Friedrichsen, Patricia; Abell, Sandra

    2013-01-01

    In order to understand how prospective teachers develop knowledge for teaching, researchers must identify the types of knowledge that are integral to effective science teaching. This case study investigated how 4 prospective secondary biology teachers' science teaching orientations, knowledge of science learners, and knowledge of instructional…

  14. Why Explicit Knowledge Cannot Become Implicit Knowledge

    ERIC Educational Resources Information Center

    VanPatten, Bill

    2016-01-01

    In this essay, I review one of the conclusions in Lindseth (2016) published in "Foreign Language Annals." That conclusion suggests that explicit learning and practice (what she called form-focused instruction) somehow help the development of implicit knowledge (or might even become implicit knowledge). I argue for a different…

  15. Teacher Knowledge-Ability and Pupil Achievement.

    ERIC Educational Resources Information Center

    Tanner, Daniel; Celso, Nicholas

    The effectiveness of schools and the levels of investment in schooling have been in question since the 1966 Coleman report "Equality of Educational Opportunity." Based on a theory of "knowledge-ability," this study challenges the assumption that given "inputs" will yield equivalent effects or "outputs." In…

  16. Down syndrome and the genes of human chromosome 21: current knowledge and future potentials. Report on the Expert workshop on the biology of chromosome 21 genes: towards gene-phenotype correlations in Down syndrome. Washington D.C., September 28-October 1, 2007.

    PubMed

    Pritchard, M; Reeves, R H; Dierssen, M; Patterson, D; Gardiner, K J

    2008-01-01

    Down syndrome (DS), trisomy of human chromosome 21, is the most common genetic cause of intellectual disability. With an incidence in some countries as high as one in approximately 700 live births, and a complex, extensive and variably severe phenotype, Down syndrome is a significant medical and social challenge. In recent years, there has been a rapid increase in information on the functions of the genes of human chromosome 21, as well as in techniques and resources for their analysis. A recent workshop brought together experts on the molecular biology of Down syndrome and chromosome 21 with interested researchers in other fields to discuss advances and potentials for generating gene-phenotype correlations. An additional goal of the workshop was to work towards identification of targets for therapeutics that will correct features of DS. A knowledge-based approach to therapeutics also requires the correlation of chromosome 21 gene function with phenotypic features.

  17. [The potentials for immunization against influenza using liposome-incorporated viral surface antigens].

    PubMed

    Burducea, O; Marcheş, F; Duţu, C; Grancea, C; Nicolau, A; Păun, C

    1989-01-01

    Studies were conducted using uni- and multilamellar liposomes to establish optimum conditions for influenza antigen incorporation in view of their transport to the target cells for experimental influenza prophylaxis in hybrid white mice. Radiometric determinations showed a good level of preparation purification, a good efficiency of incorporation in liposomes of the active biological material, the liposome linked radioactivity distribution among different organs. Charged liposomes induced solid and long lasting resistance against influenza control infection.

  18. When cell biology meets theory

    PubMed Central

    Gonzalez-Gaitan, Marcos

    2015-01-01

    Cell biologists now have tools and knowledge to generate useful quantitative data. But how can we make sense of these data, and are we measuring the correct parameters? Moreover, how can we test hypotheses quantitatively? To answer these questions, the theory of physics is required and is essential to the future of quantitative cell biology. PMID:26416957

  19. Solar Energy Project, Activities: Biology.

    ERIC Educational Resources Information Center

    Tullock, Bruce, Ed.; And Others

    This guide contains lesson plans and outlines of science activities which present concepts of solar energy in the context of biology experiments. Each unit presents an introduction; objectives; skills and knowledge needed; materials; methods; questions; recommendations for further work; and a teacher information sheet. The teacher information…

  20. Visual Learning in Field Biology.

    ERIC Educational Resources Information Center

    Stanley, Ethel D.

    Visual learning has long been recognized as an integral process in educating biology undergraduates, who must develop specific visual skills and knowledge in order to communicate and work in the extensive visual culture shared by practicing biologists. Student experiences with field observations and the development and application of verbal/visual…

  1. Collaborative Research Seed Grants for Integrating Knowledges and Creating New Knowledge

    ERIC Educational Resources Information Center

    Freitag, Amy

    2015-01-01

    Incorporating different ways of knowing in research and management has the potential to bring creativity to environmental problem-solving through integrating ways of knowing and innovation via co-producing knowledge. To gain these benefits, North Carolina Sea Grant Extension offers small annual grants called Fisheries Resource Grants to paired…

  2. Biological Oceanography

    NASA Technical Reports Server (NTRS)

    Abbott, M. R.

    1984-01-01

    Within the framework of global biogeochemical cycles and ocean productivity, there are two areas that will be of particular interest to biological oceanography in the 1990s. The first is the mapping in space time of the biomass and productivity of phytoplankton in the world ocean. The second area is the coupling of biological and physical processes as it affects the distribution and growth rate of phytoplankton biomass. Certainly other areas will be of interest to biological oceanographers, but these two areas are amenable to observations from satellites. Temporal and spatial variability is a regular feature of marine ecosystems. The temporal and spatial variability of phytoplankton biomass and productivity which is ubiquitous at all time and space scales in the ocean must be characterized. Remote sensing from satellites addresses these problems with global observations of mesocale (2 to 20 days, 10 to 200 km) features over a long period of time.

  3. Biological preconcentrator

    DOEpatents

    Manginell, Ronald P.; Bunker, Bruce C.; Huber, Dale L.

    2008-09-09

    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  4. Development of the biology card sorting task to measure conceptual expertise in biology.

    PubMed

    Smith, Julia I; Combs, Elijah D; Nagami, Paul H; Alto, Valerie M; Goh, Henry G; Gourdet, Muryam A A; Hough, Christina M; Nickell, Ashley E; Peer, Adrian G; Coley, John D; Tanner, Kimberly D

    2013-01-01

    There are widespread aspirations to focus undergraduate biology education on teaching students to think conceptually like biologists; however, there is a dearth of assessment tools designed to measure progress from novice to expert biological conceptual thinking. We present the development of a novel assessment tool, the Biology Card Sorting Task, designed to probe how individuals organize their conceptual knowledge of biology. While modeled on tasks from cognitive psychology, this task is unique in its design to test two hypothesized conceptual frameworks for the organization of biological knowledge: 1) a surface feature organization focused on organism type and 2) a deep feature organization focused on fundamental biological concepts. In this initial investigation of the Biology Card Sorting Task, each of six analytical measures showed statistically significant differences when used to compare the card sorting results of putative biological experts (biology faculty) and novices (non-biology major undergraduates). Consistently, biology faculty appeared to sort based on hypothesized deep features, while non-biology majors appeared to sort based on either surface features or nonhypothesized organizational frameworks. Results suggest that this novel task is robust in distinguishing populations of biology experts and biology novices and may be an adaptable tool for tracking emerging biology conceptual expertise.

  5. TARGET: Rapid Capture of Process Knowledge

    NASA Technical Reports Server (NTRS)

    Ortiz, C. J.; Ly, H. V.; Saito, T.; Loftin, R. B.

    1993-01-01

    TARGET (Task Analysis/Rule Generation Tool) represents a new breed of tool that blends graphical process flow modeling capabilities with the function of a top-down reporting facility. Since NASA personnel frequently perform tasks that are primarily procedural in nature, TARGET models mission or task procedures and generates hierarchical reports as part of the process capture and analysis effort. Historically, capturing knowledge has proven to be one of the greatest barriers to the development of intelligent systems. Current practice generally requires lengthy interactions between the expert whose knowledge is to be captured and the knowledge engineer whose responsibility is to acquire and represent the expert's knowledge in a useful form. Although much research has been devoted to the development of methodologies and computer software to aid in the capture and representation of some types of knowledge, procedural knowledge has received relatively little attention. In essence, TARGET is one of the first tools of its kind, commercial or institutional, that is designed to support this type of knowledge capture undertaking. This paper will describe the design and development of TARGET for the acquisition and representation of procedural knowledge. The strategies employed by TARGET to support use by knowledge engineers, subject matter experts, programmers and managers will be discussed. This discussion includes the method by which the tool employs its graphical user interface to generate a task hierarchy report. Next, the approach to generate production rules for incorporation in and development of a CLIPS based expert system will be elaborated. TARGET also permits experts to visually describe procedural tasks as a common medium for knowledge refinement by the expert community and knowledge engineer making knowledge consensus possible. The paper briefly touches on the verification and validation issues facing the CLIPS rule generation aspects of TARGET. A description of

  6. Incorporating Brokers within Collaboration Environments

    NASA Astrophysics Data System (ADS)

    Rajasekar, A.; Moore, R.; de Torcy, A.

    2013-12-01

    A collaboration environment, such as the integrated Rule Oriented Data System (iRODS - http://irods.diceresearch.org), provides interoperability mechanisms for accessing storage systems, authentication systems, messaging systems, information catalogs, networks, and policy engines from a wide variety of clients. The interoperability mechanisms function as brokers, translating actions requested by clients to the protocol required by a specific technology. The iRODS data grid is used to enable collaborative research within hydrology, seismology, earth science, climate, oceanography, plant biology, astronomy, physics, and genomics disciplines. Although each domain has unique resources, data formats, semantics, and protocols, the iRODS system provides a generic framework that is capable of managing collaborative research initiatives that span multiple disciplines. Each interoperability mechanism (broker) is linked to a name space that enables unified access across the heterogeneous systems. The collaboration environment provides not only support for brokers, but also support for virtualization of name spaces for users, files, collections, storage systems, metadata, and policies. The broker enables access to data or information in a remote system using the appropriate protocol, while the collaboration environment provides a uniform naming convention for accessing and manipulating each object. Within the NSF DataNet Federation Consortium project (http://www.datafed.org), three basic types of interoperability mechanisms have been identified and applied: 1) drivers for managing manipulation at the remote resource (such as data subsetting), 2) micro-services that execute the protocol required by the remote resource, and 3) policies for controlling the execution. For example, drivers have been written for manipulating NetCDF and HDF formatted files within THREDDS servers. Micro-services have been written that manage interactions with the CUAHSI data repository, the Data

  7. Assembly of multilayer films incorporating a viral protein cage architecture.

    PubMed

    Suci, Peter A; Klem, Michael T; Arce, Fernando T; Douglas, Trevor; Young, Mark

    2006-10-10

    Protein cage architectures such as viral capsids, heat shock proteins, ferritins, and DNA-binding proteins are nanoscale modular subunits that can be used to expand the structural and functional range of composite materials. Here, layer-by-layer (LbL) assembly was used to incorporate cowpea chlorotic mottle virus (CCMV) into multilayer films. Three types of multilayer films were prepared. In the first type, ionic interactions were employed to assemble CCMV into triple layers. In the second type, complementary biological interactions (streptavidin/biotin) were used for this purpose. In a third variation of LbL assembly, complementary biological interactions were employed to produce nanotextured films that exhibit in-plane order over a micron scale without the need to adsorb onto a prepatterned template.

  8. Bioterrorism and biological threats dominate federal health security research; other priorities get scant attention.

    PubMed

    Shelton, Shoshana R; Connor, Kathryn; Uscher-Pines, Lori; Pillemer, Francesca Matthews; Mullikin, James M; Kellermann, Arthur L

    2012-12-01

    The federal government plays a critical role in achieving national health security by providing strategic guidance and funding research to help prevent, respond to, mitigate, and recover from disasters, epidemics, and acts of terrorism. In this article we describe the first-ever inventory of nonclassified national health security-related research funded by civilian agencies of the federal government. Our analysis revealed that the US government's portfolio of health security research is currently weighted toward bioterrorism and emerging biological threats, laboratory methods, and development of biological countermeasures. Eight of ten other priorities identified in the Department of Health and Human Services' National Health Security Strategy-such as developing and maintaining a national health security workforce or incorporating recovery into planning and response-receive scant attention. We offer recommendations to better align federal spending with health security research priorities, including the creation of an interagency working group charged with minimizing research redundancy and filling persistent gaps in knowledge.

  9. Analyzing beliefs and practices of a Mexican high school biology teacher

    NASA Astrophysics Data System (ADS)

    Verjovsky, Janet; Waldegg, Guillermina

    2005-04-01

    This article explores the beliefs and practices of a high school biology teacher through three interrelated theoretical frameworks: common knowledge, collaborative learning, and communities of practice. The data were obtained from an in-depth case study of Maria, a biology teacher from a Mexican public high school that was participating in a 4-year international science project using collaborative learning and information and communication technology. Her beliefs and practices were explored by means of questionnaires, semi-structured interviews, and nonparticipant observation of classes. Through the use of the three-component framework, the degrees of coherence between practice and beliefs that guide the teacher's daily behavior became apparent, as well as the difficulties of incorporating innovations due to institutional constraints.

  10. Socioemotional, Personality, and Biological Development: Illustrations from a Multilevel Developmental Psychopathology Perspective on Child Maltreatment.

    PubMed

    Cicchetti, Dante

    2016-01-01

    Developmental theories can be affirmed, challenged, and augmented by incorporating knowledge about atypical ontogenesis. Investigations of the biological, socioemotional, and personality development in individuals with high-risk conditions and psychopathological disorders can provide an entrée into the study of system organization, disorganization, and reorganization. This article examines child maltreatment to illustrate the benefit that can be derived from the study of individuals subjected to nonnormative caregiving experiences. Relative to an average expectable environment, which consists of a species-specific range of environmental conditions that support adaptive development among genetically normal individuals, maltreating families fail to provide many of the experiences that are required for normal development. Principles gleaned from the field of developmental psychopathology provide a framework for understanding multilevel functioning in normality and pathology. Knowledge of normative developmental processes provides the impetus to design and implement randomized control trial (RCT) interventions that can promote resilient functioning in maltreated children.

  11. Designing Interventions Informed by Scientific Knowledge About Effects of Early Adversity: A Translational Neuroscience Agenda for Next Generation Addictions Research

    PubMed Central

    Fisher, Philip A.; Berkman, Elliot T.

    2015-01-01

    In spite of extensive scientific knowledge about the neurobiological systems and neural pathways underlying addictions, only limited progress has been made to reduce the population-level incidence of addictions by using prevention and treatment programs. In this area of research the translation of basic neuroscience of causal mechanisms to effective interventions has not been fully realized. In this article we describe how an understanding of the effects of early adverse experiences on brain and biological development may provide new opportunities to achieve impact at scale with respect to reduction of addictions. We propose four categories of new knowledge that translational neuroscience investigations of addictions should incorporate to be successful. We then describe a translational neuroscience-informed smoking cessation intervention based on this model. PMID:26985399

  12. Biology and ecology of the ``Pompeii worm'' (Alvinella pompejana Desbruyères and Laubier), a normal dweller of an extreme deep-sea environment: A synthesis of current knowledge and recent developments

    NASA Astrophysics Data System (ADS)

    Desbruyères, D.; Chevaldonné, P.; Alayse, A.-M.; Jollivet, D.; Lallier, F. H.; Jouin-Toulmond, C.; Zal, F.; Sarradin, P.-M.; Cosson, R.; Caprais, J.-C.; Arndt, C.; O'Brien, J.; Guezennec, J.; Hourdez, S.; Riso, R.; Gaill, F.; Laubier, L.; Toulmond, A.

    1998-01-01

    Alvinella pompejana, the "Pompeii worm" lives on active hydrothermal edifices at deep-sea vents of the East Pacific Rise. The physical and chemical patterns of its microhabitat were determined from temperature probe measurements, temperature time series, and on-board and shore-based chemical analyses based on discrete sampling (pH, H 2S, CO 2, CH 4, S 2O 2-3, Ca, Mg, Cu, Cd, Zn). The microhabitat is characterised by high temporal and microscale spatial variability, with temperature values in the range of 20°-45°C at the immediate periphery of tubes but reaching higher, still undetermined, values inside the tubes. The difference observed between in vitro temperature limits for the stability of biomolecules and metabolic rates, and suggested in situ conditions seems to indicate a significant protective role of biological interfaces (tubes and cuticle). Temporal instability possibly also plays an important role in the ability for these worms to colonise such an extreme habitat. The functional role of dominant epibiotic bacteria is discussed in the light of recent biochemical and molecular data: the tube-worm-bacteria system can be considered as a symbiotic entity where carbon is probably metabolised and recycled. Sulphide detoxification occurs by oxidation at the gill level and possibly at the intracellular haemoglobin level. Heavy metals, ingested or absorbed, are trapped in spherocrystals and bound to metallothionein-like proteins. Anatomical, physiological and molecular adaptations to hypoxia allow the worm to successfully colonise the chimneys. A. pompejana lives in an ephemeral environment and must reproduce and disperse accordingly. It is a gonochoric species that displays a pseucopulatory behaviour allowing transfer of sperm to female spermathecae, thus avoiding dispersion of the gametes. The size of the oocytes suggests a lecithotrophic or benthic development. The population size structure is polymodal, indicating discontinuous recruitment. Population

  13. Integration of aquatic ecology and biological oceanographic knowledge for development of area-based eutrophication assessment criteria leading to water resource remediation and utilization management: a case study in Tha Chin, the most eutrophic river of Thailand.

    PubMed

    Meksumpun, Charumas; Meksumpun, Shettapong

    2008-01-01

    This research was carried out in Tha Chin Watershed in the central part of Thailand with attempts to apply multidisciplinary knowledge for understanding ecosystem structure and response to anthropogenic pollution and natural impacts leading to a proposal for an appropriate zonation management approach for sustainable utilization of the area. Water quality status of the Tha Chin River and Estuary had been determined by analyzing ecological, hydrological, and coastal oceanographic information from recent field surveys (during March 2006 to November 2007) together with secondary data on irrigation, land utilization, and socio-economic status.Results indicated that the Tha Chin River and Estuary was eutrophic all year round. Almost 100% of the brackish to marine areas reflected strongly hypertrophic water condition during both dry and high-loading periods. High NH(4)(+) and PO(4)(3-) loads from surrounding agricultural land use, agro-industry, and community continuously flew into the aquatic environment. Deteriorated ecosystem was clearly observed by dramatically low DO levels (ca 1 mg/l) in riverine to coastal areas and Noctiluca and Ceratium red tide outbreaks occurred around tidal front closed to the estuary. Accordingly, fishery resources were significantly decreased. Some riverine benthic habitats became dominated by deposit-feeding worms e.g. Lumbriculus, Branchiura, and Tubifex, while estuarine benthic habitats reflected succession of polychaetes and small bivalves. Results on analysis on integrated ecosystem responses indicated that changing functions were significantly influenced by particulates and nutrients dynamics in the system.Based on the overall results, the Tha Chin River and Estuary should be divided into 4 zones (I: Upper freshwater zone; II: Middle freshwater zone; III Lower freshwater zone; and IV: Lowest brackish to marine zone) for further management schemes on water remediation. In this study, the importance of habitat morphology and water flow

  14. Use of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in ART-naïve ACTG clinical trials participants.

    PubMed

    Grady, Benjamin J; Torstenson, Eric S; McLaren, Paul J; DE Bakker, Paul I W; Haas, David W; Robbins, Gregory K; Gulick, Roy M; Haubrich, Richard; Ribaudo, Heather; Ritchie, Marylyn D

    2011-01-01

    Personalized medicine is a high priority for the future of health care. The idea of tailoring an individual's wellness plan to their unique genetic code is one which we hope to realize through the use of pharmacogenomics. There have been examples of tremendous success in pharmacogenomic associations however there are many such examples in which only a small proportion of trait variance has been explained by the genetic variation. Although the increased use of GWAS could help explain more of this variation, it is likely that a significant proportion of the genetic architecture of these pharmacogenomic traits are due to complex genetic effects such as epistasis, also known as gene-gene interactions, as well as gene-drug interactions. In this study, we utilize the Biofilter software package to look for candidate epistasis contributing to risk for virologic failure with efavirenz-containing antiretroviral therapy (ART) regimens in treatment-naïve participants of AIDS Clinical Trials Group (ACTG) randomized clinical trials. A total of 904 individuals from three ACTG trials with data on efavirenz treatment are analyzed after race-stratification into white, black, and Hispanic ethnic groups. Biofilter was run considering 245 candidate ADME (absorption, distribution, metabolism, and excretion) genes and using database knowledge of gene and protein interaction networks to produce approximately 2 million SNP-SNP interaction models within each ethnic group. These models were evaluated within the PLATO software package using pair wise logistic regression models. Although no interaction model remained significant after correction for multiple comparisons, an interaction between SNPs in the TAP1 and ABCC9 genes was one of the top models before correction. The TAP1 protein is responsible for intracellular transport of antigen to MHC class I molecules, while ABCC9 codes for a transporter which is part of the subfamily of ABC transporters associated with multi-drug resistance

  15. USE OF BIOLOGICAL KNOWLEDGE TO INFORM THE ANALYSIS OF GENE-GENE INTERACTIONS INVOLVED IN MODULATING VIROLOGIC FAILURE WITH EFAVIRENZ-CONTAINING TREATMENT REGIMENS IN ART-NAÏVE ACTG CLINICAL TRIALS PARTICIPANTS

    PubMed Central

    Grady, Benjamin J.; Torstenson, Eric S.; Mclaren, Paul J.; De Bakker, Paul I.W.; Haas, David W.; Robbins, Gregory K.; Gulick, Roy M.; Haubrich, Richard; Ribaudo, Heather; Ritchie, Marylyn D.

    2011-01-01

    Personalized medicine is a high priority for the future of health care. The idea of tailoring an individual’s wellness plan to their unique genetic code is one which we hope to realize through the use of pharmacogenomics. There have been examples of tremendous success in pharmacogenomic associations however there are many such examples in which only a small proportion of trait variance has been explained by the genetic variation. Although the increased use of GWAS could help explain more of this variation, it is likely that a significant proportion of the genetic architecture of these pharmacogenomic traits are due to complex genetic effects such as epistasis, also known as gene-gene interactions, as well as gene-drug interactions. In this study, we utilize the Biofilter software package to look for candidate epistasis contributing to risk for virologic failure with efavirenz-containing antiretroviral therapy (ART) regimens in treatment-naïve participants of AIDS Clinical Trials Group (ACTG) randomized clinical trials. A total of 904 individuals from three ACTG trials with data on efavirenz treatment are analyzed after race-stratification into white, black, and Hispanic ethnic groups. Biofilter was run considering 245 candidate ADME (absorption, distribution, metabolism, and excretion) genes and using database knowledge of gene and protein interaction networks to produce approximately 2 million SNP-SNP interaction models within each ethnic group. These models were evaluated within the PLATO software package using pair wise logistic regression models. Although no interaction model remained significant after correction for multiple comparisons, an interaction between SNPs in the TAP1 and ABCC9 genes was one of the top models before correction. The TAP1 protein is responsible for intracellular transport of antigen to MHC class I molecules, while ABCC9 codes for a transporter which is part of the subfamily of ABC transporters associated with multi-drug resistance

  16. Bayes in biological anthropology.

    PubMed

    Konigsberg, Lyle W; Frankenberg, Susan R

    2013-12-01

    In this article, we both contend and illustrate that biological anthropologists, particularly in the Americas, often think like Bayesians but act like frequentists when it comes to analyzing a wide variety of data. In other words, while our research goals and perspectives are rooted in probabilistic thinking and rest on prior knowledge, we often proceed to use statistical hypothesis tests and confidence interval methods unrelated (or tenuously related) to the research questions of interest. We advocate for applying Bayesian analyses to a number of different bioanthropological questions, especially since many of the programming and computational challenges to doing so have been overcome in the past two decades. To facilitate such applications, this article explains Bayesian principles and concepts, and provides concrete examples of Bayesian computer simulations and statistics that address questions relevant to biological anthropology, focusing particularly on bioarchaeology and forensic anthropology. It also simultaneously reviews the use of Bayesian methods and inference within the discipline to date. This article is intended to act as primer to Bayesian methods and inference in biological anthropology, explaining the relationships of various methods to likelihoods or probabilities and to classical statistical models. Our contention is not that traditional frequentist statistics should be rejected outright, but that there are many situations where biological anthropology is better served by taking a Bayesian approach. To this end it is hoped that the examples provided in this article will assist researchers in choosing from among the broad array of statistical methods currently available.

  17. Biologically inspired oxidation catalysis.

    PubMed

    Que, Lawrence; Tolman, William B

    2008-09-18

    The development of processes for selective hydrocarbon oxidation is a goal that has long been pursued. An additional challenge is to make such processes environmentally friendly, for example by using non-toxic reagents and energy-efficient catalytic methods. Excellent examples are naturally occurring iron- or copper-containing metalloenzymes, and extensive studies have revealed the key chemical principles that underlie their efficacy as catalysts for aerobic oxidations. Important inroads have been made in applying this knowledge to the development of synthetic catalysts that model enzyme function. Such biologically inspired hydrocarbon oxidation catalysts hold great promise for wide-ranging synthetic applications.

  18. (Biological dosimetry)

    SciTech Connect

    Sega, G.A.

    1990-11-06

    The traveler participated in an International Symposium on Trends in Biological Dosimetry and presented an invited paper entitled, Adducts in sperm protamine and DNA vs mutation frequency.'' The purpose of the Symposium was to examine the applicability of new methods to study quantitatively the effects of xenobiotic agents (radiation and chemicals) on molecular, cellular and organ systems, with special emphasis on human biological dosimetry. The general areas covered at the meeting included studies on parent compounds and metabolites; protein adducts; DNA adducts; gene mutations; cytogenetic end-points and reproductive methods.

  19. Prior Knowledge, Reading Skill, and Text Cohesion in the Comprehension of Science Texts

    ERIC Educational Resources Information Center

    Ozuru, Yasuhiro; Dempsey, Kyle; McNamara, Danielle S.

    2009-01-01

    This study examined how text features (i.e., cohesion) and individual differences (i.e., reading skill and prior knowledge) contribute to biology text comprehension. College students with low and high levels of biology knowledge read two biology texts, one of which was high in cohesion and the other low in cohesion. The two groups were similar in…

  20. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Presents content information and/or laboratory procedures and experiments on different biology topics including small-scale cultivation of watercress and its use in water-culture experiments, microbiology of the phylloplane, use of mouthbrooders in science class, and the gene. (DC)

  1. Marine Biology

    ERIC Educational Resources Information Center

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  2. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Describes laboratory procedures, demonstrations, and classroom activities/materials, including water relation exercise on auxin-treated artichoke tuber tissue; aerobic respiration in yeast; an improved potometer; use of mobiles in biological classification, and experiments on powdery mildews and banana polyphenol oxidase. Includes reading lists…

  3. Cancer Biology

    ERIC Educational Resources Information Center

    Dominiecki, Mary E.

    2004-01-01

    University of Colorado's Virtual Student Fellowship available at and developed by Bakemeier, Richard F. This website is designed to give students applying for a fellowship an overview of basic topics in biology and how they are used by cancer researchers to develop new treatments.

  4. (Biological dosimetry)

    SciTech Connect

    Preston, R.J.

    1990-12-17

    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  5. Bottle Biology.

    ERIC Educational Resources Information Center

    Jager, Peter

    1993-01-01

    Describes activities which utilize plastic drink bottles and are designed to foster the development of a wide range of biological and ecological concepts. Includes instructions for making a model compost column and presents a model that illustrates open versus closed ecosystems. (DDR)

  6. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1980

    1980-01-01

    Describes equipment, activities, and experiments useful in biology and environmental education instruction, including, among others, sampling in ecology using an overhead projector, the slide finder as an aid to microscopy, teaching kidney function, and teaching wildlife conservation-sand dune systems. (SK)

  7. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1984

    1984-01-01

    Presents information on the teaching of nutrition (including new information relating to many current O-level syllabi) and part 16 of a reading list for A- and S-level biology. Also includes a note on using earthworms as a source of material for teaching meiosis. (JN)

  8. Biology Excursions

    ERIC Educational Resources Information Center

    Baldock, R. N.

    1973-01-01

    Provides many useful suggestions and cautions for planning and executing a biology field excursion. Specific procedures are outlined for investigating land communities and coastal areas, and a number of follow-up laboratory activities are described. The appendix provides an extensive bibliography with useful comments on the literature. (JR)

  9. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1979

    1979-01-01

    Organized by topic is a reading list for A- and S-level biology. Described are experiments for measuring rate of water uptake in a shoot; questions to aid students in designing experiments; rise of overhead projection to demonstrate osmosis and blood cell counting; and microbial manufacture of vinegar. (CS)

  10. Biology Notes

    ERIC Educational Resources Information Center

    School Science Review, 1976

    1976-01-01

    Describes nine biology experiments, including osmosis, genetics; oxygen content of blood, enzymes in bean seedlings, preparation of bird skins, vascularization in bean seedlings, a game called "sequences" (applied to review situations), crossword puzzle for human respiration, and physiology of the woodlouse. (CS)

  11. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Outlines a variety of laboratory procedures, techniques, and materials including construction of a survey frame for field biology, a simple tidal system, isolation and applications of plant protoplasts, tropisms, teaching lung structure, and a key to statistical methods for biologists. (DS)

  12. The meaning of biological information.

    PubMed

    Koonin, Eugene V

    2016-03-13

    Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with 'meaning', i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to 'meaning' of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

  13. The meaning of biological information

    PubMed Central

    Koonin, Eugene V.

    2016-01-01

    Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to ‘meaning’ of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology. PMID:26857678

  14. Incorporating Sociology into Community Service Classes

    ERIC Educational Resources Information Center

    Hochschild, Thomas R., Jr.; Farley, Matthew; Chee, Vanessa

    2014-01-01

    Sociologists and instructors who teach about community service share an affinity for understanding and addressing social problems. While many studies have demonstrated the benefits of incorporating community service into sociology courses, we examine the benefits of incorporating sociological content into community service classes. The authors…

  15. 49 CFR 572.40 - Incorporated materials.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Incorporated materials. 572.40 Section 572.40... Percentile Male § 572.40 Incorporated materials. (a) The drawings, specifications, manual, and computer... by reference. These materials are thereby made part of this regulation. The Director of the...

  16. 49 CFR 572.40 - Incorporated materials.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 7 2011-10-01 2011-10-01 false Incorporated materials. 572.40 Section 572.40... Percentile Male § 572.40 Incorporated materials. (a) The drawings, specifications, manual, and computer... by reference. These materials are thereby made part of this regulation. The Director of the...

  17. 49 CFR 572.40 - Incorporated materials.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 7 2013-10-01 2013-10-01 false Incorporated materials. 572.40 Section 572.40... Percentile Male § 572.40 Incorporated materials. (a) The drawings, specifications, manual, and computer... by reference. These materials are thereby made part of this regulation. The Director of the...

  18. 49 CFR 572.40 - Incorporated materials.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 7 2012-10-01 2012-10-01 false Incorporated materials. 572.40 Section 572.40... Percentile Male § 572.40 Incorporated materials. (a) The drawings, specifications, manual, and computer... by reference. These materials are thereby made part of this regulation. The Director of the...

  19. Knowledge-based commodity distribution planning

    NASA Technical Reports Server (NTRS)

    Saks, Victor; Johnson, Ivan

    1994-01-01

    This paper presents an overview of a Decision Support System (DSS) that incorporates Knowledge-Based (KB) and commercial off the shelf (COTS) technology components. The Knowledge-Based Logistics Planning Shell (KBLPS) is a state-of-the-art DSS with an interactive map-oriented graphics user interface and powerful underlying planning algorithms. KBLPS was designed and implemented to support skilled Army logisticians to prepare and evaluate logistics plans rapidly, in order to support corps-level battle scenarios. KBLPS represents a substantial advance in graphical interactive planning tools, with the inclusion of intelligent planning algorithms that provide a powerful adjunct to the planning skills of commodity distribution planners.

  20. Knowledge-based flow field zoning

    NASA Technical Reports Server (NTRS)

    Andrews, Alison E.

    1988-01-01

    Automation flow field zoning in two dimensions is an important step towards easing the three-dimensional grid generation bottleneck in computational fluid dynamics. A knowledge based approach works well, but certain aspects of flow field zoning make the use of such an approach challenging. A knowledge based flow field zoner, called EZGrid, was implemented and tested on representative two-dimensional aerodynamic configurations. Results are shown which illustrate the way in which EZGrid incorporates the effects of physics, shape description, position, and user bias in a flow field zoning.