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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. Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization.

    PubMed

    Hasegawa, Takanori; Yamaguchi, Rui; Nagasaki, Masao; Miyano, Satoru; Imoto, Seiya

    2014-01-01

    Comprehensive understanding of gene regulatory networks (GRNs) is a major challenge in the field of systems biology. Currently, there are two main approaches in GRN analysis using time-course observation data, namely an ordinary differential equation (ODE)-based approach and a statistical model-based approach. The ODE-based approach can generate complex dynamics of GRNs according to biologically validated nonlinear models. However, it cannot be applied to ten or more genes to simultaneously estimate system dynamics and regulatory relationships due to the computational difficulties. The statistical model-based approach uses highly abstract models to simply describe biological systems and to infer relationships among several hundreds of genes from the data. However, the high abstraction generates false regulations that are not permitted biologically. Thus, when dealing with several tens of genes of which the relationships are partially known, a method that can infer regulatory relationships based on a model with low abstraction and that can emulate the dynamics of ODE-based models while incorporating prior knowledge is urgently required. To accomplish this, we propose a method for inference of GRNs using a state space representation of a vector auto-regressive (VAR) model with L1 regularization. This method can estimate the dynamic behavior of genes based on linear time-series modeling constructed from an ODE-based model and can infer the regulatory structure among several tens of genes maximizing prediction ability for the observational data. Furthermore, the method is capable of incorporating various types of existing biological knowledge, e.g., drug kinetics and literature-recorded pathways. The effectiveness of the proposed method is shown through a comparison of simulation studies with several previous methods. For an application example, we evaluated mRNA expression profiles over time upon corticosteroid stimulation in rats, thus incorporating corticosteroid

  3. A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments

    PubMed Central

    Larsen, Peter; Almasri, Eyad; Chen, Guanrao; Dai, Yang

    2007-01-01

    Background The incorporation of prior biological knowledge in the analysis of microarray data has become important in the reconstruction of transcription regulatory networks in a cell. Most of the current research has been focused on the integration of multiple sets of microarray data as well as curated databases for a genome scale reconstruction. However, individual researchers are more interested in the extraction of most useful information from the data of their hypothesis-driven microarray experiments. How to compile the prior biological knowledge from literature to facilitate new hypothesis generation from a microarray experiment is the focus of this work. We propose a novel method based on the statistical analysis of reported gene interactions in PubMed literature. Results Using Gene Ontology (GO) Molecular Function annotation for reported gene regulatory interactions in PubMed literature, a statistical analysis method was proposed for the derivation of a likelihood of interaction (LOI) score for a pair of genes. The LOI-score and the Pearson correlation coefficient of gene profiles were utilized to check if a pair of query genes would be in the above specified interaction. The method was validated in the analysis of two gene sets formed from the yeast Saccharomyces cerevisiae cell cycle microarray data. It was found that high percentage of identified interactions shares GO Biological Process annotations (39.5% for a 102 interaction enriched gene set and 23.0% for a larger 999 cyclically expressed gene set). Conclusion This method can uncover novel biologically relevant gene interactions. With stringent confidence levels, small interaction networks can be identified for further establishment of a hypothesis testable by biological experiment. This procedure is computationally inexpensive and can be used as a preprocessing procedure for screening potential biologically relevant gene pairs subject to the analysis with sophisticated statistical methods. PMID

  4. 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

  5. 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

  6. 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. PMID:25874581

  7. 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

  8. "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.

  9. 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

  10. 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

  11. The Social Construction of Biological Knowledge.

    ERIC Educational Resources Information Center

    Bain, Linda L.

    The influence of biological science research on the development of physical education curriculum is examined in this paper. The social construction of scientific knowledge is described as occurring in the selection of problems to be studied, the collection and interpretation of data, the dissemination of results, and the educational uses of…

  12. 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., Sr.

    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.

  13. 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

  14. 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.

  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. 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. PMID:26838891

  17. 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,…

  18. 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

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

    PubMed

    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

  20. 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…

  1. Biologic activity of antigen receptors artificially incorporated onto B lymphocytes.

    PubMed

    Peacock, J S; Londo, T R; Roess, D A; Barisas, B G

    1986-09-15

    We describe a method for incorporating monoclonal antibody molecules onto viable murine lymphocytes and summarize the biologic activity of these artificial receptors on B cells. Mouse spleen cells incubated overnight with palmitate conjugates of a monoclonal anti-DNP IgA (protein 315) in the presence of deoxycholic acid incorporate about 50,000 antibody molecules per cell. When concentrations of deoxycholate and palmitoyl-protein 315 are carefully controlled, this labeling procedure does not affect the viability or the normal functions of the receptor-decorated cells. The incorporated antibody specifically binds DNP-antigens, although it appears to be unable to communicate directly with internal cellular components. Yet when these receptor-decorated, unprimed cells are challenged with any one of several DNP-antigens, up to 42,000 per 10(6) B cells differentiate into Ig-secreting cells. This response is about 23-fold greater than that induced in normal cell cultures and is of the same magnitude as that induced by the polyclonal B cell activator LPS. This, in addition to the observation that only about 3.6% of receptor-decorated B cells responding to DNP-conjugated polymerized flagellin (DNP-POL) produce hapten-specific antibody, demonstrates that these antigens cause polyclonal B cell differentiation. Normal spleen cells in the presence of DNP-POL and irradiated spleen cells bearing the artificial receptors do not exhibit the polyclonal antibody response. Also, the response of receptor-decorated B cell is blocked by high but nontoxic concentrations of the nonimmunogenic hapten DNP-lysine. These observations demonstrate that the polyclonal B cell response in this system requires the binding of antigen to artificial receptors on functionally viable cells. The polyclonal B cell response to a thymus-dependent antigen DNP-conjugated bovine gamma-globulin (DNP-BGG) requires the presence of the carrier-primed T cells. On the other hand, T cell depletion by anti-Thy-1

  2. 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…

  3. Incorporating knowledge to databases--a solution to complex domains.

    PubMed Central

    Leão, B. de F.; Mantovani, R.; Rossi, R. I.; Zielinsky, P.

    1992-01-01

    This paper describes the design of an integrated environment to handle information on congenital heart disease patients. A three-layer model that integrates a database, a knowledge-base and a graphical user-interface is presented. The role of each layer and its connections is discussed. The advantages of using a hypertext front-end system to present and retrieve complex data are also addressed. The current status of the project and its future developments are described in the final section. PMID:1482873

  4. 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…

  5. 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. PMID:26173464

  6. 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…

  7. 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

  8. 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

  9. 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'…

  10. 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.

  11. 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

  12. Elaboration of Cognitive Knowledge of Biology from Childhood to Adulthood.

    ERIC Educational Resources Information Center

    Fisher, Kathleen M.

    Word association techniques were used to examine the growth of biological knowledge over a period of years, from fourth-grade to college students. Results were analyzed by classifying stimulus-response word pairs according to the nature of the relationship between the words in each pair. Three hypotheses were tested: (1) the proportion of enactive…

  13. 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…

  14. 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…

  15. 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…

  16. 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

  17. 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. PMID:26086662

  18. 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 plan is not…

  19. 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…

  20. 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…

  1. Developmental “Roots” in Mature Biological Knowledge

    PubMed Central

    Goldberg, Robert F.; Thompson-Schill, Sharon L.

    2009-01-01

    Young children tend to claim that moving artifacts and nonliving natural kinds are alive, but neglect to ascribe life to plants. This research tested whether adults exhibit similar confusions when verifying life status in a speeded classification task. Experiment 1 showed that undergraduates encounter greater difficulty (reduced accuracy and increased response times) in determining life status for plants, relative to animals, and for natural and moving nonliving things, relative to artifacts and non-moving things. Experiment 2 replicated these effects in university biology professors. The professors showed a significantly reduced effect size for living things, as compared with the students, but still showed greater difficulty for plants than animals, even as no differences from the students were apparent in their responses to nonliving things. These results suggest that mature biological knowledge relies on a developmental foundation that is not radically overwritten or erased with the profound conceptual changes that accompany mastery of the domain. PMID:19399979

  2. 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

  3. Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge

    PubMed Central

    Squillario, Margherita; Barbieri, Matteo; Verri, Alessandro; Barla, Annalisa

    2016-01-01

    Biological interpretability is a key requirement for the output of microarray data analysis pipelines. The most used pipeline first identifies a gene signature from the acquired measurements and then uses gene enrichment analysis as a tool for functionally characterizing the obtained results. Recently Knowledge Driven Variable Selection (KDVS), an alternative approach which performs both steps at the same time, has been proposed. In this paper, we assess the effectiveness of KDVS against standard approaches on a Parkinson’s Disease (PD) dataset. The presented quantitative analysis is made possible by the construction of a reference list of genes and gene groups associated to PD. Our work shows that KDVS is much more effective than the standard approach in enhancing the interpretability of the obtained results. PMID:27600081

  4. Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge.

    PubMed

    Squillario, Margherita; Barbieri, Matteo; Verri, Alessandro; Barla, Annalisa

    2016-01-01

    Biological interpretability is a key requirement for the output of microarray data analysis pipelines. The most used pipeline first identifies a gene signature from the acquired measurements and then uses gene enrichment analysis as a tool for functionally characterizing the obtained results. Recently Knowledge Driven Variable Selection (KDVS), an alternative approach which performs both steps at the same time, has been proposed. In this paper, we assess the effectiveness of KDVS against standard approaches on a Parkinson's Disease (PD) dataset. The presented quantitative analysis is made possible by the construction of a reference list of genes and gene groups associated to PD. Our work shows that KDVS is much more effective than the standard approach in enhancing the interpretability of the obtained results. PMID:27600081

  5. 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…

  6. 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

  7. Critical Analysis of Problems Encountered in Incorporating Indigenous Knowledge in Science Teaching by Primary School Teachers in Zimbabwe

    ERIC Educational Resources Information Center

    Shizha, Edward

    2007-01-01

    In Zimbabwe the need to incorporate indigenous knowledge in science education to reflect local cultural settings cannot be overemphasized. Current policies on science are situated in Western cultural definitions, thus marginalizing indigenous knowledge, which is misconceived as irrational and illogical. This study used qualitative research…

  8. Knowledge Transfer in Biology and Translation across External Representations: Experts' Views and Challenges for Learning

    ERIC Educational Resources Information Center

    Schonborn, Konrad J.; Bogeholz, Susanne

    2009-01-01

    Recent curriculum reform promotes core competencies such as desired "content knowledge" and "communication" for meaningful learning in biology. Understanding in biology is demonstrated when pupils can apply acquired knowledge to new tasks. This process requires the transfer of knowledge and the subordinate process of translation across external…

  9. 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

  10. 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.

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

    PubMed

    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. PMID:6716559

  12. 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 Pb for 60 days. The diet consisted of homogenized 4-wk-old cockerels raised on feed mixed with and without Pb. No kestrels died and weights did not differ among treatment groups. The control group (0.5 ppm Pb) had the lowest mean concentration of Pb and the high dietary group had the highest for the following tissues: kidney, liver, femur, brain and blood. Concentrations of Pb were significantly correlated among tissues. Treatment groups did not differ in packed cell volume, Hb concentration or erythrocyte count.

  13. 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

  14. 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.

  15. 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. PMID:26478334

  16. Proliferation of diversified clostridial species during biological soil disinfestation incorporated with plant biomass under various conditions.

    PubMed

    Mowlick, Subrata; Takehara, Toshiaki; Kaku, Nobuo; Ueki, Katsuji; Ueki, Atsuko

    2013-09-01

    Biological soil disinfestation (BSD) involves the anaerobic decomposition of plant biomass by microbial communities leading to control of plant pathogens. We analyzed bacterial communities in soil of a model experiment of BSD, as affected by biomass incorporation under various conditions, to find out the major anaerobic bacterial groups which emerged after BSD treatments. The soil was treated with Brassica juncea plants, wheat bran, or Avena strigosa plants, irrigated at 20 or 30 % moisture content and incubated at 25-30 °C for 17 days. The population of Fusarium oxysporum f. sp. spinaciae incorporated at the start of the experiment declined markedly for some BSD conditions and rather high concentrations of acetate and butyrate were detected from these BSD-treated soils. The polymerase chain reaction-denaturing gradient gel electrophoresis analysis based on the V3 region of 16S rRNA gene sequences from the soil DNA revealed that bacterial profiles greatly changed according to the treatment conditions. Based on the clone library analysis, phylogenetically diverse clostridial species appeared exceedingly dominant in the bacterial community of BSD soil incorporated with Brassica plants or wheat bran, in which the pathogen was suppressed completely. Species in the class Clostridia such as Clostridium saccharobutylicum, Clostridium acetobutylicum, Clostridium xylanovorans, Oxobacter pfennigii, Clostridium pasteurianum, Clostridium sufflavum, Clostridium cylindrosporum, etc. were commonly recognized as closely related species of the dominant clone groups from these soil samples. PMID:23132344

  17. Bayesian regression discontinuity designs: incorporating clinical knowledge in the causal analysis of primary care data

    PubMed Central

    Geneletti, Sara; O’Keeffe, Aidan G.; Sharples, Linda D.; Richardson, Sylvia; Baio, Gianluca

    2016-01-01

    The regression discontinuity (RD) design is a quasi-experimental design that estimates the causal effects of a treatment by exploiting naturally occurring treatment rules. It can be applied in any context where a particular treatment or intervention is administered according to a pre-specified rule linked to a continuous variable. Such thresholds are common in primary care drug prescription where the RD design can be used to estimate the causal effect of medication in the general population. Such results can then be contrasted to those obtained from randomised controlled trials (RCTs) and inform prescription policy and guidelines based on a more realistic and less expensive context. In this paper, we focus on statins, a class of cholesterol-lowering drugs, however, the methodology can be applied to many other drugs provided these are prescribed in accordance to pre-determined guidelines. Current guidelines in the UK state that statins should be prescribed to patients with 10-year cardiovascular disease risk scores in excess of 20%. If we consider patients whose risk scores are close to the 20% risk score threshold, we find that there is an element of random variation in both the risk score itself and its measurement. We can therefore consider the threshold as a randomising device that assigns statin prescription to individuals just above the threshold and withholds it from those just below. Thus, we are effectively replicating the conditions of an RCT in the area around the threshold, removing or at least mitigating confounding. We frame the RD design in the language of conditional independence, which clarifies the assumptions necessary to apply an RD design to data, and which makes the links with instrumental variables clear. We also have context-specific knowledge about the expected sizes of the effects of statin prescription and are thus able to incorporate this into Bayesian models by formulating informative priors on our causal parameters. PMID:25809691

  18. 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…

  19. Hemiasterlin analogues incorporating an aromatic, and heterocyclic type C-terminus: design, synthesis and biological evaluation

    PubMed Central

    Lesma, Giordano; Sacchetti, Alessandro; Bai, Rouli; Basso, Giuseppe; Bortolozzi, Roberta; Hamel, Ernest; Vaiana, Nadia; Viola, Giampietro

    2014-01-01

    A representative series of structural analogs of the antimitotic tripeptides hemiasterlins have been designed and synthesized, as potential inhibitors of tubulin polymerization. Relying also on a computational approach, we aimed to explore unknown extensive changes at the C-fragment, by incorporating the conformationally required double bond into five- and six-membered rings. Key steps of the synthetic strategy are a dynamic resolution affording the A-fragment in 97 % ee and the preparation of six new cyclic C fragments, all potentially able to interact with tubulin by means of H bonds. Unexpectedly, biological evaluation of these analogs did not provide evidences neither for cytotoxic effect nor for inhibition of tubulin polymerization. PMID:24500310

  20. 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. PMID:26818824

  1. 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…

  2. 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

  3. 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.

  4. 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

  5. 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…

  6. 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…

  7. 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…

  8. 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…

  9. 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…

  10. 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,…

  11. Transforming Biology Curriculum at Navajo Community College to Include Navajo and Western Cultural Knowledge.

    ERIC Educational Resources Information Center

    Garrison, Edward R.

    1994-01-01

    Describes how a college teacher used Navajo traditional knowledge to rethink the teaching of college biology. Suggests that teachers intimidated by the intricate Dine Philosophy of Education may integrate Navajo knowledge into their courses through focused research guided by Navajo consultants. Includes five examples of redesigned curricula for…

  12. 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…

  13. 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,...

  14. 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 ...

  15. 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

  16. 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.

  17. A multimedia Anatomy Browser incorporating a knowledge base and 3D images.

    PubMed Central

    Eno, K.; Sundsten, J. W.; Brinkley, J. F.

    1991-01-01

    We describe a multimedia program for teaching anatomy. The program, called the Anatomy Browser, displays cross-sectional and topographical images, with outlines around structures and regions of interest. The user may point to these structures and retrieve text descriptions, view symbolic relationships between structures, or view spatial relationships by accessing 3-D graphics animations from videodiscs produced specifically for this program. The software also helps students exercise what they have learned by asking them to identify structures by name and location. The program is implemented in a client-server architecture, with the user interface residing on a Macintosh, while images, data, and a growing symbolic knowledge base of anatomy are stored on a fileserver. This architecture allows us to develop practical tutorial modules that are in current use, while at the same time developing the knowledge base that will lead to more intelligent tutorial systems. PMID:1807699

  18. 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.

  19. 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.

  20. 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...

  1. 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…

  2. 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…

  3. Incorporating prior knowledge of urban scene spatial structure in aperture code designs for surveillance systems

    NASA Astrophysics Data System (ADS)

    Valenzuela, John R.; Thelen, Brian J.; Subotic, Nikola

    2010-08-01

    Two major missions of Surveillance systems are imaging and ground moving target indication (GMTI). Recent advances in coded aperture electro optical systems have enabled persistent surveillance systems with extremely large fields of regard. The areas of interest for these surveillance systems are typically urban, with spatial topologies having a very definite structure. We incorporate aspects of a priori information on this structure in our aperture code designs to enable optimized dealiasing operations for undersampled focal plane arrays. Our framework enables us to design aperture codes to minimize mean square error for image reconstruction or to maximize signal to clutter ratio for GMTI detection. In this paper we present a technical overview of our code design methodology and show the results of our designed codes on simulated DIRSIG mega-scene data.

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

    PubMed

    Marris, Claire; Jefferson, Catherine; Lentzos, Filippa

    2014-11-01

    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

  5. Knowledge management and electronic care records: Incorporating social, legal and ethical issues.

    PubMed

    Bassinder, James; Bali, Rajeev K; Naguib, Raouf

    2006-01-01

    Many challenges face developers of secure computer-based clinical systems but the technical problems are overshadowed by many obstacles, key amongst them being social and ethical issues. A sound Knowledge Management (KM) structure within clinical environments can recognise the responsibility of healthcare professionals to keep patient clinical data (for example, electronic care record (ECR) systems) secure. An arrangement is proposed that gives the most senior clinician in a healthcare facility the ultimate responsibility for security of clinical data held in the organisation. Ideally, the senior clinician would possess training and experience in information systems and their security. Contracts should be developed between healthcare facilities and their patients, defining the limits to the use and disclosure of clinical health data. However, we are observing increasing confusion about the term 'Knowledge Management' which may be limited both its efficacy and effectiveness. Health organisations are referring to the term in various contexts and health informatics articles frequently use the term and interpret it in diverse ways. Given the divergence of views, this paper will attempt to establish KM's efficacy for the implementation of electronic care record systems. PMID:17095821

  6. 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

  7. Extending (Q)SARs to incorporate proprietary knowledge for regulatory purposes: A case study using aromatic amine mutagenicity.

    PubMed

    Ahlberg, Ernst; Amberg, Alexander; Beilke, Lisa D; Bower, David; Cross, Kevin P; Custer, Laura; Ford, Kevin A; Van Gompel, Jacky; Harvey, James; Honma, Masamitsu; Jolly, Robert; Joossens, Elisabeth; Kemper, Raymond A; Kenyon, Michelle; Kruhlak, Naomi; Kuhnke, Lara; Leavitt, Penny; Naven, Russell; Neilan, Claire; Quigley, Donald P; Shuey, Dana; Spirkl, Hans-Peter; Stavitskaya, Lidiya; Teasdale, Andrew; White, Angela; Wichard, Joerg; Zwickl, Craig; Myatt, Glenn J

    2016-06-01

    Statistical-based and expert rule-based models built using public domain mutagenicity knowledge and data are routinely used for computational (Q)SAR assessments of pharmaceutical impurities in line with the approach recommended in the ICH M7 guideline. Knowledge from proprietary corporate mutagenicity databases could be used to increase the predictive performance for selected chemical classes as well as expand the applicability domain of these (Q)SAR models. This paper outlines a mechanism for sharing knowledge without the release of proprietary data. Primary aromatic amine mutagenicity was selected as a case study because this chemical class is often encountered in pharmaceutical impurity analysis and mutagenicity of aromatic amines is currently difficult to predict. As part of this analysis, a series of aromatic amine substructures were defined and the number of mutagenic and non-mutagenic examples for each chemical substructure calculated across a series of public and proprietary mutagenicity databases. This information was pooled across all sources to identify structural classes that activate or deactivate aromatic amine mutagenicity. This structure activity knowledge, in combination with newly released primary aromatic amine data, was incorporated into Leadscope's expert rule-based and statistical-based (Q)SAR models where increased predictive performance was demonstrated. PMID:26879463

  8. Liposomes incorporating cyclodextrin-drug inclusion complexes: Current state of knowledge.

    PubMed

    Gharib, Riham; Greige-Gerges, Hélène; Fourmentin, Sophie; Charcosset, Catherine; Auezova, Lizette

    2015-09-20

    Cyclodextrins (CDs) are cyclic oligosaccharides, consisting of glucopyranose units, which are able to form host-guest inclusion complexes with lipophilic molecules. The ability of CD to increase drug solubility may be used to increase drug entrapment in the aqueous compartment of liposomes and liposomes can protect CD/drug inclusion complexes until drug release. Liposomes are phospholipid vesicles composed of lipid bilayers enclosing one or more aqueous compartments. They have been widely used as safe and effective carriers for both hydrophilic and lipophilic drugs. However, lipophilic drugs incorporated in the membrane bilayers can be rapidly released, which limits the effectiveness of this drug delivery system. The coupling of both delivery systems by encapsulating CD/drug inclusion complex into liposomes is proposed to circumvent the drawbacks of each separate system. Here, we review the literature regarding the encapsulation of CD/drug inclusion complex into conventional, deformable and double loaded liposomes. The review highlights the characteristics of these systems and presents the advantages and disadvantages of each one. PMID:26050903

  9. 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.

  10. 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

  11. 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…

  12. Incorporating Climate Change Lessons Into the Biology, Chemistry and Physics Classrooms

    NASA Astrophysics Data System (ADS)

    Nadeau, J. M.

    2013-12-01

    In this session, several climate change related activities will be demonstrated, that can be used in the Biology, Chemistry and Physics Classrooms. Ms. Nadeau's book "Climate Change at Earth's Poles: 50 Research-Based Lessons for Biology, Chemistry and Physics", will be available for purchase. This publication was inspired after the IPY Oslo Science Conference in 2010, and was presented at the IPY 2012 Science Conference in Montreal, and at the Science Teachers' Conference in Coimbra, Portugal in 2013. Ms. Nadeau is a Biology, Chemistry, and Physics teacher at Gloucester High School in Ottawa, Canada. Resource Book for Teachers

  13. Incorporating domain knowledge for tubule detection in breast histopathology using O'Callaghan neighborhoods

    NASA Astrophysics Data System (ADS)

    Basavanhally, Ajay; Yu, Elaine; Xu, Jun; Ganesan, Shridar; Feldman, Michael; Tomaszewski, John; Madabhushi, Anant

    2011-03-01

    An important criterion for identifying complicated objects with multiple attributes is the use of domain knowledge which reflects the precise spatial linking of the constituent attributes. Hence, simply detecting the presence of the low-level attributes that constitute the object, even in cases where these attributes might be detected in spatial proximity to each other is usually not a robust strategy. The O'Callaghan neighborhood is an ideal vehicle for characterizing objects comprised of multiple attributes spatially connected to each other in a precise fashion because it allows for modeling and imposing spatial distance and directional constraints on the object attributes. In this work we apply the O'Callaghan neighborhood to the problem of tubule identification on hematoxylin and eosin (H & E) stained breast cancer (BCa) histopathology, where a tubule is characterized by a central lumen surrounded by cytoplasm and a ring of nuclei around the cytoplasm. The detection of tubules is important because tubular density is an important predictor in cancer grade determination. In the context of ER+ BCa, grade has been shown to be strongly linked to disease aggressiveness and patient outcome. The more standard pattern recognition approaches to detection of complex objects typically involve training classifiers for low-level attributes individually. For tubule detection, the spatial proximity of lumen, cytoplasm, and nuclei might suggest the presence of a tubule. However such an approach could also suffer from false positive errors due to the presence of fat, stroma, and other lumen-like areas that could be mistaken for tubules. In this work, tubules are identified by imposing spatial and distance constraints using O'Callaghan neighborhoods between the ring of nuclei around each lumen. In this work, cancer nuclei in each image are found via a color deconvolution scheme, which isolates the hematoxylin stain, thereby enabling automated detection of individual cell nuclei

  14. Effect of Hyaluronic Acid Incorporation Method on the Stability and Biological Properties of Polyurethane-Hyaluronic Acid Biomaterials

    PubMed Central

    Ruiz, Amaliris; Rathnam, Kashmila R.; Masters, Kristyn S.

    2014-01-01

    The high failure rate of small diameter vascular grafts continues to drive the development of new materials and modification strategies that address this clinical problem, with biomolecule incorporation typically achieved via surface-based modification of various biomaterials. In this work, we examined whether the method of biomolecule incorporation (i.e., bulk vs. surface modification) into a polyurethane (PU) polymer impacted biomaterial performance in the context of vascular applications. Specifically, hyaluronic acid (HA) was incorporated into a poly(ether urethane) via bulk copolymerization or covalent surface tethering, and the resulting PU-HA materials characterized with respect to both physical and biological properties. Modification of PU with HA by either surface or bulk methods yielded materials that, when tested under static conditions, possessed no significant differences in their ability to resist protein adsorption, platelet adhesion, and bacterial adhesion, while supporting endothelial cell culture. However, only bulk-modified PU-HA materials were able to fully retain these characteristics following material exposure to flow, demonstrating a superior ability to retain the incorporated HA and minimize enzymatic degradation, protein adsorption, platelet adhesion, and bacterial adhesion. Thus, despite bulk methods rarely being implemented in the context of biomolecule attachment, these results demonstrate improved performance of PU-HA upon bulk, rather than surface, incorporation of HA. Although explored only in the context of PU-HA, the findings revealed by these experiments have broader implications for the design and evaluation of vascular graft modification strategies. PMID:24276670

  15. 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…

  16. A Short Note on Haroutunian's View of Piaget's Biological Conception of Knowledge.

    ERIC Educational Resources Information Center

    Doll, William E., Jr.

    1981-01-01

    The author discusses major premises of a paper, by Sophie Haroutunian (Educational Theory, v30 n3), that relates Jean Piaget's conception of knowledge to his biological theory of equilibrium. Doll argues that Piaget's theory of equilibration (striving for control over the environment) is not sufficiently appreciated by Haroutunian. (PP)

  17. 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…

  18. 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...

  19. 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. PMID:25116396

  20. 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.

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

    PubMed

    Reddy, Prashant; Lakshmikumaran, Malathi

    2015-10-01

    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. PMID:26101205

  2. The experience of addiction as told by the addicted: incorporating biological understandings into self-story.

    PubMed

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

    2012-12-01

    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

  3. 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"…

  4. 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…

  5. 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

  6. 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

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

    PubMed

    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

  8. 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

  9. 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

  10. 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

  11. 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.

  12. Conscious Knowledge of Learning: Accessing Learning Strategies in a Final Year High School Biology Class. Research Report

    ERIC Educational Resources Information Center

    Conner, Lindsey; Gunstone, Richard

    2004-01-01

    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…

  13. 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

  14. 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

  15. Regulation of the biological functions of osteoblasts and bone formation by Zn-incorporated coating on microrough titanium.

    PubMed

    Shen, Xinkun; Hu, Yan; Xu, Gaoqiang; Chen, Weizhen; Xu, Kui; Ran, Qichun; Ma, Pingping; Zhang, Yarong; Li, Jinghua; Cai, Kaiyong

    2014-09-24

    To improve the biological performance of titanium implant, a series of Zn-incorporated coatings were fabricated on the microrough titanium (Micro-Ti) via sol-gel method by spin-coating technique. The successful fabrication of the coating was verified by combined techniques of scanning electron microscopy, surface profiler, X-ray diffraction, X-ray photoelectron spectroscopy, and water contact angle measurements. The incorporated zinc existed as ZnO, which released Zn ions in a sustained manner. The Zn-incorporated samples (Ti-Zn0.08, Ti-Zn0.16, and Ti-Zn0.24) efficiently inhibited the adhesion of both Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa) bacteria. The in vitro evaluations including cell activity, alkaline phosphatase (ALP), mineralization, osteogenic genes expressions (Runx2, ALP, OPG, Col I, OPN, and OC), and tartrate-resistant acid phosphatase, confirmed that Ti-Zn0.16 sample was the optimal one to regulate the proliferation or differentiation for both osteoblasts and osteoclasts. More importantly, in vivo evaluations including Micro-CT analysis, push-out test, and histological observations verified that Ti-Zn0.16 implants could efficiently promote new bone formation after implantation for 4 and 12 weeks, respectively. The resulting material thus has potential application in orthopedic field. PMID:25148131

  16. BioBIKE: a Web-based, programmable, integrated biological knowledge base.

    PubMed

    Elhai, Jeff; Taton, Arnaud; Massar, J P; Myers, John K; Travers, Mike; Casey, Johnny; Slupesky, Mark; Shrager, Jeff

    2009-07-01

    BioBIKE (biobike.csbc.vcu.edu) is a web-based environment enabling biologists with little programming expertise to combine tools, data, and knowledge in novel and possibly complex ways, as demanded by the biological problem at hand. BioBIKE is composed of three integrated components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Each of the five current BioBIKE instances provides all available information (genomic, metabolic, experimental) appropriate to a given research community. The BioBIKE programming language and graphical programming interface employ familiar operations to help users combine functions and information to conduct biologically meaningful analyses. Many commonly used tools, such as Blast and PHYLIP, are built-in, allowing users to access them within the same interface and to pass results from one to another. Users may also invent their own tools, packaging complex expressions under a single name, which is immediately made accessible through the graphical interface. BioBIKE represents a partial solution to the difficult question of how to enable those with no background in computer programming to work directly and creatively with mass biological information. BioBIKE is distributed under the MIT Open Source license. A description of the underlying language and other technical matters is available at www.Biobike.org. PMID:19433511

  17. Using Biological Knowledge to Uncover the Mystery in the Search for Epistasis in Genome-Wide Association Studies

    PubMed Central

    Ritchie, Marylyn D.

    2011-01-01

    The search for the missing heritability in genome-wide association studies (GWAS) has become an important focus for the human genetics community. One suspected location of these genetic effects is in gene-gene interactions, or epistasis. The computational burden of exploring gene-gene interactions in the wealth of data generated in GWAS, along with small to moderate sample sizes, have led to epistasis being an afterthought, rather than a primary focus of GWAS analyses. In this review, we discuss some potential approaches to filter a GWAS dataset to a smaller, more manageable dataset where searching for epistasis is considerably more feasible. We describe a number of alternative approaches, but primarily focus on the use of prior biological knowledge from databases in the public domain to guide the search for epistasis. The manner in which prior knowledge is incorporated into a GWA study can be many and these data can be extracted from a variety of database sources. We discuss a number of these approaches and propose that a comprehensive approach will likely be most fruitful for searching for epistasis in large-scale genomic studies of the current state-of-the-art and into the future. PMID:21158748

  18. Incorporating spike-rate adaptation into a rate code in mathematical and biological neurons.

    PubMed

    Ralston, Bridget N; Flagg, Lucas Q; Faggin, Eric; Birmingham, John T

    2016-06-01

    For a slowly varying stimulus, the simplest relationship between a neuron's input and output is a rate code, in which the spike rate is a unique function of the stimulus at that instant. In the case of spike-rate adaptation, there is no unique relationship between input and output, because the spike rate at any time depends both on the instantaneous stimulus and on prior spiking (the "history"). To improve the decoding of spike trains produced by neurons that show spike-rate adaptation, we developed a simple scheme that incorporates "history" into a rate code. We utilized this rate-history code successfully to decode spike trains produced by 1) mathematical models of a neuron in which the mechanism for adaptation (IAHP) is specified, and 2) the gastropyloric receptor (GPR2), a stretch-sensitive neuron in the stomatogastric nervous system of the crab Cancer borealis, that exhibits long-lasting adaptation of unknown origin. Moreover, when we modified the spike rate either mathematically in a model system or by applying neuromodulatory agents to the experimental system, we found that changes in the rate-history code could be related to the biophysical mechanisms responsible for altering the spiking. PMID:26888106

  19. Challenges of incorporating gene expression data to predict HCC prognosis in the age of systems biology

    PubMed Central

    Du, Yan; Cao, Guang-Wen

    2012-01-01

    Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. The recurrence of HCC after curative treatments is currently a major hurdle. Identification of subsets of patients with distinct prognosis provides an opportunity to tailor therapeutic approaches as well as to select the patients with specific sub-phenotypes for targeted therapy. Thus, the development of gene expression profiles to improve the prediction of HCC prognosis is important for HCC management. Although several gene signatures have been evaluated for the prediction of HCC prognosis, there is no consensus on the predictive power of these signatures. Using systematic approaches to evaluate these signatures and combine them with clinicopathologic information may provide more accurate prediction of HCC prognosis. Recently, Villanueva et al[13] developed a composite prognostic model incorporating gene expression patterns in both tumor and adjacent tissues to predict HCC recurrence. In this commentary, we summarize the current progress in using gene signatures to predict HCC prognosis, and discuss the importance, existing issues and future research directions in this field. PMID:22912544

  20. 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

  1. Incorporating small molecules or biologics into nanofibers for optimized drug release: A review.

    PubMed

    Sebe, István; Szabó, Péter; Kállai-Szabó, Barnabás; Zelkó, Romána

    2015-10-15

    Over the past several decades, the formulation of novel nanofiber-based drug delivery systems focusing on specific delivery purposes has been investigated worldwide with a continuous level of interest. The unique structure and properties of nanoscale fibrous systems, such as their high specific-area-to-volume ratio and high porosity and the possibility of controlling their crystalline-amorphous phase transitions, make them a desirable formulation pathway to satisfy the needs of recent pharmaceutical development. Fibrous delivery systems can facilitate the accelerated dissolution and increased solubility of small molecules and can also be useful in controlling drug delivery over time (for local or systemic drug administration). In the latter case, the release periods can be tuned over a wide range (from hours to weeks), e.g., by adjusting the fiber diameter and selecting the appropriate polymers. The solubility of the polymer, the fiber diameter and the fiber structure are the primary parameters affecting drug release. In addition to immediate and sustained release, other release profiles, such as biphasic release, can also be achieved. Chemical conjugation and surface functionalization offer further possibilities for the control of drug release. In the case of small molecules, developments focus mostly on overcoming the unfavorable physicochemical nature of the active agents. By contrast, in the preparation of macromolecule-loaded nanofibers, maximizing the biological activity of the macromolecules presents the greatest challenge. The authors' intent is to provide a comprehensive overview of the key parameters of advanced drug delivery systems of this type. PMID:26307263

  2. 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.

  3. 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

  4. 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

  5. Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

    PubMed Central

    von Reumont, Björn M; Meusemann, Karen; Szucsich, Nikolaus U; Dell'Ampio, Emiliano; Gowri-Shankar, Vivek; Bartel, Daniela; Simon, Sabrina; Letsch, Harald O; Stocsits, Roman R; Luan, Yun-xia; Wägele, Johann Wolfgang; Pass, Günther; Hadrys, Heike; Misof, Bernhard

    2009-01-01

    Background Whenever different data sets arrive at conflicting phylogenetic hypotheses, only testable causal explanations of sources of errors in at least one of the data sets allow us to critically choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit rRNAs are among the most popular markers for studies of deep phylogenies. However, some nodes supported by this data are suspected of being artifacts caused by peculiarities of the evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted with conflicting hypotheses which are dependent on data set and method of reconstruction. We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes. Results We analyzed a large set of arthropod sequences, applied new tools for quality control of data prior to tree reconstruction, and increased the biological realism of substitution models. Although the split-decomposition network indicated a high noise content in the data set, our measures were able to both improve the analyses and give causal explanations for some incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not completely disappear. Conclusion Analyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic

  6. 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. PMID:17445881

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    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 science department made use of technology as an integral part of teaching biology. In this study, conducted in one school in the state of New York, in the United States of America, the Students' Attitudes Toward and Knowledge of Technology Questionnaire was administered to nearly 700 high school science students. A principal component and principal factor analysis resulted in new scales from the validation of the instrument that demonstrated high reliabilities. There were statistically significant gender differences in all the scales of the questionnaire in favor of males.

  8. Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

    PubMed Central

    Shafer, Paul; Isganitis, Timothy; Yona, Golan

    2006-01-01

    Background Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. Results We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. Conclusion Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at . PMID:16480496

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

    NASA Astrophysics Data System (ADS)

    Rozenszajn, Ronit; Yarden, Anat

    2014-02-01

    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 program aimed at designing new teaching and learning materials suggested by the teachers themselves. The research presents an enlargement of previous PCK representations by focusing on a detailed representation of two main PCK domains: teaching and learning, including ten PCK components that emerged in the course of data analysis. This representation enabled revealing the unique PCK held by each teacher and to characterize the expansion of the two components of the participating teachers' PCK during the long-term professional development program. Retention of major parts of the expanded PCK a year after termination of the program implies that designing and implementing new teaching and learning materials based on the teachers' experiences, needs, and knowledge in a workshop format accompanied by biology and science education courses might provide a powerful means for PCK expansion. We recommend that designers of professional development programs be aware of the unique PCK held by each teacher in order to promote meaningful professional development of each teacher. Moreover, the PCK representations that were identified in the course of this study enabled clarifying the "orientation toward teaching science" category of PCK which appears to be unclear in current literature.

  10. 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

  11. Improving biomarker list stability by integration of biological knowledge in the learning process

    PubMed Central

    2012-01-01

    Background The identification of robust lists of molecular biomarkers related to a disease is a fundamental step for early diagnosis and treatment. However, methodologies for biomarker discovery using microarray data often provide results with limited overlap. It has been suggested that one reason for these inconsistencies may be that in complex diseases, such as cancer, multiple genes belonging to one or more physiological pathways are associated with the outcomes. Thus, a possible approach to improve list stability is to integrate biological information from genomic databases in the learning process; however, a comprehensive assessment based on different types of biological information is still lacking in the literature. In this work we have compared the effect of using different biological information in the learning process like functional annotations, protein-protein interactions and expression correlation among genes. Results Biological knowledge has been codified by means of gene similarity matrices and expression data linearly transformed in such a way that the more similar two features are, the more closely they are mapped. Two semantic similarity matrices, based on Biological Process and Molecular Function Gene Ontology annotation, and geodesic distance applied on protein-protein interaction networks, are the best performers in improving list stability maintaining almost equal prediction accuracy. Conclusions The performed analysis supports the idea that when some features are strongly correlated to each other, for example because are close in the protein-protein interaction network, then they might have similar importance and are equally relevant for the task at hand. Obtained results can be a starting point for additional experiments on combining similarity matrices in order to obtain even more stable lists of biomarkers. The implementation of the classification algorithm is available at the link: http://www.math.unipd.it/~dasan/biomarkers.html. PMID

  12. How Knowledge of Pathogen Population Biology Informs Management of Septoria Tritici Blotch.

    PubMed

    McDonald, Bruce A; Mundt, Christopher C

    2016-09-01

    Zymoseptoria tritici (previously Mycosphaerella graminicola) causes Septoria tritici blotch (STB) on wheat. The population biology of Z. tritici has been exceptionally well characterized as a result of intensive studies conducted over nearly 30 years. These studies provided important insights into the biology, epidemiology and evolutionary history of Z. tritici that will prove useful for management of STB. The well-documented, rapid adaptation of Z. tritici populations to fungicide applications and deployment of wheat cultivars carrying both major gene and quantitative resistance reflects the high evolutionary potential predicted by the large effective population size, high degree of gene flow and high levels of recombination found in field populations of Z. tritici globally. QST studies that assessed the global diversity for several important quantitative traits confirmed the adaptive potential of field populations and laid the groundwork for quantitative trait loci (QTL) mapping studies. QTL mapping elucidated the genetic architecture of each trait and led to identification of candidate genes affecting fungicide resistance, thermal adaptation, virulence, and host specialization. The insights that emerged through these analyses of Z. tritici population biology can now be used to generate actionable disease management strategies aimed at sustainably reducing losses due to STB. The high evolutionary potential found in field populations of Z. tritici requires deployment of a corresponding dynamically diverse set of control measures that integrate cultural, chemical, biological and resistance breeding strategies. In this review, we describe and prioritize STB control strategies based on current knowledge of Z. tritici population biology and propose a future research agenda oriented toward long-term STB management. PMID:27111799

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

    PubMed Central

    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. PMID:24006399

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

    NASA Astrophysics Data System (ADS)

    Barnett, Ellen; Friedrichsen, Patricia J.

    2015-11-01

    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 strategies used by a secondary biology mentor teacher to support the development of a PST's PCK. The primary data sources were the transcripts of audio-recorded, daily meetings between the mentor and the PST during two curriculum units: DNA/Protein Synthesis and Evolution. The mentor influenced the PST's teaching orientation by repeatedly comparing teacher- and student-centered approaches, asking him to consider how students learn, and asking him to self-assess whether his instruction aligned with his teaching beliefs. The mentor helped the PST develop topic-specific knowledge of instructional strategies by sharing strategies she used previously, modeling critical reflection, and inviting him to critically reflect on his own instructional strategies. Topic-specific knowledge of students' understanding of science was developed by discussing common student misconceptions revealed in students' conversations and by sharing the results of test-item analysis from previous unit tests. The mentor helped develop the PST's topic-specific knowledge of assessment by helping him critically analyze and revise previous examinations to better align with the current curriculum units. Topic-specific knowledge of curricula was developed by jointly grappling with decisions about concept sequencing within units. The study includes implications for research, science teacher education, and professional development for mentors.

  15. [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

  16. 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

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

    PubMed

    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

  18. 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

  19. Enhanced Biological Functions of Human Mesenchymal Stem-Cell Aggregates Incorporating E-Cadherin-Modified PLGA Microparticles.

    PubMed

    Zhang, Yan; Mao, Hongli; Gao, Chao; Li, Suhua; Shuai, Qizhi; Xu, Jianbin; Xu, Ke; Cao, Lei; Lang, Ren; Gu, Zhongwei; Akaike, Toshihiro; Yang, Jun

    2016-08-01

    Mesenchymal stem cells (MSCs) have emerged as a promising source of multipotent cells for various cell-based therapies due to their unique properties, and formation of 3D MSC aggregates has been explored as a potential strategy to enhance therapeutic efficacy. In this study, poly(lactic-co-glycolic acid) (PLGA) microparticles modified with human E-cadherin fusion protein (hE-cad-PLGA microparticles) have been fabricated and integrated with human MSCs to form 3D cell aggregates. The results show that, compared with the plain PLGA, the hE-cad-PLGA microparticles distribute within the aggregates more evenly and further result in a more significant improvement of cellular proliferation and secretion of a series of bioactive factors due to the synergistic effects from the bioactive E-cadherin fragments and the PLGA microparticles. Meanwhile, the hE-cad-PLGA microparticles incorporated in the aggregates upregulate the phosphorylation of epidermal growth factor receptors and activate the AKT and ERK1/2 signaling pathways in the MSCs. Additionally, the E-cadherin/β-catenin cellular membrane complex in the MSCs is markedly stimulated by the hE-cad-PLGA microparticles. Therefore, engineering 3D cell aggregates with hE-cad-PLGA microparticles can be a promising method for ex vivo multipotent stem-cell expansion with enhanced biological functions and may offer a novel route to expand multipotent stem-cell-based clinical applications. PMID:27245478

  20. 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.

  1. 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…

  2. 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

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

    PubMed

    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

  4. InCoB2012 Conference: from biological data to knowledge to technological breakthroughs

    PubMed Central

    2012-01-01

    Ten years ago when Asia-Pacific Bioinformatics Network held the first International Conference on Bioinformatics (InCoB) in Bangkok its theme was North-South Networking. At that time InCoB aimed to provide biologists and bioinformatics researchers in the Asia-Pacific region a forum to meet, interact with, and disseminate knowledge about the burgeoning field of bioinformatics. Meanwhile InCoB has evolved into a major regional bioinformatics conference that attracts not only talented and established scientists from the region but increasingly also from East Asia, North America and Europe. Since 2006 InCoB yielded 114 articles in BMC Bioinformatics supplement issues that have been cited nearly 1,000 times to date. In part, these developments reflect the success of bioinformatics education and continuous efforts to integrate and utilize bioinformatics in biotechnology and biosciences in the Asia-Pacific region. A cross-section of research leading from biological data to knowledge and to technological applications, the InCoB2012 theme, is introduced in this editorial. Other highlights included sessions organized by the Pan-Asian Pacific Genome Initiative and a Machine Learning in Immunology competition. InCoB2013 is scheduled for September 18-21, 2013 at Suzhou, China. PMID:23281929

  5. 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)

  6. 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…

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

    PubMed

    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

  8. 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.

  9. 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. PMID:25651801

  10. 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.

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

    PubMed

    Thiele, Herbert; Glandorf, Jörg; Hufnagel, Peter

    2010-01-01

    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. PMID:20508300

  12. 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. PMID:24252487

  13. 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…

  14. 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. PMID:21879517

  15. 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…

  16. Guidelines for incorporating scientific knowledge and practice on rare diseases into higher education: neuronal ceroid lipofuscinoses as a model disorder.

    PubMed

    Cismondi, Inés Adriana; Kohan, Romina; Adams, Heather; Bond, Mike; Brown, Rachel; Cooper, Jonathan D; de Hidalgo, Perla K; Holthaus, Sophia-Martha Kleine; Mole, Sara E; Mugnaini, Julia; de Ramirez, Ana María Oller; Pesaola, Favio; Rautenberg, Gisela; Platt, Frances M; Noher de Halac, Inés

    2015-10-01

    This article addresses the educational issues associated with rare diseases (RD) and in particular the Neuronal Ceroid Lipofuscinoses (NCLs, or CLN diseases) in the curricula of Health Sciences and Professional's Training Programs. Our aim is to develop guidelines for improving scientific knowledge and practice in higher education and continuous learning programs. Rare diseases (RD) are collectively common in the general population with 1 in 17 people affected by a RD in their lifetime. Inherited defects in genes involved in metabolism are the commonest group of RD with over 8000 known inborn errors of metabolism. The majority of these diseases are neurodegenerative including the NCLs. Any professional training program on NCL must take into account the medical, social and economic burdens related to RDs. To address these challenges and find solutions to them it is necessary that individuals in the government and administrative authorities, academia, teaching hospitals and medical schools, the pharmaceutical industry, investment community and patient advocacy groups all work together to achieve these goals. The logistical issues of including RD lectures in university curricula and in continuing medical education should reflect its complex nature. To evaluate the state of education in the RD field, a summary should be periodically up dated in order to assess the progress achieved in each country that signed up to the international conventions addressing RD issues in society. It is anticipated that auditing current practice will lead to higher standards and provide a framework for those educators involved in establishing RD teaching programs world-wide. PMID:26117801

  17. 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

  18. Incorporating Sedimentological Observations, Hydrogeophysics and conceptual Knowledge to Constrain 3D Numerical Heterogeneity Models of Coarse Alluvial Systems

    NASA Astrophysics Data System (ADS)

    Huber, E.; Huggenberger, P.

    2012-12-01

    Accurate predictions on groundwater flow and transport behavior within fluvial and glaciofluvial sediments, but also interaction with surface water bodies, rely on knowledge of distributed aquifer properties. The complexity of the depositional and erosional processes in fluvial systems leads to highly heterogeneous distributions of hydrogeological parameters. The system dynamics, such as aggradation rates and channel mobility of alluvial systems; its influence on the preservation potential of the key depositional elements in the geological record; and its influence on the heterogeneity scales and the relevance for groundwater hydraulics is topic of the presentation. The aims of our work are to find a relation between surface morphological structures and the sedimentary structures in vertical profiles (i.e. gravel pits or GPR sections) and to derive rules for the interpretation of horizontal time-slices from 3D GPR data. Based on these data we set-up conceptual models of the structures of coarse alluvial systems at different scales which can be tested by stochastic methods. Relevant depositional elements and a hierarchy or genetic relationship of such elements will be defined based on the knowledge of depositional processes in alluvial systems inferred from: field observations after major flood events; 2D and 3D GPR data; and from existing data derived from laboratory flumes. Extensive geophysical field experiments within the Tagliamento alluvial system gave new insights to the sedimentary structures developing at high flows. Owing to the fact that rivers often destroy at least part of their bed during or shortly after large floods and subsequently rebuild, it is not easy to establish a simple relationship between surface morphology and the sedimentary structures found in vertical sections of many alluvial outcrops. According to these findings we suppose that surface or near-surface structures will not catch the essence of heterogeneity of alluvial aquifers

  19. 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. PMID:23586746

  20. The presentation and management of victims of chemical and biological agents: a survey of knowledge of UK clinicians.

    PubMed

    Wimbush, Stephen; Davies, Gareth; Lockey, David

    2003-09-01

    A survey was conducted among acute specialty clinicians in four centres in the UK to determine their levels of knowledge of the presentation and subsequent management of victims following deliberate release of chemical or biological agents. This revealed significant gaps in knowledge and training. Of the 102 respondents, more than half did not understand the decontamination process. More than a third were unsure of the presenting features of nerve agent release. Only a minority knew the recommended treatment and only one in five have participated in relevant exercises. PMID:12969606

  1. 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. PMID:8932577

  2. 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…

  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. 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

  5. On the Growth of Scientific Knowledge: Yeast Biology as a Case Study

    PubMed Central

    He, Xionglei; Zhang, Jianzhi

    2009-01-01

    The tempo and mode of human knowledge expansion is an enduring yet poorly understood topic. Through a temporal network analysis of three decades of discoveries of protein interactions and genetic interactions in baker's yeast, we show that the growth of scientific knowledge is exponential over time and that important subjects tend to be studied earlier. However, expansions of different domains of knowledge are highly heterogeneous and episodic such that the temporal turnover of knowledge hubs is much greater than expected by chance. Familiar subjects are preferentially studied over new subjects, leading to a reduced pace of innovation. While research is increasingly done in teams, the number of discoveries per researcher is greater in smaller teams. These findings reveal collective human behaviors in scientific research and help design better strategies in future knowledge exploration. PMID:19300476

  6. 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…

  7. 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...

  8. 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…

  9. Surface characterization and biological evaluation of silver-incorporated DLC coatings fabricated by hybrid RF PACVD/MS method.

    PubMed

    Bociąga, Dorota; Jakubowski, Witold; Komorowski, Piotr; Sobczyk-Guzenda, Anna; Jędrzejczak, Anna; Batory, Damian; Olejnik, Anna

    2016-06-01

    Since the biological response of the body towards an implanted material is mainly governed by its surface properties, biomaterials are improved by various kinds of coatings. Their role is to provide good mechanical and biological characteristics, and exclude some disadvantages like post-implantation infections. This phenomenon may be reduced by introduction of silver as an antibacterial agent. This study evaluates the Ag-DLC films synthesized by the hybrid RF PACVD/MS method according to the patent number PL401955-A1 worked out inter alia by the authors. Such tests as XPS, SEM, EDS, AFM, FTIR, Raman and ICP-TOF-MS were used to determine surface properties of the coatings. The obtained results were correlated with the biological response estimated on the basis of cells viability assay (osteoblast cells line Saos-2) and bacterial colonization test (Escherichia coli strain DH5α). Results showed that the hybrid RF PACVD/MS method allows one to get tight coating preventing the diffusion of harmful elements from the metallic substrate. Ag concentration increases with the growing power density, it occurs in metallic state, does not create chemical bonds and is evenly dispersed within the DLC matrix in the form of nanoscale silver clusters. Increasing silver content above 2at.% improves bactericidal properties, but decreases cell viability. PMID:27040240

  10. An investigation of the relationship between having recent knowledge in basic biology and student success in Anatomy and Physiology I

    NASA Astrophysics Data System (ADS)

    Taylor, Edward T.

    Allied Health Programs generally require that students complete coursework in Human Anatomy and Physiology I and II as part of their Pre-Allied Health curriculum. Human Anatomy and Physiology I generally has as a prerequisite some coursework in basic biology. Basic biology as a prerequisite should provide students with the foundation of knowledge in the basic biological principles and processes that will prepare them for the material presented in a Human Anatomy and Physiology I course and the Allied Health Program. The principle question that prompted this study was, Do students need coursework in basic biology to be successful in Anatomy and Physiology I? The purpose of this study was to determine if there was a difference in the exam average obtained in Biology 202, Human Anatomy and Physiology I, for those students who have had, within the previous three years, a foundation course in basic biology as compared to those students who have not, within the previous three years, had a foundation course in basic biology. The current study analyzed data obtained on 642 students who were enrolled in Biology 202, Anatomy and Physiology I, during the Fall semester of 2000 to the Spring semester of 2003 at Wor-Wic Community College. Statistical techniques including an ANOVA, Pearson Product Moment Correlation, and a Multiple Regression Analysis were conducted to reveal any relationships in the data. The dependent variable was the exam average obtained in the independent variables included the time period since the student had taken a basic biology course, sex, age, and college GPA. The results of the ANOVA indicated that there was no relationship between the exam average between current and non-current students, where alpha = 0.05 and p = 0.783. There was statistically significance for GPA, where p = 0 .000. There was also statistically significant interactions between last biology course and GPA, p = 0.05, last biology course, sex, and GPA, p = 0.002. The Pearson Product

  11. A novel nano hydroxyapatite-incorporated Ni-P coating as an effective inter layer for biological applications.

    PubMed

    Shibli, S M A; Jayalekshmi, A C

    2009-03-01

    Hydroxyapatite (HA) coatings are normally made directly on orthopaedic implants and they possess many demerits such as cracks, irregular phase composition and poor adhesion. The present study had a novel approach of providing a nano-HA and phosphorous-rich electroless nickel (EN) coating as an interlayer on stainless steel (SS) prior to electrodeposition of pure HA coating. The interlayer had the merits of having incorporated with nano HA with rich phosphorous content. The outermost HA coating had excellent adherence and it was found to be free from any defects since it was formed only on the interlayer and not on the direct substrate. The overall coating system revealed high bioactivity when immersed in simulated body fluid (SBF). The present study also highlights the scope of using cost effective SS as the implant substrate instead of titanium as against the current trend of substrate selection. PMID:18987947

  12. Synthesis of organometallic-based biologically active compounds: In vitro antibacterial, antifungal and cytotoxic properties of some sulfonamide incorporated ferrocences.

    PubMed

    Chohan, Zahid H

    2009-02-01

    Sulfonamides incorporated ferrocene (SIF) have been synthesized by the condensation reaction of sulfonamides (sulfanilamide, sulfathiazole or sulfamethaxazole) with 1,1'-diacetylferrocene. The synthesized compounds (SIF(1)-SIF(4)) have been characterized by their physical, spectral and analytical properties and have been screened for their in vitro antibacterial properties against pathogenic bacterial strains e.g., Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis Staphylococcus aureus and Salmonella typhi and for antifungal activity against Trichophyton longifusus, Candida albicans, Aspergillus flavus, Microsporum canis, Fusarium solani and Candida glaberata using Agar-well diffusion method. Most of the compounds showed good antibacterial activity whereas, all the compounds exhibited significant antifungal activity. Brine shrimp bioassay was also carried out for in vitro cytotoxic properties against Artemia salina. PMID:18608785

  13. 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.

  14. Knowledge and Awareness Concerning Chemical and Biological Terrorism: Continuing Education Implications.

    ERIC Educational Resources Information Center

    Rose, Molly A.; Larrimore, Karen L.

    2002-01-01

    Nurses, physicians, and nursing and medical students (n=291) were surveyed about their awareness of chemical and biological terrorism. Infection control personnel and nurse educators (n=24) were surveyed about terrorism preparation. Fewer than one-quarter of questions were answered correctly, and only about 23% reported confidence in the ability…

  15. Biology and Geology Teachers' Domain-Specific Pedagogical Content Knowledge of Evolution.

    ERIC Educational Resources Information Center

    Veal, William R.; Kubasko, Dennis S., Jr.

    2003-01-01

    Interviews eight students enrolled in a secondary-science curriculum class and four experienced high school biology and geology teachers to determine reasons for disciplinary variance in the teaching of evolution. Finds variance imbedded in inherent differences in content and methodology of the two scientific disciplines. (Contains 27 references.)…

  16. 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…

  17. REFINING KNOWLEDGE OF HYPOXIA DYNAMICS: THE INTERACTION OF PHYSICS AND BIOLOGY MX964240

    EPA Science Inventory

    The specific purpose of this proposal is to expand the coupled biological/physical data acquisition by instrumenting a moored platform in the Northern Gulf of Mexico close to the Mississippi River delta off the Barataria Bay estuary. Real-time monitors for dissolved oxygen, chlo...

  18. 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…

  19. 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…

  20. 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…

  1. 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…

  2. 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.

  3. 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.

  4. Radioprotection by DMSO against the biological effects of incorporated radionuclides in vivo--Comparison with other radioprotectors and evidence for indirect action of Auger electrons.

    PubMed

    Goddu, S M; Narra, V R; Harapanhalli, R S; Howell, R W; Rao, D V

    1996-01-01

    Dimethyl sulfoxide (DMSO) was studied for its capacity to protect against the biological effects of chronic irradiation by incorporated radionuclides. Spermatogenesis in mice was used as experimental model and spermatogonial cell survival was the biological endpoint. DMSO was injected intratesticularly 4 h prior to a similar injection of the radiochemical and the spermhead survival determined. Iodine-125 was localized in either the cytoplasm (H125IPDM) or in the DNA (125IUdR) of the testicular cells. Protection was observed against the high-LET type effects of DNA-bound 125I as well as the low-LET effects of cytoplasmically localized 125I with dose modification factors (DMF) of 3.1+/-1.0 and 4.4+/-1.0 respectively. No protection (DMF = 1.1+/-0.1) was observed against the effects of high-LET 5.3 MeV alpha particles of 210Po. The present findings provide supporting evidence that the mechanism responsible for the extreme biological damage caused by DNA-bound Auger emitters is largely radical mediated and therefore indirect in nature. PMID:9004770

  5. 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.

  6. The influence of pedagogical content knowledge (PCK) for teaching macroevolution on student outcomes in a general education biology course

    NASA Astrophysics Data System (ADS)

    Walter, Emily Marie

    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 components on students' knowledge of macroevolution and evolution acceptance. The study used a mixed methods approach to understand how PCK influences student outcomes, and is one of the first to examine the influence of PCK on student outcomes at the post-secondary level. In addition, the study is one of few to document a significant relationship between knowledge of evolution and evolution acceptance, including how instruction influenced these outcomes. The case selected for study was a general education biology class: 270 students and their instructor. To examine the nature and sources of the instructor's PCK for teaching macroevolution, the course was observed in its entirety, the instructor was interviewed before, during, and after the evolution unit, and artifacts were collected from the evolution unit. Interview and observational protocols for the instructor were developed based on the Magnussson, Kracjik, & Borko (1999) model of PCK. The instructor was found to have deep knowledge of learners, and this knowledge in turn informed the other components of her PCK. Her knowledge of learners was built through reflecting on student exam outcomes, referencing the pedagogical literature, interactions with students, and discussions with colleagues. These findings have implications for faculty professional development. The influence of the course was examined both quantitatively and qualitatively. Students were surveyed using the Measure of Understanding of Macroevolution (Nadelson & Southerland, 2010a) the Measure of Acceptance of the Theory of Evolution (Rutledge & Warden, 1999, 2007). From pre- to post-test, students became

  7. BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge

    PubMed Central

    2013-01-01

    Background With the recent decreasing cost of genome sequence data, there has been increasing interest in rare variants and methods to detect their association to disease. We developed BioBin, a flexible collapsing method inspired by biological knowledge that can be used to automate the binning of low frequency variants for association testing. We also built the Library of Knowledge Integration (LOKI), a repository of data assembled from public databases, which contains resources such as: dbSNP and gene Entrez database information from the National Center for Biotechnology (NCBI), pathway information from Gene Ontology (GO), Protein families database (Pfam), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, NetPath - signal transduction pathways, Open Regulatory Annotation Database (ORegAnno), Biological General Repository for Interaction Datasets (BioGrid), Pharmacogenomics Knowledge Base (PharmGKB), Molecular INTeraction database (MINT), and evolutionary conserved regions (ECRs) from UCSC Genome Browser. The novelty of BioBin is access to comprehensive knowledge-guided multi-level binning. For example, bin boundaries can be formed using genomic locations from: functional regions, evolutionary conserved regions, genes, and/or pathways. Methods We tested BioBin using simulated data and 1000 Genomes Project low coverage data to test our method with simulated causative variants and a pairwise comparison of rare variant (MAF < 0.03) burden differences between Yoruba individuals (YRI) and individuals of European descent (CEU). Lastly, we analyzed the NHLBI GO Exome Sequencing Project Kabuki dataset, a congenital disorder affecting multiple organs and often intellectual disability, contrasted with Complete Genomics data as controls. Results The results from our simulation studies indicate type I error rate is controlled, however, power falls quickly for small sample sizes using variants with modest effect sizes. Using BioBin, we were able to find simulated

  8. 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. PMID:9213630

  9. 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

  10. Intertwining Threshold Settings, Biological Data and Database Knowledge to Optimize the Selection of Differentially Expressed Genes from Microarray

    PubMed Central

    Chuchana, Paul; Holzmuller, Philippe; Vezilier, Frederic; Berthier, David; Chantal, Isabelle; Severac, Dany; Lemesre, Jean Loup; Cuny, Gerard; Nirdé, Philippe; Bucheton, Bruno

    2010-01-01

    Background Many tools used to analyze microarrays in different conditions have been described. However, the integration of deregulated genes within coherent metabolic pathways is lacking. Currently no objective selection criterion based on biological functions exists to determine a threshold demonstrating that a gene is indeed differentially expressed. Methodology/Principal Findings To improve transcriptomic analysis of microarrays, we propose a new statistical approach that takes into account biological parameters. We present an iterative method to optimise the selection of differentially expressed genes in two experimental conditions. The stringency level of gene selection was associated simultaneously with the p-value of expression variation and the occurrence rate parameter associated with the percentage of donors whose transcriptomic profile is similar. Our method intertwines stringency level settings, biological data and a knowledge database to highlight molecular interactions using networks and pathways. Analysis performed during iterations helped us to select the optimal threshold required for the most pertinent selection of differentially expressed genes. Conclusions/Significance We have applied this approach to the well documented mechanism of human macrophage response to lipopolysaccharide stimulation. We thus verified that our method was able to determine with the highest degree of accuracy the best threshold for selecting genes that are truly differentially expressed. PMID:20976008

  11. 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. PMID:26163315

  12. 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. PMID:24688691

  13. 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

  14. Does the transition to an active-learning environment for the introductory course reduce students' overall knowledge of the various disciplines in biology?

    PubMed

    Simurda, Maryanne C

    2012-01-01

    As biology education is being redesigned toward an interdisciplinary focus and as pedagogical trends move toward active-learning strategies and investigative experiences, a restructuring of the course content for the Introductory Biology course is necessary. The introductory course in biology has typically been a survey of all the biosciences. If the total number of topics covered is reduced, is the students' overall knowledge of biology also reduced? Our introductory course has been substantially modified away from surveying the biological sciences and toward providing a deep understanding of a particular biological topic, as well as focusing on developing students' analytical and communication skills. Because of this shift to a topic-driven approach for the introductory course, we were interested in assessing our graduating students' overall knowledge of the various biological disciplines. Using the Major Field Test - Biology (Educational Testing Service (ETS), Princeton, NJ), we compared the test performance of graduating students who had a traditional lecture-based introductory course to those who had a topic-driven active-learning introductory course. Our results suggest that eliminating the traditional survey of biology and, instead, focusing on quantitative and writing skills at the introductory level do not affect our graduating students' overall breadth of knowledge of the various biosciences. PMID:23653776

  15. Gelatin-apatite bone mimetic co-precipitates incorporated within biopolymer matrix to improve mechanical and biological properties useful for hard tissue repair.

    PubMed

    Won, Jong-Eun; El-Fiqi, Ahmed; Jegal, Seung-Hwan; Han, Cheol-Min; Lee, Eun-Jung; Knowles, Jonathan C; Kim, Hae-Won

    2014-04-01

    Synthetic biopolymers are commonly used for the repair and regeneration of damaged tissues. Specifically targeting bone, the composite approach of utilizing inorganic components is considered promising in terms of improving mechanical and biological properties. We developed gelatin-apatite co-precipitates which mimic the native bone matrix composition within poly(lactide-co-caprolactone) (PLCL). Ionic reaction of calcium and phosphate with gelatin molecules enabled the co-precipitate formation of gelatin-apatite nanocrystals at varying ratios. The gelatin-apatite precipitates formed were carbonated apatite in nature, and were homogeneously distributed within the gelatin matrix. The incorporation of gelatin-apatite significantly improved the mechanical properties, including tensile strength, elastic modulus and elongation at break, and the improvement was more pronounced as the apatite content increased. Of note, the tensile strength increased to as high as 45 MPa (a four-fold increase vs. PLCL), the elastic modulus was increased up to 1500 MPa (a five-fold increase vs. PLCL), and the elongation rate was ~240% (twice vs. PLCL). These results support the strengthening role of the gelatin-apatite precipitates within PLCL. The gelatin-apatite addition considerably enhanced the water affinity and the acellular mineral-forming ability in vitro in simulated body fluid; moreover, it stimulated cell proliferation and osteogenic differentiation. Taken together, the GAp-PLCL nanocomposite composition is considered to have excellent mechanical and biological properties, which hold great potential for use as bone regenerative matrices. PMID:23985536

  16. 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.

  17. Biological variation in musculoskeletal injuries: current knowledge, future research and practical implications.

    PubMed

    Collins, Malcolm; September, Alison V; Posthumus, Michael

    2015-12-01

    Evidence from familial and genetic association studies have reported that DNA sequence variants play an important role, together with non-genetic factors, in the aetiology of both exercise-associated and occupational-associated acute and chronic musculoskeletal soft tissue injuries. The associated variants, which have been identified to date, may contribute to the interindividual variation in the structure and, by implication, mechanical properties of the collagen fibril and surrounding matrix within musculoskeletal soft tissues, as well as their response to mechanical loading and other stimuli. Future work should focus on the establishment of multidisciplinary international consortia for the identification of biologically relevant variants involved in modulating injury risk. These consortia will improve the limitations of the published hypothesis-driven genetic association studies, since they will allow resources to be pooled in recruiting large well-characterised cohorts required for whole-genome screening. Finally, clinicians and coaches need to be aware that many direct-to-consumer companies are currently marketing genetic tests directly to athletes without it being requested by an appropriately qualified healthcare professional, and without interpretation alongside other clinical indicators or lifestyle factors. These specific genetic tests are premature and are not necessarily required to evaluate susceptibility to musculoskeletal soft tissue injury. Current practice should rather consider susceptibility through known risk factors such as a positive family history of a specific injury, a history of other tendon and/or ligament injuries and participation in activities associated with the specific musculoskeletal injuries. Potential susceptible athletes may then be individually managed to reduce their risk profile. PMID:26504180

  18. 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

  19. TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics.

    PubMed

    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

  20. The Use of a Knowledge Survey as an Indicator of Student Learning in an Introductory Biology Course

    PubMed Central

    2005-01-01

    A knowledge survey (KS) is a series of content-based questions sequenced in order of presentation during a course. Students do not answer the questions; rather, they rank their confidence in their ability to answer each question. A 304-question KS was designed and implemented for a multisection, multi-instructor introductory biology course to determine whether this tool could be used to assess student learning. The KS was administered during the first 2 wk and the last 2 wk of the semester online via WebCT. Results were scored using one point for each “not confident” response (level 1), two points for each “possibly confident” response (level 2), and three points for each “confident” response (level 3). We found that scores increased significantly between the pre- and post-KS, indicating that student confidence in their knowledge of the course material increased over the semester. However, the correlation between student confidence and final grades was negligible or low, and chi-square tests show that KS scores and matched exam questions were not significantly related. We conclude that under the conditions implemented in our study, the KS does not reliably measure student learning as measured by final grades or exam questions. PMID:16341258

  1. 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.…

  2. 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

  3. Low Frequency Variants, Collapsed Based on Biological Knowledge, Uncover Complexity of Population Stratification in 1000 Genomes Project Data

    PubMed Central

    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. PMID:24385916

  4. 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. PMID:25571605

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

    ERIC Educational Resources Information Center

    Nehm, Ross H.; Schonfeld, Irvin Sam

    2007-01-01

    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…

  6. You can exercise your way out of HIV and other stories: The role of biological knowledge in adolescents' evaluation of myths

    NASA Astrophysics Data System (ADS)

    Keselman, Alla; Kaufman, David R.; Patel, Vimla L.

    2004-07-01

    A primary objective for science education is to impart robust knowledge that has applicability to real-world problems. This article presents research investigating the relationship between adolescents' conceptual understanding of the biological basis of HIV and critical reasoning. Middle and high school students were interviewed about their understanding of HIV and were subsequently asked to evaluate scenarios that contained myths about HIV. On the basis of their responses to the interview questions, students' understanding of HIV was categorized into three models, naïve, intermediate, and advanced. The results indicate that knowledge mediated students' responses in specific ways. Students at different levels of HIV knowledge reasoned in qualitatively different ways about the myths. A significant relationship was found between students' understanding of HIV biology and the level of biological reasoning. We found that students who employed cellular-level biological reasoning were more likely to reject the myths than students who employed just system-level reasoning or nonspecific biological reasoning. The findings emphasize the importance of conceptual understanding in the critical evaluation of information that may serve as a basis for making decisions about HIV. We conclude with discussing the implications of the findings for science and health education.

  7. 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

  8. 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…

  9. 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…

  10. 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.

  11. 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…

  12. 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…

  13. 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…

  14. 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.

  15. 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

  16. 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

  17. Use of antimicrobial films and edible coatings incorporating chemical and biological preservatives to control growth of Listeria monocytogenes on cold smoked salmon.

    PubMed

    Neetoo, Hudaa; 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/cm(2) (films) and 2.9 log CFU/cm(2) (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/cm(2), 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

  18. 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

  19. Preservice Biology Teachers' Knowledge Structures as a Function of Professional Teacher Education: A Year-Long Assessment.

    ERIC Educational Resources Information Center

    Gess-Newsome, Julie; Lederman, Norman G.

    1993-01-01

    Reports a study of 10 preservice biology teachers' subject matter structure (SMS). Using qualitative methods, the researchers sought to discover the nature and source of the SMS, the stability, and the relationship to the act of teaching. Among the conclusions are that these preservice teachers do not appear cognizant of their SMSs and that the…

  20. 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,…

  1. 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…

  2. 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…

  3. Validation of a Paper-and-Pencil Test Instrument Measuring Biology Teachers' Pedagogical Content Knowledge by Using Think-Aloud

    ERIC Educational Resources Information Center

    Jüttner, Melanie; Neuhaus, Birgit Jana

    2013-01-01

    The topic of "teacher professionalism" is one of the most crucial ones in quality education research. It has a potential to generate results that could inform and hence enhance the practice in classrooms. Thus, research in this field needs reliable instruments to measure the professional knowledge of our teachers to be able to generate…

  4. Testing a model of science process skills acquisition: An interaction with parents' education, preferred language, gender, science attitude, cognitive development, academic ability, and biology knowledge

    NASA Astrophysics Data System (ADS)

    Germann, Paul J.

    Path analysis techniques were used to test a hypothesized structural model of direct and indirect causal effects of student variables on science process skills. The model was tested twice using data collected at the beginning and end of the school year from 67 9th- and 10th-grade biology students who lived in a rural Franco-American community in New England. Each student variable was found to have significant effects, accounting for approximately 80% of the variance in science process skills achievement. Academic ability, biology knowledge, and language preference had significant direct effects. There were significant mediated effects by cognitive development, parents' education, and attitude toward science in school. The variables of cognitive development and academic ability had the greatest total effects on science process skills. Implications for practitioners and researchers are discussed.

  5. 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

  6. Critical review of the current knowledge of the biology of the American woodcock and its management on the breeding grounds

    USGS Publications Warehouse

    Sepik, G.F.; McAuley, D.G.; Longcore, J.R.

    1993-01-01

    We critiqued previous work on the biology and management of the American woodcock (Scolopax minor) on the breeding grounds. We determined that little is known about habitat variables and weather extremes that may limit the population. Most investigators who attempted to define habitat requirements of the woodcock used inadequate sample sizes, limited the duration of their studies, did not account for effects of weather, or failed to adequately measure habitat variables. Furthermore, the effects of hunting on local or regional populations has never been adequately studied. We concluded that obtaining data to understand the biology of the woodcock and the effects of hunting is essential before managers can reverse the long-term decline of woodcock numbers.

  7. 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.

  8. 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

  9. 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. PMID:20810966

  10. Synthesis, biological activity and dyeing performance of some novel azo disperse dyes incorporating pyrazolo[1,5-a]pyrimidines for dyeing of polyester fabrics

    NASA Astrophysics Data System (ADS)

    Sayed, Ahmed Z.; Aboul-Fetouh, Mahmoud S.; Nassar, Hesham S.

    2012-02-01

    Several novel pyrazolopyrimidine azo compounds were achieved from diazotization of 4-aminoacetanilide and coupling with malononitrile and then refluxed with hydrazine hydrate to furnish 3,5-diamino-4-(4-acetamidophenylazo)-1H-pyrazole. The later compound was diazotized and coupled with substituted α-cyanocinnamate, α-cyanocinnamonitrile, 2-cyano-3-ethoxyacrylic acid ethyl ester, chalcones and ethylacetoacetate to produce novel dyestuffs. Structures of the dyes were fully characterized by using FT-IR, 1H NMR, mass spectroscopy and elemental analysis. The dyes were applied to polyester fiber, affording satisfactory results and showed biological activity towards various microorganisms.

  11. 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. PMID:26125941

  12. 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

  13. 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. PMID:25293538

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

    USGS Publications Warehouse

    Middendorf, G.; Reynolds, R.

    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.

  15. 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

  16. 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

  17. 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. PMID:26663505

  18. 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. PMID:26001286

  19. 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. PMID:24312478

  20. 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

  1. On Crowd-verification of Biological Networks.

    PubMed

    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

  2. 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

  3. Molecular and cellular characterization of the biological effects of ruthenium(II) complexes incorporating 2-pyridyl-2-pyrimidine-4-carboxylic acid.

    PubMed

    Pierroz, Vanessa; Joshi, Tanmaya; Leonidova, Anna; Mari, Cristina; Schur, Julia; Ott, Ingo; Spiccia, Leone; Ferrari, Stefano; Gasser, Gilles

    2012-12-19

    A great majority of the Ru complexes currently studied in anticancer research exert their antiproliferative activity, at least partially, through ligand exchange. In recent years, however, coordinatively saturated and substitutionally inert polypyridyl Ru(II) compounds have emerged as potential anticancer drug candidates. In this work, we present the synthesis and detailed characterization of two novel inert Ru(II) complexes, namely, [Ru(bipy)(2)(Cpp-NH-Hex-COOH)](2+) (2) and [Ru(dppz)(2)(CppH)](2+) (3) (bipy = 2,2'-bipyridine; CppH = 2-(2'-pyridyl)pyrimidine-4-carboxylic acid; Cpp-NH-Hex-COOH = 6-(2-(pyridin-2-yl)pyrimidine-4-carboxamido)hexanoic acid; dppz = dipyrido[3,2-a:2',3'-c]phenazine). 3 is of particular interest as it was found to have IC(50) values comparable to cisplatin, a benchmark standard in the field, on three cancer cell lines and a better activity on one cisplatin-resistant cell line than cisplatin itself. The mechanism of action of 3 was then investigated in detail and it could be demonstrated that, although 3 binds to calf-thymus DNA by intercalation, the biological effects that it induces did not involve a nuclear DNA related mode of action. On the contrary, confocal microscopy colocalization studies in HeLa cells showed that 3 specifically targeted mitochondria. This was further correlated by ruthenium quantification using High-resolution atomic absorption spectrometry. Furthermore, as determined by two independent assays, 3 induced apoptosis at a relatively late stage of treatment. The generation of reactive oxygen species could be excluded as the cause of the observed cytotoxicity. It was demonstrated that the mitochondrial membrane potential in HeLa was impaired by 3 as early as 2 h after its introduction and even more with increasing time. PMID:23181418

  4. INPPO2014, First INPPO World Congress on "Plant Proteomics: Methodology to Biology"-A global platform for involving, gathering and disseminating knowledge.

    PubMed

    Lüthje, Sabine; Renaut, Jenny; Job, Dominique; Hajduch, Martin; Carpentier, Sébastien; Sarkar, Abhijit; Agrawal, Raj; Dunn, Michael J; Rakwal, Randeep; Agrawal, Ganesh Kumar

    2015-05-01

    The International Plant Proteomics Organization (INPPO) is a global platform of the plant proteomics community or, more generally, the scientific community that uses proteomics to address plant biology. Organizing an international conference is one of its initiatives to promote plant proteomics by involving and gathering scientists/researchers/students and by disseminating the acquired knowledge. In this fourth INPPO Highlights, the first INPPO World Congress 2014 (INPPO2014) is described and discussed. The INPPO2014 was held at the University of Hamburg (Germany) with the title "Plant Proteomics: Methodology to Biology" under the leadership of Sabine Lüthje (Germany). Participants (around 150) from 38 nations attended this congress covering all continents. The four-day scientific program comprised 52 lectures and 61 poster presentations in a highly professional and friendly atmosphere on mass spectrometry and gel-based proteomics. Two round-table open discussions deliberated on plant proteomics, its associated international organizations/initiatives and future INPPO perspectives. The Second INPPO World Congress 2016 (INPPO2016) "The Quest for Tolerant Varieties-Phenotyping at Plant and Cellular Level" is planned to be organized in Bratislava (Slovakia) under the leadership of Martin Hajduch (Slovak Republic) and Sébastien Carpentier (Belgium) and cosponsored by the COST action FA1306. PMID:25865070

  5. A Community College Instructor's Reflective Journey Toward Developing Pedagogical Content Knowledge for Nature of Science in a Non-majors Undergraduate Biology Course

    NASA Astrophysics Data System (ADS)

    Krajewski, Sarah J.; Schwartz, Renee

    2014-08-01

    Research supports an explicit-reflective approach to teaching about nature of science (NOS), but little is reported on teachers' journeys as they attempt to integrate NOS into everyday lessons. This participatory action research paper reports the challenges and successes encountered by an in-service teacher, Sarah, implementing NOS for the first time throughout four units of a community college biology course (genetics, molecular biology, evolution, and ecology). Through the action research cycles of planning, implementing, and reflecting, Sarah identified areas of challenge and success. This paper reports emergent themes that assisted her in successfully embedding NOS within the science content. Data include weekly lesson plans and pre/post reflective journaling before and after each lesson of this lecture/lab combination class that met twice a week. This course was taught back to back semesters, and this study is based on the results of a year-long process. Developing pedagogical content knowledge (PCK) for NOS involves coming to understand the overlaps and connections between NOS, other science subject matter, pedagogical strategies, and student learning. Sarah found that through action research she was able to grow and assimilate her understanding of NOS within the biology content she was teaching. A shift in orientation toward teaching products of science to teaching science processes was a necessary shift for NOS pedagogical success. This process enabled Sarah's development of PCK for NOS. As a practical example of putting research-based instructional recommendations into practice, this study may be very useful for other teachers who are learning to teach NOS.

  6. 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

  7. 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

  8. 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. PMID:26013981

  9. 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.

  10. Knowledge-guided gene ranking by coordinative component analysis

    PubMed Central

    2010-01-01

    Background In cancer, gene networks and pathways often exhibit dynamic behavior, particularly during the process of carcinogenesis. Thus, it is important to prioritize those genes that are strongly associated with the functionality of a network. Traditional statistical methods are often inept to identify biologically relevant member genes, motivating researchers to incorporate biological knowledge into gene ranking methods. However, current integration strategies are often heuristic and fail to incorporate fully the true interplay between biological knowledge and gene expression data. Results To improve knowledge-guided gene ranking, we propose a novel method called coordinative component analysis (COCA) in this paper. COCA explicitly captures those genes within a specific biological context that are likely to be expressed in a coordinative manner. Formulated as an optimization problem to maximize the coordinative effort, COCA is designed to first extract the coordinative components based on a partial guidance from knowledge genes and then rank the genes according to their participation strengths. An embedded bootstrapping procedure is implemented to improve statistical robustness of the solutions. COCA was initially tested on simulation data and then on published gene expression microarray data to demonstrate its improved performance as compared to traditional statistical methods. Finally, the COCA approach has been applied to stem cell data to identify biologically relevant genes in signaling pathways. As a result, the COCA approach uncovers novel pathway members that may shed light into the pathway deregulation in cancers. Conclusion We have developed a new integrative strategy to combine biological knowledge and microarray data for gene ranking. The method utilizes knowledge genes for a guidance to first extract coordinative components, and then rank the genes according to their contribution related to a network or pathway. The experimental results show that