Has Modern Biology Entered the Mouth? The Clinical Impact of Biological Research.

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Baum, Bruce J.

1991-01-01

Three areas of biological research that are beginning to have an impact on clinical medicine are examined, including molecular biology, cell biology, and biotechnology. It is concluded that oral biologists and educators must work cooperatively to bring rapid biological and biomedical advances into dental training in a meaningful way. (MSE)

Biotechnologies as a Context for Enhancing Junior High-School Students' Ability to Ask Meaningful Questions about Abstract Biological Processes.

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Olsher, G.; Dreyfus, A.

1999-01-01

Suggests a new approach to teaching about biochemical cellular processes by stimulating student interest in those biochemical processes that allowed for the outcomes of modern biotechnologies. Discusses the development of students' ability to ask meaningful questions about intra-cellular processes, and the resulting meaningful learning of relevant…

The predictive nature of transcript expression levels on protein expression in adult human brain.

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Bauernfeind, Amy L; Babbitt, Courtney C

2017-04-24

Next generation sequencing methods are the gold standard for evaluating expression of the transcriptome. When determining the biological implications of such studies, the assumption is often made that transcript expression levels correspond to protein levels in a meaningful way. However, the strength of the overall correlation between transcript and protein expression is inconsistent, particularly in brain samples. Following high-throughput transcriptomic (RNA-Seq) and proteomic (liquid chromatography coupled with tandem mass spectrometry) analyses of adult human brain samples, we compared the correlation in the expression of transcripts and proteins that support various biological processes, molecular functions, and that are located in different areas of the cell. Although most categories of transcripts have extremely weak predictive value for the expression of their associated proteins (R 2 values of < 10%), transcripts coding for protein kinases and membrane-associated proteins, including those that are part of receptors or ion transporters, are among those that are most predictive of downstream protein expression levels. The predictive value of transcript expression for corresponding proteins is variable in human brain samples, reflecting the complex regulation of protein expression. However, we found that transcriptomic analyses are appropriate for assessing the expression levels of certain classes of proteins, including those that modify proteins, such as kinases and phosphatases, regulate metabolic and synaptic activity, or are associated with a cellular membrane. These findings can be used to guide the interpretation of gene expression results from primate brain samples.

Motivational reading on education, meaningful reading realisation

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Adriana Qafa

2017-07-01

Full Text Available In this study I will present some ideas on today’s educational practice for motivation, the realization of the meaningful reading. There is a special place for the methodical ranking of the reading process, starting in school. Main requests of this reading, consist of the deep meaning of the subject, exploration of the idea, and other elements of the subject, implementation of the technique’s rules of the expressive reading, such as breathing, voice, diction, intonation, spelling, stoppages, logical emphasizes, emotional expressions, temper, timber, gesticulations, and mimic. There is also highlighted the fact that the used method comes from the pupils’ results and depends on the capability and level of the teacher, from the programming’s scale, the tools that are put into disposition, the age and the level of the pupils, and from the environment that the teacher creates during courses. At the end there are some practical guidelines for the realization of the expressive reading in the literature subject.

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes

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Paules Richard S

2007-11-01

Full Text Available Abstract Background A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisition of co-expressed genes a challenge. We developed a novel method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes, designated as EPIG. The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions. Results Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratio's, EPIG extracts a set of patterns representing co-expressed genes. The method is shown to work well with a simulated data set and microarray data obtained from time-series studies of dauer recovery and L1 starvation in C. elegans and after ultraviolet (UV or ionizing radiation (IR-induced DNA damage in diploid human fibroblasts. With the simulated data set, EPIG extracted the appropriate number of patterns which were more stable and homogeneous than the set of patterns that were determined using the CLICK or CAST clustering algorithms. However, CLICK performed better than EPIG and CAST with respect to the average correlation between clusters/patterns of the simulated data. With real biological data, EPIG extracted more dauer-specific patterns than CLICK. Furthermore, analysis of the IR/UV data revealed 18 unique patterns and 2661 genes out of approximately 17,000 that were identified as significantly expressed and categorized to the patterns by EPIG. The time-dependent patterns displayed similar and dissimilar responses between IR and UV treatments. Gene Ontology analysis applied to each pattern-related subset of co-expressed genes revealed underlying

Novel Study Guides for Biochemistry Meaningful Learning in Biology: a Design-Based Research

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Costa, C ; Galembeck, E. Costa, C ; Galembeck, E.

2017-07-01

Full Text Available One of the difficulties for biochemistry learning is the persistence of traditional teaching methods, based on transmission and memorization of abstract and detailed information, usually in a decontextualized way. Such scenario results in surface learning and content reproduction. In order to address these problems, three interventions in a discipline (Metabolism for Biology majors were applied, in the form of innovative teaching tools (study guides. OBJECTIVES: The main goal is to evaluate the impact of these interventions on interest, motivation, and learning of the metabolic pathways. MATERIALS AND METHODS: We describe the development, application, and evaluation of two study guides – one created from a problem used as a contextual connection for glycogen metabolism study and another embedding an integrative view based on glutamate metabolism. Both materials were guided by broad themes like evolution, metabolic adaptation, and comparative biochemistry. The development of the study guides combined submicroscopic (molecular and macroscopic (body, environment levels, aiming to motivate reading and discussion. A design-based research with cycles of application and assessment was carried out, by means of classroom observation, grade analysis in written exams, and students’ interviews. RESULTS AND DISCUSSION: In general, based on in-class student feedback to professors and to the researcher in the interviews, the study guides arouse curiosity and fostered peer discussion. Final average grades indicate a good global performance in all proposed activities. Whole data from study guides’ application in classroom evidenced their impact on interest, motivation, and learning. The strategy of developing problem or integrative situation linking molecular (micro and contextual (macro levels were helpful to foster critical thinking and to value topics of scientific literacy. CONCLUSIONS: Analysis and interpretation of the results point to benefits for

Downregulation of the expression of HDGF attenuates malignant biological behaviors of hilar cholangiocarcinoma cells.

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Liu, Yanfeng; Sun, Jingxian; Yang, Guangyun; Liu, Zhaojian; Guo, Sen; Zhao, Rui; Xu, Kesen; Wu, Xiaopeng; Zhang, Zhaoyang

2015-09-01

Hepatoma-derived growth factor (HDGF) has been reported to be a potential predictive and prognostic marker for several types of cancer and important in malignant biological behaviors. However, its role in human hilar cholangiocarcinoma remains to be elucidated. Our previous study demonstrated that high expression levels of HDGF in hilar cholangiocarcinoma tissues correlates with tumor progression and patient outcome. The present study aimed to elucidate the detailed functions of the HDGF protein. This was performed by downregulating the protein expression of HDGF in the FRH0201 hilar cholangiocarcinoma cell line by RNA interference (RNAi) in vitro, and revealed that downregulation of the HDGF protein significantly inhibited the malignant biological behavior of the FRH0201 cells. In addition, further investigation revealed that downregulation of the protein expression of HDGF significantly decreased the secretion of vascular endothelial growth factor, which may be the mechanism partially responsible for the inhibition of malignant biological behaviors. These findings demonstrated that HDGF is important in promoting malignant biological behaviors, including proliferation, migration and invasion of hilar cholangiocarcinoma FRH0201 cells. Inhibition of the expression of HDGF downregulated the malignant biological behaviors, suggesting that downregulation of the protein expression of HDGF by RNAi may be a novel therapeutic approach to inhibit the progression of hilar cholangiocarcinoma.

Argudas: lessons for argumentation in biology based on a gene expression use case.

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McLeod, Kenneth; Ferguson, Gus; Burger, Albert

2012-01-25

In situ hybridisation gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information online are often both incomplete and inconsistent. Non-monotonic reasoning can help resolve such difficulties - one such form of reasoning is computational argumentation. Essentially this involves asking a computer to debate (i.e. reason about) the validity of a particular statement. Arguments are produced for both sides - the statement is true and, the statement is false - then the most powerful argument is used. In this work the computer is asked to debate whether or not a gene is expressed in a particular mouse anatomical structure. The information generated during the debate can be passed to the biological end-user, enabling their own decision-making process. This paper examines the evolution of a system, Argudas, which tests using computational argumentation in an in situ gene hybridisation gene expression use case. Argudas reasons using information extracted from several different online resources that publish gene expression information for the mouse. The development and evaluation of two prototypes is discussed. Throughout a number of issues shall be raised including the appropriateness of computational argumentation in biology and the challenges faced when integrating apparently similar online biological databases. From the work described in this paper it is clear that for argumentation to be effective in the biological domain the argumentation community need to develop further the tools and resources they provide. Additionally, the biological community must tackle the incongruity between overlapping and adjacent resources, thus facilitating the integration and modelling of biological information. Finally, this work highlights both the importance of, and difficulty in creating, a good model of the domain.

Self-Determination and Meaningful Work: Exploring Socioeconomic Constraints

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Blake A Allan

2016-02-01

Full Text Available This study examined a model of meaningful work among a diverse sample of working adults. From the perspectives of Self-Determination Theory and the Psychology of Working Framework, we tested a structural model with social class and work volition predicting SDT motivation variables, which in turn predicted meaningful work. Partially supporting hypotheses, work volition was positively related to internal regulation and negatively related to amotivation, whereas social class was positively related to external regulation and amotivation. In turn, internal regulation was positively related to meaningful work, whereas external regulation and amotivation were negatively related to meaningful work. Indirect effects from work volition to meaningful work via internal regulation and amotivation were significant, and indirect effects from social class to meaningful work via external regulation and amotivaiton were significant. This study highlights the important relations between SDT motivation variables and meaningful work, especially the large positive relation between internal regulation and meaningful work. However, results also reveal that work volition and social class may play critical roles in predicting internal regulation, external regulation, and amotivation.

Self-Determination and Meaningful Work: Exploring Socioeconomic Constraints.

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Allan, Blake A; Autin, Kelsey L; Duffy, Ryan D

2016-01-01

This study examined a model of meaningful work among a diverse sample of working adults. From the perspectives of Self-Determination Theory and the Psychology of Working Framework, we tested a structural model with social class and work volition predicting SDT motivation variables, which in turn predicted meaningful work. Partially supporting hypotheses, work volition was positively related to internal regulation and negatively related to amotivation, whereas social class was positively related to external regulation and amotivation. In turn, internal regulation was positively related to meaningful work, whereas external regulation and amotivation were negatively related to meaningful work. Indirect effects from work volition to meaningful work via internal regulation and amotivation were significant, and indirect effects from social class to meaningful work via external regulation and amotivation were significant. This study highlights the important relations between SDT motivation variables and meaningful work, especially the large positive relation between internal regulation and meaningful work. However, results also reveal that work volition and social class may play critical roles in predicting internal regulation, external regulation, and amotivation.

Finding biological process modifications in cancer tissues by mining gene expression correlations

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Storari Sergio

2006-01-01

Full Text Available Abstract Background Through the use of DNA microarrays it is now possible to obtain quantitative measurements of the expression of thousands of genes from a biological sample. This technology yields a global view of gene expression that can be used in several ways. Functional insight into expression profiles is routinely obtained by using Gene Ontology terms associated to the cellular genes. In this paper, we deal with functional data mining from expression profiles, proposing a novel approach that studies the correlations between genes and their relations to Gene Ontology (GO. By using this "functional correlations comparison" we explore all possible pairs of genes identifying the affected biological processes by analyzing in a pair-wise manner gene expression patterns and linking correlated pairs with Gene Ontology terms. Results We apply here this "functional correlations comparison" approach to identify the existing correlations in hepatocarcinoma (161 microarray experiments and to reveal functional differences between normal liver and cancer tissues. The number of well-correlated pairs in each GO term highlights several differences in genetic interactions between cancer and normal tissues. We performed a bootstrap analysis in order to compute false detection rates (FDR and confidence limits. Conclusion Experimental results show the main advantage of the applied method: it both picks up general and specific GO terms (in particular it shows a fine resolution in the specific GO terms. The results obtained by this novel method are highly coherent with the ones proposed by other cancer biology studies. But additionally they highlight the most specific and interesting GO terms helping the biologist to focus his/her studies on the most relevant biological processes.

Gene expression-based biological test for major depressive disorder: an advanced study

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Watanabe S

2017-02-01

Full Text Available Shin-ya Watanabe,1 Shusuke Numata,1 Jun-ichi Iga,2 Makoto Kinoshita,1 Hidehiro Umehara,1 Kazuo Ishii,3 Tetsuro Ohmori1 1Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 2Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, 3Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan Purpose: Recently, we could distinguished patients with major depressive disorder (MDD from nonpsychiatric controls with high accuracy using a panel of five gene expression markers (ARHGAP24, HDAC5, PDGFC, PRNP, and SLC6A4 in leukocyte. In the present study, we examined whether this biological test is able to discriminate patients with MDD from those without MDD, including those with schizophrenia and bipolar disorder.Patients and methods: We measured messenger ribonucleic acid expression levels of the aforementioned five genes in peripheral leukocytes in 17 patients with schizophrenia and 36 patients with bipolar disorder using quantitative real-time polymerase chain reaction (PCR, and we combined these expression data with our previous expression data of 25 patients with MDD and 25 controls. Subsequently, a linear discriminant function was developed for use in discriminating between patients with MDD and without MDD.Results: This expression panel was able to segregate patients with MDD from those without MDD with a sensitivity and specificity of 64% and 67.9%, respectively.Conclusion: Further research to identify MDD-specific markers is needed to improve the performance of this biological test. Keywords: depressive disorder, biomarker, gene expression, schizophrenia, bipolar disorder

Expression of biologically active murine interleukin-18 in Lactococcus lactis.

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Feizollahzadeh, Sadegh; Khanahmad, Hossein; Rahimmanesh, Ilnaz; Ganjalikhani-Hakemi, Mazdak; Andalib, Alireza; Sanei, Mohammad Hossein; Rezaei, Abbas

2016-11-01

The food-grade bacterium Lactococcus lactis is increasingly used for heterologous protein expression in therapeutic and industrial applications. The ability of L. lactis to secrete biologically active cytokines may be used for the generation of therapeutic cytokines. Interleukin (IL)-18 enhances the immune response, especially on mucosal surfaces, emphasizing its therapeutic potential. However, it is produced as an inactive precursor and has to be enzymatically cleaved for maturation. We genetically manipulated L. lactis to secrete murine IL-18. The mature murine IL-18 gene was inserted downstream of a nisin promoter in pNZ8149 plasmid and the construct was used to transform L. lactis NZ3900. The transformants were selected on Elliker agar and confirmed by restriction enzyme digestion and sequencing. The expression and secretion of IL-18 protein was verified by SDS-PAGE, western blotting and ELISA. The biological activity of recombinant IL-18 was determined by its ability to induce interferon (IFN)-γ production in L. lactis co-cultured with murine splenic T cells. The amounts of IL-18 in bacterial lysates and supernatants were 3-4 μg mL -1 and 0.6-0.7 ng mL -1 , respectively. The successfully generated L. lactis strain that expressed biologically active murine IL-18 can be used to evaluate the possible therapeutic effects of IL-18 on mucosal surfaces. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Meaningful work, work engagement and organisational commitment

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Madelyn Geldenhuys

2014-03-01

Research purpose: The aim of the study was to investigate the relationships amongst psychological meaningfulness, work engagement and organisational commitment and to test for a possible mediation effect of work engagement on the relationship between psychological meaningfulness and organisational commitment. Motivation for the study: Managers have to rethink ways of improving productivity and performance at work, due to the diverse, and in some instances escalating, needs of employees (e.g. financial support to uphold their interest in and enjoyment of working. Research approach, design and method: A quantitative approach was employed to gather the data for the study, utilising a cross-sectional survey design. The sample (n = 415 consisted of working employees from various companies and positions in Gauteng, South Africa. Main findings: The results confirmed a positive relationship between psychological meaningfulness, work engagement and organisational commitment. Further, psychological meaningfulness predicts work engagement, whilst psychological meaningfulness and work engagement predict organisational commitment. Practical/managerial implications: Employers identifying their employees’ commitment patterns and mapping out strategies for enhancing those that are relevant to organisational goals will yield positive work outcomes (e.g. employees who are creative, seek growth or challenges for themselves. Contribution/value-add: This study contributes to the literature through highlighting the impact that meaningful work has on sustaining employee commitment to the organisation.

Meaningfulness of Service and Marital Satisfaction in Army Couples

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Bergmann, Jeffrey S.; Renshaw, Keith D.; Allen, Elizabeth S.; Markman, Howard J.; Stanley, Scott M.

2015-01-01

The vast numbers of military service members who have been deployed since 2001 highlights the need to better understand relationships of military couples. A unique consideration in military couples is the concept of meaningfulness of service, or the value service members and their partners place on military service in spite of the sacrifices it requires. In a sample of 606 Army couples, we used path analysis to examine how male service members’ and female spouses’ perceived meaningfulness of service added to the prediction of marital satisfaction in both members of the couple, when accounting for service members’ PTSD symptoms. Spouses’ perceived meaningfulness of service was linked with higher marital satisfaction in spouses, regardless of service member’s perceived meaningfulness of service. Service members’ perceived meaningfulness of service was also associated with increased marital satisfaction in service members, but only when their spouses also perceived higher meaningfulness. There were no significant interactions between service members’ PTSD and either partner’s perceived meaningfulness. Implications for enhanced attention to spousal perceptions of meaningfulness of service are discussed. PMID:25046347

Meaningfulness of service and marital satisfaction in Army couples.

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Bergmann, Jeffrey S; Renshaw, Keith D; Allen, Elizabeth S; Markman, Howard J; Stanley, Scott M

2014-10-01

The vast numbers of military service members who have been deployed since 2001 highlights the need to better understand relationships of military couples. A unique consideration in military couples is the concept of meaningfulness of service, or the value service members and their partners place on military service in spite of the sacrifices it requires. In a sample of 606 Army couples, the authors used path analysis to examine how male service members' and female spouses' perceived meaningfulness of service added to the prediction of marital satisfaction in both members of the couple, when accounting for service members' PTSD symptoms. Spouses' perceived meaningfulness of service was linked with higher marital satisfaction in spouses, regardless of service member's perceived meaningfulness of service. Service members' perceived meaningfulness of service was also associated with increased marital satisfaction in service members, but only when their spouses also perceived higher meaningfulness. There were no significant interactions between service members' PTSD and either partner's perceived meaningfulness. Implications for enhanced attention to spousal perceptions of meaningfulness of service are discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Relationship between meaningful work and job performance in nurses.

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Tong, Ling

2018-04-01

The present study was designed to determine the relationship between meaningful work and job performance, and the impact of meaningful work on nursing care quality. Meaningful work has been suggested as a significant factor affecting job performance, but the relationship has never been studied in nurses in China. A descriptive correlational study was designed to assess the level of meaningful work, tasks, and contextual performance as well as their relationships. We used a stratified random-sampling approach to enrol nurses from hospitals. Multivariate regression analysis was applied to determine the relationship between meaningful work and their demographic data. There were significant, positive relationships between meaningful work and task performance and contextual performance. Education level, work unit, and employment type influenced meaningful work. The work motivation score of the nurses was lower than that of the other 2 dimensions, and a negative work motivation score negatively influenced job performance. Improving meaningful work and providing more support and assistance could improve nurse performance, thereby improving the quality of nursing care. © 2018 John Wiley & Sons Australia, Ltd.

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

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Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

Sparse Bayesian classification and feature selection for biological expression data with high correlations.

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Xian Yang

Full Text Available Classification models built on biological expression data are increasingly used to predict distinct disease subtypes. Selected features that separate sample groups can be the candidates of biomarkers, helping us to discover biological functions/pathways. However, three challenges are associated with building a robust classification and feature selection model: 1 the number of significant biomarkers is much smaller than that of measured features for which the search will be exhaustive; 2 current biological expression data are big in both sample size and feature size which will worsen the scalability of any search algorithms; and 3 expression profiles of certain features are typically highly correlated which may prevent to distinguish the predominant features. Unfortunately, most of the existing algorithms are partially addressing part of these challenges but not as a whole. In this paper, we propose a unified framework to address the above challenges. The classification and feature selection problem is first formulated as a nonconvex optimisation problem. Then the problem is relaxed and solved iteratively by a sequence of convex optimisation procedures which can be distributed computed and therefore allows the efficient implementation on advanced infrastructures. To illustrate the competence of our method over others, we first analyse a randomly generated simulation dataset under various conditions. We then analyse a real gene expression dataset on embryonal tumour. Further downstream analysis, such as functional annotation and pathway analysis, are performed on the selected features which elucidate several biological findings.

G =  MAT: linking transcription factor expression and DNA binding data.

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Tretyakov, Konstantin; Laur, Sven; Vilo, Jaak

2011-01-31

Transcription factors are proteins that bind to motifs on the DNA and thus affect gene expression regulation. The qualitative description of the corresponding processes is therefore important for a better understanding of essential biological mechanisms. However, wet lab experiments targeted at the discovery of the regulatory interplay between transcription factors and binding sites are expensive. We propose a new, purely computational method for finding putative associations between transcription factors and motifs. This method is based on a linear model that combines sequence information with expression data. We present various methods for model parameter estimation and show, via experiments on simulated data, that these methods are reliable. Finally, we examine the performance of this model on biological data and conclude that it can indeed be used to discover meaningful associations. The developed software is available as a web tool and Scilab source code at http://biit.cs.ut.ee/gmat/.

G = MAT: Linking Transcription Factor Expression and DNA Binding Data

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Tretyakov, Konstantin; Laur, Sven; Vilo, Jaak

2011-01-01

Transcription factors are proteins that bind to motifs on the DNA and thus affect gene expression regulation. The qualitative description of the corresponding processes is therefore important for a better understanding of essential biological mechanisms. However, wet lab experiments targeted at the discovery of the regulatory interplay between transcription factors and binding sites are expensive. We propose a new, purely computational method for finding putative associations between transcription factors and motifs. This method is based on a linear model that combines sequence information with expression data. We present various methods for model parameter estimation and show, via experiments on simulated data, that these methods are reliable. Finally, we examine the performance of this model on biological data and conclude that it can indeed be used to discover meaningful associations. The developed software is available as a web tool and Scilab source code at http://biit.cs.ut.ee/gmat/. PMID:21297945

The Annotation, Mapping, Expression and Network (AMEN suite of tools for molecular systems biology

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Primig Michael

2008-02-01

Full Text Available Abstract Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i uploading and pre-processing data from microarray expression profiling experiments, (ii detecting groups of significantly co-expressed genes, and (iii searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.

Shaping Biological Knowledge: Applications in Proteomics

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R. Appel

2006-04-01

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

Shaping biological knowledge: applications in proteomics.

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

2004-01-01

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

The effect of occupational meaningfulness on occupational commitment

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Itai Ivtzan

2014-11-01

Full Text Available Existing research lacks a scholarly consensus on how to define and validly measure ‘meaningful work’ (e.g., Rosso, Dekas & Wrzesniewski, 2010. The following correlational study highlights the value of investigating meaningfulness in the context of occupational commitment. The study hypothesizes that occupational commitment is positively correlated with occupational meaningfulness, where meaningfulness is defined as the extent to which people’s occupations contribute to personal meaning in life. One-hundred and fifty-six full-time office based UK workers completed an online questionnaire including 18 questions measuring levels of occupational commitment (Meyer, Allen & Smith, 1993, in addition to six novel items measuring occupational meaningfulness. The results supported the hypothesis and also showed that the affective sub-type of occupational commitment had the highest correlation with occupational meaningfulness. Such results exhibit the importance of finding meaning at work, as well as the relevance of this to one’s level of commitment to his or her job. This paper argues that individuals should consider OM before choosing to take a specific role, whereas organizations ought to consider the OM of their potential candidates before recruiting them into a role. Possible directions for future research directions are also discussed.

Identification of highly synchronized subnetworks from gene expression data.

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Gao, Shouguo; Wang, Xujing

2013-01-01

There has been a growing interest in identifying context-specific active protein-protein interaction (PPI) subnetworks through integration of PPI and time course gene expression data. However the interaction dynamics during the biological process under study has not been sufficiently considered previously. Here we propose a topology-phase locking (TopoPL) based scoring metric for identifying active PPI subnetworks from time series expression data. First the temporal coordination in gene expression changes is evaluated through phase locking analysis; The results are subsequently integrated with PPI to define an activity score for each PPI subnetwork, based on individual member expression, as well topological characteristics of the PPI network and of the expression temporal coordination network; Lastly, the subnetworks with the top scores in the whole PPI network are identified through simulated annealing search. Application of TopoPL to simulated data and to the yeast cell cycle data showed that it can more sensitively identify biologically meaningful subnetworks than the method that only utilizes the static PPI topology, or the additive scoring method. Using TopoPL we identified a core subnetwork with 49 genes important to yeast cell cycle. Interestingly, this core contains a protein complex known to be related to arrangement of ribosome subunits that exhibit extremely high gene expression synchronization. Inclusion of interaction dynamics is important to the identification of relevant gene networks.

Cardiac c-Kit Biology Revealed by Inducible Transgenesis.

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Gude, Natalie A; Firouzi, Fareheh; Broughton, Kathleen M; Ilves, Kelli; Nguyen, Kristine P; Payne, Christina R; Sacchi, Veronica; Monsanto, Megan M; Casillas, Alexandria R; Khalafalla, Farid G; Wang, Bingyan J; Ebeid, David E; Alvarez, Roberto; Dembitsky, Walter P; Bailey, Barbara A; van Berlo, Jop; Sussman, Mark A

2018-06-22

Biological significance of c-Kit as a cardiac stem cell marker and role(s) of c-Kit+ cells in myocardial development or response to pathological injury remain unresolved because of varied and discrepant findings. Alternative experimental models are required to contextualize and reconcile discordant published observations of cardiac c-Kit myocardial biology and provide meaningful insights regarding clinical relevance of c-Kit signaling for translational cell therapy. The main objectives of this study are as follows: demonstrating c-Kit myocardial biology through combined studies of both human and murine cardiac cells; advancing understanding of c-Kit myocardial biology through creation and characterization of a novel, inducible transgenic c-Kit reporter mouse model that overcomes limitations inherent to knock-in reporter models; and providing perspective to reconcile disparate viewpoints on c-Kit biology in the myocardium. In vitro studies confirm a critical role for c-Kit signaling in both cardiomyocytes and cardiac stem cells. Activation of c-Kit receptor promotes cell survival and proliferation in stem cells and cardiomyocytes of either human or murine origin. For creation of the mouse model, the cloned mouse c-Kit promoter drives Histone2B-EGFP (enhanced green fluorescent protein; H2BEGFP) expression in a doxycycline-inducible transgenic reporter line. The combination of c-Kit transgenesis coupled to H2BEGFP readout provides sensitive, specific, inducible, and persistent tracking of c-Kit promoter activation. Tagging efficiency for EGFP+/c-Kit+ cells is similar between our transgenic versus a c-Kit knock-in mouse line, but frequency of c-Kit+ cells in cardiac tissue from the knock-in model is 55% lower than that from our transgenic line. The c-Kit transgenic reporter model reveals intimate association of c-Kit expression with adult myocardial biology. Both cardiac stem cells and a subpopulation of cardiomyocytes express c-Kit in uninjured adult heart

MicroRNA Expression Varies according to Glucose Tolerance, Measurement Platform, and Biological Source

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S. Dias

2017-01-01

Full Text Available Dysregulated microRNA (miRNA expression is observed during type 2 diabetes (T2D, although the consistency of miRNA expression across measurement platform and biological source is uncertain. Here we report miRNA profiling in the whole blood and serum of South African women with different levels of glucose tolerance, using next generation sequencing (NGS and quantitative real time PCR (qRT-PCR. Whole blood-derived miRNAs from women with newly diagnosed T2D (n=4, impaired glucose tolerance (IGT (n=4, and normal glucose tolerance (NGT (n=4 were subjected to NGS, whereafter transcript levels of selected miRNAs were quantified in the whole blood and serum of these women using qRT-PCR. Of the five significantly differentially expressed miRNAs identified by NGS, only the directional increase of miR-27b in women with IGT compared to NGT was confirmed in whole blood and serum, using qRT-PCR. Functional enrichment of miR-27b gene targets identified biological pathways associated with glucose transport and insulin regulation. In conclusion, this study showed poor correlation in miRNA expression profiled using NGS and qRT-PCR and in whole blood and serum. The consistent increased expression of miR-27b in women with IGT compared to NGT across measurement platform and biological source holds potential as a biomarker for risk stratification in our population.

Reflections on Meaningfulness and its Social Relevance

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Nicole Note

2010-06-01

Full Text Available Philosophers who write about the meaning of life are few nowadays. Thesubject has lost its attractiveness. Perceived from a viewpoint of logical positivism or language philosophy, the whole issue of meaningfulness seems rather pointless. It is often considered to be related to metaphysics, making it less suitable for philosophical inquiry. The topic of meaningfulness seems too intangible. Indeed, the few philosophers that have embarked on examining meaningfulness have proven to be well aware of the challenges this poses. At times they acknowledge that the more they concentrate on the subject, the more it seems to fall apart into unintelligible pieces about whichnothing of philosophical value can be said.

G =  MAT: linking transcription factor expression and DNA binding data.

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Konstantin Tretyakov

Full Text Available Transcription factors are proteins that bind to motifs on the DNA and thus affect gene expression regulation. The qualitative description of the corresponding processes is therefore important for a better understanding of essential biological mechanisms. However, wet lab experiments targeted at the discovery of the regulatory interplay between transcription factors and binding sites are expensive. We propose a new, purely computational method for finding putative associations between transcription factors and motifs. This method is based on a linear model that combines sequence information with expression data. We present various methods for model parameter estimation and show, via experiments on simulated data, that these methods are reliable. Finally, we examine the performance of this model on biological data and conclude that it can indeed be used to discover meaningful associations. The developed software is available as a web tool and Scilab source code at http://biit.cs.ut.ee/gmat/.

Towards a mathematical theory of meaningful communication

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Corominas-Murtra, Bernat; Fortuny, Jordi; Solé, Ricard V.

2014-04-01

Meaning has been left outside most theoretical approaches to information in biology. Functional responses based on an appropriate interpretation of signals have been replaced by a probabilistic description of correlations between emitted and received symbols. This assumption leads to potential paradoxes, such as the presence of a maximum information associated to a channel that creates completely wrong interpretations of the signals. Game-theoretic models of language evolution and other studies considering embodied communicating agents show that the correct (meaningful) match resulting from agent-agent exchanges is always achieved and natural systems obviously solve the problem correctly. Inspired by the concept of duality of the communicative sign stated by the swiss linguist Ferdinand de Saussure, here we present a complete description of the minimal system necessary to measure the amount of information that is consistently decoded. Several consequences of our developments are investigated, such as the uselessness of a certain amount of information properly transmitted for communication among autonomous agents.

Antecedents and outcomes of meaningful work among school teachers

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Elmari Fouché

2017-03-01

Research purpose: The aim of this study was to investigate antecedents and outcomes of meaningful work among school teachers. Motivation for the study: Meaningful work underpins people’s motivation and affects their well-being and job satisfaction. Furthermore, it is a significant pathway to healthy and authentic organisations. However, a research gap exists regarding the effects of different antecedents and outcomes of meaningful work. Research approach, design and method: A cross-sectional survey was used with a convenience sample of 513 teachers. The Work-Life Questionnaire, Revised Job Diagnostic Survey, Co-worker Relations Scale, Work and Meaning Inventory, Personal Resources Scale, Work Engagement Scale, Turnover Intention Scale and a measure of self-rated performance were administered. Main findings: A calling orientation, job design and co-worker relations were associated with meaningful work. A low calling orientation and poor co-worker relationships predicted burnout. A calling orientation, a well-designed job, good co-worker relationships and meaningful work predicted work engagement. Job design was moderately associated with self-ratings of performance. The absence of a calling orientation predicted teachers’ intention to leave the organisation. Practical/managerial implications: Educational managers should consider implementing interventions to affect teachers’ calling orientation (through job crafting, perceptions of the nature of their jobs (by allowing autonomy and co-worker relations (through teambuilding to promote perceptions of meaningful work. Promoting perceptions of meaningful work might contribute to lower burnout, higher work engagement, better self-ratings of performance and retention of teachers. Contribution/value-add: This study contributes to scientific knowledge regarding the effects of three antecedents, namely a calling orientation, job design and co-worker relationships on meaningful work. It also contributed to knowledge

BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data

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Madeira Sara C

2009-07-01

Full Text Available Abstract Background The ability to monitor changes in expression patterns over time, and to observe the emergence of coherent temporal responses using expression time series, is critical to advance our understanding of complex biological processes. Biclustering has been recognized as an effective method for discovering local temporal expression patterns and unraveling potential regulatory mechanisms. The general biclustering problem is NP-hard. In the case of time series this problem is tractable, and efficient algorithms can be used. However, there is still a need for specialized applications able to take advantage of the temporal properties inherent to expression time series, both from a computational and a biological perspective. Findings BiGGEsTS makes available state-of-the-art biclustering algorithms for analyzing expression time series. Gene Ontology (GO annotations are used to assess the biological relevance of the biclusters. Methods for preprocessing expression time series and post-processing results are also included. The analysis is additionally supported by a visualization module capable of displaying informative representations of the data, including heatmaps, dendrograms, expression charts and graphs of enriched GO terms. Conclusion BiGGEsTS is a free open source graphical software tool for revealing local coexpression of genes in specific intervals of time, while integrating meaningful information on gene annotations. It is freely available at: http://kdbio.inesc-id.pt/software/biggests. We present a case study on the discovery of transcriptional regulatory modules in the response of Saccharomyces cerevisiae to heat stress.

Meaningful work and secondary school teachers' intention to leave

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M. Janik

2015-05-01

Full Text Available The study investigates the relations between secondary school teachers' work-role fit, job enrichment, supervisor relationships, co-worker relationships, psychological meaningfulness of work and intention to leave. A cross-sectional survey was used. The participants were 502 secondary school teachers in Namibia. The following measuring instruments were used: Work-role Fit Scale, Job Enrichment Scale, Co-worker and Supervisor Relationships Scales, Psychological Meaningfulness Scale and Turnover Intention Scale. Work-role fit and job enrichment both had direct positive effect on experiences of psychological meaningfulness at work, while poor work-role fit and low psychological meaningfulness both had a direct effect on teachers' intentions to leave. An analysis of the indirect effects showed that poor work-role fit and poor job enrichment affected intention to leave due to the concomitant experience of low psychological meaningfulness. These findings have implications for the retention of teachers in secondary schools.

Biclustering methods: biological relevance and application in gene expression analysis.

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Ali Oghabian

Full Text Available DNA microarray technologies are used extensively to profile the expression levels of thousands of genes under various conditions, yielding extremely large data-matrices. Thus, analyzing this information and extracting biologically relevant knowledge becomes a considerable challenge. A classical approach for tackling this challenge is to use clustering (also known as one-way clustering methods where genes (or respectively samples are grouped together based on the similarity of their expression profiles across the set of all samples (or respectively genes. An alternative approach is to develop biclustering methods to identify local patterns in the data. These methods extract subgroups of genes that are co-expressed across only a subset of samples and may feature important biological or medical implications. In this study we evaluate 13 biclustering and 2 clustering (k-means and hierarchical methods. We use several approaches to compare their performance on two real gene expression data sets. For this purpose we apply four evaluation measures in our analysis: (1 we examine how well the considered (biclustering methods differentiate various sample types; (2 we evaluate how well the groups of genes discovered by the (biclustering methods are annotated with similar Gene Ontology categories; (3 we evaluate the capability of the methods to differentiate genes that are known to be specific to the particular sample types we study and (4 we compare the running time of the algorithms. In the end, we conclude that as long as the samples are well defined and annotated, the contamination of the samples is limited, and the samples are well replicated, biclustering methods such as Plaid and SAMBA are useful for discovering relevant subsets of genes and samples.

Synthetic Biology: Putting Synthesis into Biology

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Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

The Structure and Function of Biological Networks

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Wu, Daniel Duanqing

2010-01-01

Biology has been revolutionized in recent years by an explosion in the availability of data. Transforming this new wealth of data into meaningful biological insights and clinical breakthroughs requires a complete overhaul both in the questions being asked and the methodologies used to answer them. A major challenge in organizing and understanding…

Biologics or tofacitinib for people with rheumatoid arthritis unsuccessfully treated with biologics: a systematic review and network meta-analysis.

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Singh, Jasvinder A; Hossain, Alomgir; Tanjong Ghogomu, Elizabeth; Mudano, Amy S; Maxwell, Lara J; Buchbinder, Rachelle; Lopez-Olivo, Maria Angeles; Suarez-Almazor, Maria E; Tugwell, Peter; Wells, George A

2017-03-10

of bias for major baseline imbalance. We downgraded the quality of the evidence for most outcomes to moderate or low due to study limitations, heterogeneity, or rarity of direct comparator trials. Biologic monotherapy versus placeboCompared to placebo, biologics were associated with clinically meaningful and statistically significant improvement in RA as demonstrated by higher ACR50 and RA remission rates. RR was 4.10 for ACR50 (95% CI 1.97 to 8.55; moderate-quality evidence); absolute benefit RD 14% (95% CI 6% to 21%); and NNTB = 8 (95% CI 4 to 23). RR for RA remission was 13.51 (95% CI 1.85 to 98.45, one study available; moderate-quality evidence); absolute benefit RD 9% (95% CI 5% to 13%); and NNTB = 11 (95% CI 3 to 136). Results for withdrawals due to adverse events and serious adverse events did not show any statistically significant or clinically meaningful differences. There were no studies available for analysis for function measured by HAQ, radiographic progression, or cancer outcomes. There were not enough data for any of the outcomes to look at subgroups. Biologic + MTX versus active comparator (MTX/other traditional DMARDs)Compared to MTX/other traditional DMARDs, biologic + MTX was associated with a clinically meaningful and statistically significant improvement in ACR50, function measured by HAQ, and RA remission rates in direct comparisons. RR for ACR50 was 4.07 (95% CI 2.76 to 5.99; high-quality evidence); absolute benefit RD 16% (10% to 21%); NNTB = 7 (95% CI 5 to 11). HAQ scores showed an improvement with a mean difference (MD) of 0.29 (95% CI 0.21 to 0.36; high-quality evidence); absolute benefit RD 9.7% improvement (95% CI 7% to 12%); and NNTB = 5 (95% CI 4 to 7). Remission rates showed an improved RR of 20.73 (95% CI 4.13 to 104.16; moderate-quality evidence); absolute benefit RD 10% (95% CI 8% to 13%); and NNTB = 17 (95% CI 4 to 96), among the biologic + MTX group compared to MTX/other DMARDs. There were no studies for radiographic progression

Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm.

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Tchagang, Alain B; Phan, Sieu; Famili, Fazel; Shearer, Heather; Fobert, Pierre; Huang, Yi; Zou, Jitao; Huang, Daiqing; Cutler, Adrian; Liu, Ziying; Pan, Youlian

2012-04-04

Nowadays, it is possible to collect expression levels of a set of genes from a set of biological samples during a series of time points. Such data have three dimensions: gene-sample-time (GST). Thus they are called 3D microarray gene expression data. To take advantage of the 3D data collected, and to fully understand the biological knowledge hidden in the GST data, novel subspace clustering algorithms have to be developed to effectively address the biological problem in the corresponding space. We developed a subspace clustering algorithm called Order Preserving Triclustering (OPTricluster), for 3D short time-series data mining. OPTricluster is able to identify 3D clusters with coherent evolution from a given 3D dataset using a combinatorial approach on the sample dimension, and the order preserving (OP) concept on the time dimension. The fusion of the two methodologies allows one to study similarities and differences between samples in terms of their temporal expression profile. OPTricluster has been successfully applied to four case studies: immune response in mice infected by malaria (Plasmodium chabaudi), systemic acquired resistance in Arabidopsis thaliana, similarities and differences between inner and outer cotyledon in Brassica napus during seed development, and to Brassica napus whole seed development. These studies showed that OPTricluster is robust to noise and is able to detect the similarities and differences between biological samples. Our analysis showed that OPTricluster generally outperforms other well known clustering algorithms such as the TRICLUSTER, gTRICLUSTER and K-means; it is robust to noise and can effectively mine the biological knowledge hidden in the 3D short time-series gene expression data.

Meaningful Interaction in a Local Context

DEFF Research Database (Denmark)

Holck, Ulla

2006-01-01

This keynote is based on a Ph.D. thesis on development of socially meaningful interaction in music therapy with children with very poor communication skills (Holck 2002). The aim was to identify some of the conditions, whereby actions can be understood as meaningful - that is, whereby the child......’ Samspil i Musikterapi [Eng.: ’Commusical’ Interplay in Music Therapy. Qualitative Video Analyses of Musical and Gestural Interactions with Children with Severe Functional Limitations, including Children with Autism]. Unpubl. PhD thesis, Aalborg Universitet. Holck, U. (2004) Interaction Themes in Music...

Clustering gene expression regulators: new approach to disease subtyping.

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Mikhail Pyatnitskiy

Full Text Available One of the main challenges in modern medicine is to stratify different patient groups in terms of underlying disease molecular mechanisms as to develop more personalized approach to therapy. Here we propose novel method for disease subtyping based on analysis of activated expression regulators on a sample-by-sample basis. Our approach relies on Sub-Network Enrichment Analysis algorithm (SNEA which identifies gene subnetworks with significant concordant changes in expression between two conditions. Subnetwork consists of central regulator and downstream genes connected by relations extracted from global literature-extracted regulation database. Regulators found in each patient separately are clustered together and assigned activity scores which are used for final patients grouping. We show that our approach performs well compared to other related methods and at the same time provides researchers with complementary level of understanding of pathway-level biology behind a disease by identification of significant expression regulators. We have observed the reasonable grouping of neuromuscular disorders (triggered by structural damage vs triggered by unknown mechanisms, that was not revealed using standard expression profile clustering. For another experiment we were able to suggest the clusters of regulators, responsible for colorectal carcinoma vs adenoma discrimination and identify frequently genetically changed regulators that could be of specific importance for the individual characteristics of cancer development. Proposed approach can be regarded as biologically meaningful feature selection, reducing tens of thousands of genes down to dozens of clusters of regulators. Obtained clusters of regulators make possible to generate valuable biological hypotheses about molecular mechanisms related to a clinical outcome for individual patient.

Life is pretty meaningful.

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Heintzelman, Samantha J; King, Laura A

2014-09-01

The human experience of meaning in life is widely viewed as a cornerstone of well-being and a central human motivation. Self-reports of meaning in life relate to a host of important functional outcomes. Psychologists have portrayed meaning in life as simultaneously chronically lacking in human life as well as playing an important role in survival. Examining the growing literature on meaning in life, we address the question "How meaningful is life, in general?" We review possible answers from various psychological sources, some of which anticipate that meaning in life should be low and others that it should be high. Summaries of epidemiological data and research using two self-report measures of meaning in life suggest that life is pretty meaningful. Diverse samples rate themselves significantly above the midpoint on self-reports of meaning in life. We suggest that if meaning in life plays a role in adaptation, it must be commonplace, as our analysis suggests. (c) 2014 APA, all rights reserved.

Meaningful and Purposeful Practice

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Clementi, Donna

2014-01-01

This article describes a graphic, designed by Clementi and Terrill, the authors of "Keys to Planning for Learning" (2013), visually representing the components that contribute to meaningful and purposeful practice in learning a world language, practice that leads to greater proficiency. The entire graphic is centered around the letter…

PROMOTING MEANINGFUL LEARNING THROUGH CREATE-SHARE-COLLABORATE

OpenAIRE

Sailin, Siti Nazuar; Mahmor, Noor Aida

2017-01-01

Students in this 21st century are required to acquire these 4C skills: Critical thinking, Communication, Collaboration and Creativity. These skills can be integrated in the teaching and learning through innovative teaching that promotes active and meaningful learning. One way of integrating these skills is through collaborative knowledge creation and sharing. This paper providesan example of meaningful teaching and learning activities designed within the Create-Share-Collaborate instructional...

Helping others increases meaningful work: Evidence from three experiments.

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Allan, Blake A; Duffy, Ryan D; Collisson, Brian

2018-03-01

The aim of the current research was to examine whether manipulating task significance increased the meaningfulness of work among students (Study 1), an online sample of working adults (Study 2), and public university employees (Study 3). In Study 1, students completed a typing task for the benefit of themselves, a charity, or someone they knew would directly benefit from their work. People who worked to benefit someone else, rather than themselves, reported greater task meaningfulness. In Study 2, a representative, online sample of employees reflected on a time when they worked to benefit themselves or someone else at work. Results revealed that people who reflected on working to benefit someone else, rather than themselves, reported greater work meaningfulness. In Study 3, public university employees participated in a community intervention by working as they normally would, finding new ways to help people each day, or finding several new ways to help others on a single day. People who helped others many times in a single day experienced greater gains in work meaningfulness over time. Across 3 experimental studies, we found that people who perceived their work as helping others experienced more meaningfulness in their work. This highlights the potential mechanisms practitioners, employers, and other parties can use to increase the meaningfulness of work, which has implications for workers' well-being and productivity. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Is synthetic biology mechanical biology?

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Holm, Sune

2015-12-01

A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

Building gene co-expression networks using transcriptomics data for systems biology investigations

DEFF Research Database (Denmark)

Kadarmideen, Haja; Watson-Haigh, Nathan S.

2012-01-01

Gene co-expression networks (GCN), built using high-throughput gene expression data are fundamental aspects of systems biology. The main aims of this study were to compare two popular approaches to building and analysing GCN. We use real ovine microarray transcriptomics datasets representing four......) is connected within a network. The two GCN construction methods used were, Weighted Gene Co-expression Network Analysis (WGCNA) and Partial Correlation and Information Theory (PCIT) methods. Nodes were ranked based on their connectivity measures in each of the four different networks created by WGCNA and PCIT...... (with > 20000 genes) access to large computer clusters, particularly those with larger amounts of shared memory is recommended....

Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters.

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Hensman, James; Lawrence, Neil D; Rattray, Magnus

2013-08-20

Time course data from microarrays and high-throughput sequencing experiments require simple, computationally efficient and powerful statistical models to extract meaningful biological signal, and for tasks such as data fusion and clustering. Existing methodologies fail to capture either the temporal or replicated nature of the experiments, and often impose constraints on the data collection process, such as regularly spaced samples, or similar sampling schema across replications. We propose hierarchical Gaussian processes as a general model of gene expression time-series, with application to a variety of problems. In particular, we illustrate the method's capacity for missing data imputation, data fusion and clustering.The method can impute data which is missing both systematically and at random: in a hold-out test on real data, performance is significantly better than commonly used imputation methods. The method's ability to model inter- and intra-cluster variance leads to more biologically meaningful clusters. The approach removes the necessity for evenly spaced samples, an advantage illustrated on a developmental Drosophila dataset with irregular replications. The hierarchical Gaussian process model provides an excellent statistical basis for several gene-expression time-series tasks. It has only a few additional parameters over a regular GP, has negligible additional complexity, is easily implemented and can be integrated into several existing algorithms. Our experiments were implemented in python, and are available from the authors' website: http://staffwww.dcs.shef.ac.uk/people/J.Hensman/.

Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits

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Watson, Emma; MacNeil, Lesley T.; Ritter, Ashlyn D.; Yilmaz, L. Safak; Rosebrock, Adam P.; Caudy, Amy A.; Walhout, Albertha J. M.

2014-01-01

SUMMARY Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here we used an interspecies systems biology approach with Caenorhabditis elegans and two if its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal’s gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development and reduces fertility, but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology. PMID:24529378

Work engagement and meaningful work across generational cohorts

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Crystal Hoole

2015-08-01

Full Text Available Orientation: Engaging employees and providing employees with a sense of meaning at work is not a one-size-fits-all approach. Although research has shown that differences between work engagement and meaningful work amongst generational cohorts exist, results are still inconclusive. With age becoming increasingly more important as a diversity factor, a better understanding of the dynamics between work engagement and meaningful work across different generational cohorts is necessary to design the right strategy for each organisation’s unique parameters. Research purpose: The aim of this study was to determine whether there is a relationship between work engagement and meaningful work and whether there are significant variances between the levels of work engagement and meaningful work between different generational cohorts. Motivation for study: Work engagement has consistently been highlighted by researchers and human resources experts as a recommended solution to provide companies with the upper hand when it comes to creating a competitive edge. Yet, levels of work engagement are far from ideal, requiring intensified efforts to identify solutions towards raising overall engagement levels. In recent years, much of the focus in terms of generating engagement has been aimed in the direction of financial rewards and other benefits; some organisational experts are of the opinion that a shift is occurring towards meaningful work instead of monetary rewards as the driver of engagement. The changing nature of the work landscape also suggests that generational cohorts experience work engagement and meaningful work differently. Understanding these complexities is mandatory in creating solutions towards improving levels of engagement and meaningful work. Research approach, design and method: A cross-sectional quantitative research approach has been followed. The Utrecht Work Engagement Scale (UWES and Psychological Meaningful Scale (PMS were administered

Meaningful work and mental health: job satisfaction as a moderator.

Science.gov (United States)

Allan, Blake A; Dexter, Chelsea; Kinsey, Rebecca; Parker, Shelby

2018-02-01

Depression, anxiety and stress are common problems for modern workers. Although having meaningful work, or work that is significant, facilitates personal growth, and contributes to the greater good, has been linked to better mental health, people's work might also need to be satisfying or enjoyable to improve outcomes. The purpose of the present study was to examine meaningful work's relation to mental health (i.e. depression, anxiety and stress) and investigate job satisfaction as a moderator of this relation. The study hypotheses were tested with a large, diverse sample recruited from an online source. Partially supporting hypotheses, when controlling for job satisfaction, meaningful work negatively correlated with depression but did not have a significant relation with anxiety and stress. Similarly, job satisfaction negatively predicted depression and stress. Furthermore, the relations between meaningful work and both anxiety and stress were moderated by job satisfaction. Specifically, only people perceiving their work as meaningful and satisfying reported less anxiety and stress. Although continued research is needed, employers and employees may have to target both the meaningfulness and job satisfaction to address the issues of stress and anxiety among working adults.

Meaningful call combinations and compositional processing in the southern pied babbler

Science.gov (United States)

Engesser, Sabrina; Ridley, Amanda R.; Townsend, Simon W.

2016-01-01

Language’s expressive power is largely attributable to its compositionality: meaningful words are combined into larger/higher-order structures with derived meaning. Despite its importance, little is known regarding the evolutionary origins and emergence of this syntactic ability. Although previous research has shown a rudimentary capability to combine meaningful calls in primates, because of a scarcity of comparative data, it is unclear to what extent analog forms might also exist outside of primates. Here, we address this ambiguity and provide evidence for rudimentary compositionality in the discrete vocal system of a social passerine, the pied babbler (Turdoides bicolor). Natural observations and predator presentations revealed that babblers produce acoustically distinct alert calls in response to close, low-urgency threats and recruitment calls when recruiting group members during locomotion. On encountering terrestrial predators, both vocalizations are combined into a “mobbing sequence,” potentially to recruit group members in a dangerous situation. To investigate whether babblers process the sequence in a compositional way, we conducted systematic experiments, playing back the individual calls in isolation as well as naturally occurring and artificial sequences. Babblers reacted most strongly to mobbing sequence playbacks, showing a greater attentiveness and a quicker approach to the loudspeaker, compared with individual calls or control sequences. We conclude that the sequence constitutes a compositional structure, communicating information on both the context and the requested action. Our work supports previous research suggesting combinatoriality as a viable mechanism to increase communicative output and indicates that the ability to combine and process meaningful vocal structures, a basic syntax, may be more widespread than previously thought. PMID:27155011

Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits.

Science.gov (United States)

Watson, Emma; MacNeil, Lesley T; Ritter, Ashlyn D; Yilmaz, L Safak; Rosebrock, Adam P; Caudy, Amy A; Walhout, Albertha J M

2014-02-13

Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here, we used an interspecies systems biology approach with Caenorhabditis elegans and two of its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal's gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development, and reduces fertility but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid, preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology. Copyright © 2014 Elsevier Inc. All rights reserved.

Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap.

Science.gov (United States)

Lawhorn, Chelsea M; Schomaker, Rachel; Rowell, Jonathan T; Rueppell, Olav

2018-04-16

Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression. Neglecting this variability could therefore lead to inflated estimates of significant overlap between DEG lists. With computer simulations, we demonstrate that such biases arise from variation in the control of gene expression. Significant overlap commonly arises between two lists of DEGs that are randomly generated, assuming that the control of gene expression is variable among genes but consistent between corresponding experiments. More overlap is observed when transcription factors are specific to their binding sites and when the number of genes is considerably higher than the number of different transcription factors. In contrast, overlap between two DEG lists is always lower than expected when the genetic architecture of expression is independent between the two experiments. Thus, the current methods for determining significant overlap between DEGs are potentially confounding biologically meaningful overlap with overlap that arises due to variability in control of expression among genes, and more sophisticated approaches are needed.

Dynamics of problem setting and framing in citizen discussions on synthetic biology.

Science.gov (United States)

Betten, Afke Wieke; Broerse, Jacqueline E W; Kupper, Frank

2018-04-01

Synthetic biology is an emerging scientific field where engineers and biologists design and build biological systems for various applications. Developing synthetic biology responsibly in the public interest necessitates a meaningful societal dialogue. In this article, we argue that facilitating such a dialogue requires an understanding of how people make sense of synthetic biology. We performed qualitative research to unravel the underlying dynamics of problem setting and framing in citizen discussions on synthetic biology. We found that most people are not inherently for or against synthetic biology as a technology or development in itself, but that their perspectives are framed by core values about our relationships with science and technology and that sensemaking is much dependent on the context and general feelings of (dis)content. Given that there are many assumptions focused on a more binary idea of the public's view, we emphasize the need for frame awareness and understanding in a meaningful dialogue.

Integrative analysis of many weighted co-expression networks using tensor computation.

Directory of Open Access Journals (Sweden)

Wenyuan Li

2011-06-01

Full Text Available The rapid accumulation of biological networks poses new challenges and calls for powerful integrative analysis tools. Most existing methods capable of simultaneously analyzing a large number of networks were primarily designed for unweighted networks, and cannot easily be extended to weighted networks. However, it is known that transforming weighted into unweighted networks by dichotomizing the edges of weighted networks with a threshold generally leads to information loss. We have developed a novel, tensor-based computational framework for mining recurrent heavy subgraphs in a large set of massive weighted networks. Specifically, we formulate the recurrent heavy subgraph identification problem as a heavy 3D subtensor discovery problem with sparse constraints. We describe an effective approach to solving this problem by designing a multi-stage, convex relaxation protocol, and a non-uniform edge sampling technique. We applied our method to 130 co-expression networks, and identified 11,394 recurrent heavy subgraphs, grouped into 2,810 families. We demonstrated that the identified subgraphs represent meaningful biological modules by validating against a large set of compiled biological knowledge bases. We also showed that the likelihood for a heavy subgraph to be meaningful increases significantly with its recurrence in multiple networks, highlighting the importance of the integrative approach to biological network analysis. Moreover, our approach based on weighted graphs detects many patterns that would be overlooked using unweighted graphs. In addition, we identified a large number of modules that occur predominately under specific phenotypes. This analysis resulted in a genome-wide mapping of gene network modules onto the phenome. Finally, by comparing module activities across many datasets, we discovered high-order dynamic cooperativeness in protein complex networks and transcriptional regulatory networks.

Nutritional Systems Biology

DEFF Research Database (Denmark)

Jensen, Kasper

and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

Molecular codes in biological and chemical reaction networks.

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Dennis Görlich

Full Text Available Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio- chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries, biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades, an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

Recombinant protein expression for structural biology in HEK 293F suspension cells: a novel and accessible approach.

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Portolano, Nicola; Watson, Peter J; Fairall, Louise; Millard, Christopher J; Milano, Charles P; Song, Yun; Cowley, Shaun M; Schwabe, John W R

2014-10-16

The expression and purification of large amounts of recombinant protein complexes is an essential requirement for structural biology studies. For over two decades, prokaryotic expression systems such as E. coli have dominated the scientific literature over costly and less efficient eukaryotic cell lines. Despite the clear advantage in terms of yields and costs of expressing recombinant proteins in bacteria, the absence of specific co-factors, chaperones and post-translational modifications may cause loss of function, mis-folding and can disrupt protein-protein interactions of certain eukaryotic multi-subunit complexes, surface receptors and secreted proteins. The use of mammalian cell expression systems can address these drawbacks since they provide a eukaryotic expression environment. However, low protein yields and high costs of such methods have until recently limited their use for structural biology. Here we describe a simple and accessible method for expressing and purifying milligram quantities of protein by performing transient transfections of suspension grown HEK (Human Embryonic Kidney) 293 F cells.

Meaningful work and secondary school teachers' intention to leave ...

African Journals Online (AJOL)

The following measuring instruments were used: Work-role Fit Scale, Job Enrichment Scale, Co-worker and Supervisor Relationships Scales, Psychological Meaningfulness Scale and Turnover Intention Scale. Work-role fit and job enrichment both had direct positive effect on experiences of psychological meaningfulness at ...

Meaningful spatial and temporal sequences of activities in dwelling

NARCIS (Netherlands)

Hematalikeikha, M.A.; Coolen, H.C.C.H.; Pourdeihimi, S.

2014-01-01

Human activities based on human needs are affected by affordances and meanings that occur in the dwelling. Activities over time and space have meaningful sequences. The meaningfulness of activities in the cultural framework is conditioned by its special temporality and spatiality. Also, temporal or

Between order and chaos: The quest for meaningful information

NARCIS (Netherlands)

Adriaans, P.

2009-01-01

The notion of meaningful information seems to be associated with the sweet spot between order and chaos. This form of meaningfulness of information, which is primarily what science is interested in, is not captured by both Shannon information and Kolmogorov complexity. In this paper I develop a

Meaningful coping with chronic pain: Exploring the interplay between goal violation, meaningful coping strategies and life satisfaction in chronic pain patients.

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Dezutter, Jessie; Dewitte, Laura; Thauvoye, Evalyne; Vanhooren, Siebrecht

2017-02-01

Trying to cope with chronic pain is a highly demanding and challenging task and pain patients often need to reformulate goals or aspirations due to their pain condition. This goal violation is often related with experienced distress and requires coping processes in order to decrease the distress and stimulate a healthy adaptation. Some scholars, however, argued that in so-called unsolvable or irreparable stressors such as chronic pain, conventional coping strategies like problem-focused coping might not be the most adaptive option. In these situations, meaningful coping strategies attempting to transform the meaning of the stressful experience would be more accurate. In this study, we aim to test if goal violation triggers meaningful coping strategies over time and whether engagement in these meaningful coping strategies result in improved life satisfaction, as an indicator of adaptation. A longitudinal three wave study in a sample of paint patients (n = 125) tests whether goal violation triggers positive reappraisal and downward comparison, two possible meaningful coping strategies. The study furthermore tests if engagement in these strategies results in a better adaptation to the pain condition, reflected in higher life satisfaction. Results partially supported our hypotheses by pointing to the benevolent role of downward comparison on life satisfaction via decreased goal violation of pain patients. Our findings however did also show that positive reappraisal predicted lower life satisfaction via increased levels of appraised goal violation which questions the role of positive reappraisal as a genuine meaningful coping strategy. Implications and limitations are discussed. © 2016 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

Self-Determination and Meaningful Work: Exploring Socioeconomic Constraints

OpenAIRE

Allan, Blake A.; Autin, Kelsey L.; Duffy, Ryan D.

2016-01-01

This study examined a model of meaningful work among a diverse sample of working adults. From the perspectives of Self-Determination Theory and the Psychology of Working Framework, we tested a structural model with social class and work volition predicting SDT motivation variables, which in turn predicted meaningful work. Partially supporting hypotheses, work volition was positively related to internal regulation and negatively related to amotivation, whereas social class was positively relat...

Expression of novel rice gibberellin 2-oxidase gene is under homeostatic regulation by biologically active gibberellins.

Science.gov (United States)

Sakai, Miho; Sakamoto, Tomoaki; Saito, Tamio; Matsuoka, Makoto; Tanaka, Hiroshi; Kobayashi, Masatomo

2003-04-01

We have cloned two genes for gibberellin (GA) 2-oxidase from rice ( Oryza sativa L.). Expression of OsGA2ox2 was not observed. The other gene, OsGA2ox3, was expressed in every tissue examined and was enhanced by the application of biologically active GA. Recombinant OsGA2ox3 protein catalyzed the metabolism of GA(1) to GA(8) and GA(20) to GA(29)-catabolite. These results indicate that OsGA2ox3 is involved in the homeostatic regulation of the endogenous level of biologically active GA in rice.

Meaningful Use of Health Information Technology by Rural Hospitals

Science.gov (United States)

McCullough, Jeffrey; Casey, Michelle; Moscovice, Ira; Burlew, Michele

2011-01-01

Purpose: This study examines the current status of meaningful use of health information technology (IT) in Critical Access Hospitals (CAHs), other rural, and urban US hospitals, and it discusses the potential role of Medicare payment incentives and disincentives in encouraging CAHs and other rural hospitals to achieve meaningful use. Methods: Data…

Concept maps and the meaningful learning of science

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José Antonio C. S. Valadares

2013-03-01

Full Text Available The foundations of the Meaningful Learning Theory (MLT were laid by David Ausubel. The MLT was highly valued by the contributions of Joseph Novak and D. B. Gowin. Unlike other learning theories, the MLT has an operational component, since there are some instruments based on it and with the meaningful learning facilitation as aim. These tools were designated graphic organizers by John Trowbridge and James Wandersee (2000, pp. 100-129. One of them is the concept map created by Novak to extract meanings from an amalgam of information, having currently many applications. The other one is the Vee diagram or knowledge Vee, also called epistemological Vee or heuristic Vee. It was created by Gowin, and is an excellent organizer, for example to unpack and make transparent the unclear information from an information source. Both instruments help us in processing and becoming conceptually transparent the information, to facilitate the cognitive process of new meanings construction. In this work, after a brief introduction, it will be developed the epistemological and psychological grounds of MLT, followed by a reference to constructivist learning environments facilitators of the meaningful learning, the characterization of concept maps and exemplification of its use in various applications that have proved to be very effective from the standpoint of meaningful learning.

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

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Lo Kenneth

2012-08-01

Full Text Available Abstract Background Inference about regulatory networks from high-throughput genomics data is of great interest in systems biology. We present a Bayesian approach to infer gene regulatory networks from time series expression data by integrating various types of biological knowledge. Results We formulate network construction as a series of variable selection problems and use linear regression to model the data. Our method summarizes additional data sources with an informative prior probability distribution over candidate regression models. We extend the Bayesian model averaging (BMA variable selection method to select regulators in the regression framework. We summarize the external biological knowledge by an informative prior probability distribution over the candidate regression models. Conclusions We demonstrate our method on simulated data and a set of time-series microarray experiments measuring the effect of a drug perturbation on gene expression levels, and show that it outperforms leading regression-based methods in the literature.

Intrinsic Value and a Meaningful Life | Audi | Philosophical Papers

African Journals Online (AJOL)

I distinguish various ways in which human life may be thought to be meaningful and present an account of what might be called existential meaningfulness. The account is neutral with respect to both theism and naturalism, but each is addressed in several places and the paper's main points are harmonious with certain ...

Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

Energy Technology Data Exchange (ETDEWEB)

Manno, D; Filippo, E; Fiore, R; Serra, A [Dipartimento di Scienza dei Materiali, Universita del Salento, Lecce (Italy); Urso, E; Rizzello, A; Maffia, M [Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita del Salento, Lecce (Italy)

2010-04-23

Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP{sup C}. In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP{sup C} at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

International Nuclear Information System (INIS)

Manno, D; Filippo, E; Fiore, R; Serra, A; Urso, E; Rizzello, A; Maffia, M

2010-01-01

Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP C . In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP C at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

Values-led Participatory Design as a pursuit of meaningful alternatives

DEFF Research Database (Denmark)

Leong, Tuck Wah; Iversen, Ole Sejer

2015-01-01

Participatory Design (PD) is inherently concerned with inquiring into and supporting human values when designing IT. We argue that a PD approach that is led by a focus upon participants' values can allow participants to discover meaningful alternatives -- alternative uses and alternative...... conceptualizations for IT that are particularly meaningful to them. However, how PD works with values in the design process has not been made explicit. In this paper, we aim to (i) explicate this values-led PD approach, (ii) illustrate how this approach can lead to outcomes that are meaningful alternatives, and (iii...

Extracting biologically significant patterns from short time series gene expression data

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McGinnis Thomas

2009-08-01

Full Text Available Abstract Background Time series gene expression data analysis is used widely to study the dynamics of various cell processes. Most of the time series data available today consist of few time points only, thus making the application of standard clustering techniques difficult. Results We developed two new algorithms that are capable of extracting biological patterns from short time point series gene expression data. The two algorithms, ASTRO and MiMeSR, are inspired by the rank order preserving framework and the minimum mean squared residue approach, respectively. However, ASTRO and MiMeSR differ from previous approaches in that they take advantage of the relatively few number of time points in order to reduce the problem from NP-hard to linear. Tested on well-defined short time expression data, we found that our approaches are robust to noise, as well as to random patterns, and that they can correctly detect the temporal expression profile of relevant functional categories. Evaluation of our methods was performed using Gene Ontology (GO annotations and chromatin immunoprecipitation (ChIP-chip data. Conclusion Our approaches generally outperform both standard clustering algorithms and algorithms designed specifically for clustering of short time series gene expression data. Both algorithms are available at http://www.benoslab.pitt.edu/astro/.

A concept for biological valuation in the marine environment

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Eric Willem Maria Stienen

2007-03-01

Full Text Available In order to develop management strategies for sustainable useand conservation in the marine environment, reliable and meaningful,but integrated ecological information is needed. Biological valuationmaps that compile and summarize all available biological andecological information for a study area, and that allocate anoverall biological value to subzones, can be used as baselinemaps for future spatial planning at sea. This paper providesa concept for marine biological valuation which is based on aliterature review of existing valuation criteria and the consensusreached by a discussion group of experts.

Characteristics of meaningful chemistry education - The case of water quality

NARCIS (Netherlands)

Westbroek, Hanna Barbara

2005-01-01

This thesis addresses the question of how to involve students in meaningful chemistry education by a proper implementation of three characteristics of meaningful: a context, a need-to-know approach and attention for student input. The characteristics were adopted as solution strategies for

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Science.gov (United States)

Yang, Laurence; Tan, Justin; O'Brien, Edward J; Monk, Jonathan M; Kim, Donghyuk; Li, Howard J; Charusanti, Pep; Ebrahim, Ali; Lloyd, Colton J; Yurkovich, James T; Du, Bin; Dräger, Andreas; Thomas, Alex; Sun, Yuekai; Saunders, Michael A; Palsson, Bernhard O

2015-08-25

Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma genitalium). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in nondifferentially expressed genes and depleted in differentially expressed genes. Compared with the noncore, core gene expression levels are also similar across genetic backgrounds (two times higher Spearman rank correlation) and exhibit significantly more complex transcriptional and posttranscriptional regulatory features (40% more transcription start sites per gene, 22% longer 5'UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, validated by using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models; it de facto defines a paleome.

Biological activity of Bt proteins expressed in different structures of transgenic corn against Spodoptera frugiperda

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Daniel Bernardi

2016-06-01

Full Text Available ABSTRACT: Spodoptera frugiperda (J. E. Smith is the main target pest of Bt corn technologies, such as YieldGard VT PRO(tm (Cry1A.105/Cry2Ab2 and PowerCore(tm (Cry1A.105/Cry2Ab2/Cry1F. In this study, it was evaluated the biological activity of Bt proteins expressed in different plant structures of YieldGard VT PRO(tm and PowerCore(tm corn against S. frugiperda . Complete mortality of S. frugiperda neonates was observed on leaf-disc of both Bt corn technologies. However, the mortality in silks and grains was lower than 50 and 6%, respectively. In addition, more than 49% of the surviving larvae in silks and grains completed the biological cycle. However, all life table parameters were negatively affected in insects that developed in silks and grains of both Bt corn events. In summary, the low biological activity of Bt proteins expressed on silks and grains of YieldGard VT PRO(tm and PowerCore(tm corn can contribute to the resistance evolution in S. frugiperda populations.

Meaningful work and secondary school teachers' intention to leave

OpenAIRE

Janik, M.; Rothmann, S.

2015-01-01

The study investigates the relations between secondary school teachers' work-role fit, job enrichment, supervisor relationships, co-worker relationships, psychological meaningfulness of work and intention to leave. A cross-sectional survey was used. The participants were 502 secondary school teachers in Namibia. The following measuring instruments were used: Work-role Fit Scale, Job Enrichment Scale, Co-worker and Supervisor Relationships Scales, Psychological Meaningfulness Scale and Turnove...

Poignancy: Mixed Emotional Experience in the Face of Meaningful Endings

Science.gov (United States)

Ersner-Hershfield, Hal; Mikels, Joseph A.; Sullivan, Sarah J.; Carstensen, Laura L.

2009-01-01

The experience of mixed emotions increases with age. Socioemotional selectivity theory suggests that mixed emotions are associated with shifting time horizons. Theoretically, perceived constraints on future time increase appreciation for life, which, in turn, elicits positive emotions such as happiness. Yet, the very same temporal constraints heighten awareness that these positive experiences come to an end, thus yielding mixed emotional states. In 2 studies, the authors examined the link between the awareness of anticipated endings and mixed emotional experience. In Study 1, participants repeatedly imagined being in a meaningful location. Participants in the experimental condition imagined being in the meaningful location for the final time. Only participants who imagined “last times” at meaningful locations experienced more mixed emotions. In Study 2, college seniors reported their emotions on graduation day. Mixed emotions were higher when participants were reminded of the ending that they were experiencing. Findings suggest that poignancy is an emotional experience associated with meaningful endings. PMID:18179325

Meaningful Human Control over Autonomous Systems: A Philosophical Account

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Filippo Santoni de Sio

2018-02-01

Full Text Available Debates on lethal autonomous weapon systems have proliferated in the past 5 years. Ethical concerns have been voiced about a possible raise in the number of wrongs and crimes in military operations and about the creation of a “responsibility gap” for harms caused by these systems. To address these concerns, the principle of “meaningful human control” has been introduced in the legal–political debate; according to this principle, humans not computers and their algorithms should ultimately remain in control of, and thus morally responsible for, relevant decisions about (lethal military operations. However, policy-makers and technical designers lack a detailed theory of what “meaningful human control” exactly means. In this paper, we lay the foundation of a philosophical account of meaningful human control, based on the concept of “guidance control” as elaborated in the philosophical debate on free will and moral responsibility. Following the ideals of “Responsible Innovation” and “Value-sensitive Design,” our account of meaningful human control is cast in the form of design requirements. We identify two general necessary conditions to be satisfied for an autonomous system to remain under meaningful human control: first, a “tracking” condition, according to which the system should be able to respond to both the relevant moral reasons of the humans designing and deploying the system and the relevant facts in the environment in which the system operates; second, a “tracing” condition, according to which the system should be designed in such a way as to grant the possibility to always trace back the outcome of its operations to at least one human along the chain of design and operation. As we think that meaningful human control can be one of the central notions in ethics of robotics and AI, in the last part of the paper, we start exploring the implications of our account for the design and use of non

Using Concept Mapping in the Biology Classroom.

Science.gov (United States)

Donovan, Edward P.

Concept mapping, a technique based on David Ausubel's theory of meaningful learning, involves the organization of concepts into an hierarchical arrangement. Suggestions for incorporating this learning strategy into the biology classroom are presented and discussed. Steps in concept mapping include: (1) identifying important concepts in the study…

Toward computational cumulative biology by combining models of biological datasets.

Science.gov (United States)

Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

2014-01-01

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations-for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

Self-expression assignment as a teaching approach to enhance the interest of Kuwaiti women in biological sciences.

Science.gov (United States)

El-Sabban, Farouk

2008-06-01

Stimulating the interest of students in biological sciences necessitates the use of new teaching methods and motivating approaches. The idea of the self-expression assignment (SEA) has evolved from the prevalent environment at the College for Women of Kuwait University (Safat, State of Kuwait), a newly established college where the number of students is low and where students have varied backgrounds and interests and are being instructed biological sciences in English for the first time. This SEA requires each student to choose a topic among a long list of topics and interact with it in any way to produce a finished product without the interference of the course instructor. Students are told that the SEA will be graded based on their commitment, creative thinking, innovation in developing the idea, and finishing up of the chosen assignment. The SEA has been implemented in three introductory courses, namely, Biology, Introduction to Human Nutrition and Food Science, and The Human Body. Many interesting projects resulted from the SEA, and, based on an administered survey, students assessed this assignment very favorably. Students expressed their pleasure of experiencing freedom in choosing their own topics, interacting with such topics, learning more about them, and finishing up their projects. Students appreciated this type of exposure to biological sciences and expressed that such an experience enhanced their interest in such sciences.

Design democratization with communities: Drawing toward locally meaningful design

DEFF Research Database (Denmark)

Winschiers-Goagoses, Naska; Winschiers-Theophilus, Heike; Rodil, Kasper

2012-01-01

The authors present community drawing as meaningful representations to inform locally valid technology design. They investigate recognition within and across cultural borders, thereby exposing variances of localities. The study contributes to the still scarce body of empirical work on culturally...... meaningful development of visual representations and recognition, as part of a longitudinal research project in which we co-design a 3D visualization for a specific Namibian pilot site....

On making nursing undergraduate human reproductive physiology content meaningful and relevant: discussion of human pleasure in its biological context.

Science.gov (United States)

McClusky, Leon Mendel

2012-01-01

The traditional presentation of the Reproductive Physiology component in an Anatomy and Physiology course to nursing undergraduates focuses on the broad aspects of hormonal regulation of reproduction and gonadal anatomy, with the role of the higher centres of the brain omitted. An introductory discussion is proposed which could precede the lectures on the reproductive organs. The discussion gives an overview of the biological significance of human pleasure, the involvement of the neurotransmitter dopamine, and the role of pleasure in the survival of the individual and even species. Pleasure stimuli (positive and negative) and the biological significance of naturally-induced pleasurable experiences are briefly discussed in the context of reproduction and the preservation of genetic material with an aim to foster relevancy between subject material and human behaviour in any type of society. The tenderness of this aspect of the human existence is well-understood because of its invariable association with soul-revealing human expressions such as love, infatuation, sexual flirtations, all of which are underpinned by arousal, desire and/or pleasure. Assuming that increased knowledge correlates with increased confidence, the proposed approach may provide the nurse with an adequate knowledge base to overcome well-known barriers in communicating with their patients about matters of sexual health and intimacy. Copyright © 2011 Elsevier Ltd. All rights reserved.

A structured sparse regression method for estimating isoform expression level from multi-sample RNA-seq data.

Science.gov (United States)

Zhang, L; Liu, X J

2016-06-03

With the rapid development of next-generation high-throughput sequencing technology, RNA-seq has become a standard and important technique for transcriptome analysis. For multi-sample RNA-seq data, the existing expression estimation methods usually deal with each single-RNA-seq sample, and ignore that the read distributions are consistent across multiple samples. In the current study, we propose a structured sparse regression method, SSRSeq, to estimate isoform expression using multi-sample RNA-seq data. SSRSeq uses a non-parameter model to capture the general tendency of non-uniformity read distribution for all genes across multiple samples. Additionally, our method adds a structured sparse regularization, which not only incorporates the sparse specificity between a gene and its corresponding isoform expression levels, but also reduces the effects of noisy reads, especially for lowly expressed genes and isoforms. Four real datasets were used to evaluate our method on isoform expression estimation. Compared with other popular methods, SSRSeq reduced the variance between multiple samples, and produced more accurate isoform expression estimations, and thus more meaningful biological interpretations.

Expression Profiling of Genes Related to Endothelial Cells Biology in Patients with Type 2 Diabetes and Patients with Prediabetes

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Sara Moradipoor

2016-01-01

Full Text Available Endothelial dysfunction appears to be an early sign indicating vascular damage and predicts the progression of atherosclerosis and cardiovascular disorders. Extensive clinical and experimental evidence suggests that endothelial dysfunction occurs in Type 2 Diabetes Mellitus (T2DM and prediabetes patients. This study was carried out with an aim to appraise the expression levels in the peripheral blood of 84 genes related to endothelial cells biology in patients with diagnosed T2DM or prediabetes, trying to identify new genes whose expression might be changed under these pathological conditions. The study covered a total of 45 participants. The participants were divided into three groups: group 1, patients with T2DM; group 2, patients with prediabetes; group 3, control group. The gene expression analysis was performed using the Endothelial Cell Biology RT2 Profiler PCR Array. In the case of T2DM, 59 genes were found to be upregulated, and four genes were observed to be downregulated. In prediabetes patients, increased expression was observed for 49 genes, with two downregulated genes observed. Our results indicate that diabetic and prediabetic conditions change the expression levels of genes related to endothelial cells biology and, consequently, may increase the risk for occurrence of endothelial dysfunction.

Machine learning in computational biology to accelerate high-throughput protein expression.

Science.gov (United States)

Sastry, Anand; Monk, Jonathan; Tegel, Hanna; Uhlen, Mathias; Palsson, Bernhard O; Rockberg, Johan; Brunk, Elizabeth

2017-08-15

The Human Protein Atlas (HPA) enables the simultaneous characterization of thousands of proteins across various tissues to pinpoint their spatial location in the human body. This has been achieved through transcriptomics and high-throughput immunohistochemistry-based approaches, where over 40 000 unique human protein fragments have been expressed in E. coli. These datasets enable quantitative tracking of entire cellular proteomes and present new avenues for understanding molecular-level properties influencing expression and solubility. Combining computational biology and machine learning identifies protein properties that hinder the HPA high-throughput antibody production pipeline. We predict protein expression and solubility with accuracies of 70% and 80%, respectively, based on a subset of key properties (aromaticity, hydropathy and isoelectric point). We guide the selection of protein fragments based on these characteristics to optimize high-throughput experimentation. We present the machine learning workflow as a series of IPython notebooks hosted on GitHub (https://github.com/SBRG/Protein_ML). The workflow can be used as a template for analysis of further expression and solubility datasets. ebrunk@ucsd.edu or johanr@biotech.kth.se. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A rapid Q-PCR titration protocol for adenovirus and helper-dependent adenovirus vectors that produces biologically relevant results

Science.gov (United States)

Gallaher, Sean D.; Berk, Arnold J.

2013-01-01

Adenoviruses are employed in the study of cellular processes and as expression vectors used in gene therapy. The success and reproducibility of these studies is dependent in part on having accurate and meaningful titers of replication competent and helper-dependent adenovirus stocks, which is problematic due to the use of varied and divergent titration protocols. Physical titration methods, which quantify the total number of viral particles, are used by many, but are poor at estimating activity. Biological titration methods, such as plaque assays, are more biologically relevant, but are time consuming and not applicable to helper-dependent gene therapy vectors. To address this, a protocol was developed called “infectious genome titration” in which viral DNA is isolated from the nuclei of cells ~3 h post-infection, and then quantified by Q-PCR. This approach ensures that only biologically active virions are counted as part of the titer determination. This approach is rapid, robust, sensitive, reproducible, and applicable to all forms of adenovirus. Unlike other Q-PCR-based methods, titers determined by this protocol are well correlated with biological activity. PMID:23624118

THE MEANINGFUL ACTIVITY PARTICIPATION ASSESSMENT: A MEASURE OF ENGAGEMENT IN PERSONALLY VALUED ACTIVITIES*

Science.gov (United States)

EAKMAN, AARON M.; CARLSON, MIKE E.; CLARK, FLORENCE A.

2011-01-01

The Meaningful Activity Participation Assessment (MAPA), a recently developed 28-item tool designed to measure the meaningfulness of activity, was tested in a sample of 154 older adults. The MAPA evidenced a sufficient level of internal consistency and test-retest reliability and correlated as theoretically predicted with the Life Satisfaction Index-Z, the Satisfaction with Life Scale, the Engagement in Meaningful Activities Survey, the Purpose in Life Test, the Center for Epidemiologic Studies Depression Inventory and the Rand SF-36v2 Health Survey subscales. Zero-order correlations consistently demonstrated meaningful relationships between the MAPA and scales of psychosocial well-being and health-related quality of life. Results from multiple regression analyses further substantiated these findings, as greater meaningful activity participation was associated with better psychological well-being and health-related quality of life. The MAPA appears to be a reliable and valid measure of meaningful activity, incorporating both subjective and objective indicators of activity engagement. PMID:20649161

Making Social Studies Meaningful to Elementary Students.

Science.gov (United States)

Klein, Susan

1982-01-01

Describes a unit on Ancient Greece designed to make social studies meaningful to fourth and fifth graders. Individual projects and group activities helped students learn about ancient Greek culture. (AM)

Students’ Expectations and Experiences of Meaningful Simulation-Based Medical Education

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Tuulikki Keskitalo

2016-11-01

Full Text Available This study aims to investigate students’ expectations and experiences of meaningful learning in simulation-based learning environments. We set the following research question: How do students’ experiences of meaningful simulation-based learning correspond to their expectations? The students’ (n = 87; male 51, female 36 pre- and post-questionnaires were analyzed using statistical methods. The results indicated that students’ expectations and experiences of meaningful learning were positive, and for most statements, there were statistically significant differences between the mean pre-questionnaire rating and the mean post-questionnaire rating, thereby indicating that students’ actual experiences of simulation-based learning were more positive than their expectations. Thus, students’ experiences exceeded their expectations.

Functional Associations by Response Overlap (FARO, a functional genomics approach matching gene expression phenotypes.

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Henrik Bjørn Nielsen

2007-08-01

Full Text Available The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between experimental factors affecting a biological system. Unfortunately, direct comparisons of gene expression profiles obtained in independent, publicly available microarray experiments are typically compromised by substantial, experiment-specific biases. Here we suggest a novel yet conceptually simple approach for deriving 'Functional Association(s by Response Overlap' (FARO between microarray gene expression studies. The transcriptional response is defined by the set of differentially expressed genes independent from the magnitude or direction of the change. This approach overcomes the limited comparability between studies that is typical for methods that rely on correlation in gene expression. We apply FARO to a compendium of 242 diverse Arabidopsis microarray experimental factors, including phyto-hormones, stresses and pathogens, growth conditions/stages, tissue types and mutants. We also use FARO to confirm and further delineate the functions of Arabidopsis MAP kinase 4 in disease and stress responses. Furthermore, we find that a large, well-defined set of genes responds in opposing directions to different stress conditions and predict the effects of different stress combinations. This demonstrates the usefulness of our approach for exploiting public microarray data to derive biologically meaningful associations between experimental factors. Finally, our

Do Sophisticated Epistemic Beliefs Predict Meaningful Learning? Findings from a Structural Equation Model of Undergraduate Biology Learning

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Lee, Silvia Wen-Yu; Liang, Jyh-Chong; Tsai, Chin-Chung

2016-01-01

This study investigated the relationships among college students' epistemic beliefs in biology (EBB), conceptions of learning biology (COLB), and strategies of learning biology (SLB). EBB includes four dimensions, namely "multiple-source," "uncertainty," "development," and "justification." COLB is further…

Relationships between Flow Experience, Life Meaningfulness and Subjective Well-being in Music Students

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Martin Sedlár

2014-01-01

Full Text Available The study examines relationships between flow experience in musical activities, life meaningfulness and subjective well – being. Life meaningfulness belongs to eudaimonic good life, subjective well–being belongs to hedonic good life and flow seems to be combination of both approaches. It is supposed that flow experience in musical activity and life meaningfulness should have positive impact on subjective well –being. The research sample consisted of 96 university music students (37 males, 59 females from the Music and Dance Faculty, Academy of Performing Arts in Bratislava, Slovakia. Dispositional Flow Scale–2, which measures nine dimension of flow, was used for measuring frequency o f flow experience. Life Meaningfulness Scale, which measures three dimensions of life meaningfulness, was used for measuring meaningfulness of life. Positive and Negative Affect Schedule measured affective components of subjective well–being, and Satisfaction with Life Scale measured cognitive component of subjective well–being. Categorization revealed that the most favourite performing musical activities are creative musical activities, such as reproduction and production, during which music students relatively often experience flow. The results of correlation analysis showed that total scores of flow experience, life meaningfulness and components of subjective well–being, significantly correlate each other. Aspects of flow, clear goals and autotelic experience are positively related to cognitive and motivational dimension of life meaningfulness and also to positive affectivity. Loss of self–consciousness and autotelic experience are positively related to emotional dimension of life meaningfulness. Challenge–skill balance, action–awareness merging, clear goals, concentration on task at hand, sense of control and autotelic experience are negatively related to negative affectivity. Challenge–skill balance and autotelic experience are related to

Gene expression profiling--Opening the black box of plant ecosystem responses to global change

Energy Technology Data Exchange (ETDEWEB)

Leakey, A.D.B.; Ainsworth, E.A.; Bernard, S.M.; Markelz, R.J.C.; Ort, D.R.; Placella, S.A.P.; Rogers, A.; Smith, M.D.; Sudderth, E.A.; Weston, D.J.; Wullschleger, S.D.; Yuan, S.

2009-11-01

The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Since the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and non-model species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.

Investigation of the effect of ionizing radiation on gene expression variation by the 'DNA chips': feasibility of a biological dosimeter

International Nuclear Information System (INIS)

Gruel, G.

2005-01-01

After having described the different biological effects of ionizing radiation and the different approaches to biological dosimetry, and introduced 'DNA chips' or DNA micro-arrays, the author reports the characterization of gene expression variations in the response of cells to a gamma irradiation. Both main aspects of the use DNA chips are investigated: fundamental research and diagnosis. This research thesis thus proposes an analysis of the effect of ionizing radiation using DNA chips, notably by comparing gene expression modifications measured in mouse irradiated lung, heart and kidney. It reports a feasibility study of bio-dosimeter based on expression profiles

Audio-Visual and Meaningful Semantic Context Enhancements in Older and Younger Adults.

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Kirsten E Smayda

Full Text Available Speech perception is critical to everyday life. Oftentimes noise can degrade a speech signal; however, because of the cues available to the listener, such as visual and semantic cues, noise rarely prevents conversations from continuing. The interaction of visual and semantic cues in aiding speech perception has been studied in young adults, but the extent to which these two cues interact for older adults has not been studied. To investigate the effect of visual and semantic cues on speech perception in older and younger adults, we recruited forty-five young adults (ages 18-35 and thirty-three older adults (ages 60-90 to participate in a speech perception task. Participants were presented with semantically meaningful and anomalous sentences in audio-only and audio-visual conditions. We hypothesized that young adults would outperform older adults across SNRs, modalities, and semantic contexts. In addition, we hypothesized that both young and older adults would receive a greater benefit from a semantically meaningful context in the audio-visual relative to audio-only modality. We predicted that young adults would receive greater visual benefit in semantically meaningful contexts relative to anomalous contexts. However, we predicted that older adults could receive a greater visual benefit in either semantically meaningful or anomalous contexts. Results suggested that in the most supportive context, that is, semantically meaningful sentences presented in the audiovisual modality, older adults performed similarly to young adults. In addition, both groups received the same amount of visual and meaningful benefit. Lastly, across groups, a semantically meaningful context provided more benefit in the audio-visual modality relative to the audio-only modality, and the presence of visual cues provided more benefit in semantically meaningful contexts relative to anomalous contexts. These results suggest that older adults can perceive speech as well as younger

The relativity of biological function.

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Laubichler, Manfred D; Stadler, Peter F; Prohaska, Sonja J; Nowick, Katja

2015-12-01

Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literature to support certain claims, for instance about the fraction of "functional DNA" in the human genome. Here we argue that all biologically meaningful interpretations of function are necessarily context dependent. This implies that they derive their meaning as well as their range of applicability only within a specific theoretical and measurement context. We use this framework to shed light on the current debate about functional DNA and argue that without considering explicitly the theoretical and measurement contexts all attempts to integrate biological theories are prone to fail.

AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data

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Xia Yuannan

2006-12-01

Full Text Available Abstract Background DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amount of microarray data and make biological sense of them. Affymetrix GeneChips are widely used microarrays, where a variety of statistical algorithms have been explored and used for detecting significant genes in the experiment. These methods rely solely on the quantitative data, i.e., signal intensity; however, qualitative data are also important parameters in detecting differentially expressed genes. Results AffyMiner is a tool developed for detecting differentially expressed genes in Affymetrix GeneChip microarray data and for associating gene annotation and gene ontology information with the genes detected. AffyMiner consists of the functional modules, GeneFinder for detecting significant genes in a treatment versus control experiment and GOTree for mapping genes of interest onto the Gene Ontology (GO space; and interfaces to run Cluster, a program for clustering analysis, and GenMAPP, a program for pathway analysis. AffyMiner has been used for analyzing the GeneChip data and the results were presented in several publications. Conclusion AffyMiner fills an important gap in finding differentially expressed genes in Affymetrix GeneChip microarray data. AffyMiner effectively deals with multiple replicates in the experiment and takes into account both quantitative and qualitative data in identifying significant genes. AffyMiner reduces the time and effort needed to compare data from multiple arrays and to interpret the possible biological implications associated with significant changes in a gene's expression.

Meaningful Learning in the Cooperative Classroom

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Sharan, Yael

2015-01-01

Meaningful learning is based on more than what teachers transmit; it promotes the construction of knowledge out of learners' experience, feelings and exchanges with other learners. This educational view is based on the constructivist approach to learning and the co-operative learning approach. Researchers and practitioners in various…

The clinical implications and biologic relevance of neurofilament expression in gastroenteropancreatic neuroendocrine neoplasms.

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Schimmack, Simon; Lawrence, Ben; Svejda, Bernhard; Alaimo, Daniele; Schmitz-Winnenthal, Hubertus; Fischer, Lars; Büchler, Markus W; Kidd, Mark; Modlin, Irvin

2012-05-15

Although gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) exhibit widely divergent behavior, limited biologic information (apart from Ki-67) is available to characterize malignancy. Therefore, the identification of alternative biomarkers is a key unmet need. Given the role of internexin alpha (INA) in neuronal development, the authors assessed its function in neuroendocrine cell systems and the clinical implications of its expression as a GEP-NEN biomarker. Functional assays were undertaken to investigate the mechanistic role of INA in the pancreatic BON cell line. Expression levels of INA were investigated in 50 pancreatic NENs (43 primaries, 7 metastases), 43 small intestinal NENs (25 primaries, 18 metastases), normal pancreas (n = 10), small intestinal mucosa (n = 16), normal enterochromaffin (EC) cells (n = 9), mouse xenografts (n = 4) and NEN cell lines (n = 6) using quantitative polymerase chain reaction, Western blot, and immunostaining analyses. In BON cells, decreased levels of INA messenger RNA and protein were associated with the inhibition of both proliferation and mitogen-activated protein kinase (MAPK) signaling. INA was not expressed in normal neuroendocrine cells but was overexpressed (from 2-fold to 42-fold) in NEN cell lines and murine xenografts. In pancreatic NENs, INA was overexpressed compared with pancreatic adenocarcinomas and normal pancreas (27-fold [P = .0001], and 9-fold [P = .02], respectively). INA transcripts were correlated positively with Ki-67 (correlation coefficient [r] = 0.5; P biologic information relevant to delineation of both pancreatic NEN tumor phenotypes and clinical behavior. Copyright © 2011 American Cancer Society.

Conducting Expressively: Navigating Seven Misconceptions That Inhibit Meaningful Connection to Ensemble and Sound

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Snyder, Courtney

2016-01-01

When expressivity (ignited by imagination) is incorporated into the learning process for both the conductor (teacher) and player (student), the qualities of movement, communication, instruction, and ensemble sound all change for the better, often with less work. Expressive conducting allows the conductor to feel more connected to the music and the…

A meaningful workplace: Framework, space and context ...

African Journals Online (AJOL)

A meaningful workplace: Framework, space and context. ... PL Steenkamp, JS Basson ... The organisation experiences a loss of productivity, quality, innovation, et cetera ... This is what this article is about: to conceptualise the workplace as ...

Towards a More Biologically-meaningful Climate Characterization: Variability in Space and Time at Multiple Scales

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Christianson, D. S.; Kaufman, C. G.; Kueppers, L. M.; Harte, J.

2013-12-01

Sampling limitations and current modeling capacity justify the common use of mean temperature values in summaries of historical climate and future projections. However, a monthly mean temperature representing a 1-km2 area on the landscape is often unable to capture the climate complexity driving organismal and ecological processes. Estimates of variability in addition to mean values are more biologically meaningful and have been shown to improve projections of range shifts for certain species. Historical analyses of variance and extreme events at coarse spatial scales, as well as coarse-scale projections, show increasing temporal variability in temperature with warmer means. Few studies have considered how spatial variance changes with warming, and analysis for both temporal and spatial variability across scales is lacking. It is unclear how the spatial variability of fine-scale conditions relevant to plant and animal individuals may change given warmer coarse-scale mean values. A change in spatial variability will affect the availability of suitable habitat on the landscape and thus, will influence future species ranges. By characterizing variability across both temporal and spatial scales, we can account for potential bias in species range projections that use coarse climate data and enable improvements to current models. In this study, we use temperature data at multiple spatial and temporal scales to characterize spatial and temporal variability under a warmer climate, i.e., increased mean temperatures. Observational data from the Sierra Nevada (California, USA), experimental climate manipulation data from the eastern and western slopes of the Rocky Mountains (Colorado, USA), projected CMIP5 data for California (USA) and observed PRISM data (USA) allow us to compare characteristics of a mean-variance relationship across spatial scales ranging from sub-meter2 to 10,000 km2 and across temporal scales ranging from hours to decades. Preliminary spatial analysis at

Meaning in meaninglessness: The propensity to perceive meaningful patterns in coincident events and randomly arranged stimuli is linked to enhanced attention in early sensory processing.

Science.gov (United States)

Rominger, Christian; Schulter, Günter; Fink, Andreas; Weiss, Elisabeth M; Papousek, Ilona

2018-05-01

Perception of objectively independent events or stimuli as being significantly connected and the associated proneness to perceive meaningful patterns constitute part of the positive symptoms of schizophrenia, which are associated with altered attentional processes in lateralized speech perception. Since perceiving meaningful patterns is to some extent already prevalent in the general population, the aim of the study was to investigate whether the propensity to experience meaningful patterns in co-occurring events and random stimuli may be associated with similar altered attentional processes in lateralized speech perception. Self-reported and behavioral indicators of the perception of meaningful patterns were assessed in non-clinical individuals, along with EEG auditory evoked potentials during the performance of an attention related lateralized speech perception task (Dichotic Listening Test). A greater propensity to perceive meaningful patterns was associated with higher N1 amplitudes of the evoked potentials to the onset of the dichotically presented consonant-vowel syllables, indicating enhanced automatic attention in early sensory processing. The study suggests that more basic mechanisms in how people associate events may play a greater role in the cognitive biases that are manifest in personality expressions such as positive schizotypy, rather than that positive schizotypy moderates these cognitive biases directly. Copyright © 2017 Elsevier B.V. All rights reserved.

Operating Room Delays: Meaningful Use in Electronic Health Record.

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Van Winkle, Rachelle A; Champagne, Mary T; Gilman-Mays, Meri; Aucoin, Julia

2016-06-01

Perioperative areas are the most costly to operate and account for more than 40% of expenses. The high costs prompted one organization to analyze surgical delays through a retrospective review of their new electronic health record. Electronic health records have made it easier to access and aggregate clinical data; 2123 operating room cases were analyzed. Implementing a new electronic health record system is complex; inaccurate data and poor implementation can introduce new problems. Validating the electronic health record development processes determines the ease of use and the user interface, specifically related to user compliance with the intent of the electronic health record development. The revalidation process after implementation determines if the intent of the design was fulfilled and data can be meaningfully used. In this organization, the data fields completed through automation provided quantifiable, meaningful data. However, data fields completed by staff that required subjective decision making resulted in incomplete data nearly 24% of the time. The ease of use was further complicated by 490 permutations (combinations of delay types and reasons) that were built into the electronic health record. Operating room delay themes emerged notwithstanding the significant complexity of the electronic health record build; however, improved accuracy could improve meaningful data collection and a more accurate root cause analysis of operating room delays. Accurate and meaningful use of data affords a more reliable approach in quality, safety, and cost-effective initiatives.

Meaningful Use of School Health Data

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Johnson, Kathleen Hoy; Bergren, Martha Dewey

2011-01-01

Meaningful use (MU) of Electronic Health Records (EHRs) is an important development in the safety and security of health care delivery in the United States. Advancement in the use of EHRs occurred with the passage of the American Recovery and Reinvestment Act of 2009, which provides incentives for providers to support adoption and use of EHRs.…

Redefining meaningful age groups in the context of disease.

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Geifman, Nophar; Cohen, Raphael; Rubin, Eitan

2013-12-01

Age is an important factor when considering phenotypic changes in health and disease. Currently, the use of age information in medicine is somewhat simplistic, with ages commonly being grouped into a small number of crude ranges reflecting the major stages of development and aging, such as childhood or adolescence. Here, we investigate the possibility of redefining age groups using the recently developed Age-Phenome Knowledge-base (APK) that holds over 35,000 literature-derived entries describing relationships between age and phenotype. Clustering of APK data suggests 13 new, partially overlapping, age groups. The diseases that define these groups suggest that the proposed divisions are biologically meaningful. We further show that the number of different age ranges that should be considered depends on the type of disease being evaluated. This finding was further strengthened by similar results obtained from clinical blood measurement data. The grouping of diseases that share a similar pattern of disease-related reports directly mirrors, in some cases, medical knowledge of disease-age relationships. In other cases, our results may be used to generate new and reasonable hypotheses regarding links between diseases.

IINFLUENCE OF FREEZING AND PROLONGED STORAGE OF EXPRESSED BREAST MILK ON ITS NUTRITIVE, BIOLOGICAL VALUES AND MICROBIOLOGICAL SAFETY

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O. L. Lukoyanova

2011-01-01

Full Text Available Evaluation of prolonged storage of breast milk safety for nutrition of newborns remains actual problem of modern nutritiology. Objectives: to evaluate an influence of freezing and prolonged storage of expressed breast milk on its nutritive, biological values and microbiological safety. Methods: samples of expressed breast milk (native samples and after 1 and 3 months of storage in containers Philips AVENT in t -18°С were analyzed; levels of secretory IgA, lysozyme, transforming growth factor (TGF β1, potassium, calcium, magnesium, pH, buffer capacity and bacterial cells were detected. Results: there is no statistically significant influence of low temperature and prolonged storage of expressed breast milk on levels of secretory IgA, lysozyme, TGF β1 and bacterial cells. Potassium and calcium levels significantly decreased (on about 10% and 20% accordingly, pH increased, and buffer capacity of milk lowered after freezing during 3 months. Conclusion: children’s feeding with native and expressed breast milk defrosted after 3 months of storage is equal in nutritive and biological values and microbiological safety.

Stochastic biological response to radiation. Comprehensive analysis of gene expression

International Nuclear Information System (INIS)

Inoue, Tohru; Hirabayashi, Yoko

2012-01-01

Authors explain that the radiation effect on biological system is stochastic along the law of physics, differing from chemical effect, using instances of Cs-137 gamma-ray (GR) and benzene (BZ) exposures to mice and of resultant comprehensive analyses of gene expression. Single GR irradiation is done with Gamma Cell 40 (CSR) to C57BL/6 or C3H/He mouse at 0, 0.6 and 3 Gy. BE is given orally at 150 mg/kg/day for 5 days x 2 weeks. Bone marrow cells are sampled 1 month after the exposure. Comprehensive gene expression is analyzed by Gene Chip Mouse Genome 430 2.0 Array (Affymetrix) and data are processed by programs like case normalization, statistics, network generation, functional analysis etc. GR irradiation brings about changes of gene expression, which are classifiable in common genes variable commonly on the dose change and stochastic genes variable stochastically within each dose: e.g., with Welch-t-test, significant differences are between 0/3 Gy (dose-specific difference, 455 pbs (probe set), in stochastic 2113 pbs), 0/0.6 Gy (267 in 1284 pbs) and 0.6/3 Gy (532 pbs); and with one-way analysis of variation (ANOVA) and hierarchial/dendrographic analyses, 520 pbs are shown to involve the dose-dependent 226 and dose-specific 294 pbs. It is also shown that at 3 Gy, expression of common genes are rather suppressed, including those related to the proliferation/apoptosis of B/T cells, and of stochastic genes, related to cell division/signaling. Ven diagram of the common genes of above 520 pbs, stochastic 2113 pbs at 3 Gy and 1284 pbs at 0.6 Gy shows the overlapping genes 29, 2 and 4, respectively, indicating only 35 pbs are overlapping in total. Network analysis of changes by GR shows the rather high expression of genes around hub of cAMP response element binding protein (CREB) at 0.6 Gy, and rather variable expression around CREB hub/suppressed expression of kinesin hub at 3 Gy; in the network by BZ exposure, unchanged or low expression around p53 hub and suppression

Readiness for Meaningful Use of Health Information Tech...

Data.gov (United States)

U.S. Department of Health & Human Services — According to findings reported in Readiness for Meaningful Use of Health Information Technology and Patient Centered Medical Home Recognition Survey Results,...

The effect of biological sealants and adhesive treatments on matrix metalloproteinase expression during renal injury healing.

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José Miguel Lloris-Carsí

Full Text Available Renal injuries are relatively common in cases of abdominal trauma. Adhesives and sealants can be used to repair and preserve damaged organs. Using a rat model, this study explores the activity of different matrix metalloproteinases (MMP during the healing of renal injuries treated by two biological adhesives (TachoSil and GelitaSpon and a new synthetic elastic cyanoacrylate (Adhflex.Renal traumatic injuries were experimentally induced in 90 male Wistar rats by a Stiefel Biopsy Punch in the anterior aspect of the left kidney. Animals were divided into five groups: 1, sham non-injured (n = 3; 2, non-treated standard punch injury (n = 6; 3, punch injury treated with TachoSil (n = 27; 4, punch injury treated with GelitaSpon (n = 27; and, 5, punch injury treated with Adhflex (n = 27. Wound healing was evaluated 2, 6, and 18 days after injury by determining the expression of MMPs, and the histopathological evolution of lesions.Histologically, the wound size at 6 days post-injury was larger in Adhflex-treated samples than in the other treatments, but the scarring tissue was similar at 18 days post-injury. Only the MMPs subtypes 1, 2, 8, 9, and 13 were sufficiently expressed to be quantifiable. Both time since injury and treatment type had a significant influence on MMPs expression. Two days after injury, the expression of MMP8 and MMP9 was predominant. MMP2 expression was greater 6 days after injury. The Adhflex-treated group had a significantly higher MMPs expression than the other treatment groups at all healing stages.All three sealant treatments induced almost similar expression of MMPs than untreated animals indicating a physiological healing process. Given that all renal trauma injuries must be considered emergencies, both biological and synthetic adhesives, such as Adhflex, should be considered as a treatment options.

Reaping the benefits of meaningful work: The mediating versus moderating role of work engagement.

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Johnson, Matthew J; Jiang, Lixin

2017-08-01

This study examined whether meaningful work may improve one's quality of life outside of the workplace (i.e., work-to-life enrichment). More importantly, we proposed and tested competing hypotheses regarding the role of work engagement in the relationship between meaningful work and work-to-life enrichment. Specifically, we investigated whether work engagement served as a mediator of this relationship, as suggested by the job demands-resources model, or instead a moderator, as suggested by conservation of resources theory. Two-wave survey data were collected from 194 respondents recruited via Amazon Mechanical Turk. Analyses showed that meaningful work was positively related to work-to-life enrichment over time (i.e., 3 months later). Additionally, work engagement mediated but did not moderate the relationship between meaningful work at Time 1 and work-to-life enrichment at Time 2. We suggest that organizations foster a sense of meaningfulness in employees to facilitate engagement and in turn enrich employees' lives beyond the workplace. Therefore, not only organizations, but individuals as well may reap the benefits of meaningful work. Copyright © 2016 John Wiley & Sons, Ltd.

Annotating spatio-temporal datasets for meaningful analysis in the Web

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Stasch, Christoph; Pebesma, Edzer; Scheider, Simon

2014-05-01

More and more environmental datasets that vary in space and time are available in the Web. This comes along with an advantage of using the data for other purposes than originally foreseen, but also with the danger that users may apply inappropriate analysis procedures due to lack of important assumptions made during the data collection process. In order to guide towards a meaningful (statistical) analysis of spatio-temporal datasets available in the Web, we have developed a Higher-Order-Logic formalism that captures some relevant assumptions in our previous work [1]. It allows to proof on meaningful spatial prediction and aggregation in a semi-automated fashion. In this poster presentation, we will present a concept for annotating spatio-temporal datasets available in the Web with concepts defined in our formalism. Therefore, we have defined a subset of the formalism as a Web Ontology Language (OWL) pattern. It allows capturing the distinction between the different spatio-temporal variable types, i.e. point patterns, fields, lattices and trajectories, that in turn determine whether a particular dataset can be interpolated or aggregated in a meaningful way using a certain procedure. The actual annotations that link spatio-temporal datasets with the concepts in the ontology pattern are provided as Linked Data. In order to allow data producers to add the annotations to their datasets, we have implemented a Web portal that uses a triple store at the backend to store the annotations and to make them available in the Linked Data cloud. Furthermore, we have implemented functions in the statistical environment R to retrieve the RDF annotations and, based on these annotations, to support a stronger typing of spatio-temporal datatypes guiding towards a meaningful analysis in R. [1] Stasch, C., Scheider, S., Pebesma, E., Kuhn, W. (2014): "Meaningful spatial prediction and aggregation", Environmental Modelling & Software, 51, 149-165.

Expression and fast preparation of biologically active recombinant human coagulation factor VII in CHO-K1 cells.

Science.gov (United States)

Xiao, W; Li, C Q; Xiao, X P; Lin, F Z

2013-12-16

Human coagulation factor VII (FVII) plays an important role in the blood coagulation process and exists in micro amounts in human plasma; therefore, any attempt at the large-scale production of FVII in significant quantities is challenging. The purpose of this study was to express and obtain biologically active recombinant FVII (rFVII) from Chinese hamster ovary K1 (CHO-K1) cells. The full-length FVII cDNA was isolated from a HepG2 cell line and then subcloned in pcDNA3.1 to construct an expression vector, pcDNA-FVII. CHO-K1 cells were transfected with 1 µg pcDNA-FVII. The cell line that stably expressed secretory FVII was screened using 900 µg/mL G418. The FVII copy number in CHO-K1 cells was detected by quantitative polymerase chain reaction (qPCR). The rFVII was purified in ligand affinity chromatography medium. The purified protein was detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis. The biological activity of the purified FVII protein was determined by a prothrombin time assay. Three cell lines that permanently expressed rFVII were screened. The qPCR results demonstrated that each CHO-K1 cell harbored two FVII DNA copies. The SDS-PAGE and Western blot analysis showed that the purified protein was about 50 kDa. The purity of the target protein was 95%. The prothrombin time assay indicated that the FVII-specific activity of rFVII was 2573 ± 75 IU/mg. This method enabled the fast preparation of high-purity rFVII from CHO-K1 cells, and the purified protein had good biological activity.

BicPAMS: software for biological data analysis with pattern-based biclustering.

Science.gov (United States)

Henriques, Rui; Ferreira, Francisco L; Madeira, Sara C

2017-02-02

Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entities). However, given its computational complexity, only recent breakthroughs on pattern-based biclustering enabled efficient searches without the restrictions that state-of-the-art biclustering algorithms place on the structure and homogeneity of biclusters. As a result, pattern-based biclustering provides the unprecedented opportunity to discover non-trivial yet meaningful biological modules with putative functions, whose coherency and tolerance to noise can be tuned and made problem-specific. To enable the effective use of pattern-based biclustering by the scientific community, we developed BicPAMS (Biclustering based on PAttern Mining Software), a software that: 1) makes available state-of-the-art pattern-based biclustering algorithms (BicPAM (Henriques and Madeira, Alg Mol Biol 9:27, 2014), BicNET (Henriques and Madeira, Alg Mol Biol 11:23, 2016), BicSPAM (Henriques and Madeira, BMC Bioinforma 15:130, 2014), BiC2PAM (Henriques and Madeira, Alg Mol Biol 11:1-30, 2016), BiP (Henriques and Madeira, IEEE/ACM Trans Comput Biol Bioinforma, 2015), DeBi (Serin and Vingron, AMB 6:1-12, 2011) and BiModule (Okada et al., IPSJ Trans Bioinf 48(SIG5):39-48, 2007)); 2) consistently integrates their dispersed contributions; 3) further explores additional accuracy and efficiency gains; and 4) makes available graphical and application programming interfaces. Results on both synthetic and real data confirm the relevance of BicPAMS for biological data analysis, highlighting its essential role for the discovery of putative modules with non-trivial yet biologically significant functions from expression and network data. BicPAMS is the first biclustering tool offering the

Remedial principles and meaningful engagement in education ...

African Journals Online (AJOL)

This article evaluates the meaningful engagement doctrine in the education rights jurisprudence of the Constitutional Court in the light of a set of normative principles developed by Susan Sturm for evaluating participatory public law remedies. It commences by identifying four principles for evaluating participatory remedies ...

Fishing for meaningful units in connected speech

DEFF Research Database (Denmark)

Henrichsen, Peter Juel; Christiansen, Thomas Ulrich

2009-01-01

In many branches of spoken language analysis including ASR, the set of smallest meaningful units of speech is taken to coincide with the set of phones or phonemes. However, fishing for phones is difficult, error-prone, and computationally expensive. We present an experiment, based on machine...

Biological and immunogenic properties of rabies virus glycoprotein expressed by canine herpesvirus vector.

Science.gov (United States)

Xuan, X; Tuchiya, K; Sato, I; Nishikawa, Y; Onoderaz, Y; Takashima, Y; Yamamoto, A; Katsumata, A; Iwata, A; Ueda, S; Mikami, T; Otsuka, H

1998-01-01

In order to evaluate whether canine herpesvirus (CHV) could be used as a live vector for the expression of heterologous immunogenes, we constructed a recombinant canine herpesvirus (CHV) expressing glycoprotein (G protein) of rabies virus (RV). The gene of G protein was inserted within the thymidine kinase gene of CHV YP11mu strain under the control of the human cytomegalovirus immediate early promoter. The G protein expressed by the recombinant CHV was processed and transported to the cell surface as in RV infected cells, and showed the same biological activities such as low pH dependent cell fusion and hemadsorption. The antigenic authenticity of the recombinant G protein was confirmed by a panel of monoclonal antibodies specific for G protein. Dogs inoculated intransally with the recombinant CHV produced higher titres of virus neutralizing antibodies against RV than those inoculated with a commercial, inactivated rabies vaccine. These results suggest that the CHV recombinant expressing G protein can be used as a vaccine to control canine rabies and that CHV may be useful as a vector to develop live recombinant against other infectious diseases in dogs.

Novel topological descriptors for analyzing biological networks

Directory of Open Access Journals (Sweden)

Varmuza Kurt K

2010-06-01

Full Text Available Abstract Background Topological descriptors, other graph measures, and in a broader sense, graph-theoretical methods, have been proven as powerful tools to perform biological network analysis. However, the majority of the developed descriptors and graph-theoretical methods does not have the ability to take vertex- and edge-labels into account, e.g., atom- and bond-types when considering molecular graphs. Indeed, this feature is important to characterize biological networks more meaningfully instead of only considering pure topological information. Results In this paper, we put the emphasis on analyzing a special type of biological networks, namely bio-chemical structures. First, we derive entropic measures to calculate the information content of vertex- and edge-labeled graphs and investigate some useful properties thereof. Second, we apply the mentioned measures combined with other well-known descriptors to supervised machine learning methods for predicting Ames mutagenicity. Moreover, we investigate the influence of our topological descriptors - measures for only unlabeled vs. measures for labeled graphs - on the prediction performance of the underlying graph classification problem. Conclusions Our study demonstrates that the application of entropic measures to molecules representing graphs is useful to characterize such structures meaningfully. For instance, we have found that if one extends the measures for determining the structural information content of unlabeled graphs to labeled graphs, the uniqueness of the resulting indices is higher. Because measures to structurally characterize labeled graphs are clearly underrepresented so far, the further development of such methods might be valuable and fruitful for solving problems within biological network analysis.

Designing Meaningful Game Experiences for Rehabilitation and Sustainable Mobility Settings

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Silvia Gabrielli

2014-03-01

Full Text Available This paper presents the approach followed in two ongoing research projects aimed to designing meaningful game-based experiences to support home rehabilitation, eco-sustainable mobility goals and more in general better daily lifestyles. We first introduce the need for designing meaningful game-based experiences that are well-connected to the relevant non-game settings and can be customized by/for users, then, we show examples of how this approach can be realized in the rehabilitation and sustainable mobility contexts.

Dogs Evaluate Threatening Facial Expressions by Their Biological Validity--Evidence from Gazing Patterns.

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Sanni Somppi

Full Text Available Appropriate response to companions' emotional signals is important for all social creatures. The emotional expressions of humans and non-human animals have analogies in their form and function, suggesting shared evolutionary roots, but very little is known about how animals other than primates view and process facial expressions. In primates, threat-related facial expressions evoke exceptional viewing patterns compared with neutral or positive stimuli. Here, we explore if domestic dogs (Canis familiaris have such an attentional bias toward threatening social stimuli and whether observed emotional expressions affect dogs' gaze fixation distribution among the facial features (eyes, midface and mouth. We recorded the voluntary eye gaze of 31 domestic dogs during viewing of facial photographs of humans and dogs with three emotional expressions (threatening, pleasant and neutral. We found that dogs' gaze fixations spread systematically among facial features. The distribution of fixations was altered by the seen expression, but eyes were the most probable targets of the first fixations and gathered longer looking durations than mouth regardless of the viewed expression. The examination of the inner facial features as a whole revealed more pronounced scanning differences among expressions. This suggests that dogs do not base their perception of facial expressions on the viewing of single structures, but the interpretation of the composition formed by eyes, midface and mouth. Dogs evaluated social threat rapidly and this evaluation led to attentional bias, which was dependent on the depicted species: threatening conspecifics' faces evoked heightened attention but threatening human faces instead an avoidance response. We propose that threatening signals carrying differential biological validity are processed via distinctive neurocognitive pathways. Both of these mechanisms may have an adaptive significance for domestic dogs. The findings provide a novel

Independent component analysis reveals new and biologically significant structures in micro array data

Directory of Open Access Journals (Sweden)

Veerla Srinivas

2006-06-01

Full Text Available Abstract Background An alternative to standard approaches to uncover biologically meaningful structures in micro array data is to treat the data as a blind source separation (BSS problem. BSS attempts to separate a mixture of signals into their different sources and refers to the problem of recovering signals from several observed linear mixtures. In the context of micro array data, "sources" may correspond to specific cellular responses or to co-regulated genes. Results We applied independent component analysis (ICA to three different microarray data sets; two tumor data sets and one time series experiment. To obtain reliable components we used iterated ICA to estimate component centrotypes. We found that many of the low ranking components indeed may show a strong biological coherence and hence be of biological significance. Generally ICA achieved a higher resolution when compared with results based on correlated expression and a larger number of gene clusters with significantly enriched for gene ontology (GO categories. In addition, components characteristic for molecular subtypes and for tumors with specific chromosomal translocations were identified. ICA also identified more than one gene clusters significant for the same GO categories and hence disclosed a higher level of biological heterogeneity, even within coherent groups of genes. Conclusion Although the ICA approach primarily detects hidden variables, these surfaced as highly correlated genes in time series data and in one instance in the tumor data. This further strengthens the biological relevance of latent variables detected by ICA.

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

Directory of Open Access Journals (Sweden)

Gao Shouguo

2011-08-01

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

Callings, work role fit, psychological meaningfulness and work ...

African Journals Online (AJOL)

meaningful work experiences, which also impact individuals' work .... group 25 to 29 years. .... significant chi-squared difference tests, after these path deletions, indicated that .... Counseling Psychology, 59:479-485. doi: 10.1037/a0028949.

Construction of new synthetic biology tools for the control of gene expression in the cyanobacterium Synechococcus sp. strain PCC 7002.

Science.gov (United States)

Zess, Erin K; Begemann, Matthew B; Pfleger, Brian F

2016-02-01

Predictive control of gene expression is an essential tool for developing synthetic biological systems. The current toolbox for controlling gene expression in cyanobacteria is a barrier to more in-depth genetic analysis and manipulation. Towards relieving this bottleneck, this work describes the use of synthetic biology to construct an anhydrotetracycline-based induction system and adapt a trans-acting small RNA (sRNA) system for use in the cyanobacterium Synechococcus sp. strain PCC 7002. An anhydrotetracycline-inducible promoter was developed to maximize intrinsic strength and dynamic range. The resulting construct, PEZtet , exhibited tight repression and a maximum 32-fold induction upon addition of anhydrotetracycline. Additionally, a sRNA system based on the Escherichia coli IS10 RNA-IN/OUT regulator was adapted for use in Synechococcus sp. strain PCC 7002. This system exhibited 70% attenuation of target gene expression, providing a demonstration of the use of sRNAs for differential gene expression in cyanobacteria. These systems were combined to produce an inducible sRNA system, which demonstrated 59% attenuation of target gene expression. Lastly, the role of Hfq, a critical component of sRNA systems in E. coli, was investigated. Genetic studies showed that the Hfq homolog in Synechococcus sp. strain PCC 7002 did not impact repression by the engineered sRNA system. In summary, this work describes new synthetic biology tools that can be applied to physiological studies, metabolic engineering, or sRNA platforms in Synechococcus sp. strain PCC 7002. © 2015 Wiley Periodicals, Inc.

The journey of primary care practices to meaningful use: a Colorado Beacon Consortium study.

Science.gov (United States)

Fernald, Douglas H; Wearner, Robyn; Dickinson, W Perry

2013-01-01

The Health Information Technology for Economic and Clinical Health Act of 2009 provides for incentive payments through Medicare and Medicaid for clinicians who implement electronic health records (EHRs) and use this technology meaningfully to improve patient care. There are few comprehensive descriptions of how primary care practices achieve the meaningful use of clinical data, including the formal stage 1 meaningful use requirements. Evaluation of the Colorado Beacon Consortium project included iterative qualitative analysis of practice narratives, provider and staff interviews, and separate focus groups with quality improvement (QI) advisors and staff from the regional health information exchange (HIE). Most practices described significant realignment of practice priorities and aims, which often required substantial education and training of physicians and staff. Re-engineering office processes, data collection protocols, EHRs, staff roles, and practice culture comprised the primary effort and commitment to attest to stage 1 meaningful use and subsequent meaningful use of clinical data. While realizing important benefits, practices bore a significant burden in learning the true capabilities of their EHRs with little effective support from vendors. Attestation was an important initial milestone in the process, but practices faced substantial ongoing work to use their data meaningfully for patient care and QI. Key resources were instrumental to these practices: local technical EHR expertise; collaborative learning mechanisms; and regular contact and support from QI advisors. Meeting the stage 1 requirements for incentives under Medicare and Medicaid meaningful use criteria is the first waypoint in a longer journey by primary care practices to the meaningful use of electronic data to continuously improve the care and health of their patients. The intensive re-engineering effort for stage 1 yielded practice changes consistent with larger practice aims and goals

Multiscale Embedded Gene Co-expression Network Analysis.

Directory of Open Access Journals (Sweden)

Won-Min Song

2015-11-01

Full Text Available Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3, the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA by: i introducing quality control of co-expression similarities, ii parallelizing embedded network construction, and iii developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs. We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA. MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

Multiscale Embedded Gene Co-expression Network Analysis.

Science.gov (United States)

Song, Won-Min; Zhang, Bin

2015-11-01

Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG) has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3), the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA) by: i) introducing quality control of co-expression similarities, ii) parallelizing embedded network construction, and iii) developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs). We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA). MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

Do sophisticated epistemic beliefs predict meaningful learning? Findings from a structural equation model of undergraduate biology learning

Science.gov (United States)

Lee, Silvia Wen-Yu; Liang, Jyh-Chong; Tsai, Chin-Chung

2016-10-01

This study investigated the relationships among college students' epistemic beliefs in biology (EBB), conceptions of learning biology (COLB), and strategies of learning biology (SLB). EBB includes four dimensions, namely 'multiple-source,' 'uncertainty,' 'development,' and 'justification.' COLB is further divided into 'constructivist' and 'reproductive' conceptions, while SLB represents deep strategies and surface learning strategies. Questionnaire responses were gathered from 303 college students. The results of the confirmatory factor analysis and structural equation modelling showed acceptable model fits. Mediation testing further revealed two paths with complete mediation. In sum, students' epistemic beliefs of 'uncertainty' and 'justification' in biology were statistically significant in explaining the constructivist and reproductive COLB, respectively; and 'uncertainty' was statistically significant in explaining the deep SLB as well. The results of mediation testing further revealed that 'uncertainty' predicted surface strategies through the mediation of 'reproductive' conceptions; and the relationship between 'justification' and deep strategies was mediated by 'constructivist' COLB. This study provides evidence for the essential roles some epistemic beliefs play in predicting students' learning.

Demands–abilities fit, work beliefs, meaningful work and engagement in nature-based jobs

Directory of Open Access Journals (Sweden)

Nellie de Crom

2018-03-01

Full Text Available Orientation: Meaningful work and personal engagement are important dimensions of flourishing of employees, especially when individuals work in challenging jobs. Research purpose: This study aimed to investigate the relationship between demands–abilities fit, work beliefs, meaningful work and engagement in individuals in nature-based jobs. Motivation for the study: Individuals working in nature often work under challenging circumstances without the necessary resources. A research gap exists regarding the effects of demands–abilities fit and work beliefs on meaningful work. It is also not clear how these antecedents and meaningful work will impact the engagement of individuals working in nature. Research approach, design and method: A cross-sectional survey was used with a convenience sample of 161 nature-based employees. Data were collected using a structured online questionnaire consisting of items from the demands–abilities fit scale, work–life questionnaire, work and meaning Inventory, work engagement scale and a biographical questionnaire. Main findings: Work beliefs (calling, career and job and demands–abilities fit predicted a large percentage of the variance in meaning making. Work beliefs (calling and job and demands–abilities fit also predicted a large percentage of the variance in greater good motivations. Demands–abilities fit and a calling work orientation indirectly affected work engagement via meaningful work. The scales which measured calling and job orientations showed insufficient discriminant validity in relation to the scales which measured positive meaning and work engagement. Practical and managerial implications: Managers should consider implementing interventions to affect the demands–abilities fit (through human resource management interventions and work beliefs of individuals working in nature (through job crafting. Promoting perceptions of meaningful work might contribute to higher personal engagement

Emotional, Biological, and Cognitive Impact of a Brief Expressive Writing Intervention for Women at Familial Breast Cancer Risk

National Research Council Canada - National Science Library

Valdimarsdottir, Heiddis

2006-01-01

...) than women without familial breast cancer risk. The proposed study will examine the impact of an expressive writing intervention on emotional biological and cognitive processes among women at familial breast cancer risk...

Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species.

Science.gov (United States)

Adams, Matthew P; Collier, Catherine J; Uthicke, Sven; Ow, Yan X; Langlois, Lucas; O'Brien, Katherine R

2017-01-04

When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (T opt ) for maximum photosynthetic rate (P max ). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike.

Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species

Science.gov (United States)

Adams, Matthew P.; Collier, Catherine J.; Uthicke, Sven; Ow, Yan X.; Langlois, Lucas; O'Brien, Katherine R.

2017-01-01

When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (Topt) for maximum photosynthetic rate (Pmax). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike.

Wonderful Life : Exploring Wonder in Meaningful Moments

NARCIS (Netherlands)

van de Goor, Marie Jacqueline; Sools, Anna Maria; Westerhof, Gerben Johan; Bohlmeijer, Ernst Thomas

In this article, we bring the study of meaning together with the emerging field of study focusing on the emotions of wonder: wonder, enchantment, awe, and being moved. It is in meaningful moments that these two meet, and in our empirical study, we used the emotions of wonder as a lens to investigate

The Omaha system and meaningful use: applications for practice, education, and research.

Science.gov (United States)

Martin, Karen S; Monsen, Karen A; Bowles, Kathryn H

2011-01-01

Meaningful use has become ubiquitous in the vocabulary of health information technology. It suggests that better healthcare does not result from the adoption of technology and electronic health records, but by increasing interoperability and informing clinical decisions at the point of care. Although the initial application of meaningful use was limited to eligible professionals and hospitals, it incorporates complex processes and workflow that involve all nurses, other healthcare practitioners, and settings. The healthcare community will become more integrated, and interdisciplinary practitioners will provide enhanced patient-centered care if electronic health records adopt the priorities of meaningful use. Standardized terminologies are a necessary component of such electronic health records. The Omaha System is an exemplar of a standardized terminology that enables meaningful use of clinical data to support and improve patient-centered clinical practice, education, and research. It is user-friendly, generates data that can be shared with patients and their families, and enables healthcare providers to analyze and exchange patient-centered coded data. Use of the Omaha System is increasing steadily in diverse practice, education, and research settings nationally and internationally.

Using Mobile Tools to Support Meaningful Work-based Learning in Vocational Education

Directory of Open Access Journals (Sweden)

Hanna Vuojärvi

2016-11-01

Full Text Available This case study focused on meaningful work-based learning (WBL and the pedagogical use of mobile information and communication technologies (ICTs in vocational tourism education. The aim was to reveal how teaching/tutoring and learning are realized and how the use of smartphones supports the realization of meaningful learning characteristics during WBL periods in highly versatile environments. Within a design-based research framework, the data was collected through learning journals written by students and qualitative interviews. The results of thematic analysis were used to develop a practice-oriented pedagogical model for meaningful WBL. The model visualizes the roles of students, teachers, and companies involved in WBL, the meaningful learning characteristics that can be amplified through the use of mobile ICTs, and the outcomes for each stakeholder. The model suggests structuring WBL through four negotiations involving a student, a teacher, and a company to assure that each student has clearly formulated learning goals and possibilities to pursue those goals regardless of the mobility of their work or facilities during their WBL period.

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

Directory of Open Access Journals (Sweden)

Tintle Nathan L

2012-08-01

Full Text Available Abstract Background Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. Results We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Conclusions Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

Meaningful Use of a Confidential Adolescent Patient Portal.

Science.gov (United States)

Thompson, Lindsay A; Martinko, Thomas; Budd, Pamela; Mercado, Rebeccah; Schentrup, Anzeela M

2016-02-01

To design and evaluate the usage of an adolescent patient portal specifically adapted for adolescent health care needs that also satisfied institutional meaningful use guidelines regarding electronic health records. Key stakeholders at one academic health care center adopted an online portal and opted to designate a patient portal specifically for adolescents to maximize confidentiality in compliance with state privacy laws. This study analyzed aggregate electronic health record data of adolescents' (ages 12-17.9 years) uptake, usage, and functionality of this portal and compared it to parent portal usage for younger children (ages 0-11 years). Differences in means were calculated using paired t tests. The portal was used similarly between parents of young children and adolescents, with almost 1,000 enrollees in each group from September 1, 2012 to March 31, 2015. There were no gender differences in enrollment. Adolescents were less likely than parents of younger children to review appointments (73% vs. 85%), laboratory tests (67% vs. 79%), problem lists (40% vs. 78%), or allergies (45% vs. 77%, all p values adolescents sent 1,397 confidential messages. Institutional decisions for implementing meaningful use requirements can align with goals of adolescent health. Patient portals can enhance adolescent health care quality and adolescents readily use a confidential portal. Implementation of meaningful use requirements should be checked against adolescent health care needs to maximize confidentiality and promote health communication. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Effects of simulated microgravity on gene expression and biological phenotypes of a single generation Caenorhabditis elegans cultured on 2 different media.

Science.gov (United States)

Tee, Ling Fei; Neoh, Hui-Min; Then, Sue Mian; Murad, Nor Azian; Asillam, Mohd Fairos; Hashim, Mohd Helmy; Nathan, Sheila; Jamal, Rahman

2017-11-01

Studies of multigenerational Caenorhabditis elegans exposed to long-term spaceflight have revealed expression changes of genes involved in longevity, DNA repair, and locomotion. However, results from spaceflight experiments are difficult to reproduce as space missions are costly and opportunities are rather limited for researchers. In addition, multigenerational cultures of C. elegans used in previous studies contribute to mixture of gene expression profiles from both larvae and adult worms, which were recently reported to be different. Usage of different culture media during microgravity simulation experiments might also give rise to differences in the gene expression and biological phenotypes of the worms. In this study, we investigated the effects of simulated microgravity on the gene expression and biological phenotype profiles of a single generation of C. elegans worms cultured on 2 different culture media. A desktop Random Positioning Machine (RPM) was used to simulate microgravity on the worms for approximately 52 to 54 h. Gene expression profile was analysed using the Affymetrix GeneChip® C. elegans 1.0 ST Array. Only one gene (R01H2.2) was found to be downregulated in nematode growth medium (NGM)-cultured worms exposed to simulated microgravity. On the other hand, eight genes were differentially expressed for C. elegans Maintenance Medium (CeMM)-cultured worms in microgravity; six were upregulated, while two were downregulated. Five of the upregulated genes (C07E3.15, C34H3.21, C32D5.16, F35H8.9 and C34F11.17) encode non-coding RNAs. In terms of biological phenotype, we observed that microgravity-simulated worms experienced minimal changes in terms of lifespan, locomotion and reproductive capabilities in comparison with the ground controls. Taking it all together, simulated microgravity on a single generation of C. elegans did not confer major changes to their gene expression and biological phenotype. Nevertheless, exposure of the worms to microgravity

Sweeping the Floor or Putting a Man on the Moon: How to Define and Measure Meaningful Work.

Science.gov (United States)

Both-Nwabuwe, Jitske M C; Dijkstra, Maria T M; Beersma, Bianca

2017-01-01

Meaningful work is integral to well-being and a flourishing life. The construct of "meaningful work" is, however, consistently affected by conceptual ambiguity. Although there is substantial support for arguments to maintain the status of conceptual ambiguity, we make a case for the benefits of having consensus on a definition and scale of meaningful work in the context of paid work. The objective of this article, therefore, was twofold. Firstly, we wanted to develop a more integrative definition of meaningful work. Secondly, we wanted to establish a corresponding operationalization. We reviewed the literature on the existing definitions of meaningful work and the scales designed to measure it. We found 14 definitions of meaningful work. Based on these definitions, we identified four categories of definitions, which led us to propose an integrative and comprehensive definition of meaningful work. We identified two validated scales that were partly aligned with the proposed definition. Based on our review, we conclude that scholars in this field should coalesce rather than diverge their efforts to conceptualize and measure meaningful work.

Biological Characteristics of Caspase-14 and Its Expression in Neoplastic Diseases in the View of Translational Medicine

Directory of Open Access Journals (Sweden)

Kang-sheng LIU

2016-06-01

Full Text Available Caspase-14, a member of caspase family, only exists in mammals. As the most divergent member in the family of mammalian caspases, caspase-14 displays a variety of unique characteristics. It is expressed in a limited number of tissues and has the shortest amino acid sequence within the caspase protein family. At present, it has been found that caspase-14 is functionally different from the inflammatory reaction group of typical caspase family members. It exerts a certain effect in the promotion of final differentiation of epidermal cells and hydration of stratum corneum so as to maintain the steady state of skin barrier. In recent years, caspase-14 expression has been discovered in neoplastic diseases. Translational medicine integrates experimental research results and clinical guidance into the optimal implementation criteria for promoting the prediction, prevention and treatment of diseases. Via human genomics and molecular biology, translational medicine offers a possibility of screening molecular markers so that it can be used to diagnose the neoplastic diseases. In this article, the biological characteristics and substrates of caspase-14 as well as its expression in embryonic period and neoplastic diseases were reviewed.

Assessing Assessment: In Pursuit of Meaningful Learning

Science.gov (United States)

Rootman-le Grange, Ilse; Blackie, Margaret A. L.

2018-01-01

The challenge of supporting the development of meaningful learning is prevalent in chemistry education research. One of the core activities used in the learning process is assessments. The aim of this paper is to illustrate how the semantics dimension of Legitimation Code Theory can be a helpful tool to critique the quality of assessments and…

Gene expression analysis of zebrafish melanocytes, iridophores, and retinal pigmented epithelium reveals indicators of biological function and developmental origin.

Directory of Open Access Journals (Sweden)

Charles W Higdon

Full Text Available In order to facilitate understanding of pigment cell biology, we developed a method to concomitantly purify melanocytes, iridophores, and retinal pigmented epithelium from zebrafish, and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co-enrichment in melanocytes and retinal pigmented epithelium, as well as in melanocytes and iridophores. We found 214 genes co-enriched in melanocytes and retinal pigmented epithelium, indicating the shared functions of melanin-producing cells. We found 62 genes significantly co-enriched in melanocytes and iridophores, illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine-based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate-limiting substrate for purine synthesis, phosphoribosyl pyrophosphate, thus constituting a guanine cycle. The purification procedure and expression analysis described here, along with the accompanying transcriptome-wide expression data, provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types, and will be a useful resource for further studies of pigment cell biology.

Integration of gene expression and methylation to unravel biological networks in glioblastoma patients.

Science.gov (United States)

Gadaleta, Francesco; Bessonov, Kyrylo; Van Steen, Kristel

2017-02-01

The vast amount of heterogeneous omics data, encompassing a broad range of biomolecular information, requires novel methods of analysis, including those that integrate the available levels of information. In this work, we describe Regression2Net, a computational approach that is able to integrate gene expression and genomic or methylation data in two steps. First, penalized regressions are used to build Expression-Expression (EEnet) and Expression-Genomic or Expression-Methylation (EMnet) networks. Second, network theory is used to highlight important communities of genes. When applying our approach, Regression2Net to gene expression and methylation profiles for individuals with glioblastoma multiforme, we identified, respectively, 284 and 447 potentially interesting genes in relation to glioblastoma pathology. These genes showed at least one connection in the integrated networks ANDnet and XORnet derived from aforementioned EEnet and EMnet networks. Although the edges in ANDnet occur in both EEnet and EMnet, the edges in XORnet occur in EMnet but not in EEnet. In-depth biological analysis of connected genes in ANDnet and XORnet revealed genes that are related to energy metabolism, cell cycle control (AATF), immune system response, and several cancer types. Importantly, we observed significant overrepresentation of cancer-related pathways including glioma, especially in the XORnet network, suggesting a nonignorable role of methylation in glioblastoma multiforma. In the ANDnet, we furthermore identified potential glioma suppressor genes ACCN3 and ACCN4 linked to the NBPF1 neuroblastoma breakpoint family, as well as numerous ABC transporter genes (ABCA1, ABCB1) suggesting drug resistance of glioblastoma tumors. © 2016 WILEY PERIODICALS, INC.

Engagement and Skill Development in Biology Students through Analysis of Art

Science.gov (United States)

Milkova, Liliana; Crossman, Colette; Wiles, Stephanie; Allen, Taylor

2013-01-01

An activity involving analysis of art in biology courses was designed with the goals of piquing undergraduates’ curiosity, broadening the ways in which college students meaningfully engage with course content and concepts, and developing aspects of students’ higher-level thinking skills, such as analysis, synthesis, and evaluation. To meet these learning outcomes, the activity had three key components: preparatory readings, firsthand visual analysis of art during a visit to an art museum, and communication of the analysis. Following a presentation on the methodology of visual analysis, students worked in small groups to examine through the disciplinary lens of biology a selection of approximately 12 original artworks related in some manner to love. The groups then developed and presented for class members a mini-exhibition of several pieces addressing one of two questions: 1) whether portrayals of love in art align with the growing understanding of the biology of love or 2) whether the bodily experience of love is universal or, alternatively, is culturally influenced, as is the experience of depression. Evaluation of quantitative and qualitative assessment data revealed that the assignment engaged students, supported development of higher-level thinking skills, and prompted meaningful engagement with course material. PMID:24297295

Engagement and skill development in biology students through analysis of art.

Science.gov (United States)

Milkova, Liliana; Crossman, Colette; Wiles, Stephanie; Allen, Taylor

2013-01-01

An activity involving analysis of art in biology courses was designed with the goals of piquing undergraduates' curiosity, broadening the ways in which college students meaningfully engage with course content and concepts, and developing aspects of students' higher-level thinking skills, such as analysis, synthesis, and evaluation. To meet these learning outcomes, the activity had three key components: preparatory readings, first-hand visual analysis of art during a visit to an art museum, and communication of the analysis. Following a presentation on the methodology of visual analysis, students worked in small groups to examine through the disciplinary lens of biology a selection of approximately 12 original artworks related in some manner to love. The groups then developed and presented for class members a mini-exhibition of several pieces addressing one of two questions: 1) whether portrayals of love in art align with the growing understanding of the biology of love or 2) whether the bodily experience of love is universal or, alternatively, is culturally influenced, as is the experience of depression. Evaluation of quantitative and qualitative assessment data revealed that the assignment engaged students, supported development of higher-level thinking skills, and prompted meaningful engagement with course material.

Oral cancer cells with different potential of lymphatic metastasis displayed distinct biologic behaviors and gene expression profiles.

Science.gov (United States)

Zhuang, Zhang; Jian, Pan; Longjiang, Li; Bo, Han; Wenlin, Xiao

2010-02-01

Oral squamous cell carcinoma (OSCC) often spreads from the primary tumor to regional lymph nodes in the early stage. Better understanding of the biology of lymphatic spread of oral cancer cells is important for improving the survival rate of cancer patients. We established the cell line LNMTca8113 by repeated injections in foot pads of nude mice, which had a much higher lymphatic metastasis rate than its parental cell line Tca8113. Then, we compared the biologic behaviors of cancer cells between them. Moreover, microarray-based expression profiles between them were also compared, and a panel of differential genes was validated using real-time-PCR. In contrast to Tca8113 cells, LNMTca8113 cells were more proliferative and resistant to apoptosis in the absence of serum, and had enhanced ability of inducing capillary-like structures. Moreover, microarray-based expression profiles between them identified 1341 genes involved in cell cycle, cell adhesion, lymphangiogenesis, regulation of apoptosis, and so on. Some genes dedicating to the metastatic potential, including JAM2, TNC, CTSC, LAMB1, VEGFC, HAPLN1, ACPP, GDF9 and FGF11, were upregulated in LNMTca8113 cells. These results suggested that LNMTca8113 and Tca8113 cells were proper models for lymphatic metastasis study because there were differences in biologic behaviors and metastasis-related genes between them. Additionally, the differentially expressed gene profiles in cancer progression may be helpful in exploring therapeutic targets and provide the foundation for further functional validation of these specific candidate genes for OSCC.

Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis

Science.gov (United States)

Scott, RE; Ghule, PN; Stein, JL; Stein, GS

2015-01-01

The early stages of carcinogenesis are linked to defects in the cell cycle. A series of cell cycle checkpoints are involved in this process. The G1/S checkpoint that serves to integrate the control of cell proliferation and differentiation is linked to carcinogenesis and the mitotic spindle checkpoint with the development of chromosomal instability. This paper presents the outcome of systems biology studies designed to evaluate if networks of covariate cell cycle gene transcripts exist in proliferative mammalian tissues including mice, rats and humans. The GeneNetwork website that contains numerous gene expression datasets from different species, sexes and tissues represents the foundational resource for these studies (www.genenetwork.org). In addition, WebGestalt, a gene ontology tool, facilitated the identification of expression networks of genes that co-vary with key cell cycle targets, especially Cdc20 and Plk1 (www.bioinfo.vanderbilt.edu/webgestalt). Cell cycle expression networks of such covariate mRNAs exist in multiple proliferative tissues including liver, lung, pituitary, adipose and lymphoid tissues among others but not in brain or retina that have low proliferative potential. Sixty-three covariate cell cycle gene transcripts (mRNAs) compose the average cell cycle network with p = e−13 to e−36. Cell cycle expression networks show species, sex and tissue variability and they are enriched in mRNA transcripts associated with mitosis many of which are associated with chromosomal instability. PMID:25808367

What Do Beginner Biology Teacher Candidates Know of Genetics and Genes?

Science.gov (United States)

Oztas, Fulya; Oztas, Haydar

2016-01-01

Misconceptions are a barrier to understanding biology hence, to promote meaningful learning, it is necessary to overcome these difficulties with the help of different instructional methods rather than traditional instructional methods. Therefore it could be very interesting to find out "how students' prior knowledge of genetics affects…

Pengaruh Job Enrichment terhadap Employee Engagement melalui Psychological Meaningfulness sebagai Mediator

OpenAIRE

Sungkit, Flavia Norpina; Meiyanto, IJK Sito

2015-01-01

The purpose of the study is to investigate the influence of job enrichment toward employee engagement through psychological meaningfulness as the mediator. Research design used is a cross-sectional study of 112 employees. Data is analyzed by multiple linear regression analysis. Result shows job enrichment is able to influence employee engagement significantly through psychological meaningfulness as the mediator. The p=0,000 with significance level 0,05. The sig F change shows 0,006, which is

Protestant ethic: Contributing towards a meaningful workplace ...

African Journals Online (AJOL)

The article also indicates that the Protestant ethic can indeed contribute towards a meaningful experience whilst performing work-related tasks in workspace. The Protestant work ethic is more than a cultural norm that places a positive moral value on doing a good job. Based on a belief that work has intrinsic value for its own ...

Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes

International Nuclear Information System (INIS)

Warnat, Patrick; Oberthuer, André; Fischer, Matthias; Westermann, Frank; Eils, Roland; Brors, Benedikt

2007-01-01

Neuroblastoma patients show heterogeneous clinical courses ranging from life-threatening progression to spontaneous regression. Recently, gene expression profiles of neuroblastoma tumours were associated with clinically different phenotypes. However, such data is still rare for important patient subgroups, such as patients with MYCN non-amplified advanced stage disease. Prediction of the individual course of disease and optimal therapy selection in this cohort is challenging. Additional research effort is needed to describe the patterns of gene expression in this cohort and to identify reliable prognostic markers for this subset of patients. We combined gene expression data from two studies in a meta-analysis in order to investigate differences in gene expression of advanced stage (3 or 4) tumours without MYCN amplification that show contrasting outcomes (alive or dead) at five years after initial diagnosis. In addition, a predictive model for outcome was generated. Gene expression profiles from 66 patients were included from two studies using different microarray platforms. In the combined data set, 72 genes were identified as differentially expressed by meta-analysis at a false discovery rate (FDR) of 8.33%. Meta-analysis detected 34 differentially expressed genes that were not found as significant in either single study. Outcome prediction based on data of both studies resulted in a predictive accuracy of 77%. Moreover, the genes that were differentially expressed in subgroups of advanced stage patients without MYCN amplification accurately separated MYCN amplified tumours from low stage tumours without MYCN amplification. Our findings support the hypothesis that neuroblastoma consists of two biologically distinct subgroups that differ by characteristic gene expression patterns, which are associated with divergent clinical outcome

After the Greeting: Realizing the Potential of Physical Models in Cell Biology.

Science.gov (United States)

Paluch, Ewa K

2015-12-01

Biophysics is increasingly taking center stage in cell biology as the tools for precise quantifications of cellular behaviors expand. Interdisciplinary approaches, combining quantitative physical modeling with cell biology, are of growing interest to journal editors, funding agencies, and hiring committees. However, despite an ever-increasing emphasis on the importance of interdisciplinary research, the student trained in biology may still be at a loss as to what it actually means. I discuss here some considerations on how to achieve meaningful and high-quality interdisciplinary work. Copyright © 2015 Elsevier Ltd. All rights reserved.

BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.

Science.gov (United States)

Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; van der Lek, Adrian; Mevissen, Theo; Fluck, Juliane

2016-01-01

Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and medical text mining. Track 4 at BioCreative V attempts to approach this complexity using fragments of large-scale manually curated biological networks, represented in Biological Expression Language (BEL), as training and test data. BEL is an advanced knowledge representation format which has been designed to be both human readable and machine processable. The specific goal of track 4 was to evaluate text mining systems capable of automatically constructing BEL statements from given evidence text, and of retrieving evidence text for given BEL statements. Given the complexity of the task, we designed an evaluation methodology which gives credit to partially correct statements. We identified various levels of information expressed by BEL statements, such as entities, functions, relations, and introduced an evaluation framework which rewards systems capable of delivering useful BEL fragments at each of these levels. The aim of this evaluation method is to help identify the characteristics of the systems which, if combined, would be most useful for achieving the overall goal of automatically constructing causal biological networks from text. © The Author(s) 2016. Published by Oxford University Press.

Community-based medical education: is success a result of meaningful personal learning experiences?

Science.gov (United States)

Kelly, Len; Walters, Lucie; Rosenthal, David

2014-01-01

Community-based medical education (CBME) is the delivery of medical education in a specific social context. Learners become a part of social and medical communities where their learning occurs. Longitudinal integrated clerkships (LICs) are year-long community-based placements where the curriculum and clinical experience is typically delivered by primary care physicians. These programs have proven to be robust learning environments, where learners develop strong communication skills and excellent clinical reasoning. To date, no learning model has been offered to describe CBME. The characteristics of CBME are explored by the authors who suggest that the social and professional context provided in small communities enhances medical education. The authors postulate that meaningfulness is engendered by the authentic context, which develops over time. These relationships with preceptors, patients and the community provide meaningfulness, which in turn enhances learning. The authors develop a novel learning model. They propose that the context-rich environment of CBME allows for meaningful relationships and experiences for students and that such meaningfulness enhances learning.

Meaningful Share Generation for Increased Number of Secrets in Visual Secret-Sharing Scheme

Directory of Open Access Journals (Sweden)

Mustafa Ulutas

2010-01-01

Full Text Available This paper presents a new scheme for hiding two halftone secret images into two meaningful shares created from halftone cover images. Meaningful shares are more desirable than noise-like (meaningless shares in Visual Secret Sharing because they look natural and do not attract eavesdroppers' attention. Previous works in the field focus on either increasing number of secrets or creating meaningful shares for one secret image. The method outlined in this paper both increases the number of secrets and creates meaningful shares at the same time. While the contrast ratio of shares is equal to that of Extended Visual Cryptography, two secrets are encoded into two shares as opposed to one secret in the Extended Visual Cryptography. Any two natural-looking images can be used as cover unlike the Halftone Visual Cryptography method where one cover should be the negative of the other cover image and can only encode one secret. Effectiveness of the proposed method is verified by an experiment.

New perspectives on biological HDL-targeted therapies

OpenAIRE

Muthuramu, Ilayaraja; Amin, Md Ruhul; De Geest, Bart

2017-01-01

According to a modified high-density lipoprotein (HDL) hypothesis, improving HDL function will lead to a decrease of coronary events. The stringent requirement for proving or refuting this hypothesis is that the causal pathway between the therapeutic intervention and a clinically meaningful endpoint obligatory passes through HDL. Infusion therapy of reconstituted HDL particles and human apolipoprotein A-I gene transfer are biological HDL-targeted therapies that are distinguished by HDL specif...

A Continuum of Learning: From Rote Memorization to Meaningful Learning in Organic Chemistry

Science.gov (United States)

Grove, Nathaniel P.; Bretz, Stacey Lowery

2012-01-01

The Assimilation Theory of Ausubel and Novak has typically been used in the research literature to describe two extremes to learning chemistry: meaningful learning "versus" rote memorization. It is unlikely, however, that such discrete categories of learning exist. Rote and meaningful learning, rather, are endpoints along a continuum of…

Using adaptive processes and adverse outcome pathways to develop meaningful, robust, and actionable environmental monitoring programs.

Science.gov (United States)

Arciszewski, Tim J; Munkittrick, Kelly R; Scrimgeour, Garry J; Dubé, Monique G; Wrona, Fred J; Hazewinkel, Rod R

2017-09-01

The primary goals of environmental monitoring are to indicate whether unexpected changes related to development are occurring in the physical, chemical, and biological attributes of ecosystems and to inform meaningful management intervention. Although achieving these objectives is conceptually simple, varying scientific and social challenges often result in their breakdown. Conceptualizing, designing, and operating programs that better delineate monitoring, management, and risk assessment processes supported by hypothesis-driven approaches, strong inference, and adverse outcome pathways can overcome many of the challenges. Generally, a robust monitoring program is characterized by hypothesis-driven questions associated with potential adverse outcomes and feedback loops informed by data. Specifically, key and basic features are predictions of future observations (triggers) and mechanisms to respond to success or failure of those predictions (tiers). The adaptive processes accelerate or decelerate the effort to highlight and overcome ignorance while preventing the potentially unnecessary escalation of unguided monitoring and management. The deployment of the mutually reinforcing components can allow for more meaningful and actionable monitoring programs that better associate activities with consequences. Integr Environ Assess Manag 2017;13:877-891. © 2017 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC). © 2017 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Meaningful Gamification in an Industrial/Organizational Psychology Course

Science.gov (United States)

Stansbury, Jessica A.; Earnest, David R.

2017-01-01

Motivation and game research continue to demonstrate that the implementation of game design characteristics in the classroom can be engaging and intrinsically motivating. The present study assessed the extent to which an industrial organizational psychology course designed learning environment created with meaningful gamification elements can…

Emotional, Biological, and Cognitive Impact of a Brief Expressive Writing Intervention for African American Women at Familial Breast Cancer

National Research Council Canada - National Science Library

Valdimarsdottir, Heiddis

2007-01-01

...) than women without familial breast cancer risk. The proposed study will examine the impact of an expressive writing intervention on emotional biological, and cognitive processes among women at familial breast cancer risk...

Meaningful Experiences in Physical Education and Youth Sport: A Review of the Literature

Science.gov (United States)

Beni, Stephanie; Fletcher, Tim; Ní Chróinín, Déirdre

2017-01-01

The purpose of this research is to review the literature about young people's meaningful experiences in physical education and youth sport. We reviewed 50 empirical peer-reviewed articles published in English since 1987. Five themes were identified as central influences to young people's meaningful experiences in physical education and sport:…

The Meaningful Activity Participation Assessment: A Measure of Engagement in Personally Valued Activities

Science.gov (United States)

Eakman, Aaron M.; Carlson, Mike E.; Clark, Florence A.

2010-01-01

The Meaningful Activity Participation Assessment (MAPA), a recently developed 28-item tool designed to measure the meaningfulness of activity, was tested in a sample of 154 older adults. The MAPA evidenced a sufficient level of internal consistency and test-retest reliability and correlated as theoretically predicted with the Life Satisfaction…

Molecular Biology In Young Women With Breast Cancer: From Tumor Gene Expression To DNA Mutations.

Science.gov (United States)

Gómez-Flores-Ramos, Liliana; Castro-Sánchez, Andrea; Peña-Curiel, Omar; Mohar-Betancourt, Alejandro

2017-01-01

Young women with breast cancer (YWBC) represent roughly 15% of breast cancer (BC) cases in Latin America and other developing regions. Breast tumors occurring at an early age are more aggressive and have an overall worse prognosis compared to breast tumors in postmenopausal women. The expression of relevant proliferation biomarkers such as endocrine receptors and human epidermal growth factor receptor 2 appears to be unique in YWBC. Moreover, histopathological, molecular, genetic, and genomic studies have shown that YWBC exhibit a higher frequency of aggressive subtypes, differential tumor gene expression, increased genetic susceptibility, and specific genomic signatures, compared to older women with BC. This article reviews the current knowledge on tumor biology and genomic signatures in YWBC.

PreproVIP-derived peptides in the human female genital tract: expression and biological function

DEFF Research Database (Denmark)

Bredkjoer, H E; Palle, C; Ekblad, E

1997-01-01

The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination with immunohistoc......The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination...... with immunohistochemistry were used. The effect of preproVIP 22-79, preproVIP 111-122 and preproVIP 156-170 on genital smooth muscle activity in the Fallopian tube was investigated in vitro and compared to that of VIP. All the preproVIP-derived peptides were expressed throughout the genital tract in neuronal elements...

Expression of recombinant glycoproteins in mammalian cells: towards an integrative approach to structural biology.

Science.gov (United States)

Aricescu, A Radu; Owens, Raymond J

2013-06-01

Mammalian cells are rapidly becoming the system of choice for the production of recombinant glycoproteins for structural biology applications. Their use has enabled the structural investigation of a whole new set of targets including large, multi-domain and highly glycosylated eukaryotic cell surface receptors and their supra-molecular assemblies. We summarize the technical advances that have been made in mammalian expression technology and highlight some of the structural insights that have been obtained using these methods. Looking forward, it is clear that mammalian cell expression will provide exciting and unique opportunities for an integrative approach to the structural study of proteins, especially of human origin and medically relevant, by bridging the gap between the purified state and the cellular context. Copyright © 2013 Elsevier Ltd. All rights reserved.

Industrial systems biology and its impact on synthetic biology of yeast cell factories

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

Meaningful radiation worker training for temporary craftsmen

International Nuclear Information System (INIS)

Williams, S.L.

1976-01-01

The carefully organized Radiation Worker Training Program presented to permanently assigned personnel at a power reactor facility too often falls by the wayside when temporary craftsmen are brought in for an outage. Even though these temporary workers will frequently be assigned to outage jobs with high radiation and/or contamination exposures, their Radiation Worker Training is often squeezed into an already busy schedule, thus reducing its effectiveness. As an aid for evaluating the effectiveness of an existing Radiation Worker Training Program for temporary craftsmen or for setting up a new program, the following guides are presented and discussed in this paper: the training environment; the interest and meaningfulness of the presentation; the method or methods used for presentation of the training information; the use of demonstrations; trainee participation; and, measuring the amount and type of information retained by a trainee. Meaningful Radiation Worker Training for temporary craftsmen can pay big dividends. Craftsmen can be expected to make fewer mistakes, thus reducing radiation exposure and lessening the chance for the spread of contamination. The craftsmen will also benefit by being able to work longer and utility management will benefit by having lower outage costs

Concept Mapping Using Cmap Tools to Enhance Meaningful Learning

Science.gov (United States)

Cañas, Alberto J.; Novak, Joseph D.

Concept maps are graphical tools that have been used in all facets of education and training for organizing and representing knowledge. When learners build concept maps, meaningful learning is facilitated. Computer-based concept mapping software such as CmapTools have further extended the use of concept mapping and greatly enhanced the potential of the tool, facilitating the implementation of a concept map-centered learning environment. In this chapter, we briefly present concept mapping and its theoretical foundation, and illustrate how it can lead to an improved learning environment when it is combined with CmapTools and the Internet. We present the nationwide “Proyecto Conéctate al Conocimiento” in Panama as an example of how concept mapping, together with technology, can be adopted by hundreds of schools as a means to enhance meaningful learning.

"Meaningful use" of electronic health records and its relevance to laboratories and pathologists

Directory of Open Access Journals (Sweden)

Walter H Henricks

2011-01-01

Full Text Available Electronic health records (EHRs have emerged as a major topic in health care and are central to the federal government′s strategy for transforming healthcare delivery in the United States. Recent federal actions that aim to promote the use of EHRs promise to have significant implications for laboratories and for pathology practices. Under the HITECH (Health Information Technology Economic and Clinical Health Act, an EHR incentive program has been established through which individual physicians and hospitals can qualify to receive incentive payments if they achieve "meaningful use" of "certified" EHR technology. The rule also establishes payment penalties in future years for eligible providers who have not met the requirements for meaningful use of EHRs. Meaningful use must be achieved using EHR technology that has been certified in accordance with functional and technical criteria that are set forth a regulation that parallels the meaningful use criteria in the incentive program. These actions and regulations are important to laboratories and pathologists for a number of reasons. Several of the criteria and requirements in the meaningful use rules and EHR certification criteria relate directly or indirectly to laboratory testing and laboratory information management, and future stage requirements are expected to impact the laboratory as well. Furthermore, as EHR uptake expands, there will be greater expectations for electronic interchange of laboratory information and laboratory information system (LIS-EHR interfaces. Laboratories will need to be aware of the technical, operational, and business challenges that they may face as expectations for LIS-EHR increase. This paper reviews the important recent federal efforts aimed at accelerating EHR use, including the incentive program for EHR meaningful use, provider eligibility, and EHR certification criteria, from a perspective of their relevance for laboratories and pathology practices.

Building Bridges Through Meaningful Occupation

Directory of Open Access Journals (Sweden)

Jennifer Fortuna

2017-07-01

Full Text Available Mary Block, MS, OTR/L, an occupational therapist and artist based in Illinois, provided the cover art for the Summer 2017 issue of The Open Journal of Occupational Therapy (OJOT. Generations is a sculpture made from concrete that measures 240 x100 in. (6.096 x 2.54 m. The piece was commissioned by Mary’s home town, the Village of Deerfield, IL. Mary always knew she wanted to be an artist. When competing paradigms altered Mary’s career path, the field of occupational therapy helped her to shape a new worldview. In uncertain times, meaningful occupation empowered Mary to start over again where she originally began

Morality and a Meaningful Life | Thomas | Philosophical Papers

African Journals Online (AJOL)

... healthy dovetail with respect to leading a meaningful life. With this argument regarding psychological health I draw upon, and extend, P. F. Strawson's seminal essay “Freedom and Resentment”. Also in this regard, I extend Wittgenstein's argument against the possibility of a private language to social behavior generally.

What constitutes meaningful engagement for patients and families as partners on research teams?

Science.gov (United States)

Black, Agnes; Strain, Kimberly; Wallsworth, Christine; Charlton, Sara-Grey; Chang, Wilma; McNamee, Kate; Hamilton, Clayon

2018-01-01

Objective There is growing emphasis on health care organizations to ensure that lay people are meaningfully engaged as partners on research teams. Our aim was to explore the perspectives of patients, family members and informal caregivers who have been involved on health care research teams in Canada and elicit their recommendations for meaningful engagement. Methods We conducted a qualitative study guided by thematic analysis of transcripts of focus groups and interviews of 19 experienced patient research partners in Canada. Results We identified four main themes: research environment, expectations, support and value, which highlight participants' combined perspectives on important factors to ensure their engagement in research is meaningful. Conclusions Our findings add to the evolving evidence base on the perspectives of lay people involved in health care research and their recommendations for research leaders on meaningful engagement. Our study suggests that research leaders should provide a welcoming research environment, outline appropriate expectations for patient research partners on research teams, support patient research partners' engagement in projects and recognize the value patient research partners bring to health research.

Creating a meaningful infection control program: one home healthcare agency's lessons.

Science.gov (United States)

Poff, Renee McCoy; Browning, Sarah Via

2014-03-01

Creating a meaningful infection control program in the home care setting proved to be challenging for agency leaders of one hospital-based home healthcare agency. Challenges arose when agency leaders provided infection control (IC) data to the hospital's IC Committee. The IC Section Chief asked for national benchmark comparisons to align home healthcare reporting to that of the hospital level. At that point, it was evident that the home healthcare IC program lacked definition and structure. The purpose of this article is to share how one agency built a meaningful IC program.

Biologicals versus biosimilars the future ahead

Directory of Open Access Journals (Sweden)

A Singhal

2015-01-01

Full Text Available Biosimilars are highly similar versions of already authorized innovator biological therapies. They demonstrate no clinically meaningful difference with their innovator products in terms of efficacy, safety and quality characteristics and biological activity. Biosimilars have demonstrated growing acceptance and use, especially in the developing countries due to severe cost constraints. Global market for Indian non-innovator products is approximately worth USD 1.5 Billion/annum with an annual growth rate of 27%. Estimated exports of Indian biopharmaceutical products have been increasing at a rate of 47%. In India, there is a good acceptance of non-innovator healthcare products amongst healthcare professionals and patients. Several home grown biopharmaceutical industries are now actively developing and marketing non innovator products in India.

Measuring meaningful learning in the undergraduate chemistry laboratory

Science.gov (United States)

Galloway, Kelli R.

The undergraduate chemistry laboratory has been an essential component in chemistry education for over a century. The literature includes reports on investigations of singular aspects laboratory learning and attempts to measure the efficacy of reformed laboratory curriculum as well as faculty goals for laboratory learning which found common goals among instructors for students to learn laboratory skills, techniques, experimental design, and to develop critical thinking skills. These findings are important for improving teaching and learning in the undergraduate chemistry laboratory, but research is needed to connect the faculty goals to student perceptions. This study was designed to explore students' ideas about learning in the undergraduate chemistry laboratory. Novak's Theory of Meaningful Learning was used as a guide for the data collection and analysis choices for this research. Novak's theory states that in order for meaningful learning to occur the cognitive, affective, and psychomotor domains must be integrated. The psychomotor domain is inherent in the chemistry laboratory, but the extent to which the cognitive and affective domains are integrated is unknown. For meaningful learning to occur in the laboratory, students must actively integrate both the cognitive domain and the affective domains into the "doing" of their laboratory work. The Meaningful Learning in the Laboratory Instrument (MLLI) was designed to measure students' cognitive and affective expectations and experiences within the context of conducting experiments in the undergraduate chemistry laboratory. Evidence for the validity and reliability of the data generated by the MLLI were collected from multiple quantitative studies: a one semester study at one university, a one semester study at 15 colleges and universities across the United States, and a longitudinal study where the MLLI was administered 6 times during two years of general and organic chemistry laboratory courses. Results from

Callings, work role fit, psychological meaningfulness and work ...

African Journals Online (AJOL)

Our aim in this study was to investigate the relationships among a calling orientation, work role fit, psychological meaningfulness and work engagement of teachers in Zambia. A quantitative approach was followed and a cross-sectional survey was used. The sample (n = 150) included 75 basic and 75 secondary school ...

Synonyms, Antonyms, and Retroactive Inhibition with Meaningful Material

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Weisshed, Ethel

1973-01-01

The determination of the extent to which generalizations derived from studies of rote verbal learning, particularly paired-associate learning applied to highly meaningful materials, was the focus of this study. It was found that discriminating tags to synonyms and antonyms permitting the application of appropriate transfer rules may be attached.…

Meaningful work and work engagement : The mediating role of perceived opportunity to craft and job crafting behavior

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Van Wingerden, Jessica; van der Stoep, Joost; Poell, R.F.

2018-01-01

This study examines the impact of meaningful work on employees’ level of work engagement as mediated by perceived opportunities to craft and job crafting. Based on the literature on meaningful work and job crafting, we hypothesize that meaningful work has a positive relationship with an employee’s

Environmental regulation of plant gene expression: an RT-qPCR laboratory project for an upper-level undergraduate biochemistry or molecular biology course.

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Eickelberg, Garrett J; Fisher, Alison J

2013-01-01

We present a novel laboratory project employing "real-time" RT-qPCR to measure the effect of environment on the expression of the FLOWERING LOCUS C gene, a key regulator of floral timing in Arabidopsis thaliana plants. The project requires four 3-hr laboratory sessions and is aimed at upper-level undergraduate students in biochemistry or molecular biology courses. The project provides students with hands-on experience with RT-qPCR, the current "gold standard" for gene expression analysis, including detailed data analysis using the common 2-ΔΔCT method. Moreover, it provides a convenient starting point for many inquiry-driven projects addressing diverse questions concerning ecological biochemistry, naturally occurring genetic variation, developmental biology, and the regulation of gene expression in nature. Copyright © 2013 Wiley Periodicals, Inc.

Effects of perceptual load and socially meaningful stimuli on crossmodal selective attention in Autism Spectrum Disorder and neurotypical samples.

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Tyndall, Ian; Ragless, Liam; O'Hora, Denis

2018-04-01

The present study examined whether increasing visual perceptual load differentially affected both Socially Meaningful and Non-socially Meaningful auditory stimulus awareness in neurotypical (NT, n = 59) adults and Autism Spectrum Disorder (ASD, n = 57) adults. On a target trial, an unexpected critical auditory stimulus (CAS), either a Non-socially Meaningful ('beep' sound) or Socially Meaningful ('hi') stimulus, was played concurrently with the presentation of the visual task. Under conditions of low visual perceptual load both NT and ASD samples reliably noticed the CAS at similar rates (77-81%), whether the CAS was Socially Meaningful or Non-socially Meaningful. However, during high visual perceptual load NT and ASD participants reliably noticed the meaningful CAS (NT = 71%, ASD = 67%), but NT participants were unlikely to notice the Non-meaningful CAS (20%), whereas ASD participants reliably noticed it (80%), suggesting an inability to engage selective attention to ignore non-salient irrelevant distractor stimuli in ASD. Copyright © 2018 Elsevier Inc. All rights reserved.

Designing and evaluating a context-based lesson sequence promoting conceptual coherence in biology

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Ummels, M. H J; Kamp, M. J A; De Kroon, H.; Boersma, K. Th|info:eu-repo/dai/nl/073043141

2015-01-01

Context-based education, in which students deal with biological concepts in a meaningful way, is showing promise in promoting the development of students conceptual coherence. However, literature gives little guidance about how this kind of education should be designed. Therefore, our study aims at

Youth Perspectives on Meaningful Participation in Community Based Programs: A Qualitative Assessment

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Sherer W. Royce

2009-12-01

Full Text Available Allowing the voiceless to have a voice is a tenet of empowerment. This paper highlights research that employed a participatory action research framework to gain a better understanding of young people’s perceptions about youth empowerment and acquire their perspective (voice about the meaningfulness of participation in out-of-school advocacy and volunteer program activities. Using Photovoice, the research provides a missing point of view in youth empowerment model development. Results indicate that the quality of a youth’s participation in a community-based program is determined by 1 youth expressing themselves without censorship, 2 occasions for youth to expand their social networks with youth and adults, and 3 adults observing and valuing youth contributions. These findings raise implications for community-based, youth empowerment programs including program philosophy, program procedures, youth empowerment content and activities, and adult leadership style. The findings may assist practitioners when designing youth empowering activities and researchers when operationalizing youth empowerment.

THE EVOLUTION OF THE KREBS CYCLE: A PROMISING THEME FOR MEANINGFUL BIOCHEMISTRY LEARNING IN BIOLOGY

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C. Costa

2015-08-01

Full Text Available INTRODUCTION: Evolution has been recognized as a key concept for biologists. In order to motivate biology undergraduates for contents of central energetic metabolism, we addressed the Krebs cycle structure and functions to an evolutionary view. To this end, we created a study guide which contextualizes the emergence of the cyclic pathway, in light of the prokaryotic influence since early Earth anaerobic condition to oxygen rise in atmosphere. OBJECTIVES: The main goal is to highlight the educational potential of the material whose subject is scarcely covered in biochemistry textbooks. MATERIALS AND METHODS: The study guide is composed by three interrelated sections, the problem (Section 1, designed to arouse curiosity, inform and motivate students; an introductory text (Section 2 about life evolution, including early micro-organisms and Krebs cycle emergence, and questions (Section 3 for debate. The activity consisted on a peer discussion session, with instructors tutoring. The questions were designed to foster exchange of ideas in an ever-increasing level of complexity, and cover subjects from early atmospheric conditions to organization of the metabolism along the subsequent geological ages. RESULTS AND DISCUSSION: We noticed that students were engaged and motivated by the task, especially during group discussion. Based on students’ feedbacks and class observations, we learned that the material raised curiosity and stimulated discussion among peers. It brought a historical and purposeful way of dealing with difficult biochemical concepts. CONCLUSIONS: The whole experience suggests that the study guide was a stimulus for broadening comprehension of the Krebs cycle, reinforcing the evolutionary stance as an important theme for biology and biochemistry understanding. On the other hand, we do not underestimate the fact that approaching Krebs cycle from an evolutionary standpoint is a quite complex discussion for the majority of students

Updating biological bases of social behavior.

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O'Connor, Thomas G

2014-09-01

This month's collation of papers deals with social behaviors that operationalize key constructs in fields covered by the journal, including attachment theory and parenting; emotional regulation; psychopathology of several forms; general and specific cognitive abilities. Notably, many examples are offered of how these social behaviors link with biology. That is an obvious and important direction for clinical research insofar as it helps to erase a perceptual chasm and artificial duality between 'behavior' and 'biology'. But, although it must be the case that social behavior has biological connections of one sort or other, identifying reliable connections with practical application has proved to be a non-trivial challenge. In particular, the challenge seems to be in measuring social behavior meaningfully enough that it could be expected to have a biological pulse, and in measuring biological markers systematically enough that emergent-downstream effects would surface. Associations are not especially uncommon, but it has been a frustrating task in constructing a practically broad model from a bricolage of scattered and disconnected parts and findings in the literature. Several reports in this issue offer contrasts that may help move along this line of study. © 2014 Association for Child and Adolescent Mental Health.

9th International Conference on Practical Applications of Computational Biology and Bioinformatics

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Rocha, Miguel; Fdez-Riverola, Florentino; Paz, Juan

2015-01-01

This proceedings presents recent practical applications of Computational Biology and  Bioinformatics. It contains the proceedings of the 9th International Conference on Practical Applications of Computational Biology & Bioinformatics held at University of Salamanca, Spain, at June 3rd-5th, 2015. The International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB) is an annual international meeting dedicated to emerging and challenging applied research in Bioinformatics and Computational Biology. Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies, together with novel and ever evolving distinct types of omics data technologies, have put an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis o...

Using Meaningful Contexts to Promote Understanding of Pronumerals

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Linsell, Chris; Cavanagh, Michael; Tahir, Salma

2013-01-01

Developing a conceptual understanding of elementary algebra has been the focus of a number of recent articles in this journal. Baroudi (2006) advocated problem solving to assist students' transition from arithmetic to algebra, and Shield (2008) described the use of meaningful contexts for developing the concept of function. Samson (2011, 2012)…

Using Community-Based Participatory Research to Investigate Meaningful Prenatal Care Among African American Women.

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Nypaver, Cynthia F; Shambley-Ebron, Donna

2016-11-01

In the United States, African American babies die more than twice as often as White babies. The cause for this difference remains elusive, yet is likely complex with one factor being inadequate cultural care of pregnant African American women. The purpose of this study was to explore African American women's perspectives of meaningful prenatal care. Community-based participatory research was employed for this study using photovoice. The sample included 11 African American mothers in an urban community in Midwestern United States. Five themes were abstracted from the data: (1) Access to Care; (2) Soul Nourishment; (3) Companionship; (4) Help Me, Teach Me; and (5) The Future. Meaningful prenatal care is influenced by culture. African American women need physical, social, and soulful support to enhance meaningfulness of care during pregnancy. The findings support that meaningfulness of prenatal care for African American women may be enhanced by accessible and uniquely designed, culturally congruent models of prenatal care. © The Author(s) 2015.

Clinicopathological variables of sporadic schwannomas of peripheral nerve in 291 patients and expression of biologically relevant markers.

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Young, Eric D; Ingram, Davis; Metcalf-Doetsch, William; Khan, Dilshad; Al Sannaa, Ghadah; Le Loarer, Francois; Lazar, Alexander J F; Slopis, John; Torres, Keila E; Lev, Dina; Pollock, Raphael E; McCutcheon, Ian E

2017-09-08

OBJECTIVE While sporadic peripheral schwannomas (SPSs) are generally well treated with surgery, their biology is not well understood. Consequently, treatment options are limited. The aim of this study was to provide a comprehensive description of SPS. The authors describe clinicopathological features and treatment outcomes of patients harboring these tumors, and they assess expression of biomarkers using a clinically annotated tissue microarray. Together, these data give new insight into the biology and management of SPS. METHODS Patients presenting with a primary SPS between 1993 and 2011 (n = 291) were selected from an institutional registry to construct a clinical database. All patients underwent follow-up, and short- and long-term outcomes were assessed. Expression of relevant biomarkers was assessed using a new tissue microarray (n = 121). RESULTS SPSs were generally large (mean 5.5 cm) and frequently painful at presentation (55%). Most patients were treated with surgery (80%), the majority of whom experienced complete resolution (52%) or improvement (18%) of their symptoms. Tumors that were completely resected (85%) did not recur. Some patients experienced short-term (16%) and long-term (4%) complications postoperatively. Schwannomas expressed higher levels of platelet-derived growth factor receptor-β (2.1) than malignant peripheral nerve sheath tumors (MPNSTs) (1.5, p = 0.004) and neurofibromas (1.33, p = 0.007). Expression of human epidermal growth factor receptor-2 was greater in SPSs (0.91) than in MPNSTs (0.33, p = 0.002) and neurofibromas (0.33, p = 0.026). Epidermal growth factor receptor was expressed in far fewer SPS cells (10%) than in MPNSTs (58%, p SPSs more frequently expressed cytoplasmic survivin (66% of tumor cells) than normal nerve (46% of cells), but SPS expressed nuclear survivin in fewer tumor cells than in MPNSTs (24% and 50%, respectively; p = 0.018). CONCLUSIONS Complete resection is curative for SPS. Left untreated, however, these

Mathematical Biology Modules Based on Modern Molecular Biology and Modern Discrete Mathematics

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Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network. PMID:20810955

Mathematical biology modules based on modern molecular biology and modern discrete mathematics.

Science.gov (United States)

Robeva, Raina; Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network.

Hospital IT adoption strategies associated with implementation success: implications for achieving meaningful use.

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Ford, Eric W; Menachemi, Nir; Huerta, Timothy R; Yu, Feliciano

2010-01-01

Health systems are facing significant pressure to either implement health information technology (HIT) systems that have "certified" electronic health record applications and that fulfill the federal government's definition of "meaningful use" or risk substantial financial penalties in the near future. To this end, hospitals have adopted one of three strategies, described as "best of breed," "best of suite," and "single vendor," to meet organizational and regulatory demands. The single-vendor strategy is used by the simple majority of U.S. hospitals, but is it the most effective mode for achieving full implementation? Moreover, what are the implications of adopting this strategy for achieving meaningful use? The simple answer to the first question is that the hospitals using the hybrid best of suite strategy had fully implemented HIT systems in significantly greater proportions than did hospitals employing either of the other strategies. Nonprofit and system-affiliated hospitals were more likely to have fully implemented their HIT systems. In addition, increased health maintenance organization market penetration rates were positively correlated with complete implementation rates. These results have ongoing implications for achieving meaningful use in the near term. The federal government's rewards and incentives program related to the meaningful use of HIT in hospitals has created an organizational imperative to implement such systems. For hospitals that have not begun systemwide implementation, pursuing a best of suite strategy may provide the greatest chance for achieving all or some of the meaningful use targets in the near term or at least avoiding future penalties scheduled to begin in 2015.

Biological activity evaluation of cloned and expressed caprine growth hormone from local Pakistani goat breed beetal

International Nuclear Information System (INIS)

Butt, H.I.; Shahzad, M.I.; Bashir, Q.

2011-01-01

Growth hormone cDNA of local goat breed-beetal was amplified by RT PCR and gene including leader sequence was cloned in pTZR57 cloning vector. The cGH-pTZR57 clone was confirmed by restriction digestion and sequence analyses before finally sub-cloning the gene in pND- a mammalian expression vector. The clones were again confirmed by restriction digestion and PCR analyses. Highly purified, supercoiled cGH-pND construct was used to transfect Vero cell lines for expression studies. The in vitro expression of cGH was checked by dot-ELISA technique. After confirming its in vitro cell line based expression, the construct was injected to 4 weeks old balb/c mice intramuscularly. Two animals were euthanized per week till four weeks to monitor the in vivo biological activity by evaluating the tibia epiphyseal width and body weight gain assays. Significant increase in tibia epiphyseal width and gain in body weight was observed from vaccinated animals. The study supports the concept that DNA based therapeutics are an efficient and cost effective method for gene delivery and in vivo transgene expressions. (author)

Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum.

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Pengfei Cai

2016-04-01

Full Text Available Schistosomiasis is a chronic and debilitating disease caused by blood flukes (digenetic trematodes of the genus Schistosoma. Schistosomes are sexually dimorphic and exhibit dramatic morphological changes during a complex lifecycle which requires subtle gene regulatory mechanisms to fulfil these complex biological processes. In the current study, a 41,982 features custom DNA microarray, which represents the most comprehensive probe coverage for any schistosome transcriptome study, was designed based on public domain and local databases to explore differential gene expression in S. japonicum. We found that approximately 1/10 of the total annotated genes in the S. japonicum genome are differentially expressed between adult males and females. In general, genes associated with the cytoskeleton, and motor and neuronal activities were readily expressed in male adult worms, whereas genes involved in amino acid metabolism, nucleotide biosynthesis, gluconeogenesis, glycosylation, cell cycle processes, DNA synthesis and genome fidelity and stability were enriched in females. Further, miRNAs target sites within these gene sets were predicted, which provides a scenario whereby the miRNAs potentially regulate these sex-biased expressed genes. The study significantly expands the expressional and regulatory characteristics of gender-biased expressed genes in schistosomes with high accuracy. The data provide a better appreciation of the biological and physiological features of male and female schistosome parasites, which may lead to novel vaccine targets and the development of new therapeutic interventions.

Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum.

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Cai, Pengfei; Liu, Shuai; Piao, Xianyu; Hou, Nan; Gobert, Geoffrey N; McManus, Donald P; Chen, Qijun

2016-04-01

Schistosomiasis is a chronic and debilitating disease caused by blood flukes (digenetic trematodes) of the genus Schistosoma. Schistosomes are sexually dimorphic and exhibit dramatic morphological changes during a complex lifecycle which requires subtle gene regulatory mechanisms to fulfil these complex biological processes. In the current study, a 41,982 features custom DNA microarray, which represents the most comprehensive probe coverage for any schistosome transcriptome study, was designed based on public domain and local databases to explore differential gene expression in S. japonicum. We found that approximately 1/10 of the total annotated genes in the S. japonicum genome are differentially expressed between adult males and females. In general, genes associated with the cytoskeleton, and motor and neuronal activities were readily expressed in male adult worms, whereas genes involved in amino acid metabolism, nucleotide biosynthesis, gluconeogenesis, glycosylation, cell cycle processes, DNA synthesis and genome fidelity and stability were enriched in females. Further, miRNAs target sites within these gene sets were predicted, which provides a scenario whereby the miRNAs potentially regulate these sex-biased expressed genes. The study significantly expands the expressional and regulatory characteristics of gender-biased expressed genes in schistosomes with high accuracy. The data provide a better appreciation of the biological and physiological features of male and female schistosome parasites, which may lead to novel vaccine targets and the development of new therapeutic interventions.

Additional Prognostic Value of SUVmax Measured by F-18 FDG PET/CT over Biological Marker Expressions in Surgically Resected Cervical Cancer Patients.

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Yun, Man Soo; Kim, Seong-Jang; Pak, Kyoungjune; Lee, Chang Hun

2015-01-01

We compared the prognostic ability of the maximum standardized uptake value (SUVmax) and various biological marker expressions to predict recurrence in patients with surgically resected cervical cancer. A retrospective review identified 60 patients with cervical cancer who received [18F]fluorodeoxyglucose positron emission tomography/computed tomography (F-18 FDG PET/CT) at the time of the diagnosis of cancer. The SUVmax, expressions of carbonic anhydrase-IX (CA-IX), glucose transporter 1 (GLUT-1), and vascular endothelial growth factor (VEGF), and known prognostic factors were investigated. The median follow-up time was 22.2 months (range 3.4-43.1 months). Using univariate analyses, the stage (stage II, p = 0.0066), SUVmax (> 6, p = 0.027), parametrial involvement (p value than biological marker expression in patients with surgically resected cervical cancer. © 2015 S. Karger GmbH, Freiburg.

Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species

OpenAIRE

Matthew P. Adams; Catherine J. Collier; Sven Uthicke; Yan X. Ow; Lucas Langlois; Katherine R. O’Brien

2017-01-01

When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluat...

MO-DE-207B-03: Improved Cancer Classification Using Patient-Specific Biological Pathway Information Via Gene Expression Data

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Young, M; Craft, D [Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States)

2016-06-15

Purpose: To develop an efficient, pathway-based classification system using network biology statistics to assist in patient-specific response predictions to radiation and drug therapies across multiple cancer types. Methods: We developed PICS (Pathway Informed Classification System), a novel two-step cancer classification algorithm. In PICS, a matrix m of mRNA expression values for a patient cohort is collapsed into a matrix p of biological pathways. The entries of p, which we term pathway scores, are obtained from either principal component analysis (PCA), normal tissue centroid (NTC), or gene expression deviation (GED). The pathway score matrix is clustered using both k-means and hierarchical clustering, and a clustering is judged by how well it groups patients into distinct survival classes. The most effective pathway scoring/clustering combination, per clustering p-value, thus generates various ‘signatures’ for conventional and functional cancer classification. Results: PICS successfully regularized large dimension gene data, separated normal and cancerous tissues, and clustered a large patient cohort spanning six cancer types. Furthermore, PICS clustered patient cohorts into distinct, statistically-significant survival groups. For a suboptimally-debulked ovarian cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00127) showed significant improvement over that of a prior gene expression-classified study (p = .0179). For a pancreatic cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00141) showed significant improvement over that of a prior gene expression-classified study (p = .04). Pathway-based classification confirmed biomarkers for the pyrimidine, WNT-signaling, glycerophosphoglycerol, beta-alanine, and panthothenic acid pathways for ovarian cancer. Despite its robust nature, PICS requires significantly less run time than current pathway scoring methods. Conclusion: This work validates the PICS method to improve

Emotional, Biological, and Cognitive Impact of a Brief Expressive Writing Intervention for African American Women at Familial Breast Cancer Risk

National Research Council Canada - National Science Library

Valdimarsdottir, Heiddie; Bovbjerg, Dana

2005-01-01

... to their fatalistic attitudes towards the disease. The proposed study will examine the impact of an expressive writing intervention on emotional, biological, and cognitive processes among women of African descent at familial breast cancer risk...

Biological and clinical meaning of myeloid antigen expression in the acute lymphocytic leukemia in children

International Nuclear Information System (INIS)

Marsan Suarez, Vianed; Sanchez Segura, Miriam; Socarras Ferrer, Bertha B; Valle Perez, Lazaro O del

2009-01-01

In 238 children presenting with acute lymphoid leukemia (ALL) authors studied the possible association between the myeloid antigens expression with determined biologic and clinic features at disease onset. The cellular immunophenotyping was performed by ultraimmunocytochemical method. From the total of diagnosed ALLs, the 21,8% were LLA-Mi+. There was a lymphadenopathies predominance (71,2%), splenomegaly (65,4%) and hepatomegaly (57,7%) in patients with LLA-Mi+ and very significant differences (p =0,003, p = 0,0068, and p = 0,000, respectively. There was also alight predominance of mediastinum adenopathies, CNS infiltration and hemorrahagic manifestations in patients with LLA-Mi+, no statistically significant. Results showed that in our patients the myeloid antigen expression on the lymphoid blasts influenced on appearance of determined presentation of morphologic and clinical features in children

Probabilistic biological network alignment.

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Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

A novel summary report of colonoscopy: timeline visualization providing meaningful colonoscopy video information.

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Cho, Minwoo; Kim, Jee Hyun; Kong, Hyoun Joong; Hong, Kyoung Sup; Kim, Sungwan

2018-05-01

The colonoscopy adenoma detection rate depends largely on physician experience and skill, and overlooked colorectal adenomas could develop into cancer. This study assessed a system that detects polyps and summarizes meaningful information from colonoscopy videos. One hundred thirteen consecutive patients had colonoscopy videos prospectively recorded at the Seoul National University Hospital. Informative video frames were extracted using a MATLAB support vector machine (SVM) model and classified as bleeding, polypectomy, tool, residue, thin wrinkle, folded wrinkle, or common. Thin wrinkle, folded wrinkle, and common frames were reanalyzed using SVM for polyp detection. The SVM model was applied hierarchically for effective classification and optimization of the SVM. The mean classification accuracy according to type was over 93%; sensitivity was over 87%. The mean sensitivity for polyp detection was 82.1%, and the positive predicted value (PPV) was 39.3%. Polyps detected using the system were larger (6.3 ± 6.4 vs. 4.9 ± 2.5 mm; P = 0.003) with a more pedunculated morphology (Yamada type III, 10.2 vs. 0%; P < 0.001; Yamada type IV, 2.8 vs. 0%; P < 0.001) than polyps missed by the system. There were no statistically significant differences in polyp distribution or histology between the groups. Informative frames and suspected polyps were presented on a timeline. This summary was evaluated using the system usability scale questionnaire; 89.3% of participants expressed positive opinions. We developed and verified a system to extract meaningful information from colonoscopy videos. Although further improvement and validation of the system is needed, the proposed system is useful for physicians and patients.

Modeling Meaningful Learning in Chemistry Using Structural Equation Modeling

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Brandriet, Alexandra R.; Ward, Rose Marie; Bretz, Stacey Lowery

2013-01-01

Ausubel and Novak's construct of "meaningful learning" stipulates that substantive connections between new knowledge and what is already known requires the integration of thinking, feeling, and performance (Novak J. D., (2010), "Learning, creating, and using knowledge: concept maps as facilitative tools in schools and…

Meaningfulness in work - experiences among employed individuals with persistent mental illness.

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Leufstadius, Christel; Eklund, Mona; Erlandsson, Lena-Karin

2009-01-01

The aim of the present study was to investigate how people with persistent mental illness, with various types of work and employment conditions, experience and describe the meaningfulness of work. The study had a qualitative approach and twelve informants living in the community were purposefully selected and interviewed according to overarching themes. The interviews were analysed using qualitative content analysis, and all of the authors were involved in the analysis process. The findings resulted in four main themes: 1) work per se has certain characteristics, 2) participation in different contexts gives a feeling of normality, acceptance, belonging and fulfilment of norms and values, 3) work affords structure, energy and a balanced daily life, and 4) work increases well-being and strengthens one's identity. A tentative model is described concerning perceived meaningfulness in work among individuals with persistent mental illness, in which the first three aspects of meaning are a prerequisite for meaning in terms of increased well-being and strengthened identity. Furthermore, it seems important that work has to bring the just right challenge to the individual in order for him or her to perceive the identified aspects of meaningfulness.

Industrial systems biology and its impact on synthetic biology of yeast cell factories.

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Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-06-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Improving students' meaningful learning on the predictive nature of quantum mechanics

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Rodolfo Alves de Carvalho Neto

2009-03-01

Full Text Available This paper deals with research about teaching quantum mechanics to 3rd year high school students and their meaningful learning of its predictive aspect; it is based on the Master’s dissertation of one of the authors (CARVALHO NETO, 2006. While teaching quantum mechanics, we emphasized its predictive and essentially probabilistic nature, based on Niels Bohr’s complementarity interpretation (BOHR, 1958. In this context, we have discussed the possibility of predicting measurement results in well-defined experimental contexts, even for individual events. Interviews with students reveal that they have used quantum mechanical ideas, suggesting their meaningful learning of the essentially probabilistic predictions of quantum mechanics.

Using Variable Precision Rough Set for Selection and Classification of Biological Knowledge Integrated in DNA Gene Expression

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Calvo-Dmgz D.

2012-12-01

Full Text Available DNA microarrays have contributed to the exponential growth of genomic and experimental data in the last decade. This large amount of gene expression data has been used by researchers seeking diagnosis of diseases like cancer using machine learning methods. In turn, explicit biological knowledge about gene functions has also grown tremendously over the last decade. This work integrates explicit biological knowledge, provided as gene sets, into the classication process by means of Variable Precision Rough Set Theory (VPRS. The proposed model is able to highlight which part of the provided biological knowledge has been important for classification. This paper presents a novel model for microarray data classification which is able to incorporate prior biological knowledge in the form of gene sets. Based on this knowledge, we transform the input microarray data into supergenes, and then we apply rough set theory to select the most promising supergenes and to derive a set of easy interpretable classification rules. The proposed model is evaluated over three breast cancer microarrays datasets obtaining successful results compared to classical classification techniques. The experimental results shows that there are not significat differences between our model and classical techniques but it is able to provide a biological-interpretable explanation of how it classifies new samples.

Meaningful Work and Secondary School Teachers' Intention to Leave

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Janik, M.; Rothmann, S.

2015-01-01

The study investigates the relations between secondary school teachers' work-role fit, job enrichment, supervisor relationships, co-worker relationships, psychological meaningfulness of work and intention to leave. A cross-sectional survey was used. The participants were 502 secondary school teachers in Namibia. The following measuring instruments…

Development of an Assessment Tool to Measure Students' Meaningful Learning in the Undergraduate Chemistry Laboratory

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Galloway, Kelli R.; Bretz, Stacey Lowery

2015-01-01

Research on learning in the undergraduate chemistry laboratory necessitates an understanding of students' perspectives of learning. Novak's Theory of Meaningful Learning states that the cognitive (thinking), affective (feeling), and psychomotor (doing) domains must be integrated for meaningful learning to occur. The psychomotor domain is the…

Can a multimedia tool help students' learning performance in complex biology subjects?

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Pinar Koseoglu

2015-11-01

Full Text Available The aim of the present study was to determine the effects of multimedia-based biology teaching (Mbio and teacher-centered biology (TCbio instruction approaches on learners' biology achievements, as well as their views towards learning approaches. During the research process, an experimental design with two groups, TCbio (n = 22 and Mbio (n = 26, were used. The results of the study proved that the Mbio approach was more effective than the TCbio approach with regard to supporting meaningful learning, academic achievement, enjoyment and motivation. Moreover, the TCbio approach is ineffective in terms of time management, engaging attention, and the need for repetition of subjects. Additionally, the results were discussed in terms of teaching, learning, multimedia design as well as biology teaching/learning.

Dissecting Redox Biology Using Fluorescent Protein Sensors.

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Schwarzländer, Markus; Dick, Tobias P; Meyer, Andreas J; Morgan, Bruce

2016-05-01

Fluorescent protein sensors have revitalized the field of redox biology by revolutionizing the study of redox processes in living cells and organisms. Within one decade, a set of fundamental new insights has been gained, driven by the rapid technical development of in vivo redox sensing. Redox-sensitive yellow and green fluorescent protein variants (rxYFP and roGFPs) have been the central players. Although widely used as an established standard tool, important questions remain surrounding their meaningful use in vivo. We review the growing range of thiol redox sensor variants and their application in different cells, tissues, and organisms. We highlight five key findings where in vivo sensing has been instrumental in changing our understanding of redox biology, critically assess the interpretation of in vivo redox data, and discuss technical and biological limitations of current redox sensors and sensing approaches. We explore how novel sensor variants may further add to the current momentum toward a novel mechanistic and integrated understanding of redox biology in vivo. Antioxid. Redox Signal. 24, 680-712.

Are all certified EHRs created equal? Assessing the relationship between EHR vendor and hospital meaningful use performance.

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Holmgren, A Jay; Adler-Milstein, Julia; McCullough, Jeffrey

2017-11-24

The federal electronic health record (EHR) certification process was intended to ensure a baseline level of system quality and the ability to support meaningful use criteria. We sought to assess whether there was variation across EHR vendors in the degree to which hospitals using products from those vendors were able to achieve high levels of performance on meaningful use criteria. We created a cross-sectional national hospital sample from the Office of the National Coordinator for Health Information Technology EHR Products Used for Meaningful Use Attestation public use file and the Centers for Medicare & Medicaid Services Medicare EHR Incentive Program Eligible Hospitals public use file. We used regression models to assess the relationship between vendor and hospital performance on 6 Stage 2 Meaningful Use criteria, controlling for hospital characteristics. We also calculated how much variation in performance is explained by vendor choice. We found significant associations between specific vendor and level of hospital performance for all 6 meaningful use criteria. Epic was associated with significantly higher performance on 5 of the 6 criteria; relationships for other vendors were mixed, with some associated with significantly worse performance on multiple criteria. EHR vendor choice accounted for between 7% and 34% of performance variation across the 6 criteria. A nontrivial proportion of variation in hospital meaningful use performance is explained by vendor choice, and certain vendors are more often associated with better meaningful use performance than others. Our results suggest that policy-makers should improve the certification process by including more "real-world" scenario testing and provider feedback or ratings to reduce this variation. Hospitals can use these results to guide interactions with vendors. Vendor choice accounts for a meaningful proportion of variation in hospital meaningful use performance, and specific vendors are consistently associated

Initial Development of the Meaningful Learning with Technology Scale (MeLTS) for High-School Students

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Lee, Chwee Beng

2018-01-01

With the rapid developments in emerging technologies and the emphasis on technologies in learning environments, the connection between technologies and meaningful learning has strengthened. Developing an understanding of the components of meaningful learning with technology is pivotal, as this may enable educators to make more informed decisions…

Biological signals classification and analysis

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Kiasaleh, Kamran

2015-01-01

This authored monograph presents key aspects of signal processing analysis in the biomedical arena. Unlike wireless communication systems, biological entities produce signals with underlying nonlinear, chaotic nature that elude classification using the standard signal processing techniques, which have been developed over the past several decades for dealing primarily with standard communication systems. This book separates what is random from that which appears to be random, and yet is truly deterministic with random appearance. At its core, this work gives the reader a perspective on biomedical signals and the means to classify and process such signals. In particular, a review of random processes along with means to assess the behavior of random signals is also provided. The book also includes a general discussion of biological signals in order to demonstrate the inefficacy of the well-known techniques to correctly extract meaningful information from such signals. Finally, a thorough discussion of recently ...

Pedagogical Principles of Learning to Teach Meaningful Physical Education

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Ní Chróinín, Déirdre; Fletcher, Tim; O'Sullivan, Mary

2018-01-01

Background: Concerns that current forms of physical education teacher education (PETE) are not adequately providing teachers with the tools necessary for working with the realities and challenges of teaching physical education in contemporary schools has led some scholars to advocate for an approach that prioritises meaningfulness in physical…

A technology training protocol for meeting QSEN goals: Focusing on meaningful learning.

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Luo, Shuhong; Kalman, Melanie

2018-01-01

The purpose of this paper is to describe and discuss how we designed and developed a 12-step technology training protocol. The protocol is meant to improve meaningful learning in technology education so that nursing students are able to meet the informatics requirements of Quality and Safety Education in Nursing competencies. When designing and developing the training protocol, we used a simplified experiential learning model that addressed the core features of meaningful learning: to connect new knowledge with students' prior knowledge and real-world workflow. Before training, we identified students' prior knowledge and workflow tasks. During training, students learned by doing, reflected on their prior computer skills and workflow, designed individualized procedures for integration into their workflow, and practiced the self-designed procedures in real-world settings. The trainer was a facilitator who provided a meaningful learning environment, asked the right questions to guide reflective conversation, and offered scaffoldings at critical moments. This training protocol could significantly improve nurses' competencies in using technologies and increase their desire to adopt new technologies. © 2017 Wiley Periodicals, Inc.

Experimental and Modeling Approaches for Understanding the Effect of Gene Expression Noise in Biological Development

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David M. Holloway

2018-04-01

Full Text Available Biological development involves numerous chemical and physical processes which must act in concert to reliably produce a cell, a tissue, or a body. To be successful, the developing organism must be robust to variability at many levels, such as the environment (e.g., temperature, moisture, upstream information (such as long-range positional information gradients, or intrinsic noise due to the stochastic nature of low concentration chemical kinetics. The latter is especially relevant to the regulation of gene expression in cell differentiation. The temporal stochasticity of gene expression has been studied in single celled organisms for nearly two decades, but only recently have techniques become available to gather temporally-resolved data across spatially-distributed gene expression patterns in developing multicellular organisms. These demonstrate temporal noisy “bursting” in the number of gene transcripts per cell, raising the question of how the transcript number defining a particular cell type is produced, such that one cell type can reliably be distinguished from a neighboring cell of different type along a tissue boundary. Stochastic spatio-temporal modeling of tissue-wide expression patterns can identify signatures for specific types of gene regulation, which can be used to extract regulatory mechanism information from experimental time series. This Perspective focuses on using this type of approach to study gene expression noise during the anterior-posterior segmentation of the fruit fly embryo. Advances in experimental and theoretical techniques will lead to an increasing quantification of expression noise that can be used to understand how regulatory mechanisms contribute to embryonic robustness across a range of developmental processes.

Enhancing the Meaningfulness of Work for Astronauts on Long Duration Space Exploration Missions.

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Britt, Thomas W; Sytine, Anton; Brady, Ashley; Wilkes, Russ; Pittman, Rebecca; Jennings, Kristen; Goguen, Kandice

2017-08-01

Numerous authors have identified the stressors likely to be encountered on long duration space exploration missions (e.g., to Mars), including the possibility of significant crises, separation from family, boredom/monotony, and interpersonal conflict. Although many authors have noted that meaningful work may be beneficial for astronauts on these missions, none have detailed the sources of meaningful work for astronauts and how these sources may differ between astronauts. The present article identifies how engagement in meaningful work during long duration missions may mitigate the adverse effects of demands and increase the potential for benefits resulting from the missions. Semistructured interviews were conducted with nine NASA personnel, including astronauts, flight directors, and flight surgeons. Questions addressed sources of meaning for astronauts, characteristics of tasks that enhance vs. detract from meaning, and recommendations for enhancing meaning. Personnel mentioned contributing to humanity and the next generation, contributing to the mission, and exploration as the most meaningful aspects of their work. Characteristics of tasks that enhanced meaning included using a variety of skills, feeling personal control over their schedule, autonomy in the execution of tasks, and understanding the importance of the experiments conducted on the mission. Top recommendations to sustain meaning were insuring social needs were met through such activities as the strategic use of social media, giving astronauts autonomy as well as structure, and conducting training during transit. Implications are addressed for tailoring meaning-based interventions for astronauts participating on long duration missions and assessing the effectiveness of these interventions.Britt TW, Sytine A, Brady A, Wilkes R, Pittman R, Jennings K, Goguen K. Enhancing the meaningfulness of work for astronauts on long duration space exploration missions. Aerosp Med Hum Perform. 2017; 88(8):779-783.

Bodily Movement and Facial Actions in Expressive Musical Performance by Solo and Duo Instrumentalists: Two Distinctive Case Studies

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Davidson, Jane W.

2012-01-01

The research literature concerning gesture in musical performance increasingly reports that musically communicative and meaningful performances contain highly expressive bodily movements. These movements are involved in the generation of the musically expressive performance, but enquiry into the development of expressive bodily movement has been…

Authentic Leadership and Altruism: The Mediating Role of Meaningfulness

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Sagnak, Mesut; Kuruöz, Mehmet

2017-01-01

The purpose of this study was to investigate the mediating effects of meaningfulness on the relationship between authentic leadership and altruistic behavior. The participants consisted of 356 teachers randomly selected from 14 primary and secondary schools in Nigde. Three different instruments were used in this study. The scales were translated…

Seeing through Symbols: The Case of Equivalent Expressions.

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Kieran, Carolyn; Sfard, Anna

1999-01-01

Presents a teaching experiment to turn students from external observers into active participants in a game of algebra learning where students use graphs to build meaning for equivalence of algebraic expressions. Concludes that the graphic-functional approach seems to make the introduction to algebra much more meaningful for the learner. (ASK)

Evolution of meanings of the concept of gen in students of higher education in the teaching of biology

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Dalia Diez de Tancredi

2012-01-01

Full Text Available The aim of the study was to identify initial meanings of the concept of the gene among 50 students from the career training of teachers of biology at the University Pedagogical Experimental Libertador (UPEL, Pedagogical Institute of Caracas, who enrolled in Cell Biology (BC and General Genetics (GG, as well as those built from a didactic intervention that formed part of Participatory Action Research (PAR. The work is based on the Theory of Meaningful Learning of Ausubel, on the principles of critical meaningful learning facilitators of Moreira, and on elements of the educational act of Novak. To investigate the evolution of meaning of this concept were used: questionnaires, interviews, maps and graphic representations of concepts developed by students. The data analysis provides a differentiated evolution of the meaning of the gene in the students, which corresponds to the didactic intervention and teachers, actions in both courses. It shows the importance of organizing the teaching in a potentially meaningful way to reflect on the content and learning, so that abstract concepts such as gene, must be presented with a critical and reflexive epistemology.

Meaningful Words and Non-Words Repetitive Articulatory Rate (Oral Diadochokinesis) in Persian Speaking Children.

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Zamani, Peyman; Rezai, Hossein; Garmatani, Neda Tahmasebi

2017-08-01

Repetitive articulatory rate or Oral Diadochokinesis (oral-DDK) shows a guideline for appraisal and diagnosis of subjects with oral-motor disorder. Traditionally, meaningless words repetition has been utilized in this task and preschool children have challenges with them. Therefore, we aimed to determine some meaningful words in order to test oral-DDK in Persian speaking preschool children. Participants were 142 normally developing children, (age range 4-6 years), who were asked to produce /motæka, golabi/ as two meaningful Persian words and /pa-ta-ka/ as non-word in conventional oral-DDK task. We compared the time taken for 10-times fast repetitions of two meaningful Persian words and the tri-syllabic nonsense word /pa-ta-ka/. Praat software was used to calculate the average time that subjects took to produce the target items. In 4-5 year old children, [Formula: see text] of time taken for 10-times repetitions of /pa-ta-ka, motæka, golabi/ were [Formula: see text], and [Formula: see text] seconds respectively, and in 5-6 year old children were [Formula: see text], and [Formula: see text] seconds respectively. Findings showed that the main effect of type of words on oral diadochokinesis was significant ([Formula: see text]). Children repeated meaningful words /motæka, golabi/ faster than the non-word /pa-ta-ka/. Sex and age factors had no effect on time taken for repetition of oral-DDK test. It is suggested that Speech Therapists can use meaningful words to facilitate oral-DDK test for children.

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data

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Trifonov, Vladimir; Pasqualucci, Laura; Dalla-Favera, Riccardo; Rabadan, Raul

2011-12-01

Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing (HTS), expression profiles, proteomics, and electronic health records (EHR) are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of fractal-like distributions that commonly appear in the analysis of such data. The first set of examples are drawn from a HTS experiment. Here, the distributions appear as part of the evaluation of the error rate of the sequencing and the identification of tumorogenic genomic alterations. The other examples are obtained from risk factor evaluation and analysis of relative disease prevalence and co-mordbidity as these appear in EHR. The distributions are also relevant to identification of subclonal populations in tumors and the study of quasi-species and intrahost diversity of viral populations.

Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

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Ina Aretz

2016-04-01

Full Text Available Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

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Aretz, Ina; Meierhofer, David

2016-04-27

Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

WHATSAPP CONTRIBUTIONS IN SPANISH TEACHING: A PERSPECTIVE OF MEANINGFUL AND COLLABORATIVE LEARNING

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Iandra Maria Weirich da Silva Coelho

2017-08-01

Full Text Available This article describes a didactic proposal, mediated by the use of WhatsApp as a potential tool for the teaching of Spanish as an additional language. Activities are drawn from collaborative and meaningful practice with authentic situations of the language usage, taking by reference the theoretical construct of the Theory of Meaningful Learning (AUSUBEL, 2003 and Collaborative Practice of Writing. The results identify positive contributions about the increased interest and motivation of students, promotion of discursive competence, interactivity, autonomy, about actions involving the authorship and collaborative construction in information network for knowledge sharing.

End user programming with personally meaningful objects

CSIR Research Space (South Africa)

Smith, Andrew C

2016-09-01

Full Text Available (Kimchi et al., 2003). Perceptual organisation is a neuro-cognitive process that dictates how we perceive objects in physical space and how we interpret some objects as being distinct from others and yet other objects as part of a whole (Helm, 2014... called the designer-cum-user. Using this approach, the user creates a personally meaningful artefact that represents the target product. Although not confirmed, we anticipate that this approach reduces the initial cognitive load on the user when he uses...

Differentially expressed genes distributed over chromosomes and implicated in certain biological processes for site insertion genetically modified rice Kemingdao.

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Liu, Zhi; Li, Yunhe; Zhao, Jie; Chen, Xiuping; Jian, Guiliang; Peng, Yufa; Qi, Fangjun

2012-01-01

Release of genetically modified (GM) plants has sparked off intensive debates worldwide partly because of concerns about potential adverse unintended effects of GM plants to the agro system and the safety of foods. In this study, with the aim of revealing the molecular basis for unintended effects of a single site insertion GM Kemingdao (KMD) rice transformed with a synthetic cry1Ab gene, and bridging unintended effects of KMD rice through clues of differentially expressed genes, comparative transcriptome analyses were performed for GM KMD rice and its parent rice of Xiushui11 (XS11). The results showed that 680 differentially expressed transcripts were identified from 30-day old seedlings of GM KMD rice. The absolute majority of these changed expression transcripts dispersed and located over all rice chromosomes, and existed physical distance on chromosome from the insertion site, while only two transcripts were found to be differentially expressed within the 21 genes located within 100 kb up and down-stream of the insertion site. Pathway and biology function analyses further revealed that differentially expressed transcripts of KMD rice were involved in certain biological processes, and mainly implicated in two types of pathways. One type was pathways implicated in plant stress/defense responses, which were considerably in coordination with the reported unintended effects of KMD rice, which were more susceptible to rice diseases compared to its parent rice XS11; the other type was pathways associated with amino acids metabolism. With this clue, new unintended effects for changes in amino acids synthesis of KMD rice leaves were successfully revealed. Such that an actual case was firstly provided for identification of unintended effects in GM plants by comparative transciptome analysis.

Are estimates of meaningful decline in mobility performance consistent among clinically important subgroups? (Health ABC Study).

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Perera, S.; Studenski, S.; Newman, A.; Simonsick, E.; Harris, T.; Schwartz, A.; Visser, M.

2014-01-01

Background: Meaningful change criteria help determine if function has improved or declined, but their magnitudes may vary across clinically relevant subgroups. We estimate meaningful decline in four common measures of physical performance in subgroups of older adults based on initial performance,

Comprehension for What? Preparing Students for Their Meaningful Future

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Conley, Mark W.; Wise, Antoinette

2011-01-01

Researchers, policymakers, and educators face a daunting task these days concerning literacy education for the here and now and literacy for the future. Even though one clings to the romantic notion that education provides the building blocks in a straight line to a meaningful future, the reality is that mixed goals and instructional messages…

Biological Roles of Aberrantly Expressed Glycosphingolipids and Related Enzymes in Human Cancer Development and Progression

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Dinghao Zhuo

2018-05-01

Full Text Available Glycosphingolipids (GSLs, which consist of a hydrophobic ceramide backbone and a hydrophilic carbohydrate residue, are an important type of glycolipid expressed in surface membranes of all animal cells. GSLs play essential roles in maintenance of plasma membrane stability, in regulation of numerous cellular processes (including adhesion, proliferation, apoptosis, and recognition, and in modulation of signal transduction pathways. GSLs have traditionally been classified as ganglio-series, lacto-series, or globo-series on the basis of their diverse types of oligosaccharide chains. Structures and functions of specific GSLs are also determined by their oligosaccharide chains. Different cells and tissues show differential expression of GSLs, and changes in structures of GSL glycan moieties occur during development of numerous types of human cancer. Association of GSLs and/or related enzymes with initiation and progression of cancer has been documented in 100s of studies, and many such GSLs are useful markers or targets for cancer diagnosis or therapy. In this review, we summarize (i recent studies on aberrant expression and distribution of GSLs in common human cancers (breast, lung, colorectal, melanoma, prostate, ovarian, leukemia, renal, bladder, gastric; (ii biological functions of specific GSLs in these cancers.

Towards physical principles of biological evolution

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Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

2018-03-01

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice

In search of meaningfulness: nostalgia as an antidote to boredom.

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van Tilburg, Wijnand A P; Igou, Eric R; Sedikides, Constantine

2013-06-01

We formulated, tested, and supported, in 6 studies, a theoretical model according to which individuals use nostalgia as a way to reinject meaningfulness in their lives when they experience boredom. Studies 1-3 established that induced boredom causes increases in nostalgia when participants have the opportunity to revert to their past. Studies 4 and 5 examined search for meaning as a mediator of the effect of boredom on nostalgia. Specifically, Study 4 showed that search for meaning mediates the effect of state boredom on nostalgic memory content, whereas Study 5 demonstrated that search for meaning mediates the effect of dispositional boredom on dispositional nostalgia. Finally, Study 6 examined the meaning reestablishment potential of nostalgia during boredom: Nostalgia mediates the effect of boredom on sense of meaningfulness and presence of meaning in one's life. Nostalgia counteracts the meaninglessness that individuals experience when they are bored.

Engaging Axiology: Enabling MeaningfulTransdisciplinary Collaboration in Adapted Physical Activity.

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Peers, Danielle

2018-07-01

In this article, I explore the concept of axiology in the context of adapted physical activity research and analyze its connection to the more commonly discussed paradigmatic assumptions of epistemology and ontology. Following methodological scholars, I argue for an acknowledgment of the pivotal role that axiology already plays in adapted physical activity research and for the potential interdisciplinary and transdisciplinary opportunities that could be enabled by engaging with axiology in more explicit ways. I discuss a number of potential axiological gaps between the field of adapted physical activity and disability communities, arguing that such differences may undermine attempts at doing meaningful transdisciplinary research with such communities. I offer strategies for bridging these axiological gaps, encouraging us to work together in axiologically reflexive ways in order to increase meaningful opportunities for more people with disabilities to be engaged in the movement-based activities and communities of their choice.

Expression of Truncated Neurokinin-1 Receptor in Childhood Neuroblastoma is Independent of Tumor Biology and Stage.

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Pohl, Alexandra; Kappler, Roland; Mühling, Jakob; VON Schweinitz, Dietrich; Berger, Michael

2017-11-01

Neuroblastoma is an embryonal malignancy arising from the aberrant growth of neural crest progenitor cells of the sympathetic nervous system. The tachykinin receptor 1 (TACR1) - substance P complex is associated with tumoral angiogenesis and cell proliferation in a variety of cancer types. Inhibition of TACR1 was recently described to impede growth of NB cell lines. However, the relevance of TACR1 in clinical settings is unknown. We investigated gene expression levels of full-length and truncated TACR1 in 59 neuroblastomas and correlated these data with the patients' clinical parameters such as outcome, metastasis, International Neuroblastoma Staging System (INSS) status, MYCN proto-oncogene, bHLH transcription factor (MYCN) status, gender and age. Our results indicated that TACR1 is ubiquitously expressed in neuroblastoma but expression levels are independent of clinical parameters. Our data suggest that TACR1 might serve as a potent anticancer target in a large variety of patients with neuroblastoma, independent of tumor biology and clinical stage. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Relationship between attachment to God and meaningful life parents of mentally retarded children in Zahedan city

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H Jenaabadi

2014-07-01

Conclusion: Given a significant positive correlation between appeal to God and meaningful life, it is suggested including spirituality therapy sessions and teaching religious coping methods to reduce stress and thus make meaningful life in these parents by welfare, education of exceptional children, and radio and television organizations.

Meaningful learning: The essential factor for conceptual change in limited or inappropriate propositional hierarchies leading to empowerment of learners

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Novak, Joseph D.

2002-07-01

The construction and reconstruction of meanings by learners requires that they actively seek to integrate new knowledge with knowledge already in their cognitive structure. Ausubel's assimilation theory of cognitive learning has been shown to be effective in guiding research and instructional design to facilitate meaningful learning (Ausubel, The psychology of meaningful verbal learning, New York: Grune and Stratton, 1963; Educational psychology: A cognitive view, New York: Holt, Rinehart and Winston, 1968; The acquisition and retention of knowledge, Dordrecht: Kluwer, 2000). Gowin's Vee heuristic has been employed effectively to aid teachers and students in understanding the constructed nature of knowledge (Gowin, Educating, Ithaca, NY: Cornell University Press, 1981). Situated learning occurs when learning is by rote or at a lower level of meaningful learning. Concept mapping has been used effectively to aid meaningful learning with resulting modification of student's knowledge structures. When these knowledge structures are limited or faulty in some way, they may be referred to as Limited or Inappropriate Propositional Hierarchies (LIPH's). Conceptual change, or more accurately conceptual reconstrution, requires meaningful learning to modify LIPH's. Collaborative group learning facilitates meaningful learning and new knowledge construction. World-wide economic changes are forcing major changes in business and industry placing a premium on the power and value of knowledge and new knowledge production. These changes require changes in school and university education that centers on the nature and power of meaningful learning. New computer tools are available to facilitate teaching activities targeted at modifying LIPH's, and aiding meaningful learning in general.

Effects of CPG ODN on biological behavior of PANC-1 and expression of TLR9 in pancreatic cancer.

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Wu, Han-Qing; Wang, Bo; Zhu, Shi-Kai; Tian, Yuan; Zhang, Jing-Hui; Wu, He-Shui

2011-02-28

To determine the expression of toll-like receptor 9 (TLR9) in pancreatic tumor and the effects of cytosine phosphate-guanosine oligodeoxynucleotides 2216 (CPG ODN2216) on biological behavior of pancreatic carcinoma cell line PANC-1 and explore their clinical significance. The immunohistochemistry and Western blot were used to determine the expression of TLR9 protein in pancreatic cancer tissues, and immunofluorescence staining was performed to detect the TLR9 protein expression in pancreatic carcinoma cell line PANC-1. To assess the effects of CPG ODN2216 on the invasive property of Panc-1 cells, in vitro cell adhesion, wound-healing scrape, and invasion and cell colony formation were evaluated. TLR9 was highly expressed in pancreatic cancer tissues and PANC-1 cells. The percentage of positive cells expressing TLR9 protein in human pancreatic tissues, paracancerous tissues and normal tissues were 73.3%, 33.3% and 20.0%, respectively, and the protein expression level of TLR9 was gradually descending (P PANC-1 cells in CPG ODN 2216 treatment group were significantly lower than in the control group (P PANC-1 cells in treatment group was significantly decreased and CPG ODN2216 had an inhibitive effect in the growth of Panc-1 cells in a dose and time-dependent manner (P Panc-1 cells.

11th International Conference on Practical Applications of Computational Biology & Bioinformatics

CERN Document Server

Mohamad, Mohd; Rocha, Miguel; Paz, Juan; Pinto, Tiago

2017-01-01

Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next-generation sequencing technologies, together with novel and constantly evolving, distinct types of omics data technologies, have created an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis of the datasets produced and their integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Clearly, Biology is more and more a science of information and requires tools from the computational sciences. In the last few years, we have seen the rise of a new generation of interdisciplinary scientists with a strong background in the biological and computational sciences. In this context, the interaction of r...

8th International Conference on Practical Applications of Computational Biology & Bioinformatics

CERN Document Server

Rocha, Miguel; Fdez-Riverola, Florentino; Santana, Juan

2014-01-01

Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies, together with novel and ever evolving distinct types of omics data technologies, have put an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis of the datasets produced and their integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Clearly, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researche...

10th International Conference on Practical Applications of Computational Biology & Bioinformatics

CERN Document Server

Rocha, Miguel; Fdez-Riverola, Florentino; Mayo, Francisco; Paz, Juan

2016-01-01

Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies, together with novel and ever evolving distinct types of omics data technologies, have put an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis of the datasets produced and their integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Clearly, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researche...

How Do Novice Art Teachers Define and Implement Meaningful Curriculum?

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Bain, Christina; Newton, Connie; Kuster, Deborah; Milbrandt, Melody

2010-01-01

Four researchers collaborated on this qualitative case study that examined 11 first-year novice art teachers' understanding and implementation of meaningful curriculum. Participants were selected through a criterion method sampling strategy; the subjects were employed in rural, urban, and suburban public school districts. In order to conduct a…

Cultural study in design : In search of a meaningful approach

NARCIS (Netherlands)

van Boeijen, A.G.C.

2014-01-01

Does the Circuit of Culture help design students to do a cultural study that is meaningful for their design project? Indeed, it provides a good view on the phenomenon culture, its complexity and how contemporary cultures can be studied, providing an overview and structure of the processes that

The importance of culturally meaningful activity for health benefits among older Korean immigrant living in the United States.

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Kim, Junhyoung; Kim, May; Han, Areum; Chin, Seungtae

2015-01-01

Research indicates that participation in culturally meaningful activity is beneficial for immigrants' health and well-being, yet older Korean immigrants struggle with accepting new cultural perspectives, which can negatively affect their health and well-being. Using in-depth interviews, this study was designed to capture the value of culturally meaningful activities for health among older Korean immigrants. Three themes were identified: (a) improved psychological well-being, (b) enhanced positive emotions and feelings, and (c) social connections developed with others. The findings suggest that by engaging in various culturally meaningful activities, older Korean immigrants gain a sense of social, cultural, and psychological significance in life. This study also provided evidence that older Korean immigrants maintain and develop their cultural identity through culturally meaningful activities.

The importance of culturally meaningful activity for health benefits among older Korean immigrant living in the United States

Directory of Open Access Journals (Sweden)

Junhyoung Kim

2015-06-01

Full Text Available Research indicates that participation in culturally meaningful activity is beneficial for immigrants’ health and well-being, yet older Korean immigrants struggle with accepting new cultural perspectives, which can negatively affect their health and well-being. Using in-depth interviews, this study was designed to capture the value of culturally meaningful activities for health among older Korean immigrants. Three themes were identified: (a improved psychological well-being, (b enhanced positive emotions and feelings, and (c social connections developed with others. The findings suggest that by engaging in various culturally meaningful activities, older Korean immigrants gain a sense of social, cultural, and psychological significance in life. This study also provided evidence that older Korean immigrants maintain and develop their cultural identity through culturally meaningful activities.

Meaningful and efficient? Enduring challenges to Aboriginal participation in environmental assessment

International Nuclear Information System (INIS)

Udofia, Aniekan; Noble, Bram; Poelzer, Greg

2017-01-01

This paper explores the underlying practice-based challenges to meaningful and efficient Aboriginal participation in environmental assessment (EA) - participation that provides meaningful opportunities for Aboriginal communities to shape EA, yet assures a degree of efficiency for project proponents who need to obtain EA approvals in a timely and financially viable manner. We do so based on an analysis of the EA policy community's experience with uranium exploration and mining in Saskatchewan, Canada. Many of the challenges to meaningful and efficient Aboriginal participation that emerged are multi-dimensional, often concerning participation processes, decision-making, and relationships. Although scholars have explored many of these issues and have proposed numerous solutions, challenges persist in practice. Several other issues also emerged from our study that have received limited attention, including the non-commitment to early and ongoing participation by smaller project proponents, and the EA exemption of exploration projects; the limited availability of information to project developers on local right holders and Aboriginal interests; expectations about the integration of traditional knowledge and land use in EA not aligning with the information that is available to proponents; confusion about who is responsible for initiating early participation and consultation processes; the lack of early relationship building with potentially affected communities, particularly by governments; and the lack of other viable avenues, outside EA, for Aboriginal communities to raise more strategic issues of concern that affect traditional lands and treaty rights.

‘Killing Me Softly With His/Her Song’: How Leaders Dismantle Followers’ Sense of Work Meaningfulness

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Petra Kipfelsberger

2018-05-01

Full Text Available Leaders influence followers’ meaning and play a key role in shaping their employees’ experience of work meaningfulness. While the dominant perspective in theory and in empirical work focuses on the positive influence of leaders on followers’ work meaningfulness, our conceptual model explores conditions in which leaders may harm followers’ sense of meaning. We introduce six types of conditions: leaders’ personality traits, leaders’ behaviors, the relationship between leader and follower, followers’ attributions, followers’ characteristics, and job design under which leaders’ meaning making efforts might harm or ‘kill’ followers’ sense of work meaningfulness. Accordingly, we explore how these conditions may interact with leaders’ meaning making efforts to lower levels of followers’ sense of meaning, and in turn, lead to negative personal outcomes (cynicism, lower well-being, and disengagement, as well as negative organizational outcomes (corrosive organizational energy, higher turnover rates, and lower organizational productivity. By doing so, our research extends the current literature, enabling a more comprehensive understanding of leaders’ influence on followers’ work meaningfulness, while considering the dark side of meaning making.

Meaningful community involvement in protected area issues: a dialogue session

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Laurie Yung

2000-01-01

The current effort to rethink public involvement in decision-making processes for federal lands is gaining momentum. Advocates of alternative decision-making processes seek to involve communities in more meaningful ways than traditional NEPA-style public participation. These new processes take the form of citizen monitoring, partnerships, and most often, collaboration...

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

DEFF Research Database (Denmark)

Yang, Laurence; Tan, Justin; O'Brien, Edward J.

2015-01-01

based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma......Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood...... at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass...

Sweeping the floor or putting a man on the moon : How to define and measure meaningful work

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Both-Nwabuwe, Jitske M.C.; Dijkstra, Maria T.M.; Beersma, Bianca

2017-01-01

Meaningful work is integral to well-being and a flourishing life. The construct of "meaningful work" is, however, consistently affected by conceptual ambiguity. Although there is substantial support for arguments to maintain the status of conceptual ambiguity, we make a case for the benefits of

An investigation of meaningful understanding and effectiveness of the implementation of Piagetian and Ausubelian theories in physics instruction

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Williams, Karen Ann

One section of college students (N = 25) enrolled in an algebra-based physics course was selected for a Piagetian-based learning cycle (LC) treatment while a second section (N = 25) studied in an Ausubelian-based meaningful verbal reception learning treatment (MVRL). This study examined the students' overall (concept + problem solving + mental model) meaningful understanding of force, density/Archimedes Principle, and heat. Also examined were students' meaningful understanding as measured by conceptual questions, problems, and mental models. In addition, students' learning orientations were examined. There were no significant posttest differences between the LC and MVRL groups for students' meaningful understanding or learning orientation. Piagetian and Ausubelian theories explain meaningful understanding for each treatment. Students from each treatment increased their meaningful understanding. However, neither group altered their learning orientation. The results of meaningful understanding as measured by conceptual questions, problem solving, and mental models were mixed. Differences were attributed to the weaknesses and strengths of each treatment. This research also examined four variables (treatment, reasoning ability, learning orientation, and prior knowledge) to find which best predicted students' overall meaningful understanding of physics concepts. None of these variables were significant predictors at the.05 level. However, when the same variables were used to predict students' specific understanding (i.e. concept, problem solving, or mental model understanding), the results were mixed. For forces and density/Archimedes Principle, prior knowledge and reasoning ability significantly predicted students' conceptual understanding. For heat, however, reasoning ability was the only significant predictor of concept understanding. Reasoning ability and treatment were significant predictors of students' problem solving for heat and forces. For density

Evidence of inflammatory immune signaling in chronic fatigue syndrome: A pilot study of gene expression in peripheral blood

Directory of Open Access Journals (Sweden)

Vernon Suzanne D

2008-09-01

Full Text Available Abstract Background Genomic profiling of peripheral blood reveals altered immunity in chronic fatigue syndrome (CFS however interpretation remains challenging without immune demographic context. The object of this work is to identify modulation of specific immune functional components and restructuring of co-expression networks characteristic of CFS using the quantitative genomics of peripheral blood. Methods Gene sets were constructed a priori for CD4+ T cells, CD8+ T cells, CD19+ B cells, CD14+ monocytes and CD16+ neutrophils from published data. A group of 111 women were classified using empiric case definition (U.S. Centers for Disease Control and Prevention and unsupervised latent cluster analysis (LCA. Microarray profiles of peripheral blood were analyzed for expression of leukocyte-specific gene sets and characteristic changes in co-expression identified from topological evaluation of linear correlation networks. Results Median expression for a set of 6 genes preferentially up-regulated in CD19+ B cells was significantly lower in CFS (p = 0.01 due mainly to PTPRK and TSPAN3 expression. Although no other gene set was differentially expressed at p Conclusion Dissection of blood microarray profiles points to B cell dysfunction with coordinated immune activation supporting persistent inflammation and antibody-mediated NK cell modulation of T cell activity. This has clinical implications as the CD19+ genes identified could provide robust and biologically meaningful basis for the early detection and unambiguous phenotyping of CFS.

Health information technology: integration of clinical workflow into meaningful use of electronic health records.

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Bowens, Felicia M; Frye, Patricia A; Jones, Warren A

2010-10-01

This article examines the role that clinical workflow plays in successful implementation and meaningful use of electronic health record (EHR) technology in ambulatory care. The benefits and barriers of implementing EHRs in ambulatory care settings are discussed. The researchers conclude that widespread adoption and meaningful use of EHR technology rely on the successful integration of health information technology (HIT) into clinical workflow. Without successful integration of HIT into clinical workflow, clinicians in today's ambulatory care settings will continue to resist adoption and implementation of EHR technology.

The effects of meaningful irrelevant speech and road traffic noise on teachers' attention, episodic and semantic memory.

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Enmarker, Ingela

2004-11-01

The aim of the present experiment was to examine the effects of meaningful irrelevant speech and road traffic noise on attention, episodic and semantic memory, and also to examine whether the noise effects were age-dependent. A total of 96 male and female teachers in the age range of 35-45 and 55-65 years were randomly assigned to a silent or the two noise conditions. Noise effects found in episodic memory were limited to a meaningful text, where cued recall contrary to expectations was equally impaired by the two types of noise. However, meaningful irrelevant speech also deteriorated recognition of the text, whereas road traffic noise caused no decrement. Retrieval from two word fluency tests in semantic memory showed strong effects of noise exposure, one affected by meaningful irrelevant speech and the other by road traffic noise. The results implied that both acoustic variation and the semantic interference could be of importance for noise impairments. The expected age-dependent noise effects did not show up.

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

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Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

2016-01-01

Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

Evaluating meaningful learning using concept mapping in dental hygiene education: a pilot study.

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Canasi, Dina M; Amyot, Cynthia; Tira, Daniel

2014-02-01

Concept mapping, as a teaching strategy, has been shown to promote critical thinking and problem solving in educational settings. Dental clinicians must distinguish between critical and irrelevant characteristics in the delivery of care, thus necessitating reasoning skills to do so. One of the aims of the American Dental Education Association Commission on Change and Innovation (ADEA-CCI) is to identify deficiencies in curriculum which were meant to improve critical thinking and problem solving skills necessary in clinical practice. The purpose of this study was to compare 2 teaching strategies, traditional lecture and lecture supported by concept mapping exercises within collaborative working groups, to determine if there is a beneficial effect on meaningful learning. For this pilot study, the study population consisted of students from 2 geographically separated associate level dental hygiene programs in the southeastern U.S. A quasi-experimental control group pre- and post-test design was used. The degree of meaningful learning achieved by both programs was assessed by comparing pre- and post-test results. Both programs experienced a significant degree of meaningful learning from pre- to post-test. However, there was no statistically significant difference between the programs on the post-test. These results were in direct contrast to research in other disciplines on concept mapping and its effect on promoting meaningful learning. Further investigation into the study's outcome was obtained through a follow-up focus group. In spite of careful attention to methodology in the development of this research project, the focus group illuminated methodological failings that potentially impacted the outcome of the study. Recommendations are underscored for future conduct of educational research of this kind.

Assessing clinically meaningful treatment effects in controlled trials: chronic migraine as an example.

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Dodick, David W; Turkel, Catherine C; DeGryse, Ronald E; Diener, Hans-Christoph; Lipton, Richard B; Aurora, Sheena K; Nolan, Marissa E; Silberstein, Stephen D

2015-02-01

In addition to headache, persons with chronic migraine (CM) experience multiple symptoms, both ictal and interictal, that may contribute to their suffering. Translating clinical trial results into practice requires assessment of the results' clinical meaningfulness. When examining treatment benefit in this disabled patient population, multiple headache-symptom measures should be considered to fully reflect clinical relevance. Currently, only onabotulinumtoxinA is approved specifically for headache prophylaxis in adults with CM. Topiramate is the only other therapeutic agent with double-blind, placebo-controlled evidence in this population. Herein we evaluate the clinical meaningfulness of onabotulinumtoxinA and topiramate as headache prophylaxis in CM by comparing primary endpoints from the placebo-controlled, double-blind phase of the Phase 3 REsearch Evaluating Migraine Prophylaxis Therapy (PREEMPT) clinical program and the topiramate clinical trial (frequency of headache days [primary endpoint in PREEMPT; secondary in topiramate trial] and migraine/migrainous days [primary in topiramate trial, or "migraine/probable-migraine days"; secondary in PREEMPT]). Additionally, outcome measures such as responder rates, health-related quality of life, discontinuation rates, safety, and tolerability profiles are important clinical considerations. The clinical data indicate that statistically significant, clinically relevant treatment benefits exist for both onabotulinumtoxinA and topiramate. These data support these treatments as meaningful headache prophylaxis in adults with CM. CM is a chronic pain condition. We sought to determine the clinical relevance of recent trials in this disabled population. Clinical data indicate that statistically significant, clinically relevant treatment benefits exist for both onabotulinumtoxinA and topiramate, and support use of these treatments as meaningful headache prophylaxis in CM. Copyright © 2015 American Pain Society. Published

Modeling biological pathway dynamics with timed automata.

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Schivo, Stefano; Scholma, Jetse; Wanders, Brend; Urquidi Camacho, Ricardo A; van der Vet, Paul E; Karperien, Marcel; Langerak, Rom; van de Pol, Jaco; Post, Janine N

2014-05-01

Living cells are constantly subjected to a plethora of environmental stimuli that require integration into an appropriate cellular response. This integration takes place through signal transduction events that form tightly interconnected networks. The understanding of these networks requires capturing their dynamics through computational support and models. ANIMO (analysis of Networks with Interactive Modeling) is a tool that enables the construction and exploration of executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The tool is based on the formalism of Timed Automata, which can be analyzed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signaling pathways, contributing to the integration of isolated signaling events into complex network models. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic behavior of the network of interest. A user-friendly interface hides the use of Timed Automata from the user, while keeping the expressive power intact. Abstraction to single-parameter kinetics speeds up construction of models that remain faithful enough to provide meaningful insight. The resulting dynamic behavior of the network components is displayed graphically, allowing for an intuitive and interactive modeling experience.

Association between clinically meaningful behavior problems and overweight in children.

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Lumeng, Julie C; Gannon, Kate; Cabral, Howard J; Frank, Deborah A; Zuckerman, Barry

2003-11-01

To determine whether there is a relationship between clinically meaningful behavior problems and concurrent and future overweight in 8- to 11-year-old children. 1998 National Longitudinal Survey of Youth interview data for 8- to 11-year-old children and their mothers were analyzed. A Behavior Problems Index score >90th percentile was considered clinically meaningful. Child overweight was defined as a body mass index (BMI) >or=95th percentile for age and sex. Multiple logistic regression was used to control for potential confounders (selected a priori): child's sex, race, use of behavior-modifying medication, history of academic retention, and hours of television per day; maternal obesity, smoking status, marital status, education, and depressive symptoms; family poverty status; and Home Observation for Measurement of the Environment-Short Form (HOME-SF) cognitive stimulation score. In an attempt to elucidate temporal sequence, a second analysis was conducted with a subsample of normal-weight children who became overweight between 1996 and 1998 while controlling for BMI z score in 1996. The sample included 755 mother-child pairs. Of the potential confounding variables, race, maternal obesity, academic grade retention, maternal education, poverty status, and HOME-SF cognitive stimulation score acted as joint confounders, altering the relationship between behavior problems and overweight in the multiple logistic regression model. With these covariates in the final model, behavior problems were independently associated with concurrent child overweight (adjusted odds ratio: 2.95; 95% confidence interval: 1.34-6.49). The relationship was strengthened in the subsample of previously normal-weight children, with race, maternal obesity, HOME-SF cognitive stimulation score, and 1996 BMI z score acting as confounders (adjusted odds ratio: 5.23; 95% confidence interval: 1.37-19.9). Clinically meaningful behavior problems in 8- to 11-year-old children were independently

Finding pathways to more equitable and meaningful public-scientist partnerships

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Daniela Soleri; Jonathan W. Long; Monica D. Ramirez-Andreotta; Ruth Eitemiller; Rajul Pandyaǁ

2016-01-01

For many, citizen science is exciting because of the possibility for more diverse, equitable partnerships in scientific research with outcomes considered meaningful and useful by all, including public participants. This was the focus of a symposium we organized at the 2015 conference of the Citizen Science Association. Here we synthesize points made by symposium...

Potential biological process of X-linked inhibitor of apoptosis protein in renal cell carcinoma based upon differential protein expression analysis.

Science.gov (United States)

Chen, Chao; Zhao, Si Cong; Yang, Wen Zheng; Chen, Zong Ping; Yan, Yong

2018-01-01

The X-linked inhibitor of apoptosis protein (XIAP) is the best characterized member of the IAP family and is a potent inhibitor of the caspase/apoptosis pathway. It has also been revealed that XIAP has additional biological functions that rely on its direct inhibition of apoptosis. In the present study, stably transfected Caki-1 cells with XIAP-knockdown were generated, and an isobaric tag for relative and absolute quantitation-based proteomics approach was employed to investigate the regulatory mechanism of XIAP in renal cell carcinoma (RCC). The results demonstrate that the sensitivity of the RCC cell line to apoptotic stimulation increased markedly with XIAP-knockdown. A number of differentially expressed proteins were detected between the original Caki-1 cell line and the XIAP-knockdown Caki-1 cell line; 87 at 0 h (prior to etoposide treatment), 178 at 0.5 h and 169 at 3 h, while no differentially expressed proteins were detected (ratio >1.5 or <0.5; P<0.05) at 12 h after etoposide treatment. Through analysis of the differentially expressed proteins, it was revealed that XIAP may participate in the tumor protein p53 pathway, the Wnt signaling pathway, glucose metabolism, endoplasmic reticulum stress, cytoskeletal regulation and DNA repair. These results indicate that XIAP may have a number of biological functions and may provide an insight into the biomedical significance of XIAP overexpression in RCC.

A systems biology approach for miRNA-mRNA expression patterns analysis in non-small cell lung cancer.

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Najafi, Ali; Tavallaei, Mahmood; Hosseini, Sayed Mostafa

2016-01-01

Non-small cell lung cancers (NSCLCs) is a prevalent and heterogeneous subtype of lung cancer accounting for 85 percent of patients. MicroRNAs (miRNAs), a class of small endogenous non-coding RNAs, incorporate into regulation of gene expression post-transcriptionally. Therefore, deregulation of miRNAs' expression has provided further layers of complexity to the molecular etiology and pathogenesis of different diseases and malignancies. Although, until now considerable number of studies has been carried out to illuminate this complexity in NSCLC, they have remained less effective in their goal due to lack of a holistic and integrative systems biology approach which considers all natural elaborations of miRNAs' function. It is able to reliably nominate most affected signaling pathways and therapeutic target genes by deregulated miRNAs during a particular pathological condition. Herein, we utilized a holistic systems biology approach, based on appropriate re-analyses of microarray datasets followed by reliable data filtering, to analyze integrative and combinatorial deregulated miRNA-mRNA interaction network in NSCLC, aiming to ascertain miRNA-dysregulated signaling pathway and potential therapeutic miRNAs and mRNAs which represent a lion' share during various aspects of NSCLC's pathogenesis. Our systems biology approach introduced and nominated 1) important deregulated miRNAs in NSCLCs compared with normal tissue 2) significant and confident deregulated mRNAs which were anti-correlatively targeted by deregulated miRNA in NSCLCs and 3) dysregulated signaling pathways in association with deregulated miRNA-mRNAs interactions in NSCLCs. These results introduce possible mechanism of function of deregulated miRNAs and mRNAs in NSCLC that could be used as potential therapeutic targets.

Hospital budget increase for information technology during phase 1 meaningful use.

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Neumeier, Harold; Berner, Eta S; Burke, Darrell E; Azuero, Andres

2015-01-01

Federal policies have a significant effect on how businesses spend money. The 2009 HITECH (Health Information Technology for Economic and Clinical Health Act) authorized incentive payments through Medicare and Medicaid to clinicians and hospitals when they use certified electronic health records privately and securely to achieve specified improvements in care delivery. Federal incentive payments were offered in 2011 for hospitals that had satisfied "meaningful use" criteria. A longitudinal study of nonfederal hospital information technology (IT) budgets (N = 493) during the years 2009 to 2011 found increases in the percentage of hospital annual operating budgets allocated to IT in the years leading up to these federal incentives. This increase was most pronounced among hospitals receiving high proportions of their reimbursements from Medicaid, followed by hospitals receiving high proportions of their reimbursements from Medicare, possibly indicating a budget shift during this period to more IT spending to achieve meaningful-use policy guidelines.

Designing meaningful educational spaces for the development of competencies in childhood

Directory of Open Access Journals (Sweden)

Yenny Otálora Sevilla

2010-11-01

Full Text Available A meaningful educational space is a learning environment that promotes and strengthens the development of social and cognitive competencies in children. This article offers conceptual and methodological elements from Educational Psychology that facilitates the design of significant educational spaces for the development of child competencies, both in and out of school. On the one hand, the learning environment is defined as a dynamic and complex space of construction of knowledge. On the other it takes into account some considerations about child development which help set five criteria to characterize learning environments as meaningful educational spaces: They are structured, intensive, extensive, generative and interactive situations. Each of these criteria is illustrated through learning environments designed by educators in Colombia, based on the use of cultural practices inherent their communities of origin. Cultural practices were found to be relevant to the development of their children’s competencies.

Expression of long non-coding RNA-HOTAIR in oral squamous cell carcinoma Tca8113 cells and its associated biological behavior

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Liu, Huawei; Li, Zhiyong; Wang, Chao; Feng, Lin; Huang, Haitao; Liu, Changkui; Li, Fengxia

2016-01-01

As a long noncoding RNA, HOX transcript antisense intergenic RNA (HOTAIR) is highly expressed in many types of tumors. However, its expression and function in oral squamous cell carcinoma (OSCC) cells and tissues remains largely unknown. We herein studied the biological functions of HOTAIR in OSCC Tca8113 cells. Real-time quantitative PCR showed that HOTAIR, p21 and p53 mRNA expressions in doxorubicin (DOX)-treated or γ-ray-irradiated Tca8113 cells were up-regulated. Knockdown of p53 expression inhibited DOX-induced HOTAIR up-regulation, suggesting that DNA damage-induced HOTAIR expression may be associated with p53. Transfection and CCK-8 assays showed that compared with the control group, overexpression of HOTAIR promoted the proliferation of Tca8113 cells, while interfering with its expression played an opposite role. Flow cytometry exhibited that HOTAIR overexpression decreased the rate of DOX-induced apoptosis. When HOTAIR expression was inhibited by siRNA, the proportions of cells in G2/M and S phases increased and decreased respectively. Meanwhile, the rate of DOX-induced apoptosis rose. DNA damage-induced HOTAIR expression facilitated the proliferation of Tca8113 cells and decreased their apoptosis. However, whether the up-regulation depends on p53 still needs in-depth studies. PMID:27904675

Computing health quality measures using Informatics for Integrating Biology and the Bedside.

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Klann, Jeffrey G; Murphy, Shawn N

2013-04-19

The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)'s Query Health platform to move toward this goal. Our goal is to integrate i2b2 with the Query Health HQMF architecture, to prepare for other HQMF use-cases (such as MU2 and MU3), and to articulate the functional overlap between i2b2 and HQMF. Therefore, we analyze the structure of HQMF, and then we apply this understanding to HQMF computation on the i2b2 clinical analytical database platform. Specifically, we develop a translator between two query languages, HQMF and i2b2, so that the i2b2 platform can compute HQMF queries. We use the HQMF structure of queries for aggregate reporting, which define clinical data elements and the temporal and logical relationships between them. We use the i2b2 XML format, which allows flexible querying of a complex clinical data repository in an easy-to-understand domain-specific language. The translator can represent nearly any i2b2-XML query as HQMF and execute in i2b2 nearly any HQMF query expressible in i2b2-XML. This translator is part of the freely available reference implementation of the QueryHealth initiative. We analyze limitations of the conversion and find it covers many, but not all, of the complex temporal and logical operators required by quality measures. HQMF is an expressive language for defining quality measures, and it will be important to understand and implement for CQM computation, in both meaningful use and population health. However, its current form might allow

Host cell proteins in biologics development: Identification, quantitation and risk assessment.

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Wang, Xing; Hunter, Alan K; Mozier, Ned M

2009-06-15

Host cell proteins (HCPs) are those produced or encoded by the organisms and unrelated to the intended recombinant product. Some are necessary for growth, survival, and normal cellular processing whereas others may be non-essential, simply carried along as baggage. Like the recombinant product, HCPs may also be modified by the host with a number of post-translational modifications. Regardless of the utility, or lack thereof, HCPs are undesirable in the final drug substance. Though commonly present in small quantities (parts per million expressed as nanograms per milligrams of the intended recombinant protein) much effort and cost is expended by industry to remove them. The purpose of this review is to summarize what is of relevance in regards to the biology, the impact of genomics and proteomics on HCP evaluation, the regulatory expectations, analytical approaches, and various methodologies to remove HCPs with bioprocessing. Historical data, bioinformatics approaches and industrial case study examples are provided. Finally, a proposal for a risk assessment tool is provided which brings these facets together and proposes a means for manufacturers to classify and organize a control strategy leading to meaningful product specifications. 2009 Wiley Periodicals, Inc.

Craniopharyngioma: Survivin expression and ultrastructure

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ZHU, JIANG; YOU, CHAO

2015-01-01

The aim of the present study was to investigate the significance of survivin protein expression levels in craniopharyngioma. Tumor samples and clinical data were obtained from 50 patients with craniopharyngioma who were admitted to the West China Hospital of Sichuan University (Chengdu, China). The morphology of the craniopharyngioma samples was observed using optical and electron microscopes, and survivin expression was investigated in the samples by immunohistochemical analysis. The immunohistochemical results revealed survivin expression in all of the craniopharyngioma samples, but not in the healthy brain tissue samples. It was identified that survivin was expressed at a higher level in cases of the adamantinomatous type compared with those of the squamous-papillary type, in male patients compared with female patients, in children compared with adults and in recurrent cases compared with non-recurrent cases. Furthermore, no significant difference was detected in survivin expression levels among the tumors of different subtypes and different disease stages. The results of the present study indicate that survivin is significant in the development of craniopharyngioma, and that survivin protein expression levels are a meaningful indicator for assessing craniopharyngioma recurrence. PMID:25435936

A generic algorithm for layout of biological networks.

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Schreiber, Falk; Dwyer, Tim; Marriott, Kim; Wybrow, Michael

2009-11-12

Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration. We present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks. The presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.

Can Ausubel's Theory of Meaningful Learning Become an Alternative to Piagetian Psychology?

Science.gov (United States)

Albert, Edna

1979-01-01

Discusses Novak's views that Ausubel's meaningful learning can become an alternative to Piagetian psychology and argues that Ausubel does not provide a theory that can be an alternative to Piaget's developmental psychology. (HM)

Predicting Translation Initiation Rates for Designing Synthetic Biology

International Nuclear Information System (INIS)

Reeve, Benjamin; Hargest, Thomas; Gilbert, Charlie; Ellis, Tom

2014-01-01

In synthetic biology, precise control over protein expression is required in order to construct functional biological systems. A core principle of the synthetic biology approach is a model-guided design and based on the biological understanding of the process, models of prokaryotic protein production have been described. Translation initiation rate is a rate-limiting step in protein production from mRNA and is dependent on the sequence of the 5′-untranslated region and the start of the coding sequence. Translation rate calculators are programs that estimate protein translation rates based on the sequence of these regions of an mRNA, and as protein expression is proportional to the rate of translation initiation, such calculators have been shown to give good approximations of protein expression levels. In this review, three currently available translation rate calculators developed for synthetic biology are considered, with limitations and possible future progress discussed.

Merit-Based Incentive Payment System: Meaningful Changes in the Final Rule Brings Cautious Optimism.

Science.gov (United States)

Manchikanti, Laxmaiah; Helm Ii, Standiford; Calodney, Aaron K; Hirsch, Joshua A

2017-01-01

The Medicare Access and CHIP Reauthorization Act of 2015 (MACRA) eliminated the flawed Sustainable Growth Rate (SGR) act formula - a longstanding crucial issue of concern for health care providers and Medicare beneficiaries. MACRA also included a quality improvement program entitled, "The Merit-Based Incentive Payment System, or MIPS." The proposed rule of MIPS sought to streamline existing federal quality efforts and therefore linked 4 distinct programs into one. Three existing programs, meaningful use (MU), Physician Quality Reporting System (PQRS), value-based payment (VBP) system were merged with the addition of Clinical Improvement Activity category. The proposed rule also changed the name of MU to Advancing Care Information, or ACI. ACI contributes to 25% of composite score of the four programs, PQRS contributes 50% of the composite score, while VBP system, which deals with resource use or cost, contributes to 10% of the composite score. The newest category, Improvement Activities or IA, contributes 15% to the composite score. The proposed rule also created what it called a design incentive that drives movement to delivery system reform principles with the inclusion of Advanced Alternative Payment Models (APMs).Following the release of the proposed rule, the medical community, as well as Congress, provided substantial input to Centers for Medicare and Medicaid Services (CMS),expressing their concern. American Society of Interventional Pain Physicians (ASIPP) focused on 3 important aspects: delay the implementation, provide a 3-month performance period, and provide ability to submit meaningful quality measures in a timely and economic manner. The final rule accepted many of the comments from various organizations, including several of those specifically emphasized by ASIPP, with acceptance of 3-month reporting period, as well as the ability to submit non-MIPS measures to improve real quality and make the system meaningful. CMS also provided a mechanism for

An Integrated Approach for RNA-seq Data Normalization.

Science.gov (United States)

Yang, Shengping; Mercante, Donald E; Zhang, Kun; Fang, Zhide

2016-01-01

DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization. In this article, we propose an integrated approach for RNA-seq data normalization. Comparisons show that the proposed normalization can improve power for downstream differentially expressed gene detection and generate more biologically meaningful results in gene profiling. In addition, our findings show that due to the effects of copy number changes, some housekeeping genes are not always suitable internal controls for studying gene expression. Using information from DNA copy number, integrated approach is successful in reducing noises due to both biological and nonbiological causes in RNA-seq data, thus increasing the accuracy of gene profiling.

Types of Meaningfulness of Life and Values of Future Teachers

Science.gov (United States)

Salikhova, Nailia R.

2016-01-01

The leading role of meaning of life in regulation of human's activity of all types provides the relevance of the research. The goal of the paper is to identify and describe types of meaningfulness of life in future teachers, and to reveal the specificity of values hierarchy indicative of each type. The leading approach applied in the research was…

The categorisation of dysthymic disorder: Can its constituents be meaningfully apportioned?

NARCIS (Netherlands)

Rhebergen, D.; Graham, R.; Hadzi-Pavlovic, D.; Stek, M.L.; Friend, P.; Barrett, M.; Parker, G.

2012-01-01

Background: Since its introduction in DSM-III, the validity of dysthymia has been debated. Our objective is to further examine the concept of dysthymia in an outpatient sample, and explore whether its constituents can be meaningfully apportioned. Methods: 318 patients attending the Black Dog

MOLECULAR CLONING, SEQUENCING, EXPRESSION AND BIOLOGICAL ACTIVITY OF GIANT PANDA (AILUROPODA MELANOLEUCA) INTERFERON-GAMMA.

Science.gov (United States)

Zhu, Hui; Wang, Wen-Xiu; Wang, Bao-Qin; Zhu, Xiao-Fu; Wu, Xu-Jin; Ma, Qing-Yi; Chen, De-Kun

2012-06-29

The giant panda (Ailuropoda melanoleuca) is an endangered species and indigenous to China. Interferon-gamma (IFN-γ) is the only member of type □ IFN and is vital for the regulation of host adapted immunity and inflammatory response. Little is known aboutthe FN-γ gene and its roles in giant panda.In this study, IFN-γ gene of Qinling giant panda was amplified from total blood RNA by RT-CPR, cloned, sequenced and analysed. The open reading frame (ORF) of Qinling giant panda IFN-γ encodes 152 amino acidsand is highly similar to Sichuan giant panda with an identity of 99.3% in cDNA sequence. The IFN-γ cDNA sequence was ligated to the pET32a vector and transformed into E. coli BL21 competent cells. Expression of recombinant IFN-γ protein of Qinling giant panda in E. coli was confirmed by SDS-PAGE and Western blot analysis. Biological activity assay indicated that the recombinant IFN-γ protein at the concentration of 4-10 µg/ml activated the giant panda peripheral blood lymphocytes,while at 12 µg/mlinhibited. the activation of the lymphocytes.These findings provide insights into the evolution of giant panda IFN-γ and information regarding amino acid residues essential for their biological activity.

Vesicular monoamine transporter protein expression correlates with clinical features, tumor biology, and MIBG avidity in neuroblastoma: a report from the Children's Oncology Group

International Nuclear Information System (INIS)

Temple, William; Mendelsohn, Lori; Nekritz, Erin; Gustafson, W.C.; Matthay, Katherine K.; Kim, Grace E.; Lin, Lawrence; Giacomini, Kathy; Naranjo, Arlene; Van Ryn, Collin; Yanik, Gregory A.; Kreissman, Susan G.; Hogarty, Michael; DuBois, Steven G.

2016-01-01

Vesicular monoamine transporters 1 and 2 (VMAT1 and VMAT2) are thought to mediate MIBG uptake in adult neuroendocrine tumors. In neuroblastoma, the norepinephrine transporter (NET) has been investigated as the principal MIBG uptake protein, though some tumors without NET expression concentrate MIBG. We investigated VMAT expression in neuroblastoma and correlated expression with MIBG uptake and clinical features. We evaluated VMAT1 and VMAT2 expression by immunohistochemistry (IHC) in neuroblastoma tumors from 76 patients with high-risk metastatic disease treated in a uniform cooperative group trial (COG A3973). All patients had baseline MIBG diagnostic scans centrally reviewed. IHC results were scored as the product of intensity grading (0 - 3+) and percent of tumor cells expressing the protein of interest. The association between VMAT1 and VMAT2 scores and clinical and biological features was tested using Wilcoxon rank-sum tests. Patient characteristics were typical of high-risk neuroblastoma, though the cohort was intentionally enriched in patients with MIBG-nonavid tumors (n = 20). VMAT1 and VMAT2 were expressed in 62 % and 75 % of neuroblastoma tumors, respectively. VMAT1 and VMAT2 scores were both significantly lower in MYCN amplified tumors and in tumors with high mitotic karyorrhectic index. MIBG-avid tumors had significantly higher VMAT2 scores than MIBG-nonavid tumors (median 216 vs. 45; p = 0.04). VMAT1 expression did not correlate with MIBG avidity. VMAT1 and VMAT2 are expressed in the majority of neuroblastomas. Expression correlates with other biological features. The expression level of VMAT2 but not that of VMAT1 correlates with avidity for MIBG. (orig.)

Vesicular monoamine transporter protein expression correlates with clinical features, tumor biology, and MIBG avidity in neuroblastoma: a report from the Children's Oncology Group

Energy Technology Data Exchange (ETDEWEB)

Temple, William; Mendelsohn, Lori; Nekritz, Erin; Gustafson, W.C.; Matthay, Katherine K. [UCSF School of Medicine, Department of Pediatrics, San Francisco, CA (United States); UCSF Benioff Children' s Hospital, San Francisco, CA (United States); Kim, Grace E. [UCSF School of Medicine, Department of Pathology, San Francisco, CA (United States); Lin, Lawrence; Giacomini, Kathy [UCSF School of Pharmacy, Department of Bioengineering and Therapeutic Sciences, San Francisco, CA (United States); Naranjo, Arlene; Van Ryn, Collin [University of Florida, Children' s Oncology Group Statistics and Data Center, Gainesville, FL (United States); Yanik, Gregory A. [University of Michigan, CS Mott Children' s Hospital, Ann Arbor, MI (United States); Kreissman, Susan G. [Duke University Medical Center, Durham, NC (United States); Hogarty, Michael [University of Pennsylvania, Children' s Hospital of Philadelphia and Perelman School of Medicine, Philadelphia, PA (United States); DuBois, Steven G. [UCSF School of Medicine, Department of Pediatrics, San Francisco, CA (United States); UCSF Benioff Children' s Hospital, San Francisco, CA (United States); UCSF School of Medicine, San Francisco, CA (United States)

2016-03-15

Vesicular monoamine transporters 1 and 2 (VMAT1 and VMAT2) are thought to mediate MIBG uptake in adult neuroendocrine tumors. In neuroblastoma, the norepinephrine transporter (NET) has been investigated as the principal MIBG uptake protein, though some tumors without NET expression concentrate MIBG. We investigated VMAT expression in neuroblastoma and correlated expression with MIBG uptake and clinical features. We evaluated VMAT1 and VMAT2 expression by immunohistochemistry (IHC) in neuroblastoma tumors from 76 patients with high-risk metastatic disease treated in a uniform cooperative group trial (COG A3973). All patients had baseline MIBG diagnostic scans centrally reviewed. IHC results were scored as the product of intensity grading (0 - 3+) and percent of tumor cells expressing the protein of interest. The association between VMAT1 and VMAT2 scores and clinical and biological features was tested using Wilcoxon rank-sum tests. Patient characteristics were typical of high-risk neuroblastoma, though the cohort was intentionally enriched in patients with MIBG-nonavid tumors (n = 20). VMAT1 and VMAT2 were expressed in 62 % and 75 % of neuroblastoma tumors, respectively. VMAT1 and VMAT2 scores were both significantly lower in MYCN amplified tumors and in tumors with high mitotic karyorrhectic index. MIBG-avid tumors had significantly higher VMAT2 scores than MIBG-nonavid tumors (median 216 vs. 45; p = 0.04). VMAT1 expression did not correlate with MIBG avidity. VMAT1 and VMAT2 are expressed in the majority of neuroblastomas. Expression correlates with other biological features. The expression level of VMAT2 but not that of VMAT1 correlates with avidity for MIBG. (orig.)

Mediating role of meaningful work between resources and work engagement in Bangladesh’s private banks

Directory of Open Access Journals (Sweden)

Nawrin Rubaba

2018-03-01

Full Text Available Engaged employees are considered as the most desired assets for the organization. Although significant contributions have been observed in the engagement literature, a holistic approach is yet to be untouched in terms of developing relationship between various resources, work engagement and psychological mechanism such as meaningful work. The purpose of this study is to explore the mediating role of meaningful work between resources and work engagement in private banks in Bangladesh. This study followed the quantitative methodological approach and based on Bakker and Demerouti’s (2007 Job demand-resources model. A survey questionnaire was prepared and used to collect data. 440 respondents participated in this study, who is currently working in private banks in Bangladesh. Multiple regression analysis along with Sobel test was performed to analyze the data. The findings confirmed that the relationships between organizational, job, personal resources and work engagement were partially mediated through meaningful work. It has been observed that all determinates had a significant influence on work engagement. For practical implications, the organization can align various resources to uplift the engagement level of the employees. Since meaningful work was found to be a significant predictor, managers can develop jobs where employees can relate their purpose to their work. This study recommends that future research can apply this model to different contexts as well as to different groups of respondents.

Early- versus Late-Onset Dysthymia: A Meaningful Clinical Distinction?

OpenAIRE

Sansone, Randy A.; Sansone, Lori A.

2009-01-01

In the current Diagnostic and Statistical Manual of Mental Disorders, dysthymic disorder is categorized as either early-onset or late-onset, based upon the emergence of symptoms before or after the age of 21, respectively. Does this diagnostic distinction have any meaningful clinical implications? In this edition of The Interface, we present empirical studies that have, within a single study, compared individuals with early-versus late-onset dysthymia. In this review, we found that, compared ...

Nitrogen-use-efficiency: a biologically meaningful definition?

NARCIS (Netherlands)

Berendse, F.; Aerts, R.

1987-01-01

A parameter to measure the efficiency of nitrogen use should include 1) the mean residence time of the N in the plant, ie the period during which the absorbed N can be used for C-fixation; and 2) the instantaneous rate of C-fixation per unit of N in the plant. It is essential to distinguish between

Bridging cancer biology with the clinic: relative expression of a GRHL2-mediated gene-set pair predicts breast cancer metastasis.

Directory of Open Access Journals (Sweden)

Xinan Yang

Full Text Available Identification and characterization of crucial gene target(s that will allow focused therapeutics development remains a challenge. We have interrogated the putative therapeutic targets associated with the transcription factor Grainy head-like 2 (GRHL2, a critical epithelial regulatory factor. We demonstrate the possibility to define the molecular functions of critical genes in terms of their personalized expression profiles, allowing appropriate functional conclusions to be derived. A novel methodology, relative expression analysis with gene-set pairs (RXA-GSP, is designed to explore the potential clinical utility of cancer-biology discovery. Observing that Grhl2-overexpression leads to increased metastatic potential in vitro, we established a model assuming Grhl2-induced or -inhibited genes confer poor or favorable prognosis respectively for cancer metastasis. Training on public gene expression profiles of 995 breast cancer patients, this method prioritized one gene-set pair (GRHL2, CDH2, FN1, CITED2, MKI67 versus CTNNB1 and CTNNA3 from all 2717 possible gene-set pairs (GSPs. The identified GSP significantly dichotomized 295 independent patients for metastasis-free survival (log-rank tested p = 0.002; severe empirical p = 0.035. It also showed evidence of clinical prognostication in another independent 388 patients collected from three studies (log-rank tested p = 3.3e-6. This GSP is independent of most traditional prognostic indicators, and is only significantly associated with the histological grade of breast cancer (p = 0.0017, a GRHL2-associated clinical character (p = 6.8e-6, Spearman correlation, suggesting that this GSP is reflective of GRHL2-mediated events. Furthermore, a literature review indicates the therapeutic potential of the identified genes. This research demonstrates a novel strategy to integrate both biological experiments and clinical gene expression profiles for extracting and elucidating the genomic

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

Science.gov (United States)

Kang, Tianyu; Ding, Wei; Zhang, Luoyan; Ziemek, Daniel; Zarringhalam, Kourosh

2017-12-19

Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers. In this paper, we develop a biological network-based regularized artificial neural network model for prediction of phenotype from transcriptomic measurements in clinical trials. To improve model sparsity and the overall reproducibility of the model, we incorporate regularization for simultaneous shrinkage of gene sets based on active upstream regulatory mechanisms into the model. We benchmark our method against various regression, support vector machines and artificial neural network models and demonstrate the ability of our method in predicting the clinical outcomes using clinical trial data on acute rejection in kidney transplantation and response to Infliximab in ulcerative colitis. We show that integration of prior biological knowledge into the classification as developed in this paper, significantly improves the robustness and generalizability of predictions to independent datasets. We provide a Java code of our algorithm along with a parsed version of the STRING DB database. In summary, we present a method for prediction of clinical phenotypes using baseline genome-wide expression data that makes use of prior biological knowledge on gene-regulatory interactions in order to increase robustness and reproducibility of omic-scale markers. The integrated group-wise regularization methods increases the interpretability of biological signatures and gives stable performance estimates across independent test sets.

Towards happiness: Experiences of work-role fit, meaningfulness and work engagement of industrial/organisational psychologists in South Africa

Directory of Open Access Journals (Sweden)

Llewellyn E. van Zyl

2010-10-01

Research purpose: The aim of this study was to determine how I/O psychologists experience the meaning of their work and to investigate the relationships between their experiences of work-role fit, meaning of work, psychological meaningfulness and work engagement, utilising the happiness framework proposed by Seligman (2002. Motivation for the study: I/O psychologists spend more than 88% of their working day with people, and they are primary role models for happiness in the workplace. Information about their work engagement and experiences of meaning is therefore needed. Research design, approach and method: A survey design was used. A convenience sample (n = 106 was taken of I/O psychologists in South Africa. A biographical questionnaire, the Work-Role Fit Scale, the Work-Life Questionnaire, the Psychological Meaningfulness Scale, the Work Engagement Scale and a survey measuring the actual and desired time spent on six broad categories of work were administered. Main findings: Work-role fit predicted psychological meaningfulness and work engagement. The calling orientation to work predicted both psychological meaningfulness and work engagement. Work-role fit mediated the relationship between the meaning of work and psychological meaningfulness. Work-role fit partially mediated the relationship between a calling orientation to work and work engagement. Practical implications: A calling orientation to work should be fostered in I/O psychologists because it contributes to experiences of work-role fit, psychological meaningfulness and work engagement. Contribution/value-add: The results of this study contribute to scientific knowledge about work-role fit, engagement and meaning as components of happiness of I/O psychologists.

The Right to Appropriate and Meaningful Education for Children with ASD

Science.gov (United States)

Marshall, David; Goodall, Craig

2015-01-01

This paper will explore from a "child's rights perspective" the "right" of children with autistic spectrum disorder (ASD) to appropriate and meaningful education. Human "rights" principles within international law will be evaluated in relation to how they have been interpreted and applied in relation to achieving this…

The co-creation of meaningful action: bridging enaction and interactional sociology.

Science.gov (United States)

De Jaegher, Hanne; Peräkylä, Anssi; Stevanovic, Melisa

2016-05-05

What makes possible the co-creation of meaningful action? In this paper, we go in search of an answer to this question by combining insights from interactional sociology and enaction. Both research schools investigate social interactions as such, and conceptualize their organization in terms of autonomy. We ask what it could mean for an interaction to be autonomous, and discuss the structures and processes that contribute to and are maintained in the so-called interaction order. We also discuss the role played by individual vulnerability as well as the vulnerability of social interaction processes in the co-creation of meaningful action. Finally, we outline some implications of this interdisciplinary fraternization for the empirical study of social understanding, in particular in social neuroscience and psychology, pointing out the need for studies based on dynamic systems approaches on origins and references of coordination, and experimental designs to help understand human co-presence. © 2016 The Authors.

The co-creation of meaningful action: bridging enaction and interactional sociology

Science.gov (United States)

Peräkylä, Anssi; Stevanovic, Melisa

2016-01-01

What makes possible the co-creation of meaningful action? In this paper, we go in search of an answer to this question by combining insights from interactional sociology and enaction. Both research schools investigate social interactions as such, and conceptualize their organization in terms of autonomy. We ask what it could mean for an interaction to be autonomous, and discuss the structures and processes that contribute to and are maintained in the so-called interaction order. We also discuss the role played by individual vulnerability as well as the vulnerability of social interaction processes in the co-creation of meaningful action. Finally, we outline some implications of this interdisciplinary fraternization for the empirical study of social understanding, in particular in social neuroscience and psychology, pointing out the need for studies based on dynamic systems approaches on origins and references of coordination, and experimental designs to help understand human co-presence. PMID:27069055

The challenge of a meaningful job

DEFF Research Database (Denmark)

Jepsen, Ingrid

and the feeling of doing high quality care generate job satisfaction. The obligation and pressure to perform well and the disadvantages on the midwives’ private lives is counterbalanced by the feeling of doing a meaningful and important job. Working in caseload midwifery creates a feeling of working in a self....... The methodology was inspired by ethnography, and applied methods were field observations followed by interviews. Participants: Thirteen out of eighteen midwives working in caseloads were observed during one or two days in the antenatal clinic and interviewed at a later occasion. Findings: The recognition......-governing model within the public hospital, without losing the technological benefits of a modern birth unit. For pregnant women with a challenging personality or attitude towards others, Caseload midwifery may provide an extra opportunity to feel recognized and respected. Key conclusions: Caseload midwifery...

A strategy for full interrogation of prognostic gene expression patterns: exploring the biology of diffuse large B cell lymphoma.

Directory of Open Access Journals (Sweden)

Lisa M Rimsza

Full Text Available Gene expression profiling yields quantitative data on gene expression used to create prognostic models that accurately predict patient outcome in diffuse large B cell lymphoma (DLBCL. Often, data are analyzed with genes classified by whether they fall above or below the median expression level. We sought to determine whether examining multiple cut-points might be a more powerful technique to investigate the association of gene expression with outcome.We explored gene expression profiling data using variable cut-point analysis for 36 genes with reported prognostic value in DLBCL. We plotted two-group survival logrank test statistics against corresponding cut-points of the gene expression levels and smooth estimates of the hazard ratio of death versus gene expression levels. To facilitate comparisons we also standardized the expression of each of the genes by the fraction of patients that would be identified by any cut-point. A multiple comparison adjusted permutation p-value identified 3 different patterns of significance: 1 genes with significant cut-point points below the median, whose loss is associated with poor outcome (e.g. HLA-DR; 2 genes with significant cut-points above the median, whose over-expression is associated with poor outcome (e.g. CCND2; and 3 genes with significant cut-points on either side of the median, (e.g. extracellular molecules such as FN1.Variable cut-point analysis with permutation p-value calculation can be used to identify significant genes that would not otherwise be identified with median cut-points and may suggest biological patterns of gene effects.

An empirically based conceptual framework for fostering meaningful patient engagement in research.

Science.gov (United States)

Hamilton, Clayon B; Hoens, Alison M; Backman, Catherine L; McKinnon, Annette M; McQuitty, Shanon; English, Kelly; Li, Linda C

2018-02-01

Patient engagement in research (PEIR) is promoted to improve the relevance and quality of health research, but has little conceptualization derived from empirical data. To address this issue, we sought to develop an empirically based conceptual framework for meaningful PEIR founded on a patient perspective. We conducted a qualitative secondary analysis of in-depth interviews with 18 patient research partners from a research centre-affiliated patient advisory board. Data analysis involved three phases: identifying the themes, developing a framework and confirming the framework. We coded and organized the data, and abstracted, illustrated, described and explored the emergent themes using thematic analysis. Directed content analysis was conducted to derive concepts from 18 publications related to PEIR to supplement, confirm or refute, and extend the emergent conceptual framework. The framework was reviewed by four patient research partners on our research team. Participants' experiences of working with researchers were generally positive. Eight themes emerged: procedural requirements, convenience, contributions, support, team interaction, research environment, feel valued and benefits. These themes were interconnected and formed a conceptual framework to explain the phenomenon of meaningful PEIR from a patient perspective. This framework, the PEIR Framework, was endorsed by the patient research partners on our team. The PEIR Framework provides guidance on aspects of PEIR to address for meaningful PEIR. It could be particularly useful when patient-researcher partnerships are led by researchers with little experience of engaging patients in research. © 2017 The Authors Health Expectations Published by John Wiley & Sons Ltd.

Functional characterizations of venom phenotypes in the eastern diamondback rattlesnake (Crotalus adamanteus) and evidence for expression-driven divergence in toxic activities among populations

Science.gov (United States)

Margres, Mark J.; Walls, Robert; Suntravat, Montamas; Lucena, Sara; Sánchez, Elda E.; Rokyta, Darin R.

2016-01-01

Phenotypes frequently vary across and within species. The connection between specific phenotypic effects and function, however, is less understood despite being essential to our understanding of the adaptive process. Snake venoms are ideal for identifying functionally important phenotypic variation because venom variation is common, and venoms can be functionally characterized through simple assays and toxicity measurements. Previous work with the eastern diamondback rattlesnake (Crotalus adamanteus) used multivariate statistical approaches to identify six unique venom phenotypes. We functionally characterized hemolytic, gelatinase, fibrinogenolytic, and coagulant activity for all six phenotypes, as well as one additional venom, to determine if the statistically significant differences in toxin expression levels previously documented corresponded to differences in venom activity. In general, statistical differences in toxin expression predicted the identified functional differences, or lack thereof, in toxic activity, demonstrating that the statistical approach used to characterize C. adamanteus venoms was a fair representation of biologically meaningful differences. Minor differences in activity not accounted for by the statistical model may be the result of amino-acid differences and/or post-translational modifications, but overall we were able to link variation in protein expression levels to variation in function as predicted by multivariate statistical approaches. PMID:27179420

Cloning and expression of adiponectin and its globular domain, and measurement of the biological activity in vivo.

Science.gov (United States)

Hu, Xiao-Bo; Zhang, Yu-Jian; Zhang, Hui-Tang; Yang, Sheng-Li; Gong, Yi

2003-11-01

3T3-L1-adipocytes produce the adipocyte complement related protein of 30 kD (ACRP30), which is exclusively expressed in differentiated adipocytes. Decreased expression of ACRP30 correlates with insulin resistance in mouse models of altered insulin sensitivity. Adiponectin, the human homologue of ACRP30, circulates in human plasma at high levels. Plasma adiponectin levels have been reported to be decreased in some insulin-resistant states, such as obesity and type II diabetes mellitus. Here, full-length adiponectin and its C-terminal globular head domain (gAdiponectin) were expressed in Escherichia coli and gAdiponectin was used to immunize a rabbit to obtain polyclonal antiserum with titer of 10,000. Adiponectin was detected in human plasma with the use of gAdiponectin anti-serum by Western blot analysis, which was also detected by gACRP30 anti-serum. Injection in alloxan-treated rats with purified recombinant fusion adiponectin or gAdiponectin transiently abolished hyperglycemia. So adiponectin and gAdiponectin might have activity as a glucose lowering agent and potentially as a therapeutic for metabolic disease. All these results suggested that the recombinant protein had biological activity, and provided a useful tool in further studies.

Adjuvant Biological Therapies in Chronic Leg Ulcers

Directory of Open Access Journals (Sweden)

Natalia Burgos-Alonso

2017-11-01

Full Text Available Current biological treatments for non-healing wounds aim to address the common deviations in healing mechanisms, mainly inflammation, inadequate angiogenesis and reduced synthesis of extracellular matrix. In this context, regenerative medicine strategies, i.e., platelet rich plasmas and mesenchymal stromal cell products, may form part of adjuvant interventions in an integral patient management. We synthesized the clinical experience on ulcer management using these two categories of biological adjuvants. The results of ten controlled trials that are included in this systematic review favor the use of mesenchymal stromal cell based-adjuvants for impaired wound healing, but the number and quality of studies is moderate-low and are complicated by the diversity of biological products. Regarding platelet-derived products, 18 controlled studies investigated their efficacy in chronic wounds in the lower limb, but the heterogeneity of products and protocols hinders clinically meaningful quantitative synthesis. Most patients were diabetic, emphasizing an unmet medical need in this condition. Overall, there is not sufficient evidence to inform routine care, and further clinical research is necessary to realize the full potential of adjuvant regenerative medicine strategies in the management of chronic leg ulcers.

Anticipation: Beyond synthetic biology and cognitive robotics.

Science.gov (United States)

Nasuto, Slawomir J; Hayashi, Yoshikatsu

2016-10-01

The aim of this paper is to propose that current robotic technologies cannot have intentional states any more than is feasible within the sensorimotor variant of embodied cognition. It argues that anticipation is an emerging concept that can provide a bridge between both the deepest philosophical theories about the nature of life and cognition and the empirical biological and cognitive sciences steeped in reductionist and Newtonian conceptions of causality. The paper advocates that in order to move forward, cognitive robotics needs to embrace new platforms and a conceptual framework that will enable it to pursue, in a meaningful way, questions about autonomy and purposeful behaviour. We suggest that hybrid systems, part robotic and part cultures of neurones, offer experimental platforms where different dimensions of enactivism (sensorimotor, constitutive foundations of biological autonomy, including anticipation), and their relative contributions to cognition, can be investigated in an integrated way. A careful progression, mindful to the deep philosophical concerns but also respecting empirical evidence, will ultimately lead towards unifying theoretical and empirical biological sciences and may offer advancement where reductionist sciences have been so far faltering. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Towards a More Meaningful Involvement of Librarians in Academic Program Reviews

Science.gov (United States)

Bowker, Lynne

2018-01-01

Purpose: Using a descriptive case study approach, this paper aims to validate academic librarians' perceptions that they are marginalized by faculty during academic program reviews, and recommends ways for the two groups to collaborate more effectively to make program reviews more meaningful. Design/methodology/approach: The paper describes a case…

Meaningfulness for creation of growth in Small- and Medium-sized enterprises

DEFF Research Database (Denmark)

Brink, Tove; Neville, Mette

2016-01-01

The research in this paper reveals how meaningfulness of growth can be created in Small- and Medium-sized Enterprises (SMEs). The research is conducted in a four-year period with 24 SMEs participating from different industry branches. The research is now in the late part of the 3rd. year starting...

Transforming City Schools through Art: Approaches to Meaningful K-12 Learning

Science.gov (United States)

Hutzel, Karen; Bastos, Flavia M. C.; Cozier, Kimberly J.

2012-01-01

This anthology places art at the center of meaningful urban education reform. Providing a fresh perspective on urban education, the contributors describe a positive, asset-based community development model designed to tap into the teaching/learning potential already available in urban cities. Rather than focusing on a lack of resources, this…

Comparison of co-expression measures: mutual information, correlation, and model based indices.

Science.gov (United States)

Song, Lin; Langfelder, Peter; Horvath, Steve

2012-12-09

Co-expression measures are often used to define networks among genes. Mutual information (MI) is often used as a generalized correlation measure. It is not clear how much MI adds beyond standard (robust) correlation measures or regression model based association measures. Further, it is important to assess what transformations of these and other co-expression measures lead to biologically meaningful modules (clusters of genes). We provide a comprehensive comparison between mutual information and several correlation measures in 8 empirical data sets and in simulations. We also study different approaches for transforming an adjacency matrix, e.g. using the topological overlap measure. Overall, we confirm close relationships between MI and correlation in all data sets which reflects the fact that most gene pairs satisfy linear or monotonic relationships. We discuss rare situations when the two measures disagree. We also compare correlation and MI based approaches when it comes to defining co-expression network modules. We show that a robust measure of correlation (the biweight midcorrelation transformed via the topological overlap transformation) leads to modules that are superior to MI based modules and maximal information coefficient (MIC) based modules in terms of gene ontology enrichment. We present a function that relates correlation to mutual information which can be used to approximate the mutual information from the corresponding correlation coefficient. We propose the use of polynomial or spline regression models as an alternative to MI for capturing non-linear relationships between quantitative variables. The biweight midcorrelation outperforms MI in terms of elucidating gene pairwise relationships. Coupled with the topological overlap matrix transformation, it often leads to more significantly enriched co-expression modules. Spline and polynomial networks form attractive alternatives to MI in case of non-linear relationships. Our results indicate that MI

Meaningful real-life relationships in massively multiplayer online roleplaying games

OpenAIRE

Mansikkamäki, E. (Eetu)

2014-01-01

Abstract Massively Multiplayer Online Roleplaying Games are extremely popular with millions and millions of players spending large portions of their free time in these virtual environments. Still the social value and the meaningfulness of the relationships formed within them are questioned by most non-gamers and even some gamers. In the past even academia was mainly concentrating on the negative aspects of gaming but lately...

From noise to synthetic nucleoli: can synthetic biology achieve new insights?

Science.gov (United States)

Ciechonska, Marta; Grob, Alice; Isalan, Mark

2016-04-18

Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."

Mining rare associations between biological ontologies.

Science.gov (United States)

Benites, Fernando; Simon, Svenja; Sapozhnikova, Elena

2014-01-01

The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations.

Mining rare associations between biological ontologies.

Directory of Open Access Journals (Sweden)

Fernando Benites

Full Text Available The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations.

Aging, culture, and memory for socially meaningful item-context associations: an East-West cross-cultural comparison study.

Science.gov (United States)

Yang, Lixia; Li, Juan; Spaniol, Julia; Hasher, Lynn; Wilkinson, Andrea J; Yu, Jing; Niu, Yanan

2013-01-01

Research suggests that people in Eastern interdependent cultures process information more holistically and attend more to contextual information than do people in Western independent cultures. The current study examined the effects of culture and age on memory for socially meaningful item-context associations in 71 Canadians of Western European descent (35 young and 36 older) and 72 native Chinese citizens (36 young and 36 older). All participants completed two blocks of context memory tasks. During encoding, participants rated pictures of familiar objects. In one block, objects were rated either for their meaningfulness in the independent living context or their typicality in daily life. In the other block, objects were rated for their meaningfulness in the context of fostering relationships with others or for their typicality in daily life. The encoding in each block was followed by a recognition test in which participants identified pictures and their associated contexts. The results showed that Chinese outperformed Canadians in context memory, though both culture groups showed similar age-related deficits in item and context memory. The results suggest that Chinese are at an advantage in memory for socially meaningful item-context associations, an advantage that continues from young adulthood into old age.

Clustering-based approaches to SAGE data mining

Directory of Open Access Journals (Sweden)

Wang Haiying

2008-07-01

Full Text Available Abstract Serial analysis of gene expression (SAGE is one of the most powerful tools for global gene expression profiling. It has led to several biological discoveries and biomedical applications, such as the prediction of new gene functions and the identification of biomarkers in human cancer research. Clustering techniques have become fundamental approaches in these applications. This paper reviews relevant clustering techniques specifically designed for this type of data. It places an emphasis on current limitations and opportunities in this area for supporting biologically-meaningful data mining and visualisation.

Gadd45β expression in chondrosarcoma: A pilot study for diagnostic and biological implications in histological grading

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Ishido Yasuhiro

2010-10-01

Full Text Available Abstract Background Although the diagnosis of chondrosarcoma, especially the distinction between enchondroma and low-grade chondrosarcoma or low-grade chondrosarcoma and high-grade chondrosarcoma, is pathologically difficult, differential diagnosis is very important because the treatment strategies for these diseases are completely different. The grading system is crucial in predicting biologic behavior and prognosis, however, exact pathological grading is difficult using only routine examinations because the criteria of the grading system are not necessarily definitive. Growth arrest and DNA damage-inducible protein 45β (GADD45β is an essential molecule for chondrocytes during terminal differentiation. In the present study, we investigated the immunohistochemical expression of GADD45β in enchondroma, and chondrosarcoma of histological grades I, II, and III, to clarify the diagnostic significance of GADD45β in pathological grading of chondrosarcoma. Methods Twenty samples (enchondroma = 6, chondrosarcoma grade I = 7, grade II = 6, grade III = 1 were used for immunohistochemical analysis to investigate the expression of GADD45β. Quantitative analysis was performed to compare the number of GADD45β positive cells and pathological grading. Results Over 70% of the cells in enchondromas expressed GADD45β. On the other hand, the expression of GADD45β decreased significantly according to the histological grade of chondrosarcoma (grade I: 45%; grade II: 13.8%; and grade III: 3.8%. Conclusions The association of GADD45β expression and pathological grading of chondrosarcoma in the present study suggests that the immunohistochemical study of GADD45β may be a specific diagnostic parameter for chondrosarcoma cell differentiation.

Sentence Processing as a Function of Syntax, Short Term Memory Capacity, the Meaningfulness of the Stimulus and Age

Science.gov (United States)

Gamlin, Peter J.

1971-01-01

Examines the effects of short term memory (STM) capacity, meaningfulness of stimuli, and age upon listeners' structuring of sentences. Results show that the interaction between STM capacity and meaningfulness (1) approached significance when data were collapsed over both age levels, and (2) was significant for one age level. Tables and references.…

Tunable promoters in systems biology

DEFF Research Database (Denmark)

Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

2005-01-01

The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

Does (Non-)Meaningful Sensori-Motor Engagement Promote Learning With Animated Physical Systems?

NARCIS (Netherlands)

Pouw, Wim T J L; Eielts, Charly; van Gog, Tamara; Zwaan, Rolf A.; Paas, Fred

2016-01-01

Previous research indicates that sensori-motor experience with physical systems can have a positive effect on learning. However, it is not clear whether this effect is caused by mere bodily engagement or the intrinsically meaningful information that such interaction affords in performing the

Pedagogical Background for Technology Education--Meaningful Learning in Theory and Practice

Science.gov (United States)

Autio, Ossi

2009-01-01

One important theme in technology education is the growing need to develop the type of pedagogies that encourage pupils in authentic and meaningful learning experiences. Often, the teaching strategies of technology education are only a matter of teaching the handling of materials and tools, and the production of mere objects does not consider how…

Meaningful Statistics in Professional Practices as a Bridge between Mathematics and Science: An Evaluation of a Design Research Project

Science.gov (United States)

Dierdorp, Adri; Bakker, Arthur; van Maanen, Jan A.; Eijkelhof, Harrie M. C.

2014-01-01

Background: Creating coherence between school subjects mathematics and science and making these school subjects meaningful are still topical challenges. This study investigates how students make meaningful connections between mathematics, statistics, science and applications when they engage in a specially developed unit that is based on…

Exploitation of complex network topology for link prediction in biological interactomes

KAUST Repository

Alanis Lobato, Gregorio

2014-06-01

The network representation of the interactions between proteins and genes allows for a holistic perspective of the complex machinery underlying the living cell. However, the large number of interacting entities within the cell makes network construction a daunting and arduous task, prone to errors and missing information. Fortunately, the structure of biological networks is not different from that of other complex systems, such as social networks, the world-wide web or power grids, for which growth models have been proposed to better understand their structure and function. This means that we can design tools based on these models in order to exploit the topology of biological interactomes with the aim to construct more complete and reliable maps of the cell. In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable and biologically meaningful information that enriches the datasets to which we have access today.

Tunable promoters in synthetic and systems biology

DEFF Research Database (Denmark)

Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

2012-01-01

in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...... for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

Developing an instrument to measure emotional behaviour abilities of meaningful learning through the Delphi technique.

Science.gov (United States)

Cadorin, Lucia; Bagnasco, Annamaria; Tolotti, Angela; Pagnucci, Nicola; Sasso, Loredana

2017-09-01

To identify items for a new instrument that measures emotional behaviour abilities of meaningful learning, according to Fink's Taxonomy. Meaningful learning is an active process that promotes a wider and deeper understanding of concepts. It is the result of an interaction between new and previous knowledge and produces a long-term change of knowledge and skills. To measure meaningful learning capability, it is very important in the education of health professionals to identify problems or special learning needs. For this reason, it is necessary to create valid instruments. A Delphi Study technique was implemented in four phases by means of e-mail. The study was conducted from April-September 2015. An expert panel consisting of ten researchers with experience in Fink's Taxonomy was established to identify the items of the instrument. Data were analysed for conceptual description and item characteristics and attributes were rated. Expert consensus was sought in each of these phases. An 87·5% consensus cut-off was established. After four rounds, consensus was obtained for validation of the content of the instrument 'Assessment of Meaningful learning Behavioural and Emotional Abilities'. This instrument consists of 56 items evaluated on a 6-point Likert-type scale. Foundational Knowledge, Application, Integration, Human Dimension, Caring and Learning How to Learn were the six major categories explored. This content validated tool can help educators (teachers, trainers and tutors) to identify and improve the strategies to support students' learning capability, which could increase their awareness of and/or responsibility in the learning process. © 2017 John Wiley & Sons Ltd.

Semantic integration of gene expression analysis tools and data sources using software connectors

Science.gov (United States)

2013-01-01

Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools

Social networking for language learners: Creating meaningful output with Web 2.0 tools

Directory of Open Access Journals (Sweden)

Robert Chartrand

2012-03-01

Full Text Available The Internet has the potential to provide language learners with vast resources of authentic written, audio, and video materials to supplement lessons. Educators can find a wide assortment of materials for learners to study in class or after class for independent learning and to encourage learner autonomy. More recently, however, the immense popularity of social networking websites has created new opportunities for language learners to interact in authentic ways that were previously difficult to achieve. Advances in technology mean that today, learners of a language can easily interact with their peers in meaningful practice that helps foster language acquisition and motivation. That is, tasks that make use of Web 2.0 interactivity can significantly raise students’ potential to generate meaningful output and stimulate their interest in language learning.

Perspective: The missing link in academic career planning and development: pursuit of meaningful and aligned work.

Science.gov (United States)

Lieff, Susan J

2009-10-01

Retention of faculty in academic medicine is a growing challenge. It has been suggested that inattention to the humanistic values of the faculty is contributing to this problem. Professional development should consider faculty members' search for meaning, purpose, and professional fulfillment and should support the development of an ability to reflect on these issues. Ensuring the alignment of academic physicians' inner direction with their outer context is critical to professional fulfillment and effectiveness. Personal reflection on the synergy of one's strengths, passions, and values can help faculty members define meaningful work so as to enable clearer career decision making. The premise of this article is that an awareness of and the pursuit of meaningful work and its alignment with the academic context are important considerations in the professional fulfillment and retention of academic faculty. A conceptual framework for understanding meaningful work and alignment and ways in which that framework can be applied and taught in development programs are presented and discussed.

Myasthenia Gravis Impairment Index: Responsiveness, meaningful change, and relative efficiency.

Science.gov (United States)

Barnett, Carolina; Bril, Vera; Kapral, Moira; Kulkarni, Abhaya V; Davis, Aileen M

2017-12-05

To study responsiveness and meaningful change of the Myasthenia Gravis Impairment Index (MGII) and its relative efficiency compared to other measures. We enrolled 95 patients receiving prednisone, IV immunoglobulin (IVIg), or plasma exchange (PLEX) and 54 controls. Patients were assessed with the MGII and other measures-including the Quantitative Myasthenia Gravis Score, Myasthenia Gravis Composite, and Myasthenia Gravis Activities of Daily Living-at baseline and 3-4 weeks after treatment. Statistical markers of responsiveness included between-groups and within-group differences, and we estimated the relative efficiency of the MGII compared to other measures. Patient-meaningful change was assessed with an anchor-based method, using the patient's impression of change. We determined the minimal detectable change (MDC) and the minimal important difference (MID) at the group and individual level. Treated patients had a higher change in MGII scores than controls (analysis of covariance p 1 favoring the MGII. The MGII demonstrated responsiveness to prednisone, IVIg, and PLEX in patients with myasthenia. There is a differential response in ocular and generalized symptoms to type of therapy. The MGII has higher relative efficiency than comparison measures and is viable for use in clinical trials. Copyright © 2017 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

Meaningful Gamification and Students' Motivation: A Strategy for Scaffolding Reading Material

Science.gov (United States)

Ling, Lynette Tan Yuen

2018-01-01

Gamification is an innovative pedagogical strategy where digital games are used in an educational setting and as an aid to learning. Recent publications on gamification in the classroom investigate the concept of "meaningful gamification," where, in line with Ryan and Deci's self-determination theory, competency, autonomy, and…

Aging, Culture, and Memory for Socially Meaningful Item-Context Associations: An East-West Cross-Cultural Comparison Study

Science.gov (United States)

Yang, Lixia; Li, Juan; Spaniol, Julia; Hasher, Lynn; Wilkinson, Andrea J.; Yu, Jing; Niu, Yanan

2013-01-01

Research suggests that people in Eastern interdependent cultures process information more holistically and attend more to contextual information than do people in Western independent cultures. The current study examined the effects of culture and age on memory for socially meaningful item-context associations in 71 Canadians of Western European descent (35 young and 36 older) and 72 native Chinese citizens (36 young and 36 older). All participants completed two blocks of context memory tasks. During encoding, participants rated pictures of familiar objects. In one block, objects were rated either for their meaningfulness in the independent living context or their typicality in daily life. In the other block, objects were rated for their meaningfulness in the context of fostering relationships with others or for their typicality in daily life. The encoding in each block was followed by a recognition test in which participants identified pictures and their associated contexts. The results showed that Chinese outperformed Canadians in context memory, though both culture groups showed similar age-related deficits in item and context memory. The results suggest that Chinese are at an advantage in memory for socially meaningful item-context associations, an advantage that continues from young adulthood into old age. PMID:23593288

Aging, culture, and memory for socially meaningful item-context associations: an East-West cross-cultural comparison study.

Directory of Open Access Journals (Sweden)

Lixia Yang

Full Text Available Research suggests that people in Eastern interdependent cultures process information more holistically and attend more to contextual information than do people in Western independent cultures. The current study examined the effects of culture and age on memory for socially meaningful item-context associations in 71 Canadians of Western European descent (35 young and 36 older and 72 native Chinese citizens (36 young and 36 older. All participants completed two blocks of context memory tasks. During encoding, participants rated pictures of familiar objects. In one block, objects were rated either for their meaningfulness in the independent living context or their typicality in daily life. In the other block, objects were rated for their meaningfulness in the context of fostering relationships with others or for their typicality in daily life. The encoding in each block was followed by a recognition test in which participants identified pictures and their associated contexts. The results showed that Chinese outperformed Canadians in context memory, though both culture groups showed similar age-related deficits in item and context memory. The results suggest that Chinese are at an advantage in memory for socially meaningful item-context associations, an advantage that continues from young adulthood into old age.

Mesenchymal stromal cells express GARP/LRRC32 on their surface: effects on their biology and immunomodulatory capacity.

Science.gov (United States)

Carrillo-Galvez, Ana Belén; Cobo, Marién; Cuevas-Ocaña, Sara; Gutiérrez-Guerrero, Alejandra; Sánchez-Gilabert, Almudena; Bongarzone, Pierpaolo; García-Pérez, Angélica; Muñoz, Pilar; Benabdellah, Karim; Toscano, Miguel G; Martín, Francisco; Anderson, Per

2015-01-01

Mesenchymal stromal cells (MSCs) represent a promising tool for therapy in regenerative medicine, transplantation, and autoimmune disease due to their trophic and immunomodulatory activities. However, we are still far from understanding the mechanisms of action of MSCs in these processes. Transforming growth factor (TGF)-β1 is a pleiotropic cytokine involved in MSC migration, differentiation, and immunomodulation. Recently, glycoprotein A repetitions predominant (GARP) was shown to bind latency-associated peptide (LAP)/TGF-β1 to the cell surface of activated Foxp3(+) regulatory T cells (Tregs) and megakaryocytes/platelets. In this manuscript, we show that human and mouse MSCs express GARP which presents LAP/TGF-β1 on their cell surface. Silencing GARP expression in MSCs increased their secretion and activation of TGF-β1 and reduced their proliferative capacity in a TGF-β1-independent manner. Importantly, we showed that GARP expression on MSCs contributed to their ability to inhibit T-cell responses in vitro. In summary, we have found that GARP is an essential molecule for MSC biology, regulating their immunomodulatory and proliferative activities. We envision GARP as a new target for improving the therapeutic efficacy of MSCs and also as a novel MSC marker. © 2014 AlphaMed Press.

Elevated mammaglobin (h-MAM) expression in breast cancer is associated with clinical and biological features defining a less aggressive tumour phenotype

International Nuclear Information System (INIS)

Núñez-Villar, MJ; Martínez-Arribas, F; Pollán, M; Lucas, AR; Sánchez, J; Tejerina, A; Schneider, J

2003-01-01

Mammaglobin (h-MAM) is expressed mainly by breast epithelial cells, and this feature has been used to detect circulating breast cancer cells and occult metastases in sentinel axillary lymph nodes of breast cancer patients. However, the biological role of mammaglobin is completely unknown. We studied 128 fresh-frozen breast cancer specimens by means of reverse transcriptase–polymerase chain reaction and quantified their h-MAM mRNA expression. This was then correlated with histological and nuclear grade, oestrogen and progesterone receptor expression, c-erb-B2 and mutant p53 expression, as well as with cellular proliferation measured by means of the Ki67 labelling index, DNA ploidy and S-phase, and finally with the presence or not of invaded axillary nodes in the mastectomy specimen. In the univariate analysis, high h-MAM expression (above the median for the whole group) correlated significantly (P < 0.05) with oestrogen and progesterone receptor expression, diploid DNA content, low Ki67 labelling index, low nuclear grade and almost significantly (P = 0.058) with the absence of axillary nodal invasion in the mastectomy specimen. In a final, multivariate model, only progesterone receptor expression, diploid DNA content and absence of nodal invasion were found to be independently associated with high h-MAM expression. All of the features associated with mammaglobin expression reflect, without exception, a less aggressive tumour phenotype. Further studies are needed to clarify whether this is attributable to h-MAM expression itself, or to another mechanism of which mammaglobin expression forms part

Pilot Study of Flow and Meaningfulness as Psychological Learning Concepts in Patient Education: A Short Report

DEFF Research Database (Denmark)

Nicic, Sara; Nørby, Karina; Bruun Johansen, Clea

2014-01-01

of this study was to investigate the applicability of these concepts of positive psychological theory in a patient education setting. Methods: This pilot study combines participating observation of group based patient education and 8 qualitative interviews with 4 patients with type 2 diabetes. Meaning......Abstract Background: The aim of this pilot study was to explore patient experiences of meaningfulness and flow related to group based patient education in type 2 diabetes. Meaningfulness and flow are underexposed as psychological learning concepts in patient education, and the ambition...

Creating Visual Design and Meaningful Audience Experiences

DEFF Research Database (Denmark)

Steijn, Arthur; Ion Wille, Jakob

2014-01-01

The main purpose of the EU Interreg funded Classical Composition Music and Experience Design project, was to rethink audience experiences and develop knowledge of applied technologies connected to classical music and live concerts. The project and its main objectives was motivated by at least thee...... conditions. The most important being 1) the development in new technology creating new expectations in audiences attending cultural events, including classical concerts, 2) resent decline in audiences attending classical music and 3) a will to strengthen relations between cultural institutions, creative...... businesses and educational institutions in the Øresund region (including the city and surroundings of Malmø and Copenhagen). Therefore the project Classical Composition Music and Experience Design focused on developing new and meaningful audience experiences where live classical music meets new digital...

Isolation and expression of recombinant antibody fragments to the biological warfare pathogen Brucella melitensis.

Science.gov (United States)

Hayhurst, Andrew; Happe, Scott; Mabry, Robert; Koch, Zephyr; Iverson, Brent L; Georgiou, George

2003-05-01

Brucella melitensis is a highly infectious animal pathogen able to cause a recurring debilitating disease in humans and is therefore high on the list of biological warfare agents. Immunoglobulin genes from mice immunized with gamma-irradiated B. melitensis strain 16M were used to construct a library that was screened by phage display against similarly prepared bacteria. The selected phage particles afforded a strong enzyme-linked immunosorbent assay (ELISA) signal against gamma-irradiated B. melitensis cells. However, extensive efforts to express the respective single chain antibody variable region fragment (scFv) in soluble form failed due to: (i) poor solubility and (ii) in vivo degradation of the c-myc tag used for the detection of the recombinant antibodies. Both problems could be addressed by: (i) fusing a human kappa light chain constant domain (Ck) chain to the scFv to generate single chain antibody fragment (scAb) antibody fragments and (ii) by co-expression of the periplasmic chaperone Skp. While soluble, functional antibodies could be produced in this manner, phage-displaying scFvs or scAbs were still found to be superior ELISA reagents for immunoassays, due to the large signal amplification afforded by anti-phage antibodies. The isolated phage antibodies were shown to be highly specific to B. melitensis and did not recognize Yersinia pseudotuberculosis in contrast to the existing diagnostic monoclonal YST 9.2.1.

PageRank analysis reveals topologically expressed genes correspond to psoriasis and their functions are associated with apoptosis resistance.

Science.gov (United States)

Zeng, Xue; Zhao, Jingjing; Wu, Xiaohong; Shi, Hongbo; Liu, Wali; Cui, Bingnan; Yang, Li; Ding, Xu; Song, Ping

2016-05-01

Psoriasis is an inflammatory skin disease. Deceleration in keratinocyte apoptosis is the most significant pathological change observed in psoriasis. To detect a meaningful correlation between the genes and gene functions associated with the mechanism underlying psoriasis, 927 differentially expressed genes (DEGs) were identified using the Gene Expression Omnibus database, GSE13355 [false discovery rate (FDR) 1] with the package in R langue. The selected DEGs were further constructed using the search tool for the retrieval of interacting genes, in order to analyze the interaction network between the DEGs. Subsequent to PageRank analysis, 14 topological hub genes were identified, and the functions and pathways in the hub genes network were analyzed. The top‑ranked hub gene, estrogen receptor‑1 (ESR1) is downregulated in psoriasis, exhibited binding sites enriched with genes possessing anti‑apoptotic functions. The ESR1 gene encodes estrogen receptor α (ERα); a reduced level of ERα expression provides a crucial foundation in response to the anti‑apoptotic activity of psoriatic keratinocytes by activating the expression of anti‑apoptotic genes. Furthermore, it was detected that the pathway that is associated most significantly with psoriasis is the pathways in cancer. Pathways in cancer may protect psoriatic cells from apoptosis by inhibition of ESR1 expression. The present study provides support towards the investigation of ESR1 gene function and elucidates that the interaction with anti‑apoptotic genes is involved in the underlying biological mechanisms of resistance to apoptosis in psoriasis. However, further investigation is required to confirm the present results.

Molecular characterization and differential expression of olfactory genes in the antennae of the black cutworm moth Agrotis ipsilon.

Directory of Open Access Journals (Sweden)

Shao-Hua Gu

Full Text Available Insects use their sensitive and selective olfactory system to detect outside chemical odorants, such as female sex pheromones and host plant volatiles. Several groups of olfactory proteins participate in the odorant detection process, including odorant binding proteins (OBPs, chemosensory proteins (CSPs, odorant receptors (ORs, ionotropic receptors (IRs and sensory neuron membrane proteins (SNMPs. The identification and functional characterization of these olfactory proteins will enhance our knowledge of the molecular basis of insect chemoreception. In this study, we report the identification and differential expression profiles of these olfactory genes in the black cutworm moth Agrotis ipsilon. In total, 33 OBPs, 12 CSPs, 42 ORs, 24 IRs, 2 SNMPs and 1 gustatory receptor (GR were annotated from the A. ipsilon antennal transcriptomes, and further RT-PCR and RT-qPCR revealed that 22 OBPs, 3 CSPs, 35 ORs, 14 IRs and the 2 SNMPs are uniquely or primarily expressed in the male and female antennae. Furthermore, one OBP (AipsOBP6 and one CSP (AipsCSP2 were exclusively expressed in the female sex pheromone gland. These antennae-enriched OBPs, CSPs, ORs, IRs and SNMPs were suggested to be responsible for pheromone and general odorant detection and thus could be meaningful target genes for us to study their biological functions in vivo and in vitro.

An enhanced topologically significant directed random walk in cancer classification using gene expression datasets

Directory of Open Access Journals (Sweden)

Choon Sen Seah

2017-12-01

Full Text Available Microarray technology has become one of the elementary tools for researchers to study the genome of organisms. As the complexity and heterogeneity of cancer is being increasingly appreciated through genomic analysis, cancerous classification is an emerging important trend. Significant directed random walk is proposed as one of the cancerous classification approach which have higher sensitivity of risk gene prediction and higher accuracy of cancer classification. In this paper, the methodology and material used for the experiment are presented. Tuning parameter selection method and weight as parameter are applied in proposed approach. Gene expression dataset is used as the input datasets while pathway dataset is used to build a directed graph, as reference datasets, to complete the bias process in random walk approach. In addition, we demonstrate that our approach can improve sensitive predictions with higher accuracy and biological meaningful classification result. Comparison result takes place between significant directed random walk and directed random walk to show the improvement in term of sensitivity of prediction and accuracy of cancer classification.

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

Semantic Web meets Integrative Biology: a survey.

Science.gov (United States)

Chen, Huajun; Yu, Tong; Chen, Jake Y

2013-01-01

Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB.

The consistency and complementarity between critical meaningful learning theory and the epistemology of Paul Feyerabend

Directory of Open Access Journals (Sweden)

Felipe Damasio

2015-12-01

Full Text Available Researchers in science teaching have advocated concomitant education about and of science. To approach the nature and history of science in basic education is necessary to have an epistemological approach that can go between of rationalism of Bunge and relativism of Feyerabend. In this paper, it is argued that Feyerabend's epistemological stance is that more can help promote meaningful learning critical, so as to form inquiring, flexible, creative, innovative, tolerant and liberal people. In addition, the suggestions Feyerabend's epistemology also complement the Theory of Meaningful Learning Critical to propose a curriculum and a context for the principles of the theory are in science classrooms.

Beyond Needs Analysis: Soft Systems Methodology for Meaningful Collaboration in EAP Course Design

Science.gov (United States)

Tajino, Akira; James, Robert; Kijima, Kyoichi

2005-01-01

Designing an EAP course requires collaboration among various concerned stakeholders, including students, subject teachers, institutional administrators and EAP teachers themselves. While needs analysis is often considered fundamental to EAP, alternative research methodologies may be required to facilitate meaningful collaboration between these…

If meaningfulness is not always fulfilling, why then does it matter?

Directory of Open Access Journals (Sweden)

Nicole Note

2014-12-01

Full Text Available We start from a quandary in the field of meaningfulness introduced by Susan Wolf, who attempts to make clear why meaning in life would matter. In common sense terms, fulfilment is considered to play a main role in the conceptualisation of meaningfulness. While initially taking this also for granted Wolf gradually comprehends that fulfilment is not the overall reason why meaning in life matters. She leaves however open the paramount question of what would make it then so particular. In this article, we explore this query to a fuller extent, and maintain that a promising road to an answer lays in the understanding that meaning in life is directive in an ineffable way. In order to fathom what this entails, a distinction between meaningfulness’ and ‘meaning in life’ will prove helpful. Both have often been considered synonyms, but we argue that they are quite distinct, yet intrinsically related. Starting from a subject that is mainly discussed in analytic philosophy, we build a bridge to phenomenological praxis, indicating that we can only understand its core function - its ineffable way of being directive - through phenomenology.

The meaningfulness of participating in support groups for informal caregivers of older adults with dementia: a systematic review

DEFF Research Database (Denmark)

Lauritzen, Jette; Pedersen, Preben Ulrich; Sørensen, Erik Elgaard

2015-01-01

of participants: Informal caregivers of older adults aged 65 years and over with dementia. The informal caregiver was a family member, and care was performed at home. Phenomena of interest: How the informal caregivers perceived the meaningfulness of participating in support groups. The setting was all locations......BACKGROUND Informal caregivers who perform at-home care of older people with dementia might have feelings of a meaningless existence, burden, anxiety, stress and fatigue. Support groups are considered an especially effective and economical way to relieve informal caregivers’ stress and burden......, although it is unclear if participating in group meetings produces a meaningful outcome for the informal caregiver. OBJECTIVES To identify the meaningfulness of participating in support groups for informal caregivers of older adults with dementia living in their own home. INCLUSION CRITERIA Types...

Meaningful Engagement in Scientific Practices: How Classroom Communities Develop Authentic Epistemologies for Science

Science.gov (United States)

Krist, Christina Rae

Recent reforms in science education, based on decades of learning research, emphasize engaging students in science and engineering practices as the means to develop and refine disciplinary ideas. These reforms advocate an epistemic shift in how school science is done: from students learning about science ideas to students figuring out core science ideas. This shift is challenging to implement: how do we bring the goals and practices of a discipline into classroom communities in meaningful ways that go beyond simply following rote scientific procedures? In this dissertation, I investigate how classroom communities learn to engage meaningfully in scientific practices, characterizing their engagement as a process of epistemic learning. I take a situated perspective that defines learning as shifts in how members engage in communities of practice. I examine students' epistemic learning as a function of their participation in a classroom community of scientific practice along two dimensions: what they do, or the practical epistemic heuristics they use to guide how they build knowledge; and who they are, or how ownership and authorship of ideas is negotiated and affectively marked through interaction. I focus on a cohort of students as they move from 6th to 8 th grade. I analyze three science units, one from each grade level, to look at the epistemic heuristics implicit in student and teacher talk and how the use of those heuristics shifts over time. In addition, I examine one anomalous 8th grade class to look at how students and the teacher position themselves and each other with respect to the ideas in their classroom and how that positioning supports epistemic learning. Taken together, these analyses demonstrate how students' engagement in scientific practices evolves in terms of what they do and who they are in relation to the knowledge and ideas in their classroom over time. I propose a model for epistemic learning that articulates how classroom communities develop

Helper-dependent adenovirus achieve more efficient and persistent liver transgene expression in non-human primates under immunosuppression.

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Unzu, C; Melero, I; Hervás-Stubbs, S; Sampedro, A; Mancheño, U; Morales-Kastresana, A; Serrano-Mendioroz, I; de Salamanca, R E; Benito, A; Fontanellas, A

2015-11-01

Helper-dependent adenoviral (HDA) vectors constitute excellent gene therapy tools for metabolic liver diseases. We have previously shown that an HDA vector encoding human porphobilinogen deaminase (PBGD) corrects acute intermittent porphyria mice. Now, six non-human primates were injected in the left hepatic lobe with the PBGD-encoding HDA vector to study levels and persistence of transgene expression. Intrahepatic administration of 5 × 10(12) viral particles kg(-1) (10(10) infective units kg(-1)) of HDA only resulted in transient (≈14 weeks) transgene expression in one out of three individuals. In contrast, a more prolonged 90-day immunosuppressive regimen (tacrolimus, mycophenolate, rituximab and steroids) extended meaningful transgene expression for over 76 weeks in two out of two cases. Transgene expression under immunosuppression (IS) reached maximum levels 6 weeks after HDA administration and gradually declined reaching a stable plateau within the therapeutic range for acute porphyria. The non-injected liver lobes also expressed the transgene because of vector circulation. IS controlled anticapsid T-cell responses and decreased the induction of neutralizing antibodies. Re-administration of HDA-hPBGD at week +78 achieved therapeutically meaningful transgene expression only in those animals receiving IS again at the time of this second vector exposure. Overall, immunity against adenoviral capsids poses serious hurdles for long-term HDA-mediated liver transduction, which can be partially circumvented by pharmacological IS.

The nucleic acid revolution continues - will forensic biology become forensic molecular biology?

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Gunn, Peter; Walsh, Simon; Roux, Claude

2014-01-01

Molecular biology has evolved far beyond that which could have been predicted at the time DNA identity testing was established. Indeed we should now perhaps be referring to "forensic molecular biology." Aside from DNA's established role in identifying the "who" in crime investigations, other developments in medical and developmental molecular biology are now ripe for application to forensic challenges. The impact of DNA methylation and other post-fertilization DNA modifications, plus the emerging role of small RNAs in the control of gene expression, is re-writing our understanding of human biology. It is apparent that these emerging technologies will expand forensic molecular biology to allow for inferences about "when" a crime took place and "what" took place. However, just as the introduction of DNA identity testing engendered many challenges, so the expansion of molecular biology into these domains will raise again the issues of scientific validity, interpretation, probative value, and infringement of personal liberties. This Commentary ponders some of these emerging issues, and presents some ideas on how they will affect the conduct of forensic molecular biology in the foreseeable future.

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

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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

Profiling of Candida albicans Gene Expression During Intra-abdominal Candidiasis Identifies Biologic Processes Involved in Pathogenesis

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Cheng, Shaoji; Clancy, Cornelius J.; Xu, Wenjie; Schneider, Frank; Hao, Binghua; Mitchell, Aaron P.; Nguyen, M. Hong

2013-01-01

Background. The pathogenesis of intra-abdominal candidiasis is poorly understood. Methods. Mice were intraperitoneally infected with Candida albicans (1 × 106 colony-forming units) and sterile stool. nanoString assays were used to quantitate messenger RNA for 145 C. albicans genes within the peritoneal cavity at 48 hours. Results. Within 6 hours after infection, mice developed peritonitis, characterized by high yeast burdens, neutrophil influx, and a pH of 7.9 within peritoneal fluid. Organ invasion by hyphae and early abscess formation were evident 6 and 24 hours after infection, respectively; abscesses resolved by day 14. nanoString assays revealed adhesion and responses to alkaline pH, osmolarity, and stress as biologic processes activated in the peritoneal cavity. Disruption of the highly-expressed gene RIM101, which encodes an alkaline-regulated transcription factor, did not impact cellular morphology but reduced both C. albicans burden during early peritonitis and C. albicans persistence within abscesses. RIM101 influenced expression of 49 genes during intra-abdominal candidiasis, including previously unidentified Rim101 targets. Overexpression of the RIM101-dependent gene SAP5, which encodes a secreted protease, restored the ability of a rim101 mutant to persist within abscesses. Conclusions. A mouse model of intra-abdominal candidiasis is valuable for studying pathogenesis and C. albicans gene expression. RIM101 contributes to persistence within intra-abdominal abscesses, at least in part through activation of SAP5. PMID:24006479

Proposal for inclusion of topics of particle physics integrated electric charge through a potentially meaningful teaching units

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Lisiane Barcellos Calheiro

2014-03-01

Full Text Available In this article the results of the analysis of free and concept maps produced are presented from the application and evaluation of a Potentially Meaningful Teaching Units – PMTU, which is a teaching sequence based on various learning theories and seeks to promote meaningful student learning. Presents, in this work, part of a research Masters in Science Education which deals with the inclusion of topics of particle physics integrated with traditional content of the third year of high school. It was implemented in a third grade high school class of a State School in Santa Maria, Rio Grande do Sul, and Brazil. The PMTU aimed to address in an integrated manner threads for Particle Physics and Electronics. A didactic sequence that integrated the topics of electric charge, atomic models, elementary particles, quantization and process electrification was applied. Such integration aimed at stimulating the interest on topics related to Modern and Contemporary Physics. It was developed using PMTU activities that aimed at promoting meaningful learning and knowledge construction in the classroom, Since the topics involved were quite complex, this made their integration a real challenge to the high school teachers, and resulted in changes in their teaching practices. Research showed that the inclusion of topics on physics of elementary particles the and electricity, through Potentially Meaningful Teaching Units, show satisfactory results in the students’ learning.

Heterologous expression of biologically active chicken granulocyte ...

African Journals Online (AJOL)

After being screened by yeast peptone dextrose (YPD) containing high concentrations of Zeocin and direct PCR, the positive clone was cultured in flask with buffered minimal methanol (BMMY) and expression induced by methanol. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot ...

TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes.

Science.gov (United States)

Jung, Inuk; Jo, Kyuri; Kang, Hyejin; Ahn, Hongryul; Yu, Youngjae; Kim, Sun

2017-12-01

Identifying biologically meaningful gene expression patterns from time series gene expression data is important to understand the underlying biological mechanisms. To identify significantly perturbed gene sets between different phenotypes, analysis of time series transcriptome data requires consideration of time and sample dimensions. Thus, the analysis of such time series data seeks to search gene sets that exhibit similar or different expression patterns between two or more sample conditions, constituting the three-dimensional data, i.e. gene-time-condition. Computational complexity for analyzing such data is very high, compared to the already difficult NP-hard two dimensional biclustering algorithms. Because of this challenge, traditional time series clustering algorithms are designed to capture co-expressed genes with similar expression pattern in two sample conditions. We present a triclustering algorithm, TimesVector, specifically designed for clustering three-dimensional time series data to capture distinctively similar or different gene expression patterns between two or more sample conditions. TimesVector identifies clusters with distinctive expression patterns in three steps: (i) dimension reduction and clustering of time-condition concatenated vectors, (ii) post-processing clusters for detecting similar and distinct expression patterns and (iii) rescuing genes from unclassified clusters. Using four sets of time series gene expression data, generated by both microarray and high throughput sequencing platforms, we demonstrated that TimesVector successfully detected biologically meaningful clusters of high quality. TimesVector improved the clustering quality compared to existing triclustering tools and only TimesVector detected clusters with differential expression patterns across conditions successfully. The TimesVector software is available at http://biohealth.snu.ac.kr/software/TimesVector/. sunkim.bioinfo@snu.ac.kr. Supplementary data are available at

Microfluidic Technologies for Synthetic Biology

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Sung Kuk Lee

2011-06-01

Full Text Available Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

Inferring gene dependency network specific to phenotypic alteration based on gene expression data and clinical information of breast cancer.

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Zhou, Xionghui; Liu, Juan

2014-01-01

Although many methods have been proposed to reconstruct gene regulatory network, most of them, when applied in the sample-based data, can not reveal the gene regulatory relations underlying the phenotypic change (e.g. normal versus cancer). In this paper, we adopt phenotype as a variable when constructing the gene regulatory network, while former researches either neglected it or only used it to select the differentially expressed genes as the inputs to construct the gene regulatory network. To be specific, we integrate phenotype information with gene expression data to identify the gene dependency pairs by using the method of conditional mutual information. A gene dependency pair (A,B) means that the influence of gene A on the phenotype depends on gene B. All identified gene dependency pairs constitute a directed network underlying the phenotype, namely gene dependency network. By this way, we have constructed gene dependency network of breast cancer from gene expression data along with two different phenotype states (metastasis and non-metastasis). Moreover, we have found the network scale free, indicating that its hub genes with high out-degrees may play critical roles in the network. After functional investigation, these hub genes are found to be biologically significant and specially related to breast cancer, which suggests that our gene dependency network is meaningful. The validity has also been justified by literature investigation. From the network, we have selected 43 discriminative hubs as signature to build the classification model for distinguishing the distant metastasis risks of breast cancer patients, and the result outperforms those classification models with published signatures. In conclusion, we have proposed a promising way to construct the gene regulatory network by using sample-based data, which has been shown to be effective and accurate in uncovering the hidden mechanism of the biological process and identifying the gene signature for

Integrating Concept Mapping into Information Systems Education for Meaningful Learning and Assessment

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Wei, Wei; Yue, Kwok-Bun

2017-01-01

Concept map (CM) is a theoretically sound yet easy to learn tool and can be effectively used to represent knowledge. Even though many disciplines have adopted CM as a teaching and learning tool to improve learning effectiveness, its application in IS curriculum is sparse. Meaningful learning happens when one iteratively integrates new concepts and…

Meaningful Learning in the Teaching of Culture: The Project Based Learning Approach

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Kean, Ang Chooi; Kwe, Ngu Moi

2014-01-01

This paper reports on a collaborative effort taken by a team of three teacher educators in using the Project Based Learning (PBL) approach in the teaching of Japanese culture with the aim to investigate the presence of actual "meaningful learning" among 15 students of a 12-Week Preparatory Japanese Language course under a teacher…

Older Adults Co-Creating Meaningful Individualized Social Activities Online for Healthy Ageing.

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Blusi, Madeleine; Nilsson, Ingeborg; Lindgren, Helena

2018-01-01

Social isolation and loneliness among older people is a growing problem with negative effects on physical and mental health. In co-creation with older adults individualized social activities were designed where older adults through computer mediated communication were able to participate in social activities without leaving their homes. Four types of activities were designed; outdoor activity, music event, visiting a friend and leisure activity. A participatory action research design was applied, where end users together with scientists from two research fields developed, tested and evaluated online participation in the activities. Usability and safety of the systems were major concerns among older adults. The evaluation pointed out that level of simplicity, usability and audio-video quality determined the level of satisfaction with the human interaction during the activity, thereby affecting the meaningfulness of the activity. The research presented in this paper constitutes the first step in a long-term research process aiming at developing a digital coaching system that gives older adults personalized support for increasing participation in meaningful social activities.

Engaging in Work Even When It Is Meaningless: Positive Affective Disposition and Meaningful Work Interact in Relation to Work Engagement

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Steger, Michael F.; Littman-Ovadia, Hadassah; Miller, Michal; Menger, Lauren; Rothmann, Sebastiaan

2013-01-01

The central aim of the present study was to assess the predictive value of affective disposition and meaningful work on employee engagement. Specifically, it was proposed that meaningful work moderates the relationship between affective disposition and engagement. Questionnaires were completed by 252 white-collar employees, working in a variety of…

The relative biological effectiveness of antiprotons

DEFF Research Database (Denmark)

Holzscheiter, Michael H.; Alsner, Jan; Bassler, Niels

2016-01-01

Background and purpose: Aside from the enhancement of physical dose deposited by antiprotons annihilating in tissue-like material compared to protons of the same range a further increase of biological effective dose has been demonstrated. This enhancement can be expressed in an increase of the re......Background and purpose: Aside from the enhancement of physical dose deposited by antiprotons annihilating in tissue-like material compared to protons of the same range a further increase of biological effective dose has been demonstrated. This enhancement can be expressed in an increase...... of the relative biological effectiveness (RBE) of antiprotons near the end of range. We have performed the first-ever direct measurement of the RBE of antiprotons both at rest and in flight. Materials and methods: Experimental data were generated on the RBE of an antiproton beam entering a tissue-like target...

Evaluation of Biological Toxicity of CdTe Quantum Dots with Different Coating Reagents according to Protein Expression of Engineering Escherichia coli

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Wei Xu

2015-01-01

Full Text Available The results obtained from toxicity assessment of quantum dots (QDs can be used to establish guidelines for the application of QDs in bioimaging. This paper focused on the design of a novel method to evaluate the toxicity of CdTe QDs using engineering Escherichia coli as a model. The toxicity of mercaptoacetic acid (MPA, glutathione (GSH, and L-cysteine (Cys capped CdTe QDs was analyzed according to the heterologous protein expression in BL21/DE3, engineering Escherichia coli extensively used for protein expression. The results showed that the MPA-CdTe QDs had more serious toxicity than the other two kinds of CdTe QDs. The microscopic images and SEM micrographs further proved that both the proliferation and the protein expression of engineering Escherichia coli were inhibited after treatment with MPA-CdTe QDs. The proposed method is important to evaluate biological toxicity of both QDs and other nanoparticles.

Athero Express : ATHERO-sclerotic plaque EXPRESSion in relation to vascular events and patient characteristics

NARCIS (Netherlands)

Verhoeven, B.A.N.

2006-01-01

Athero-Express is a tissue bank study, designed to investigate the expression of atherosclerotic derived biological variables in relation to the long-term outcome of patients undergoing carotid endarterectomy. Its design includes both cross-sectional and follow-up studies, the results from which

Expression Patterns and Potential Biological Roles of Dip2a.

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Luqing Zhang

Full Text Available Disconnected (disco-interacting protein 2 homolog A is a member of the DIP2 protein family encoded by Dip2a gene. Dip2a expression pattern has never been systematically studied. Functions of Dip2a in embryonic development and adult are not known. To investigate Dip2a gene expression and function in embryo and adult, a Dip2a-LacZ mouse model was generated by insertion of β-Gal cDNA after Dip2a promoter using CRISPR/Cas9 technology. Dip2a-LacZ mouse was designed to be a lacZ reporter mouse as well as a Dip2a knockout mouse. Heterozygous mice were used to study endogenous Dip2a expression and homozygotes to study DIP2A-associated structure and function. LacZ staining indicated that Dip2a is broadly expressed in neuronal, reproductive and vascular tissues, as well as in heart, kidney, liver and lung. Results demonstrate that Dip2a is expressed in ectoderm-derived tissues in developing embryos. Adult tissues showed rich staining in neurons, mesenchymal, endothelial, smooth muscle cells and cardiomyocytes by cell types. The expression pattern highly overlaps with FSTL1 and supports previous report that DIP2A to be potential receptor of FSTL1 and its protective roles of cardiomyocytes. Broad and intense embryonic and adult expression of Dip2a has implied their multiple structural and physiological roles.

Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation

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Alessandro Giuliani

2017-12-01

Full Text Available A statistical mechanical mean-field approach to the temporal development of biological regulation provides a phenomenological, but basic description of the dynamical behavior of genome expression in terms of autonomous self-organization with a critical transition (Self-Organized Criticality: SOC. This approach reveals the basis of self-regulation/organization of genome expression, where the extreme complexity of living matter precludes any strict mechanistic approach. The self-organization in SOC involves two critical behaviors: scaling-divergent behavior (genome avalanche and sandpile-type critical behavior. Genome avalanche patterns—competition between order (scaling and disorder (divergence reflect the opposite sequence of events characterizing the self-organization process in embryo development and helper T17 terminal cell differentiation, respectively. On the other hand, the temporal development of sandpile-type criticality (the degree of SOC control in mouse embryo suggests the existence of an SOC control landscape with a critical transition state (i.e., the erasure of zygote-state criticality. This indicates that a phase transition of the mouse genome before and after reprogramming (immediately after the late 2-cell state occurs through a dynamical change in a control parameter. This result provides a quantitative open-thermodynamic appreciation of the still largely qualitative notion of the epigenetic landscape. Our results suggest: (i the existence of coherent waves of condensation/de-condensation in chromatin, which are transmitted across regions of different gene-expression levels along the genome; and (ii essentially the same critical dynamics we observed for cell-differentiation processes exist in overall RNA expression during embryo development, which is particularly relevant because it gives further proof of SOC control of overall expression as a universal feature.

Meaningful Academic Work as Praxis in Emergence

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Keijo Räsänen

2008-01-01

Full Text Available The managerial form of university governance has changed the conditions of academic work in many countries. While some academics consider this a welcome development, others experience it as a threat to their autonomy and to the meaningfulness of their work. This essay suggests a stance in response to the current conditions that should serve especially the latter group of academics. The claim is that by approaching academic work as a potential praxis in emergence, it is possible to appreciate local, autonomous activity in renewing academic work. Even if such efforts remain difficult, dispersed in space, discontinuous in time, and incomplete, they may provide a sense of direction and keep up hope. The conception of praxis is a way of articulating the mission of such efforts; simultaneously, it is also a way of defining an epistemic object for research on academic work.

Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions.

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Evans, Ciaran; Hardin, Johanna; Stoebel, Daniel M

2017-02-27

RNA-Seq is a widely used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct comparison of expression measures. Errors in normalization can have a significant impact on downstream analysis, such as inflated false positives in differential expression analysis. An underemphasized feature of normalization is the assumptions on which the methods rely and how the validity of these assumptions can have a substantial impact on the performance of the methods. In this article, we explain how assumptions provide the link between raw RNA-Seq read counts and meaningful measures of gene expression. We examine normalization methods from the perspective of their assumptions, as an understanding of methodological assumptions is necessary for choosing methods appropriate for the data at hand. Furthermore, we discuss why normalization methods perform poorly when their assumptions are violated and how this causes problems in subsequent analysis. To analyze a biological experiment, researchers must select a normalization method with assumptions that are met and that produces a meaningful measure of expression for the given experiment. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Attentional Networks and Biological Motion

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Chandramouli Chandrasekaran

2010-03-01

Full Text Available Our ability to see meaningful actions when presented with pointlight traces of human movement is commonly referred to as the perception of biological motion. While traditionalexplanations have emphasized the spontaneous and automatic nature of this ability, morerecent findings suggest that attention may play a larger role than is typically assumed. Intwo studies we show that the speed and accuracy of responding to point-light stimuli is highly correlated with the ability to control selective attention. In our first experiment we measured thresholds for determining the walking direction of a masked point-light figure, and performance on a range of attention-related tasks in the same set of observers. Mask-density thresholds for the direction discrimination task varied quite considerably from observer to observer and this variation was highly correlated with performance on both Stroop and flanker interference tasks. Other components of attention, such as orienting, alerting and visual search efficiency, showed no such relationship. In a second experiment, we examined the relationship between the ability to determine the orientation of unmasked point-light actions and Stroop interference, again finding a strong correlation. Our results are consistent with previous research suggesting that biological motion processing may requite attention, and specifically implicate networks of attention related to executive control and selection.

Elemental analysis of biological materials. Current problems and techniques with special reference to trace elements

International Nuclear Information System (INIS)

1980-01-01

Selected techniques were reviewed for the assay of trace and minor elements in biological materials. Other relevant information is also presented on the need for such analyses, sampling, sample preparation and analytical quality control. In order to evaluate and compare the applicability of the various analytical techniques on a meaningful and objective basis, the materials chosen for consideration were intended to be typical of a wide range of biological matrics of different elemental compositions, namely Bowen's kale, representing a plant material, and NBS bovine liver, IAEA animal muscle, and blood serum, representing animal tissues. The subject is reviewed under the following headings: on the need for trace element analyses in the life sciences (4 papers); sampling and sample preparation for trace element analysis (2 papers); analytical techniques for trace and minor elements in biological materials (7 papers); analytical quality control (2 papers)

Monod and the spirit of molecular biology

OpenAIRE

Morange , Michel

2015-01-01

International audience; The founders of molecular biology shared views on the place of biology within science, as well as on the relations of molecular biology to Darwinism. Jacques Monod was no exception, but the study of his writings is particularly interesting because he expressed his point of view very clearly and pushed the implications of some of his choices further than most of his contemporaries. The spirit of molecular biology is no longer the same as in the 1960s but, interestingly,...

Implementing a Social Knowledge Networking (SKN) system to enable meaningful use of an EHR medication reconciliation system.

Science.gov (United States)

Rangachari, Pavani

2018-01-01

Despite the regulatory impetus toward meaningful use of electronic health record (EHR) Medication Reconciliation (MedRec) to prevent medication errors during care transitions, hospital adherence has lagged for one chief reason: low physician engagement, stemming from lack of consensus about which physician is responsible for managing a patient's medication list. In October 2016, Augusta University received a 2-year grant from the Agency for Healthcare Research and Quality to implement a Social Knowledge Networking (SKN) system for enabling its health system (AU Health) to progress from "limited use" of EHR MedRec technology to "meaningful use." The hypothesis is that SKN would bring together a diverse group of practitioners, to facilitate tacit knowledge exchange on issues related to EHR MedRec, which in turn is expected to increase practitioners' engagement in addressing those issues and enable meaningful use of EHR. The specific aims are to examine: 1) user-engagement in the SKN system, and 2) associations between "SKN use" and "meaningful use" of EHR. The 2-year project uses an exploratory mixed-method design and consists of three phases: 1) development; 2) SKN implementation; and 3) analysis. Phase 1, completed in May 2017, sought to identify a comprehensive set of issues related to EHR MedRec from practitioners directly involved in the MedRec process. This process facilitated development of a "Reporting Tool" on issues related to EHR MedRec, which, along with an existing "SKN/Discussion Tool," was integrated into the EHR at AU Health. Phase 2 (launched in June 2017) involves implementing the EHR-integrated SKN system over a 52-week period in inpatient and outpatient medicine units. The prospective implementation design is expected to generate context-sensitive strategies for meaningful use and successful implementation of EHR MedRec and thereby make substantial contributions to the patient safety and risk management literature. From a health care policy

Parent Perceptions of Time Spent Meaningfully by Young Adults with Pervasive Support Needs

Science.gov (United States)

Rossetti, Zachary; Lehr, Donna; Lederer, Leslie; Pelerin, Dana; Huang, Shuoxi

2015-01-01

This article describes a qualitative study that examined how 23 young adults with pervasive support needs and limited functional communication spent their time and how their parents (n = 23) and direct support professionals (DSPs; n = 2) defined meaningfulness in relation to the young adults' experiences. Data were collected through…

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

Science.gov (United States)

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.

Patient-perceived satisfactory improvement (PPSI): interpreting meaningful change in pain from the patient's perspective

NARCIS (Netherlands)

ten Klooster, Peter M.; Drossaers-Bakker, K.W.; Taal, Erik; van de Laar, Mart A F J

2006-01-01

The assessment of clinically meaningful changes in patient-reported pain has become increasingly important when interpreting results of clinical studies. However, proposed response criteria, such as the minimal clinically important difference, do not correspond with the growing need for information

Meaningful cultural learning by imitative participation: the case of abstract thinking in primary school

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van Oers, B.

2012-01-01

The article describes a theory-driven approach to meaningful learning in primary schools, based on the Vygotskian cultural-historical theory of human development and learning. This approach is elaborated into an educational concept called 'developmental education' that is implemented in the

Measuring Meaningful Learning in the Undergraduate Chemistry Laboratory: A National, Cross-Sectional Study

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Galloway, Kelli R.; Bretz, Stacey Lowery

2015-01-01

Research on laboratory learning points to the need to better understand what and how students learn in the undergraduate chemistry laboratory. The Meaningful Learning in the Laboratory Instrument (MLLI) was administered to general and organic chemistry students from 15 colleges and universities across the United States in order to measure the…

Representing and Practising Meaningful Differences in a Well-Structured but Complex Art Curriculum

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Cunliffe, Leslie

2010-01-01

This paper conceptualizes the secondary art curriculum as a well-structured but complex knowledge-domain, with the aim of emphasizing meaningful differences in the way creative grammar operates in the following gatherings of art practices: Pre-historic and non-European cultures; Ancient and European cultures before c. 1800; Romantic and Modern…

Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

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2005-08-01

Full Text Available Although several reports have characterized the hematopoietic stem cell (HSC transcriptome, the roles of HSC-specific genes in hematopoiesis remain elusive. To identify candidate regulators of HSC fate decisions, we compared the transcriptome of human umbilical cord blood and bone marrow (CD34+(CD33-(CD38-Rho(lo(c-kit+ cells, enriched for hematopoietic stem/progenitor cells with (CD34+(CD33-(CD38-Rho(hi cells, enriched in committed progenitors. We identified 277 differentially expressed transcripts conserved in these ontogenically distinct cell sources. We next performed a morpholino antisense oligonucleotide (MO-based functional screen in zebrafish to determine the hematopoietic function of 61 genes that had no previously known function in HSC biology and for which a likely zebrafish ortholog could be identified. MO knock down of 14/61 (23% of the differentially expressed transcripts resulted in hematopoietic defects in developing zebrafish embryos, as demonstrated by altered levels of circulating blood cells at 30 and 48 h postfertilization and subsequently confirmed by quantitative RT-PCR for erythroid-specific hbae1 and myeloid-specific lcp1 transcripts. Recapitulating the knockdown phenotype using a second MO of independent sequence, absence of the phenotype using a mismatched MO sequence, and rescue of the phenotype by cDNA-based overexpression of the targeted transcript for zebrafish spry4 confirmed the specificity of MO targeting in this system. Further characterization of the spry4-deficient zebrafish embryos demonstrated that hematopoietic defects were not due to more widespread defects in the mesodermal development, and therefore represented primary defects in HSC specification, proliferation, and/or differentiation. Overall, this high-throughput screen for the functional validation of differentially expressed genes using a zebrafish model of hematopoiesis represents a major step toward obtaining meaningful information from global

Supporting students in building interdisciplinary connections across physics and biology

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Turpen, Chandra

2014-03-01

Our research team has been engaged in the iterative redesign of an Introductory Physics course for Life Science (IPLS) majors to explicitly bridge biology and physics in ways that are authentic to the disciplines. Our interdisciplinary course provides students opportunities to examine how modeling decisions (e.g. knowing when and how to use different concepts, identifying implicit assumptions, making and justifying assumptions) may differ depending on canonical disciplinary aims and interests. Our focus on developing students' interdisciplinary reasoning skills requires 1) shifting course topics to focus on core ideas that span the disciplines, 2) shifting epistemological expectations, and 3) foregrounding typically tacit disciplinary assumptions. In working to build an authentic interdisciplinary course that bridges physics and biology, we pay careful attention to supporting students in constructing these bridges. This course has been shown to have important impacts: a) students seek meaningful connections between the disciplines, b) students perceive relevance and utility of ideas from different disciplines, and c) students reconcile challenging disciplinary ideas. Although our focus has been on building interdisciplinary coherence, we have succeeded in maintaining strong student learning gains on fundamental physics concepts and allowed students to deepen their understanding of challenging concepts in thermodynamics. This presentation will describe the shifts in course content and the modern pedagogical approaches that have been integrated into the course, and provide an overview of key research results from this project. These results may aid physicists in reconsidering how they can meaningfully reach life-science students. This work is supported by NSF-TUES DUE 11-22818, the HHMI NEXUS grant, and a NSF Graduate Research Fellowship (DGE 0750616).

IMRT optimization with pseudo-biologic objective function

International Nuclear Information System (INIS)

Yi, B. Y.; Ahn, S. D.; Kim, J. H.; Lee, S. W.; Choi, E. K.

2002-01-01

The pseudo-biologic objective function has been proposed for the IMRT optimization. It is similar to the biological objective function in mathematical shape, but uses physical parameters. The pseudo-biologic objective function concept is consisted of the target coverage index (TCI) and the organ score index (OSI), was introduced. The TCI was expressed as the sum of all of the weighted bins of target dose volume histogram (DVH). The weights were given as the normal distribution of which the average is 100 % and the standard deviation is ±. The OSI was expressed as similar way. The average of the normal distribution was 0% of the dose and that of standard deviation was selected as a function of limiting dose and its importance. The objective function could be calculated as the product of the TCI and OSI's. The RTP Tool Box (RTB) was used for this study. The constraints applied in the optimization was intuitively clinical experience based numbers, while the physical objective function asks just numbers which are not necessarily based on the clinic, and the parameters for the biologic objective functions are uncertain. The OSI's from the pseudo-biological function showed better results than from the physical functions, while TCI's showed similar tendency. We could show that the pseudo-biologic function can be used for an IMRT objective function on behalf of the biological objective function

Meaningful Understanding and Systems Thinking in Organic Chemistry: Validating Measurement and Exploring Relationships

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Vachliotis, Theodoros; Salta, Katerina; Tzougraki, Chryssa

2014-01-01

The purpose of this study was dual: First, to develop and validate assessment schemes for assessing 11th grade students' meaningful understanding of organic chemistry concepts, as well as their systems thinking skills in the domain. Second, to explore the relationship between the two constructs of interest based on students' performance…

CONCEPTUAL APPROACHES TO THE EDUCATION OF LIFE-MEANINGFUL VALUES OF TEENAGERS AND EARLY ADOLESCENCE IN UKRAINE

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Katherinа Zhurba

2015-04-01

Full Text Available The article presents the conceptual approaches to the upbringing in the education of life-meaningful values of teenagers and early adolescence in Ukraine. The definition of life-meaningful values has been given up. The major problems and contradictions in the upbringing of the Ukrainian children were paid attention to. The dependence of the result of upbringing, from the desire and the participation of all actors: children, parents, teachers is pointed out. Conceptual approaches to education of life values meaning are analyzed on the methodological, theoretical and practical levels. The aspects of the previous researches have been underlined. In this context, a systematic approach determines the integrity of the educational process in primary and high school. Synergetic approach combines the organization and self-organization of the growing personality. Humanistic approach recognizes each child's highest value at school, family, and society. Personal-centered approach provides individual attention to him, to free choice of that or other life-meaningful values. Activity approach provides practice and deed activity of children and shows how the value of the meaning of life affects the behavior of the individual. The theoretical level of substantiation of the concept of education of children of teenagers and early youth gives ability to define key points and concepts. Practical level implies the corresponding experimental activity, the determination of propriate pedagogical conditions, the selection of content, forms and methods of education of teenagers and early adolescence. Conceptual approaches offer the opportunity to develop a modern system of education of the values of the meaning of life of teenagers and early adolescence in Ukraine. Implementation of conceptual approaches aimed at qualitative changes in the education of life-meaningful values among of teenagers and early adolescence.

The Meaningful Roles Intervention: An Evolutionary Approach to Reducing Bullying and Increasing Prosocial Behavior.

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Ellis, Bruce J; Volk, Anthony A; Gonzalez, Jose-Michael; Embry, Dennis D

2016-12-01

Bullying is a problem that affects adolescents worldwide. Efforts to prevent bullying have been moderately successful at best, or iatrogenic at worst. We offer an explanation for this limited success by employing an evolutionary-psychological perspective to analyze antibullying interventions. We argue that bullying is a goal-directed behavior that is sensitive to benefits as well as costs, and that interventions must address these benefits. This perspective led us to develop a novel antibullying intervention, Meaningful Roles, which offers bullies prosocial alternatives-meaningful roles and responsibilities implemented through a school jobs program and reinforced through peer-to-peer praise notes-that effectively meet the same status goals as bullying behavior. We describe this new intervention and how its theoretical evolutionary roots may be applicable to other intervention programs. © 2015 The Authors. Journal of Research on Adolescence © 2015 Society for Research on Adolescence.

Detection of EGFR and COX-2 Expression by Immunohistochemical Method on a Tissue Microarray Section in Lung Cancer and Biological Significance

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Xinyun WANG

2010-02-01

Full Text Available Background and objective Epidermal growth factor receptor (EGFR and cyclooxygenase-2 (COX-2, which can regulate growth, invasion and metastasis of tumor through relevant signaling pathway, have been detected in a variety of solid tumors. The aim of this study is to investigate the biological significance of EGFR and COX-2 expression in lung cancer and the relationship between them. Methods The expression of EGFR and COX-2 was detected in 89 primary lung cancer tissues, 12 premaliganant lesions, 12 lymph node metastases, and 10 normal lung tissues as the control by immunohistochemical method on a tissue microarray section. Results EGFR protein was detectable in 59.6%, 41.7%, and 66.7% of primary lung cancer tissues, premalignant lesions and lymph node metastases, respectively; COX-2 protein was detectable in 52.8%, 41.7%, and 66.7% of primary lung cancer tissues, premalignant lesions and lymph node metastases, respectively, which were significantly higher than those of the control (P 0.05. COX-2 expression was related to gross type (P < 0.05. A highly positive correlation was observed between EGFR and COX-2 expression (P < 0.01. Conclusion Overexpression of EGFR and COX-2 may play an important role in the tumorgenesis, progression and malignancy of lung cancer. Detection of EGFR and COX-2 expression might be helpful to diagnosis and prognosis of lung cancer.

Enhanced heterologous expression of biologically active human granulocyte colony stimulating factor in transgenic tobacco BY-2 cells by localization to endoplasmic reticulum.

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Nair, Nisha R; Chidambareswaren, M; Manjula, S

2014-09-01

Tobacco Bright Yellow-2 (BY-2) cells, one of the best characterized cell lines is an attractive expression system for heterologous protein expression. However, the expression of foreign proteins is currently hampered by their low yield, which is partially the result of proteolytic degradation. Human granulocyte colony stimulating factor (hG-CSF) is a hematopoietic cytokine. Recombinant hG-CSF is successfully being used for the treatment of chemotherapy-induced neutropenia in cancer patients. Here, we describe a simple strategy for producing biologically active hG-CSF in tobacco BY-2 cells, localized in the apoplast of BY-2 cells, as well as targeted to the endoplasmic reticulum (ER). ER targeting significantly enhanced recombinant production which scaled to 17.89 mg/l from 4.19 mg/l when expressed in the apoplasts. Southern blotting confirmed the stable integration of hG-CSF in the BY-2 nuclear genome, and the expression of hG-CSF was analysed by Western blotting. Total soluble protein containing hG-CSF isolated from positive calli showed proliferative potential when tested on HL-60 cell lines by MTT assay. We also report the potential of a Fluorescence-activated cell sorting approach for an efficient sorting of the hG-CSF-expressing cell lines, which will enable the generation of homogenous high-producing cell lines.

History of the molecular biology of cytomegaloviruses.

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Stinski, Mark F

2014-01-01

The history of the molecular biology of cytomegaloviruses from the purification of the virus and the viral DNA to the cloning and expression of the viral genes is reviewed. A key genetic element of cytomegalovirus (the CMV promoter) contributed to our understanding of eukaryotic cell molecular biology and to the development of lifesaving therapeutic proteins. The study of the molecular biology of cytomegaloviruses also contributed to the development of antivirals to control the viral infection.

Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis

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Kaur Parminder

2012-08-01

Full Text Available Abstract Background An approach to molecular classification based on the comparative expression of protein pairs is presented. The method overcomes some of the present limitations in using peptide intensity data for class prediction for problems such as the detection of a disease, disease prognosis, or for predicting treatment response. Data analysis is particularly challenging in these situations due to sample size (typically tens being much smaller than the large number of peptides (typically thousands. Methods based upon high dimensional statistical models, machine learning or other complex classifiers generate decisions which may be very accurate but can be complex and difficult to interpret in simple or biologically meaningful terms. A classification scheme, called ProtPair, is presented that generates simple decision rules leading to accurate classification which is based on measurement of very few proteins and requires only relative expression values, providing specific targeted hypotheses suitable for straightforward validation. Results ProtPair has been tested against clinical data from 21 patients following a bone marrow transplant, 13 of which progress to idiopathic pneumonia syndrome (IPS. The approach combines multiple peptide pairs originating from the same set of proteins, with each unique peptide pair providing an independent measure of discriminatory power. The prediction rate of the ProtPair for IPS study as measured by leave-one-out CV is 69.1%, which can be very beneficial for clinical diagnosis as it may flag patients in need of closer monitoring. The “top ranked” proteins provided by ProtPair are known to be associated with the biological processes and pathways intimately associated with known IPS biology based on mouse models. Conclusions An approach to biomarker discovery, called ProtPair, is presented. ProtPair is based on the differential expression of pairs of peptides and the associated proteins. Using mass

Callings, Work Role Fit, Psychological Meaningfulness and Work Engagement among Teachers in Zambia

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Rothmann, Sebastiaan; Hamukang'andu, Lukondo

2013-01-01

Our aim in this study was to investigate the relationships among a calling orientation, work role fit, psychological meaningfulness and work engagement of teachers in Zambia. A quantitative approach was followed and a cross-sectional survey was used. The sample (n = 150) included 75 basic and 75 secondary school teachers in the Choma district of…

Body language in the brain: constructing meaning from expressive movement

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Christine Marie Tipper

2015-08-01

Full Text Available This fMRI study investigated neural systems that interpret body language - the meaningful emotive expressions conveyed by body movement. Participants watched videos of performers engaged in modern dance or pantomime that conveyed specific themes such as hope, agony, lust, or exhaustion. We tested whether the meaning of an affectively laden performance was decoded in localized brain substrates as a distinct property of action separable from other superficial features, such as choreography, kinematics, performer, and low-level visual stimuli. A repetition suppression (RS procedure was used to identify brain regions that decoded the meaningful affective state of a performer, as evidenced by decreased activity when emotive themes were repeated in successive performances. Because the theme was the only feature repeated across video clips that were otherwise entirely different, the occurrence of RS identified brain substrates that differentially coded the specific meaning of expressive performances. RS was observed bilaterally, extending anteriorly along middle and superior temporal gyri into temporal pole, medially into insula, rostrally into inferior orbitofrontal cortex, and caudally into hippocampus and amygdala. Behavioral data on a separate task indicated that interpreting themes from modern dance was more difficult than interpreting pantomime; a result that was also reflected in the fMRI data. There was greater RS in left hemisphere, suggesting that the more abstract metaphors used to express themes in dance compared to pantomime posed a greater challenge to brain substrates directly involved in decoding those themes. We propose that the meaning-sensitive temporal-orbitofrontal regions observed here comprise a superordinate functional module of a known hierarchical action observation network, which is critical to the construction of meaning from expressive movement. The findings are discussed with respect to a predictive coding model of action

The association of meaningfulness, well-being, and engagement with absenteeism : A moderated mediation model

NARCIS (Netherlands)

Soane, E.; Shantz, A.; Alfes, K.; Truss, C.; Rees, C.; Gatenby, M.

2013-01-01

We theorized that absence from work is a resource-based process that is related to perceived meaningfulness of work, well-being, and engagement. Broaden-and-build theory (Fredrickson, 1998, 2001) and engagement theory (Bakker, Schaufeli, Leiter, & Taris, 2008; Kahn, 1990) were used to develop a

A Mixed-Methods Study of the Recovery Concept, "A Meaningful Day," in Community Mental Health Services for Individuals with Serious Mental Illnesses.

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Myers, Neely A L; Smith, Kelly; Pope, Alicia; Alolayan, Yazeed; Broussard, Beth; Haynes, Nora; Compton, Michael T

2016-10-01

The recovery concept encompasses overcoming or managing one's illness, being physically and emotionally healthy, and finding meaningful purpose through work, school, or volunteering, which connects one to others in mutually fulfilling ways. Using a mixed-methods approach, we studied the emphasis on "a meaningful day" in the new Opening Doors to Recovery (ODR) program in southeast Georgia. Among 100 participants, we measured the meaningful day construct using three quantitative items at baseline (hospital discharge) and at 4-, 8-, and 12-month follow-up, finding statistically significant linear trends over time for all three measures. Complementary qualitative interviews with 30 individuals (ODR participants, family members, and ODR's Community Navigation Specialists and program leaders) revealed themes pertaining to companionship, productivity, achieving stability, and autonomy, as well as the concern about insufficient resources. The concept of "a meaningful day" can be a focus of clinical attention and measured as a person-centered outcome for clients served by recovery-oriented community mental health services.

Mutually Beneficial Foreign Language Learning: Creating Meaningful Interactions through Video-Synchronous Computer-Mediated Communication

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Kato, Fumie; Spring, Ryan; Mori, Chikako

2016-01-01

Providing learners of a foreign language with meaningful opportunities for interactions, specifically with native speakers, is especially challenging for instructors. One way to overcome this obstacle is through video-synchronous computer-mediated communication tools such as Skype software. This study reports quantitative and qualitative data from…

Meaningful metrics a 21st-century librarian's guide to bibliometrics, altmetrics, and research impact

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Roemer, Robin Chin

2015-01-01

What does it mean to have meaningful metrics in today's complex higher education landscape? With a foreword by Heather Piwowar and Jason Priem, this highly engaging and activity-laden book serves to introduce readers to the fast-paced world of research metrics from the unique perspective of academic librarians and LIS practitioners. Starting with the essential histories of bibliometrics and altmetrics, and continuing with in-depth descriptions of the core tools and emerging issues at stake in the future of both fields, Meaningful Metrics is a convenient all-in-one resource that is designed to be used by a range of readers, from those with little to no background on the subject to those looking to become movers and shakers in the current scholarly metrics movement. Authors Borchardt and Roemer, offer tips, tricks, and real-world examples illustrate how librarians can support the successful adoption of research metrics, whether in their institutions or across academia as a whole.

Positive Bioluminescence Imaging of MicroRNA Expression in Small Animal Models Using an Engineered Genetic-Switch Expression System, RILES.

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Baril, Patrick; Pichon, Chantal

2016-01-01

MicroRNAs (miRNAs) are a class of small, noncoding RNAs which regulate gene expression by directing their target mRNA for degradation or translational repression. Since their discovery in the early 1990s, miRNAs have emerged as key components in the posttranscriptional regulation of gene networks, shaping many biological processes from development, morphogenesis, differentiation, proliferation and apoptosis. Although understanding of the molecular basis of miRNA biology is improving, methods to monitor the dynamic and the spatiotemporal aspects of miRNA expression under physiopathological conditions are required. However, monitoring of miRNAs is difficult due to their small size, low abundance, high degree of sequence similarity, and their dynamic expression pattern which is subjected to tight transcriptional and post-transcriptional controls. Recently, we developed a miRNA monitoring system called RILES, standing for RNAi-inducible expression system, which relies on an engineered regulatable expression system, to switch on the expression of the luciferase gene when the targeted miRNA is expressed in cells. We demonstrated that RILES is a specific, sensitive, and robust method to determine the fine-tuning of miRNA expression during the development of an experimental pathological process in mice. Because RILES offers the possibility for longitudinal studies on individual subjects, sharper insights into miRNA regulation can be generated, with applications in physiology, pathophysiology and development of RNAi-based therapies. This chapter describes methods and protocols to monitor the expression of myomiR-206, -1, and -133 in the tibialis anterior muscle of mice. These protocols can be used and adapted to monitor the expression of other miRNAs in other biological processes.

Energy key performance indicators : a european benchmark and assessment of meaningful indicators for the use of energy in large corporations

OpenAIRE

Friedrichs, Katja

2013-01-01

This study aims to identify and analyze energy key performance indicators among large European companies. Energy usage has become a very meaningful topic for both internal management as well as external stakeholders of a company. A review of current literature suggests that while environmental indicators in general have found broad attention and plenty of theories concerning good and meaningful indicators are published, no study investigating actually applied energy indicators ...

A novel validation algorithm allows for automated cell tracking and the extraction of biologically meaningful parameters.

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Daniel H Rapoport

Full Text Available Automated microscopy is currently the only method to non-invasively and label-free observe complex multi-cellular processes, such as cell migration, cell cycle, and cell differentiation. Extracting biological information from a time-series of micrographs requires each cell to be recognized and followed through sequential microscopic snapshots. Although recent attempts to automatize this process resulted in ever improving cell detection rates, manual identification of identical cells is still the most reliable technique. However, its tedious and subjective nature prevented tracking from becoming a standardized tool for the investigation of cell cultures. Here, we present a novel method to accomplish automated cell tracking with a reliability comparable to manual tracking. Previously, automated cell tracking could not rival the reliability of manual tracking because, in contrast to the human way of solving this task, none of the algorithms had an independent quality control mechanism; they missed validation. Thus, instead of trying to improve the cell detection or tracking rates, we proceeded from the idea to automatically inspect the tracking results and accept only those of high trustworthiness, while rejecting all other results. This validation algorithm works independently of the quality of cell detection and tracking through a systematic search for tracking errors. It is based only on very general assumptions about the spatiotemporal contiguity of cell paths. While traditional tracking often aims to yield genealogic information about single cells, the natural outcome of a validated cell tracking algorithm turns out to be a set of complete, but often unconnected cell paths, i.e. records of cells from mitosis to mitosis. This is a consequence of the fact that the validation algorithm takes complete paths as the unit of rejection/acceptance. The resulting set of complete paths can be used to automatically extract important biological parameters

Statistical approach for selection of biologically informative genes.

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Das, Samarendra; Rai, Anil; Mishra, D C; Rai, Shesh N

2018-05-20

Selection of informative genes from high dimensional gene expression data has emerged as an important research area in genomics. Many gene selection techniques have been proposed so far are either based on relevancy or redundancy measure. Further, the performance of these techniques has been adjudged through post selection classification accuracy computed through a classifier using the selected genes. This performance metric may be statistically sound but may not be biologically relevant. A statistical approach, i.e. Boot-MRMR, was proposed based on a composite measure of maximum relevance and minimum redundancy, which is both statistically sound and biologically relevant for informative gene selection. For comparative evaluation of the proposed approach, we developed two biological sufficient criteria, i.e. Gene Set Enrichment with QTL (GSEQ) and biological similarity score based on Gene Ontology (GO). Further, a systematic and rigorous evaluation of the proposed technique with 12 existing gene selection techniques was carried out using five gene expression datasets. This evaluation was based on a broad spectrum of statistically sound (e.g. subject classification) and biological relevant (based on QTL and GO) criteria under a multiple criteria decision-making framework. The performance analysis showed that the proposed technique selects informative genes which are more biologically relevant. The proposed technique is also found to be quite competitive with the existing techniques with respect to subject classification and computational time. Our results also showed that under the multiple criteria decision-making setup, the proposed technique is best for informative gene selection over the available alternatives. Based on the proposed approach, an R Package, i.e. BootMRMR has been developed and available at https://cran.r-project.org/web/packages/BootMRMR. This study will provide a practical guide to select statistical techniques for selecting informative genes

Are there meaningful individual differences in temporal inconsistency in self-reported personality?

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Soubelet, Andrea; Salthouse, Timothy A; Oishi, Shigehiro

2014-11-01

The current project had three goals. The first was to examine whether it is meaningful to refer to across-time variability in self-reported personality as an individual differences characteristic. The second was to investigate whether negative affect was associated with variability in self-reported personality, while controlling for mean levels, and correcting for measurement errors. The third goal was to examine whether variability in self-reported personality would be larger among young adults than among older adults, and whether the relation of variability with negative affect would be stronger at older ages than at younger ages. Two moderately large samples of participants completed the International Item Pool Personality questionnaire assessing the Big Five personality dimensions either twice or thrice, in addition to several measures of negative affect. Results were consistent with the hypothesis that within-person variability in self-reported personality is a meaningful individual difference characteristic. Some people exhibited greater across-time variability than others after removing measurement error, and people who showed temporal instability in one trait also exhibited temporal instability across the other four traits. However, temporal variability was not related to negative affect, and there was no evidence that either temporal variability or its association with negative affect varied with age.

Monod and the spirit of molecular biology.

Science.gov (United States)

Morange, Michel

2015-06-01

The founders of molecular biology shared views on the place of biology within science, as well as on the relations of molecular biology to Darwinism. Jacques Monod was no exception, but the study of his writings is particularly interesting because he expressed his point of view very clearly and pushed the implications of some of his choices further than most of his contemporaries. The spirit of molecular biology is no longer the same as in the 1960s but, interestingly, Monod anticipated some recent evolutions of this discipline. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Computational mediation as factor of motivation and meaningful learning in education of sciences of 9th grade: astronomy topics

Science.gov (United States)

Da Silva, F. M.; Furtado, W. W.

2012-10-01

The main purpose of this study was to analyze the contribution of using hypertext and pedagogic mediation in search of a Meaningful Learning Process in Sciences. We investigate the usage of hypertext in the teaching and learning methods of Astronomy modules. A survey was conducted with students from the 9th grade of Primary School of a public school in the city of Goiânia, Goiás in Brazil. We have analyzed the possibilities that hypermedia can offer in the teaching and learning process, using as reference David Ausubel's Theory of Meaningful Learning. The study was divided into four phases: application of an initial questionnaire on students, development of didactic material (hypertext), six classes held in a computer lab with the use of hypermedia and a final questionnaire applied in the lab after classes. This research indicated that the use of hypertext linked to pedagogical mediation processes is seen as a motivational tool and has potential to foster to Meaningful Learning.

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

Science.gov (United States)

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthetic biology: Emerging bioengineering in Indonesia

Science.gov (United States)

Suhandono, Sony

2017-05-01

The development of synthetic biology will shape the new era of science and technology. It is an emerging bioengineering technique involving genetic engineering which can alter the phenotype and behavior of the cell or the new product. Synthetic biology may produce biomaterials, drugs, vaccines, biosensors, and even a recombinant secondary metabolite used in herbal and complementary medicine, such as artemisinin, a malaria drug which is usually extracted from the plant Artemisia annua. The power of synthetic biology has encouraged scientists in Indonesia, and is still in early development. This paper also covers some research from an Indonesian research institute in synthetic biology such as observing the production of bio surfactants and the enhanced production of artemisinin using a transient expression system. Synthetic biology development in Indonesia may also be related to the iGEM competition, a large synthetic biology research competition which was attended by several universities in Indonesia. The application of synthetic biology for drug discovery will be discussed.

BiologicalNetworks 2.0 - an integrative view of genome biology data

Directory of Open Access Journals (Sweden)

Ponomarenko Julia

2010-12-01

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

Population-expression models of immune response

International Nuclear Information System (INIS)

Stromberg, Sean P; Antia, Rustom; Nemenman, Ilya

2013-01-01

The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an initial naive phenotype to an effector phenotype which controls the pathogen, and subsequently to a memory phenotype that is maintained and responsible for long-term protection. The expansion and the differentiation have been considered largely independently. Changes in cell populations are typically described using ecologically based ordinary differential equation models. In contrast, differentiation of single cells is studied within systems biology and is frequently modeled by considering changes in gene and protein expression in individual cells. Recent advances in experimental systems biology make available for the first time data to allow the coupling of population and high dimensional expression data of immune cells during infections. Here we describe and develop population-expression models which integrate these two processes into systems biology on the multicellular level. When translated into mathematical equations, these models result in non-conservative, non-local advection-diffusion equations. We describe situations where the population-expression approach can make correct inference from data while previous modeling approaches based on common simplifying assumptions would fail. We also explore how model reduction techniques can be used to build population-expression models, minimizing the complexity of the model while keeping the essential features of the system. While we consider problems in immunology in this paper, we expect population-expression models to be more broadly applicable. (paper)

Sustaining "meaningful use" of health information technology in low-resource practices.

Science.gov (United States)

Green, Lee A; Potworowski, Georges; Day, Anya; May-Gentile, Rachelle; Vibbert, Danielle; Maki, Bruce; Kiesel, Leslie

2015-01-01

The implementation of electronic health records (EHRs) has been extensively studied, but their maintenance once implemented has not. The Regional Extension Center (REC) program provides implementation assistance to priority practices-those with limited financial, technical, and organizational resources-but the assistance is time limited. Our objective was to identify potential barriers to maintenance of meaningful use of EHRs in priority primary care practices using a qualitative observational study for federally qualified health centers (FQHCs) and priority practices in Michigan. We conducted cognitive task analysis (CTA) interviews and direct observations of health information technology implementation in FQHCs. In addition, we conducted semistructured interviews with implementation specialists serving priority practices to detect emergent themes relevant to maintenance. Maintaining EHR technology will require ongoing expert technical support indefinitely beyond implementation to address upgrades and security needs. Maintaining meaningful use for quality improvement will require ongoing support for leadership and change management. Priority practices not associated with larger systems lack access to the necessary technical expertise, financial resources, and leverage with vendors to continue alone. Rural priority practices are particularly challenged, because expertise is often not available locally. Priority practices, especially in rural areas, are at high risk for falling on the wrong side of a "digital divide" as payers and regulators enact increasing expectations for EHR use and information management. For those without affiliation to maintain the necessary expert staff, ongoing support will be needed for those practices to remain viable. © 2015 Annals of Family Medicine, Inc.

Selection and validation of reference genes for miRNA expression studies during porcine pregnancy.

Directory of Open Access Journals (Sweden)

Jocelyn M Wessels

Full Text Available MicroRNAs comprise a family of small non-coding RNAs that modulate several developmental and physiological processes including pregnancy. Their ubiquitous presence is confirmed in mammals, worms, flies and plants. Although rapid advances have been made in microRNA research, information on stable reference genes for validation of microRNA expression is still lacking. Real time PCR is a widely used tool to quantify gene transcripts. An appropriate reference gene must be chosen to minimize experimental error in this system. A small difference in miRNA levels between experimental samples can be biologically meaningful as these entities can affect multiple targets in a pathway. This study examined the suitability of six commercially available reference genes (RNU1A, RNU5A, RNU6B, SNORD25, SCARNA17, and SNORA73A in maternal-fetal tissues from healthy and spontaneously arresting/dying conceptuses from sows were separately analyzed at gestation day 20. Comparisons were also made with non-pregnant endometrial tissues from sows. Spontaneous fetal loss is a prime concern to the commercial pork industry. Our laboratory has previously identified deficits in vasculature development at maternal-fetal interface as one of the major participating causes of fetal loss. Using this well-established model, we have extended our studies to identify suitable microRNA reference genes. A methodical approach to assessing suitability was adopted using standard curve and melting curve analysis, PCR product sequencing, real time PCR expression in a panel of gestational tissues, and geNorm and NormFinder analysis. Our quantitative real time PCR analysis confirmed expression of all 6 reference genes in maternal and fetal tissues. All genes were uniformly expressed in tissues from healthy and spontaneously arresting conceptus attachment sites. Comparisons between tissue types (maternal/fetal/non-pregnant revealed significant differences for RNU5A, RNU6B, SCARNA17, and SNORA73A

A complex pattern of chemokine receptor expression is seen in osteosarcoma

International Nuclear Information System (INIS)

Luettichau, Irene von; Huss, Ralf; Nelson, Peter J; Segerer, Stephan; Wechselberger, Alexandra; Notohamiprodjo, Mike; Nathrath, Michaela; Kremer, Markus; Henger, Anna; Djafarzadeh, Roghieh; Burdach, Stefan

2008-01-01

Osteosarcoma is the most frequent bone tumor in childhood and adolescence. Patients with primary metastatic disease have a poor prognosis. It is therefore important to better characterize the biology of this tumor to define new prognostic markers or therapeutic targets for tailored therapy. Chemokines and their receptors have been shown to be involved in the development and progression of malignant tumors. They are thought to be active participants in the biology of osteosarcoma. The function of specific chemokines and their receptors is strongly associated with the biological context and microenvironment of their expression. In this report we characterized the expression of a series of chemokine receptors in the complex environment that defines osteosarcoma. The overall level of chemokine receptor mRNA expression was determined using TaqMan RT-PCR of microdissected archival patient biopsy samples. Expression was then verified at the protein level by immunohistochemistry using a series of receptor specific antibody reagents to elucidate the cellular association of expression. Expression at the RNA level was found for most of the tested receptors. CCR1 expression was found on infiltrating mononuclear and polynuclear giant cells in the tumor. Cells associated with the lining of intratumoral vessels were shown to express CCR4. Infiltrating mononuclear cells and tumor cells both showed expression of the receptor CCR5, while CCR7 was predominantly expressed by the mononuclear infiltrate. CCR10 was only very rarely detected in few scattered infiltrating cells. Our data elucidate for the first time the cellular context of chemokine receptor expression in osteosarcoma. This is an important issue for better understanding potential chemokine/chemokine receptor function in the complex biologic processes that underlie the development and progression of osteosarcoma. Our data support the suggested involvement of chemokines and their receptors in diverse aspects of the biology

Cell-free synthetic biology for environmental sensing and remediation.

Science.gov (United States)

Karig, David K

2017-06-01

The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications. Cell-free protein expression systems offer a path towards leveraging synthetic biology, while preventing the spread of engineered organisms in nature. Recent efforts in the areas of cell-free approaches for sensing, regulation, and metabolic pathway implementation, as well as for preserving and deploying cell-free expression components, embody key steps towards realizing the potential of cell-free systems for environmental sensing and remediation. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

No impact of Bt soybean that express Cry1Ac protein on biological traits of Euschistus heros (Hemiptera, Pentatomidae and its egg parasitoid Telenomus podisi (Hymenoptera, Platygastridae

Directory of Open Access Journals (Sweden)

Gabriela Vieira Silva

2014-09-01

Full Text Available No impact of Bt soybean that express Cry1Ac protein on biological traits of Euschistus heros (Hemiptera, Pentatomidae and its egg parasitoid Telenomus podisi (Hymenoptera, Platygastridae. Biological traits of the stink bug Euschistus heros and its main biological control agent Telenomus podisi were evaluated under controlled environmental conditions (25 ± 2ºC; 60 ± 10% RH; and 14/10 h photoperiod by placing first instar nymphs into Petri dishes with pods originating from two soybean isolines (Bt-soybean MON 87701 × MON 89788, which expresses the Cry1Ac protein, and its near non-Bt isoline A5547 where they remained until the adult stage. Due to gregarious behavior exhibited by first instar nymphs, they were individualized only when at the second instar. Adults were separated by sex and weighed, and pronotum width of each individual was subsequently measured. They were placed into plastic boxes containing soybean grains of the same soybean isoline as food source. Egg viability and female fecundity were assessed in adult individuals. Adult females of T. podisi (up to 24h old were placed with eggs of E. heros from mothers reared on both soybean isolines. Nymphal development time, insect weight, pronotum width, sex ratio, female fecundity, and egg viability (% emergence of Euschistus heros did not differ between treatments. Eggto-adult development time, female longevity, sex ratio, and percentage of parasitized eggs were not impacted by the Bt-soybean (expressing Cry1Ac protein. Results indicate that the Bt-soybean, MON 87701 × MON 89788, has no direct significant impact on the two studied species.

Uncovering the molecular secrets of inflammatory breast cancer biology: an integrated analysis of three distinct affymetrix gene expression datasets.

Science.gov (United States)

Van Laere, Steven J; Ueno, Naoto T; Finetti, Pascal; Vermeulen, Peter; Lucci, Anthony; Robertson, Fredika M; Marsan, Melike; Iwamoto, Takayuki; Krishnamurthy, Savitri; Masuda, Hiroko; van Dam, Peter; Woodward, Wendy A; Viens, Patrice; Cristofanilli, Massimo; Birnbaum, Daniel; Dirix, Luc; Reuben, James M; Bertucci, François

2013-09-01

Inflammatory breast cancer (IBC) is a poorly characterized form of breast cancer. So far, the results of expression profiling in IBC are inconclusive due to various reasons including limited sample size. Here, we present the integration of three Affymetrix expression datasets collected through the World IBC Consortium allowing us to interrogate the molecular profile of IBC using the largest series of IBC samples ever reported. Affymetrix profiles (HGU133-series) from 137 patients with IBC and 252 patients with non-IBC (nIBC) were analyzed using unsupervised and supervised techniques. Samples were classified according to the molecular subtypes using the PAM50-algorithm. Regression models were used to delineate IBC-specific and molecular subtype-independent changes in gene expression, pathway, and transcription factor activation. Four robust IBC-sample clusters were identified, associated with the different molecular subtypes (Pmolecular subtype-independent 79-gene signature, which held independent prognostic value in a series of 871 nIBCs. Functional analysis revealed attenuated TGF-β signaling in IBC. We show that IBC is transcriptionally heterogeneous and that all molecular subtypes described in nIBC are detectable in IBC, albeit with a different frequency. The molecular profile of IBC, bearing molecular traits of aggressive breast tumor biology, shows attenuation of TGF-β signaling, potentially explaining the metastatic potential of IBC tumor cells in an unexpected manner. ©2013 AACR.

Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review.

Science.gov (United States)

Raddatz, Barbara B; Spitzbarth, Ingo; Matheis, Katja A; Kalkuhl, Arno; Deschl, Ulrich; Baumgärtner, Wolfgang; Ulrich, Reiner

2017-09-01

High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms. The scientific literature concerning high-throughput data-mining techniques usually addresses mathematicians or computer scientists as the target audience. In contrast, the present review provides the reader with a clear and systematic basis from a veterinary pathologist's perspective. Therefore, the aims are (1) to introduce the reader to the necessary methodological background; (2) to introduce the sequential steps commonly performed in a microarray analysis including quality control, annotation, normalization, selection of differentially expressed genes, clustering, gene ontology and pathway analysis, analysis of manually selected genes, and biomarker discovery; and (3) to provide references to publically available and user-friendly software suites. In summary, the data analysis methods presented within this review will enable veterinary pathologists to analyze high-throughput transcriptome data obtained from their own experiments, supplemental data that accompany scientific publications, or public repositories in order to obtain a more in-depth insight into underlying disease mechanisms.

Effect of Community-Based Occupational Therapy on Health-Related Quality of Life and Engagement in Meaningful Activities of Women with Breast Cancer

Directory of Open Access Journals (Sweden)

Daiva Petruseviciene

2018-01-01

Full Text Available We aimed to evaluate the short-term effects of community-based occupational therapy on health-related quality of life and engagement in meaningful activities among women with breast cancer. An open label randomized controlled trial study design was applied. The participants were members of various societies of women with cancer. In total, 22 women have participated in the study. Participants of the experimental group (n=11 participated in a 6-week community-based occupational therapy program and the usual activities of various societies, whereas the control group (n=11 women participated in the usual activities of the societies only. 1 of the participants withdrew during the course; therefore 21 completed the study successfully. Participants of both groups were assessed for health-related quality of life and the participants of the experimental group were assessed for engagement in meaningful activities. The evaluation was carried out during the nonacute period of the disease—at the beginning of the study and after 6 weeks. Women of the experimental group demonstrated statistically significantly better scores in the global quality of life, role functions, physical, emotional, cognitive, and social functions, fatigue, insomnia, financial impact, systemic therapy side effects, and breast symptoms scales compared to the control group participants (p<0.05 after the 6 weeks, as measured by the EORTC QLQ-C30 questionnaire and its breast cancer module QLQ-BR23. Furthermore, women of the experimental group demonstrated significant greater engagement in meaningful activities when applying community-based occupational therapy (p<0.05, as measured by using the Engagement in Meaningful Activities Survey (EMAS. The evaluation of the associations between the women’s engagement in meaningful activities and changes in health-related quality of life showed that greater engagement in meaningful activities was associated with better emotional functions and a

Synthetic biology and biosecurity: challenging the "myths".

OpenAIRE

Jefferson, C; Lentzos, F; Marris, C

2014-01-01

15.10.14 KB. Ok to add published version to spiral, OA paper under cc by Synthetic biology, a field that aims to make biology easier to engineer, is routinely described as leading to an increase in the dual-use threat, i.e., the potential for the same scientific research to be used for peaceful purposes or misused for warfare or terrorism. Fears have been expressed that the de-skilling of biology, combined with online access to the genomic DNA sequences of pathogenic organisms an...

Node fingerprinting: an efficient heuristic for aligning biological networks.

Science.gov (United States)

Radu, Alex; Charleston, Michael

2014-10-01

With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

Third international congress of plant molecular biology: Molecular biology of plant growth and development

Energy Technology Data Exchange (ETDEWEB)

Hallick, R.B. [ed.

1995-02-01

The Congress was held October 6-11, 1991 in Tucson with approximately 3000 scientists attending and over 300 oral presentations and 1800 posters. Plant molecular biology is one of the most rapidly developing areas of the biological sciences. Recent advances in the ability to isolate genes, to study their expression, and to create transgenic plants have had a major impact on our understanding of the many fundamental plant processes. In addition, new approaches have been created to improve plants for agricultural purposes. This is a book of presentation and posters from the conference.

Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals.

Science.gov (United States)

Yum, Lauren K; Baumgarten, Sebastian; Röthig, Till; Roder, Cornelia; Roik, Anna; Michell, Craig; Voolstra, Christian R

2017-07-25

Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.

Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals

KAUST Repository

Yum, Lauren

2017-07-19

Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.

Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals

KAUST Repository

Yum, Lauren; Baumgarten, Sebastian; Rö thig, Till; Roder, Cornelia; Roik, Anna Krystyna; Michell, Craig; Voolstra, Christian R.

2017-01-01

Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

Directory of Open Access Journals (Sweden)

Madeira Sara C

2009-06-01

Full Text Available Abstract Background The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters. Methods In this work, we propose e-CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with approximate expression patterns in time polynomial in the size of the time series gene expression matrix. This polynomial time complexity is achieved by manipulating a discretized version of the original matrix using efficient string processing techniques. We also propose extensions to deal with missing values, discover anticorrelated and scaled expression patterns, and different ways to compute the errors allowed in the expression patterns. We propose a scoring criterion combining the statistical significance of expression patterns with a similarity measure between overlapping biclusters. Results We present results in real data showing the effectiveness of e-CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in Saccharomyces cerevisiae in response to heat stress. In particular, the results show the advantage of considering approximate patterns when compared to state of

An improved Pearson's correlation proximity-based hierarchical clustering for mining biological association between genes.

Science.gov (United States)

Booma, P M; Prabhakaran, S; Dhanalakshmi, R

2014-01-01

Microarray gene expression datasets has concerned great awareness among molecular biologist, statisticians, and computer scientists. Data mining that extracts the hidden and usual information from datasets fails to identify the most significant biological associations between genes. A search made with heuristic for standard biological process measures only the gene expression level, threshold, and response time. Heuristic search identifies and mines the best biological solution, but the association process was not efficiently addressed. To monitor higher rate of expression levels between genes, a hierarchical clustering model was proposed, where the biological association between genes is measured simultaneously using proximity measure of improved Pearson's correlation (PCPHC). Additionally, the Seed Augment algorithm adopts average linkage methods on rows and columns in order to expand a seed PCPHC model into a maximal global PCPHC (GL-PCPHC) model and to identify association between the clusters. Moreover, a GL-PCPHC applies pattern growing method to mine the PCPHC patterns. Compared to existing gene expression analysis, the PCPHC model achieves better performance. Experimental evaluations are conducted for GL-PCPHC model with standard benchmark gene expression datasets extracted from UCI repository and GenBank database in terms of execution time, size of pattern, significance level, biological association efficiency, and pattern quality.

Environmental radiation: basic principles, biological facts, potential risks

International Nuclear Information System (INIS)

Rodemann, H.P.

2000-01-01

This book describes the complex processes that underlie the effects of different types of radiation at the cellular, organ and organismic level. Technical terms central to the subject matter are printed in italicize and explained in a glossary along with all physical quantities and dimensional units referred to. Through a systematic presentation of various aspects of the effects of environmental radiation on humans the author has endeavoured to make it clear that any discussion on potential health hazards must be conducted specific to the type of radiation in question. Furthermore, to study these issues meaningfully one must have a knowledge of the scientific basis of interactions between the various types of radiation and biological systems and be able to assess the relative impact of environmental radiation compared with other environmental health hazards

Progeny Clustering: A Method to Identify Biological Phenotypes

Science.gov (United States)

Hu, Chenyue W.; Kornblau, Steven M.; Slater, John H.; Qutub, Amina A.

2015-01-01

Estimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset. PMID:26267476

Measuring Meaningful Learning in the Undergraduate General Chemistry and Organic Chemistry Laboratories: A Longitudinal Study

Science.gov (United States)

Galloway, Kelli R.; Bretz, Stacey Lowery

2015-01-01

Understanding how students learn in the undergraduate chemistry teaching laboratory is an essential component to developing evidence-based laboratory curricula. The Meaningful Learning in the Laboratory Instrument (MLLI) was developed to measure students' cognitive and affective expectations and experiences for learning in the chemistry…

The Effect of Case Teaching on Meaningful and Retentive Learning When Studying Genetic Engineering

Science.gov (United States)

Güccük, Ahmet; Köksal, Mustafa Serdar

2017-01-01

The purpose of this study is to investigate the effects of case teaching on how students learn about genetic engineering, in terms of meaningful learning and retention of learning. The study was designed as quasi-experimental research including 63 8th graders (28 boys and 35 girls). To collect data, genetic engineering achievement tests were…

Rule-Based Design of Plant Expression Vectors Using GenoCAD.

Science.gov (United States)

Coll, Anna; Wilson, Mandy L; Gruden, Kristina; Peccoud, Jean

2015-01-01

Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It includes a library of plant biological parts organized in structural categories and a set of rules describing how to assemble these parts into large constructs. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.

Robust Transgene Expression from Bicistronic mRNA in the Green Alga Chlamydomonas reinhardtii

Directory of Open Access Journals (Sweden)

Masayuki Onishi

2016-12-01

Full Text Available The unicellular green alga Chlamydomonas reinhardtii is a model organism that provides an opportunity to understand the evolution and functional biology of the lineage that includes the land plants, as well as aspects of the fundamental core biology conserved throughout the eukaryotic phylogeny. Although many tools are available to facilitate genetic, molecular biological, biochemical, and cell biological studies in Chlamydomonas, expression of unselected transgenes of interest (GOIs has been challenging. In most methods used previously, the GOI and a selectable marker are expressed from two separate mRNAs, so that their concomitant expression is not guaranteed. In this study, we developed constructs that allow expression of an upstream GOI and downstream selectable marker from a single bicistronic mRNA. Although this approach in other systems has typically required a translation-enhancing element such as an internal ribosome entry site for the downstream marker, we found that a short stretch of unstructured junction sequence was sufficient to obtain adequate expression of the downstream gene, presumably through post-termination reinitiation. With this system, we obtained robust expression of both endogenous and heterologous GOIs, including fluorescent proteins and tagged fusion proteins, in the vast majority of transformants, thus eliminating the need for tedious secondary screening for GOI-expressing transformants. This improved efficiency should greatly facilitate a variety of genetic and cell-biological studies in Chlamydomonas and also enable new applications such as expression-based screens and large-scale production of foreign proteins.

Identifying meaningful activities among elderly people with demenitia: the developing process of an observation taxonomy

DEFF Research Database (Denmark)

Andresen, Mette

2014-01-01

, values and beliefs in the center formed the base in the development of the tool. Aim: To develop an observational tool which can identify meaningful activities among elderly demented nursing home residents and thereby provide staff with more knowledge and possibilities for inviting and engaging residents...

Magnitude and meaningfulness of change in SF-36 scores in four types of orthopedic surgery

DEFF Research Database (Denmark)

Busija, Lucy; Osborne, Richard H; Nilsdotter, Anna

2008-01-01

BACKGROUND: The Medical Outcomes General Health Survey (SF-36) is a widely used health status measure; however, limited evidence is available for its performance in orthopedic settings. The aim of this study was to examine the magnitude and meaningfulness of change and sensitivity of SF-36...

Security, Dignity, Caring Relationships, and Meaningful Work: Needs Motivating Participation in a Job-Training Program

Science.gov (United States)

Ayers, David F.; Miller-Dyce, Cherrel; Carlone, David

2008-01-01

Researchers asked 17 participants in a job-training program to describe their personal struggles following an economic restructuring. Examined through a critical theoretical lens, findings indicate that the learners enrolled in the program to reclaim security, dignity, meaningful work, and caring relationships. Program planners at community…

Versatile and on-demand biologics co-production in yeast.

Science.gov (United States)

Cao, Jicong; Perez-Pinera, Pablo; Lowenhaupt, Ky; Wu, Ming-Ru; Purcell, Oliver; de la Fuente-Nunez, Cesar; Lu, Timothy K

2018-01-08

Current limitations to on-demand drug manufacturing can be addressed by technologies that streamline manufacturing processes. Combining the production of two or more drugs into a single batch could not only be useful for research, clinical studies, and urgent therapies but also effective when combination therapies are needed or where resources are scarce. Here we propose strategies to concurrently produce multiple biologics from yeast in single batches by multiplexing strain development, cell culture, separation, and purification. We demonstrate proof-of-concept for three biologics co-production strategies: (i) inducible expression of multiple biologics and control over the ratio between biologic drugs produced together; (ii) consolidated bioprocessing; and (iii) co-expression and co-purification of a mixture of two monoclonal antibodies. We then use these basic strategies to produce drug mixtures as well as to separate drugs. These strategies offer a diverse array of options for on-demand, flexible, low-cost, and decentralized biomanufacturing applications without the need for specialized equipment.

Gene Expression Commons: an open platform for absolute gene expression profiling.

Directory of Open Access Journals (Sweden)

Jun Seita

Full Text Available Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000 of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named "Gene Expression Commons" (https://gexc.stanford.edu/ which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples.

Prediction of Associations between microRNAs and Gene Expression in Glioma Biology.

Directory of Open Access Journals (Sweden)

Stefan Wuchty

Full Text Available Despite progress in the determination of miR interactions, their regulatory role in cancer is only beginning to be unraveled. Utilizing gene expression data from 27 glioblastoma samples we found that the mere knowledge of physical interactions between specific mRNAs and miRs can be used to determine associated regulatory interactions, allowing us to identify 626 associated interactions, involving 128 miRs that putatively modulate the expression of 246 mRNAs. Experimentally determining the expression of miRs, we found an over-representation of over(under-expressed miRs with various predicted mRNA target sequences. Such significantly associated miRs that putatively bind over-expressed genes strongly tend to have binding sites nearby the 3'UTR of the corresponding mRNAs, suggesting that the presence of the miRs near the translation stop site may be a factor in their regulatory ability. Our analysis predicted a significant association between miR-128 and the protein kinase WEE1, which we subsequently validated experimentally by showing that the over-expression of the naturally under-expressed miR-128 in glioma cells resulted in the inhibition of WEE1 in glioblastoma cells.

Network Security via Biometric Recognition of Patterns of Gene Expression

Science.gov (United States)

Shaw, Harry C.

2016-01-01

Molecular biology provides the ability to implement forms of information and network security completely outside the bounds of legacy security protocols and algorithms. This paper addresses an approach which instantiates the power of gene expression for security. Molecular biology provides a rich source of gene expression and regulation mechanisms, which can be adopted to use in the information and electronic communication domains. Conventional security protocols are becoming increasingly vulnerable due to more intensive, highly capable attacks on the underlying mathematics of cryptography. Security protocols are being undermined by social engineering and substandard implementations by IT organizations. Molecular biology can provide countermeasures to these weak points with the current security approaches. Future advances in instruments for analyzing assays will also enable this protocol to advance from one of cryptographic algorithms to an integrated system of cryptographic algorithms and real-time expression and assay of gene expression products.

Consumers’ social media brand behaviors: uncovering underlying motivators and deriving meaningful consumer segments

OpenAIRE

Dimitriu, Radu; Guesalaga Trautmann, Rodrigo

2017-01-01

The current research identifies the range of social media brand behaviors (i.e., brand touch points) that consumers can exhibit on social media, and subsequently queries a representative sample of consumers with regard to such behaviors. The analysis reveals four underlying motivators for consumers’ social media behaviors, including brand tacit engagement, brand exhibiting, brand patronizing and brand deal seeking. These motivators are used to derive meaningful consumer segments identified as...

Doing the Project and Learning the Content: Designing Project-Based Science Curricula for Meaningful Understanding

Science.gov (United States)

Kanter, David E.

2010-01-01

Project-based science curricula can improve students' usable or meaningful understanding of the science content underlying a project. However, such curricula designed around "performances" wherein students design or make something do not always do this. We researched ways to design performance project-based science curricula (pPBSc) to better…

"Seeing the Whole Elephant": Changing Mindsets and Empowering Stakeholders to Meaningfully Manage Accountability and Improvement

Science.gov (United States)

Bush-Mecenas, Susan; Marsh, Julie A.; Montes de Oca, David; Hough, Heather

2018-01-01

School accountability and improvement policy are on the precipice of a paradigm shift. While the multiple-measure dashboard accountability approach holds great promise for promoting more meaningful learning opportunities for all students, our research indicates that this can come with substantial challenges in practice. We reflect upon the lessons…

Classification, expression pattern and comparative analysis of sugarcane expressed sequences tags (ESTs encoding glycine-rich proteins (GRPs

Directory of Open Access Journals (Sweden)

Fusaro Adriana

2001-01-01

Full Text Available Since the isolation of the first glycine-rich proteins (GRPs in plants a wealth of new GRPs have been identified. The highly specific but diverse expression pattern of grp genes, taken together with the distinct sub-cellular localization of some GRP groups, clearly indicate that these proteins are involved in several independent physiological processes. Notwithstanding the absence of a clear definition of the role of GRPs in plant cells, studies conducted with these proteins have provided new and interesting insights into the molecular biology and cell biology of plants. Complexly regulated promoters and distinct mechanisms for the regulation of gene expression have been demonstrated and new protein targeting pathways, as well as the exportation of GRPs from different cell types have been discovered. These data show that GRPs can be useful as markers and/or models to understand distinct aspects of plant biology. In this paper, the structural and functional features of these proteins in sugarcane (Saccharum officinarum L. are summarized. Since this is the first description of GRPs in sugarcane, special emphasis has been given to the expression pattern of these GRP genes by studying their abundance and prevalence in the different cDNA-libraries of the Sugarcane Expressed Sequence Tag (SUCEST project . The comparison of sugarcane GRPs with GRPs from other species is also discussed.

Systems biology: the reincarnation of systems theory applied in biology?

Science.gov (United States)

Wolkenhauer, O

2001-09-01

With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

Molecular biology of Plasmodiophora brassicae

DEFF Research Database (Denmark)

Siemens, Johannes; Bulman, Simon; Rehn, Frank

2009-01-01

of several genes have been revealed, and the expression of those genes has been linked to development of clubroot to some extent. In addition, the sequence data have reinforced the inclusion of the plasmodiophorids within the Cercozoa. The recent successes in molecular biology have produced new approaches...

Interpretation of biological and mechanical variations between the Lowry versus Bradford method for protein quantification

OpenAIRE

Tzong-Shi Lu; Szu-Yu Yiao; Kenneth Lim; Roderick V. Jensen; Li-Li Hsiao

2010-01-01

Background: The identification of differences in protein expression resulting from methodical variations is an essential component to the interpretation of true, biologically significant results. Aims: We used the Lowry and Bradford methods- two most commonly used methods for protein quantification, to assess whether differential protein expressions are a result of true biological or methodical variations. Material & Methods: Differential protein expression patterns was assessed by western bl...

Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

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Tung Shu-Yun

2011-04-01

Full Text Available Abstract Background Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as Arabidopsis thaliana do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied. Results Several molecular biology tools were used to isolate flower-specific gene promoters from Oncidium 'Gower Ramsey' (Onc. GR. A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in Onc. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (TI genes (OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable A. thaliana transformation analyses. Conclusions By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.

COURSERA ONLINE COURSE: A PLATFORM FOR ENGLISH TEACHERS’ MEANINGFUL AND VIBRANT PROFESSIONAL DEVELOPMENT

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Arnis Silvia

2015-07-01

Full Text Available This article reports on English teachers‘ attitudes towards a professional development program run by Coursera (coursera.org. These teachers were participants of Foundation of Teaching for Learning 1: Introduction online course. Using a survey case study, the findings reveal that most of the participants perceive the course as a well-organized and effective platform to engage in professional learning. Coursera is an online learning platform offering various courses for teacher educators which are meaningful (closely related to their daily teaching practice and vibrant (involves active collaboration among peer participants to review and assess their projects. Albeit this nature, another finding shows that the participants lament that their institutions do not provide professional development (PD support. In fact, PD programs are not constrained to face-to-face encounters, since it can be designed using online platforms such as Coursera, a massive open online course (MOOC. Accordingly, the contribution of the article is to show how online platforms make meaningful and vibrant teacher professional development (TPD possible. The implication of the study is that school administrators and policy makers should provide support for their teachers to take online PD programs. This professional learning should contribute to the best teaching practice and student learning attainment.

Expression and characterization of recombinant single-chain salmon class I MHC fused with beta2-microglobulin with biological activity

DEFF Research Database (Denmark)

Zhao, Heng; Stet, René J M; Skjødt, Karsten

2008-01-01

Heterodimeric class I major histocompatibility complex (MHC) molecules consist of a putative 45-kDa heavy chain and a 12-kDa beta2-microglobulin (beta2m) light chain. The knowledge about MHC genes in Atlantic salmon accumulated during the last decade has allowed us to generate soluble and stable ...... MHC class I molecules with biological activity. We report here the use of a bacterial expression system to produce the recombinant single-chain MHC molecules based on a specific allele Sasa-UBA*0301. This particular allele was selected because previous work has shown its association...... antibodies were successfully produced against both the MHC class I heavy chain and beta(2)m, and showed binding to the recombinant molecule. The recombinant complex Sasabeta2mUBA*0301 was expressed and isolated; the production was scaled up by adjusting to its optimal conditions. Subsequently......, the recombinant proteins were purified by affinity chromatography using mAb against beta2m and alpha3. Eluates were analyzed by Western blot and refolded by the removal of denaturant. The correct folding was confirmed by measuring its binding capacity against mAb produced to recognize the native form of MHC...

Using Cluster Analysis to Characterize Meaningful Learning in a First-Year University Chemistry Laboratory Course

Science.gov (United States)

Galloway, Kelli R.; Bretz, Stacey Lowery

2015-01-01

The Meaningful Learning in the Laboratory Instrument (MLLI) was designed to measure students' cognitive and affective learning in the university chemistry laboratory. The MLLI was administered at the beginning and the end of the first semester to first-year university chemistry students to measure their expectations and experiences for learning in…

75 FR 28331 - Meaningful Access to United States Currency for Blind and Visually Impaired Persons

Science.gov (United States)

2010-05-20

... feature is used in some foreign currency, and the Study's data indicated that this feature was more... Currency for Blind and Visually Impaired Persons AGENCY: Bureau of Engraving and Printing, Department of... meaningful access to U.S. currency to people who are blind and visually impaired pursuant to section 504 of...

The Search for Meaningful E-Learning at Canadian Universities: A Multi-Institutional Research Study

Science.gov (United States)

Salyers, Vincent; Carter, Lorraine; Carter, Alanna; Myers, Sue; Barrett, Penelope

2014-01-01

While e-learning is now characterized by a past and trends within that past, there continues to be uncertainty about how e-learning is defined and conceptualized, whether or not we like e-learning, and whether or not it is as meaningful to us as face to face learning. The purpose of this study was to document the e-learning perceptions of students…

Taking a leap of faith: Meaningful participation of people with experiences of homelessness in solutions to address homelessness

Directory of Open Access Journals (Sweden)

Trudy Laura Norman

2015-12-01

Full Text Available Participation of people with experiences of homelessness is critical to the development of meaningful strategies to end homelessness. The purpose of this study was to gain insights from people who have been homeless in a mid-sized Canadian city, as to strategies that facilitate meaningful participation in solutions to end homelessness. Within an overarching framework of collaborative research, we collected data through seven focus groups and employed interpretive description as our approach to data analysis. In our analysis, we identified both exclusionary and inclusionary forces that impact participation. Exclusionary forces included being ‘caught in the homelessness industry’, ‘homelessness is a full time job’ and facing stigma/discrimination that make participation a ‘leap of faith’. Inclusionary forces included earning respect and building trust to address unequal power relations, and restoring often ‘taken for granted’ social relations. Specific strategies to enhance participation include listening, valuing skills and stories, and supporting advocacy efforts. The study findings illuminate ways in which power imbalances are lived out in the daily lives of people who experience homelessness, as well as mitigating forces that provide direction as to strategies for addressing power inequities that seek to make participation and social inclusion meaningful. Keywords: homelessness, social policy, social exclusion, social inclusion, advocacy

Expression of biologically active human interferon alpha 2 in aloe vera

Science.gov (United States)

We have developed a system for transgenic expression of proteins in Aloe Vera. Using this approach we have generated plants expressing the human gene interferon alpha 2, IFNa2. IFNa2 is a small secreted cytokine that plays a vital role in regulating the body’s immune response to viral infections a...

Construction of a high-EGFR expression cell line and its biological ...

African Journals Online (AJOL)

Targeted screening of EGFR compounds has become one of the medical research focuses for tumor therapy. A431, which naturally expresses high levels of EGFR, was compared with the stably high expressing EGFR cell line HEK293. Flow cytometry was used to analyze cell growth and Western blot was used to ...

Using PCR to Target Misconceptions about Gene Expression

Directory of Open Access Journals (Sweden)

Leslie K. Wright

2013-02-01

Full Text Available We present a PCR-based laboratory exercise that can be used with first- or second-year biology students to help overcome common misconceptions about gene expression. Biology students typically do not have a clear understanding of the difference between genes (DNA and gene expression (mRNA/protein and often believe that genes exist in an organism or cell only when they are expressed. This laboratory exercise allows students to carry out a PCR-based experiment designed to challenge their misunderstanding of the difference between genes and gene expression. Students first transform E. coli with an inducible GFP gene containing plasmid and observe induced and un-induced colonies. The following exercise creates cognitive dissonance when actual PCR results contradict their initial (incorrect predictions of the presence of the GFP gene in transformed cells. Field testing of this laboratory exercise resulted in learning gains on both knowledge and application questions on concepts related to genes and gene expression.

Qualitative Insights from a Canadian Multi-Institutional Research Study: In Search of Meaningful E-Learning

Science.gov (United States)

Carter, Lorraine M.; Salyers, Vince; Myers, Sue; Hipfner, Carol; Hoffart, Caroline; MacLean, Christa; White, Kathy; Matus, Theresa; Forssman, Vivian; Barrett, Penelope

2014-01-01

This paper reports the qualitative findings of a mixed methods research study conducted at three Canadian post-secondary institutions. Called the Meaningful E-learning or MEL project, the study was an exploration of the teaching and learning experiences of faculty and students as well as their perceptions of the benefits and challenges of…

The Relationship Between Magnet Designation, Electronic Health Record Adoption, and Medicare Meaningful Use Payments.

Science.gov (United States)

Lippincott, Christine; Foronda, Cynthia; Zdanowicz, Martin; McCabe, Brian E; Ambrosia, Todd

2017-08-01

The objective of this study was to examine the relationship between nursing excellence and electronic health record adoption. Of 6582 US hospitals, 4939 were eligible for the Medicare Electronic Health Record Incentive Program, and 6419 were eligible for evaluation on the HIMSS Analytics Electronic Medical Record Adoption Model. Of 399 Magnet hospitals, 330 were eligible for the Medicare Electronic Health Record Incentive Program, and 393 were eligible for evaluation in the HIMSS Analytics Electronic Medical Record Adoption Model. Meaningful use attestation was defined as receipt of a Medicare Electronic Health Record Incentive Program payment. The adoption electronic health record was defined as Level 6 and/or 7 on the HIMSS Analytics Electronic Medical Record Adoption Model. Logistic regression showed that Magnet-designated hospitals were more likely attest to Meaningful Use than non-Magnet hospitals (odds ratio = 3.58, P electronic health records than non-Magnet hospitals (Level 6 only: odds ratio = 3.68, P electronic health record use, which involves earning financial incentives for successful adoption. Continued investigation is needed to examine the relationships between the quality of nursing care, electronic health record usage, financial implications, and patient outcomes.

Linking job-relevant personality traits, transformational leadership, and job performance via perceived meaningfulness at work: A moderated mediation model.

Science.gov (United States)

Frieder, Rachel E; Wang, Gang; Oh, In-Sue

2018-03-01

By integrating the fundamental principles of the theory of purposeful work behavior (TPWB; Barrick, Mount, & Li, 2013) with cognitive-affective personality system (CAPS) theory (Mischel, 1977; Mischel & Shoda, 1995), we examine how and when salespeople's job-relevant personality traits relate to their performance. We argue that individuals with personality traits that fit outdoor sales jobs (i.e., conscientious, extraversion, openness to experience) will perceive their work as more meaningful and as a result achieve heightened performance. Moreover, drawing from TPWB and CAPS theory, we expect that as an important element of the social context, transformational leadership moderates the indirect effect of salespeople's job-relevant personality traits on their job performance via enhanced perceptions of meaningfulness at work. Results based on data from 496 outdoor salespeople and their 218 supervisors and regional managers provide support for the hypotheses pertaining to conscientiousness and openness, but not extraversion. Specifically, the conditional indirect effects of conscientiousness or openness on performance through perceived meaningfulness are more positive under low, rather than high, levels of transformational leadership. Implications for research and practice are discussed along with study limitations and future research directions. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Agent-based modelling in synthetic biology.

Science.gov (United States)

Gorochowski, Thomas E

2016-11-30

Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. © 2016 The Author(s).

Action video game players' visual search advantage extends to biologically relevant stimuli.

Science.gov (United States)

Chisholm, Joseph D; Kingstone, Alan

2015-07-01

Research investigating the effects of action video game experience on cognition has demonstrated a host of performance improvements on a variety of basic tasks. Given the prevailing evidence that these benefits result from efficient control of attentional processes, there has been growing interest in using action video games as a general tool to enhance everyday attentional control. However, to date, there is little evidence indicating that the benefits of action video game playing scale up to complex settings with socially meaningful stimuli - one of the fundamental components of our natural environment. The present experiment compared action video game player (AVGP) and non-video game player (NVGP) performance on an oculomotor capture task that presented participants with face stimuli. In addition, the expression of a distractor face was manipulated to assess if action video game experience modulated the effect of emotion. Results indicate that AVGPs experience less oculomotor capture than NVGPs; an effect that was not influenced by the emotional content depicted by distractor faces. It is noteworthy that this AVGP advantage emerged despite participants being unaware that the investigation had to do with video game playing, and participants being equivalent in their motivation and treatment of the task as a game. The results align with the notion that action video game experience is associated with superior attentional and oculomotor control, and provides evidence that these benefits can generalize to more complex and biologically relevant stimuli. Copyright © 2015 Elsevier B.V. All rights reserved.

Using gene expression noise to understand gene regulation

NARCIS (Netherlands)

Munsky, B.; Neuert, G.; van Oudenaarden, A.

2012-01-01

Phenotypic variation is ubiquitous in biology and is often traceable to underlying genetic and environmental variation. However, even genetically identical cells in identical environments display variable phenotypes. Stochastic gene expression, or gene expression "noise," has been suggested as a

Impact of Instructor Expressiveness and some Students' Personal ...

African Journals Online (AJOL)

This study investigated the effects of Instructor Expressiveness (a teaching behaviour), Students' Locus of Control (LOC), gender and cognitive entry behaviour (CEB) on secondary school students' attitude towards biology. After determining the LOC, CEB, gender and attitude towards biology of the study sample, the ...

Age by Disease Biological Interactions: Implications for Late-Life Depression

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Brandon eMcKinney

2012-11-01

Full Text Available Onset of depressive symptoms after the age of 65, or late-life depression (LLD, is common and poses a significant burden on affected individuals, caretakers and society. Evidence suggests a unique biological basis for LLD, but current hypotheses do not account for its pathophysiological complexity. Here we propose a novel etiological framework for LLD, the age-by-disease biological interaction hypothesis, based on the observations that the subset of genes that undergoes lifelong progressive changes in expression is restricted to a specific set of biological processes, and that a disproportionate number of these age-dependent genes have been previously and similarly implicated in neurodegenerative and neuropsychiatric disorders, including depression. The age-by-disease biological interaction hypothesis posits that age-dependent biological processes (i are pushed in LLD-promoting directions by changes in gene expression naturally occurring during brain aging, which (ii directly contribute to pathophysiological mechanisms of LLD, and (iii that individual variability in rates of age-dependent changes determines risk or resiliency to develop age-related disorders, including LLD. We review observations supporting this hypothesis, including consistent and specific age-dependent changes in brain gene expression, and their overlap with neuropsychiatric and neurodegenerative disease pathways. We then review preliminary reports supporting the genetic component of this hypothesis. Other potential biological mediators of age-dependent gene changes are proposed. We speculate that studies examining the relative contribution of these mechanisms to age-dependent changes and related disease mechanisms will not only provide critical information on the biology of normal aging of the human brain, but will inform our understanding our age-dependent diseases, in time fostering the development of new interventions for prevention and treatment of age-dependent diseases

Molecular biology approaches in bioadhesion research

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Marcelo Rodrigues

2014-07-01

Full Text Available The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1 generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2 setting up a BLAST search facility, (3 perform an in situ hybridization screen, and (4 functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.

Establishing meaningful cut points for online user ratings.

Science.gov (United States)

Hirschfeld, Gerrit; Thielsch, Meinald T

2015-01-01

Subjective perceptions of websites can be reliably measured with questionnaires. But it is unclear how such scores should be interpreted in practice, e.g. is an aesthetics score of 4 points on a seven-point-scale satisfactory? The current paper introduces a receiver-operating characteristic (ROC)-based methodology to establish meaningful cut points for the VisAWI (visual aesthetics of websites inventory) and its short form the VisAWI-S. In two studies we use users' global ratings (UGRs) and website rankings as anchors. A total of 972 participants took part in the studies which yielded similar results. First, one-item UGRs correlate highly with the VisAWI. Second, cut points on the VisAWI reliably differentiate between sites that are perceived as attractive versus unattractive. Third, these cut points are variable, but only within a certain range. Together the research presented here establishes a score of 4.5 on the VisAWI which is a reasonable goal for website designers and highlights the utility of the ROC methodology to derive relevant scores for rating scales.

Possibilities of creating meaningful encounters in anesthesia nursing

DEFF Research Database (Denmark)

Aagaard, Karin

Anesthesia nursing is performed in a highly technological environment with restricted time for interaction with patients. Patients are in a vulnerable position, which can be characterized by anxiety regarding the anesthetic and surgical procedure. The bedrock of effective nursing care is to facil......Anesthesia nursing is performed in a highly technological environment with restricted time for interaction with patients. Patients are in a vulnerable position, which can be characterized by anxiety regarding the anesthetic and surgical procedure. The bedrock of effective nursing care...... of nursing. In this dissertation, focused ethnography is used to explore the interactions between patients and nurse anesthetists before general anesthesia. Moreover, it will explore the professional identity of nurse anesthetists, in relation to the situation of preparing patients for general anesthesia....... A micro-substantive theory is developed regarding the opportunities for creating meaningful encounters between patients and nurse anesthetists. The theory is based on three dominant motivations for interaction in anesthesia nursing. The context of care is not committed and responsive to the core elements...

Modeling LIDAR Detection of Biological Aerosols to Determine Optimum Implementation Strategy

Energy Technology Data Exchange (ETDEWEB)

Sheen, David M.; Aker, Pam M.

2007-09-19

This report summarizes work performed for a larger multi-laboratory project named the Background Interferent Measurement and Standards project. While originally tasked to develop algorithms to optimize biological warfare agent detection using UV fluorescence LIDAR, the current uncertainties in the reported fluorescence profiles and cross sections the development of any meaningful models. It was decided that a better approach would be to model the wavelength-dependent elastic backscattering from a number of ambient background aerosol types, and compare this with that generated from representative sporulated and vegetative bacterial systems. Calculations in this report show that a 266, 355, 532 and 1064 nm elastic backscatter LIDAR experiment will allow an operator to immediately recognize when sulfate, VOC-based or road dust (silicate) aerosols are approaching, independent of humidity changes. It will be more difficult to distinguish soot aerosols from biological aerosols, or vegetative bacteria from sporulated bacteria. In these latter cases, the elastic scattering data will most likely have to be combined with UV fluorescence data to enable a more robust categorization.

Visual attention to meaningful stimuli by 1- to 3-year olds: implications for the measurement of memory.

Science.gov (United States)

Hayne, Harlene; Jaeger, Katja; Sonne, Trine; Gross, Julien

2016-11-01

The visual recognition memory (VRM) paradigm has been widely used to measure memory during infancy and early childhood; it has also been used to study memory in human and nonhuman adults. Typically, participants are familiarized with stimuli that have no special significance to them. Under these conditions, greater attention to the novel stimulus during the test (i.e., novelty preference) is used as the primary index of memory. Here, we took a novel approach to the VRM paradigm and tested 1-, 2-, and 3-year olds using photos of meaningful stimuli that were drawn from the participants' own environment (e.g., photos of their mother, father, siblings, house). We also compared their performance to that of participants of the same age who were tested in an explicit pointing version of the VRM task. Two- and 3-year olds exhibited a strong familiarity preference for some, but not all, of the meaningful stimuli; 1-year olds did not. At no age did participants exhibit the kind of novelty preference that is commonly used to define memory in the VRM task. Furthermore, when compared to pointing, looking measures provided a rough approximation of recognition memory, but in some instances, the looking measure underestimated retention. The use of meaningful stimuli raise important questions about the way in which visual attention is interpreted in the VRM paradigm, and may provide new opportunities to measure memory during infancy and early childhood. © 2016 Wiley Periodicals, Inc.

Meaningful experiences in science education: Engaging the space researcher in a cultural transformation to greater science literacy

Science.gov (United States)

Morrow, Cherilynn A.

1993-01-01

The visceral appeal of space science and exploration is a very powerful emotional connection to a very large and diverse collection of people, most of whom have little or no perspective about what it means to do science and engineering. Therein lies the potential of space for a substantially enhanced positive impact on culture through education. This essay suggests that through engaging more of the space research and development community in enabling unique and 'meaningful educational experiences' for educators and students at the pre-collegiate levels, space science and exploration can amplify its positive feedback on society and act as an important medium for cultural transformation to greater science literacy. I discuss the impact of space achievements on people and define what is meant by a 'meaningful educational experience,' all of which points to the need for educators and students to be closer to the practice of real science. I offer descriptions of two nascent science education programs associated with NASA which have the needed characteristics for providing meaningful experiences that can cultivate greater science literacy. Expansion of these efforts and others like it will be needed to have the desired impact on culture, but I suggest that the potential for the needed resources is there in the scientific research communities. A society in which more people appreciate and understand science and science methods would be especially conducive to human progress in space and on Earth.

School nurse evaluations: making the process meaningful and motivational.

Science.gov (United States)

McDaniel, Kathryn H; Overman, Muriel; Guttu, Martha; Engelke, Martha Keehner

2013-02-01

The professional standards of school nursing practice provide a framework to help school nurses focus on their unique mission of promoting health and academic achievement for all students. Without the standards, the nurse's role can become task oriented and limited in scope. By using an evaluation tool that reflects the standards, nurses not only become aware and begin to understand the standards; they also become directly accountable for meeting them. In addition, developing an evaluation process based on the standards of school nurse practice increases the visibility of school nurses and helps school administrators understand the role of the school nurse. This article describes how one school district integrated the scope and standards of school nursing into the job description and performance evaluation of the nurse. The process which is used to complete the evaluation in a manner that is meaningful and motivational to the school nurse is described.

A Systems’ Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks

Directory of Open Access Journals (Sweden)

Xin Lai

2013-01-01

Full Text Available MicroRNAs (miRNAs are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. To demonstrate the application of this approach, we adopt it to investigate mechanisms of collective repression on p21 by multiple miRNAs. We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts.

Unified Modeling of Filtration and Expression of Biological Sludge