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Sample records for biologically meaningful expression

  1. An integrative approach to inferring biologically meaningful gene modules

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    Wang Kai

    2011-07-01

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

  2. Behavioral meaningful opioidergic stimulation activates kappa receptor gene expression

    International Nuclear Information System (INIS)

    Teodorov, E.; Ferrari, M.F.R.; Fior-Chadi, D.R.; Camarini, R.; Felício, L.F.

    2012-01-01

    The periaqueductal gray (PAG) has been reported to be a location for opioid regulation of pain and a potential site for behavioral selection in females. Opioid-mediated behavioral and physiological responses differ according to the activity of opioid receptor subtypes. The present study investigated the effects of the peripheral injection of the kappa-opioid receptor agonist U69593 into the dorsal subcutaneous region of animals on maternal behavior and on Oprk1 gene activity in the PAG of female rats. Female Wistar rats weighing 200-250 g at the beginning of the study were randomly divided into 2 groups for maternal behavior and gene expression experiments. On day 5, pups were removed at 7:00 am and placed in another home cage that was distant from their mother. Thirty minutes after removing the pups, the dams were treated with U69593 (0.15 mg/kg, sc) or 0.9% saline (up to 1 mL/kg) and after 30 min were evaluated in the maternal behavior test. Latencies in seconds for pup retrieval, grouping, crouching, and full maternal behavior were scored. The results showed that U69593 administration inhibited maternal behavior (P < 0.05) because a lower percentage of U69593 group dams showed retrieval of first pup, retrieving all pups, grouping, crouching and displaying full maternal behavior compared to the saline group. Opioid gene expression was evaluated using real-time reverse-transcription polymerase chain reaction (RT-PCR). A single injection of U69593 increased Oprk1 PAG expression in both virgin (P < 0.05) and lactating female rats (P < 0.01), with no significant effect on Oprm1 or Oprd1 gene activity. Thus, the expression of kappa-opioid receptors in the PAG may be modulated by single opioid receptor stimulation and behavioral meaningful opioidergic transmission in the adult female might occur simultaneously to specific changes in gene expression of kappa-opioid receptor subtype. This is yet another alert for the complex role of the opioid system in female

  3. Behavioral meaningful opioidergic stimulation activates kappa receptor gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Teodorov, E. [Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Paulo, SP (Brazil); Ferrari, M.F.R. [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil); Fior-Chadi, D.R. [Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil); Camarini, R. [Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP (Brazil); Felício, L.F. [Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP (Brazil)

    2012-06-01

    The periaqueductal gray (PAG) has been reported to be a location for opioid regulation of pain and a potential site for behavioral selection in females. Opioid-mediated behavioral and physiological responses differ according to the activity of opioid receptor subtypes. The present study investigated the effects of the peripheral injection of the kappa-opioid receptor agonist U69593 into the dorsal subcutaneous region of animals on maternal behavior and on Oprk1 gene activity in the PAG of female rats. Female Wistar rats weighing 200-250 g at the beginning of the study were randomly divided into 2 groups for maternal behavior and gene expression experiments. On day 5, pups were removed at 7:00 am and placed in another home cage that was distant from their mother. Thirty minutes after removing the pups, the dams were treated with U69593 (0.15 mg/kg, sc) or 0.9% saline (up to 1 mL/kg) and after 30 min were evaluated in the maternal behavior test. Latencies in seconds for pup retrieval, grouping, crouching, and full maternal behavior were scored. The results showed that U69593 administration inhibited maternal behavior (P < 0.05) because a lower percentage of U69593 group dams showed retrieval of first pup, retrieving all pups, grouping, crouching and displaying full maternal behavior compared to the saline group. Opioid gene expression was evaluated using real-time reverse-transcription polymerase chain reaction (RT-PCR). A single injection of U69593 increased Oprk1 PAG expression in both virgin (P < 0.05) and lactating female rats (P < 0.01), with no significant effect on Oprm1 or Oprd1 gene activity. Thus, the expression of kappa-opioid receptors in the PAG may be modulated by single opioid receptor stimulation and behavioral meaningful opioidergic transmission in the adult female might occur simultaneously to specific changes in gene expression of kappa-opioid receptor subtype. This is yet another alert for the complex role of the opioid system in female

  4. Behavioral meaningful opioidergic stimulation activates kappa receptor gene expression

    Directory of Open Access Journals (Sweden)

    E. Teodorov

    2012-10-01

    Full Text Available The periaqueductal gray (PAG has been reported to be a location for opioid regulation of pain and a potential site for behavioral selection in females. Opioid-mediated behavioral and physiological responses differ according to the activity of opioid receptor subtypes. The present study investigated the effects of the peripheral injection of the kappa-opioid receptor agonist U69593 into the dorsal subcutaneous region of animals on maternal behavior and on Oprk1 gene activity in the PAG of female rats. Female Wistar rats weighing 200-250 g at the beginning of the study were randomly divided into 2 groups for maternal behavior and gene expression experiments. On day 5, pups were removed at 7:00 am and placed in another home cage that was distant from their mother. Thirty minutes after removing the pups, the dams were treated with U69593 (0.15 mg/kg, sc or 0.9% saline (up to 1 mL/kg and after 30 min were evaluated in the maternal behavior test. Latencies in seconds for pup retrieval, grouping, crouching, and full maternal behavior were scored. The results showed that U69593 administration inhibited maternal behavior (P < 0.05 because a lower percentage of kappa group dams showed retrieval of first pup, retrieving all pups, grouping, crouching and displaying full maternal behavior compared to the saline group. Opioid gene expression was evaluated using real-time reverse-transcription polymerase chain reaction (RT-PCR. A single injection of U69593 increased Oprk1 PAG expression in both virgin (P < 0.05 and lactating female rats (P < 0.01, with no significant effect on Oprm1 or Oprd1 gene activity. Thus, the expression of kappa-opioid receptors in the PAG may be modulated by single opioid receptor stimulation and behavioral meaningful opioidergic transmission in the adult female might occur simultaneously to specific changes in gene expression of kappa-opioid receptor subtype. This is yet another alert for the complex role of the opioid system in

  5. Novel study guides for biochemistry meaningful learning in biology: a design-based research

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    Caetano da Costa

    2017-12-01

    Full Text Available To address the usually decontextualized transmission of information in biochemistry teaching, three interventions in a discipline (Metabolism for Biology majors were applied as innovative study guides. We describe the development, application, and evaluation of two study guides, contextualized with a real problem or an integrative view, using broad themes like evolution and metabolic adaptation. In order to evaluate the impact of both interventions on interest, motivation, and learning of the metabolic pathways, 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. Analysis and interpretation of the results point to benefits for teaching and learning, with helpful information to guide elaboration and refinement of new teaching materials and to make active learning more meaningful.

  6. Identifying biologically meaningful hot-weather events using threshold temperatures that affect life-history.

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    Susan J Cunningham

    Full Text Available Increases in the frequency, duration and intensity of heat waves are frequently evoked in climate change predictions. However, there is no universal definition of a heat wave. Recent, intense hot weather events have caused mass mortalities of birds, bats and even humans, making the definition and prediction of heat wave events that have the potential to impact populations of different species an urgent priority. One possible technique for defining biologically meaningful heat waves is to use threshold temperatures (T(thresh above which known fitness costs are incurred by species of interest. We set out to test the utility of this technique using T(thresh values that, when exceeded, affect aspects of the fitness of two focal southern African bird species: the southern pied babbler Turdiodes bicolor (T(thresh = 35.5 °C and the common fiscal Lanius collaris (T(thresh = 33 °C. We used these T(thresh values to analyse trends in the frequency, duration and intensity of heat waves of magnitude relevant to the focal species, as well as the annual number of hot days (maximum air temperature > T(thresh, in north-western South Africa between 1961 and 2010. Using this technique, we were able to show that, while all heat wave indices increased during the study period, most rapid increases for both species were in the annual number of hot days and in the maximum intensity (and therefore intensity variance of biologically meaningful heat waves. Importantly, we also showed that warming trends were not uniform across the study area and that geographical patterns in warming allowed both areas of high risk and potential climate refugia to be identified. We discuss the implications of the trends we found for our focal species, and the utility of the T(thresh technique as a conservation tool.

  7. 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

  8. 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

  9. Science literacy and meaningful learning: status of public high school students from Rio de Janeiro face to molecular biology concepts

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    Daniel Alves Escodino

    2013-12-01

    Full Text Available In this work we aimed to determine the level of Molecular Biology (MB science literacy of students from two Brazilian public schools which do not consider the rogerian theory for class planning and from another institution, Cap UERJ, which favours this theory. We applied semiclosed questionnaires specific to the different groups of science literacy levels. Besides, we have asked them to perform conceptual maps with MB concepts in order to observe if they have experienced meaningful learning. Finally, we prepared MB classes for students of the three schools, considering their conceptual maps and tried to evaluate, through a second map execution, if the use of alternative didactics material, which consider meaningful learning process, would have any effect over the appropriation of new concepts. We observed that most students are placed at Functional literacy level. Nonetheless, several students from CAp were also settled at the higher Conceptual and Procedural levels. We found that most students have not experienced meaningful learning and that the employment of didactic material and implementation of proposals which consider the cognitive structure of the students had a significant effect on the appropriation of several concepts.

  10. 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

  11. 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

  12. 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…

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

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

    2009-02-01

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

  14. 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…

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

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    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.

  16. 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…

  17. 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

    2016-10-01

    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.

  18. 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 ...

  19. Interactive analysis of systems biology molecular expression data

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    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  20. El cuerpo: silencioso pero significativo en expresión O corpo: silencioso mas significativo em expressão The body: silent but meaningful in expression

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    Martha Cecilia Madrigal Ramírez

    2011-07-01

    Full Text Available Investigación en salas de espera de servicios de urgencias de la ciudad de Medellín, Colombia. Objetivo: identificar las maneras en que las personas expresan sus emociones durante la espera en los servicios de urgencias. Metodología: enfoque cualitativo, con herramientas de la etnografía focalizada; se realizaron 50 horas de observación. Análisis a partir de diarios de campo y entrevistas; se extractaron códigos que se agruparon en categorías para obtener una visión total del fenómeno; se garantizó la confidencialidad. Resultados y discusión: las salas de espera de los servicios de urgencias son espacios impersonales que limitan la comunicación y el acompañamiento entre las personas, y hacen que se generen diferentes estados emocionales que se expresan a través del cuerpo. Se suscitan conversaciones con extraños, movimientos, miradas y gestos con diferentes significados. Reflexión: el conocimiento de las diferentes formas de expresión de las experiencias emocionales de los pacientes y sus familias permite implementar, en las instituciones de salud, mecanismos para favorecer la comunicación asertiva entre usuarios y personal de salud, para la toma de decisiones oportunas y adecuadas a cada situación, de manera que la atención de urgencias sea un proceso humanizado.Pesquisa feita nas salas de espera dos serviços de emergência da cidade de Medellín, Colómbia. Objetivo: Identificar as formas de expressão das emoções pessoais durante a espera nos serviços de emergência. Metodologia: Abordagem qualitativa, com instrumentos saídos da etnografia focalizada. Foram realizadas 50 horas de observações. Analisaramse os diários de campo e entrevistas, e códigos foram extraídos e foram agrupados em categorias para obter uma visão global do fenómeno; garantindo sempre a confidencialidade. Resultados e discussão: as salas de espera dos serviços de emergência são espaços impessoais que limitam a comunicação e isolam as

  1. 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.

  2. Students' Meaningful Learning Orientation and Their Meaningful Understandings of Meiosis and Genetics.

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    Cavallo, Ann Liberatore

    This 1-week study explored the extent to which high school students (n=140) acquired meaningful understanding of selected biological topics (meiosis and the Punnett square method) and the relationship between these topics. This study: (1) examined "mental modeling" as a technique for measuring students' meaningful understanding of the…

  3. Psychological context of work meaningfulness

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    Karel Paulík

    2014-12-01

    Full Text Available There is a significant shift of approach to the management of organizations and workers in recent decades. This shift in management philosophy is characterized by converting from traditional, conventional (rather bureaucratic management models to rather humanistic/existential oriented models. This transition comes partly from the understanding that human resources are the most promising and effective way for organization development, partly from a shift in the understanding of the role of organizations in society. The key point of these approaches has become a "meaning" or "meaningfulness" in relation to the work and organization. The importance of work meaningfulness is not only in its potential to increase the competitiveness of organizations, but especially in its major (mostly positive impacts on the employee himself and his work (and by that the organization and its performance. Work meaningfulness is strongly connected to the work engagement, which represents the active personal participation in the work process, manifested by vigor, active cooperation, willingness to contribute to the company's success and dedication to work. Work engagement seems to be next important factor affecting work attitudes and achievements of employees. The paper gives an overview of various approaches to work meaningfulness and work engagement, on the basis of which authors propose new model of work meaningfulness with overlap to work engagement. The work meaningfulness is not seen as one-dimensional variable, but consists of complex of interacting factors and processes that define an individual perceived meaning and importance of the work. Meaningful work is influenced by three areas. The first is the organizational culture. This is defined as a specific pattern of values, norms, beliefs, attitudes and assumptions that are often not clearly expressed, but affect the way individuals behave in an organization and how things are done. The second area is the work

  4. The Retention of Meaningful Understanding of Meiosis and Genetics.

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    Cavallo, Ann Liberatore

    This study investigated the retention of meaningful understanding of the biological topics of meiosis, the Punnett square method and the relations between these two topics. This study also explored the predictive influence of students' general tendency to learn meaningfully or by rote (meaningful learning orientation), prior knowledge of meiosis,…

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

    Directory of Open Access Journals (Sweden)

    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.

  6. Meaningful and Purposeful Practice

    Science.gov (United States)

    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…

  7. 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

  8. Life is pretty meaningful.

    Science.gov (United States)

    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.

  9. An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks.

    Science.gov (United States)

    Botía, Juan A; Vandrovcova, Jana; Forabosco, Paola; Guelfi, Sebastian; D'Sa, Karishma; Hardy, John; Lewis, Cathryn M; Ryten, Mina; Weale, Michael E

    2017-04-12

    Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of clusters of genes (modules). We propose k-means clustering as an additional processing step to conventional WGCNA, which we have implemented in the R package km2gcn (k-means to gene co-expression network, https://github.com/juanbot/km2gcn ). We assessed our method on networks created from UKBEC data (10 different human brain tissues), on networks created from GTEx data (42 human tissues, including 13 brain tissues), and on simulated networks derived from GTEx data. We observed substantially improved module properties, including: (1) few or zero misplaced genes; (2) increased counts of replicable clusters in alternate tissues (x3.1 on average); (3) improved enrichment of Gene Ontology terms (seen in 48/52 GCNs) (4) improved cell type enrichment signals (seen in 21/23 brain GCNs); and (5) more accurate partitions in simulated data according to a range of similarity indices. The results obtained from our investigations indicate that our k-means method, applied as an adjunct to standard WGCNA, results in better network partitions. These improved partitions enable more fruitful downstream analyses, as gene modules are more biologically meaningful.

  10. Beyond meaningful use: getting meaningful value from IT.

    Science.gov (United States)

    Fortin, Jason; Zywiak, Walt

    2010-02-01

    The HITECH provisions of ARRA include financial incentives for providers to demonstrate meaningful use of certified EHR technology. However, to maximize the value of IT under new payment models, provider organizations will need to go beyond meaningful use criteria in three key areas: Delivering high-quality care. Ensuring coordinated care. Integrating financial systems.

  11. Expression Patterns and Potential Biological Roles of Dip2a.

    Directory of Open Access Journals (Sweden)

    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.

  12. Integration of biological networks and gene expression data using Cytoscape

    DEFF Research Database (Denmark)

    Cline, M.S.; Smoot, M.; Cerami, E.

    2007-01-01

    of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules......Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context...... and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape....

  13. Research on prokaryocyte expression and biological activity of the ...

    African Journals Online (AJOL)

    Furthermore, the ATPase activity of the protein was also assayed using ultraviolet spectrophotometry based on PiColorLock Gold reagent. An effective expression method was established for BLM protein in E. coli. The obvious bioactivities of the protein were observed in binding to ssDNA or dsDNA, unwinding the dsDNA in ...

  14. Unified Modeling of Filtration and Expression of Biological Sludge

    DEFF Research Database (Denmark)

    Sørensen, Peter Borgen

    Dewatering is a costly operation in both industry, e.g . when dewatering drilling mud, harbor sludge or biomass, and at municipal wastewater treatment plants when dewatering biological sludges. In practice, design and operation of dewatering equipment are mostly based on empirical knowledge, and ......, and normally results are not satisfactory, e.g. in terms of cake solids or capacity of equipment. Thus, there is a need for theoretical and technical developments to improve dewatering performance, based on better scientific knowledge and well defined principles and rules....

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  18. 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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. 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....

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. 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.

  5. 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.

    2014-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  8. Water Habitat Study: Prediction Makes It More Meaningful.

    Science.gov (United States)

    Glasgow, Dennis R.

    1982-01-01

    Suggests a teaching strategy for water habitat studies to help students make a meaningful connection between physiochemical data (dissolved oxygen content, pH, and water temperature) and biological specimens they collect. Involves constructing a poster and using it to make predictions. Provides sample poster. (DC)

  9. Towards a mathematical theory of meaningful communication

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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

  16. 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

  17. Motivational reading on education, meaningful reading realisation

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. 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)

  2. Extracting biologically significant patterns from short time series gene expression data

    Directory of Open Access Journals (Sweden)

    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/.

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

    Science.gov (United States)

    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.

  4. 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...

  5. 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.

  6. 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.

  7. 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

  8. 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...

  9. 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...

  10. 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...

  11. 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

  12. 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.

  13. 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

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. 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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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

  20. Reflections on Meaningfulness and its Social Relevance

    Directory of Open Access Journals (Sweden)

    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.

  1. 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.

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

    Science.gov (United States)

    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/.

  3. 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.

  4. 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 ...

  5. 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)

  6. Meaningful work, work engagement and organisational commitment

    Directory of Open Access Journals (Sweden)

    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.

  7. 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

  8. Nonparametric testing for DNA copy number induced differential mRNA gene expression

    NARCIS (Netherlands)

    van Wieringen, W.N.; van de Wiel, M.A.

    2009-01-01

    The central dogma of molecular biology relates DNA with mRNA. Array CGH measures DNA copy number and gene expression microarrays measure the amount of mRNA. Methods that integrate data from these two platforms may uncover meaningful biological relationships that further our understanding of cancer.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. 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...

  11. Heterologous Expression and Delivery of Biologically Active Exendin-4 by Lactobacillus paracasei L14.

    Directory of Open Access Journals (Sweden)

    Zhu Zeng

    Full Text Available Exendin-4, a glucagon-like protein-1 (GLP-1 receptor agonist, is an excellent therapeutic peptide drug for type 2 diabetes due to longer lasting biological activity compared to GLP-1. This study explored the feasibility of using probiotic Lactobacillus paracasei as an oral vector for recombinant exendin-4 peptide delivery, an alternative to costly chemical synthesis and inconvenient administration by injection. L. paracasei transformed with a plasmid encoding the exendin-4 gene (L. paracasei L14/pMG76e-exendin-4 with a constitutive promotor was successfully constructed and showed efficient secretion of exendin-4. The secreted exendin-4 significantly enhanced insulin secretion of INS-1 β-cells, along with an increment in their proliferation and inhibition of their apoptosis, corresponding to the effect of GLP-1 on these cells. The transcription level of the pancreatic duodenal homeobox-1 gene (PDX-1, a key transcription factor for cellular insulin synthesis and secretion, was upregulated by the treatment with secreted exendin-4, paralleling the upregulation of insulin gene expression. Caco-2 cell monolayer permeability assay showed a 34-fold increase in the transport of exendin-4 delivered by L. paracasei vs. that of free exendin-4 (control, suggesting effective facilitation of exendin-4 transport across the intestinal barrier by this delivery system. This study demonstrates that the probiotic Lactobacillus can be engineered to secrete bioactive exendin-4 and facilitate its transport through the intestinal barrier, providing a novel strategy for oral exendin-4 delivery using this lactic acid bacterium.

  12. 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 ...

  13. 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 ...

  14. Meaningful Learning in the Cooperative Classroom

    Science.gov (United States)

    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…

  15. Meaningful Use of School Health Data

    Science.gov (United States)

    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.…

  16. 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

  17. 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…

  18. 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...

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

    Science.gov (United States)

    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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

    Science.gov (United States)

    Tsou, Ann-Ping; Sun, Yi-Ming; Liu, Chia-Lin; Huang, Hsien-Da; Horng, Jorng-Tzong; Tsai, Meng-Feng; Liu, Baw-Juine

    2006-07-01

    Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. 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.

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

    Science.gov (United States)

    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.

  10. Design-Based Learning for Biology: Genetic Engineering Experience Improves Understanding of Gene Expression

    Science.gov (United States)

    Ellefson, Michelle R.; Brinker, Rebecca A.; Vernacchio, Vincent J.; Schunn, Christian D.

    2008-01-01

    Gene expression is a difficult topic for students to learn and comprehend, at least partially because it involves various biochemical structures and processes occurring at the microscopic level. Designer Bacteria, a design-based learning (DBL) unit for high-school students, applies principles of DBL to the teaching of gene expression. Throughout…

  11. 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...

  12. 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 ...

  13. 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.

  14. 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.

  15. 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...

  16. Construction of a high-EGFR expression cell line and its biological ...

    African Journals Online (AJOL)

    USER

    2010-07-26

    Jul 26, 2010 ... activator of transcription (STAT) pathways, which regulate cell transformation ... Construction of a EGFR eukaryotic expression vector. The plasmid .... was 4-5 times greater in the Aft-HEK293 cells following transfection. EGFR ...

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

    OpenAIRE

    McLeod, Kenneth; Ferguson, Gus; Burger, Albert

    2012-01-01

    Background 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...

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

    Science.gov (United States)

    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.

  19. Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology.

    Science.gov (United States)

    Blount, Benjamin A; Weenink, Tim; Vasylechko, Serge; Ellis, Tom

    2012-01-01

    Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex "multi-wire" logic functions.

  20. Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology

    Science.gov (United States)

    Blount, Benjamin A.; Weenink, Tim; Vasylechko, Serge; Ellis, Tom

    2012-01-01

    Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex “multi-wire” logic functions. PMID:22442681

  1. 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.

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

    Science.gov (United States)

    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

  3. 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

  4. 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...

  5. The role of CD40 expression in dendritic cells in cancer biology; a systematic review.

    Science.gov (United States)

    Lee, Gui Han; Askari, Alan; Malietzis, George; Bernardo, David; Clark, Susan K; Knight, Stella C; Al-Hassi, Hafid Omar

    2014-01-01

    CD40 is a co-stimulatory molecule belonging to the tumor necrosis factor superfamily and is essential in activation of dendritic cells. Dendritic cells (DCs) are antigen-presenting cells capable of initiating cytotoxic T-lymphocyte immune response against cancer cells. However, there are few studies on the characterization of DCs in cancer, specifically their expression of CD40, despite its implication in cancer immunotherapy. We reviewed available data on the expression of CD40 on DCs in various cancers, and its implications for cancer immunotherapy. A systematic review on CD40 expression on DCs in cancer was performed with reference to preferred reporting items for systematic reviews and meta-analyses (PRISMA). Studies that satisfied the inclusion and exclusion criteria were 21 out of 927. Variations in type and status of the cancers, source of DCs and methodology for detecting CD40 expression amongst the studies resulted in contrasting results. DCs generally expressed low CD40 in tumor infiltrating DCs (tiDCs), in DCs derived by in vitro culture from blood monocytes using cytokine stimulation (MoDCs) and in DCs exposed in vitro to tumor cells lines; the studies suggested that CD40 expression in DCs is impaired in cancer particularly in metastatic disease. However, DCs identified in fresh peripheral blood mononuclear cells (PBMC) expressed higher numbers of CD40 positive cells in some cancer patients, which could be due to tumor-derived factors leading to partially-stimulated DCs. The results provide evidence that some cancer patients may show partial systemic DC activation and expression of increased CD40 in response to the presence of tumor but that such activity may become abortive in the presence of factors produced by the tumor. This review has thus identified key papers on CD40 expression on DCs in various cancers and discusses the limitations and contrasting results of these studies in relation to variations in methodology. The results highlight the need

  6. Molecular biology of breast cancer metastasis Molecular expression of vascular markers by aggressive breast cancer cells

    International Nuclear Information System (INIS)

    Hendrix, Mary JC; Seftor, Elisabeth A; Kirschmann, Dawn A; Seftor, Richard EB

    2000-01-01

    During embryogenesis, the formation of primary vascular networks occurs via the processes of vasculogenesis and angiogenesis. In uveal melanoma, vasculogenic mimicry describes the 'embryonic-like' ability of aggressive, but not nonaggressive, tumor cells to form networks surrounding spheroids of tumor cells in three-dimensional culture; these recapitulate the patterned networks seen in patients' aggressive tumors and correlates with poor prognosis. The molecular profile of these aggressive tumor cells suggests that they have a deregulated genotype, capable of expressing vascular phenotypes. Similarly, the embryonic-like phenotype expressed by the aggressive human breast cancer cells is associated with their ability to express a variety of vascular markers. These studies may offer new insights for consideration in breast cancer diagnosis and therapeutic intervention strategies

  7. Expression of DNA repair genes in ovarian cancer samples: biological and clinical considerations.

    Science.gov (United States)

    Ganzinelli, M; Mariani, P; Cattaneo, D; Fossati, R; Fruscio, R; Corso, S; Ricci, F; Broggini, M; Damia, G

    2011-05-01

    The purpose of this study was to investigate retrospectively the mRNA expression of genes involved in different DNA repair pathways implicated in processing platinum-induced damage in 171 chemotherapy-naïve ovarian tumours and correlate the expression of the different genes with clinical parameters. The expression of genes involved in DNA repair pathways (PARP1, ERCC1, XPA, XPF, XPG, BRCA1, FANCA, FANCC, FANCD2, FANCF and PolEta), and in DNA damage transduction (Chk1 and Claspin) was measured by RT-PCR in 13 stage I borderline and 77 stage I and 88 III ovarian carcinomas. ERCC1, XPA, XPF and XPG genes were significantly less expressed in stage III than in stage I carcinoma; BRCA1, FANCA, FANCC, FANCD2 gene expressions were low in borderline tumours, higher in stage I carcinomas and lower in stage III samples. High levels of ERCC1, XPA, FANCC, XPG and PolEta correlated with an increase in Overall Survival (OS) and Progression Free Survival (PFS), whilst high BRCA1 levels were associated with PFS on univariate analysis. With multivariate analyses no genes retained an association when adjusted by stage, grade and residual tumour. A tendency towards a better PFS was observed in patients with the highest level of ERCC1 and BRCA1 after platinum-based therapy than those given both platinum and taxol. The expression of DNA repair genes differed in borderline stage I, stage I and stage III ovarian carcinomas. The role of DNA repair genes in predicting the response in ovarian cancer patients seems far from being established. Copyright © 2010 Elsevier Ltd. All rights reserved.

  8. [Biological characteristics of a chimeric rabies virus expressing canine parvovirus VP2 protein].

    Science.gov (United States)

    Niu, Xue-Feng; Liu, Xiao-Hui; Sun, Zhao-Jin; Shi, He-He; Chen, Jing; Jiang, Bido; Sun, Jing-Chen; Guo, Xiao-Feng

    2009-09-01

    To obtain a bivalence vaccine against canine rabies virus and canine parvovirus, a chimeric rabies virus expressing canine parvovirus VP2 protein was generated by the technique of reverse genetics. It was shown that the chimeric virus designated as HEP-Flury (VP2) grew well on BHK-21 cells and the VP2 gene could still be stably expressed after ten passages on BHK-21 cells. Experiments on the mice immunized with the chimeric virus HEP-Flury (VP2) demonstrated that specific antibodies against rabies virus and canine parvovirus were induced in immunized mice after vaccination with the live chimeric virus.

  9. 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.

  10. The Expression and Biological Significance of PD-L1 on Lung Cancer Cell Lines

    Directory of Open Access Journals (Sweden)

    Cheng CHEN

    2009-08-01

    Full Text Available Background and objective Tumor-associated PD-L1 expression was recently shown to promote T-cell apoptosis and proposed as a potential mechanism of immune evasion by tumors. On the basis of the ability of tumor-associated PD-L1 to mediate activated T-cell death, it is likely that manipulation of the PD-L1 pathway at defined time points during the development of the T-cell antitumor immune response can enhance the efficacy of T-cell-based immunotherapy. Here, the levels of expression of PD-L1 on lung cancer cell lines and its role in interaction of CTL and target cells was investigated. Methods Human PBMC derived DCs were loaded with apoptotic tumor cells and stimulated by CD40 mAb (5C11. Tumor specific CTL was generated in vitro by autologous T cells co-cultured with mature DCs. Expression of PD-L1 on lung cancer cell lines H1299 and A549 were analyzed by FCM. JAM assay was used to detect the cytolytic activity of CTL with or without blocking PD-L1 by PD-L1 mAb respectively. The concentrations of IFN-γ in supernatants from distinct groups were analyzed by ELISA. Results Tumor cells-loaded mature DCs could induce the generation of the tumor specific CTL. Expression of PD-L1 was low on A549 cell, but high on H1299 cell. Blockade of PD-L1 on A549 could not improve cytolytic effect of CTL on target cells and IFN-γ production, but fragmentation of H1299 cells and IFN-γ production were significantly enhanced by the combination of PD-L1 mAb and CTL. Conclusion Expression of PD-L1 on lung cancer cell line can decrease the cytolytic effect of CTL on target cells.

  11. 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...

  12. 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...

  13. Meaningful Academic Work as Praxis in Emergence

    Directory of Open Access Journals (Sweden)

    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.

  14. Computational biology of genome expression and regulation--a review of microarray bioinformatics.

    Science.gov (United States)

    Wang, Junbai

    2008-01-01

    Microarray technology is being used widely in various biomedical research areas; the corresponding microarray data analysis is an essential step toward the best utilizing of array technologies. Here we review two components of the microarray data analysis: a low level of microarray data analysis that emphasizes the designing, the quality control, and the preprocessing of microarray experiments, then a high level of microarray data analysis that focuses on the domain-specific microarray applications such as tumor classification, biomarker prediction, analyzing array CGH experiments, and reverse engineering of gene expression networks. Additionally, we will review the recent development of building a predictive model in genome expression and regulation studies. This review may help biologists grasp a basic knowledge of microarray bioinformatics as well as its potential impact on the future evolvement of biomedical research fields.

  15. A circadian gene expression atlas in mammals: implications for biology and medicine.

    Science.gov (United States)

    Zhang, Ray; Lahens, Nicholas F; Ballance, Heather I; Hughes, Michael E; Hogenesch, John B

    2014-11-11

    To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional "rush hours" preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  20. Identification of differentially expressed genes and biological pathways in bladder cancer

    Science.gov (United States)

    Tang, Fucai; He, Zhaohui; Lei, Hanqi; Chen, Yuehan; Lu, Zechao; Zeng, Guohua; Wang, Hangtao

    2018-01-01

    The purpose of the present study was to identify key genes and investigate the related molecular mechanisms of bladder cancer (BC) progression. From the Gene Expression Omnibus database, the gene expression dataset GSE7476 was downloaded, which contained 43 BC samples and 12 normal bladder tissues. GSE7476 was analyzed to screen the differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for the DEGs using the DAVID database, and a protein-protein interaction (PPI) network was then constructed using Cytoscape software. The results of the GO analysis showed that the upregulated DEGs were significantly enriched in cell division, nucleoplasm and protein binding, while the downregulated DEGs were significantly enriched in ‘extracellular matrix organization’, ‘proteinaceous extracellular matrix’ and ‘heparin binding’. The results of the KEGG pathway analysis showed that the upregulated DEGs were significantly enriched in the ‘cell cycle’, whereas the downregulated DEGs were significantly enriched in ‘complement and coagulation cascades’. JUN, cyclin-dependent kinase 1, FOS, PCNA, TOP2A, CCND1 and CDH1 were found to be hub genes in the PPI network. Sub-networks revealed that these gene were enriched in significant pathways, including the ‘cell cycle’ signaling pathway and ‘PI3K-Akt signaling pathway’. In summary, the present study identified DEGs and key target genes in the progression of BC, providing potential molecular targets and diagnostic biomarkers for the treatment of BC. PMID:29532898

  1. Towards a unified system for expression of biological damage by ionising radiation

    International Nuclear Information System (INIS)

    Watt, D.E.; Chen, C.Z.; Kadiri, L.; Younis, A.

    1987-01-01

    Limitations to current systems of radiation dosimetry are discussed. Analyses of a wide range of published data on inactivation of enzymes, viruses, bacteria, plant and mammalian cells by electrons, X and γ-rays, and accelerated ions leads to the conclusion that the main radiosensitive sites in higher cells are the double-stranded segments of DNA. The probability of damage is determined by the mean free path for ionization along the charged particle tracks and is optimum when the spacing matches the mean chord length (2 nm) through a DNA segment. Interpretation of these findings leads to the possibility of a more accurate unified system of dosimetry and to the specification of absolute biological effectiveness. (author)

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

    DEFF Research Database (Denmark)

    Sastry, Anand; Monk, Jonathan M.; Tegel, Hanna

    2017-01-01

    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. Availability and implementation: 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...

  3. 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.

  4. 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.

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

    Science.gov (United States)

    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

  6. 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.

  7. Mathematical and Biological Modelling of RNA Secondary Structure and Its Effects on Gene Expression

    Directory of Open Access Journals (Sweden)

    T. A. Hughes

    2006-01-01

    Full Text Available Secondary structures within the 5′ untranslated regions of messenger RNAs can have profound effects on the efficiency of translation of their messages and thereby on gene expression. Consequently they can act as important regulatory motifs in both physiological and pathological settings. Current approaches to predicting the secondary structure of these RNA sequences find the structure with the global-minimum free energy. However, since RNA folds progressively from the 5′ end when synthesised or released from the translational machinery, this may not be the most probable structure. We discuss secondary structure prediction based on local-minimisation of free energy with thermodynamic fluctuations as nucleotides are added to the 3′ end and show that these can result in different secondary structures. We also discuss approaches for studying the extent of the translational inhibition specified by structures within the 5′ untranslated region.

  8. Five different piscidins from Nile tilapia, Oreochromis niloticus: analysis of their expressions and biological functions.

    Directory of Open Access Journals (Sweden)

    Kuan-Chieh Peng

    Full Text Available Piscidins are antimicrobial peptides (AMPs that play important roles in helping fish resist pathogenic infections. Through comparisons of tilapia EST clones, the coding sequences of five piscidin-like AMPs (named TP1∼5 of Nile tilapia, Oreochromis niloticus, were determined. The complete piscidin coding sequences of TP1, -2, -3, -4, and -5 were respectively composed of 207, 234, 231, 270, and 195 bases, and each contained a translated region of 68, 77, 76, 89, and 64 amino acids. The tissue-specific, Vibrio vulnificus stimulation-specific, and Streptococcus agalactiae stimulation-specific expressions of TP2, -3, and -4 mRNA were determined by a comparative RT-PCR. Results of the tissue distribution analysis revealed high expression levels of TP2 mRNA in the skin, head kidneys, liver, and spleen. To study bacterial stimulation, S. agalactiae (SA47 was injected, and the TP4 transcript was upregulated by >13-fold (compared to the wild-type (WT control, without injection and was 60-fold upregulated (compared to the WT control, without injection 24 h after the S. agalactiae (SA47 injection in the spleen and gills. Synthesized TP3 and TP4 peptides showed antimicrobial activities against several bacteria in this study, while the synthesized TP1, -2, and -5 peptides did not. The synthesized TP2, -3, and -4 peptides showed hemolytic activities and synthesized TP3 and TP4 peptides inhibited tilapia ovary cell proliferation with a dose-dependent effect. In summary, the amphiphilic α-helical cationic peptides of TP3 and TP4 may represent novel and potential antimicrobial agents for further peptide drug development.

  9. Significant Deregulated Pathways in Diabetes Type II Complications Identified through Expression Based Network Biology

    Science.gov (United States)

    Ukil, Sanchaita; Sinha, Meenakshee; Varshney, Lavneesh; Agrawal, Shipra

    Type 2 Diabetes is a complex multifactorial disease, which alters several signaling cascades giving rise to serious complications. It is one of the major risk factors for cardiovascular diseases. The present research work describes an integrated functional network biology approach to identify pathways that get transcriptionally altered and lead to complex complications thereby amplifying the phenotypic effect of the impaired disease state. We have identified two sub-network modules, which could be activated under abnormal circumstances in diabetes. Present work describes key proteins such as P85A and SRC serving as important nodes to mediate alternate signaling routes during diseased condition. P85A has been shown to be an important link between stress responsive MAPK and CVD markers involved in fibrosis. MAPK8 has been shown to interact with P85A and further activate CTGF through VEGF signaling. We have traced a novel and unique route correlating inflammation and fibrosis by considering P85A as a key mediator of signals. The next sub-network module shows SRC as a junction for various signaling processes, which results in interaction between NF-kB and beta catenin to cause cell death. The powerful interaction between these important genes in response to transcriptionally altered lipid metabolism and impaired inflammatory response via SRC causes apoptosis of cells. The crosstalk between inflammation, lipid homeostasis and stress, and their serious effects downstream have been explained in the present analyses.

  10. Design, Recombinant Fusion Expression and Biological Evaluation of Vasoactive Intestinal Peptide Analogue as Novel Antimicrobial Agent

    Directory of Open Access Journals (Sweden)

    Chunlan Xu

    2017-11-01

    Full Text Available Antimicrobial peptides represent an emerging category of therapeutic agents with remarkable structural and functional diversity. Modified vasoactive intestinal peptide (VIP (VIP analogue 8 with amino acid sequence “FTANYTRLRRQLAVRRYLAAILGRR” without haemolytic activity and cytotoxicity displayed enhanced antimicrobial activities against Staphylococcus aureus (S. aureus ATCC 25923 and Escherichia coli (E. coli ATCC 25922 than parent VIP even in the presence of 180 mM NaCl or 50 mM MgCl2, or in the range of pH 4–10. VIP analogue 8 was expressed as fusion protein thioredoxin (Trx-VIP8 in E. coli BL21(DE at a yield of 45.67 mg/L. The minimum inhibitory concentration (MIC of the recombinant VIP analogue 8 against S. aureus ATCC 25923 and E. coli ATCC 25922 were 2 μM. These findings suggest that VIP analogue 8 is a promising candidate for application as a new and safe antimicrobial agent.

  11. A meaningful MESS (Medical Education Scholarship Support

    Directory of Open Access Journals (Sweden)

    Shari A. Whicker

    2016-07-01

    Full Text Available Background: Graduate medical education faculty bear the responsibility of demonstrating active research and scholarship; however, faculty who choose education-focused careers may face unique obstacles related to the lack of promotion tracks, funding, career options, and research opportunities. Our objective was to address education research and scholarship barriers by providing a collaborative peer-mentoring environment and improve the production of research and scholarly outputs. Methods: We describe a Medical Education Scholarship Support (MESS group created in 2013. MESS is an interprofessional, multidisciplinary peer-mentoring education research community that now spans multiple institutions. This group meets monthly to address education research and scholarship challenges. Through this process, we develop new knowledge, research, and scholarly products, in addition to meaningful collaborations. Results: MESS originated with eight founding members, all of whom still actively participate. MESS has proven to be a sustainable unfunded local community of practice, encouraging faculty to pursue health professions education (HPE careers and fostering scholarship. We have met our original objectives that involved maintaining 100% participant retention; developing increased knowledge in at least seven content areas; and contributing to the development of 13 peer-reviewed publications, eight professional presentations, one Masters of Education project, and one educational curriculum. Discussion: The number of individuals engaged in HPE research continues to rise. The MESS model could be adapted for use at other institutions, thereby reducing barriers HPE researchers face, providing an effective framework for trainees interested in education-focused careers, and having a broader impact on the education research landscape.

  12. Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

    Directory of Open Access Journals (Sweden)

    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.

  13. 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...

  14. Cross-species comparison of the gut: Differential gene expression sheds light on biological differences in closely related tenebrionids.

    Science.gov (United States)

    Oppert, Brenda; Perkin, Lindsey; Martynov, Alexander G; Elpidina, Elena N

    2018-04-01

    The gut is one of the primary interfaces between an insect and its environment. Understanding gene expression profiles in the insect gut can provide insight into interactions with the environment as well as identify potential control methods for pests. We compared the expression profiles of transcripts from the gut of larval stages of two coleopteran insects, Tenebrio molitor and Tribolium castaneum. These tenebrionids have different life cycles, varying in the duration and number of larval instars. T. castaneum has a sequenced genome and has been a model for coleopterans, and we recently obtained a draft genome for T. molitor. We assembled gut transcriptome reads from each insect to their respective genomes and filtered mapped reads to RPKM>1, yielding 11,521 and 17,871 genes in the T. castaneum and T. molitor datasets, respectively. There were identical GO terms in each dataset, and enrichment analyses also identified shared GO terms. From these datasets, we compiled an ortholog list of 6907 genes; 45% of the total assembled reads from T. castaneum were found in the top 25 orthologs, but only 27% of assembled reads were found in the top 25 T. molitor orthologs. There were 2281 genes unique to T. castaneum, and 2088 predicted genes unique to T. molitor, although improvements to the T. molitor genome will likely reduce these numbers as more orthologs are identified. We highlight a few unique genes in T. castaneum or T. molitor that may relate to distinct biological functions. A large number of putative genes expressed in the larval gut with uncharacterized functions (36 and 68% from T. castaneum and T. molitor, respectively) support the need for further research. These data are the first step in building a comprehensive understanding of the physiology of the gut in tenebrionid insects, illustrating commonalities and differences that may be related to speciation and environmental adaptation. Published by Elsevier Ltd.

  15. Are students ready for meaningful use?

    Directory of Open Access Journals (Sweden)

    Gary S. Ferenchick

    2013-11-01

    Full Text Available Background: The meaningful use (MU of electronic medical records (EMRs is being implemented in three stages. Key objectives of stage one include electronic analysis of data entered into structured fields, using decision-support tools (e.g., checking drug–drug interactions [DDI] and electronic information exchange. Objective: The authors assessed the performance of medical students on 10 stage-one MU tasks and measured the correlation between students’ MU performance and subsequent end-of-clerkship professionalism assessments and their grades on an end-of-year objective structured clinical examination. Participants: Two-hundred and twenty-two third-year medical students on the internal medicine (IM clerkship. Design/main measures: From July 2010 to February 2012, all students viewed 15 online tutorials covering MU competencies. The authors measured student MU documentation and performance in the chart of a virtual patient using a fully functional training EMR. Specific MU measurements included, adding: a new problem, a new medication, an advanced directive, smoking status, the results of screening tests; and performing a DDI (in which a major interaction was probable, and communicating a plan for this interaction. Key results: A total of 130 MU errors were identified. Sixty-eight (30.6% students had at least one error, and 30 (13.5% had more than one (range 2–6. Of the 130 errors, 90 (69.2% were errors in structured data entry. Errors occurred in medication dosing and instructions (18%, DDI identification (12%, documenting smoking status (15%, and colonoscopy results (23%. Students with MU errors demonstrated poorer performance on end-of-clerkship professionalism assessments (r=−0.112, p=0.048 and lower observed structured clinical examination (OSCE history-taking skills (r=−0.165, p=0.008 and communication scores (r=− 0.173, p=0.006. Conclusions: MU errors among medical students are common and correlate with subsequent poor

  16. Redefining meaningful age groups in the context of disease.

    Science.gov (United States)

    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.

  17. Meaningfulness of Service and Marital Satisfaction in Army Couples

    Science.gov (United States)

    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

  18. 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 ...

  19. Meaningfulness of service and marital satisfaction in Army couples.

    Science.gov (United States)

    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).

  20. 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…

  1. 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

  2. Relationship between meaningful work and job performance in nurses.

    Science.gov (United States)

    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.

  3. Self-Determination and Meaningful Work: Exploring Socioeconomic Constraints

    Directory of Open Access Journals (Sweden)

    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.

  4. Self-Determination and Meaningful Work: Exploring Socioeconomic Constraints.

    Science.gov (United States)

    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.

  5. 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 ...

  6. 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

  7. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  9. ON THE DERIVATIVE OF SMOOTH MEANINGFUL FUNCTIONS

    Directory of Open Access Journals (Sweden)

    Sanjo Zlobec

    2011-02-01

    Full Text Available The derivative of a function f in n variables at a point x* is one of the most important tools in mathematical modelling. If this object exists, it is represented by the row n-tuple f(x* = [∂f/∂xi(x*] called the gradient of f at x*, abbreviated: “the gradient”. The evaluation of f(x* is usually done in two stages, first by calculating the n partials and then their values at x = x*. In this talk we give an alternative approach. We show that one can characterize the gradient without differentiation! The idea is to fix an arbitrary row n-tuple G and answer the following question: What is a necessary and sufficient condition such that G is the gradient of a given f at a given x*? The answer is given after adjusting the quadratic envelope property introduced in [3]. We work with smooth, i.e., continuously differentiable, functions with a Lipschitz derivative on a compact convex set with a non-empty interior. Working with this class of functions is not a serious restriction. In fact, loosely speaking, “almost all” smooth meaningful functions used in modelling of real life situations are expected to have a bounded “acceleration” hence they belong to this class. In particular, the class contains all twice differentiable functions [1]. An important property of the functions from this class is that every f can be represented as the difference of some convex function and a convex quadratic function. This decomposition was used in [3] to characterize the zero derivative points. There we obtained reformulations and augmentations of some well known classic results on optimality such as Fermats extreme value theorem (known from high school and the Lagrange multiplier theorem from calculus [2, 3]. In this talk we extend the results on zero derivative points to characterize the relation G = f(x*, where G is an arbitrary n-tuple. Some special cases: If G = O, we recover the results on zero derivative points. For functions of a single

  10. Expression

    Directory of Open Access Journals (Sweden)

    Wang-Xia Wang

    2014-02-01

    Full Text Available The miR-15/107 family comprises a group of 10 paralogous microRNAs (miRNAs, sharing a 5′ AGCAGC sequence. These miRNAs have overlapping targets. In order to characterize the expression of miR-15/107 family miRNAs, we employed customized TaqMan Low-Density micro-fluid PCR-array to investigate the expression of miR-15/107 family members, and other selected miRNAs, in 11 human tissues obtained at autopsy including the cerebral cortex, frontal cortex, primary visual cortex, thalamus, heart, lung, liver, kidney, spleen, stomach and skeletal muscle. miR-103, miR-195 and miR-497 were expressed at similar levels across various tissues, whereas miR-107 is enriched in brain samples. We also examined the expression patterns of evolutionarily conserved miR-15/107 miRNAs in three distinct primary rat brain cell preparations (enriched for cortical neurons, astrocytes and microglia, respectively. In primary cultures of rat brain cells, several members of the miR-15/107 family are enriched in neurons compared to other cell types in the central nervous system (CNS. In addition to mature miRNAs, we also examined the expression of precursors (pri-miRNAs. Our data suggested a generally poor correlation between the expression of mature miRNAs and their precursors. In summary, we provide a detailed study of the tissue and cell type-specific expression profile of this highly expressed and phylogenetically conserved family of miRNA genes.

  11. Antecedents and outcomes of meaningful work among school teachers

    Directory of Open Access Journals (Sweden)

    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

  12. Thymoma calcification: Is it clinically meaningful?

    Directory of Open Access Journals (Sweden)

    Alkaied Homam

    2011-08-01

    Full Text Available Abstract Among anterior mediastinal lesions, thymoma is the most common. Thymomas are tumors of thymic epithelial cell origin that are distinguished by inconsistent histological and biologic behavior. Chest imaging studies typically show a round or lobulated tumor in the anterior mediastinum. Calcifications in thymomas are classically punctuate or amorphous, positioned within the lesion. Chest computed tomography (CT features suggesting higher risk thymoma consist of tumor heterogeneity, vascular involvement, lobulation, pulmonary nodules, lymphadenopathy, and pleural manifestations. Imaging findings have an imperfect ability to predict stage and prognosis for thymoma patients. Our objective is to highlight the clinical implications of thymoma calcifications on the diagnosis, clinical manifestation and prognosis. A pubmed and google search was performed using the following words: thymoma calcification, calcified thymus, mediastinal calcification, anterior mediastinal calcification, and calcified thymoma. After reviewing 370 articles, 32 eligible articles describing thymoma calcifications were found and included in this review. Although the presence of thymus calcifications was more common in patients with invasive thymomas, they were present in significant portion of non-invasive thymomas. The presence of calcifications was not a significant factor in differentiating between benign and malignant thymoma. As a result, the type, location, size or other characteristics of thymus gland calcifications were not relevant features in clinical and radiologic diagnosis of thymoma. The histopathological diagnosis is still the only possible way to confirm the neoplastic nature of thymoma. All types of thymomas should be evaluated and managed independently of the presence of calcifications.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  15. 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.)

  16. 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.)

  17. Is synthetic biology mechanical biology?

    Science.gov (United States)

    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.

  18. Online Analytical Processing (OLAP: A Fast and Effective Data Mining Tool for Gene Expression Databases

    Directory of Open Access Journals (Sweden)

    Alkharouf Nadim W.

    2005-01-01

    Full Text Available Gene expression databases contain a wealth of information, but current data mining tools are limited in their speed and effectiveness in extracting meaningful biological knowledge from them. Online analytical processing (OLAP can be used as a supplement to cluster analysis for fast and effective data mining of gene expression databases. We used Analysis Services 2000, a product that ships with SQLServer2000, to construct an OLAP cube that was used to mine a time series experiment designed to identify genes associated with resistance of soybean to the soybean cyst nematode, a devastating pest of soybean. The data for these experiments is stored in the soybean genomics and microarray database (SGMD. A number of candidate resistance genes and pathways were found. Compared to traditional cluster analysis of gene expression data, OLAP was more effective and faster in finding biologically meaningful information. OLAP is available from a number of vendors and can work with any relational database management system through OLE DB.

  19. Online analytical processing (OLAP): a fast and effective data mining tool for gene expression databases.

    Science.gov (United States)

    Alkharouf, Nadim W; Jamison, D Curtis; Matthews, Benjamin F

    2005-06-30

    Gene expression databases contain a wealth of information, but current data mining tools are limited in their speed and effectiveness in extracting meaningful biological knowledge from them. Online analytical processing (OLAP) can be used as a supplement to cluster analysis for fast and effective data mining of gene expression databases. We used Analysis Services 2000, a product that ships with SQLServer2000, to construct an OLAP cube that was used to mine a time series experiment designed to identify genes associated with resistance of soybean to the soybean cyst nematode, a devastating pest of soybean. The data for these experiments is stored in the soybean genomics and microarray database (SGMD). A number of candidate resistance genes and pathways were found. Compared to traditional cluster analysis of gene expression data, OLAP was more effective and faster in finding biologically meaningful information. OLAP is available from a number of vendors and can work with any relational database management system through OLE DB.

  20. 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.

  1. 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

  2. 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,...

  3. Expression and biological activity of the cystine knot bioinsecticide PA1b (Pea Albumin 1 Subunit b.

    Directory of Open Access Journals (Sweden)

    Vanessa Eyraud

    Full Text Available The PA1b (Pea Albumin 1, subunit b peptide is an entomotoxin extract from Legume seeds with lethal activity on several insect pests, such as mosquitoes, some aphids and cereal weevils. This 37 amino-acid cysteine-rich peptide has been, until now, obtained by biochemical purification or chemical synthesis. In this paper, we present our results for the transient production of the peptide in Nicotiana benthamiana by agro-infiltration, with a yield of about 35 µg/g of fresh leaves and maximum production 8 days after infiltration. PA1b is part of the PA1 gene which, after post-translational modifications, encodes two peptides (PA1b and PA1a. We show that transforming tobacco with the PA1b cDNA alone does not result in production of the toxin and, in fact, the entire cDNA is necessary, raising the question of the role of PA1a. We constructed a PA1-cassette, allowing for the quick "cut/paste" of different PA1b mutants within a conserved PA1 cDNA. This cassette enabled us to produce the six isoforms of PA1b which exist in pea seeds. Biological tests revealed that all the isoforms display similar activity, with the exception of one which is inactive. The lack of activity in this isoform led us to conclude that the amphiphilic nature of the peptide is necessary for activity. The possible applications of this expression system for other cysteine-rich biomolecules are discussed.

  4. 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...

  5. 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....

  6. 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...

  7. 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...

  8. The effect of occupational meaningfulness on occupational commitment

    Directory of Open Access Journals (Sweden)

    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.

  9. Helping others increases meaningful work: Evidence from three experiments.

    Science.gov (United States)

    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).

  10. 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.

  11. 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.

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

    Science.gov (United States)

    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

  13. 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

  14. Design of a Comprehensive Biochemistry and Molecular Biology Experiment: Phase Variation Caused by Recombinational Regulation of Bacterial Gene Expression

    Science.gov (United States)

    Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

    2014-01-01

    Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about "Salmonella enterica" serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation,…

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  17. EXPRESS

    International Nuclear Information System (INIS)

    Ancelin, C.; Le, P.; DeSaint-Quentin, S.; Villatte, N.

    1987-01-01

    This paper presents EXPRESS, an expert system developed for the automation of reliability studies. The first part consists in the description of the method for static thermohydraulic systems. In this step, the authors define the knowledge representation based on the two inference engines - ALOUETTE and LCR developed by EDF. They explain all the process to construct a fault tree from a topological and functional description of the system. Numerous examples are exhibited in illustration of the method. This is followed by the lessons derived from the studies performed on some safety systems of the PALUEL nuclear plant. The development of the same approach for electric power systems is described, insisting on the difference resulting from the sequential nature of these systems. Finally, they show the main advantages identified during the studies

  18. 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

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

    Science.gov (United States)

    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.

  20. [From synthetic biology to synthetic humankind].

    Science.gov (United States)

    Nouvel, Pascal

    2015-01-01

    In this paper, we propose an historical survey of the expression "synthetic biology" in order to identify its main philosophical components. The result of the analysis is then used to investigate the meaning of the notion of "synthetic man". It is shown that both notions share a common philosophical background that can be summed up by the short but meaningful assertion: "biology is technology". The analysis allows us to distinguish two notions that are often confused in transhumanist literature: the notion of synthetic man and the notion of renewed man. The consequences of this crucial distinction are discussed. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  1. Designing Meaningful Game Experiences for Rehabilitation and Sustainable Mobility Settings

    Directory of Open Access Journals (Sweden)

    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.

  2. A systems biology analysis of the changes in gene expression via silencing of HPV-18 E1 expression in HeLa cells.

    Science.gov (United States)

    Castillo, Andres; Wang, Lu; Koriyama, Chihaya; Eizuru, Yoshito; Jordan, King; Akiba, Suminori

    2014-10-01

    Previous studies have reported the detection of a truncated E1 mRNA generated from HPV-18 in HeLa cells. Although it is unclear whether a truncated E1 protein could function as a replicative helicase for viral replication, it would still retain binding sites for potential interactions with different host cell proteins. Furthermore, in this study, we found evidence in support of expression of full-length HPV-18 E1 mRNA in HeLa cells. To determine whether interactions between E1 and cellular proteins play an important role in cellular processes other than viral replication, genome-wide expression profiles of HPV-18 positive HeLa cells were compared before and after the siRNA knockdown of E1 expression. Differential expression and gene set enrichment analysis uncovered four functionally related sets of genes implicated in host defence mechanisms against viral infection. These included the toll-like receptor, interferon and apoptosis pathways, along with the antiviral interferon-stimulated gene set. In addition, we found that the transcriptional coactivator E1A-binding protein p300 (EP300) was downregulated, which is interesting given that EP300 is thought to be required for the transcription of HPV-18 genes in HeLa cells. The observed changes in gene expression produced via the silencing of HPV-18 E1 expression in HeLa cells indicate that in addition to its well-known role in viral replication, the E1 protein may also play an important role in mitigating the host's ability to defend against viral infection.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  5. Gene expression profiling with principal component analysis depicts the biological continuum from essential thrombocythemia over polycythemia vera to myelofibrosis

    DEFF Research Database (Denmark)

    Skov, Vibe; Thomassen, Mads; Riley, Caroline H

    2012-01-01

    The recent discovery of the Janus activating kinase 2 V617F mutation in most patients with polycythemia vera (PV) and half of those with essential thrombocythemia (ET) and primary myelofibrosis (PMF) has favored the hypothesis of a biological continuum from ET over PV to PMF. We performed gene...... with biological relevant overlaps between the different entities. Moreover, the analysis separates Janus activating kinase 2-negative ET patients from Janus activating kinase 2-positive ET patients. Functional annotation analysis demonstrates that clusters of gene ontology terms related to inflammation, immune...... system, apoptosis, RNA metabolism, and secretory system were the most significantly deregulated terms in the three different disease groups. Our results yield further support for the hypothesis of a biological continuum originating from ET over PV to PMF. Functional analysis suggests an important...

  6. Meaningful Work and Secondary School Teachers' Intention to Leave

    Science.gov (United States)

    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…

  7. Meaningful community involvement in protected area issues: a dialogue session

    Science.gov (United States)

    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...

  8. Pedagogical Principles of Learning to Teach Meaningful Physical Education

    Science.gov (United States)

    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…

  9. 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 ...

  10. 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.

  11. 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

  12. 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…

  13. Using Meaningful Contexts to Promote Understanding of Pronumerals

    Science.gov (United States)

    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)…

  14. Comprehension for What? Preparing Students for Their Meaningful Future

    Science.gov (United States)

    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…

  15. Concept maps and the meaningful learning of science

    Directory of Open Access Journals (Sweden)

    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.

  16. Operating Room Delays: Meaningful Use in Electronic Health Record.

    Science.gov (United States)

    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.

  17. Synonyms, Antonyms, and Retroactive Inhibition with Meaningful Material

    Science.gov (United States)

    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.…

  18. 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…

  19. How Do Novice Art Teachers Define and Implement Meaningful Curriculum?

    Science.gov (United States)

    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…

  20. Authentic Leadership and Altruism: The Mediating Role of Meaningfulness

    Science.gov (United States)

    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…

  1. Modeling Meaningful Learning in Chemistry Using Structural Equation Modeling

    Science.gov (United States)

    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…

  2. [Relationship between the expression of beta-cat, cyclin D1 and c-myc and the occurance and biological behavior of pancreatic cancer].

    Science.gov (United States)

    Li, Yu-jun; Ji, Xiang-rui

    2003-06-01

    unchecked proliferation and differentiation, which may play an important role in the genesis of the pancreatic cancer. The abnormal expression of beta-cat is one of the mechanisms for the spread of pancreatic cancer and an index in the molecular biology to determine the metastasis and prognosis of pancreatic cancer.

  3. Work engagement and meaningful work across generational cohorts

    Directory of Open Access Journals (Sweden)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  5. 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.

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

    Science.gov (United States)

    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)

  7. Canine placental prostaglandin E2 synthase: expression, localization, and biological functions in providing substrates for prepartum PGF2alpha synthesis.

    Science.gov (United States)

    Gram, Aykut; Fox, Barbara; Büchler, Urs; Boos, Alois; Hoffmann, Bernd; Kowalewski, Mariusz P

    2014-12-01

    The prepartum output of PGF2alpha in the bitch is associated with increased placental PGE2-synthase (PTGES) mRNA levels. Contrasting with this is a decreased expression of PGF2alpha-synthase (PGFS/AKR1C3) in uteroplacental compartments during prepartum luteolysis, suggesting an involvement of alternative synthetic pathways in PGF2alpha synthesis, for example, conversion of PGE2 to PGF2alpha. However, because the expression and possible functions of the respective PTGES proteins remained unknown, no further conclusion could be drawn. Therefore, a canine-specific PTGES antibody was generated and used to investigate the expression, cellular localization, and biochemical activities of canine uteroplacental PTGES throughout pregnancy and at prepartum luteolysis. Additionally, the biochemical activities of these tissues involved in the conversion of PGE2 to PGF2alpha were investigated. The endometrial PTGES was localized in the uterine surface epithelium at preimplantation and in superficial and deep uterine glands, endothelial cells, and myometrium throughout pregnancy and at parturition. Placental signals were mostly in the trophoblast. The biochemical properties of recombinant PTGES protein were confirmed. Additionally, expression of two PGE2-receptors, PTGER2/EP2 and PTGER4/EP4, revealed their decreasing expression during luteolysis. In contrast, the uteroplacental expression of prostaglandin transporter (PGT) was strongly elevated prior to parturition. These localization patterns resembled that of PTGES. The increased expression of PTGES and PGT at parturition, together with the accompanying decreased levels of PGE2-receptors and the capability of canine uterine and placental homogenates to take part in the conversion of PGE2 to PGF2alpha, as found in this study, suggest that PGE2 could be used locally as a substrate for prepartum PGF2alpha synthesis in the dog. © 2014 by the Society for the Study of Reproduction, Inc.

  8. Gene expression of hematoregulatory cytokines is elevated endogenously after sublethal gamma irradiation and is differentially enhanced by therapeutic administration of biologic response modifiers

    International Nuclear Information System (INIS)

    Peterson, V.M.; Adamovicz, J.J.; Madonna, G.S.; Gause, W.C.; Elliott, T.B.; Moore, M.M.; Ledney, G.D.; Jackson, W.E. III

    1994-01-01

    Prompt, cytokine-mediated restoration of hematopoiesis is a prerequisite for survival after irradiation. Therapy with biologic response modifiers (BRMs), such as LPS, 3D monophosphoryl lipid A (MPL), and synthetic trehalose dicrynomycolate (S-TDCM) presumably accelerates hematopoietic recovery after irradiation are poorly defined. One hour after sublethal (7.0 Gy) 60 Co gamma irradiation, B6D2F1/J female mice received a single i.p. injection of LPS, MPL, S-TDCM, an extract from Serratia marcescens (Sm-BRM), or Tween 80 in saline (TS). Five hours later, a quantitative reverse transcription-PCR assay demonstrated marked splenic gene expression for IL-1β, IL-3, IL-6, and granulocyte-CSF (G-CSF). Enhanced gene expression for TNF-α, macrophage-CSF (M-CSF), and stem cell factor (SCF) was not detected. Injection of any BRM further enhanced cytokine gene expression and plasma levels of CSF activity within 24 h after irradiation and hastened bone marrow recovery. Mice injected with S-TDCM or Sm-BRM sustained expression of the IL-6 gene for at least 24 h after irradiation. Sm-BRM-treated mice exhibited greater gene expression for IL-1β, IL-3, TNF-α, and G-CSF at day 1 than any other BRM. When challenged with 2 LD 50/30 of Klebsiella pneumoniae 4 days after irradiation, 100% of Sm-BRM-treated mice and 70% of S-TDCM-treated mice survived, whereas ≤30% of mice treated with LPS, MPL, or TS survived. Thus, sublethal irradiation induces transient, splenic cytokine gene expression that can be differentially amplified and prolonged by BRMs. BRMs that sustained and/or enhanced irradiation-induced expression of specific cytokine genes improved survival after experimental infection. 67 refs., 7 figs., 1 tab

  9. Endothelin-2/Vasoactive Intestinal Contractor: Regulation of Expression via Reactive Oxygen Species Induced by CoCl22, and Biological Activities Including Neurite Outgrowth in PC12 Cells

    Directory of Open Access Journals (Sweden)

    Eiichi Kotake-Nara

    2006-01-01

    Full Text Available This paper reviews the local hormone endothelin-2 (ET-2, or vasoactive intestinal contractor (VIC, a member of the vasoconstrictor ET peptide family, where ET-2 is the human orthologous peptide of the murine VIC. While ET-2/VIC gene expression has been observed in some normal tissues, ET-2 recently has been reported to act as a tumor marker and as a hypoxia-induced autocrine survival factor in tumor cells. A recently published study reported that the hypoxic mimetic agent CoCl2 at 200 µM increased expression of the ET-2/VIC gene, decreased expression of the ET-1 gene, and induced intracellular reactive oxygen species (ROS increase and neurite outgrowth in neuronal model PC12 cells. The ROS was generated by addition of CoCl2 to the culture medium, and the CoCl2-induced effects were completely inhibited by the antioxidant N-acetyl cysteine. Furthermore, interleukin-6 (IL-6 gene expression was up-regulated upon the differentiation induced by CoCl2. These results suggest that expression of ET-2/VIC and ET-1 mediated by CoCl2-induced ROS may be associated with neuronal differentiation through the regulation of IL-6 expression. CoCl2 acts as a pro-oxidant, as do Fe(II, III and Cu(II. However, some biological activities have been reported for CoCl2 that have not been observed for other metal salts such as FeCl3, CuSO4, and NiCl2. The characteristic actions of CoCl2 may be associated with the differentiation of PC12 cells. Further elucidation of the mechanism of neurite outgrowth and regulation of ET-2/VIC expression by CoCl2 may lead to the development of treatments for neuronal disorders.

  10. 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.

  11. 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

  12. Synthesis and Biological Evaluation of a New Acyclic Pyrimidine Derivative as a Probe for Imaging Herpes Simplex Virus Type 1 Thymidine Kinase Gene Expression

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    Simon M. Ametamey

    2013-07-01

    Full Text Available With the idea of finding a more selective radiotracer for imaging herpes simplex virus type 1 thymidine kinase (HSV1-tk gene expression by means of positron emission tomography (PET, a novel [18F]fluorine radiolabeled pyrimidine with 4-hydroxy-3-(hydroxymethylbutyl side chain at N-1 (HHB-5-[18F]FEP was prepared and evaluated as a potential PET probe. Unlabeled reference compound, HHB-5-FEP, was synthesized via a five-step reaction sequence starting from 5-(2-acetoxyethyl-4-methoxypyrimidin-2-one. The radiosynthesis of HHB-[18F]-FEP was accomplished by nucleophilic radiofluorination of a tosylate precursor using [18F]fluoride-cryptate complex in 45% ± 4 (n = 4 radiochemical yields and high purity (>99%. The biological evaluation indicated the feasibility of using HHB-5-[18F]FEP as a PET radiotracer for monitoring HSV1-tk expression in vivo.

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

    Science.gov (United States)

    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.

  14. 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.

  15. Expression of Caspase-3, P53 in EL-4 cells induced by ionizing radiation and its biological implications

    International Nuclear Information System (INIS)

    Ju Guizhi; Shen Bo; Sun Shilong; Yan Fengqin; Fu Shibo; Li Pengwu

    2006-01-01

    Objective: To investigate the effect of ionizing radiation on the expressions of Caspase-3 and P53 proteins in EL-4 cells and its implications in the induction of apoptosis and polyploid cells. Methods: EL- 4 cells were irradiated with 4.0 Gy X-rays (180 kV, 15 mA, 0.287 Gy/min). Fluorescent staining and flow cytometry analysis were used to measure protein expression, apoptosis and polyploid cells. Results: It was found that the expression of Caspase-3 protein was increased significantly at 8 h and 12 h after the irradiation compared with sham-irradiated control (P<0.05), and the expression of P53 protein was also increased significantly at 2,4,8,12 and 24 h after the irradiation compared with sham-irradiated control (P<0.05 or P<0.01). The results showed that apoptosis of EL-4 cells was increased significantly at 2,4,8,12,24,48, and 72 h after 4.0 Gy irradiation compared with sham-irradiated control (P<0.05 or P<0.01 or P<0.001). However, no significant change in the number of polyploidy cells was found during the period from 2 to 48 h after the irradiation with 4.0 Gy X-rays. Conclusions: It is indicated that the expressions of Caspase-3 and P53 protein in EL-4 cells can be induced by ionizing radiation, and play an important role in the induction of apoptosis; the molecular pathway for polyploid formation might be P53-independent. (authors)

  16. Follow-up study of abnormal biological indicators and gene expression in the peripheral blood of three accidentally exposed persons

    International Nuclear Information System (INIS)

    Chi Cuiping; Wang Haiyan; Wei Jinping; Guo Jianping; Li Shufang; Tian Rong; Guo Fengling; Liu Huifang

    2013-01-01

    In order to identify biomarkers for early diagnosis and/or for therapeutic targets in the delayed health effects of ionizing radiation, we analyzed the subgroups of lymphocytes, serum protein levels and gene expression profiles in the peripheral blood of three 60 Co γ-ray accidentally exposed persons during the three years after irradiation. Flow cytometry analyses and agarose gel electrophoresis were applied to investigate the subgroups of lymphocytes and the composition of serum proteins, respectively. Gene expression profiling was obtained using a whole genome gene expression chip assay. Both the percentage of CD4+ T lymphocytes and the ratio of Th to Ts were reduced compared with the normal control values. The percentage of albumin decreased whereas beta globulin increased. There were 285 up-regulated and 446 down-regulated genes in irradiated samples relative to the control samples. The expression of KDR, CEACAM8 and OSM was validated by RT-PCR. The majority of the differentially expressed genes encode proteins associated with the immune response, inflammation, oncogenesis, cell structure, oxidative stress, neuro-hormone regulation, reproduction, susceptibility to psychiatric disorders, or transcriptional regulation. We have identified a number of promising novel candidates that have potential for serving as biomarkers for delayed damage. Furthermore, the changes in the immunological indicator CD4+ T cells, and the ratio of CD4+ T to CD8+ T cells may be biomarkers for the prediction of delayed damage by ionizing radiation. The findings of our study are useful for forming a comprehensive understanding of the mechanisms underlying the delayed effects of ionizing radiation. (author)

  17. 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 ...

  18. 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.

  19. Immunophenotyping of Waldenstroms macroglobulinemia cell lines reveals distinct patterns of surface antigen expression: potential biological and therapeutic implications.

    Directory of Open Access Journals (Sweden)

    Aneel Paulus

    Full Text Available Waldenströms macroglobulinemia (WM is a subtype of Non-Hodgkin's lymphoma in which the tumor cell population is markedly heterogeneous, consisting of immunoglobulin-M secreting B-lymphocytes, plasmacytoid lymphocytes and plasma cells. Due to rarity of disease and scarcity of reliable preclinical models, many facets of WM molecular and phenotypic architecture remain incompletely understood. Currently, there are 3 human WM cell lines that are routinely used in experimental studies, namely, BCWM.1, MWCL-1 and RPCI-WM1. During establishment of RPCI-WM1, we observed loss of the CD19 and CD20 antigens, which are typically present on WM cells. Intrigued by this observation and in an effort to better define the immunophenotypic makeup of this cell line, we conducted a more comprehensive analysis for the presence or absence of other cell surface antigens that are present on the RPCI-WM1 model, as well as those on the two other WM cell lines, BCWM.1 and MWCL-1. We examined expression of 65 extracellular and 4 intracellular antigens, comprising B-cell, plasma cell, T-cell, NK-cell, myeloid and hematopoietic stem cell surface markers by flow cytometry analysis. RPCI-WM1 cells demonstrated decreased expression of CD19, CD20, and CD23 with enhanced expression of CD28, CD38 and CD184, antigens that were differentially expressed on BCWM.1 and MWCL-1 cells. Due to increased expression of CD184/CXCR4 and CD38, RPCI-WM1 represents a valuable model in which to study the effects anti-CXCR4 or anti-CD38 targeted therapies that are actively being developed for treatment of hematologic cancers. Overall, differences in surface antigen expression across the 3 cell lines may reflect the tumor clone population predominant in the index patients, from whom the cell lines were developed. Our analysis defines the utility of the most commonly employed WM cell lines as based on their immunophenotype profiles, highlighting unique differences that can be further studied for

  20. Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes.

    Science.gov (United States)

    Henriques, Rui; Madeira, Sara C

    2015-01-01

    Genes can participate in multiple biological processes at a time and thus their expression can be seen as a composition of the contributions from the active processes. Biclustering under a plaid assumption allows the modeling of interactions between transcriptional modules or biclusters (subsets of genes with coherence across subsets of conditions) by assuming an additive composition of contributions in their overlapping areas. Despite the biological interest of plaid models, few biclustering algorithms consider plaid effects and, when they do, they place restrictions on the allowed types and structures of biclusters, and suffer from robustness problems by seizing exact additive matchings. We propose BiP (Biclustering using Plaid models), a biclustering algorithm with relaxations to allow expression levels to change in overlapping areas according to biologically meaningful assumptions (weighted and noise-tolerant composition of contributions). BiP can be used over existing biclustering solutions (seizing their benefits) as it is able to recover excluded areas due to unaccounted plaid effects and detect noisy areas non-explained by a plaid assumption, thus producing an explanatory model of overlapping transcriptional activity. Experiments on synthetic data support BiP's efficiency and effectiveness. The learned models from expression data unravel meaningful and non-trivial functional interactions between biological processes associated with putative regulatory modules.

  1. Understanding facial expressivity in autism spectrum disorder: An inside out review of the biological basis and clinical implications.

    Science.gov (United States)

    Deutsch, Stephen I; Raffaele, C Teal

    2018-05-16

    Deficits in decoding and understanding facially expressed emotions occur commonly in persons with autism spectrum disorder (ASD), which contribute to the impairment of social communication that serves as one of its core diagnostic criteria. Research suggests that abnormalities of visual scanning of the face, activation of key nodes within the "social brain" by facially expressed emotions, functional connectivity within and between nodes of the "social brain", and transduction of specific neurotransmitter/neuromodulatory signals contribute to the pathogenesis of these deficits in at least some persons with ASD. Importantly, the etiologies of these deficits are heterogeneous and include genetic, immunologic, and inflammatory mechanisms, as well as in utero exposures to drugs and toxins. The manifestation and severity of these deficits can also be influenced by developmental age, IQ and genetic background. Consistent with the goals of the Special Issue, the current Review is intended to familiarize the readership with several of the leading neurobiological mechanisms proposed to underlie these deficits in decoding facially expressed emotions and stimulate interest in translational preclinical and clinical investigations, whose ultimate purpose is to attenuate their severity and, thereby, improve functional outcomes of persons with ASD. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. Dioxin exposure of human CD34+ hemopoietic cells induces gene expression modulation that recapitulates its in vivo clinical and biological effects

    International Nuclear Information System (INIS)

    Fracchiolla, Nicola Stefano; Todoerti, Katia; Bertazzi, Pier Alberto; Servida, Federica; Corradini, Paolo; Carniti, Cristiana; Colombi, Antonio; Cecilia Pesatori, Angela; Neri, Antonino; Deliliers, Giorgio Lambertenghi

    2011-01-01

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) has a large number of biological effects, including skin, cardiovascular, neurologic diseases, diabetes, infertility, cancers and immunotoxicity. We analysed the in vitro TCDD effects on human CD34 + cells and tested the gene expression modulation by means of microarray analyses before and after TCDD exposure. We identified 257 differentially modulated probe sets, identifying 221 well characterized genes. A large part of these resulted associated to cell adhesion and/or angiogenesis and to transcription regulation. Synaptic transmission and visual perception functions, with the particular involvement of the GABAergic pathway were also significantly modulated. Numerous transcripts involved in cell cycle or cell proliferation, immune response, signal transduction, ion channel activity or calcium ion binding, tissue development and differentiation, female or male fertility or in several metabolic pathways were also affected after dioxin exposure. The transcriptional profile induced by TCDD treatment on human CD34 + cells strikingly reproduces the clinical and biological effects observed in individuals exposed to dioxin and in biological experimental systems. Our data support a role of dioxin in the neoplastic transformation of hemopoietic stem cells and in immune modulation processes after in vivo exposure, as indicated by the epidemiologic data in dioxin accidentally exposed populations, providing a molecular basis for it. In addition, TCDD alters genes associated to glucidic and lipidic metabolisms, to GABAergic transmission or involved in male and female fertility, thus providing a possible explanation of the diabetogenic, dyslipidemic, neurologic and fertility effects induced by TCDD in vivo exposure.

  3. 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

  4. Distinct gene subsets in pterygia formation and recurrence: dissecting complex biological phenomenon using genome wide expression data

    Directory of Open Access Journals (Sweden)

    Ang Leonard PK

    2009-03-01

    Full Text Available Abstract Background Pterygium is a common ocular surface disease characterized by fibrovascular invasion of the cornea and is sight-threatening due to astigmatism, tear film disturbance, or occlusion of the visual axis. However, the mechanisms for formation and post-surgical recurrence of pterygium are not understood, and a valid animal model does not exist. Here, we investigated the possible mechanisms of pterygium pathogenesis and recurrence. Methods First we performed a genome wide expression analysis (human Affymetrix Genechip, >22000 genes with principal component analysis and clustering techniques, and validated expression of key molecules with PCR. The controls for this study were the un-involved conjunctival tissue of the same eye obtained during the surgical resection of the lesions. Interesting molecules were further investigated with immunohistochemistry, Western blots, and comparison with tear proteins from pterygium patients. Results Principal component analysis in pterygium indicated a signature of matrix-related structural proteins, including fibronectin-1 (both splice-forms, collagen-1A2, keratin-12 and small proline rich protein-1. Immunofluorescence showed strong expression of keratin-6A in all layers, especially the superficial layers, of pterygium epithelium, but absent in the control, with up-regulation and nuclear accumulation of the cell adhesion molecule CD24 in the pterygium epithelium. Western blot shows increased protein expression of beta-microseminoprotein, a protein up-regulated in human cutaneous squamous cell carcinoma. Gene products of 22 up-regulated genes in pterygium have also been found by us in human tears using nano-electrospray-liquid chromatography/mass spectrometry after pterygium surgery. Recurrent disease was associated with up-regulation of sialophorin, a negative regulator of cell adhesion, and never in mitosis a-5, known to be involved in cell motility. Conclusion Aberrant wound healing is therefore

  5. 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).

  6. 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.

  7. 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.

  8. 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.

  9. Alteration of runt-related transcription factor 3 gene expression and biologic behavior of esophageal carcinoma TE-1 cells after 5-azacytidine intervention.

    Science.gov (United States)

    Wang, Shuai; Liu, Hong; Akhtar, Javed; Chen, Hua-Xia; Wang, Zhou

    2013-01-01

    5-Azacytidine (5-azaC) was originally identified as an anticancer drug (NSC102876) which can cause hypomethylation of tumor suppressor genes. To assess its effects on runt-related transcription factor 3 (RUNX3), expression levels and the promoter methylation status of the RUNX3 gene were assessed. We also investigated alteration of biologic behavior of esophageal carcinoma TE-1 cells. MTT assays showed 5-azaC inhibited the proliferation of TE-1 cells in a time and dose-dependent way. Although other genes could be demethylated after 5-azaC intervention, we focused on RUNX3 gene in this study. The expression level of RUNX3 mRNA increased significantly in TE-1 cells after treatment with 5-azaC at hypotoxic levels. RT-PCR showed 5-azaC at 50 μM had the highest RUNX3-induction activity. Methylation-specific PCR indicated that 5-azaC induced RUNX3 expression through demethylation. Migration and invasion of TE-1 cells were inhibited by 5-azaC, along with growth of Eca109 xenografts in nude mice. In conclusion, we demonstrate that the RUNX3 gene can be reactivated by the demethylation reagent 5-azaC, which inhibits the proliferation, migration and invasion of esophageal carcinoma TE-1 cells.

  10. 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

  11. Association between clinically meaningful behavior problems and overweight in children.

    Science.gov (United States)

    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

  12. 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

  13. NKT Cell-TCR Expression Activates Conventional T Cells in Vivo, but Is Largely Dispensable for Mature NKT Cell Biology

    Science.gov (United States)

    Vahl, J. Christoph; Heger, Klaus; Knies, Nathalie; Hein, Marco Y.; Boon, Louis; Yagita, Hideo; Polic, Bojan; Schmidt-Supprian, Marc

    2013-01-01

    Natural killer T (NKT) cell development depends on recognition of self-glycolipids via their semi-invariant Vα14i-TCR. However, to what extent TCR-mediated signals determine identity and function of mature NKT cells remains incompletely understood. To address this issue, we developed a mouse strain allowing conditional Vα14i-TCR expression from within the endogenous Tcrα locus. We demonstrate that naïve T cells are activated upon replacement of their endogenous TCR repertoire with Vα14i-restricted TCRs, but they do not differentiate into NKT cells. On the other hand, induced TCR ablation on mature NKT cells did not affect their lineage identity, homeostasis, or innate rapid cytokine secretion abilities. We therefore propose that peripheral NKT cells become unresponsive to and thus are independent of their autoreactive TCR. PMID:23853545

  14. NKT cell-TCR expression activates conventional T cells in vivo, but is largely dispensable for mature NKT cell biology.

    Directory of Open Access Journals (Sweden)

    J Christoph Vahl

    Full Text Available Natural killer T (NKT cell development depends on recognition of self-glycolipids via their semi-invariant Vα14i-TCR. However, to what extent TCR-mediated signals determine identity and function of mature NKT cells remains incompletely understood. To address this issue, we developed a mouse strain allowing conditional Vα14i-TCR expression from within the endogenous Tcrα locus. We demonstrate that naïve T cells are activated upon replacement of their endogenous TCR repertoire with Vα14i-restricted TCRs, but they do not differentiate into NKT cells. On the other hand, induced TCR ablation on mature NKT cells did not affect their lineage identity, homeostasis, or innate rapid cytokine secretion abilities. We therefore propose that peripheral NKT cells become unresponsive to and thus are independent of their autoreactive TCR.

  15. [Effect of down-regulation of HE4 gene expression on biologic behavior of ovarian cancer cells].

    Science.gov (United States)

    Zhou, Lei; Xiao, Ran; Chen, Ying; Zhang, Jing; Lu, Ren-quan; Guo, Lin

    2013-10-01

    To investigate the effects of HE4 gene knockdown on the proliferation, adhesion and invasion of the ovarian cancer cells SKOV3. The knockdown of HE4 gene was performed by RNAi technology. The recombinant plasmids (pSUPER-HE4 shDNAs) were constructed and transfected into human ovarian cancer cells SKOV3. HE4 expression was then identified by real-time PCR and Western blot analysis. The invasion and adhesion ability of transduced cells were determined. In addition, cell proliferation and growth were analyzed by colonies formation assay. Knockdown of HE4 was achieved, and further confirmed by real-time PCR and Western blot. The proliferation of HE4-down-regulated cells was not affected, but the invasion ability of the transfected cells was reduced (P cells.

  16. The induction of a tumor suppressor gene (p53) expression by low-dose radiation and its biological meaning

    International Nuclear Information System (INIS)

    Ohnishi, Takeo

    1997-01-01

    I report the induced accumulation of wild-type p53 protein of a tumor suppressor gene within 12 h in various organs of rats exposed to X-ray irradiation at low doses (10-50 cGy). The levels of p53 in some organs of irradiated rats were increased about 2- to 3-fold in comparison with the basal p53 levels in non-irradiated rats. Differences in the levels of p53 induction after low-dose X-ray irradiation were observed among the small intestine, bone marrow, brain, liver, adrenal gland, spleen, hypophysis and skin. In contrast, there was no obvious accumulation of p53 protein in the testis and ovary. Thus, the induction of cellular p.53 accumulation by low-dose X-ray irradiation in rats seems to be organ-specific. I consider that cell type, and interactions with other signal transduction pathways of the hormone system, immune system and nervous system may contribute to the variable induction of p53 by low-dose X-ray irradiation. I discussed the induction of p53 by radiation and its biological meaning from an aspect of the defense system for radiation-induced cancer. (author)

  17. Integrative miRNA-Gene Expression Analysis Enables Refinement of Associated Biology and Prediction of Response to Cetuximab in Head and Neck Squamous Cell Cancer

    Directory of Open Access Journals (Sweden)

    Loris De Cecco

    2017-01-01

    Full Text Available This paper documents the process by which we, through gene and miRNA expression profiling of the same samples of head and neck squamous cell carcinomas (HNSCC and an integrative miRNA-mRNA expression analysis, were able to identify candidate biomarkers of progression-free survival (PFS in patients treated with cetuximab-based approaches. Through sparse partial least square–discriminant analysis (sPLS-DA and supervised analysis, 36 miRNAs were identified in two components that clearly separated long- and short-PFS patients. Gene set enrichment analysis identified a significant correlation between the miRNA first-component and EGFR signaling, keratinocyte differentiation, and p53. Another significant correlation was identified between the second component and RAS, NOTCH, immune/inflammatory response, epithelial–mesenchymal transition (EMT, and angiogenesis pathways. Regularized canonical correlation analysis of sPLS-DA miRNA and gene data combined with the MAGIA2 web-tool highlighted 16 miRNAs and 84 genes that were interconnected in a total of 245 interactions. After feature selection by a smoothed t-statistic support vector machine, we identified three miRNAs and five genes in the miRNA-gene network whose expression result was the most relevant in predicting PFS (Area Under the Curve, AUC = 0.992. Overall, using a well-defined clinical setting and up-to-date bioinformatics tools, we are able to give the proof of principle that an integrative miRNA-mRNA expression could greatly contribute to the refinement of the biology behind a predictive model.

  18. Biologically meaningful scents: a framework for understanding predator-prey research across disciplines.

    Science.gov (United States)

    Parsons, Michael H; Apfelbach, Raimund; Banks, Peter B; Cameron, Elissa Z; Dickman, Chris R; Frank, Anke S K; Jones, Menna E; McGregor, Ian S; McLean, Stuart; Müller-Schwarze, Dietland; Sparrow, Elisa E; Blumstein, Daniel T

    2018-02-01

    Fear of predation is a universal motivator. Because predators hunt using stealth and surprise, there is a widespread ability among prey to assess risk from chemical information - scents - in their environment. Consequently, scents often act as particularly strong modulators of memory and emotions. Recent advances in ecological research and analytical technology are leading to novel ways to use this chemical information to create effective attractants, repellents and anti-anxiolytic compounds for wildlife managers, conservation biologists and health practitioners. However, there is extensive variation in the design, results, and interpretation of studies of olfactory-based risk discrimination. To understand the highly variable literature in this area, we adopt a multi-disciplinary approach and synthesize the latest findings from neurobiology, chemical ecology, and ethology to propose a contemporary framework that accounts for such disparate factors as the time-limited stability of chemicals, highly canalized mechanisms that influence prey responses, and the context within which these scents are detected (e.g. availability of alternative resources, perceived shelter, and ambient physical parameters). This framework helps to account for the wide range of reported responses by prey to predator scents, and explains, paradoxically, how the same individual predator scent can be interpreted as either safe or dangerous to a prey animal depending on how, when and where the cue was deposited. We provide a hypothetical example to illustrate the most common factors that influence how a predator scent (from dingoes, Canis dingo) may both attract and repel the same target organism (kangaroos, Macropus spp.). This framework identifies the catalysts that enable dynamic scents, odours or odorants to be used as attractants as well as deterrents. Because effective scent tools often relate to traumatic memories (fear and/or anxiety) that cause future avoidance, this information may also guide the development of appeasement, enrichment and anti-anxiolytic compounds, and help explain the observed variation in post-traumatic-related behaviours (including post-traumatic stress disorder, PTSD) among diverse terrestrial taxa, including humans. © 2017 Cambridge Philosophical Society.

  19. 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.

  20. Temporal variations in the gene expression levels of cyanobacterial anti-oxidant enzymes through geological history: implications for biological evolution during the Great Oxidation Event

    Science.gov (United States)

    Harada, M.; Furukawa, R.; Yokobori, S. I.; Tajika, E.; Yamagishi, A.

    2016-12-01

    expression levels of Fe-SOD occurred in response to the GOE. We propose that this is the first direct evidence of the evolution of cyanobacteria related to the rise of O2, and that the methodologies of ancestral promoter analysis used in this study can be a novel tools to reveal the biological adaptation to such a significant geologic event.

  1. Biological and biochemical characterization of mice expressing prion protein devoid of the octapeptide repeat region after infection with prions.

    Science.gov (United States)

    Yamaguchi, Yoshitaka; Miyata, Hironori; Uchiyama, Keiji; Ootsuyama, Akira; Inubushi, Sachiko; Mori, Tsuyoshi; Muramatsu, Naomi; Katamine, Shigeru; Sakaguchi, Suehiro

    2012-01-01

    Accumulating lines of evidence indicate that the N-terminal domain of prion protein (PrP) is involved in prion susceptibility in mice. In this study, to investigate the role of the octapeptide repeat (OR) region alone in the N-terminal domain for the susceptibility and pathogenesis of prion disease, we intracerebrally inoculated RML scrapie prions into tg(PrPΔOR)/Prnp(0/0) mice, which express mouse PrP missing only the OR region on the PrP-null background. Incubation times of these mice were not extended. Protease-resistant PrPΔOR, or PrP(Sc)ΔOR, was easily detectable but lower in the brains of these mice, compared to that in control wild-type mice. Consistently, prion titers were slightly lower and astrogliosis was milder in their brains. However, in their spinal cords, PrP(Sc)ΔOR and prion titers were abundant and astrogliosis was as strong as in control wild-type mice. These results indicate that the role of the OR region in prion susceptibility and pathogenesis of the disease is limited. We also found that the PrP(Sc)ΔOR, including the pre-OR residues 23-50, was unusually protease-resistant, indicating that deletion of the OR region could cause structural changes to the pre-OR region upon prion infection, leading to formation of a protease-resistant structure for the pre-OR region.

  2. Differential receptor dependencies: expression and significance of muscarinic M1 receptors in the biology of prostate cancer.

    Science.gov (United States)

    Mannan Baig, Abdul; Khan, Naveed A; Effendi, Vardah; Rana, Zohaib; Ahmad, H R; Abbas, Farhat

    2017-01-01

    Recent reports on acetylcholine muscarinic receptor subtype 3 (CHRM3) have shown its growth-promoting role in prostate cancer. Additional studies report the proliferative effect of the cholinergic agonist carbachol on prostate cancer by its agonistic action on CHRM3. This study shows that the type 1 acetylcholine muscarinic receptor (CHRM1) contributes toward the proliferation and growth of prostate cancer. We used growth and cytotoxic assays, the prostate cancer microarray database and CHRM downstream pathways' homology of CHRM subtypes to uncover multiple signals leading to the growth of prostate cancer. Growth assays showed that pilocarpine stimulates the proliferation of prostate cancer. Moreover, it shows that carbachol exerts an additional agonistic action on nicotinic cholinergic receptor of prostate cancer cells that can be blocked by tubocurarine. With the use of selective CHRM1 antagonists such as pirenzepine and dicyclomine, a considerable inhibition of proliferation of prostate cancer cell lines was observed in dose ranging from 15-60 µg/ml of dicyclomine. The microarray database of prostate cancer shows a dominant expression of CHRM1 in prostate cancer compared with other cholinergic subtypes. The bioinformatics of prostate cancer and CHRM pathways show that the downstream signalling include PIP3-AKT-CaM-mediated growth in LNCaP and PC3 cells. Our study suggests that antagonism of CHRM1 may be a potential therapeutic target against prostate cancer.

  3. Cross-species comparison of biological themes and underlying genes on a global gene expression scale in a mouse model of colorectal liver metastasis and in clinical specimens

    Directory of Open Access Journals (Sweden)

    Schirmacher Peter

    2008-09-01

    Full Text Available Abstract Background Invasion-related genes over-expressed by tumor cells as well as by reacting host cells represent promising drug targets for anti-cancer therapy. Such candidate genes need to be validated in appropriate animal models. Results This study examined the suitability of a murine model (CT26/Balb/C of colorectal liver metastasis to represent clinical liver metastasis specimens using a global gene expression approach. Cross-species similarity was examined between pure liver, liver invasion, tumor invasion and pure tumor compartments through overlap of up-regulated genes and gene ontology (GO-based biological themes on the level of single GO-terms and of condensed GO-term families. Three out of four GO-term families were conserved in a compartment-specific way between the species: secondary metabolism (liver, invasion (invasion front, and immune response (invasion front and liver. Among the individual GO-terms over-represented in the invasion compartments in both species were "extracellular matrix", "cell motility", "cell adhesion" and "antigen presentation" indicating that typical invasion related processes are operating in both species. This was reflected on the single gene level as well, as cross-species overlap of potential target genes over-expressed in the combined invasion front compartments reached up to 36.5%. Generally, histopathology and gene expression correlated well as the highest single gene overlap was found to be 44% in syn-compartmental comparisons (liver versus liver whereas cross-compartmental overlaps were much lower (e.g. liver versus tumor: 9.7%. However, single gene overlap was surprisingly high in some cross-compartmental comparisons (e.g. human liver invasion compartment and murine tumor invasion compartment: 9.0% despite little histolopathologic similarity indicating that invasion relevant genes are not necessarily confined to histologically defined compartments. Conclusion In summary, cross

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

    Directory of Open Access Journals (Sweden)

    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.

  5. The measurement of water scarcity: Defining a meaningful indicator.

    Science.gov (United States)

    Damkjaer, Simon; Taylor, Richard

    2017-09-01

    Metrics of water scarcity and stress have evolved over the last three decades from simple threshold indicators to holistic measures characterising human environments and freshwater sustainability. Metrics commonly estimate renewable freshwater resources using mean annual river runoff, which masks hydrological variability, and quantify subjectively socio-economic conditions characterising adaptive capacity. There is a marked absence of research evaluating whether these metrics of water scarcity are meaningful. We argue that measurement of water scarcity (1) be redefined physically in terms of the freshwater storage required to address imbalances in intra- and inter-annual fluxes of freshwater supply and demand; (2) abandons subjective quantifications of human environments and (3) be used to inform participatory decision-making processes that explore a wide range of options for addressing freshwater storage requirements beyond dams that include use of renewable groundwater, soil water and trading in virtual water. Further, we outline a conceptual framework redefining water scarcity in terms of freshwater storage.

  6. 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.

  7. 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...

  8. The Structure and Function of Biological Networks

    Science.gov (United States)

    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…

  9. Expression of Msx-1 is suppressed in bisphosphonate associated osteonecrosis related jaw tissue-etiopathology considerations respecting jaw developmental biology-related unique features.

    Science.gov (United States)

    Wehrhan, Falk; Hyckel, Peter; Ries, Jutta; Stockmann, Phillip; Nkenke, Emeka; Schlegel, Karl A; Neukam, Friedrich W; Amann, Kerstin

    2010-10-13

    Bone-destructive disease treatments include bisphosphonates and antibodies against the osteoclast differentiator, RANKL (aRANKL); however, osteonecrosis of the jaw (ONJ) is a frequent side-effect. Current models fail to explain the restriction of bisphosphonate (BP)-related and denosumab (anti-RANKL antibody)-related ONJ to jaws. Msx-1 is exclusively expressed in craniofacial structures and pivotal to cranial neural crest (CNC)-derived periodontal tissue remodeling. We hypothesised that Msx-1 expression might be impaired in bisphosphonate-related ONJ. The study aim was to elucidate Msx-1 and RANKL-associated signal transduction (BMP-2/4, RANKL) in ONJ-altered and healthy periodontal tissue. Twenty ONJ and twenty non-BP exposed periodontal samples were processed for RT-PCR and immunohistochemistry. An automated staining-based alkaline phosphatase-anti-alkaline phosphatase method was used to measure the stained cells:total cell-number ratio (labelling index, Bonferroni adjustment). Real-time RT-PCR was performed on ONJ-affected and healthy jaw periodontal samples (n = 20 each) to quantitatively compare Msx-1, BMP-2, RANKL, and GAPDH mRNA levels. Semi-quantitative assessment of the ratio of stained cells showed decreased Msx-1 and RANKL and increased BMP-2/4 (all p Msx-1 (p Msx-1 suppression in ONJ-adjacent periodontal tissue suggested a bisphosphonate-related impairment in cellular differentiation that occurred exclusively jaw remodelling. Further research on developmental biology-related unique features of jaw bone structures will help to elucidate pathologies restricted to maxillofacial tissue.

  10. Expression of Msx-1 is suppressed in bisphosphonate associated osteonecrosis related jaw tissue-etiopathology considerations respecting jaw developmental biology-related unique features

    Directory of Open Access Journals (Sweden)

    Schlegel Karl A

    2010-10-01

    Full Text Available Abstract Background Bone-destructive disease treatments include bisphosphonates and antibodies against the osteoclast differentiator, RANKL (aRANKL; however, osteonecrosis of the jaw (ONJ is a frequent side-effect. Current models fail to explain the restriction of bisphosphonate (BP-related and denosumab (anti-RANKL antibody-related ONJ to jaws. Msx-1 is exclusively expressed in craniofacial structures and pivotal to cranial neural crest (CNC-derived periodontal tissue remodeling. We hypothesised that Msx-1 expression might be impaired in bisphosphonate-related ONJ. The study aim was to elucidate Msx-1 and RANKL-associated signal transduction (BMP-2/4, RANKL in ONJ-altered and healthy periodontal tissue. Methods Twenty ONJ and twenty non-BP exposed periodontal samples were processed for RT-PCR and immunohistochemistry. An automated staining-based alkaline phosphatase-anti-alkaline phosphatase method was used to measure the stained cells:total cell-number ratio (labelling index, Bonferroni adjustment. Real-time RT-PCR was performed on ONJ-affected and healthy jaw periodontal samples (n = 20 each to quantitatively compare Msx-1, BMP-2, RANKL, and GAPDH mRNA levels. Results Semi-quantitative assessment of the ratio of stained cells showed decreased Msx-1 and RANKL and increased BMP-2/4 (all p Conclusions These results explain the sclerotic and osteopetrotic changes of periodontal tissue following BP application and substantiate clinical findings of BP-related impaired remodeling specific to periodontal tissue. RANKL suppression substantiated the clinical finding of impaired bone remodelling in BP- and aRANKL-induced ONJ-affected bone structures. Msx-1 suppression in ONJ-adjacent periodontal tissue suggested a bisphosphonate-related impairment in cellular differentiation that occurred exclusively jaw remodelling. Further research on developmental biology-related unique features of jaw bone structures will help to elucidate pathologies restricted to

  11. Sacrifice: an ethical dimension of caring that makes suffering meaningful.

    Science.gov (United States)

    Helin, Kaija; Lindström, Unni A

    2003-07-01

    This article is intended to raise the question of whether sacrifice can be regarded stituting a deep ethical structure in the relationship between patient and carer. The significance of sacrifice in a patient-carer relationship cannot, however, be fully understood from the standpoint of the consistently utilitarian ethic that characterizes today's ethical discourse. Deontological ethics, with its universal principles, also does not provide a suitable point of departure. Ethical recommendations and codices are important and serve as general sources of knowledge when making decisions, but they should be supplemented by an ethic that takes into consideration contextual and situational factors that make every encounter between patient and carer unique. Caring science research literature presents, on the whole, general agreement on the importance of responsibility and devotian with regard to sense of duty, warmth and genuine engagement in caring. That sacrifice may also constitute an important ethical element in the patient-carer relationship is, however, a contradictory and little considered theme. Caring literature that deals with sacrifice/self-sacrifice indicates contradictory import. It is nevertheless interesting to notice that both the negative and the positive aspects bring out importance of the concept for the professional character of caring. The tradition of ideas in medieval Christian mysticism with reference to Lévinas' ethic of responsibility offers a deeper perspective in which the meaningfulness of sacrifice in the caring relationship can be sought. The theme of sacrifice is not of interest merely as a carer's ethical outlook, but sacrifice can also be understood as a potential process of transformation health. The instinctive or conscious experience of sacrifice on the part of the individual patient can, on a symbolic level, be regarded as analogous to the cultic or religious sacrifice aiming at atonement. Sacrifice appears to the patient as an act of

  12. Synthetic Biology: Putting Synthesis into Biology

    Science.gov (United States)

    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

  13. Job enrichment: creating meaningful career development opportunities for nurses.

    Science.gov (United States)

    Duffield, Christine; Baldwin, Richard; Roche, Michael; Wise, Sarah

    2014-09-01

    This paper presents an evaluation of a career development policy in South Australia which increased the number of senior staff nurse positions and provided senior registered nurses with time away from clinical duties to undertake agreed projects. We use Kanter's model of structural power and commitment theory to understand the dimensions of this policy. Development strategies for experienced staff who wish to remain at the bedside are needed, especially in smaller health services with limited opportunities for horizontal or vertical mobility. Face-to-face semistructured interviews were conducted with 54 senior staff nurses who participated in the career structure arrangements. The policy enhanced the structure of opportunity in three ways: by increasing the number of senior staff nurse positions, the ladder steps were improved; undertaking strategic projects developed new skills; and the job enrichment approach facilitated time out from the immediate pressures of ward work and challenged nurses in a different way. Through job enrichment, South Australia has found a novel way of providing meaningful career development opportunities for experienced nurses. Methods of job enrichment need to be considered as part of career development policy, especially where movement between clinical facilities is limited and staff wish to remain at the bedside. © 2013 John Wiley & Sons Ltd.

  14. 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.

  15. Contributions of meaningful experiences gatherings to artistic education field

    Directory of Open Access Journals (Sweden)

    Bernardo Bustamante Cardona

    2012-06-01

    Full Text Available This article shows a theoretical approach to and a description of some contributions of a work of transformation of educational and sociocultural reality carried out by a group of people and institutions, among which are San Buenaventura University, Antioquia Museum, Ediarte Inc. and Antioquia University. Such intervention aims at contributing to the improvement of Artistic Education quality in Antioquia and the nation. In order to understand the significance of these Gatherings, a short historical framework is explained in which global and regional processes of academic activities having an impact on the structure of the Artistic Education field are pointed out. Likewise, some perspectives in the definition of artistic education are tackled and then a definition of Pierre Bourdieu´s concept of fieldis presented. Therefore, Meaningful Experiences Gatherings in Artistic Education (MEGAE are presented and the three first gatherings are described. Finally, it is shown the panorama of the contributions of the gatherings both in the theoretical formulation and relational structure of the field.

  16. Do family physicians electronic health records support meaningful use?

    Science.gov (United States)

    Peterson, Lars E; Blackburn, Brenna; Ivins, Douglas; Mitchell, Jason; Matson, Christine; Phillips, Robert L

    2015-03-01

    Spurred by government incentives, the use of electronic health records (EHRs) in the United States has increased; however, whether these EHRs have the functionality necessary to meet meaningful use (MU) criteria remains unknown. Our objective was to characterize family physician access to MU functionality when using a MU-certified EHR. Data were obtained from a convenience survey of family physicians accessing their American Board of Family Medicine online portfolio in 2011. A brief survey queried MU functionality. We used descriptive statistics to characterize the responses and bivariate statistics to test associations between MU and patient communication functions by presence of a MU-certified EHR. Out of 3855 respondents, 60% reported having an EHR that supports MU. Physicians with MU-certified EHRs were more likely than physicians without MU-certified EHRs to report patient registry activities (49.7% vs. 32.3%, p-valuevs. 56.4%, p-valuecommunication abilities were low regardless of EHR capabilities. Family physicians with MU-certified EHRs are more likely to report MU functionality; however, a sizeable minority does not report MU functions. Many family physicians with MU-certified EHRs may not successfully meet the successively stringent MU criteria and may face significant upgrade costs to do so. Cross sectional survey. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Measuring Patient Experiences: Is It Meaningful and Actionable?

    Science.gov (United States)

    Wong, Sabrina T; Johnston, Sharon; Burge, Fred; McGrail, Kim; Hogg, William

    2017-10-01

    Performance measurement must be meaningful to those being asked to contribute data and to the clinicians who are collecting the information. It must be actionable if performance measurement and reporting is to influence health system transformation. To date, measuring patient experiences in all parts of the healthcare system in Canada lags behind other countries. More attention needs to be paid to capturing patients with complex intersecting health and social problems that result from inequitable distribution of wealth and/or underlying structural inequities related to systemic issues such as racism and discrimination, colonialism and patriarchy. Efforts to better capture the experiences of patients who do not regularly access care and who speak English or French as a second language are also needed. Before investing heavily into collecting patient experience data as part of a performance measurement system the following ought to be considered: (1) ensuring value for and buy-in from clinicians who are being asked to collect the data and/or act on the results; (2) investment in the infrastructure to administer iterative, cost-effective patient/family experience data collection, analysis and reporting (e.g., automated software tools) and (3) incorporating practice support (e.g., facilitation) and health system opportunities to integrate the findings from patient experience surveys into policy and practice. Investment into the infrastructure of measuring, reporting and engaging clinicians in improving practice is needed for patient/caregiver experiences to be acted upon. © 2017 Longwoods Publishing.

  18. 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...

  19. PSK, a biological response modifier, modifies p53 expression, mitosis and apoptosis in X-ray irradiated mouse embryos. Possible cellular mechanism of the anti-teratogenic effect

    International Nuclear Information System (INIS)

    Kagohashi, Yukiko; Naora, Hiroyuki; Otani, Hiroki

    2002-01-01

    We previously showed that PSK, a biological response modifier, suppressed X-ray irradiation induced ocular anomalies in mouse embryos. In the present study, in mouse embryos irradiated at E7.5, PSK, when administered immediately after irradiation, suppressed mitosis and increased apoptosis as compared with embryos not treated with PSK at 12 hrs after irradiation. In the irradiated embryos, p53, which is normally expressed at a high level in early embryos, increased at 6 hrs and decreased at 12 hrs after irradiation. In the irradiated and PSK-treated embryos, the p53 level did not change at 6 hrs, increased at 12 hrs and decreased at 24 hrs after irradiation. This timing of PSK-induced delayed increase of p53 coincided with that of the PSK-induced decrease in mitosis and increase in apoptosis. These results suggested that PSK modified the p53 level and affected cell proliferation and apoptosis, which might contribute to the suppression of teratogenesis. (author)

  20. Heterologous expression of a truncated form of human recombinant vascular endothelial growth factor-A and its biological activity in wound healing.

    Science.gov (United States)

    Khaki, Mohsen; Salmanian, Ali Hatef; Mosayebi, Ghasem; Baazm, Maryam; Babaei, Saeed; Molaee, Neda; Abtahi, Hamid

    2017-07-01

    Vascular endothelial growth factor (VEGF) is one of the most effective proteins in angiogenesis, mesenchymal stem cells (MSCs) differentiation and wound healing. These abilities are therapeutic potential of VEGF in diabetic retinopathy, nephropathy and other tissue damage circumstances. In this study, recombinant VEGF was produced in Escherichia coli ( E. coli ) system and then biological activity of this protein was evaluated in animal wound healing. E. coli BL21 (DE3) competent cells were transformed with pET32a-VEGF clone and induced by isopropyl-β-D-thio-galactoside (IPTG). The recombinant protein was purified by affinity chromatography. Recombinant VEGF-A-based ointment (VEGF/Vaseline 0.8 mg/100 w/w) was used for external wound (25×15mm thickness) healing in animal model. In vivo activity of ointment was evaluated by clinical evidences and cytological microscopic assessment. The recombinant protein with molecular weight of 45 kilodaltons (kDa) and concentration of 0.8 mg/ml was produced. Immunoblotting data showed that the antigenic region of VEGF can be expressed in E. coli and the recombinant protein has similar epitopes with close antigenic properties to the natural form. Macroscopic findings and microscopic data showed that the recombinant VEGF-A ointment was effective on excisional wound healing. Recombinant VEGF-A produced by pET32a in E. coli , possesses acceptable structure and has wound healing capability.

  1. Heterologous expression of a truncated form of human recombinant vascular endothelial growth factor-A and its biological activity in wound healing

    Directory of Open Access Journals (Sweden)

    Mohsen Khaki

    2017-07-01

    Full Text Available Objective(s: Vascular endothelial growth factor (VEGF is one of the most effective proteins in angiogenesis, mesenchymal stem cells (MSCs differentiation and wound healing. These abilities are therapeutic potential of VEGF in diabetic retinopathy, nephropathy and other tissue damage circumstances. In this study, recombinant VEGF was produced in Escherichia coli (E. coli system and then biological activity of this protein was evaluated in animal wound healing. Materials and Methods: E. coli BL21 (DE3 competent cells were transformed with pET32a-VEGF clone and induced by isopropyl-β-D-thio-galactoside (IPTG. The recombinant protein was purified byaffinity chromatography. Recombinant VEGF-A-based ointment (VEGF/Vaseline 0.8 mg/100 w/w was used for external wound (25×15mm thickness healing in animal model. In vivo activity of ointment was evaluated by clinical evidences and cytological microscopic assessment. Results: The recombinant protein with molecular weight of 45 kilodaltons (kDa and concentration of 0.8 mg/ml was produced.Immunoblotting data showed that the antigenic region of VEGF can be expressed in E. coli and the recombinant protein has similar epitopes with close antigenic properties to the natural form. Macroscopic findings and microscopic data showed that the recombinant VEGF-A ointment was effective on excisional wound healing. Conclusion: Recombinant VEGF-A produced by pET32a in E. coli, possesses acceptable structure and has wound healing capability.

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

    Science.gov (United States)

    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.

  3. 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.

  4. Is the diagnostic threshold for bulimia nervosa clinically meaningful?

    Science.gov (United States)

    Chapa, Danielle A N; Bohrer, Brittany K; Forbush, Kelsie T

    2018-01-01

    The DSM-5 differentiates full- and sub-threshold bulimia nervosa (BN) according to average weekly frequencies of binge eating and inappropriate compensatory behaviors. This study was the first to evaluate the modified frequency criterion for BN published in the DSM-5. The purpose of this study was to test whether community-recruited adults (N=125; 83.2% women) with current full-threshold (n=77) or sub-threshold BN (n=48) differed in comorbid psychopathology and eating disorder (ED) illness duration, symptom severity, and clinical impairment. Participants completed the Clinical Impairment Assessment and participated in semi-structured clinical interviews of ED- and non-ED psychopathology. Differences between the sub- and full-threshold BN groups were assessed using MANOVA and Chi-square analyses. ED illness duration, age-of-onset, body mass index (BMI), alcohol and drug misuse, and the presence of current and lifetime mood or anxiety disorders did not differ between participants with sub- and full-threshold BN. Participants with full-threshold BN had higher levels of clinical impairment and weight concern than those with sub-threshold BN. However, minimal clinically important difference analyses suggested that statistically significant differences between participants with sub- and full-threshold BN on clinical impairment and weight concern were not clinically significant. In conclusion, sub-threshold BN did not differ from full-threshold BN in clinically meaningful ways. Future studies are needed to identify an improved frequency criterion for BN that better distinguishes individuals in ways that will more validly inform prognosis and effective treatment planning for BN. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Knowledge construction in the classroom: a meaningful pedagogical dialogue

    Directory of Open Access Journals (Sweden)

    Jesuína Lopes de Almeida Pacca

    2015-12-01

    Full Text Available Teacher’s performance at their real classroom was analyzed in regard to the applied pedagogical interaction. These teachers were participating in a long range continuous formation course that uses the strategy of analyzing pedagogical planning while it was being elaborated , applied and continuously evaluated by the teacher; the course aimed to the construction of professional competence with an adequate sight of the classroom interaction, within constructivist parameters. The teacher pedagogical planning was the study object: it was discussed continuously by the peers group and the coordinator who intended to point out to the explicit pedagogical content and to the content objectives that were declared for every class plan. The learning objectives and the procedures contained within it were confronted with the real evidence of learning. In these discussions learning concepts that were coherent with constructivism were invoked in addition to science contents and their nature. Dialogue was important in these discussions and stressed as a means for teaching and continuous evaluation. In this dynamical process, the teacher planning was being constantly redrafted, changing the adjustment of that classroom students to the planned knowledge acquisition. This course dynamics, led by the coordinator, intended to be reproduced by participants with their students, at least in part. We noticed surprising results in these teachers professional development besides those that were concretely planned: the transference of the course procedures to the classroom seems to happen in regard to the presence of dialogue but the most meaningful part was individual and particular progress that was included in the development of their classes and led to an improvement of abilities. We concluded that unexpected results can be converted into poles of professional performance growth and performance evolution . These results have led us to give special importance to the

  6. 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.

  7. Identification of highly synchronized subnetworks from gene expression data.

    Science.gov (United States)

    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.

  8. 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

  9. Becoming Butterflies: Making Metamorphosis Meaningful for Young Children

    Science.gov (United States)

    Giles, Rebecca M.; Baggett, Paige V.; Shaw, Edward L., Jr.

    2010-01-01

    Although butterflies are a common topic of study in many early childhood classrooms, integrating art production broadens the scope of the study and allows children to deepen their knowledge and understanding through creative self-expression. This article presents a set of integrated activities that focus on helping children fully grasp the process…

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

    Directory of Open Access Journals (Sweden)

    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.

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

    NARCIS (Netherlands)

    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,

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

    Science.gov (United States)

    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…

  13. 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:…

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

    Directory of Open Access Journals (Sweden)

    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.

  15. 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…

  16. 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…

  17. Meaningful Watershed Experiences for Middle and High School Students

    Science.gov (United States)

    Landry, Melinda; Smith, Cynthia; Greene, Joy

    2014-05-01

    Prince William County Public Schools and George Mason University in Virginia, USA, partnered to provide Meaningful Watershed Educational Experiences (MWEEs) for over 25,000 middle and high school students (11-18 year olds) across 34 schools. This school district, situated in a rapidly growing region 55 km southwest of Washington DC, has over 82,000 K-12 students. As native forest cover has been replaced with farming and urbanization, water quality has significantly degraded in the 166,534 km2 Chesapeake Bay watershed. This project was designed to increase student awareness of their impact on the land and waters of the largest estuary in the United States. MWEE is a long-term comprehensive project that incorporates a classroom preparation phase, a hands-on outdoor field investigation, and a reflection and data-sharing component. Training and technical assistance enhances the capacity of teachers of 6th grade, high school Earth Science and Environmental Science to deliver MWEEs which includes schoolyard stewardship, inquiry driven field study, use of hand-held technology and computer based mapping and analysis, project sharing and outreach. George Mason University researchers worked closely with K-12 science educators to create a comprehensive watershed-focused curriculum. Graduate and undergraduate students with strong interests in environmental science and education were trained to deliver the field investigation component of the MWEE. Representative teachers from each school were provided 3 days of professional development and were responsible for the training of their school's science education team. A comprehensive curriculum provided teachers with activities and tools designed to enhance students' mastery of state science objectives. Watershed concepts were used as the unifying theme to support student understanding of curriculum and STEM objectives including: scientific investigation, data collection and communication, chemistry, energy, erosion, human

  18. Regulation of HtrA2 on WT1 gene expression under imatinib stimulation and its effects on the cell biology of K562 cells.

    Science.gov (United States)

    Zhang, Lixia; Li, Yan; Li, Xiaoyan; Zhang, Qing; Qiu, Shaowei; Zhang, Qi; Wang, Min; Xing, Haiyan; Rao, Qing; Tian, Zheng; Tang, Kejing; Wang, Jianxiang; Mi, Yingchang

    2017-09-01

    The aim of the present study was to investigate the regulation of Wilms Tumor 1 (WT1) by serine protease high-temperature requirement protein A2 (HtrA2), a member of the Htr family, in K562 cells. In addition, the study aimed to observe the effect of this regulation on cell biological functions and its associated mechanisms. Expression of WT1 and HtrA2 mRNA, and proteins following imatinib and the HtrA2 inhibitor 5-[5-(2-nitrophenyl) furfuryl iodine]-1, 3-diphenyl-2-thiobarbituric acid (UCF-101) treatment was detected with reverse transcription-quantitative polymerase chain reaction and western blot analysis. Subsequent to treatment with drugs and UCF-101, the proliferative function of K562 cells was detected using MTT assays, and the rate of apoptosis was detected using Annexin V with propidium iodide flow cytometry in K562 cells. The protein levels in the signaling pathway were analyzed using western blotting following treatment with imatinib and UCF-101. In K562 cells, imatinib treatment activated HtrA2 gene at a transcription level, while the WT1 gene was simultaneously downregulated. Following HtrA2 inhibitor (UCF-101) treatment, the downregulation of WT1 increased gradually. At the protein level, imatinib induced the increase in HtrA2 protein level and concomitantly downregulated WT1 protein level. Subsequent to HtrA2 inhibition by UCF-101, the WT1 protein level decreased temporarily, but eventually increased. Imatinib induced apoptosis in K562 cells, but this effect was attenuated by the HtrA2 inhibitor UCF-101, resulting in the upregulation of the WT1 protein level. However; UCF-101 did not markedly change the proliferation inhibition caused by imatinib. Imatinib activated the p38 mitogen activated protein kinase (p38 MAPK) signaling pathway in K562 cells, and UCF-101 affected the activation of imatinib in the p38 MAPK signaling pathway. Imatinib inhibited the extracellular signal-related kinase (ERK1/2) pathway markedly and persistently, but UCF-101

  19. Biologic significance of receptor-binding cancer antigen expressed on SiSo cells (RCAS1) as a pivotal regulator of tumor growth through angiogenesis in human uterine cancer.

    Science.gov (United States)

    Sonoda, Kenzo; Miyamoto, Shingo; Yamazaki, Ayano; Kobayashi, Hiroaki; Nakashima, Manabu; Mekada, Eisuke; Wake, Norio

    2007-11-01

    The expression of receptor-binding cancer antigen expressed on SiSo cells (RCAS1) is related significantly to the overall survival of patients with various cancers. RCAS1 reportedly induces apoptotic cell death in peripheral lymphocytes, which may contribute to the escape of tumor cells from immune surveillance. RCAS1 expression also has been related to tumor invasiveness and size in uterine cervical cancer. To clarify whether RCAS1 exacerbates tumor progression, the authors investigated the association between RCAS1 expression and tumor growth potential. The authors constructed small interfering ribonucleic acid (RNA) (siRNA) to target RCAS1. After transfection of siRNA and the RCAS1-encoding gene, growth of tumor cells was assessed in vitro and in vivo. The correlation between RCAS1 expression and angiogenesis was investigated in the transfected cells and in inoculated tumors from nude mice. In addition, the same association was investigated immunohistochemically with tissue samples from patients with uterine cervical cancer. Knockdown of RCAS1 expression by siRNA significantly suppressed the in vivo growth of SiSo and HOUA tumor cells (P cell growth was not affected significantly. Enhanced RCAS1 expression significantly promoted in vivo growth, but not in vitro growth, of tumors derived from COS-7 cells (P = .0039). Introduction of the RCAS1-encoding gene increased expression of vascular endothelial growth factor (VEGF). In uterine cervical cancer, RCAS1 expression was associated significantly with VEGF expression (P = .0407) and with microvessel density (P = .0108). RCAS1 may be a pivotal regulator of tumor growth through angiogenesis. Continued exploration of the biologic function of RCAS1 may allow the development of novel therapeutic strategies for uterine cancer.

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

    Science.gov (United States)

    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/.

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

    Directory of Open Access Journals (Sweden)

    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/.

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

    Science.gov (United States)

    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

  3. 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

  4. MetaboAnalyst 3.0--making metabolomics more meaningful.

    Science.gov (United States)

    Xia, Jianguo; Sinelnikov, Igor V; Han, Beomsoo; Wishart, David S

    2015-07-01

    MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has experienced more than a 50X growth in user traffic (>50 000 jobs processed each month). In order to keep up with the rapidly increasing computational demands and a growing number of requests to support translational and systems biology applications, we performed a substantial rewrite and major feature upgrade of the server. The result is MetaboAnalyst 3.0. By completely re-implementing the MetaboAnalyst suite using the latest web framework technologies, we have been able substantially improve its performance, capacity and user interactivity. Three new modules have also been added including: (i) a module for biomarker analysis based on the calculation of receiver operating characteristic curves; (ii) a module for sample size estimation and power analysis for improved planning of metabolomics studies and (iii) a module to support integrative pathway analysis for both genes and metabolites. In addition, popular features found in existing modules have been significantly enhanced by upgrading the graphical output, expanding the compound libraries and by adding support for more diverse organisms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. 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...

  6. Molecular codes in biological and chemical reaction networks.

    Directory of Open Access Journals (Sweden)

    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.

  7. 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…

  8. Managerial strategies to make incentives meaningful and motivating.

    Science.gov (United States)

    Korlén, Sara; Essén, Anna; Lindgren, Peter; Amer-Wahlin, Isis; von Thiele Schwarz, Ulrica

    2017-04-10

    Purpose Policy makers are applying market-inspired competition and financial incentives to drive efficiency in healthcare. However, a lack of knowledge exists about the process whereby incentives are filtered through organizations to influence staff motivation, and the key role of managers is often overlooked. The purpose of this paper is to explore the strategies managers use as intermediaries between financial incentives and the individual motivation of staff. The authors use empirical data from a local case in Swedish specialized care. Design/methodology/approach The authors conducted an exploratory qualitative case study of a patient-choice reform, including financial incentives, in specialized orthopedics in Sweden. In total, 17 interviews were conducted with professionals in managerial positions, representing six healthcare providers. A hypo-deductive, thematic approach was used to analyze the data. Findings The results show that managers applied alignment strategies to make the incentive model motivating for staff. The managers' strategies are characterized by attempts to align external rewards with professional values based on their contextual and practical knowledge. Managers occasionally overruled the financial logic of the model to safeguard patient needs and expressed an interest in having a closer dialogue with policy makers about improvements. Originality/value Externally imposed incentives do not automatically motivate healthcare staff. Managers in healthcare play key roles as intermediaries by aligning external rewards with professional values. Managers' multiple perspectives on healthcare practices and professional culture can also be utilized to improve policy and as a source of knowledge in partnership with policy makers.

  9. Cardiac c-Kit Biology Revealed by Inducible Transgenesis.

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  11. 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)

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  14. 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

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

    Science.gov (United States)

    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.

  16. 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

  17. 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.

  18. The relativity of biological function.

    Science.gov (United States)

    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.

  19. Optimizing Placement of Weather Stations: Exploring Objective Functions of Meaningful Combinations of Multiple Weather Variables

    Science.gov (United States)

    Snyder, A.; Dietterich, T.; Selker, J. S.

    2017-12-01

    Many regions of the world lack ground-based weather data due to inadequate or unreliable weather station networks. For example, most countries in Sub-Saharan Africa have unreliable, sparse networks of weather stations. The absence of these data can have consequences on weather forecasting, prediction of severe weather events, agricultural planning, and climate change monitoring. The Trans-African Hydro-Meteorological Observatory (TAHMO.org) project seeks to address these problems by deploying and operating a large network of weather stations throughout Sub-Saharan Africa. To design the TAHMO network, we must determine where to place weather stations within each country. We should consider how we can create accurate spatio-temporal maps of weather data and how to balance the desired accuracy of each weather variable of interest (precipitation, temperature, relative humidity, etc.). We can express this problem as a joint optimization of multiple weather variables, given a fixed number of weather stations. We use reanalysis data as the best representation of the "true" weather patterns that occur in the region of interest. For each possible combination of sites, we interpolate the reanalysis data between selected locations and calculate the mean average error between the reanalysis ("true") data and the interpolated data. In order to formulate our multi-variate optimization problem, we explore different methods of weighting each weather variable in our objective function. These methods include systematic variation of weights to determine which weather variables have the strongest influence on the network design, as well as combinations targeted for specific purposes. For example, we can use computed evapotranspiration as a metric that combines many weather variables in a way that is meaningful for agricultural and hydrological applications. We compare the errors of the weather station networks produced by each optimization problem formulation. We also compare these

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

    NARCIS (Netherlands)

    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

  1. Expression of human beta-defensins-1-4 in thyroid cancer cells and new insight on biologic activity of hBD-2 in vitro.

    Science.gov (United States)

    Zhuravel, O V; Gerashchenko, O L; Khetsuriani, M R; Soldatkina, M A; Pogrebnoy, P V

    2014-09-01

    The study was aimed on analysis of human beta-defensin-1-4 (hBDs) mRNA expression in cultured thyroid cancer cells and evaluation of effects of recombinant hBD-2 (rec-hBD-2) on growth patterns, migration properties and expression of E-cadherin and vimentin in these cells. The study was performed on cultured follicular thyroid cancer WRO cells, papillary thyroid cancer TPC1 cells, and anaplastic thyroid cancer KTC-2 cells. For analysis of hBD-1-4 mRNA expression in thyroid cancer cells, semiquantitative RT-PCR was used. Effects of rec-hBD-2 on cell proliferation, viability, and migration were analyzed using direct cell counting, MTT test, and scratch assay respectively. Expression of vimentin and E-cadherin was evaluated by quantitative PCR (qPCR). By the data of RT-PCR, all three studied thyroid cancer cell lines express hBD-1 and -4 mRNA, but not hBD-2 mRNA, while hBD-3 expression was detected in WRO and KTC-2 cells. The treatment of TPC-1, WRO, and KTC-2 cells with 100-1000 nM rec-hBD-2 resulted in significant concentration-dependent suppression of cell proliferation, viability, and migratory property. By the data of qPCR, significant up-regulation of vimentin expression was registered in KTC-2 and WRO cells treated with 500 nM rec-hBD-2. Significant down-regulation of E-cadherin expression (p cells treated with the defensin. Also, it has been shown that TPC-1 cells treated with 500 nM rec-hBD-2 acquired more elongated morphology. The data demonstrate that hBD-2 in concentrations higher than 100 nM exerts significant concentration-dependent suppression of thyroid cancer cell growth and migration, and affects vimentin and E-cadherin expression dependent on histologic type of thyroid cancer cells.

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

    Directory of Open Access Journals (Sweden)

    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

  3. Biological Agents

    Science.gov (United States)

    ... E-Tools Safety and Health Topics / Biological Agents Biological Agents This page requires that javascript be enabled ... 202) 693-2300 if additional assistance is required. Biological Agents Menu Overview In Focus: Ebola Frederick A. ...

  4. 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

  5. Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals

    OpenAIRE

    Yum, L. K.; Baumgarten, S.; Röthig, T.; Roder, C.; Roik, Anna; Michell, C.; Voolstra, C. 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 studie...

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

    Science.gov (United States)

    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/.

  7. Biological activity and safety of adenoviral vector-expressed wild-type p53 after intratumoral injection in melanoma and breast cancer patients with p53-overexpressing tumors

    NARCIS (Netherlands)

    Dummer, R; Bergh, J; Karlsson, Y; Horovitz, JA; Mulder, NH; Huinin, DT; Burg, G; Hofbauer, G; Osanto, S

    p53 mutations are common genetic alterations in human cancer. Gene transfer of a wild-type (wt) p53 gene reverses the loss of normal p53 function in vitro and in vivo. A phase I dose escalation study of single intratumoral (i.t.) injection of a replication-defective adenoviral expression vector

  8. Environmental Regulation of Plant Gene Expression: An Rt-qPCR Laboratory Project for an Upper-Level Undergraduate Biochemistry or Molecular Biology Course

    Science.gov (United States)

    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…

  9. Shaping Biological Knowledge: Applications in Proteomics

    Directory of Open Access Journals (Sweden)

    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.

  10. Shaping biological knowledge: applications in proteomics.

    Science.gov (United States)

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

    2004-01-01

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

  11. Modeling biological pathway dynamics with timed automata.

    Science.gov (United States)

    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.

  12. Meaningful Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2004-05-26

    We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Biologically active, magnICON®-expressed EPO-Fc from stably transformed Nicotiana benthamiana plants presenting tetra-antennary N-glycan structures.

    Science.gov (United States)

    Nagels, Bieke; Van Damme, Els J M; Callewaert, Nico; Zabeau, Lennart; Tavernier, Jan; Delanghe, Joris R; Boets, Annemie; Castilho, Alexandra; Weterings, Koen

    2012-08-31

    In the past two decades plants have emerged as a valuable alternative for the production of pharmaceutical proteins. Since N-glycosylation influences functionality and stability of therapeutic proteins, the plant N-glycosylation pathway should be humanized. Here, we report the transient magnICON(®) expression of the erythropoietin fusion protein (EPO-Fc) in Nicotiana benthamiana plants that produce multi-antennary N-glycans without the plant-specific β1,2-xylose and α1,3-fucose residues in a stable manner (Nagels et al., 2011). The EPO-Fc fusion protein consists of EPO with a C-terminal-linked IgG-Fc domain and is used for pulmonary delivery of recombinant EPO to patients (Bitonti et al., 2004). Plant expressed EPO-Fc was quantified using a paramagnetic-particle chemiluminescent immunoassay and shown to be active in vitro via receptor binding experiments in HEK293T cells. Mass spectrometry-based N-glycan analysis confirmed the presence of multi-antennary N-glycans on plant-expressed EPO-Fc. The described research is the next step towards the development of a production platform for pharmaceutical proteins in plants. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. "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.

  17. 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.

  18. Probabilistic biological network alignment.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  20. 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.

  1. 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...

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. Construction of a plasmid for co-expression of mouse membrane-bound form of IL-15 and RAE-1ε and its biological activity.

    Science.gov (United States)

    Qian, Li; Ji, Ming-Chun; Pan, Xin-Yuan; Gong, Wei-Juan; Tian, Fang; Duan, Qiu-Fang

    2011-05-01

    Interleukin 15 (IL-15) is a pivotal cytokine for the proliferation and activation of a specific group of immune cells such as natural killer (NK), IFN-producing killer dendritic cells (IKDC) and CD8 T cells. RAE-1ε, the ligand for the activating NKG2D receptor, which also play an important role in the proliferation and activation of NK cells and IKDCs. In this study, a membrane-bound form of IL-15 (termed mb15) encoding sequence and RAE-1ε gene were obtained by SOE-PCR or PCR amplification. The amplified mb15 and RAE-1ε gene were then digested and inserted into the multiple cloning site1 (MCS1) and MCS2 of pVITRO2-mcs vector, respectively. A recombinant eukaryotic expression vector for co-expression of mb15 and RAE-1ε was successfully constructed. After it was transfected to BaF3 cells, the expression of IL-15 and RAE-1ε in recombinant BaF3/mb15/RAE-1ε cells were verified by RT-PCR, western blot and FCM analysis. Furthermore, BaF3/mb15/RAE-1ε cells had the ability of promoting NK cells proliferation and IFN-γ secretion. In conclusion, BaF3/mb15/RAE-1ε cells were successfully constructed, which is very useful for further studies, especially for the expansion and activation of certain subsets of immune cells such as NK cells and IKDCs. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi.

    Science.gov (United States)

    Huang, Xuena; Gao, Yangchun; Jiang, Bei; Zhou, Zunchun; Zhan, Aibin

    2016-01-15

    As invasive species have successfully colonized a wide range of dramatically different local environments, they offer a good opportunity to study interactions between species and rapidly changing environments. Gene expression represents one of the primary and crucial mechanisms for rapid adaptation to local environments. Here, we aim to select reference genes for quantitative gene expression analysis based on quantitative Real-Time PCR (qRT-PCR) for a model invasive ascidian, Ciona savignyi. We analyzed the stability of ten candidate reference genes in three tissues (siphon, pharynx and intestine) under two key environmental stresses (temperature and salinity) in the marine realm based on three programs (geNorm, NormFinder and delta Ct method). Our results demonstrated only minor difference for stability rankings among the three methods. The use of different single reference gene might influence the data interpretation, while multiple reference genes could minimize possible errors. Therefore, reference gene combinations were recommended for different tissues - the optimal reference gene combination for siphon was RPS15 and RPL17 under temperature stress, and RPL17, UBQ and TubA under salinity treatment; for pharynx, TubB, TubA and RPL17 were the most stable genes under temperature stress, while TubB, TubA and UBQ were the best under salinity stress; for intestine, UBQ, RPS15 and RPL17 were the most reliable reference genes under both treatments. Our results suggest that the necessity of selection and test of reference genes for different tissues under varying environmental stresses. The results obtained here are expected to reveal mechanisms of gene expression-mediated invasion success using C. savignyi as a model species. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Expression and biological-clinical significance of hTR, hTERT and CKS2 in washing fluids of patients with bladder cancer

    Directory of Open Access Journals (Sweden)

    Talesa Vincenzo N

    2010-10-01

    Full Text Available Abstract Background at present, pathogenesis of bladder cancer (BC has not been fully elucidated. Aim of this study is to investigate the role of human telomerase RNA (hTR, human telomerase reverse transcriptase (hTERT and CDC28 protein kinase regulatory subunit 2 (CKS2 in bladder carcinogenesis and their possible clinical significance; Methods the transcript levels of hTR, hTERT and CKS2 were quantified by Real time reverse transcriptase chain reaction in exfoliated cells from bladder washings of 36 patients with BC and 58 controls. The statistical significance of differences between BC bearing patients and control groups, in the general as well as in the stratified analysis (superficial or invasive BC, was assessed by Student's t test. Non parametric Receiver Operating Characteristics analysis (ROC was performed to ascertain the accuracy of study variables to discriminate between BC and controls. The clinical value of concomitant examination of hTR, hTERT and CKS2 was evaluated by logistic regression analysis; Results a significant decrease in hTR and a significant increase in hTERT or CKS2 gene expression were found between BC bearing patients and controls, as well as in the subgroups analysis. The area under the curve (AUC indicated an average discrimination power for the three genes, both in the general and subgroups analysis, when singularly considered. The ability to significantly discriminate between superficial and invasive BC was observed only for hTR transcript levels. A combined model including hTR and CKS2 was the best one in BC diagnosis; Conclusions our results, obtained from a sample set particularly rich of exfoliated cells, provide further molecular evidence on the involvement of hTR, hTERT and CKS2 gene expression in BC carcinogenesis. In particular, while hTERT and CKS2 gene expression seems to have a major involvement in the early stages of the disease, hTR gene expression, seems to be more involved in progression. In

  8. pcaGoPromoter--an R package for biological and regulatory interpretation of principal components in genome-wide gene expression data

    DEFF Research Database (Denmark)

    Hansen, Morten; Gerds, Thomas Alexander; Nielsen, Ole Haagen

    2012-01-01

    Analyzing data obtained from genome-wide gene expression experiments is challenging due to the quantity of variables, the need for multivariate analyses, and the demands of managing large amounts of data. Here we present the R package pcaGoPromoter, which facilitates the interpretation of genome.......g., cell cycle progression and the predicted involvement of expected transcription factors, including E2F. In addition, unexpected results, e.g., cholesterol synthesis in serum-depleted cells and NF-¿B activation in inhibitor treated cells, were noted. In summary, the pcaGoPromoter R package provides...

  9. Meaningful interpretation by reanalyzing the publicly available dataset: A case study of Salvia miltiorrhiza

    Directory of Open Access Journals (Sweden)

    Maulik Patel

    2017-10-01

    Full Text Available MicroRNAs are a newly discovered class of non-protein small RNAs with 22-24 nucleotides and evolutionary conserved post-transcriptional regulatory RNAs, which shows an enormous role in several biological and metabolic process. Plant derived miRNA entered into the body fluid and regulated the expression of host mRNA. Salvia miltiorrhiza is an important medicinal plant known for its potent cardiovascular and anticancer activity and hence, it was selected to identify the cross kingdom regulatory mechanism between medicinal plant and human. In this study, total 8 highly stable putative novel miRNA were predicted from the publically available ESTs of Salvia miltiorrhiza, out of which 2 miRNA were found to be regulating 32 target genes in human. Functional annotation, gene ontology and network analysis were carried out based on their significance and find out the association with the prominent disease like cancer and cardiac diseases. The network analysis showed the some important network protein like SOCS2, CD274, STAT3, TRAF3 and CXCL2 with their associated pathways. The predicted miRNA have a significant potential role in cytokine, Apoptosis and EGFR receptor signaling pathways and its biological regulation. It may be further validated using in-vivo experiment for broader picture into their miRNA epigenetic mechanism and action.

  10. Biological Mechanisms Underlying the Ultraviolet Radiation-Induced Formation of Skin Wrinkling and Sagging II: Over-Expression of Neprilysin Plays an Essential Role

    Directory of Open Access Journals (Sweden)

    Genji Imokawa

    2015-04-01

    Full Text Available Our previous studies strongly indicated that the up-regulated activity of skin fibroblast-derived elastase plays a pivotal role in wrinkling and/or sagging of the skin via the impairment of elastic fiber configuration and the subsequent loss of skin elasticity. Fortunately, we succeeded in identifying human skin fibroblast-derived elastase as a previously known enzyme, neprilysin or neutral endopeptidase (NEP. We have also characterized epithelial-mesenchymal paracrine cytokine interactions between UVB-exposed-keratinocytes and dermal fibroblasts and found that interleukin-1α and granulocyte macrophage colony stimulatory factor (GM-CSF are intrinsic cytokines secreted by UVB-exposed keratinocytes that stimulate the expression of neprilysin by fibroblasts. On the other hand, direct UVA exposure of human fibroblasts significantly stimulates the secretion of IL-6 and also elicits a significant increase in the gene expression of matrix metallo-protease(MMP-1 as well as neprilysin (to a lesser extent, which is followed by distinct increases in their protein and enzymatic activity levels. Direct UVA exposure of human keratinocytes also stimulates the secretion of IL-6, IL-8 and GM-CSF but not of IL-1 and endothelin-1. These findings suggest that GM-CSF secreted by UVA-exposed keratinocytes as well as IL-6 secreted by UVA-exposed dermal fibroblasts play important and additional roles in UVA-induced sagging and wrinkling by up-regulation of neprilysin and MMP-1, respectively, in dermal fibroblasts.

  11. 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…

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

    Science.gov (United States)

    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…

  13. 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…

  14. 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…

  15. 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…

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

    Science.gov (United States)

    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…

  17. 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.

  18. 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

  19. 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...

  20. 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...

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

    Science.gov (United States)

    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…

  2. 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…

  3. 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…

  4. "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…

  5. 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…

  6. 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...

  7. 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.

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

    Science.gov (United States)

    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…

  9. 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...

  10. Finding pathways to more equitable and meaningful public-scientist partnerships

    Science.gov (United States)

    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...

  11. 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

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

    Science.gov (United States)

    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…

  13. 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.

  14. 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.

  15. 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…

  16. 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

  17. 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…

  18. 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.

  19. 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…

  20. 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…

  1. 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

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

    Science.gov (United States)

    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…

  3. 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.

  4. Which role for Life Cycle Thinking in the definition of meaningful indicators for the circular economy?

    DEFF Research Database (Denmark)

    Niero, Monia

    2017-01-01

    at the micro level. We discuss the role of Life Cycle Thinking (LCT) in the development of meaningful circularity indicators at the product level taking into account the absolute perspective on CE. Our analysis is limited to the environmental aspect of sustainability with a focus on the climate change impact...

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

    Science.gov (United States)

    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…

  6. Application of Ausubel's Theory of Meaningful Verbal Learning to Curriculum, Teaching and Learning of Deaf Students.

    Science.gov (United States)

    Biser, Eileen

    Implications of D. Ausubel's Theory of Meaningful Verbal Learning and its derivative, the Advance Organizer Model of Teaching, for deaf students are examined. Ausubel believes that complex intellectual processes (thinking, language, problem-solving, concept formation) are the major aspects of learning, and that primary emphasis should be placed on…

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

    NARCIS (Netherlands)

    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

  8. 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…

  9. Clustering gene expression regulators: new approach to disease subtyping.

    Directory of Open Access Journals (Sweden)

    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.

  10. Annotating spatio-temporal datasets for meaningful analysis in the Web

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. Tumor suppressor p53 biology, its role in radioresponse and the analysis of p53 mutation/expression among Filipino breast cancers

    International Nuclear Information System (INIS)

    Deocaris, Custer C.

    2004-01-01

    Ionizing radiation remains one of the most effective tools for the treatment of breast cancer. It combines properties of a potent DNA-damaging agent and high degree of spatial specificity to the target tissue. Nonetheless, there remain considerable differences in the outcome for treatment of tumors of differing histological type treated by radiotherapy. The identification of predictive indicators of radiosensitivity is crucial for selecting patients suited for preoperative radiotherapy as well as those unwarranted for postoperative treatments. To improve prognostication, numerous genes involved in the breast carcinogenesis have been studied and thus far over the last decade several multi-center researches converge on the role of tumor suppressor p53 in tumor biology. The p53 gene is located on the short arm of chromosome 17 and encodes a 53-kd nuclear protein, p-53, also referred to as 'the guardian of the genome', it orchestrates multiple cellular processes such as cell growth control, DNA repair and programmed cell death. During radiotherapy, genotoxic damage induces p53 overexpression in order to control the rate of proliferating damaged cells, repair damage or induce the apoptotic pathway. Its molecular inactivation in a tumor cell, typically by a point mutation, leads to chemo/radio resistance due to the inability of the molecule to trigger p53-dependent programmed cell death

  15. Modern Biology

    OpenAIRE

    ALEKSIC, Branko

    2014-01-01

    The purpose of this course is to learn the philosophy, principles, and techniques of modern biology. The course is particularly designed for those who have not learned biology previously or whose major is other than biology, and who may think that they do not need to know any biology at all. The topics are covered in a rather general, overview manner, but certain level of diligence in grasping concepts and memorizing the terminology is expected.

  16. Meaningful interpretation of subdiffusive measurements in living cells (crowded environment) by fluorescence fluctuation microscopy.

    Science.gov (United States)

    Baumann, Gerd; Place, Robert F; Földes-Papp, Zeno

    2010-08-01

    (temporal) randomness in cellular systems.We have already derived an analytical solution gamma for in the special case of gamma = 3/2. In the case of two-color crosscorrelation or/and two-color fluorescence imaging (co-localization experiments), the second component is also a two-color species gr, for example a different molecular complex with an additional ligand. Here, we first show that plausible biological mechanisms from FCS/ FCCS and fluorescence imaging in living cells are highly questionable without proper quantitative physical models of subdiffusive motion and temporal randomness. At best, such quantitative FCS/ FCCS and fluorescence imaging data are difficult to interpret under crowding and heterogeneous conditions. It is challenging to translate proper physical models of anomalous (spatial) and heterogeneous (temporal) randomness in living cells and their cellular compartments like the nucleus into biological models of the cell biological process under study testable by single-molecule approaches. Otherwise, quantitative FCS/FCCS and fluorescence imaging measurements in living cells are not well described and cannot be interpreted in a meaningful way.

  17. Leaving out control groups: an internal contrast analysis of gene expression profiles in atrial fibrillation patients--a systems biology approach to clinical categorization.

    Science.gov (United States)

    Vanhoutte, Kurt; de Asmundis, Carlo; Francesconi, Anna; Figysl, Jurgen; Steurs, Griet; Boussy, Tim; Roos, Markus; Mueller, Andreas; Massimo, Lucio; Paparella, Gaetano; Van Caelenberg, Kristien; Chierchia, Gian Battista; Sarkozy, Andrea; Terradellas, Pedro Brugada Y; Zizi, Martin

    2009-01-01

    Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical focus on potential entry pathways into the disease. We used a RMA (Robust Multichip Average) normalized Affymetrix micro-array data set from 10 AF patients (geo_accession #GSE2240). Four series of probes were selected based on physiopathogenic links with AF entryways: apoptosis (remodeling), MAP kinase (cell remodeling), OXPHOS (ability to sustain hemodynamic workload) and glycolysis (ischemia). Annotated probe lists were polled with Bioconductor packages in R (version 2.7.1). Genetic profile contrasts were analysed with hierarchical clustering and principal component analysis. The analysis revealed distinct patient groups for all probe sets. A substantial part (54% till 67%) of the variance is explained in the first 2 principal components. Genes in PC1/2 with high discriminatory value were selected and analyzed in detail. We aim for reliable molecular stratification of AF. We show that stratification is possible based on physiologically relevant gene sets. Genes with high contrast value are likely to give pathophysiological insight into permanent AF subtypes.

  18. Mathematical biology

    CERN Document Server

    Murray, James D

    1993-01-01

    The book is a textbook (with many exercises) giving an in-depth account of the practical use of mathematical modelling in the biomedical sciences. The mathematical level required is generally not high and the emphasis is on what is required to solve the real biological problem. The subject matter is drawn, e.g. from population biology, reaction kinetics, biological oscillators and switches, Belousov-Zhabotinskii reaction, reaction-diffusion theory, biological wave phenomena, central pattern generators, neural models, spread of epidemics, mechanochemical theory of biological pattern formation and importance in evolution. Most of the models are based on real biological problems and the predictions and explanations offered as a direct result of mathematical analysis of the models are important aspects of the book. The aim is to provide a thorough training in practical mathematical biology and to show how exciting and novel mathematical challenges arise from a genuine interdisciplinary involvement with the biosci...

  19. Emerging role of Hippo signalling in pancreatic biology: YAP re-expression and plausible link to islet cell apoptosis and replication.

    Science.gov (United States)

    Sharma, Anjana; Yerra, Veera Ganesh; Kumar, Ashutosh

    2017-02-01

    Diabetes mellitus is an ailment that develops when the functional capacity of the pancreas does not meet the metabolic requirements of the whole body, either due to insulin insufficiency or resistance to insulin action. Current therapies that control glycaemia are limited by their unwanted effects or their inability to prevent the development of long-term complications. Regeneration and replacement of beta cell therapies are shaping the goals of future management of diabetes. The Hippo pathway, first discovered in Drosophila melanogaster, plays a vital role in controlling the organ size. Nuclear recruitment of YAP/TAZ (Yes-associated protein/transcriptional co-activator with PDZ-binding motif), a mammalian analogue of Yorkie protein found in Drosophila, activates cell proliferation and inhibits apoptosis. YAP was found to regulate early pancreatic development followed by downregulation during Ngn3-specific endocrine lineage maturation corresponding to their mitotic quiescence. Recent evidences have shown that optimum modulation of upstream kinases in the Hippo signalling pathway may lead to apoptosis inhibition and renewal of progenitor as well as stem cells in case of tissue or cell injury. This article reviews the evidences linking the role of various components of the Hippo pathway to pancreatic regeneration. In particular, the focus is on the beneficial role of induced YAP expression and its nuclear distribution on apoptosis and replication of adult pancreatic β islets. This approach may be of immense significance towards our fight against diabetes; thus, more insightful research is warranted in the area of Hippo signalling pathway and its involvement in pancreatic regeneration. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  20. Synthesis and biological evaluation of a 99mTc-labelled cyclic RGD peptide for imaging the αvβ3 expression

    International Nuclear Information System (INIS)

    Haubner, F.; Bock, M.; Schwaiger, M.; Wester, H.J.; Bruchertseifer, F.; Kessler, H.

    2004-01-01

    Aim: The αvβ3 integrin is involved in tumour induced angiogenesis and tumour metastasis. We describe the synthesis and evaluation of a 99m Tc-labelled RGD analogue for the visualisation of αvβ3 integrin expression. Methods: The linear peptides were assembled on a solid support. Cyclisation was performed under high dilution conditions. For conjugation with the chelator peptide, a water soluble carbodiimide was used. Radiolabelling was carried out due to standard procedures with high radiochemical yield and radiochemical purity. For in vivo evaluation, nude mice bearing αvβ3-positive human melanoma M21 and αv-negative human melanoma M21-L or Balb / c mice bearing αv-positive murine osteosarcoma were used. Results: Activity accumulation of 99m Tc-DKCK-RGD 240 min p.i. was 1.1% ID/g in the αvβ3-positive melanoma and 0.3% ID/g in the negative control tumour. In the osteosarcoma model 2.2% ID/g was found 240 min p.i. Planar gamma camera images allowed contrasting visualisation of αvβ3-positive tumours 240 min p.i. Blocking of the tumour using the αvβ3-selective pentapeptide cyclo(-Arg-Gly-Asp-D-Phe-Val-) reduces activity accumulation in the tumour to background level. However, 240 min p.i. highest activity concentration was found in kidneys resulting in low tumour / kidney ratios. Metabolite analysis 240 min p.i. showed approximately 60% intact tracer in kidneys and 80% in the tumour. Only 24% intact tracer was found in blood 30 min p.i. Conclusion: 99m Tc-DKCK-RGD allows imaging of αvβ3-positive tumours in mice. However, pharmacokinetics as well as metabolic stability of the tracer have to be improved for potential clinical application. (orig.)

  1. Cloning, characterization, expression and antifungal activity of an alkaline serine protease of Aureobasidium pullulans PL5 involved in the biological control of postharvest pathogens.

    Science.gov (United States)

    Zhang, Dianpeng; Spadaro, Davide; Valente, Silvia; Garibaldi, Angelo; Gullino, Maria Lodovica

    2012-02-15

    An alkaline protease gene was amplified from genomic DNA and cDNA of the antagonistic yeast-like fungus Aureobasidium pullulans PL5, a biocontrol agent effective against Monilinia laxa on stone fruit and Botrytis cinerea and Penicillium expansum on pome fruits. An open reading frame of 1248 bp encoding a 415-amino acid (aa) protein with a calculated molecular weight (M(r)) of 42.9 kDa and an isoelectric point (pI) of 4.5 was characterized. The cDNAALP5 gene had an 18-amino acid signal peptide, one N-gylcosylation, one histidine active site, and one serine active site. The ALP5 gene with a M(r) of 1351 bp contained two introns. One intron was of 54 bp, while the other was of 50 bp. Protein BLAST and phylogenetic tree analysis of the deduced amino sequences from the cDNAALP5 gene showed that the encoded protein had 100% homology to a protease enzyme (ALP2) of a sea strain of A. pullulans, suggesting that the protein ALP5 was an alkaline serine protease. Expression of ALP5 in Escherichia coli BL21 (DE3), followed by identification with Western-blotting, purification with Ni-NTA and analysis of enzymatic activity, yielded an homogeneous recombinant ALP5 which hydrolysed the substrate casein and inhibited the mycelial growth of the pathogens. At its optimal pH of 10.0 and reaction temperature of 50°C, the recombinant protease exhibited the highest activity towards the substrate casein, though the highest stability was at lower temperatures and pH between 7.0 and 9.0. This study provided the direct evidence that extracellular proteases secreted by the antagonist A. pullulans PL5 played a role in the biocontrol activities against some postharvest pathogens of apple and peach. Copyright © 2011 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    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.

  3. Expression analysis and biological characterization of Babesia sp. BQ1 (Lintan) (Babesia motasi-like) rhoptry-associated protein 1 and its potential use in serodiagnosis via ELISA.

    Science.gov (United States)

    Niu, Qingli; Liu, Zhijie; Yang, Jifei; Yu, Peifa; Pan, Yuping; Zhai, Bintao; Luo, Jianxun; Moreau, Emmanuelle; Guan, Guiquan; Yin, Hong

    2016-05-31

    In China, ovine babesiosis is one of the most important tick-borne haemoparasitic diseases of small ruminants. It has a significant economic impact, and several Babesia motasi-like isolates have been recently shown to be responsible for ovine babesiosis in this country. Full-length and C-terminal-truncated forms of the rap-1a61-1 gene of Babesia sp. BQ1 (Lintan) were cloned into the pET-30a plasmid and subsequently expressed as His-fusion proteins. The resulting recombinant RAP-1a proteins (rRAP-1a61-1 and rRAP-1a61-1/CT) were purified and evaluated as diagnostic antigens using Western blot analysis and ELISA. The native Babesia sp. BQ1 (Lintan) RAP-1 protein was recognized using Western blots and IFAT by antibodies that were raised in rabbits against rRAP-1a61-1/CT. The specificity, sensitivity and positive threshold values for rRAP-1a61-1/CT in ELISA were evaluated. Cross-reactivity was observed between rRAP-1a61-1/CT and positive sera for Babesia sp. BQ1 (Lintan), Babesia sp. BQ1 (Ningxian) and Babesia sp. Tianzhu isolates obtained from infected sheep. At one week post-inoculation, a significant increase was observed in the amount of antibodies produced against RAP-1a, and high levels of antibodies against RAP-1a were observed for 3 months (at 84 days p.i.). A total of 3198 serum samples were collected from small ruminants in 54 different regions in 23 provinces of China. These samples were tested using ELISA based on the rRAP-1a61-1/CT protein. The results indicated that the average positive rate was 36.02 %. The present study suggests that rRAP-1a61-1/CT might be a potential diagnostic antigen for detecting several isolates of B. motasi-like parasites infection.

  4. 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.

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

    CERN Document Server

    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.

  6. 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

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

    Science.gov (United States)

    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.

  8. 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.

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

    Science.gov (United States)

    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.

  10. 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.

  11. Engaging Axiology: Enabling MeaningfulTransdisciplinary Collaboration in Adapted Physical Activity.

    Science.gov (United States)

    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.

  12. Biological signals classification and analysis

    CERN Document Server

    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 ...

  13. Qualitative Insights from a Canadian Multiinstitutional Research Study: In Search of Meaningful E-learning

    OpenAIRE

    Lorraine M. Carter; Vince Salyers; Sue Myers; Carol Hipfner; Caroline Hoffart; Christa MacLean; Kathy White; Theresa Matus; Vivian Forssman; Penelope Barrett

    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 e-learning. Importantly, e-learning was conceptualized as the integration of pedagogy, instructional technology, and the Internet into teaching ...

  14. The Relationship between Psychological Meaningfulness and Employee Engagement: Moderating Effect of Age and Gender

    OpenAIRE

    Ruswahida Ibnu Ruslan; Md. Aminul Islam; Idris Mohd Noor

    2014-01-01

    There has been a great deal of interest in employee engagement over the years, and it has become a popular term. However, there is no one universally acceptable definition for employee engagement until now. Employee engagement has been defined in many ways, and its assessment also seems to be similar, as developed by scholars such as Kahn [1] who coins the term psychological meaningfulness. This paper reviews the literature surrounding employee engagement, especially in terms of psychological...

  15. 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...

  16. Contested Spaces. Meaningful Places. Contemporary Performances of Place and Belonging in Spain and Brazil

    Directory of Open Access Journals (Sweden)

    Maria J. C. Krom

    2009-12-01

    Full Text Available This essay aims to contribute to current anthropological debate on space and place, analysing in two instances of festival performance how, on the one hand the politics of appropriation of space contributes to the configuration of power relations, and how on the other hand, participants in these festivals engage individually and collectively with physical space(s to create places which they experience as meaningful in terms of identity and belonging.

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

    Science.gov (United States)

    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

  18. 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.

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

    Science.gov (United States)

    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.

  20. 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…

  1. A cost-effective method of achieving meaningful citizen participation in public roadway pipeline studies

    Energy Technology Data Exchange (ETDEWEB)

    Buszynski, M.E.

    1996-12-31

    Many proponents of gas pipeline studies using the public roadway for their facilities have trouble encouraging public participation. Problems resulting from a lack of public involvement are documented. A public participation process designed to gather meaningful public input is presented through a case study of a public roadway pipeline study in southern Ontario. Techniques are outlined to effectively stimulate public interest and document the public involvement process. Recommendations are made as to the transferability of this process to other jurisdictions.

  2. 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...

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

    Science.gov (United States)

    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…

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

    NARCIS (Netherlands)

    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

  5. 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.

  6. 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.…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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.

  9. 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…

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  12. 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.

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

    Science.gov (United States)

    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.

  14. 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.

  15. Biological therapeutics

    National Research Council Canada - National Science Library

    Greenstein, Ben; Brook, Daniel A

    2011-01-01

    This introductory textbook covers all the main categories of biological medicines, including vaccines, hormonal preparations, drugs for rheumatoid arthritis and other connective tissue diseases, drugs...

  16. 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.

  17. Computational biology

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved t...

  18. Mesoscopic biology

    Indian Academy of Sciences (India)

    In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological ...

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

    Directory of Open Access Journals (Sweden)

    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

  20. [LincRNA-ROR functions as a ceRNA to regulate Oct4, Sox2, and Nanog expression by sponging miR-145 and its effect on biologic characteristics of colonic cancer stem cells].

    Science.gov (United States)

    Yan, Z Y; Sun, X C

    2018-04-08

    Objective: To investigate the impact of lincRNA-ROR, a ceRNA by binding miR-145 on the expression of the downstream genes Oct4, Sox2 and Nanog, and related biological characteristics of colon cancer stem cells, and to elucidate the clinical significance of this molecular regulatory network. Methods: Fifty-two cases of colorectal cancer tissue and adjacent tissue were collected at Nanyang City Central Hospital and Nanyang Second Hospital, Henan Province, from 2014 to 2016. Real-time quantitative polymerase chain reaction (qPCR) was used to detect the expression of lincRNA-ROR and miR-145 in colorectal cancer tissue and isolated colon cancer cells. The correlation between the expression of lincRNA-ROR, miR-145 and the clinicopathologic features of colon cancer was performed. CD44(-)CD133(-) and CD44(+) CD133(+) cells were isolated from SW1116 by using flow cytometry. The expression of CD44, CD133, Oct4, Sox2, Nanog, lincRNA-ROR and miR-145 in cells were detected by qPCR. The relationship between lincRNA-ROR, miR-145, Oct4, Sox2 and Nanog was analyzed by bioinformatics, dual luciferase reporter assay, qPCR and Western blot. The effects of silencing lincRNA-ROR on the proliferation and chemosensitivity of colon cancer stem cells were detected by MTT, colony formation. Results: LincRNA-ROR was frequently up-regulated and inversely correlated with miR-145 down-regulation in the colon cancer specimens( P cells were successfully isolated from SW1116 by flow cytometry. The levels of CD44, CD133, Oct4, Sox2, Nanog, lincRNA-ROR in CD44(+) CD133(+) cells were significantly increased, while miR-145 was decreased compared with CD44(-)CD133(-)cells( P cells were significantly reduced upon cell adherence, while miR-145 was significantly increased( P cancer stem cells proliferation and increased the sensitivity to chemotherapy. Conclusions: Linc-ROR functions as a key ceRNA to prevent core TFs, e. g., Oct4, Sox2, Nanog, from miR-145-mediated suppression in colon cancer stem cells

  1. 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...

  2. 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.

  3. A concept for biological valuation in the marine environment

    Directory of Open Access Journals (Sweden)

    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.

  4. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

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

    Science.gov (United States)

    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

  6. Biological desulfurisation

    Energy Technology Data Exchange (ETDEWEB)

    Arena, B.J. [UOP LLC (United States); Benschop, A.; Janssen, A. [Paques Natural Solutions (Netherlands); Kijlstra, S. [Shell Global Solutions (Netherlands)

    2001-03-01

    This article focuses on the biological THIOPAQ process for removing hydrogen sulphide from refinery gases and recovering elemental sulphur. Details are given of the process which absorbs hydrogen sulphide-containing gas in alkaline solution prior to oxidation of the dissolved sulphur to elemental sulphur in a THIOPAQ aerobic biological reactor, with regeneration of the caustic solution. Sulphur handling options including sulphur wash, the drying of the sulphur cake, and sulphur smelting by pressure liquefaction are described. Agricultural applications of the biologically recovered sulphur, and application of the THIOPAQ process to sulphur recovery are discussed.

  7. Improving the user experience through practical data analytics gain meaningful insight and increase your bottom line

    CERN Document Server

    Fritz, Mike

    2015-01-01

    Improving the User Experience through Practical Data Analytics is your must-have resource for making UX design decisions based on data, rather than hunches. Authors Fritz and Berger help the UX professional recognize and understand the enormous potential of the ever-increasing user data that is often accumulated as a by-product of routine UX tasks, such as conducting usability tests, launching surveys, or reviewing clickstream information. Then, step-by-step, they explain how to utilize both descriptive and predictive statistical techniques to gain meaningful insight with that data. You'll be

  8. Cogent:A Case Study of Meaningful Gamification in Education with Virtual Currency

    Directory of Open Access Journals (Sweden)

    Yang Chen

    2015-02-01

    Full Text Available This paper analyzes students’ experience with Cogent, a virtual economy system used throughout the 4 years of a B.S. degree in a Technology major. The case study explains the rules of the Cogent system and investigates its effectiveness to motivate students to learn. Using focus groups and interviews, we collected qualitative data from students about their experience and perceptions of Cogent. The results indicate that Cogent played an encouraging and motivational role for these students and suggest potential for the successful design and implementation of meaningful gamification systems to promote student motivation and engagement within an educational context.

  9. On the meaningfulness of testing preference axioms in stated preference discrete choice experiments

    DEFF Research Database (Denmark)

    Hougaard, Jens Leth; Tjur, Carl Tue; Østerdal, Lars Peter Raahave

    2012-01-01

    A stream of studies on evaluation of health care services and public goods have developed tests of the preference axioms of completeness and transitivity and methods for detecting other preference phenomena such as unstability, learning- and tiredness effects, and random error, in stated preference...... discrete choice experiments. This methodological paper tries to identify the role of the preference axioms and other preference phenomena in the context of such experiments and discusses whether or howsuch axioms and phenomena can be subject to meaningful (statistical) tests....

  10. Medicare incentive payments for meaningful use of electronic health records: accounting and reporting developments.

    Science.gov (United States)

    2012-02-01

    The Healthcare Financial Management Association through its Principles and Practices (P&P) Board publishes issue analyses to provide short-term practical assistance on emerging issues in healthcare financial management. In a new issue analysis excerpted in this article, HFMA's P&P Board provides some clarity to the healthcare industry on certain accounting and reporting issues resulting from incentive payments under the Medicare program for the meaningful use of electronic health record (EHR) technology. Consultation on these matters with independent auditors is highly recommended.

  11. Heterologous expression of biologically active chicken granulocyte ...

    African Journals Online (AJOL)

    user

    2012-02-07

    Feb 7, 2012 ... CD4+ T cells to enhance the ability of secreting antibody and also enhance the function of CD8+ T cells. (Papatriantafyllou, 2011; Tovey and Lallemand, 2010). GM-CSF also is a key regulator of IL-1beta production. Furthermore, It was reported that GM-CSF play a key role in the activation of Th1 and Th17 ...

  12. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

  13. Evaluation of Short-Term Changes in Serum Creatinine Level as a Meaningful End Point in Randomized Clinical Trials.

    Science.gov (United States)

    Coca, Steven G; Zabetian, Azadeh; Ferket, Bart S; Zhou, Jing; Testani, Jeffrey M; Garg, Amit X; Parikh, Chirag R

    2016-08-01

    Observational studies have shown that acute change in kidney function (specifically, AKI) is a strong risk factor for poor outcomes. Thus, the outcome of acute change in serum creatinine level, regardless of underlying biology or etiology, is frequently used in clinical trials as both efficacy and safety end points. We performed a meta-analysis of clinical trials to quantify the relationship between positive or negative short-term effects of interventions on change in serum creatinine level and more meaningful clinical outcomes. After a thorough literature search, we included 14 randomized trials of interventions that altered risk for an acute increase in serum creatinine level and had reported between-group differences in CKD and/or mortality rate ≥3 months after randomization. Seven trials assessed interventions that, compared with placebo, increased risk of acute elevation in serum creatinine level (pooled relative risk, 1.52; 95% confidence interval, 1.22 to 1.89), and seven trials assessed interventions that, compared with placebo, reduced risk of acute elevation in serum creatinine level (pooled relative risk, 0.57; 95% confidence interval, 0.44 to 0.74). However, pooled risks for CKD and mortality associated with interventions did not differ from those with placebo in either group. In conclusion, several interventions that affect risk of acute, mild to moderate, often temporary elevation in serum creatinine level in placebo-controlled randomized trials showed no appreciable effect on CKD or mortality months later, raising questions about the value of using small to moderate changes in serum creatinine level as end points in clinical trials. Copyright © 2016 by the American Society of Nephrology.

  14. Today's 'meaningful use' standard for medication orders by hospitals may save few lives; later stages may do more.

    NARCIS (Netherlands)

    Jones, S.S.; Heaton, P.; Friedberg, M.W.; Schneider, E.C.

    2011-01-01

    The federal government is currently offering bonus payments through Medicare and Medicaid to hospitals, physicians, and other eligible health professionals who meet new standards for "meaningful use" of health information technology. Whether these incentives will improve care, reduce errors, and

  15. 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.

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

    Science.gov (United States)

    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.

  17. Are there meaningful individual differences in temporal inconsistency in self-reported personality?

    Science.gov (United States)

    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.

  18. Meaningful Ways of Understanding and Measuring Change for People with Borderline Personality Disorder: A Thematic Analysis.

    Science.gov (United States)

    McCusker, Louise; Turner, Marie-Louise; Pike, Georgina; Startup, Helen

    2018-02-19

    The effective treatment of Borderline Personality Disorder (BPD) presents healthcare providers with a significant challenge. The evidence base remains limited partially due to a lack of professional consensus and service user involvement regarding ways of measuring change. As a result, the limited evidence that is available draws on such a wide range of outcome measures, that comparison across treatment types is hindered, maintaining a lack of clarity regarding the clinical needs of this group. This investigation aimed to follow the National Institute of Clinical Excellence (NICE, 2009) research recommendations by asking service users about meaningful change within their recovery. This forms a starting point for the future development of a tailored outcome measure. Fifteen service users with a diagnosis of BPD participated in three focus groups across two specialist Personality Disorder services. The focus groups were analysed using Thematic Analysis. Two superordinate themes were synthesized from the data: (1) recovery to what?: 'How do you rewrite who you are?'; and (2) conditions for change. Each superordinate theme further consisted of three subordinate themes which elucidated the over-arching themes. This investigation highlights the complex nature of measuring change in people who have received a BPD diagnosis. Further research is needed to develop meaningful ways of measuring change according to the needs and priorities of people with BPD.

  19. 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.

  20. 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.

  1. 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.

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

    Science.gov (United States)

    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.

  3. A business case for HIT adoption: effects of "meaningful use" EHR financial incentives on clinic revenue.

    Science.gov (United States)

    Behkami, Nima A; Dorr, David A; Morrice, Stuart

    2010-01-01

    The goal of this study is to describe a framework that allows decision makers to efficiently evaluate factors that affect Electronic Health Record (EHR) adoption and test suitable interventions; specifically financial incentives. The United States healthcare delivery system is experiencing a transformation to improve population health. There is strong agreement that "meaningful use" of Health Information Technology (HIT) is a major enabler in this effort. However it's also understood that the high cost of implementing an EHR is an obstacle for adoption. To help understand these complexities we developed a simulation model designed to capture the dynamic nature of policy interventions that affect the adoption of EHR. We found that "Effective" use of HIT approaches break-even-point and larger clinic revenue many times faster that "average" or "poor" use of HIT. This study uses a systems perspective to the evaluate EHR adoption process through the "meaningful use" redesign as proposed in the American Reinvestment and Recovery Act 2009 in the United States healthcare industry by utilizing the System Dynamics methodology and Scenario Analysis.

  4. COURSERA ONLINE COURSE: A PLATFORM FOR ENGLISH TEACHERS’ MEANINGFUL AND VIBRANT PROFESSIONAL DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    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.

  5. Predicting loss of employment over three years in multiple sclerosis: clinically meaningful cognitive decline.

    Science.gov (United States)

    Morrow, Sarah A; Drake, Allison; Zivadinov, Robert; Munschauer, Frederick; Weinstock-Guttman, Bianca; Benedict, Ralph H B

    2010-10-01

    Cognitive dysfunction is common in multiple sclerosis (MS), yet the magnitude of change on objective neuropsychological (NP) tests that is clinically meaningful is unclear. We endeavored to determine NP markers of the transition from employment to work disability in MS, as indicated by degree of decline on individual tests. Participants were 97 employed MS patients followed over 41.3 ± 17.6 months with a NP battery covering six domains of cognitive function. Deterioration at follow-up was designated as documented and paid disability benefits (conservative definition) or a reduction in hours/work responsibilities (liberal definition). Using the conservative definition, 28.9% reported deteriorated employment status and for the liberal definition, 45.4%. The Symbol Digit Modalities Test (SDMT) and California Verbal Learning Test, Total Learning (CVLT2-TL) measures distinguished employed and disabled patients at follow-up. Controlling for demographic and MS characteristics, the odds ratio of a deterioration based on a change of 2.0 on the CVLT2-TL was 3.7 (95% CI 1.2-11.4 and SDMT by 4.0 was 4.2 (95% CI 1.2-14.8), accounting for 86.7% of the area under the ROC curve. We conclude that decline on NP testing over time is predictive of deterioration in vocational status, establishing a magnitude of decline on NP tests that is clinically meaningful.

  6. 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

  7. 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 ...

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

    Science.gov (United States)

    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

  9. Microfluidic Technologies for Synthetic Biology

    Directory of Open Access Journals (Sweden)

    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.

  10. 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

  11. [Biological agents].

    Science.gov (United States)

    Amano, Koichi

    2009-03-01

    There are two types of biological agents for the treatment of rheumatoid arthritis (RA); monoclonal antibodies and recombinant proteins. Among the latter, etanercept, a recombinant fusion protein of soluble TNF receptor and IgG was approved in 2005 in Japan. The post-marketing surveillance of 13,894 RA patients revealed the efficacy and safety profiles of etanercept in the Japanese population, as well as overseas studies. Abatacept, a recombinant fusion protein of CTLA4 and IgG, is another biological agent for RA. Two clinical trials disclosed the efficacy of abatacept for difficult-to-treat patients: the AIM for MTX-resistant cases and the ATTAIN for patients who are resistant to anti-TNF. The ATTEST trial suggested abatacept might have more acceptable safety profile than infliximab. These biologics are also promising for the treatment of RA for not only relieving clinical symptoms and signs but retarding structural damage.

  12. Biological preconcentrator

    Science.gov (United States)

    Manginell, Ronald P [Albuquerque, NM; Bunker, Bruce C [Albuquerque, NM; Huber, Dale L [Albuquerque, NM

    2008-09-09

    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  13. Change in CD3 positive T-cell expression in psoriatic arthritis synovium correlates with change in DAS28 and magnetic resonance imaging synovitis scores following initiation of biologic therapy - a single centre, open-label study

    LENUS (Irish Health Repository)

    Pontifex, Eliza K

    2011-01-27

    Abstract Introduction With the development of increasing numbers of potential therapeutic agents in inflammatory disease comes the need for effective biomarkers to help screen for drug efficacy and optimal dosing regimens early in the clinical trial process. This need has been recognized by the Outcome Measures in Rheumatology Clinical Trials (OMERACT) group, which has established guidelines for biomarker validation. To seek a candidate synovial biomarker of treatment response in psoriatic arthritis (PsA), we determined whether changes in immunohistochemical markers of synovial inflammation correlate with changes in disease activity scores assessing 28 joints (ΔDAS28) or magnetic resonance imaging synovitis scores (ΔMRI) in patients with PsA treated with a biologic agent. Methods Twenty-five consecutive patients with PsA underwent arthroscopic synovial biopsies and MRI scans of an inflamed knee joint at baseline and 12 weeks after starting treatment with either anakinra (first 10 patients) or etanercept (subsequent 15 patients) in two sequential studies of identical design. DAS28 scores were measured at both time points. Immunohistochemical staining for CD3, CD68 and Factor VIII (FVIII) was performed on synovial samples and scored by digital image analysis (DIA). MRI scans performed at baseline and at 12 weeks were scored for synovitis semi-quantitatively. The ΔDAS28 of the European League Against Rheumatism good response definition (>1.2) was chosen to divide patients into responder and non-responder groups. Differences between groups (Mann Whitney U test) and correlations between ΔDAS28 with change in immunohistochemical and MRI synovitis scores (Spearman\\'s rho test) were calculated. Results Paired synovial samples and MRI scans were available for 21 patients (8 anakinra, 13 etanercept) and 23 patients (8 anakinra, 15 etanercept) respectively. Change in CD3 (ΔCD3) and CD68 expression in the synovial sublining layer (ΔCD68sl) was significantly greater in

  14. Ageing towards meaningful work? Age, labour-market change, and attitudes to work in the Swedish workforce, 1979–2003

    Directory of Open Access Journals (Sweden)

    Johan Örestig

    2014-11-01

    Full Text Available A central finding in earlier research on work orientation is that there are substantial age-differences regarding attitudes to work. Generally, more older workers describe their jobs as intrinsically meaningful than younger workers. This result has been interpreted in three different ways, the psychological, the cultural, and the structural hypotheses, where the first emphasizes cognitive age-differences, the second sees age-differences as outcomes of generational differences, and the third regards them as expressions of labour-market inequalities. These different approaches lead to quite different hypotheses regarding recent developments, but the relevant research is limited. Drawing on data from the Swedish survey of living conditions (ULF, this study has examined attitudinal change within the Swedish workforce during 1979–2003. Three sub-periods, 1986-1987, 1994-1996, and 2001-2003 were compared with 1979, the year of reference. The results showed that a consistently smaller share of the workforce held extrinsic work values in the subsequent periods, and that this applied to all age-groups. Further, the results did not support the assumption of broader cultural differences between generations. Rather, the results provide support for the structural hypothesis. Older workers held extrinsic work values to a lesser degree than younger workers regardless of period. Most strikingly, the gap between the youngest group on the labour market (ages 16–29 and the older groups widened during the period. Furthermore, class differences in the distribution of the extrinsic attitude were intact throughout the study period; manual employees were consistently more likely to hold an extrinsic attitude than were service-class employees. This implies that differences in the probability of extrinsic work attitudes have been identifiable regardless of period, but that their prevalence has decreased as jobs involving features related to extrinsic work values

  15. 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.

  16. Environmental biology

    International Nuclear Information System (INIS)

    Tschumi, P.A.

    1981-01-01

    Environmental biology illustrates the functioning of ecosystems and the dynamics of populations with many examples from limnology and terrestrial ecology. On this basis, present environmental problems are analyzed. The present environmental crisis is seen as a result of the failure to observe ecological laws. (orig.) [de

  17. Biological timekeeping

    DEFF Research Database (Denmark)

    Lloyd, David

    2016-01-01

    , the networks that connect differenttime domains and the oscillations, rhythms and biological clocks that coordinate andsynchronise the complexity of the living state.“It is the pattern maintained by this homeostasis, which is the touchstone ofour personal identity. Our tissues change as we live: the food we...

  18. Scaffolded biology.

    Science.gov (United States)

    Minelli, Alessandro

    2016-09-01

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

  19. Biological digestion

    International Nuclear Information System (INIS)

    Rosevear, A.

    1988-01-01

    This paper discusses the biological degradation of non-radioactive organic material occurring in radioactive wastes. The biochemical steps are often performed using microbes or isolated enzymes in combination with chemical steps and the aim is to oxidise the carbon, hydrogen, nitrogen and sulphur to their respective oxides. (U.K.)

  20. Marine Biology

    Science.gov (United States)

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  1. 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,...

  2. Towards physical principles of biological evolution

    Science.gov (United States)

    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

  3. 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.

  4. 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.

  5. Binge eating as a meaningful experience in bulimia nervosa and anorexia nervosa: a qualitative analysis.

    Science.gov (United States)

    Eli, Karin

    2015-12-01

    Clinical studies describe binge eating as a reaction to hunger, negative affect, or the need to dissociate. However, little is known about the meanings that women with bulimia nervosa and anorexia nervosa associate with binge eating. To examine how women with anorexia nervosa and bulimia nervosa interpret their experiences of binge eating. Sixteen women who engaged in binge eating and had been diagnosed with anorexia nervosa, bulimia nervosa, or their subclinical variants were interviewed about their experiences of eating disorder. Interview data were analyzed using phenomenologically-informed thematic analysis. Participants described binge eating as a practice through which the self experiences a sense of release, and existential emptiness is replaced by overwhelming fullness. Meaningful experiences of release and fullness are central to binge eating in bulimia nervosa and anorexia nervosa, and may contribute to the long-term maintenance of this practice.

  6. Implementing the legal criteria of meaningful consent in the concept of mobile advertising

    DEFF Research Database (Denmark)

    Cleff, Evelyne Beatrix

    2006-01-01

    Advancements of the wired Internet and mobile telecommunication networks offer companies new advertising opportunities but this development also creates a need to consider acceptance and usability issues in order to ensure permission-based advertising. According to the law of the European Union (EU......), only permission-based mobile advertising is allowed. In order to obtain consent from the mobile user, the advertiser is obliged to make an effective disclosure. However, these rules are not specific to this new context. It will be a great challenge for advertisers to translate the requirements...... into actual business practices in order to obtain meaningful consent from the mobile user. This article focuses on the evaluation of legal problems related to these issues in order to find adequate technical solutions concerning m-advertising. It is assumed that a technological design, which is in line...

  7. Implementing the legal criteria for meaningful consent in the concept of mobile advertising

    DEFF Research Database (Denmark)

    Cleff, Evelyne Beatrix

    2007-01-01

    Advancements of the wired Internet and mobile telecommunication networks offer companies new advertising opportunities but this development creates a need to consider acceptance and usability issues in order to ensure permission-based advertising. According to the law of the European Union (EU......), only permission-based mobile advertising is allowed. In order to obtain consent from the mobile user, the advertiser is obliged to make an effective disclosure. However, these rules are not specific to this new context. It will be a great challenge for advertisers to translate the requirements...... into actual business practices in order to obtain meaningful consent from the mobile user. This article focuses on the evaluation of legal problems related to these issues in order to find adequate technical solutions concerning m-advertising. It is assumed that a technological design, which is in line...

  8. The dynamics of meaningful social interactions and the emergence of collective knowledge

    Science.gov (United States)

    Dankulov, Marija Mitrović; Melnik, Roderick; Tadić, Bosiljka

    2015-07-01

    Collective knowledge as a social value may arise in cooperation among actors whose individual expertise is limited. The process of knowledge creation requires meaningful, logically coordinated interactions, which represents a challenging problem to physics and social dynamics modeling. By combining two-scale dynamics model with empirical data analysis from a well-known Questions & Answers system Mathematics, we show that this process occurs as a collective phenomenon in an enlarged network (of actors and their artifacts) where the cognitive recognition interactions are properly encoded. The emergent behavior is quantified by the information divergence and innovation advancing of knowledge over time and the signatures of self-organization and knowledge sharing communities. These measures elucidate the impact of each cognitive element and the individual actor’s expertise in the collective dynamics. The results are relevant to stochastic processes involving smart components and to collaborative social endeavors, for instance, crowdsourcing scientific knowledge production with online games.

  9. ONTOLOGY BASED MEANINGFUL SEARCH USING SEMANTIC WEB AND NATURAL LANGUAGE PROCESSING TECHNIQUES

    Directory of Open Access Journals (Sweden)

    K. Palaniammal

    2013-10-01

    Full Text Available The semantic web extends the current World Wide Web by adding facilities for the machine understood description of meaning. The ontology based search model is used to enhance efficiency and accuracy of information retrieval. Ontology is the core technology for the semantic web and this mechanism for representing formal and shared domain descriptions. In this paper, we proposed ontology based meaningful search using semantic web and Natural Language Processing (NLP techniques in the educational domain. First we build the educational ontology then we present the semantic search system. The search model consisting three parts which are embedding spell-check, finding synonyms using WordNet API and querying ontology using SPARQL language. The results are both sensitive to spell check and synonymous context. This paper provides more accurate results and the complete details for the selected field in a single page.

  10. Fostering Self-Reflection and Meaningful Learning: Earth Science Professional Development for Middle School Science Teachers

    Science.gov (United States)

    Monet, Julie A.; Etkina, Eugenia

    2008-10-01

    This paper describes the analysis of teachers’ journal reflections during an inquiry-based professional development program. As a part of their learning experience, participants reflected on what they learned and how they learned. Progress of subject matter and pedagogical content knowledge was assessed though surveys and pre- and posttests. We found that teachers have difficulties reflecting on their learning and posing meaningful questions. The teachers who could describe how they reasoned from evidence to understand a concept had the highest learning gains. In contrast those teachers who seldom or never described learning a concept by reasoning from evidence showed the smallest learning gains. This analysis suggests that learning to reflect on one’s learning should be an integral part of teachers’ professional development experiences.

  11. A Knowledge Comparison Environment for Supporting Meaningful Learning of E-Book Users

    Directory of Open Access Journals (Sweden)

    Jingyun Wang

    2016-05-01

    Full Text Available In this paper, we present an ontology-based visualization support system which can provide a meaningful learning environment to help e-book learners to effectively construct their knowledge frameworks. In this personalized visualization support system, learners are encouraged to actively locate new knowledge in their own knowledge framework and check the logical consistency of their ideas for clearing up misunderstandings; on the other hand, instructors will be able to decide the group distribution for collaborative learning activities based on the knowledge structure of learners. For facilitating those visualization supports, a method to semi-automatically construct a course-centered ontology to describe the required information in a map structure is presented. To automatically manipulate this course-centered ontology to provide visualization learning supports, a prototype system is designed and developed.

  12. The significance of meaningful and enjoyable activities for nursing home resident's experiences of dignity

    DEFF Research Database (Denmark)

    Slettebø, Åshild; Saeteren, Berit; Caspari, Synnøve

    2017-01-01

    BACKGROUND: Living in a nursing home may be challenging to the residents' experience of dignity. Residents' perception of how their dignity is respected in everyday care is important. AIM: To examine how nursing home residents experience dignity through the provision of activities that foster...... meaning and joy in their daily life. METHOD: A qualitative design was used and 28 individual semistructured interviews conducted with nursing home residents from six nursing homes in Denmark, Norway and Sweden. The data were analysed with qualitative content analysis. Independent ethical committees in all...... participating countries granted their approval for the study. FINDINGS: The participants highlight two dimensions of the activities that foster experiences of dignity in nursing homes in Scandinavia. These two categories were (i) fostering dignity through meaningful participation and (ii) fostering dignity...

  13. The Concept Maps as a Didactic Resource Tool of Meaningful Learning in Astronomy Themes

    Science.gov (United States)

    Silveira, Felipa Pacífico Ribeiro de Assis; Mendonça, Conceição Aparecida Soares

    2015-07-01

    This article presents the results of an investigation that sought to understand the performance of the conceptual map (MC) as a teaching resource facilitator of meaningful learning of scientific concepts on astronomical themes, developed with elementary school students. The methodology employed to obtain and process the data was based on a quantitative and qualitative approach. On the quantitative level we designed a quasi-experimental research with a control group that did not use the MC and an experimental group that used the MC, both being evaluated in the beginning and end of the process. In this case, the performance of both groups is displayed in a descriptive and analytical study. In the qualitative approach, the MCs were interpreted using the structuring and assigned meanings shared by the student during his/her presentation. The results demonstrated through the improvement of qualifications that the MC made a difference in conceptual learning and in certain skills revealed by learning indicators.

  14. The right to appropriate and meaningful education for children with ASD.

    Science.gov (United States)

    Marshall, David; Goodall, Craig

    2015-10-01

    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 'right'. The International Convention of the Rights of the Child (United Nations in Convention on the rights of the child, office of the high commissioner, United Nations, Geneva, 1989) and the convention on the rights of the person with disability (United Nations in Convention on the rights of person's with disabilities and optional protocol, office of the high commissioner, United Nations, Geneva, 2006) amongst others will be utilised to argue the case for 'inclusive' educational opportunities to be a 'right' of every child on the autistic spectrum. The efficacy of mainstream inclusion is explored, identifying the position that a 'one size fits all' model of education is not appropriate for all children with ASD.

  15. In Quest of a Meaningful Model of Human Self and Behaviour

    Directory of Open Access Journals (Sweden)

    Manzurul Huq

    1994-06-01

    Full Text Available There is a growing awareness among many modern psychologists that the will to meaning is a highly distinctive feature of man, distinguishing him from animals. Accordingly, a behaviour model for man, to be truly representative, must include the drive for meaning as a significant dimension of human personality. In the light of this realization, some major psychological models of personality, e.g., the psychoanalytical model, behaviouristic model, humanistic model, and the existential model have been briefly examined, and a model based on transcendental nature of man is proposed. According to this model, the realization of an abiding comprehensive meaning of life and the consequent all­ inclusive meaningful behaviour, both at the individual and social levels, is the junction of man's perception and belief in a transcendentally anchored integrated framework of life.

  16. The electronic patient record as a meaningful audit tool - Accountability and autonomy in general practitioner work

    DEFF Research Database (Denmark)

    Winthereik, Brit Ross; van der Ploeg, I.; Berg, Marc

    2007-01-01

    Health authorities increasingly request that general practitioners (GPs) use information and communication technologies such as electronic patient records (EPR) for accountability purposes. This article deals with the use of EPRs among general practitioners in Britain. It examines two ways in which...... makes them active in finding ways that turn the EPR into a meaningful tool for them, that is, a tool that helps them provide what they see as good care. The article's main contribution is to show how accountability and autonomy are coproduced; less professional autonomy does not follow from more...... GPs use the EPR for accountability purposes. One way is to generate audit reports on the basis of the information that has been entered into the record. The other is to let the computer intervene in the clinical process through prompts. The article argues that GPs' ambivalence toward using the EPR...

  17. Can business impact analysis play a meaningful role in planning a cost-saving programme?

    Science.gov (United States)

    Wright, Trevor

    2011-02-01

    Business continuity as it exists today would appear to have reached something of a plateau. Considering the history of the discipline, and how it has developed from 'simple' disaster recovery to its present position, it is clear that the trend has been to move from a reactive discipline to a proactive process. Following on from this broadly-accepted point, it is perhaps time to consider how the discipline may develop and what wider and deeper contribution the business continuity profession may make to add further value for our clients. In the present climate, it seems appropriate to consider how (and if) business continuity practice can make a meaningful contribution to a cost saving exercise. The public and private sectors are considered and the differences are compared.

  18. Sensitivity of Claims-Based Algorithms to Ascertain Smoking Status More Than Doubled with Meaningful Use.

    Science.gov (United States)

    Huo, Jinhai; Yang, Ming; Tina Shih, Ya-Chen

    2018-03-01

    The "meaningful use of certified electronic health record" policy requires eligible professionals to record smoking status for more than 50% of all individuals aged 13 years or older in 2011 to 2012. To explore whether the coding to document smoking behavior has increased over time and to assess the accuracy of smoking-related diagnosis and procedure codes in identifying previous and current smokers. We conducted an observational study with 5,423,880 enrollees from the year 2009 to 2014 in the Truven Health Analytics database. Temporal trends of smoking coding, sensitivity, specificity, positive predictive value, and negative predictive value were measured. The rate of coding of smoking behavior improved significantly by the end of the study period. The proportion of patients in the claims data recorded as current smokers increased 2.3-fold and the proportion of patients recorded as previous smokers increased 4-fold during the 6-year period. The sensitivity of each International Classification of Diseases, Ninth Revision, Clinical Modification code was generally less than 10%. The diagnosis code of tobacco use disorder (305.1X) was the most sensitive code (9.3%) for identifying smokers. The specificities of these codes and the Current Procedural Terminology codes were all more than 98%. A large improvement in the coding of current and previous smoking behavior has occurred since the inception of the meaningful use policy. Nevertheless, the use of diagnosis and procedure codes to identify smoking behavior in administrative data is still unreliable. This suggests that quality improvements toward medical coding on smoking behavior are needed to enhance the capability of claims data for smoking-related outcomes research. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

  19. Qualitative Insights from a Canadian Multiinstitutional Research Study: In Search of Meaningful E-learning

    Directory of Open Access Journals (Sweden)

    Lorraine M. Carter

    2014-11-01

    Full Text Available 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 e-learning. Importantly, e-learning was conceptualized as the integration of pedagogy, instructional technology, and the Internet into teaching and learning environments. Based on this definition, participants reflected on e-learning in relation to one or more of the following contexts: face-to-face (f2f classrooms in which instructional technologies (e.g. learning management systems, video and webconferencing, mobile devices, etc. are used; blended or web-enhanced learning environments; and fully online learning environments. Data collected for the study included survey data (n=1377 for students, n=187 for faculty; narrative comments (n=269 for students, n=74 for faculty; and focus groups (n=16 for students, n=33 for faculty. The latter two sets of data comprise the basis of this paper. Four major themes emerged based on the responses of students and faculty. Represented by the acronym HIDI, the themes include human connection (H, IT support (I, design (D, and institutional infrastructure (I. These themes and sub-themes are presented in the paper as well as recommendations for educators and administrators who aspire to make e-learning a pedagogically meaningful experience for both learners and their teachers.

  20. Health Information Technology: Meaningful Use and Next Steps to Improving Electronic Facilitation of Medication Adherence.

    Science.gov (United States)

    Bosworth, Hayden B; Zullig, Leah L; Mendys, Phil; Ho, Michael; Trygstad, Troy; Granger, Christopher; Oakes, Megan M; Granger, Bradi B

    2016-03-15

    The use of health information technology (HIT) may improve medication adherence, but challenges for implementation remain. The aim of this paper is to review the current state of HIT as it relates to medication adherence programs, acknowledge the potential barriers in light of current legislation, and provide recommendations to improve ongoing medication adherence strategies through the use of HIT. We describe four potential HIT barriers that may impact interoperability and subsequent medication adherence. Legislation in the United States has incentivized the use of HIT to facilitate and enhance medication adherence. The Health Information Technology for Economic and Clinical Health (HITECH) was recently adopted and establishes federal standards for the so-called "meaningful use" of certified electronic health record (EHR) technology that can directly impact medication adherence. The four persistent HIT barriers to medication adherence include (1) underdevelopment of data reciprocity across clinical, community, and home settings, limiting the capture of data necessary for clinical care; (2) inconsistent data definitions and lack of harmonization of patient-focused data standards, making existing data difficult to use for patient-centered outcomes research; (3) inability to effectively use the national drug code information from the various electronic health record and claims datasets for adherence purposes; and (4) lack of data capture for medication management interventions, such as medication management therapy (MTM) in the EHR. Potential recommendations to address these issues are discussed. To make meaningful, high quality data accessible, and subsequently improve medication adherence, these challenges will need to be addressed to fully reach the potential of HIT in impacting one of our largest public health issues.