Integrating cell biology and proteomic approaches in plants.

Science.gov (United States)

Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

2017-10-03

Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

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

Science.gov (United States)

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

2003-01-01

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

An Integrated Approach to Biology

Indian Academy of Sciences (India)

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

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

Science.gov (United States)

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

2009-12-01

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

Broadening Participation in the Society for Integrative and Comparative Biology.

Science.gov (United States)

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

2017-07-01

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

Integration of genomic information with biological networks using Cytoscape.

Science.gov (United States)

Bauer-Mehren, Anna

2013-01-01

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

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

Science.gov (United States)

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

2011-01-01

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

A "weight of evidence" approach for the integration of environmental "triad" data to assess ecological risk and biological vulnerability.

Science.gov (United States)

Dagnino, Alessandro; Sforzini, Susanna; Dondero, Francesco; Fenoglio, Stefano; Bona, Elisa; Jensen, John; Viarengo, Aldo

2008-07-01

A new Expert Decision Support System (EDSS) that can integrate Triad data for assessing environmental risk and biological vulnerability at contaminated sites has been developed. Starting with ecosystem relevance, the EDSS assigns different weights to the results obtained from Triad disciplines. The following parameters have been employed: 1) chemical soil analyses (revealing the presence of potentially dangerous substances), 2) ecotoxicological bioassays (utilizing classical endpoints such as survival and reproduction rates), 3) biomarkers (showing sublethal pollutant effects), and 4) ecological parameters (assessing changes in community structure and functions). For each Triad discipline, the EDSS compares the data obtained at the studied field sites with reference values and calculates different 0-1 indexes (e.g., Chemical Risk Index, Ecotoxicological Risk Index, and Ecological Risk Index). The EDSS output consists of 3 indexes: 1) Environmental Risk index (EnvRI), quantifying the levels of biological damage at population-community level, 2) Biological Vulnerability Index (BVI), assessing the potential threats to biological equilibriums, and 3) Genotoxicity Index (GTI), screening genotoxicity effects. The EDSS has been applied in the integration of a battery of Triad data obtained during the European Union-funded Life Intervention in the Fraschetta Area (LINFA) project, which has been carried out in order to estimate the potential risk from soils of a highly anthropized area (Alessandria, Italy) mainly impacted by deposition of atmospheric pollutants. Results obtained during 4 seasonal sampling campaigns (2004-2005) show maximum values of EnvRI in sites A and B (characterized by industrial releases) and lower levels in site D (affected by vehicular traffic emissions). All 3 potentially polluted sites have shown high levels of BVI and GTI, suggesting a general change from reference conditions (site C).

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

Science.gov (United States)

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

2018-05-01

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

Semiconductor Devices Inspired By and Integrated With Biology

Energy Technology Data Exchange (ETDEWEB)

Rogers, John [University of Illinois

2012-04-25

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

Can lip prints provide biologic evidence?

Science.gov (United States)

Sharma, Preeti; Sharma, Neeraj; Wadhwan, Vijay; Aggarwal, Pooja

2016-01-01

Lip prints are unique and can be used in personal identification. Very few studies are available which establish them as biological evidence in the court of law. Thus, the objective of this study was to attempt to isolate DNA and obtain full short tandem repeat (STR) loci of the individual from the lip prints on different surfaces. Twelve lip prints were procured on different surfaces such as tissue paper, cotton cloth, ceramic tile, and glass surface. Latent lip prints were developed using fingerprint black powder. Lipstick-coated lip prints were also collected on the same supporting items. DNA was isolated, quantified, and amplified using Identifiler™ kit to type 15 STR loci. Ample quantity of DNA was extracted from all the lip print impressions and 15 loci were successfully located in seven samples. Fourteen loci were successfully typed in 3 lip impressions while 13 loci were typed in 2 samples. This study emphasizes the relevance of lip prints at the scene of crime. Extraction of DNA followed by typing of STR loci establishes the lip prints as biological evidence too. Tissue papers, napkins, cups, and glasses may have imprints of the suspect's lips. Thus, the full genetic profile is extremely useful for the forensic team.

Protecting Digital Evidence Integrity by Using Smart Cards

Science.gov (United States)

Saleem, Shahzad; Popov, Oliver

RFC 3227 provides general guidelines for digital evidence collection and archiving, while the International Organization on Computer Evidence offers guidelines for best practice in the digital forensic examination. In the light of these guidelines we will analyze integrity protection mechanism provided by EnCase and FTK which is mainly based on Message Digest Codes (MDCs). MDCs for integrity protection are not tamper proof, hence they can be forged. With the proposed model for protecting digital evidence integrity by using smart cards (PIDESC) that establishes a secure platform for digitally signing the MDC (in general for a whole range of cryptographic services) in combination with Public Key Cryptography (PKC), one can show that this weakness might be overcome.

West-Life, Tools for Integrative Structural Biology

CERN Multimedia

CERN. Geneva

2018-01-01

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

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

Science.gov (United States)

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

2007-01-01

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

Neurocognitive capabilities modulate the integration of evidence in schizophrenia

NARCIS (Netherlands)

Eifler, Sarah; Rausch, Franziska; Schirmbeck, Frederike; Veckenstedt, Ruth; Englisch, Susanne; Meyer-Lindenberg, Andreas; Kirsch, Peter; Zink, Mathias

2014-01-01

Previous studies have demonstrated a cognitive bias in the integration of disconfirmatory evidence (BADE) in patients with schizophrenia. This bias has been associated with delusions. So far, it is unclear how the integration of evidence is associated with neurocognitive capabilities. In the current

Integrative radiation systems biology

International Nuclear Information System (INIS)

Unger, Kristian

2014-01-01

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

An integrative approach to inferring biologically meaningful gene modules

Directory of Open Access Journals (Sweden)

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.

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

Science.gov (United States)

Desai, Sanket; Burra, Prasad

2015-01-01

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

WISB: Warwick Integrative Synthetic Biology Centre.

Science.gov (United States)

McCarthy, John

2016-06-15

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

Decision-Making Under Risk: Integrating Perspectives From Biology, Economics, and Psychology.

Science.gov (United States)

Mishra, Sandeep

2014-08-01

Decision-making under risk has been variably characterized and examined in many different disciplines. However, interdisciplinary integration has not been forthcoming. Classic theories of decision-making have not been amply revised in light of greater empirical data on actual patterns of decision-making behavior. Furthermore, the meta-theoretical framework of evolution by natural selection has been largely ignored in theories of decision-making under risk in the human behavioral sciences. In this review, I critically examine four of the most influential theories of decision-making from economics, psychology, and biology: expected utility theory, prospect theory, risk-sensitivity theory, and heuristic approaches. I focus especially on risk-sensitivity theory, which offers a framework for understanding decision-making under risk that explicitly involves evolutionary considerations. I also review robust empirical evidence for individual differences and environmental/situational factors that predict actual risky decision-making that any general theory must account for. Finally, I offer steps toward integrating various theoretical perspectives and empirical findings on risky decision-making. © 2014 by the Society for Personality and Social Psychology, Inc.

Integrating Evidence Within and Across Evidence Streams Using Qualitative Methods

Science.gov (United States)

There is high demand in environmental health for adoption of a structured process that evaluates and integrates evidence while making decisions transparent. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework holds promise to address this deman...

Aligning ontologies and integrating textual evidence for pathway analysis of microarray data

Energy Technology Data Exchange (ETDEWEB)

Gopalan, Banu; Posse, Christian; Sanfilippo, Antonio P.; Stenzel-Poore, Mary; Stevens, S.L.; Castano, Jose; Beagley, Nathaniel; Riensche, Roderick M.; Baddeley, Bob; Simon, R.P.; Pustejovsky, James

2006-10-08

Expression arrays are introducing a paradigmatic change in biology by shifting experimental approaches from single gene studies to genome-level analysis, monitoring the ex-pression levels of several thousands of genes in parallel. The massive amounts of data obtained from the microarray data needs to be integrated and interpreted to infer biological meaning within the context of information-rich pathways. In this paper, we present a methodology that integrates textual information with annotations from cross-referenced ontolo-gies to map genes to pathways in a semi-automated way. We illustrate this approach and compare it favorably to other tools by analyzing the gene expression changes underlying the biological phenomena related to stroke. Stroke is the third leading cause of death and a major disabler in the United States. Through years of study, researchers have amassed a significant knowledge base about stroke, and this knowledge, coupled with new technologies, is providing a wealth of new scientific opportunities. The potential for neu-roprotective stroke therapy is enormous. However, the roles of neurogenesis, angiogenesis, and other proliferative re-sponses in the recovery process following ischemia and the molecular mechanisms that lead to these processes still need to be uncovered. Improved annotation of genomic and pro-teomic data, including annotation of pathways in which genes and proteins are involved, is required to facilitate their interpretation and clinical application. While our approach is not aimed at replacing existing curated pathway databases, it reveals multiple hidden relationships that are not evident with the way these databases analyze functional groupings of genes from the Gene Ontology.

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

Science.gov (United States)

Chen, Bor-Sen; Wu, Chia-Chou

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2013-10-01

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

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

Directory of Open Access Journals (Sweden)

Ji Yoon Kim

2015-11-01

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

PathJam: a new service for integrating biological pathway information

Directory of Open Access Journals (Sweden)

Glez-Peña Daniel

2010-03-01

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

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

Science.gov (United States)

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

2015-01-07

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

An Integrated Biological Control System At Hanford

International Nuclear Information System (INIS)

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

2010-01-01

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

AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

Energy Technology Data Exchange (ETDEWEB)

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

2010-02-11

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

Data Integration and Mining for Synthetic Biology Design.

Science.gov (United States)

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

2016-10-21

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

FIA: An Open Forensic Integration Architecture for Composing Digital Evidence

Science.gov (United States)

Raghavan, Sriram; Clark, Andrew; Mohay, George

The analysis and value of digital evidence in an investigation has been the domain of discourse in the digital forensic community for several years. While many works have considered different approaches to model digital evidence, a comprehensive understanding of the process of merging different evidence items recovered during a forensic analysis is still a distant dream. With the advent of modern technologies, pro-active measures are integral to keeping abreast of all forms of cyber crimes and attacks. This paper motivates the need to formalize the process of analyzing digital evidence from multiple sources simultaneously. In this paper, we present the forensic integration architecture (FIA) which provides a framework for abstracting the evidence source and storage format information from digital evidence and explores the concept of integrating evidence information from multiple sources. The FIA architecture identifies evidence information from multiple sources that enables an investigator to build theories to reconstruct the past. FIA is hierarchically composed of multiple layers and adopts a technology independent approach. FIA is also open and extensible making it simple to adapt to technological changes. We present a case study using a hypothetical car theft case to demonstrate the concepts and illustrate the value it brings into the field.

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

Science.gov (United States)

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

2014-08-01

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

Integrated Biological Control

International Nuclear Information System (INIS)

JOHNSON, A.R.

2002-01-01

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

Towards Integration of Biological and Physiological Functions at Multiple Levels

Directory of Open Access Journals (Sweden)

Taishin eNomura

2010-12-01

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

Psychology and evolutionary biology; Causal analysis, evidence, and nomothetic laws

NARCIS (Netherlands)

Van Hezewijk, René

2008-01-01

Published as a chapter in Van Hezewijk, R. (2003). Psychology and evolutionary biology; Causal analysis, evidence, and nomothetic laws. In N. Stephenson, L. Radtke, R. Jorna & H. J. Stam (Eds.), Theoretical psychology; Critical contributions (pp. 405-415). Concord, Ontario: Captus Press.

Integration and Task Allocation: Evidence from Patient Care.

Science.gov (United States)

David, Guy; Rawley, Evan; Polsky, Daniel

2013-01-01

Using the universe of patient transitions from inpatient hospital care to skilled nursing facilities and home health care in 2005, we show how integration eliminates task misallocation problems between organizations. We find that vertical integration allows hospitals to shift patient recovery tasks downstream to lower-cost organizations by discharging patients earlier (and in poorer health) and increasing post-hospitalization service intensity. While integration facilitates a shift in the allocation of tasks and resources, health outcomes either improved or were unaffected by integration on average. The evidence suggests that integration solves coordination problems that arise in market exchange through improvements in the allocation of tasks across care settings.

Integration and Task Allocation: Evidence from Patient Care*

Science.gov (United States)

David, Guy; Rawley, Evan; Polsky, Daniel

2013-01-01

Using the universe of patient transitions from inpatient hospital care to skilled nursing facilities and home health care in 2005, we show how integration eliminates task misallocation problems between organizations. We find that vertical integration allows hospitals to shift patient recovery tasks downstream to lower-cost organizations by discharging patients earlier (and in poorer health) and increasing post-hospitalization service intensity. While integration facilitates a shift in the allocation of tasks and resources, health outcomes either improved or were unaffected by integration on average. The evidence suggests that integration solves coordination problems that arise in market exchange through improvements in the allocation of tasks across care settings. PMID:24415893

Systematic integration of experimental data and models in systems biology.

Science.gov (United States)

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

2010-11-29

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

Integrating phosphoproteomics in systems biology

Directory of Open Access Journals (Sweden)

Yu Liu

2014-07-01

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

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

Directory of Open Access Journals (Sweden)

L.A. Azzalis

2008-05-01

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

The Virtual Institute for Integrative Biology (VIIB)

International Nuclear Information System (INIS)

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

2007-01-01

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

Biologics in dermatology: An integrated review

Directory of Open Access Journals (Sweden)

Virendra N Sehgal

2014-01-01

Full Text Available The advent of biologics in dermatologic treatment armentarium has added refreshing dimensions, for it is a major breakthrough. Several agents are now available for use. It is therefore imperative to succinctly comprehend their pharmacokinetics for their apt use. A concerted endeavor has been made to delve on this subject. The major groups of biologics have been covered and include: Drugs acting against TNF-α, Alefacept, Ustekinumab, Rituximab, IVIG and Omalizumab. The relevant pharmacokinetic characteristics have been detailed. Their respective label (approved and off-label (unapproved indications have been defined, highlighting their dosage protocol, availability and mode of administration. The evidence level of each indication has also been discussed to apprise the clinician of their current and prospective uses. Individual anti-TNF drugs are not identical in their actions and often one is superior to the other in a particular disease. Hence, the section on anti-TNF agents mentions the literature on each drug separately, and not as a group. The limitations for their use have also been clearly brought out.

Integrated Network Analysis and Effective Tools in Plant Systems Biology

Directory of Open Access Journals (Sweden)

Atsushi eFukushima

2014-11-01

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

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

DEFF Research Database (Denmark)

Pfreundt, Andrea

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

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

DEFF Research Database (Denmark)

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

2016-01-01

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

Data mining and data integration in biology

DEFF Research Database (Denmark)

Ólason, Páll Ísólfur

2008-01-01

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

Cyber integrated MEMS microhand for biological applications

Science.gov (United States)

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

2009-05-01

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

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

Science.gov (United States)

Boes, Katie E.

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

Carole L. Palmer

2007-12-01

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

Integrative biology approach identifies cytokine targeting strategies for psoriasis.

Science.gov (United States)

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

2014-02-12

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

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

Science.gov (United States)

2013-01-01

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

Evidence-based music therapy practice: an integral understanding.

Science.gov (United States)

Abrams, Brian

2010-01-01

The American Music Therapy Association has recently put into action a plan called its Research Strategic Priority, with one of its central purposes to advance the music therapy field through research promoting Evidence-Based Practice of music therapy. The extant literature on music therapy practice, theory, and research conveys a range of very different perspectives on what may count as the "evidence" upon which practice is based. There is therefore a need to conceptualize evidence-based music therapy practice in a multifaceted, yet coherent and balanced way. The purpose of this paper is to illustrate a framework based upon four distinct epistemological perspectives on evidence-based music therapy practice that together represent an integral understanding.

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

Science.gov (United States)

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

2011-01-01

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

Integrating research evidence and physical activity policy making-REPOPA project

NARCIS (Netherlands)

Aro, A.R.; Bertram, M.; Hamalainen, R.-M.; van de Goor, L.A.M.; Skovgaard, T.; Valente, A.; Castellani, T.; Chereches, R.; Edwards, N.

2016-01-01

Evidence shows that regular physical activity is enhanced by supporting environment. Studies are needed to integrate research evidence into health enhancing, cross-sector physical activity (HEPA) policy making. This article presents the rationale, study design, measurement procedures and the initial

Integrative assessment of Evolutionary theory acceptance and knowledge levels of Biology undergraduate students from a Brazilian university

Science.gov (United States)

Tavares, Gustavo Medina; Bobrowski, Vera Lucia

2018-03-01

The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students' perceptions towards evolution, and studies can help to reveal those factors. We used a conceptual questionnaire, the Measure of Acceptance of the Theory of Evolution (MATE) instrument, and a Knowledge test to assess (1) the level of acceptance and understanding of 23 undergraduate Biology students nearing the end of their course, (2) other factors that could affect these levels, including course structure, and (3) the most difficult topics regarding evolutionary biology. The results of this study showed that the students, on average, had a 'Very High Acceptance' (89.91) and a 'Very Low Knowledge' (59.42%) of Evolutionary theory, and also indicated a moderate positive correlation between the two (r = 0.66, p = .001). The most difficult topics were related to the definition of evolution and dating techniques. We believe that the present study provides evidence for policymakers to reformulate current school and university curricula in order to improve the teachers' acceptance and understanding of evolution and other biological concepts, consequently, helping students reduce their misconceptions related to evolutionary biology.

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

Science.gov (United States)

Bisbee, Gregory D.; Kaiser, Cheryl A.

1997-01-01

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

[Problems of world outlook and methodology of science integration in biological studies].

Science.gov (United States)

Khododova, Iu D

1981-01-01

Problems of worldoutlook and methodology of the natural-science knowledge are considered basing on the analysis of tendencies in the development of the membrane theory of cell processes and the use of principles of biological membrane functioning when solving some scientific and applied problems pertaining to different branches of chemistry and biology. The notion scientific knowledge integration is defined as interpenetration of approaches, methods and ideas of different branches of knowledge and enrichment on this basis of their content resulting in knowledge augmentation in each field taken separately. These processes are accompanied by appearance of new branches of knowledge - sciences "on junction" and their subsequent differentiations. The analysis of some gnoseological situations shows that integration of sciences contributes to coordination and some agreement of thinking styles of different specialists, puts forward keen personality of a scientist demanding, in particular, his high professional mobility. Problems of scientific activity organization are considered, which involve social sciences into the integration processes. The role of philosophy in the integration processes is emphasized.

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

Science.gov (United States)

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

2012-04-05

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

Evidence-based integrative medicine in clinical veterinary oncology.

Science.gov (United States)

Raditic, Donna M; Bartges, Joseph W

2014-09-01

Integrative medicine is the combined use of complementary and alternative medicine with conventional or traditional Western medicine systems. The demand for integrative veterinary medicine is growing, but evidence-based research on its efficacy is limited. In veterinary clinical oncology, such research could be translated to human medicine, because veterinary patients with spontaneous tumors are valuable translational models for human cancers. An overview of specific herbs, botanics, dietary supplements, and acupuncture evaluated in dogs, in vitro canine cells, and other relevant species both in vivo and in vitro is presented for their potential use as integrative therapies in veterinary clinical oncology. Published by Elsevier Inc.

DNA barcodes for assessment of the biological integrity of aquatic ecosystems

Science.gov (United States)

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

Functional brain networks underlying detection and integration of disconfirmatory evidence.

Science.gov (United States)

Lavigne, Katie M; Metzak, Paul D; Woodward, Todd S

2015-05-15

Processing evidence that disconfirms a prior interpretation is a fundamental aspect of belief revision, and has clear social and clinical relevance. This complex cognitive process requires (at minimum) an alerting stage and an integration stage, and in the current functional magnetic resonance imaging (fMRI) study, we used multivariate analysis methodology on two datasets in an attempt to separate these sequentially-activated cognitive stages and link them to distinct functional brain networks. Thirty-nine healthy participants completed one of two versions of an evidence integration experiment involving rating two consecutive animal images, both of which consisted of two intact images of animal faces morphed together at different ratios (e.g., 70/30 bird/dolphin followed by 10/90 bird/dolphin). The two versions of the experiment differed primarily in terms of stimulus presentation and timing, which facilitated functional interpretation of brain networks based on differences in the hemodynamic response shapes between versions. The data were analyzed using constrained principal component analysis for fMRI (fMRI-CPCA), which allows distinct, simultaneously active task-based networks to be separated, and these were interpreted using both temporal (task-based hemodynamic response shapes) and spatial (dominant brain regions) information. Three networks showed increased activity during integration of disconfirmatory relative to confirmatory evidence: (1) a network involved in alerting to the requirement to revise an interpretation, identified as the salience network (dorsal anterior cingulate cortex and bilateral insula); (2) a sensorimotor response-related network (pre- and post-central gyri, supplementary motor area, and thalamus); and (3) an integration network involving rostral prefrontal, orbitofrontal and posterior parietal cortex. These three networks were staggered in their peak activity (alerting, responding, then integrating), but at certain time points (e

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

Science.gov (United States)

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

2017-01-01

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

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

International Nuclear Information System (INIS)

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

2006-01-01

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

Integrated pathway clusters with coherent biological themes for target prioritisation.

Directory of Open Access Journals (Sweden)

Yi-An Chen

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

Conservation Biology and Traditional Ecological Knowledge: Integrating Academic Disciplines for Better Conservation Practice

Directory of Open Access Journals (Sweden)

Joshua A. Drew

2006-12-01

Full Text Available Conservation biology and environmental anthropology are disciplines that are both concerned with the identification and preservation of diversity, in one case biological and in the other cultural. Both conservation biology and the study of traditional ecoloigcal knowledge function at the nexus of the social and natural worlds, yet historically there have been major impediments to integrating the two. Here we identify linguistic, cultural, and epistemological barriers between the two disciplines. We argue that the two disciplines are uniquely positioned to inform each other and to provide critical insights and new perspectives on the way these sciences are practiced. We conclude by synthesizing common themes found in conservation success stories, and by making several suggestions on integration. These include cross-disciplinary publication, expanding memberships in professional societies and conducting multidisciplinary research based on similar interests in ecological process, taxonomy, or geography. Finally, we argue that extinction threats, be they biological or cultural/linguistic are imminent, and that by bringing these disciplines together we may be able to forge synergistic conservation programs capable of protecting the vivid splendor of life on Earth.

Teaching the fundamentals of biological data integration using classroom games.

Directory of Open Access Journals (Sweden)

Maria Victoria Schneider

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

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

Science.gov (United States)

Kohl, Kevin D

2017-10-01

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

The Navigation Guide—Evidence-Based Medicine Meets Environmental Health: Integration of Animal and Human Evidence for PFOA Effects on Fetal Growth

Science.gov (United States)

Koustas, Erica; Sutton, Patrice; Johnson, Paula I.; Atchley, Dylan S.; Sen, Saunak; Robinson, Karen A.; Axelrad, Daniel A.; Woodruff, Tracey J.

2014-01-01

Background: The Navigation Guide is a novel systematic review method to synthesize scientific evidence and reach strength of evidence conclusions for environmental health decision making. Objective: Our aim was to integrate scientific findings from human and nonhuman studies to determine the overall strength of evidence for the question “Does developmental exposure to perfluorooctanoic acid (PFOA) affect fetal growth in humans?” Methods: We developed and applied prespecified criteria to systematically and transparently a) rate the quality of the scientific evidence as “high,” “moderate,” or “low”; b) rate the strength of the human and nonhuman evidence separately as “sufficient,” “limited,” “moderate,” or “evidence of lack of toxicity”; and c) integrate the strength of the human and nonhuman evidence ratings into a strength of the evidence conclusion. Results: We identified 18 epidemiology studies and 21 animal toxicology studies relevant to our study question. We rated both the human and nonhuman mammalian evidence as “moderate” quality and “sufficient” strength. Integration of these evidence ratings produced a final strength of evidence rating in which review authors concluded that PFOA is “known to be toxic” to human reproduction and development based on sufficient evidence of decreased fetal growth in both human and nonhuman mammalian species. Conclusion: We concluded that developmental exposure to PFOA adversely affects human health based on sufficient evidence of decreased fetal growth in both human and nonhuman mammalian species. The results of this case study demonstrate the application of a systematic and transparent methodology, via the Navigation Guide, for reaching strength of evidence conclusions in environmental health. Citation: Lam J, Koustas E, Sutton P, Johnson PI, Atchley DS, Sen S, Robinson KA, Axelrad DA, Woodruff TJ. 2014. The Navigation Guide—evidence-based medicine meets environmental health

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

Science.gov (United States)

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

2012-03-08

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

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

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Hagen, Joel B

2015-01-01

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

Multi-omic data integration enables discovery of hidden biological regularities

DEFF Research Database (Denmark)

Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin

2016-01-01

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

Systems biology in critical-care nursing.

Science.gov (United States)

Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

2011-01-01

Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

The Navigation Guide - evidence-based medicine meets environmental health: integration of animal and human evidence for PFOA effects on fetal growth.

Science.gov (United States)

Lam, Juleen; Koustas, Erica; Sutton, Patrice; Johnson, Paula I; Atchley, Dylan S; Sen, Saunak; Robinson, Karen A; Axelrad, Daniel A; Woodruff, Tracey J

2014-10-01

The Navigation Guide is a novel systematic review method to synthesize scientific evidence and reach strength of evidence conclusions for environmental health decision making. Our aim was to integrate scientific findings from human and nonhuman studies to determine the overall strength of evidence for the question "Does developmental exposure to perfluorooctanoic acid (PFOA) affect fetal growth in humans?" We developed and applied prespecified criteria to systematically and transparently a) rate the quality of the scientific evidence as "high," "moderate," or "low"; b) rate the strength of the human and nonhuman evidence separately as "sufficient," "limited," "moderate," or "evidence of lack of toxicity"; and c) integrate the strength of the human and nonhuman evidence ratings into a strength of the evidence conclusion. We identified 18 epidemiology studies and 21 animal toxicology studies relevant to our study question. We rated both the human and nonhuman mammalian evidence as "moderate" quality and "sufficient" strength. Integration of these evidence ratings produced a final strength of evidence rating in which review authors concluded that PFOA is "known to be toxic" to human reproduction and development based on sufficient evidence of decreased fetal growth in both human and nonhuman mammalian species. We concluded that developmental exposure to PFOA adversely affects human health based on sufficient evidence of decreased fetal growth in both human and nonhuman mammalian species. The results of this case study demonstrate the application of a systematic and transparent methodology, via the Navigation Guide, for reaching strength of evidence conclusions in environmental health.

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

Science.gov (United States)

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

2016-06-01

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

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

Directory of Open Access Journals (Sweden)

Andra Waagmeester

2016-06-01

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

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

Science.gov (United States)

Waagmeester, Andra; Pico, Alexander R.

2016-01-01

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

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

Directory of Open Access Journals (Sweden)

Ivo D Dinov

2008-05-01

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

Improving integrative searching of systems chemical biology data using semantic annotation

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Chen Bin

2012-03-01

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

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

Science.gov (United States)

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

2018-03-01

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

Housing interventions and control of asthma-related indoor biologic agents: a review of the evidence.

Science.gov (United States)

Krieger, James; Jacobs, David E; Ashley, Peter J; Baeder, Andrea; Chew, Ginger L; Dearborn, Dorr; Hynes, H Patricia; Miller, J David; Morley, Rebecca; Rabito, Felicia; Zeldin, Darryl C

2010-01-01

Subject matter experts systematically reviewed evidence on the effectiveness of housing interventions that affect health outcomes, primarily asthma, associated with exposure to moisture, mold, and allergens. Three of the 11 interventions reviewed had sufficient evidence for implementation: multifaceted, in-home, tailored interventions for reducing asthma morbidity; integrated pest management to reduce cockroach allergen; and combined elimination of moisture intrusion and leaks and removal of moldy items to reduce mold and respiratory symptoms. Four interventions needed more field evaluation, 1 needed formative research, and 3 either had no evidence of effectiveness or were ineffective. The 3 interventions with sufficient evidence all applied multiple, integrated strategies. This evidence review shows that selected interventions that improve housing conditions will reduce morbidity from asthma and respiratory allergies.

Integrating research evidence and physical activity policy making

DEFF Research Database (Denmark)

Aro, Arja R.; Bertram, Maja; Hämäläinen, Riitta-Maija

2016-01-01

Evidence shows that regular physical activity is enhanced by supporting environment. Studies are needed to integrate research evidence into health enhancing, cross-sector physical activity (HEPA) policy making. This article presents the rationale, study design, measurement procedures...... and the initial results of the first phase of six European countries in a five-year research project (2011-2016), REsearch into POlicy to enhance Physical Activity (REPOPA). REPOPA is programmatic research; it consists of linked studies; the first phase studied the use of evidence in 21 policies in implementation...... to learn more in depth from the policy making process and carried out 86 qualitative stakeholder interviews. The second, ongoing phase builds on the central findings of the first phase in each country; it consists of two sets of interventions: game simulations to study cross-sector collaboration...

Integrating evidence-based practice into RN-to-BSN clinical nursing education.

Science.gov (United States)

Oh, Eui Geum; Kim, Sunah; Kim, So Sun; Kim, Sue; Cho, Eun Yong; Yoo, Ji-Soo; Kim, Hee Soon; Lee, Ju Hee; You, Mi Ae; Lee, Hyejung

2010-07-01

This study examines the effects of integrating evidence-based practice (EBP) into clinical practicum on EBP efficacy and barriers to research utilization among Korean RN-to-BSN students. A one-group pretest-posttest design was used. Eighty-one students were recruited from a school of nursing in Korea. Evidence-based practice clinical practicum was composed of two consecutive programs during one semester. Lectures, individual mentoring on EBP practicum, small group, and wrap-up conferences were provided. Outcomes of EBP efficacy and barriers to research utilization were analyzed using paired t tests for 74 final participants. Evidence-based practice efficacy scores increased significantly (p effectiveness of EBP education among RN-to-BSN students. These results may help health educators develop effective educational strategies to integrate EBP concepts into a clinical practicum. Copyright 2010, SLACK Incorporated.

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

Science.gov (United States)

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

2009-05-04

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

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

Directory of Open Access Journals (Sweden)

Mosca Ettore

2007-08-01

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

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

Science.gov (United States)

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

2013-09-01

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

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

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Christley Scott

2010-08-01

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

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

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Deusiano Florêncio dos Reis

2017-01-01

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

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

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

2015-12-01

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

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

Science.gov (United States)

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

2012-12-15

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

The effects of integrated care: a systematic review of UK and international evidence.

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Baxter, Susan; Johnson, Maxine; Chambers, Duncan; Sutton, Anthea; Goyder, Elizabeth; Booth, Andrew

2018-05-10

Healthcare systems around the world have been responding to the demand for better integrated models of service delivery. However, there is a need for further clarity regarding the effects of these new models of integration, and exploration regarding whether models introduced in other care systems may achieve similar outcomes in a UK national health service context. The study aimed to carry out a systematic review of the effects of integration or co-ordination between healthcare services, or between health and social care on service delivery outcomes including effectiveness, efficiency and quality of care. Electronic databases including MEDLINE; Embase; PsycINFO; CINAHL; Science and Social Science Citation Indices; and the Cochrane Library were searched for relevant literature published between 2006 to March 2017. Online sources were searched for UK grey literature, and citation searching, and manual reference list screening were also carried out. Quantitative primary studies and systematic reviews, reporting actual or perceived effects on service delivery following the introduction of models of integration or co-ordination, in healthcare or health and social care settings in developed countries were eligible for inclusion. Strength of evidence for each outcome reported was analysed and synthesised using a four point comparative rating system of stronger, weaker, inconsistent or limited evidence. One hundred sixty seven studies were eligible for inclusion. Analysis indicated evidence of perceived improved quality of care, evidence of increased patient satisfaction, and evidence of improved access to care. Evidence was rated as either inconsistent or limited regarding all other outcomes reported, including system-wide impacts on primary care, secondary care, and health care costs. There were limited differences between outcomes reported by UK and international studies, and overall the literature had a limited consideration of effects on service users. Models of

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

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Hawkins, Charles P

2006-08-01

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

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

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

2014-02-01

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

Quantum Mechanics predicts evolutionary biology.

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Torday, J S

2018-07-01

Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018 Elsevier Ltd. All rights reserved.

Integration of Evidence Base into a Probabilistic Risk Assessment

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Saile, Lyn; Lopez, Vilma; Bickham, Grandin; Kerstman, Eric; FreiredeCarvalho, Mary; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

2011-01-01

INTRODUCTION: A probabilistic decision support model such as the Integrated Medical Model (IMM) utilizes an immense amount of input data that necessitates a systematic, integrated approach for data collection, and management. As a result of this approach, IMM is able to forecasts medical events, resource utilization and crew health during space flight. METHODS: Inflight data is the most desirable input for the Integrated Medical Model. Non-attributable inflight data is collected from the Lifetime Surveillance for Astronaut Health study as well as the engineers, flight surgeons, and astronauts themselves. When inflight data is unavailable cohort studies, other models and Bayesian analyses are used, in addition to subject matters experts input on occasion. To determine the quality of evidence of a medical condition, the data source is categorized and assigned a level of evidence from 1-5; the highest level is one. The collected data reside and are managed in a relational SQL database with a web-based interface for data entry and review. The database is also capable of interfacing with outside applications which expands capabilities within the database itself. Via the public interface, customers can access a formatted Clinical Findings Form (CLiFF) that outlines the model input and evidence base for each medical condition. Changes to the database are tracked using a documented Configuration Management process. DISSCUSSION: This strategic approach provides a comprehensive data management plan for IMM. The IMM Database s structure and architecture has proven to support additional usages. As seen by the resources utilization across medical conditions analysis. In addition, the IMM Database s web-based interface provides a user-friendly format for customers to browse and download the clinical information for medical conditions. It is this type of functionality that will provide Exploratory Medicine Capabilities the evidence base for their medical condition list

Implementing the Integrated Strategy for the Cultural Adaptation of Evidence-Based Interventions: An Illustration.

Science.gov (United States)

Sidani, Souraya; Ibrahim, Sarah; Lok, Jana; Fan, Lifeng; Fox, Mary

2018-01-01

Background Persons' cultural beliefs about a health problem can affect their perceived acceptability of evidence-based interventions, undermining evidence-based interventions' adherence, and uptake to manage the problem. Cultural adaptation has the potential to enhance the acceptability, uptake, and adherence to evidence-based interventions. Purpose To illustrate the implementation of the first two phases of the integrated strategy for cultural adaptation by examining Chinese Canadians' perceptions of chronic insomnia and evidence-based behavioral therapies for insomnia. Methods Chinese Canadians ( n = 14) with chronic insomnia attended a group session during which they completed established instruments measuring beliefs about sleep and insomnia, and their perceptions of factors that contribute to chronic insomnia. Participants rated the acceptability of evidence-based behavioral therapies and discussed their cultural perspectives regarding chronic insomnia and its treatment. Results Participants actively engaged in the activities planned for the first two phases of the integrated strategy and identified the most significant factor contributing to chronic insomnia and the evidence-based intervention most acceptable for their cultural group. Conclusions The protocol for implementing the two phases of the integrated strategy for cultural adaptation of evidence-based interventions was feasible, acceptable, and useful in identifying culturally relevant evidence-based interventions.

What is the evidence for the use of biologic or biosynthetic meshes in abdominal wall reconstruction?

Science.gov (United States)

Köckerling, F; Alam, N N; Antoniou, S A; Daniels, I R; Famiglietti, F; Fortelny, R H; Heiss, M M; Kallinowski, F; Kyle-Leinhase, I; Mayer, F; Miserez, M; Montgomery, A; Morales-Conde, S; Muysoms, F; Narang, S K; Petter-Puchner, A; Reinpold, W; Scheuerlein, H; Smietanski, M; Stechemesser, B; Strey, C; Woeste, G; Smart, N J

2018-04-01

Although many surgeons have adopted the use of biologic and biosynthetic meshes in complex abdominal wall hernia repair, others have questioned the use of these products. Criticism is addressed in several review articles on the poor standard of studies reporting on the use of biologic meshes for different abdominal wall repairs. The aim of this consensus review is to conduct an evidence-based analysis of the efficacy of biologic and biosynthetic meshes in predefined clinical situations. A European working group, "BioMesh Study Group", composed of invited surgeons with a special interest in surgical meshes, formulated key questions, and forwarded them for processing in subgroups. In January 2016, a workshop was held in Berlin where the findings were presented, discussed, and voted on for consensus. Findings were set out in writing by the subgroups followed by consensus being reached. For the review, 114 studies and background analyses were used. The cumulative data regarding biologic mesh under contaminated conditions do not support the claim that it is better than synthetic mesh. Biologic mesh use should be avoided when bridging is needed. In inguinal hernia repair biologic and biosynthetic meshes do not have a clear advantage over the synthetic meshes. For prevention of incisional or parastomal hernias, there is no evidence to support the use of biologic/biosynthetic meshes. In complex abdominal wall hernia repairs (incarcerated hernia, parastomal hernia, infected mesh, open abdomen, enterocutaneous fistula, and component separation technique), biologic and biosynthetic meshes do not provide a superior alternative to synthetic meshes. The routine use of biologic and biosynthetic meshes cannot be recommended.

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

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

2016-01-01

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

PathText: a text mining integrator for biological pathway visualizations

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

2010-01-01

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

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

Directory of Open Access Journals (Sweden)

Kempa Stefan

2009-05-01

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

Informing biological design by integration of systems and synthetic biology.

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Smolke, Christina D; Silver, Pamela A

2011-03-18

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

Climate change and biological invasions: evidence, expectations, and response options.

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Hulme, Philip E

2017-08-01

A changing climate may directly or indirectly influence biological invasions by altering the likelihood of introduction or establishment, as well as modifying the geographic range, environmental impacts, economic costs or management of alien species. A comprehensive assessment of empirical and theoretical evidence identified how each of these processes is likely to be shaped by climate change for alien plants, animals and pathogens in terrestrial, freshwater and marine environments of Great Britain. The strongest contemporary evidence for the potential role of climate change in the establishment of new alien species is for terrestrial arthropods, as a result of their ectothermic physiology, often high dispersal rate and their strong association with trade as well as commensal relationships with human environments. By contrast, there is little empirical support for higher temperatures increasing the rate of alien plant establishment due to the stronger effects of residence time and propagule pressure. The magnitude of any direct climate effect on the number of new alien species will be small relative to human-assisted introductions driven by socioeconomic factors. Casual alien species (sleepers) whose population persistence is limited by climate are expected to exhibit greater rates of establishment under climate change assuming that propagule pressure remains at least at current levels. Surveillance and management targeting sleeper pests and diseases may be the most cost-effective option to reduce future impacts under climate change. Most established alien species will increase their distribution range in Great Britain over the next century. However, such range increases are very likely be the result of natural expansion of populations that have yet to reach equilibrium with their environment, rather than a direct consequence of climate change. To assess the potential realised range of alien species will require a spatially explicit approach that not only

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

Science.gov (United States)

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

2018-03-01

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

Integrated MEMS/NEMS Resonant Cantilevers for Ultrasensitive Biological Detection

Directory of Open Access Journals (Sweden)

Xinxin Li

2009-01-01

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

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

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Nottale, Laurent; Auffray, Charles

2008-05-01

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

Continuous track paths reveal additive evidence integration in multistep decision making.

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Buc Calderon, Cristian; Dewulf, Myrtille; Gevers, Wim; Verguts, Tom

2017-10-03

Multistep decision making pervades daily life, but its underlying mechanisms remain obscure. We distinguish four prominent models of multistep decision making, namely serial stage, hierarchical evidence integration, hierarchical leaky competing accumulation (HLCA), and probabilistic evidence integration (PEI). To empirically disentangle these models, we design a two-step reward-based decision paradigm and implement it in a reaching task experiment. In a first step, participants choose between two potential upcoming choices, each associated with two rewards. In a second step, participants choose between the two rewards selected in the first step. Strikingly, as predicted by the HLCA and PEI models, the first-step decision dynamics were initially biased toward the choice representing the highest sum/mean before being redirected toward the choice representing the maximal reward (i.e., initial dip). Only HLCA and PEI predicted this initial dip, suggesting that first-step decision dynamics depend on additive integration of competing second-step choices. Our data suggest that potential future outcomes are progressively unraveled during multistep decision making.

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

Science.gov (United States)

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

2015-12-07

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

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

DEFF Research Database (Denmark)

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

2017-01-01

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

F229. THE BIOLOGICAL UNDERPINNINGS OF TREATMENT RESPONSE IN DELUSIONAL DISORDER: A SYSTEMATIC REVIEW OF QUALITATIVE EVIDENCE-TO-DATE

Science.gov (United States)

González-Rodríguez, Alexandre; Estrada, Francesc; Montalvo, Itziar; Monreal, José Antonio; Palao, Diego; Labad, Javier

2018-01-01

identified, of which 12 met our inclusion criteria. Four hypotheses were addressed: (1) Dopaminergic dysfunction (n=4): ziprasidone-induced supersensitivity psychosis by chronic blockade of D2 Dopamine Receptor (DRD2) (n=1); pretreatment levels of plasma homovallinic acid (pHVA) (n=1); dopamine transporter (DAT) dysfunction (n=1) and effectiveness of aripiprazole (DRD2 agonist) (n=1). (2) Serotonergic dysfunction (n=6): drug occupancy in 5-HT1A and 5-HT2A receptors (n=3) and efficacy of 5-HT2 antagonists (n=3). Brain dysfunction (n=7): hypoperfusion in cerebral blood flow in temporal and parietal lobes, left side (n=5), right side (n=1) and lack of basal ganglia and subcortical gray matter lesions (n=1). Genetic evidence (n=1): implications of DRD2 Ser311Cys, DRD3 Ser9Gly and TH VNTR polymorphisms. Discussion The strongests biological contributors for treatment response in delusional disorder seem to be those implicating monoaminergic systems, particularly dopamine and serotonergic neurotransmitters. Although the low level of evidence, the serotonergic dysfunction may be associated with response rates, especially in delusional disorder somatic type. The link between genetic variants of dopamine receptors and neuroimaging findings in delusional disorder may open new avenues for the search of the biological underpinnings of treatment response. The evidence for an integrated model involving dopamine and serotonin systems bears further investigations.

The validation of forensic DNA extraction systems to utilize soil contaminated biological evidence.

Science.gov (United States)

Kasu, Mohaimin; Shires, Karen

2015-07-01

The production of full DNA profiles from biological evidence found in soil has a high failure rate due largely to the inhibitory substance humic acid (HA). Abundant in various natural soils, HA co-extracts with DNA during extraction and inhibits DNA profiling by binding to the molecular components of the genotyping assay. To successfully utilize traces of soil contaminated evidence, such as that found at many murder and rape crime scenes in South Africa, a reliable HA removal extraction system would often be selected based on previous validation studies. However, for many standard forensic DNA extraction systems, peer-reviewed publications detailing the efficacy on soil evidence is either lacking or is incomplete. Consequently, these sample types are often not collected or fail to yield suitable DNA material due to the use of unsuitable methodology. The aim of this study was to validate the common forensic DNA collection and extraction systems used in South Africa, namely DNA IQ, FTA elute and Nucleosave for processing blood and saliva contaminated with HA. A forensic appropriate volume of biological evidence was spiked with HA (0, 0.5, 1.5 and 2.5 mg/ml) and processed through each extraction protocol for the evaluation of HA removal using QPCR and STR-genotyping. The DNA IQ magnetic bead system effectively removed HA from highly contaminated blood and saliva, and generated consistently acceptable STR profiles from both artificially spiked samples and crude soil samples. This system is highly recommended for use on soil-contaminated evidence over the cellulose card-based systems currently being preferentially used for DNA sample collection. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

Science.gov (United States)

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

2004-11-01

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

Using Integrative Medicine in Pain Management: An Evaluation of Current Evidence.

Science.gov (United States)

Lin, Yuan-Chi; Wan, Limeng; Jamison, Robert N

2017-12-01

Complementary medicine therapies are frequently used to treat pain conditions such as headaches and neck, back, and joint pain. Chronic pain, described as pain lasting longer than 3-6 months, can be a debilitating condition that has a significant socioeconomic impact. Pharmacologic approaches are often used for alleviating chronic pain, but recently there has been a reluctance to prescribe opioids for chronic noncancer pain because of concerns about tolerance, dependence, and addiction. As a result, there has been increased interest in integrative medicine strategies to help manage pain and to reduce reliance on prescription opioids to manage pain. This article offers a brief critical review of integrative medical therapies used to treat chronic pain, including nutritional supplements, yoga, relaxation, tai chi, massage, spinal manipulation, and acupuncture. The goal of this article is to identify those treatments that show evidence of efficacy and to identify gaps in the literature where additional studies and controlled trials are needed. An electronic search of the databases of PubMed, The Cochrane Library, EMBASE, PsycINFO, and Science Citation Index Expanded was conducted. Overall, weak positive evidence was found for yoga, relaxation, tai chi, massage, and manipulation. Strong evidence for acupuncture as a complementary treatment for chronic pain that has been shown to decrease the usage of opioids was found. Few studies were found in which integrative medicine approaches were used to address opioid misuse and abuse among chronic pain patients. Additional controlled trials to address the use of integrative medicine approaches in pain management are needed.

Modeling Cancer Metastasis using Global, Quantitative and Integrative Network Biology

DEFF Research Database (Denmark)

Schoof, Erwin; Erler, Janine

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

The integral biologically effective dose to predict brain stem toxicity of hypofractionated stereotactic radiotherapy

International Nuclear Information System (INIS)

Clark, Brenda G.; Souhami, Luis; Pla, Conrado; Al-Amro, Abdullah S.; Bahary, Jean-Paul; Villemure, Jean-Guy; Caron, Jean-Louis; Olivier, Andre; Podgorsak, Ervin B.

1998-01-01

Purpose: The aim of this work was to develop a parameter for use during fractionated stereotactic radiotherapy treatment planning to aid in the determination of the appropriate treatment volume and fractionation regimen that will minimize risk of late damage to normal tissue. Materials and Methods: We have used the linear quadratic model to assess the biologically effective dose at the periphery of stereotactic radiotherapy treatment volumes that impinge on the brain stem. This paper reports a retrospective study of 77 patients with malignant and benign intracranial lesions, treated between 1987 and 1995, with the dynamic rotation technique in 6 fractions over a period of 2 weeks, to a total dose of 42 Gy prescribed at the 90% isodose surface. From differential dose-volume histograms, we evaluated biologically effective dose-volume histograms and obtained an integral biologically-effective dose (IBED) in each case. Results: Of the 77 patients in the study, 36 had target volumes positioned so that the brain stem received more than 1% of the prescribed dose, and 4 of these, all treated for meningioma, developed serious late damage involving the brain stem. Other than type of lesion, the only significant variable was the volume of brain stem exposed. An analysis of the IBEDs received by these 36 patients shows evidence of a threshold value for late damage to the brain stem consistent with similar thresholds that have been determined for external beam radiotherapy. Conclusions: We have introduced a new parameter, the IBED, that may be used to represent the fractional effective dose to structures such as the brain stem that are partially irradiated with stereotactic dose distributions. The IBED is easily calculated prior to treatment and may be used to determine appropriate treatment volumes and fractionation regimens minimizing possible toxicity to normal tissue

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

International Nuclear Information System (INIS)

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

2013-01-01

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

Joint development of evidence-based medical record by doctors and patients through integrated Chinese and Western medicine on digestive system diseases.

Science.gov (United States)

Li, Bo; Gao, Hong-yang; Gao, Rui; Zhao, Ying-pan; Li, Qing-na; Zhao, Yang; Tang, Xu-dong; Shang, Hong-cai

2016-02-01

Building the clinical therapeutic evaluation system by combing the evaluation given by doctors and patients can form a more comprehensive and objective evaluation system. A literature search on the practice of evidence-based evaluation was conducted in key biomedical databases, i.e. PubMed, Excerpt Medica Database, China Biology Medicine disc and China National Knowledge Infrastructure. However, no relevant study on the subjects of interest was identified. Therefore, drawing on the principles of narrative medicine and expert opinion from systems of Chinese medicine and Western medicine, we propose to develop and pilot-test a novel evidence-based medical record format that captures the perspectives of both patients and doctors in a clinical trial. Further, we seek to evaluate a strategic therapeutic approach that integrates the wisdom of Chinese medicine with the scientific basis of Western medicine in the treatment of digestive system disorders. Evaluation of therapeutic efficacy of remedies under the system of Chinese medicine is an imperative ongoing research. The present study intends to identify a novel approach to assess the synergistic benefits achievable from an integrated therapeutic approach combining Chinese and Western system of medicine to treat digestive system disorders.

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

Science.gov (United States)

Lacy, Timothy; Hughes, John D.

2006-01-01

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

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

Data.gov (United States)

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

Engaging Nursing Students: Integrating Evidence-Based Inquiry, Informatics, and Clinical Practice.

Science.gov (United States)

Keiffer, Melanie R

2017-12-05

The nursing research class requires faculty to create a spirit of inquiry while integrating technology, flexibility, and responsiveness to student needs. This article discusses new pedagogies to actively engage students in the evidence-based nursing process and the achievement of course learning outcomes. Through course exemplar, the author demonstrates a creative method to engage traditional baccalaureate nursing students in a nursing project that links evidence to improved patient outcomes.

The Math–Biology Values Instrument: Development of a Tool to Measure Life Science Majors’ Task Values of Using Math in the Context of Biology

Science.gov (United States)

Andrews, Sarah E.; Runyon, Christopher; Aikens, Melissa L.

2017-01-01

In response to calls to improve the quantitative training of undergraduate biology students, there have been increased efforts to better integrate math into biology curricula. One challenge of such efforts is negative student attitudes toward math, which are thought to be particularly prevalent among biology students. According to theory, students’ personal values toward using math in a biological context will influence their achievement and behavioral outcomes, but a validated instrument is needed to determine this empirically. We developed the Math–Biology Values Instrument (MBVI), an 11-item college-level self-­report instrument grounded in expectancy-value theory, to measure life science students’ interest in using math to understand biology, the perceived usefulness of math to their life science career, and the cost of using math in biology courses. We used a process that integrates multiple forms of validity evidence to show that scores from the MBVI can be used as a valid measure of a student’s value of math in the context of biology. The MBVI can be used by instructors and researchers to help identify instructional strategies that influence math–biology values and understand how math–biology values are related to students’ achievement and decisions to pursue more advanced quantitative-based courses. PMID:28747355

Integration of an Evidence Base into a Probabilistic Risk Assessment Model. The Integrated Medical Model Database: An Organized Evidence Base for Assessing In-Flight Crew Health Risk and System Design

Science.gov (United States)

Saile, Lynn; Lopez, Vilma; Bickham, Grandin; FreiredeCarvalho, Mary; Kerstman, Eric; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

2011-01-01

This slide presentation reviews the Integrated Medical Model (IMM) database, which is an organized evidence base for assessing in-flight crew health risk. The database is a relational database accessible to many people. The database quantifies the model inputs by a ranking based on the highest value of the data as Level of Evidence (LOE) and the quality of evidence (QOE) score that provides an assessment of the evidence base for each medical condition. The IMM evidence base has already been able to provide invaluable information for designers, and for other uses.

Opportunities for Merging Chemical and Biological Synthesis

Science.gov (United States)

Wallace, Stephen; Balskus, Emily P.

2014-01-01

Organic chemists and metabolic engineers use largely orthogonal technologies to access small molecules like pharmaceuticals and commodity chemicals. As the use of biological catalysts and engineered organisms for chemical production grows, it is becoming increasingly evident that future efforts for chemical manufacture will benefit from the integration and unified expansion of these two fields. This review will discuss approaches that combine chemical and biological synthesis for small molecule production. We highlight recent advances in combining enzymatic and non-enzymatic catalysis in vitro, discuss the application of design principles from organic chemistry for engineering non-biological reactivity into enzymes, and describe the development of biocompatible chemistry that can be interfaced with microbial metabolism. PMID:24747284

Improving the International Agency for Research on Cancer's consideration of mechanistic evidence

International Nuclear Information System (INIS)

Goodman, Julie; Lynch, Heather

2017-01-01

Background: The International Agency for Research on Cancer (IARC) recently developed a framework for evaluating mechanistic evidence that includes a list of 10 key characteristics of carcinogens. This framework is useful for identifying and organizing large bodies of literature on carcinogenic mechanisms, but it lacks sufficient guidance for conducting evaluations that fully integrate mechanistic evidence into hazard assessments. Objectives: We summarize the framework, and suggest approaches to strengthen the evaluation of mechanistic evidence using this framework. Discussion: While the framework is useful for organizing mechanistic evidence, its lack of guidance for implementation limits its utility for understanding human carcinogenic potential. Specifically, it does not include explicit guidance for evaluating the biological significance of mechanistic endpoints, inter- and intra-individual variability, or study quality and relevance. It also does not explicitly address how mechanistic evidence should be integrated with other realms of evidence. Because mechanistic evidence is critical to understanding human cancer hazards, we recommend that IARC develop transparent and systematic guidelines for the use of this framework so that mechanistic evidence will be evaluated and integrated in a robust manner, and concurrently with other realms of evidence, to reach a final human cancer hazard conclusion. Conclusions: IARC does not currently provide a standardized approach to evaluating mechanistic evidence. Incorporating the recommendations discussed here will make IARC analyses of mechanistic evidence more transparent, and lead to assessments of cancer hazards that reflect the weight of the scientific evidence and allow for scientifically defensible decision-making. - Highlights: • IARC has a revised framework for evaluating literature on carcinogenic mechanisms. • The framework is based on 10 key characteristics of carcinogens. • IARC should develop transparent

Improving the International Agency for Research on Cancer's consideration of mechanistic evidence

Energy Technology Data Exchange (ETDEWEB)

Goodman, Julie, E-mail: jgoodman@gradientcorp.com; Lynch, Heather

2017-03-15

Background: The International Agency for Research on Cancer (IARC) recently developed a framework for evaluating mechanistic evidence that includes a list of 10 key characteristics of carcinogens. This framework is useful for identifying and organizing large bodies of literature on carcinogenic mechanisms, but it lacks sufficient guidance for conducting evaluations that fully integrate mechanistic evidence into hazard assessments. Objectives: We summarize the framework, and suggest approaches to strengthen the evaluation of mechanistic evidence using this framework. Discussion: While the framework is useful for organizing mechanistic evidence, its lack of guidance for implementation limits its utility for understanding human carcinogenic potential. Specifically, it does not include explicit guidance for evaluating the biological significance of mechanistic endpoints, inter- and intra-individual variability, or study quality and relevance. It also does not explicitly address how mechanistic evidence should be integrated with other realms of evidence. Because mechanistic evidence is critical to understanding human cancer hazards, we recommend that IARC develop transparent and systematic guidelines for the use of this framework so that mechanistic evidence will be evaluated and integrated in a robust manner, and concurrently with other realms of evidence, to reach a final human cancer hazard conclusion. Conclusions: IARC does not currently provide a standardized approach to evaluating mechanistic evidence. Incorporating the recommendations discussed here will make IARC analyses of mechanistic evidence more transparent, and lead to assessments of cancer hazards that reflect the weight of the scientific evidence and allow for scientifically defensible decision-making. - Highlights: • IARC has a revised framework for evaluating literature on carcinogenic mechanisms. • The framework is based on 10 key characteristics of carcinogens. • IARC should develop transparent

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

Science.gov (United States)

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

2016-02-01

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

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

Science.gov (United States)

He, Yongqun

2014-07-01

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

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

Directory of Open Access Journals (Sweden)

Thomas eEissing

2011-02-01

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

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

Science.gov (United States)

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

2010-11-01

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

Integration of ecological-biological thresholds in conservation decision making.

Science.gov (United States)

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

2016-12-01

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

The Dominance Behavioral System and Psychopathology: Evidence from Self-Report, Observational, and Biological Studies

Science.gov (United States)

Johnson, Sheri L.; Leedom, Liane J.; Muhtadie, Luma

2012-01-01

The dominance behavioral system (DBS) can be conceptualized as a biologically based system that guides dominance motivation, dominant and subordinate behavior, and responsivity to perceptions of power and subordination. A growing body of research suggests that problems with the DBS are evident across a broad range of psychopathologies. We begin by…

Interchangeability of biosimilar and biological reference product: updated regulatory positions and pre- and post-marketing evidence.

Science.gov (United States)

Trifirò, Gianluca; Marcianò, Ilaria; Ingrasciotta, Ylenia

2018-03-01

Since 2006, biosimilars have been available in several countries worldwide, thus allowing for potential savings in pharmaceutical expenditure. However, there have been numerous debates about the interchangeability of biosimilars and reference products based on concerns of immunogenicity by switching between biological products, which may cause lack of effect and toxicity. Areas covered: The authors provide the reader with an overview of the different positions of regulatory authorities on the interchangeability and automatic substitution of biosimilars and reference products. Presently, the FDA allows automatic substitution without prescriber intervention if the biosimilar is interchangeable with reference products, while the European Medicines Agency delegate to each single EU member state. Expert opinion: Different approaches in defining interchangeability and automatic substitution call for harmonization to increase confidence of healthcare professionals and patients about the clinical impact of switching. Networks of electronic healthcare records and administrative databases, potentially linkable to clinical charts and registries may rapidly assess frequency and benefit-risk profile of different switching patterns in routine care at different levels, thus integrating and strengthening pre-marketing evidence.

The challenge of integrating evidence-based design.

Science.gov (United States)

Martin, Caren S

2009-01-01

This paper discusses the integration of evidence-based design (EBD) into the design process as an innovation, illuminates the significance and progress of the diffusion of this innovation, and identifies EBD advocates and the consequences of meeting the EBD challenge. A free tool for engaging in EBD is explored. Healthcare designers are leading the EBD charge, because their clients depend on it. But not all designers engage in EBD, because it may be beyond the resources of a firm or outside its culture. However, as with other meaningful design innovations, designers who do not practice EBD could fall by the wayside. EBD is a product of the diffusion of the innovation of evidence-based medicine. The academy (i.e., the collective of institutions of higher education), design organizations, design communities, and the media all contribute to the diffusion of EBD. However, the quantity, quality, and understandability of evidence continue to challenge its broad adoption. InformeDesign®, a free, Internet-based tool, presents information to designers in a concise, understandable way. Firms must invest in EBD incrementally as a value-added component of design to meet current and future challenges. It is important for designers to realize that engaging in EBD is not a rejection of creativity, but a means by which to elevate their design solutions. ©2009 VENDOME GROUP, LLC

Influence of evidence, time, source and interferents in the observation of biological fluids with forensic lights

OpenAIRE

Laverde-Angarita, Lilia Judith; Clavijo-Bolívar, Yolanda

2015-01-01

Introduction: The laboratory receives different evidence for analysis, which maycontain fluids such as blood, semen, saliva or urine. A support tool in identifying nonvisible biological stains is observation with forensic lights. At present, there have been research advances in reference to wavelength and combination of different filters for the observation of biological fluids. Methodology: For this research, the alternate lights equipment Polilight® Flare with blue light was used, along wit...

Reproductive Biology Including Evidence for Superfetation in the European Badger Meles meles (Carnivora: Mustelidae.

Directory of Open Access Journals (Sweden)

Leigh A L Corner

Full Text Available The reproductive biology of the European badger (Meles meles is of wide interest because it is one of the few mammal species that show delayed implantation and one of only five which are suggested to show superfetation as a reproductive strategy. This study aimed to describe the reproductive biology of female Irish badgers with a view to increasing our understanding of the process of delayed implantation and superfetation. We carried out a detailed histological examination of the reproductive tract of 264 female badgers taken from sites across 20 of the 26 counties in the Republic of Ireland. The key results show evidence of multiple blastocysts at different stages of development present simultaneously in the same female, supporting the view that superfetation is relatively common in this population of badgers. In addition we present strong evidence that the breeding rate in Irish badgers is limited by failure to conceive, rather than failure at any other stages of the breeding cycle. We show few effects of age on breeding success, suggesting no breeding suppression by adult females in this population. The study sheds new light on this unusual breeding strategy of delayed implantation and superfetation, and highlights a number of significant differences between the reproductive biology of female Irish badgers and those of Great Britain and Swedish populations.

Biological evidence of low ionizing radiation doses

International Nuclear Information System (INIS)

Mirsch, Johanna

2017-01-01

Throughout life, every person is constantly exposed to different types of ionising radiation, without even noticing the exposure. The mean radiation exposure for people living in Germany amounts to approximately 4 mSv per year and encompasses the exposure from natural and man-made sources. The risks associated with exposure to low doses of radiation are still the subject of intense and highly controversial discussions, emphasizing the social relevance of studies investigating the effects of low radiation doses. In this thesis, DNA double-strand breaks (DSBs) were analyzed within three projects covering different aspects. DSBs are among the most hazardous DNA lesions induced by ionizing radiation, because this type of damage can easily lead to the loss of genetic information. Consequently, the DSB presents a high risk for the genetic integrity of the cell. In the first project, extensive results uncovered the track structure of charged particles in a biological model tissue. This provided the first biological data that could be used for comparison with data that were measured or predicted using theoretical physical dosimetry methods and mathematical simulations. Charged particles contribute significantly to the natural radiation exposure and are used increasingly in cancer radiotherapy because they are more efficient in tumor cell killing than X- or γ-rays. The difference in the biological effects of high energy charged particles compared with X- or γ-rays is largely determined by the spatial distribution of their energy deposition and the track structure inducing a three-dimensional damage pattern in living cells. This damage pattern consists of cells directly hit by the particle receiving a high dose and neighboring cells not directly hit by primary particles but exposed to far-reaching secondary electrons (δ-electrons). These cells receive a much lower dose deposition in the order of a few mGy. The radial dose distribution of single particle tracks was

“Turn-on” fluorescence probe integrated polymer nanoparticles for sensing biological thiol molecules

Science.gov (United States)

Ang, Chung Yen; Tan, Si Yu; Lu, Yunpeng; Bai, Linyi; Li, Menghuan; Li, Peizhou; Zhang, Quan; Selvan, Subramanian Tamil; Zhao, Yanli

2014-11-01

A ``turn-on'' thiol-responsive fluorescence probe was synthesized and integrated into polymeric nanoparticles for sensing intracellular thiols. There is a photo-induced electron transfer process in the off state of the probe, and this process is terminated upon the reaction with thiol compounds. Configuration interaction singles (CIS) calculation was performed to confirm the mechanism of this process. A series of sensing studies were carried out, showing that the probe-integrated nanoparticles were highly selective towards biological thiol compounds over non-thiolated amino acids. Kinetic studies were also performed to investigate the relative reaction rate between the probe and the thiolated amino acids. Subsequently, the Gibbs free energy of the reactions was explored by means of the electrochemical method. Finally, the detection system was employed for sensing intracellular thiols in cancer cells, and the sensing selectivity could be further enhanced with the use of a cancer cell-targeting ligand in the nanoparticles. This development paves a path for the sensing and detection of biological thiols, serving as a potential diagnostic tool in the future.

Optimization of total arc degree for stereotactic radiotherapy by using integral biologically effective dose and irradiated volume

International Nuclear Information System (INIS)

Lim, Do Hoon; Kim, Dae Yong; Lee, Myung Za; Chun, Ha Chung

2001-01-01

To find the optimal values of total arc degree to protect the normal brain tissue from high dose radiation in stereotactic radiotherapy planning. With Xknife-3 planning system and 4 MV linear accelerator, the authors planned under various values of parameters. One isocenter, 12, 20, 30, 40, 50, and 60 mm of collimator diameters, 100 deg, 200 deg, 300 deg, 400 deg, 500 deg, 600 deg, of total arc degrees, and 30 deg or 45 deg of arc intervals were used. After the completion of planning, the plans were compared each other using V 50 (the volume of normal brain that is delivered high dose radiation) and integral biologically effective dose. At 30 deg of arc interval, the values of V 50 had the decreased pattern with the increase of total arc degree in any collimator diameter. At 45 deg arc interval, up to 400 deg of total arc degree, the values of V 50 decreased with the increase of total arc degree, but at 500 deg and 600 deg of total arc degrees, the values increased. At 30 deg of arc interval, integral biologically effective dose showed the decreased pattern with the increase of total arc degree in any collimator diameter. At 45 deg arc interval with less than 40 mm collimator diameter, the integral biologically effective dose decreased with the increase of total arc degree, but with 50 and 60 mm of collimator diameters, up to 400 deg of total arc degree, integral biologically effective dose decreased with the increase of total arc degree, but at 500 deg and 600 deg of total arc degrees, the values increased. In the stereotactic radiotherapy planning for brain lesions, planning with 400 deg of total arc degree is optimal. Especially, when the larger collimator more than 50 mm diameter should be used, the uses of 500 deg and 600 deg of total arc degrees make the increase of V 50 and integral biologically effective dose, Therefore stereotactic radiotherapy planning using 400 deg of total arc degree can increase the therapeutic ratio and produce the effective outcome

MAS Integration and Controllership Effectiveness: Evidence of a Preparer-User Perception Gap

OpenAIRE

Weißenberger, Barbara E.; Angelkort, Hendrik; Holthoff, Gero

2012-01-01

Recent evidence suggests that managers establish a positive link between management accounting system (MAS) integration and controllership effectiveness, which is fully mediated by the perceived consistency of financial language. Our paper extends this research by analyzing whether controllers have similar perceptions on MAS design. Testing a series of multi-group structural equation models, we find evidence for a preparer-user perception gap with respect to the mediating impact of a consiste...

Promoting Student Learning through the Integration of Lab and Lecture: The Seamless Biology Curriculum

Science.gov (United States)

Burrowes, Patricia; Nazario, Gladys

2008-01-01

The authors engaged in an education experiment to determine if the integration of lab and lecture activities in zoology and botany proved beneficial to student learning and motivation toward biology. Their results revealed that this strategy positively influenced students' academic achievement, conceptual understanding, and ability to apply…

Should different impact assessment instruments be integrated? Evidence from English spatial planning

International Nuclear Information System (INIS)

Tajima, Ryo; Fischer, Thomas B.

2013-01-01

This paper aims at providing empirical evidence to the question as to whether integration of different instruments is achieving its aim in supporting sustainable decision making, focusing on SEA inclusive sustainability appraisal (SA) and other impact assessments (IAs) currently used in English spatial planning. Usage of IAs in addition to SA is established and an analysis of the integration approach (in terms of process, output, and assessor) as well as its effectiveness is conducted. It is found that while integration enhances effectiveness to some extent, too much integration, especially in terms of the procedural element, appears to diminish the overall effectiveness of each IA in influencing decisions as they become captured by the balancing function of SA. -- Highlights: ► The usage of different impact assessments in English spatial planning is clarified. ► The relationship between integration approach and effectiveness is analyzed. ► Results suggest that integration does not necessarily lead to more sustainable decisions. ► Careful consideration is recommended upon process integration

Should different impact assessment instruments be integrated? Evidence from English spatial planning

Energy Technology Data Exchange (ETDEWEB)

Tajima, Ryo, E-mail: tajima.ryo@nies.go.jp [Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259-G5-9 Nagatsuta-cho, Midori-ku, Yokoyama City, Kanagawa, 226-8502 (Japan); Fischer, Thomas B., E-mail: fischer@liverpool.ac.uk [Department of Geography and Planning, School of Environmental Sciences, University of Liverpool, 74 Bedford Street South, Liverpool L69 7ZQ (United Kingdom)

2013-07-15

This paper aims at providing empirical evidence to the question as to whether integration of different instruments is achieving its aim in supporting sustainable decision making, focusing on SEA inclusive sustainability appraisal (SA) and other impact assessments (IAs) currently used in English spatial planning. Usage of IAs in addition to SA is established and an analysis of the integration approach (in terms of process, output, and assessor) as well as its effectiveness is conducted. It is found that while integration enhances effectiveness to some extent, too much integration, especially in terms of the procedural element, appears to diminish the overall effectiveness of each IA in influencing decisions as they become captured by the balancing function of SA. -- Highlights: ► The usage of different impact assessments in English spatial planning is clarified. ► The relationship between integration approach and effectiveness is analyzed. ► Results suggest that integration does not necessarily lead to more sustainable decisions. ► Careful consideration is recommended upon process integration.

Electrophysiological evidence for a self-processing advantage during audiovisual speech integration.

Science.gov (United States)

Treille, Avril; Vilain, Coriandre; Kandel, Sonia; Sato, Marc

2017-09-01

Previous electrophysiological studies have provided strong evidence for early multisensory integrative mechanisms during audiovisual speech perception. From these studies, one unanswered issue is whether hearing our own voice and seeing our own articulatory gestures facilitate speech perception, possibly through a better processing and integration of sensory inputs with our own sensory-motor knowledge. The present EEG study examined the impact of self-knowledge during the perception of auditory (A), visual (V) and audiovisual (AV) speech stimuli that were previously recorded from the participant or from a speaker he/she had never met. Audiovisual interactions were estimated by comparing N1 and P2 auditory evoked potentials during the bimodal condition (AV) with the sum of those observed in the unimodal conditions (A + V). In line with previous EEG studies, our results revealed an amplitude decrease of P2 auditory evoked potentials in AV compared to A + V conditions. Crucially, a temporal facilitation of N1 responses was observed during the visual perception of self speech movements compared to those of another speaker. This facilitation was negatively correlated with the saliency of visual stimuli. These results provide evidence for a temporal facilitation of the integration of auditory and visual speech signals when the visual situation involves our own speech gestures.

Integration and macroevolutionary patterns in the pollination biology of conifers.

Science.gov (United States)

Leslie, Andrew B; Beaulieu, Jeremy M; Crane, Peter R; Knopf, Patrick; Donoghue, Michael J

2015-06-01

Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. To explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through to enter the ovule. We use a well-sampled phylogeny of conifers to test correlated evolution among these characters and specific sequences of character change. Using likelihood models of character evolution, we find that pollen morphology and ovule characters evolve in a concerted manner, where the flotation mechanism breaks down irreversibly following changes in orientation or drop production. The breakdown of this functional constraint, which may be facilitated by the lack of developmental integration among the constituent traits, is associated with increased trait variation and more diverse pollination strategies. Although this functional "release" increases diversity in some ways, the irreversible way in which the flotation mechanism is lost may eventually result in its complete disappearance from seed plant reproductive biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Integrated anaerobic/aerobic biological treatment for intensive swine production.

Science.gov (United States)

Bortone, Giuseppe

2009-11-01

Manure processing could help farmers to effectively manage nitrogen (N) surplus load. Many pig farms have to treat wastewater. Piggery wastewater treatment is a complex challenge, due to the high COD and N concentrations and low C/N ratio. Anaerobic digestion (AD) could be a convenient pre-treatment, particularly from the energetic view point and farm income, but this causes further reduction of C/N ratio and makes denitrification difficult. N removal can only be obtained integrating anaerobic/aerobic treatment by taking into account the best use of electron donors. Experiences gained in Italy during development of integrated biological treatment approaches for swine manure, from bench to full scale, are reported in this paper. Solid/liquid separation as pre-treatment of raw manure is an efficient strategy to facilitate liquid fraction treatment without significantly lowering C/N ratio. In Italy, two full scale SBRs showed excellent efficiency and reliability. Current renewable energy policy and incentives makes economically attractive the application of AD to the separated solid fraction using high solid anaerobic digester (HSAD) technology. Economic evaluation showed that energy production can reduce costs up to 60%, making sustainable the overall treatment.

Integrating best evidence into patient care: a process facilitated by a seamless integration with informatics tools.

Science.gov (United States)

Giuse, Nunzia B; Williams, Annette M; Giuse, Dario A

2010-07-01

The Vanderbilt University paper discusses how the Eskind Biomedical Library at Vanderbilt University Medical Center transitioned from a simplistic approach that linked resources to the institutional electronic medical record system, StarPanel, to a value-added service that is designed to deliver highly relevant information. Clinical teams formulate complex patient-specific questions via an evidence-based medicine literature request basket linked to individual patient records. The paper transitions into discussing how the StarPanel approach acted as a springboard for two additional projects that use highly trained knowledge management librarians with informatics expertise to integrate evidence into both order sets and a patient portal, MyHealth@Vanderbilt.

Evidence for replacement of an infected synthetic by a biological mesh in abdominal wall hernia repair

Directory of Open Access Journals (Sweden)

Agneta eMontgomery

2016-01-01

Full Text Available The incidence of deep infection using a synthetic mesh in inguinal hernia repair is low and reported to be well below 1%. This is in contrast to incisional hernia surgery where the reported incidence is 3% respective 13% comparing laparoscopic to open mesh repair reported in a Cochrane review. Main risk factors were long operation time, surgical site contamination and early wound complications. An infected mesh can be preserved using conservative treatment were negative pressure wound therapy (VAC® could play an important role. If strategy fails, the mesh needs to be removed. This review aims to look at evidence for situations were a biological mesh would work as a replacement of a removed infected synthetic mesh. Material and MethodsA literature search of the Medline database was performed using the PubMed search engine. Twenty publications were found relevant for this review.ResultsFor studies reviewed three options are presented: removal of the infected synthetic mesh alone, replacement with either a new synthetic or a new biological mesh. Operations were all performed at specialist centers. Removal of the mesh alone was an option limited to inguinal hernias. In ventral/incisional hernias the use of a biological mesh for replacement resulted in a very high recurrence rate, if bridging was required. Either a synthetic or a biological mesh seems to work as a replacement when fascial closure can be achieved. Evidence is though very low. ConclusionWhen required, either a synthetic or a biological meshes seems to work as a replacement for an infected synthetic mesh if the defect can be closed. It is however not recommended to use a biological mesh for bridging. Mesh replacement surgery is demanding and is recommended to be performed in a specialist center.

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

Science.gov (United States)

Holford, Matthew E; McCusker, James P; Cheung, Kei-Hoi; Krauthammer, Michael

2012-01-25

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

CHOmine: an integrated data warehouse for CHO systems biology and modeling.

Science.gov (United States)

Gerstl, Matthias P; Hanscho, Michael; Ruckerbauer, David E; Zanghellini, Jürgen; Borth, Nicole

2017-01-01

The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. http://www.chogenome.org. © The Author(s) 2017. Published by Oxford University Press.

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

Science.gov (United States)

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

2013-10-12

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

Cochrane Qualitative and Implementation Methods Group guidance series-paper 5: methods for integrating qualitative and implementation evidence within intervention effectiveness reviews.

Science.gov (United States)

Harden, Angela; Thomas, James; Cargo, Margaret; Harris, Janet; Pantoja, Tomas; Flemming, Kate; Booth, Andrew; Garside, Ruth; Hannes, Karin; Noyes, Jane

2018-05-01

The Cochrane Qualitative and Implementation Methods Group develops and publishes guidance on the synthesis of qualitative and mixed-method evidence from process evaluations. Despite a proliferation of methods for the synthesis of qualitative research, less attention has focused on how to integrate these syntheses within intervention effectiveness reviews. In this article, we report updated guidance from the group on approaches, methods, and tools, which can be used to integrate the findings from quantitative studies evaluating intervention effectiveness with those from qualitative studies and process evaluations. We draw on conceptual analyses of mixed methods systematic review designs and the range of methods and tools that have been used in published reviews that have successfully integrated different types of evidence. We outline five key methods and tools as devices for integration which vary in terms of the levels at which integration takes place; the specialist skills and expertise required within the review team; and their appropriateness in the context of limited evidence. In situations where the requirement is the integration of qualitative and process evidence within intervention effectiveness reviews, we recommend the use of a sequential approach. Here, evidence from each tradition is synthesized separately using methods consistent with each tradition before integration takes place using a common framework. Reviews which integrate qualitative and process evaluation evidence alongside quantitative evidence on intervention effectiveness in a systematic way are rare. This guidance aims to support review teams to achieve integration and we encourage further development through reflection and formal testing. Copyright © 2017 Elsevier Inc. All rights reserved.

Integration of Principles of Systems Biology and Radiation Biology: Toward Development of in silico Models to Optimize IUdR-Mediated Radiosensitization of DNA Mismatch Repair Deficient (Damage Tolerant) Human Cancers

International Nuclear Information System (INIS)

Kinsella, Timothy J.; Gurkan-Cavusoglu, Evren; Du, Weinan; Loparo, Kenneth A.

2011-01-01

Over the last 7 years, we have focused our experimental and computational research efforts on improving our understanding of the biochemical, molecular, and cellular processing of iododeoxyuridine (IUdR) and ionizing radiation (IR) induced DNA base damage by DNA mismatch repair (MMR). These coordinated research efforts, sponsored by the National Cancer Institute Integrative Cancer Biology Program (ICBP), brought together system scientists with expertise in engineering, mathematics, and complex systems theory and translational cancer researchers with expertise in radiation biology. Our overall goal was to begin to develop computational models of IUdR- and/or IR-induced base damage processing by MMR that may provide new clinical strategies to optimize IUdR-mediated radiosensitization in MMR deficient (MMR − ) “damage tolerant” human cancers. Using multiple scales of experimental testing, ranging from purified protein systems to in vitro (cellular) and to in vivo (human tumor xenografts in athymic mice) models, we have begun to integrate and interpolate these experimental data with hybrid stochastic biochemical models of MMR damage processing and probabilistic cell cycle regulation models through a systems biology approach. In this article, we highlight the results and current status of our integration of radiation biology approaches and computational modeling to enhance IUdR-mediated radiosensitization in MMR − damage tolerant cancers.

Integration of evidence-based practice in bedside teaching paediatrics supported by e-learning.

Science.gov (United States)

Potomkova, Jarmila; Mihal, Vladimir; Zapletalova, Jirina; Subova, Dana

2010-03-01

Bedside teaching with evidence-based practice elements, supported by e-learning activities, can play an important role in modern medical education. Teachers have to incorporate evidence from the medical literature to increase student motivation and interactivity. An integral part of the medical curricula at Palacky University Olomouc (Czech Republic) are real paediatric scenarios supplemented with a review of current literature to enhance evidence-based bedside teaching & learning. Searching for evidence is taught through librarian-guided interactive hands-on sessions and/or web-based tutorials followed by clinical case presentations and feedback. Innovated EBM paediatric clerkship demonstrated students' preferences towards web-based interactive bedside teaching & learning. In two academic years (2007/2008, 2008/2009), learning-focused feedback from 106 and 131 students, resp. was obtained about their attitudes towards evidence-based bedside teaching. The assessment included among others the overall level of instruction, quality of practical evidence-based training, teacher willingness and impact of instruction on increased interest in the specialty. There was some criticism about excessive workload. A parallel survey was carried out on the perceived values of different forms of information skills training (i.e. demonstration, online tutorials, and librarian-guided interactive search sessions) and post-training self-reported level of search skills. The new teaching/learning paediatric portfolio is a challenge for further activities, including effective knowledge translation, continuing medical & professional development of teachers, and didactic, clinically integrated teaching approaches.

Evidence of dark matter from biological observations

International Nuclear Information System (INIS)

Zioutas, K.

1990-01-01

In accordance with the generally accepted properties of dark matter (DM) candidates, the probability of their interaction with living matter must be equal to that for inorganic matter, and the expected effects might be unique and provide the etiology related to the appearance of several biological phenomena having sometimes fatal late effects. Although collisions with DM are rare, the charged secondaries (recoiling atoms) are expected to be high linear energy transfer particles favouring the highest relative biological effectiveness values for this, as yet invisible, part of the natural background radiation. A few cases are given, where a correlation between DM interaction and phenomena in living matter might already exist, or can show up in existing data: biorhythms with periodicities identical to known cosmic frequencies are explainable with gravitationally clustered DM around the sun, the moon, the earth, etc. The observed arrhythmia, when biological probes are moved (in airplanes, satellites, etc.) support this idea strongly. It is also proposed to implement some of the biological properties and processes (such as element composition and chemical reactions) in future DM detectors in order to improve their sensitivity. The interdisciplinary feedback is bidirectional: huge DM detectors could be used in attempt to understand enigmatic biological behaviour. (orig.)

Using reefcheck monitoring database to develop the coral reef index of biological integrity

DEFF Research Database (Denmark)

Nguyen, Hai Yen T.; Pedersen, Ole; Ikejima, Kou

2009-01-01

The coral reef indices of biological integrity was constituted based on the reef check monitoring data. Seventy six minimally disturbed sites and 72 maximallv disturbed sites in shallow water and 39 minimally disturbed sites and 37 maximally disturbed sites in deep water were classified based...... on the high-end and low-end percentages and ratios of hard coral, dead coral and fieshy algae. A total of 52 candidate metrics was identified and compiled, Eight and four metrics were finally selected to constitute the shallow and deep water coral reef indices respectively. The rating curve was applied.......05) and coral damaged by other factors -0.283 (pcoral reef indices were sensitive responses to stressors and can be capable to use as the coral reef biological monitoring tool....

The ASM-NSF Biology Scholars Program: An Evidence-Based Model for Faculty Development

Directory of Open Access Journals (Sweden)

Amy L. Chang

2016-05-01

Full Text Available The American Society for Microbiology (ASM established its ASM-NSF (National Science Foundation Biology Scholars Program (BSP to promote undergraduate education reform by 1 supporting biologists to implement evidence-based teaching practices, 2 engaging life science professional societies to facilitate biologists’ leadership in scholarly teaching within the discipline, and 3 participating in a teaching community that fosters disciplinary-level science, technology, engineering, and mathematics (STEM reform. Since 2005, the program has utilized year-long residency training to provide a continuum of learning and practice centered on principles from the scholarship of teaching and learning (SoTL to more than 270 participants (“scholars” from biology and multiple other disciplines. Additionally, the program has recruited 11 life science professional societies to support faculty development in SoTL and discipline-based education research (DBER. To identify the BSP’s long-term outcomes and impacts, ASM engaged an external evaluator to conduct a study of the program’s 2010­–2014 scholars (n = 127 and society partners. The study methods included online surveys, focus groups, participant observation, and analysis of various documents. Study participants indicate that the program achieved its proposed goals relative to scholarship, professional society impact, leadership, community, and faculty professional development. Although participants also identified barriers that hindered elements of their BSP participation, findings suggest that the program was essential to their development as faculty and provides evidence of the BSP as a model for other societies seeking to advance undergraduate science education reform. The BSP is the longest-standing faculty development program sponsored by a collective group of life science societies. This collaboration promotes success across a fragmented system of more than 80 societies representing the life

The ASM-NSF Biology Scholars Program: An Evidence-Based Model for Faculty Development.

Science.gov (United States)

Chang, Amy L; Pribbenow, Christine M

2016-05-01

The American Society for Microbiology (ASM) established its ASM-NSF (National Science Foundation) Biology Scholars Program (BSP) to promote undergraduate education reform by 1) supporting biologists to implement evidence-based teaching practices, 2) engaging life science professional societies to facilitate biologists' leadership in scholarly teaching within the discipline, and 3) participating in a teaching community that fosters disciplinary-level science, technology, engineering, and mathematics (STEM) reform. Since 2005, the program has utilized year-long residency training to provide a continuum of learning and practice centered on principles from the scholarship of teaching and learning (SoTL) to more than 270 participants ("scholars") from biology and multiple other disciplines. Additionally, the program has recruited 11 life science professional societies to support faculty development in SoTL and discipline-based education research (DBER). To identify the BSP's long-term outcomes and impacts, ASM engaged an external evaluator to conduct a study of the program's 2010-2014 scholars (n = 127) and society partners. The study methods included online surveys, focus groups, participant observation, and analysis of various documents. Study participants indicate that the program achieved its proposed goals relative to scholarship, professional society impact, leadership, community, and faculty professional development. Although participants also identified barriers that hindered elements of their BSP participation, findings suggest that the program was essential to their development as faculty and provides evidence of the BSP as a model for other societies seeking to advance undergraduate science education reform. The BSP is the longest-standing faculty development program sponsored by a collective group of life science societies. This collaboration promotes success across a fragmented system of more than 80 societies representing the life sciences and helps

A novel integration of three-dimensional electro-Fenton and biological activated carbon and its application in the advanced treatment of biologically pretreated Lurgi coal gasification wastewater.

Science.gov (United States)

Hou, Baolin; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Jia, Shengyong; Li, Kun

2015-11-01

A novel integrated process with three-dimensional electro-Fenton (3D EF) and biological activated carbon (BAC) was employed in advanced treatment of biologically pretreated Lurgi coal gasification wastewater. SAC-Fe (sludge deserved activated carbon from sewage and iron sludge) and SAC (sludge deserved activated carbon) were used in 3D EF as catalytic particle electrodes (CPEs) and in BAC as carriers respectively. Results indicated that 3D EF with SAC-Fe as CPEs represented excellent pollutants and COLOR removals as well as biodegradability improvement. The efficiency enhancement attributed to generating more H2O2 and OH. The integrated process exhibited efficient performance of COD, BOD5, total phenols, TOC, TN and COLOR removals at a much shorter retention time, with the corresponding concentrations in effluent of 31.18, 6.69, 4.29, 17.82, 13.88mg/L and <20 times, allowing discharge criteria to be met. The integrated system was efficient, cost-effective and ecological sustainable and could be a promising technology for engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integrating evidence-based interventions into client care plans.

Science.gov (United States)

Doran, Diane; Carryer, Jennifer; Paterson, Jane; Goering, Paula; Nagle, Lynn; Kushniruk, Andre; Bajnok, Irmajean; Clark, Carrie; Srivastava, Rani

2009-01-01

Within the mental health care system, there is an opportunity to improve patient safety and the overall quality of care by integrating clinical practice guidelines with the care planning process through the use of information technology. Electronic assessment tools such as the Resident Assessment Inventory - Mental Health (RAI-MH) are widely used to identify the health care needs and outcomes of clients. In this knowledge translation initiative, an electronic care planning tool was enhanced to include evidence-based clinical interventions from schizophrenia guidelines. This paper describes the development of a mental health decision support prototype, a field test by clinicians, and user experiences with the application.

Integrating interactive computational modeling in biology curricula.

Directory of Open Access Journals (Sweden)

Tomáš Helikar

2015-03-01

Full Text Available While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Integrating interactive computational modeling in biology curricula.

Science.gov (United States)

Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

2015-03-01

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Consumer preferences and values as an integral key to evidence-based practice.

Science.gov (United States)

Melnyk, Bernadette Mazurek; Fineout-Overholt, Ellen

2006-01-01

Although evidence-based practice (EBP) integrates the best evidence from well-designed studies with a clinician's expertise and patient preferences and values, most of what is emphasized in books and reports on EBP is the 5-step EBP process. However, the consideration of patient values and preferences in making clinical decisions is essential to deliver the highest quality of care. This article briefly reviews the status of EBP in the United States, described the ARCC mentorship model, and highlights how to engage consumers in the EBP process.

The evidence for biologic immunotherapy in Sarcoidosis: A systematic review

Directory of Open Access Journals (Sweden)

Pooja Shah

2017-09-01

Full Text Available Background Sarcoidosis is a chronic inflammatory disease with a myriad of clinical manifestations. Treatment involves immunosuppression with corticosteroids or steroid-sparing agents. A proportion of patients does not respond to or are intolerant to therapy. Targeted immunotherapy with biologic agents has emerged as a novel approach with plausible mechanistic reasons to warrant study. Aims The aim of this review was to evaluate the evidence for the efficacy of biological therapy in sarcoidosis. Methods We conducted a systematic literature review and meta-analysis of all published randomised-controlled trials (RCT evaluating biological therapy in sarcoidosis, using MEDLINE and Embase databases, through to September 2017. The search terms included sarcoidosis, infliximab, adalimumab, etanercept, golimumab, certolizumab, rituximab, abatacept, tocilizumab, anakinra, ustekinumab, secukinumab. Only articles reporting RCTs were selected. Improvements in respiratory disease were assessed by changes in forced vital capacity (FVC by weighted mean difference (WMD. There were insufficient data on outcome measures in other organ systems to comparatively assess efficacy. Results The search identified 2,324 studies of which only 5 provided relevant and original data. This comprised a total of 364 patients, evaluating pulmonary, cutaneous and ocular sarcoidosis. One study in pulmonary disease and one study in cutaneous disease demonstrated improvements in the primary outcome. In pulmonary disease, meta-analysis of the treatment effect of anti-TNF therapy versus placebo on FVC revealed a WMD of 1.69 per cent (95 per cent confidence interval, 1.44–1.94. Conclusion There are insufficient data to suggest the long-term efficacy of anti-TNFα inhibitors in the treatment of sarcoidosis. This may be due to heterogeneity, small sample sizes and the lack of consistent reporting of outcome measures.

Does the Internet Accelerate the Integration of Domestic Markets? Evidence from China

Institute of Scientific and Technical Information of China (English)

Lijuan Xie; Wenwei Ai; Hao Zhang

2016-01-01

This paper employs a hybrid methodology that combines case study and econometric research to examine the impact of the Internet on domestic market integration.There is not much research on this issue in the literature.From the multi-case analysis,this paper firstly obtains two main indications which are clear yet contrary to each other about how the Internet influences the market integration process.To be specific,although the Internet has both the ability and the potential to promote market integration,it is not always effective and could even harm this process due to several constraints.Using a provincial-level panel dataset from 2007 to 2013 in China,this paper empirically investigates whether the Intemet plays a positive role in the market integration process.Contradictory to common expectations,we do not find any empirical evidence that the Internet accelerates the integration of domestic markets.Thus,when compared with taking advantage of Internet tools,manmade obstacles to market integration that exist in current trading systems and business models deserve more attention.

Delivering The Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA (ACS Fall meeting)

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Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intent...

Impact of Interdisciplinary Undergraduate Research in mathematics and biology on the development of a new course integrating five STEM disciplines.

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Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

2010-01-01

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics.

Biological and photocatalytic treatment integrated with separation and reuse of titanium dioxide on the removal of chlorophenols in tap water

International Nuclear Information System (INIS)

Suryaman, Dhanus; Hasegawa, Kiyoshi

2010-01-01

We investigated biological, photocatalytic, and combination of biological and photocatalytic treatments in order to remove a mixture of 2-chlorophenol, 2,4-dichlorophenol, 2,4,5-trichlorophenol, and pentachlorophenol in tap water (total: 100 mg L -1 , each: 25 mg L -1 ). The removal of chlorinated phenols was conducted with a flow biological treatment and a circulative flow photocatalytic treatment under black light and sunlight irradiations integrated with titanium dioxide separation and reuse. The combined biological-photocatalytic treatment significantly shortened the degradation and mineralization time of both the biological treatment and the photocatalytic treatment. The removed chlorophenols per hour by the combined biological-photocatalytic treatment was 25.8 mg h -1 , whereas by the combined photocatalytic-biological treatment was 10.5 mg h -1 . After a large portion of biodegradable 2-chlorophenol and 2,4-dichlorophenol, and around half amount of slightly biodegradable 2,4,5-trichlorophenol were removed by the biological treatment, the remained three chlorophenols, biorecalcitrant pentachlorophenol, and biodegradation products were completely removed by the subsequent photocatalytic treatment. Since titanium dioxide particles in tap water spontaneously sedimented on standing after the photocatalytic treatment, the combined treatment can be operated by integrating with the titanium dioxide separation and reuse. The TiO 2 particles were recovered and reused at least three times without significantly decreasing the removal efficiency.

Biological and photocatalytic treatment integrated with separation and reuse of titanium dioxide on the removal of chlorophenols in tap water

Energy Technology Data Exchange (ETDEWEB)

Suryaman, Dhanus, E-mail: dhanussuryaman@yahoo.com [Agency for the Assessment and Application of Technology, M.H. Thamrin No. 8, Jakarta 10340 (Indonesia); Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan); Hasegawa, Kiyoshi [Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan)

2010-11-15

We investigated biological, photocatalytic, and combination of biological and photocatalytic treatments in order to remove a mixture of 2-chlorophenol, 2,4-dichlorophenol, 2,4,5-trichlorophenol, and pentachlorophenol in tap water (total: 100 mg L{sup -1}, each: 25 mg L{sup -1}). The removal of chlorinated phenols was conducted with a flow biological treatment and a circulative flow photocatalytic treatment under black light and sunlight irradiations integrated with titanium dioxide separation and reuse. The combined biological-photocatalytic treatment significantly shortened the degradation and mineralization time of both the biological treatment and the photocatalytic treatment. The removed chlorophenols per hour by the combined biological-photocatalytic treatment was 25.8 mg h{sup -1}, whereas by the combined photocatalytic-biological treatment was 10.5 mg h{sup -1}. After a large portion of biodegradable 2-chlorophenol and 2,4-dichlorophenol, and around half amount of slightly biodegradable 2,4,5-trichlorophenol were removed by the biological treatment, the remained three chlorophenols, biorecalcitrant pentachlorophenol, and biodegradation products were completely removed by the subsequent photocatalytic treatment. Since titanium dioxide particles in tap water spontaneously sedimented on standing after the photocatalytic treatment, the combined treatment can be operated by integrating with the titanium dioxide separation and reuse. The TiO{sub 2} particles were recovered and reused at least three times without significantly decreasing the removal efficiency.

Periodontal manifestations of inflammatory bowel disease: emerging epidemiologic and biologic evidence.

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Agossa, K; Dendooven, A; Dubuquoy, L; Gower-Rousseau, C; Delcourt-Debruyne, E; Capron, M

2017-06-01

Inflammatory bowel disease and periodontitis are both described as a disproportionate mucosal inflammatory response to a microbial environment in susceptible patients. Moreover, these two conditions share major environmental and lifestyle-related risk factors. Despite this intriguing pathogenic parallel, large-scale studies and basic research have only recently considered periodontal outcomes as relevant data. There are mounting and consistent arguments, from recent epidemiologic studies and animal models, that these two conditions might be related. This article is a comprehensive and critical up-to-date review of the current evidence and future prospects in understanding the biologic and epidemiologic relationships between periodontal status and inflammatory bowel disease. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The Math-Biology Values Instrument: Development of a Tool to Measure Life Science Majors' Task Values of Using Math in the Context of Biology.

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Andrews, Sarah E; Runyon, Christopher; Aikens, Melissa L

2017-01-01

In response to calls to improve the quantitative training of undergraduate biology students, there have been increased efforts to better integrate math into biology curricula. One challenge of such efforts is negative student attitudes toward math, which are thought to be particularly prevalent among biology students. According to theory, students' personal values toward using math in a biological context will influence their achievement and behavioral outcomes, but a validated instrument is needed to determine this empirically. We developed the Math-Biology Values Instrument (MBVI), an 11-item college-level self--report instrument grounded in expectancy-value theory, to measure life science students' interest in using math to understand biology, the perceived usefulness of math to their life science career, and the cost of using math in biology courses. We used a process that integrates multiple forms of validity evidence to show that scores from the MBVI can be used as a valid measure of a student's value of math in the context of biology. The MBVI can be used by instructors and researchers to help identify instructional strategies that influence math-biology values and understand how math-biology values are related to students' achievement and decisions to pursue more advanced quantitative-based courses. © 2017 S. E. Andrews et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Evidence and Feasibility of Implementing an Integrated Wellness Program in Northeast Georgia.

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Flanigan, Amber; Salm Ward, Trina

2017-08-01

Evidence for the connection between physical and mental health is growing, as is interest in providing a holistic, mind-body approach to improving mental health and wellness. A needs assessment in northeast Georgia identified several regional health priorities, including mental health and substance abuse, access to care, and cardiovascular health. The study's purpose is threefold: to (1) review evidence for integrated mind-body wellness services, (2) explore the feasibility of implementing wellness services in a small mental health agency serving northeast Georgia, and (3) conduct a brief survey assessing interest in a wellness program. The literature search identified articles within the past 10 years with these key words: "yoga," "mental health," "wellness program," "complementary alternative medicine," "tai chi," "mindfulness," "meditation," and "nutrition." The survey was distributed to the agency's affiliates. The literature review identified strong evidence for an integrated mind-body wellness program that includes yoga, tai chi, mindfulness meditation, and nutrition education. Among 73 survey respondents, 86 percent indicated interest in wellness services, and 85 percent agreed that wellness services are important to mental health and well-being. Authors suggest a model to incorporate a holistic wellness program to complement mental health services and help facilitate physical and mental health. © 2017 National Association of Social Workers.

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

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Schmitz, L.

2016-01-01

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. PMID:26977068

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology.

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Price, S A; Schmitz, L

2016-04-05

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s).

Wiring Together Synthetic Bacterial Consortia to Create a Biological Integrated Circuit.

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Perry, Nicolas; Nelson, Edward M; Timp, Gregory

2016-12-16

The promise of adapting biology to information processing will not be realized until engineered gene circuits, operating in different cell populations, can be wired together to express a predictable function. Here, elementary biological integrated circuits (BICs), consisting of two sets of transmitter and receiver gene circuit modules with embedded memory placed in separate cell populations, were meticulously assembled using live cell lithography and wired together by the mass transport of quorum-sensing (QS) signal molecules to form two isolated communication links (comlinks). The comlink dynamics were tested by broadcasting "clock" pulses of inducers into the networks and measuring the responses of functionally linked fluorescent reporters, and then modeled through simulations that realistically captured the protein production and molecular transport. These results show that the comlinks were isolated and each mimicked aspects of the synchronous, sequential networks used in digital computing. The observations about the flow conditions, derived from numerical simulations, and the biofilm architectures that foster or silence cell-to-cell communications have implications for everything from decontamination of drinking water to bacterial virulence.

Clinical practice guidelines on the evidence-based use of integrative therapies during and following breast cancer treatment

Science.gov (United States)

Greenlee, Heather; DuPont-Reyes, Melissa J.; Balneaves, Lynda G.; Carlson, Linda E.; Cohen, Misha R.; Deng, Gary; Johnson, Jillian A.; Mumber, Matthew; Seely, Dugald; Zick, Suzanna; Boyce, Lindsay; Tripathy, Debu

2018-01-01

Patients with breast cancer commonly use complementary and integrative therapies as supportive care during cancer treatment and to manage treatment-related side effects. However, evidence supporting the use of such therapies in the oncology setting is limited. This report provides updated clinical practice guidelines from the Society for Integrative Oncology on the use of integrative therapies for specific clinical indications during and after breast cancer treatment, including anxiety/stress, depression/mood disorders, fatigue, quality of life/physical functioning, chemotherapy-induced nausea and vomiting, lymphedema, chemotherapy-induced peripheral neuropathy, pain, and sleep disturbance. Clinical practice guidelines are based on a systematic literature review from 1990 through 2015. Music therapy, meditation, stress management, and yoga are recommended for anxiety/stress reduction. Meditation, relaxation, yoga, massage, and music therapy are recommended for depression/mood disorders. Meditation and yoga are recommended to improve quality of life. Acupressure and acupuncture are recommended for reducing chemotherapy-induced nausea and vomiting. Acetyl-L-carnitine is not recommended to prevent chemotherapy-induced peripheral neuropathy due to a possibility of harm. No strong evidence supports the use of ingested dietary supplements to manage breast cancer treatment-related side effects. In summary, there is a growing body of evidence supporting the use of integrative therapies, especially mind-body therapies, as effective supportive care strategies during breast cancer treatment. Many integrative practices, however, remain understudied, with insufficient evidence to be definitively recommended or avoided. PMID:28436999

The effect of different P fertilizer application (chemical, biologic and integrated on forage quality of two barely varieties (Bahman and Fasieh

Directory of Open Access Journals (Sweden)

Lezhia Zandiyeh

2016-05-01

Full Text Available Abstract To evaluate the effect of different sources of P fertilizer on grain yield and yield components of two barely varieties, this experiment was conducted in Research Farm, College of Agriculture, University of Tehran in 2010. The experimental treatments were arranged as factorial based on randomized complete block design with three replications. The treatments consisted of two barely varieties (Bahman and Fasieh and 7 levels of P fertilizer viz: 1. Control (no fertilizer application, 2. Chemical P fertilizer (based on the soil test, 3. Biological P fertilizer (P solubilizing bacteria, 4. Biological P fertilizer + 100% chemical P fertilizer, 5. Biological P fertilizer + 75% chemical P fertilizer, 6. Biological P fertilizer + 50% chemical P fertilizer, 7. Biological P fertilizer + 25% chemical P fertilizer. The results indicated that the ash percentage in Fasieh was significantly higher than Bahman at Chemical P fertilizer, integrated and Biological P fertilizer + 50% chemical P fertilizer. Except for Biological P fertilizer, DMD percentage was significantly higher in Fasieh compared to Bahman. The highest crude protein percentage was obtained for Fasieh in Biological P fertilizer + 50% chemical P fertilizer for Bahman in Biological P fertilizer + 75% chemical P fertilizer, respectively. The water soluble carbohydrate content was significantly higher in Fasieh at Chemical P fertilizer and integrated fertilizer treatments compared to Bahman variety. The highest NDF in Bahman was observed when received Biological P fertilizer + 50% chemical P fertilizer treatment, while the same results was obtained for Fasieh when received Biological P fertilizer + 100% chemical P fertilizer and Biological P fertilizer + 75% chemical P fertilizer.

Root Systems Biology: Integrative Modeling across Scales, from Gene Regulatory Networks to the Rhizosphere1

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Hill, Kristine; Porco, Silvana; Lobet, Guillaume; Zappala, Susan; Mooney, Sacha; Draye, Xavier; Bennett, Malcolm J.

2013-01-01

Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond the examination of interactions at the genetic network scale and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism, and rhizosphere scales. Understanding the underlying biological mechanisms and the complex interplay between systems at these different scales requires an integrative approach. Here, we describe examples of such approaches and discuss the merits of developing models to span multiple scales, from network to population levels, and to address dynamic interactions between plants and their environment. PMID:24143806

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

Science.gov (United States)

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

2014-07-01

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

Harnessing the Power of Integrated Mitochondrial Biology and Physiology: A Special Report on the NHLBI Mitochondria in Heart Diseases Initiative.

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Ping, Peipei; Gustafsson, Åsa B; Bers, Don M; Blatter, Lothar A; Cai, Hua; Jahangir, Arshad; Kelly, Daniel; Muoio, Deborah; O'Rourke, Brian; Rabinovitch, Peter; Trayanova, Natalia; Van Eyk, Jennifer; Weiss, James N; Wong, Renee; Schwartz Longacre, Lisa

2015-07-17

Mitochondrial biology is the sum of diverse phenomena from molecular profiles to physiological functions. A mechanistic understanding of mitochondria in disease development, and hence the future prospect of clinical translations, relies on a systems-level integration of expertise from multiple fields of investigation. Upon the successful conclusion of a recent National Institutes of Health, National Heart, Lung, and Blood Institute initiative on integrative mitochondrial biology in cardiovascular diseases, we reflect on the accomplishments made possible by this unique interdisciplinary collaboration effort and exciting new fronts on the study of these remarkable organelles. © 2015 American Heart Association, Inc.

Defending the scientific integrity of conservation-policy processes.

Science.gov (United States)

Carroll, Carlos; Hartl, Brett; Goldman, Gretchen T; Rohlf, Daniel J; Treves, Adrian; Kerr, Jeremy T; Ritchie, Euan G; Kingsford, Richard T; Gibbs, Katherine E; Maron, Martine; Watson, James E M

2017-10-01

Government agencies faced with politically controversial decisions often discount or ignore scientific information, whether from agency staff or nongovernmental scientists. Recent developments in scientific integrity (the ability to perform, use, communicate, and publish science free from censorship or political interference) in Canada, Australia, and the United States demonstrate a similar trajectory. A perceived increase in scientific-integrity abuses provokes concerted pressure by the scientific community, leading to efforts to improve scientific-integrity protections under a new administration. However, protections are often inconsistently applied and are at risk of reversal under administrations publicly hostile to evidence-based policy. We compared recent challenges to scientific integrity to determine what aspects of scientific input into conservation policy are most at risk of political distortion and what can be done to strengthen safeguards against such abuses. To ensure the integrity of outbound communications from government scientists to the public, we suggest governments strengthen scientific integrity policies, include scientists' right to speak freely in collective-bargaining agreements, guarantee public access to scientific information, and strengthen agency culture supporting scientific integrity. To ensure the transparency and integrity with which information from nongovernmental scientists (e.g., submitted comments or formal policy reviews) informs the policy process, we suggest governments broaden the scope of independent reviews, ensure greater diversity of expert input and transparency regarding conflicts of interest, require a substantive response to input from agencies, and engage proactively with scientific societies. For their part, scientists and scientific societies have a responsibility to engage with the public to affirm that science is a crucial resource for developing evidence-based policy and regulations in the public interest. �

The Dominance Behavioral System and Psychopathology: Evidence from Self-Report, Observational, and Biological Studies

Science.gov (United States)

Johnson, Sheri L.; Leedom, Liane J.; Muhtadie, Luma

2012-01-01

The dominance behavioral system (DBS) can be conceptualized as a biologically-based system which guides dominance motivation, dominant and subordinate behavior, and responsivity to perceptions of power and subordination. A growing body of research suggests that problems with the DBS are evident across a broad range of psychopathologies. We begin by describing psychological, social, and biological correlates of the dominance behavioral system (DBS). Extensive research suggests that externalizing disorders, mania-proneness, and narcissistic traits are related to heightened dominance motivation and behaviors. Mania and narcissistic traits also appear related to inflated self-perceptions of power. Anxiety and depression are related to subordination and submissiveness, as well as a desire to avoid subordination. Models of the DBS have received support from research with humans and animals; from self-report, observational, and biological methods; and using naturalistic and experimental paradigms. Limitations of available research include the relative lack of longitudinal studies using multiple measures of the DBS and the absence of relevant studies using diagnosed samples to study narcissistic personality disorder and bipolar disorder. We provide suggestions for future research on the DBS and psychopathology, including investigations of whether the DBS can be used to differentiate specific disorder outcomes; the need for more sophisticated biological research; and the value of longitudinal dynamical research. Implications of using the DBS as a tool in clinical assessment and treatment are discussed. PMID:22506751

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

Directory of Open Access Journals (Sweden)

Gregorio Sergio E

2009-05-01

Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

The Tobacco mosaic virus Movement Protein Associates with but Does Not Integrate into Biological Membranes

Science.gov (United States)

Peiró, Ana; Martínez-Gil, Luis; Tamborero, Silvia; Pallás, Vicente

2014-01-01

ABSTRACT Plant positive-strand RNA viruses require association with plant cell endomembranes for viral translation and replication, as well as for intra- and intercellular movement of the viral progeny. The membrane association and RNA binding of the Tobacco mosaic virus (TMV) movement protein (MP) are vital for orchestrating the macromolecular network required for virus movement. A previously proposed topological model suggests that TMV MP is an integral membrane protein with two putative α-helical transmembrane (TM) segments. Here we tested this model using an experimental system that measured the efficiency with which natural polypeptide segments were inserted into the ER membrane under conditions approximating the in vivo situation, as well as in planta. Our results demonstrated that the two hydrophobic regions (HRs) of TMV MP do not span biological membranes. We further found that mutations to alter the hydrophobicity of the first HR modified membrane association and precluded virus movement. We propose a topological model in which the TMV MP HRs intimately associate with the cellular membranes, allowing maximum exposure of the hydrophilic domains of the MP to the cytoplasmic cellular components. IMPORTANCE To facilitate plant viral infection and spread, viruses encode one or more movement proteins (MPs) that interact with ER membranes. The present work investigated the membrane association of the 30K MP of Tobacco mosaic virus (TMV), and the results challenge the previous topological model, which predicted that the TMV MP behaves as an integral membrane protein. The current data provide greatly needed clarification of the topological model and provide substantial evidence that TMV MP is membrane associated only at the cytoplasmic face of the membrane and that neither of its domains is integrated into the membrane or translocated into the lumen. Understanding the topology of MPs in the ER is vital for understanding the role of the ER in plant virus transport

Pollution control in pulp and paper industrial effluents using integrated chemical-biological treatment sequences.

Science.gov (United States)

El-Bestawy, Ebtesam; El-Sokkary, Ibrahim; Hussein, Hany; Keela, Alaa Farouk Abu

2008-11-01

The main objective of the present study was to improve the quality of pulp and paper industrial wastewater of two local mills RAKTA and El-Ahlia, Alexandria, Egypt, and to bring their pollutant contents to safe discharge levels. Quality improvement was carried out using integrated chemical and biological treatment approaches after their optimization. Chemical treatment (alum, lime, and ferric chloride) was followed by oxidation using hydrogen peroxide and finally biological treatment using activated sludge (90 min for RAKTA and 60 min for El-Ahlia effluents). Chemical coagulation produced low-quality effluents, while pH adjustment during coagulation treatment did not enhance the quality of the effluents. Maximum removal of the tested pollutants was achieved using the integrated treatment and the pollutants recorded residual concentrations (RCs) of 34.67, 17.33, 0.13, and 0.43 mg/l and 15.0, 11.0, 0.0, and 0.13 mg/l for chemical oxygen demand (COD), biochemical oxygen demand (BOD5), tannin and lignin, and silica in RAKTA and El-Ahlia effluents, respectively, all of which were below their maximum permissible limits (MPLs) for the safe discharge into water courses. Specific oxygen uptake rate (SOUR) and sludge volume index (SVI) values reflect good conditions and healthy activated sludge. Based on the previous results, optimized conditions were applied as bench scale on the raw effluents of RAKTA and El-Ahlia via the batch chemical and the biological treatment sequences proposed. For RAKTA effluents, the sequence was as follows: (1) coagulation with 375 mg/l FeCl3, (2) oxidation with 50 mg/l hydrogen peroxide, and (3) biological treatment using activated sludge with 2,000 mg/l initial concentration and 90 min hydraulic retention time (HRT), while for El-Ahlia raw effluents, the sequence was (1) coagulation with 250 mg/l FeCl3, (2) oxidation with 45 mg/l hydrogen peroxide, and (3) biological treatment using activated sludge with 2,000 mg/l initial concentration and 60

Achieving Adherence to Evidence-Based Practices: Are Health IT and Hospital-Physician Integration Complementary or Substitutive Strategies?

Science.gov (United States)

Everson, Jordan; Lee, Shoou-Yih Daniel; Adler-Milstein, Julia

2016-12-01

In response to evolving policies and conditions, hospitals have increased health information technology (HIT) adoption and strived to improve hospital-physician integration. While evidence suggests that both HIT and integration confer independent benefits, when combined, they may provide complementary means to achieve high performance or overlap to offset each other's contribution. We explore this relationship in the context of hospital adherence to evidence-based practices (EBPs). Using the American Hospital Association's Annual and IT Supplement surveys, and Centers for Medicare and Medicaid Services's Hospital Compare, we estimate the independent relationships and interactions between HIT and hospital-physician integration with respect to EBP adherence. HIT adoption and tight (but not loose) integration are independently associated with greater adherence to EBPs. The interaction between HIT adoption and tight integration is negative, consistent with an offsetting association between HIT adoption and integration in their relationship to EBP adherence. This finding reveals the need to be aware of potential substitutive effects from simultaneous pursuit of multiple approaches to performance improvement. © The Author(s) 2016.

Using dual classifications in the development of avian wetland indices of biological integrity for wetlands in West Virginia, USA.

Science.gov (United States)

Veselka, Walter; Anderson, James T; Kordek, Walter S

2010-05-01

Considerable resources are being used to develop and implement bioassessment methods for wetlands to ensure that "biological integrity" is maintained under the United States Clean Water Act. Previous research has demonstrated that avian composition is susceptible to human impairments at multiple spatial scales. Using a site-specific disturbance gradient, we built avian wetland indices of biological integrity (AW-IBI) specific to two wetland classification schemes, one based on vegetative structure and the other based on the wetland's position in the landscape and sources of water. The resulting class-specific AW-IBI was comprised of one to four metrics that varied in their sensitivity to the disturbance gradient. Some of these metrics were specific to only one of the classification schemes, whereas others could discriminate varying levels of disturbance regardless of classification scheme. Overall, all of the derived biological indices specific to the vegetative structure-based classes of wetlands had a significant relation with the disturbance gradient; however, the biological index derived for floodplain wetlands exhibited a more consistent response to a local disturbance gradient. We suspect that the consistency of this response is due to the inherent nature of the connectivity of available habitat in floodplain wetlands.

Redox-capacitor to connect electrochemistry to redox-biology.

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Kim, Eunkyoung; Leverage, W Taylor; Liu, Yi; White, Ian M; Bentley, William E; Payne, Gregory F

2014-01-07

It is well-established that redox-reactions are integral to biology for energy harvesting (oxidative phosphorylation), immune defense (oxidative burst) and drug metabolism (phase I reactions), yet there is emerging evidence that redox may play broader roles in biology (e.g., redox signaling). A critical challenge is the need for tools that can probe biologically-relevant redox interactions simply, rapidly and without the need for a comprehensive suite of analytical methods. We propose that electrochemistry may provide such a tool. In this tutorial review, we describe recent studies with a redox-capacitor film that can serve as a bio-electrode interface that can accept, store and donate electrons from mediators commonly used in electrochemistry and also in biology. Specifically, we (i) describe the fabrication of this redox-capacitor from catechols and the polysaccharide chitosan, (ii) discuss the mechanistic basis for electron exchange, (iii) illustrate the properties of this redox-capacitor and its capabilities for promoting redox-communication between biology and electrodes, and (iv) suggest the potential for enlisting signal processing strategies to "extract" redox information. We believe these initial studies indicate broad possibilities for enlisting electrochemistry and signal processing to acquire "systems level" redox information from biology.

Emerging concepts for management of river ecosystems and challenges to applied integration of physical and biological sciences in the Pacific Northwest, USA

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Bruce E. Rieman; Jason B. Dunham; James L. Clayton

2006-01-01

Integration of biological and physical concepts is necessary to understand and conserve the ecological integrity of river systems. Past attempts at integration have often focused at relatively small scales and on mechanistic models that may not capture the complexity of natural systems leaving substantial uncertainty about ecological responses to management actions....

Meeting the Challenge of Preparing Social Workers for Integrated Health Practice: Evidence from Two MSW Cohorts

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Rishel, Carrie W.; Hartnett, Helen P.

2017-01-01

Changes in health care policy have led to an expansion of integrated care models that rely on collaboration among interprofessional health teams. Recent federal funding has encouraged the development of innovative training models to prepare social workers for integrated health practice. This article presents evidence from the first two MSW cohorts…

Integrating evidence into practice: use of McKenzie-based treatment for mechanical low back pain

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Clarke S

2011-11-01

Full Text Available Angela Dunsford1, Saravana Kumar1,2, Sarah Clarke1 1International Centre for Allied Health Evidence, 2School of Health Sciences, University of South Australia, Adelaide, South Australia, Australia Abstract: Low back pain (LBP is a major health issue with significant socioeconomic implications in most Western countries. Many forms of treatment have been proposed and investigated in the past, with exercise being a commonly prescribed intervention. Within allied health, in particular physiotherapy, there has been a growing movement that recognizes the role of the McKenzie method in treating LBP. Within the McKenzie framework, directional preference (DP exercises are one such intervention, with preliminary data demonstrating its effectiveness in the management of LBP. In this paper, we aim to integrate the evidence from current research, identified using a systematic review, and utilize a practical real-life case scenario to outline how evidence from the literature can be implemented in clinical practice. The findings from the systematic review indicate that DP exercises may have positive effects in the management of LBP. While the body of evidence to support this is limited (only four studies and therefore modest at best, it does provide some emerging evidence to support the use of DP exercises in clinical practice. Despite this, gaps also persist in the literature on DP exercises, and this relates to the exercise parameters and the compliance rates. Recognizing this dichotomy (modest evidence in some areas and evidence gaps in other areas, which is likely to confront health practitioners, using a practical approach with a real-life clinical scenario, we outline how the evidence from the systematic review can be implemented in clinical practice. This approach builds on the philosophy of evidence-based practice of integrating research evidence with clinical expertise and patient values. Keywords: low back pain, McKenzie method, directional

[What else is Evidence-based Medicine?].

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Hauswaldt, Johannes

2010-01-01

The practice of evidence-based medicine means integrating individual clinical expertise with the best available external clinical evidence. Strange enough, scientific discussion focuses on external evidence from systematic research, but neglects its counterpart, i.e., individual clinical expertise. Apart from a lack of appropriate intellectual tools for approaching the latter, this might be due to the mutual concealment of thought and action, of sensor and motor activity (Viktor von Weizsaecker's principle of the revolving door). Behind this, and incommensurably different from each other, lie the world of physics and the world of biology with an ego animal, that is, the dilemma of the self-conscious subject in a world of objects. When practicing medicine, this dilemma of self-reference is being resolved but only through a holistic approach combining rational and external evidence with biographical, spiritual, emotional and pre-rational elements represented in the physician's individual clinical expertise. Copyright © 2010. Published by Elsevier GmbH.

Gauss-Kronrod-Trapezoidal Integration Scheme for Modeling Biological Tissues with Continuous Fiber Distributions

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Hou, Chieh; Ateshian, Gerard A.

2015-01-01

Fibrous biological tissues may be modeled using a continuous fiber distribution (CFD) to capture tension-compression nonlinearity, anisotropic fiber distributions, and load-induced anisotropy. The CFD framework requires spherical integration of weighted individual fiber responses, with fibers contributing to the stress response only when they are in tension. The common method for performing this integration employs the discretization of the unit sphere into a polyhedron with nearly uniform triangular faces (finite element integration or FEI scheme). Although FEI has proven to be more accurate and efficient than integration using spherical coordinates, it presents three major drawbacks: First, the number of elements on the unit sphere needed to achieve satisfactory accuracy becomes a significant computational cost in a finite element analysis. Second, fibers may not be in tension in some regions on the unit sphere, where the integration becomes a waste. Third, if tensed fiber bundles span a small region compared to the area of the elements on the sphere, a significant discretization error arises. This study presents an integration scheme specialized to the CFD framework, which significantly mitigates the first drawback of the FEI scheme, while eliminating the second and third completely. Here, integration is performed only over the regions of the unit sphere where fibers are in tension. Gauss-Kronrod quadrature is used across latitudes and the trapezoidal scheme across longitudes. Over a wide range of strain states, fiber material properties, and fiber angular distributions, results demonstrate that this new scheme always outperforms FEI, sometimes by orders of magnitude in the number of computational steps and relative accuracy of the stress calculation. PMID:26291492

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.

Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

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Resendis-Antonio Osbaldo

2011-07-01

Full Text Available Abstract Background Bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. In practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. Currently, the advent of high-throughput technology supplies with valuable data that contribute to understanding the metabolic activity during bacterial nitrogen fixation. This undertaking is not trivial, and the development of computational methods useful in accomplishing an integrative, descriptive and predictive framework is a crucial issue to decoding the principles that regulated the metabolic activity of this biological process. Results In this work we present a systems biology description of the metabolic activity in bacterial nitrogen fixation. This was accomplished by an integrative analysis involving high-throughput data and constraint-based modeling to characterize the metabolic activity in Rhizobium etli bacteroids located at the root nodules of Phaseolus vulgaris (bean plant. Proteome and transcriptome technologies led us to identify 415 proteins and 689 up-regulated genes that orchestrate this biological process. Taking into account these data, we: 1 extended the metabolic reconstruction reported for R. etli; 2 simulated the metabolic activity during symbiotic nitrogen fixation; and 3 evaluated the in silico results in terms of bacteria phenotype. Notably, constraint-based modeling simulated nitrogen fixation activity in such a way that 76.83% of the enzymes and 69.48% of the genes were experimentally justified. Finally, to further assess the predictive scope of the computational model, gene deletion analysis was carried out on nine metabolic enzymes. Our model concluded that an altered metabolic activity on these enzymes induced

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

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Lo Kenneth

2012-08-01

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

Evidence for the possible biological significance of the igf-1 gene alternative splicing in prostate cancer

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Anastassios ePhilippou

2013-03-01

Full Text Available Insulin-like growth factor I (IGF-I has been implicated in the pathogenesis of prostate cancer (PCa, since it plays a key role in cell proliferation, differentiation and apoptosis. The IGF-I actions are mediated mainly via its binding to the type I IGF receptor (IGF-IR, however IGF-I signaling via insulin receptor (IR and hybrid IGF-I/IR is also evident. Different IGF-I mRNA splice variants, namely IGF-IEa, IGF-IEb and IGF-IEc, are expressed in human cells and tissues. These transcripts encode several IGF-I precursor proteins which contain the same bioactive product (mature IGF-I, however, they differ by the length of their signal peptides on the amino-terminal end and the structure of the extension peptides (E-peptides on the carboxy-terminal end. There is an increasing interest in the possible different role of the IGF-I transcripts and their respective non-(matureIGF-I products in the regulation of distinct biological activities. Moreover, there is strong evidence of a differential expression profile of the IGF-I splice variants in normal vs. PCa tissues and PCa cells, implying that the expression pattern of the various IGF-I transcripts and their respective protein products may possess different functions in cancer biology. Herein, the evidence that the IGF-IEc transcript regulates PCa growth via Ec-peptide specific and IGF-IR/IR-independent signaling is discussed.

Principles for integrating reactive species into in vivo biological processes: Examples from exercise physiology.

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Margaritelis, Nikos V; Cobley, James N; Paschalis, Vassilis; Veskoukis, Aristidis S; Theodorou, Anastasios A; Kyparos, Antonios; Nikolaidis, Michalis G

2016-04-01

The equivocal role of reactive species and redox signaling in exercise responses and adaptations is an example clearly showing the inadequacy of current redox biology research to shed light on fundamental biological processes in vivo. Part of the answer probably relies on the extreme complexity of the in vivo redox biology and the limitations of the currently applied methodological and experimental tools. We propose six fundamental principles that should be considered in future studies to mechanistically link reactive species production to exercise responses or adaptations: 1) identify and quantify the reactive species, 2) determine the potential signaling properties of the reactive species, 3) detect the sources of reactive species, 4) locate the domain modified and verify the (ir)reversibility of post-translational modifications, 5) establish causality between redox and physiological measurements, 6) use selective and targeted antioxidants. Fulfilling these principles requires an idealized human experimental setting, which is certainly a utopia. Thus, researchers should choose to satisfy those principles, which, based on scientific evidence, are most critical for their specific research question. Copyright © 2015 Elsevier Inc. All rights reserved.

Toward the Integration of Meditation into Higher Education: A Review of Research Evidence

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Shapiro, Shauna L.; Brown, Kirk Warren; Astin, John A.

2011-01-01

Context: There is growing interest in the integration of meditation in higher education. Purpose: Here, we review evidence bearing on the utility of meditation to facilitate the achievement of traditional educational goals and to enhance education of the "whole person." Research Design: We examine how meditation practices may help foster important…

Integrative structure modeling with the Integrative Modeling Platform.

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Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano; Pellarin, Riccardo; Greenberg, Charles H; Saltzberg, Daniel; Sali, Andrej

2018-01-01

Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use. © 2017 The Protein Society.

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

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Marcio Katsumi Oikawa

2004-01-01

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

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

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Tavares, Gustavo Medina; Bobrowski, Vera Lucia

2018-01-01

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

The Evidence-base for Using Ontologies and Semantic Integration Methodologies to Support Integrated Chronic Disease Management in Primary and Ambulatory Care: Realist Review. Contribution of the IMIA Primary Health Care Informatics WG.

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Liyanage, H; Liaw, S-T; Kuziemsky, C; Terry, A L; Jones, S; Soler, J K; de Lusignan, S

2013-01-01

Most chronic diseases are managed in primary and ambulatory care. The chronic care model (CCM) suggests a wide range of community, technological, team and patient factors contribute to effective chronic disease management. Ontologies have the capability to enable formalised linkage of heterogeneous data sources as might be found across the elements of the CCM. To describe the evidence base for using ontologies and other semantic integration methods to support chronic disease management. We reviewed the evidence-base for the use of ontologies and other semantic integration methods within and across the elements of the CCM. We report them using a realist review describing the context in which the mechanism was applied, and any outcome measures. Most evidence was descriptive with an almost complete absence of empirical research and important gaps in the evidence-base. We found some use of ontologies and semantic integration methods for community support of the medical home and for care in the community. Ubiquitous information technology (IT) and other IT tools were deployed to support self-management support, use of shared registries, health behavioural models and knowledge discovery tools to improve delivery system design. Data quality issues restricted the use of clinical data; however there was an increased use of interoperable data and health system integration. Ontologies and semantic integration methods are emergent with limited evidence-base for their implementation. However, they have the potential to integrate the disparate community wide data sources to provide the information necessary for effective chronic disease management.

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

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

2017-01-01

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

SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance.

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Chowbina, Sudhir; Hammamieh, Rasha; Kumar, Raina; Chakraborty, Nabarun; Yang, Ruoting; Mudunuri, Uma; Jett, Marti; Palma, Joseph M; Stephens, Robert

2013-01-01

SysBioCube is an integrated data warehouse and analysis platform for experimental data relating to diseases of military relevance developed for the US Army Medical Research and Materiel Command Systems Biology Enterprise (SBE). It brings together, under a single database environment, pathophysio-, psychological, molecular and biochemical data from mouse models of post-traumatic stress disorder and (pre-) clinical data from human PTSD patients.. SysBioCube will organize, centralize and normalize this data and provide an access portal for subsequent analysis to the SBE. It provides new or expanded browsing, querying and visualization to provide better understanding of the systems biology of PTSD, all brought about through the integrated environment. We employ Oracle database technology to store the data using an integrated hierarchical database schema design. The web interface provides researchers with systematic information and option to interrogate the profiles of pan-omics component across different data types, experimental designs and other covariates.

Answering biological questions: Querying a systems biology database for nutrigenomics

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Evelo, C.T.; Bochove, K. van; Saito, J.T.

2011-01-01

The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

Integrative activities content (aic: an auxiliary tool for the teaching of Biochemistry in the course of biological sciences at UFRN

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F. D. Silva

2015-08-01

Full Text Available There are constant changes in the development of science, technology, politics, culture and society; the need for change is also evident in the training of teachers. The ease of access to information makes us realize that traditional teaching needs to be updated.The increasing demotivation of students,followed by high reprobation rates, has become a real challenge to the teaching practice.The objective of this work was to awaken in students enrolled in the discipline of MOLECULAR DIVERSITY (MD, a required curricular component in the Course of Biological Sciences at UFRN, an interest in studying the chemistry and functions of biomolecules, better relating the two to each other, and the content already studied in the course, in order to improve the teaching-learning process. This work was developed in a tutoring project registered at PROGRAD/UFRN. This discipline, MD, addresses chemical and structural features of the main organic molecules.The methodology focused on applying problem integrators called INTEGRATIVE ACTIVITIES OF CONTENT. This refers specifically to the application of problems that integrate the topics taught in the discipline, and also those administered in the disciplines processed in parallel, or even in previous semesters. In this way students realize that molecules relate and interact in all bodies; this gives rise to life through metabolism. The discipline is expected to promote meaningful and inter-related learning. We obtained the following results: greater participation and involvement of students in answering the questions posed; greater interest in the discipline;positive changes regarding the number of students who dropped the class, and in reprobation;and greater integration between teachers, students, and teaching assistants. The methodology used in this work was extremely important to achieve the proposed objectives, helping to facilitate the process of teaching-learning, as also to important relate content.

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

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Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick

2014-02-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.

Integrating biological redesign: where synthetic biology came from and where it needs to go.

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Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

2014-03-27

Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

An integrative review of the enjoyment of sadness associated with music.

OpenAIRE

Eerola, T.; Vuoskoski, J. K.; Peltola, H.-R.; Putkinen, V.; Schäfer, K.

2017-01-01

The recent surge of interest towards the paradoxical pleasure produced by sad music has generated a handful of theories and an array of empirical explorations on the topic. However, none of these have attempted to weigh the existing evidence in a systematic fashion. The present work puts forward an integrative framework laid out over three levels of explanation – biological, psycho-social, and cultural – to compare and integrate the existing findings in a meaningful way. First, we review the ...

Content-rich biological network constructed by mining PubMed abstracts

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Sharp Burt M

2004-10-01

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

Introduction to the history and current status of evidence-based korean medicine: a unique integrated system of allopathic and holistic medicine.

Science.gov (United States)

Yin, Chang Shik; Ko, Seong-Gyu

2014-01-01

Objectives. Korean medicine, an integrated allopathic and traditional medicine, has developed unique characteristics and has been active in contributing to evidence-based medicine. Recent developments in Korean medicine have not been as well disseminated as traditional Chinese medicine. This introduction to recent developments in Korean medicine will draw attention to, and facilitate, the advancement of evidence-based complementary alternative medicine (CAM). Methods and Results. The history of and recent developments in Korean medicine as evidence-based medicine are explored through discussions on the development of a national standard classification of diseases and study reports, ranging from basic research to newly developed clinical therapies. A national standard classification of diseases has been developed and revised serially into an integrated classification of Western allopathic and traditional holistic medicine disease entities. Standard disease classifications offer a starting point for the reliable gathering of evidence and provide a representative example of the unique status of evidence-based Korean medicine as an integration of Western allopathic medicine and traditional holistic medicine. Conclusions. Recent developments in evidence-based Korean medicine show a unique development in evidence-based medicine, adopting both Western allopathic and holistic traditional medicine. It is expected that Korean medicine will continue to be an important contributor to evidence-based medicine, encompassing conventional and complementary approaches.

Introduction to the History and Current Status of Evidence-Based Korean Medicine: A Unique Integrated System of Allopathic and Holistic Medicine

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Chang Shik Yin

2014-01-01

Full Text Available Objectives. Korean medicine, an integrated allopathic and traditional medicine, has developed unique characteristics and has been active in contributing to evidence-based medicine. Recent developments in Korean medicine have not been as well disseminated as traditional Chinese medicine. This introduction to recent developments in Korean medicine will draw attention to, and facilitate, the advancement of evidence-based complementary alternative medicine (CAM. Methods and Results. The history of and recent developments in Korean medicine as evidence-based medicine are explored through discussions on the development of a national standard classification of diseases and study reports, ranging from basic research to newly developed clinical therapies. A national standard classification of diseases has been developed and revised serially into an integrated classification of Western allopathic and traditional holistic medicine disease entities. Standard disease classifications offer a starting point for the reliable gathering of evidence and provide a representative example of the unique status of evidence-based Korean medicine as an integration of Western allopathic medicine and traditional holistic medicine. Conclusions. Recent developments in evidence-based Korean medicine show a unique development in evidence-based medicine, adopting both Western allopathic and holistic traditional medicine. It is expected that Korean medicine will continue to be an important contributor to evidence-based medicine, encompassing conventional and complementary approaches.

Data Integration for Health and Stress Monitoring: Biological Metabolites, Wearables Data, and Self-Reporting

Science.gov (United States)

Dunn, Jocelyn T.

Integrative and unobtrusive approaches to monitoring health and stress can assist in preventative medicine and disease management, and provide capabilities for complex work environments, such as military deployments and long-duration human space exploration missions. With many data streams that could potentially provide critical information about the health, behavior, and psychosocial states of individuals or small groups, the central question of this research is how to reliably measure health and stress states over time. This integrative approach to health and stress monitoring has implemented biological metabolite profiling, wearables data analysis, and survey assessment for comparing biological, behavioral, and psychological perspectives. Health monitoring technologies aim to provide objective data about health status. Providing objective information can help mitigate biases or blind spots in an individual's perception. Consider an individual who is unwilling to openly admit to psychosocial distress and unhealthy habits, or an individual who has habituated to long-term stressors and is unable to recognize a chronic state of high stress. Both honesty and self-awareness are required for accurate self-reporting. Digital health technologies, such as wearable devices, provide objective data for health monitoring. Compared to surveys, wearables are less influenced by participant openness, and compared to biological samples, wearables require less equipment and less labor for analysis. However, inherent to every data stream are limitations due to uncertainty and sensitivity. This research has been conducted in collaboration with Hawaii Space Exploration Analog and Simulation (HI-SEAS), which is a Mars analog research site on the slopes on Mauna Loa volcano in Hawaii. During 8-month and 12-month HI-SEAS missions in the 2014-2016 timeframe, twelve individuals provided hair and urine samples for metabolite profiling, utilized consumer-grade wearables to monitor sleep and

Using pedagogical approaches to influence evidence-based practice integration - processes and recommendations: findings from a grounded theory study.

Science.gov (United States)

Malik, Gulzar; McKenna, Lisa; Griffiths, Debra

2017-04-01

The study aimed to explore the processes undertaken by nurse academics when integrating evidence-based practice (EBP) into their teaching and learning practices. This article focuses on pedagogical approaches employed by academics to influence evidence-based practice integration into undergraduate programs across Australian universities. Nursing academics are challenged to incorporate a variety of teaching and learning strategies to teach evidence-based practice and determine their effectiveness. However, literature suggests that there are limited studies available focusing on pedagogical approaches in evidence-based practice education. A constructivist grounded theory methodology, informed by Charmaz was used for this study. Data were collected during 2014 from 23 nurse academics across Australian universities through semi-structured interviews. Additionally, nine were observed during teaching of undergraduate students. Twenty subject outlines were also analysed following Charmaz's approach of data analysis. 'Influencing EBP integration' describes the pedagogical approaches employed by academics to incorporate EBP knowledge and skills into undergraduate curricula. With the use of various teaching and learning strategies, academics attempted to contextualize EBP by engaging students with activities aiming to link evidence to practice and with the EBP process. Although, some strategies appeared to be engaging, others were traditional and seemed to be disengaging for students due to the challenges experienced by participants that impeded the use of the most effective teaching methods. Study findings offer valuable insights into the teaching practices and identify some key challenges that require the adoption of appropriate strategies to ensure future nurses are well prepared in the paradigm of evidence-based practice. © 2016 John Wiley & Sons Ltd.

Applicability of Computational Systems Biology in Toxicology

DEFF Research Database (Denmark)

Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

2014-01-01

be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method......Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources...... and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search...

7th Annual Systems Biology Symposium: Systems Biology and Engineering

Energy Technology Data Exchange (ETDEWEB)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

A Gauss-Kronrod-Trapezoidal integration scheme for modeling biological tissues with continuous fiber distributions.

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Hou, Chieh; Ateshian, Gerard A

2016-01-01

Fibrous biological tissues may be modeled using a continuous fiber distribution (CFD) to capture tension-compression nonlinearity, anisotropic fiber distributions, and load-induced anisotropy. The CFD framework requires spherical integration of weighted individual fiber responses, with fibers contributing to the stress response only when they are in tension. The common method for performing this integration employs the discretization of the unit sphere into a polyhedron with nearly uniform triangular faces (finite element integration or FEI scheme). Although FEI has proven to be more accurate and efficient than integration using spherical coordinates, it presents three major drawbacks: First, the number of elements on the unit sphere needed to achieve satisfactory accuracy becomes a significant computational cost in a finite element (FE) analysis. Second, fibers may not be in tension in some regions on the unit sphere, where the integration becomes a waste. Third, if tensed fiber bundles span a small region compared to the area of the elements on the sphere, a significant discretization error arises. This study presents an integration scheme specialized to the CFD framework, which significantly mitigates the first drawback of the FEI scheme, while eliminating the second and third completely. Here, integration is performed only over the regions of the unit sphere where fibers are in tension. Gauss-Kronrod quadrature is used across latitudes and the trapezoidal scheme across longitudes. Over a wide range of strain states, fiber material properties, and fiber angular distributions, results demonstrate that this new scheme always outperforms FEI, sometimes by orders of magnitude in the number of computational steps and relative accuracy of the stress calculation.

Biologic and clinical aspects of integration of different bone substitutes in oral surgery: a literature review.

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Zizzari, Vincenzo Luca; Zara, Susi; Tetè, Giulia; Vinci, Raffaele; Gherlone, Enrico; Cataldi, Amelia

2016-10-01

Many bone substitutes have been proposed for bone regeneration, and researchers have focused on the interactions occurring between grafts and host tissue, as the biologic response of host tissue is related to the origin of the biomaterial. Bone substitutes used in oral and maxillofacial surgery could be categorized according to their biologic origin and source as autologous bone graft when obtained from the same individual receiving the graft; homologous bone graft, or allograft, when harvested from an individual other than the one receiving the graft; animal-derived heterologous bone graft, or xenograft, when derived from a species other than human; and alloplastic graft, made of bone substitute of synthetic origin. The aim of this review is to describe the most commonly used bone substitutes, according to their origin, and to focus on the biologic events that ultimately lead to the integration of a biomaterial with the host tissue. Copyright © 2016 Elsevier Inc. All rights reserved.

Is ASEAN Ready for Banking Integration? Evidence from Interest Rate Convergence

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Fazelina Sahul Hamid

2016-07-01

Full Text Available Convergence in prices or returns of assets with similar characteristics indicates that the financial market is integrated with regional markets. This paper is the first that test of the movements of interest rates in ASEAN banking sector for the period 1990 - 2012. The empirical analysis is based on a yearly panel of commercial bank interest rate data from 5 ASEAN countries, namely, Indonesia, Malaysia, Philippines, Singapore and Thailand. We assessed the degree and speed of interest rate convergence using beta and sigma convergence method. The findings show that the difference and the dispersion in the interbank rates have reduced since the Asian financial crisis and this trend has become stronger after the Global financial crisis. The findings of this study confirm that interest rates in the ASEAN banking sector are converging. This provides evidence that the ASEAN banking sector is ready for financial integration.

The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

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Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

2012-01-01

Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

Exploring Visuomotor Priming Following Biological and Non-Biological Stimuli

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Gowen, E.; Bradshaw, C.; Galpin, A.; Lawrence, A.; Poliakoff, E.

2010-01-01

Observation of human actions influences the observer's own motor system, termed visuomotor priming, and is believed to be caused by automatic activation of mirror neurons. Evidence suggests that priming effects are larger for biological (human) as opposed to non-biological (object) stimuli and enhanced when viewing stimuli in mirror compared to…

Cross-border integration in the European electricity market. Evidence from the pricing behavior of Norwegian and Swiss exporters

International Nuclear Information System (INIS)

Balaguer, Jacint

2011-01-01

This paper examines the electricity market integration process in two European areas based on the pricing behavior of Norwegian and Swiss exporters. The aim is to gain evidence for the period after the adoption of the 'Second Legislative Package' (2003). The pricing behavior of Norwegian exporters indicates that the wholesale markets for Denmark and Sweden are highly integrated. Moreover, results are fully compatible with the existence of a very competitive marketplace for electricity. This clearly contrasts with the evidence provided by Swiss exporters. In this last case, analysis revealed differences in pricing-to-market behavior between Italy, France and Germany, which indicates that exporters take advantage of international market segmentation and divergences between market structures. This outcome provides a reasonable explanation as to why price differences between countries cannot be fully attributed to transmission costs, as has been claimed in previous research. We also found cross-country convergence in levels of markups and in pricing-to-market behavior of the Swiss exporters for the first part of the period that was analyzed. The evidence is fully consistent with an initial impulse toward market integration originated by reforms implemented at the beginning of the last decade. - Highlights: → We exploit a model based on pricing-to-market behavior. → Price discrimination by Swiss exporters is found. → Nordic electricity markets are found to be already highly integrated. → Market integration was recently improved in continental area. → Results are consistent with reforms under the 'Second Legislative Package'.

Cross-border integration in the European electricity market. Evidence from the pricing behavior of Norwegian and Swiss exporters

Energy Technology Data Exchange (ETDEWEB)

Balaguer, Jacint, E-mail: jacint.balaguer@eco.uji.es [Department of Economics, Universitat Jaume I, 12071 Castellon (Spain)

2011-09-15

This paper examines the electricity market integration process in two European areas based on the pricing behavior of Norwegian and Swiss exporters. The aim is to gain evidence for the period after the adoption of the 'Second Legislative Package' (2003). The pricing behavior of Norwegian exporters indicates that the wholesale markets for Denmark and Sweden are highly integrated. Moreover, results are fully compatible with the existence of a very competitive marketplace for electricity. This clearly contrasts with the evidence provided by Swiss exporters. In this last case, analysis revealed differences in pricing-to-market behavior between Italy, France and Germany, which indicates that exporters take advantage of international market segmentation and divergences between market structures. This outcome provides a reasonable explanation as to why price differences between countries cannot be fully attributed to transmission costs, as has been claimed in previous research. We also found cross-country convergence in levels of markups and in pricing-to-market behavior of the Swiss exporters for the first part of the period that was analyzed. The evidence is fully consistent with an initial impulse toward market integration originated by reforms implemented at the beginning of the last decade. - Highlights: > We exploit a model based on pricing-to-market behavior. > Price discrimination by Swiss exporters is found. > Nordic electricity markets are found to be already highly integrated. > Market integration was recently improved in continental area. > Results are consistent with reforms under the 'Second Legislative Package'.

Emerging concepts for management of river ecosystems and challenges to applied integration of physical and biological sciences in the Pacific Northwest, USA

Science.gov (United States)

Rieman, Bruce; Dunham, Jason B.; Clayton, James

2006-01-01

Integration of biological and physical concepts is necessary to understand and conserve the ecological integrity of river systems. Past attempts at integration have often focused at relatively small scales and on mechanistic models that may not capture the complexity of natural systems leaving substantial uncertainty about ecological responses to management actions. Two solutions have been proposed to guide management in the face of that uncertainty: the use of “natural variability” in key environmental patterns, processes, or disturbance as a reference; and the retention of some areas as essentially unmanaged reserves to conserve and represent as much biological diversity as possible. Both concepts are scale dependent because dominant processes or patterns that might be referenced will change with scale. Context and linkages across scales may be as important in structuring biological systems as conditions within habitats used by individual organisms. Both ideas view the physical environment as a template for expression, maintenance, and evolution of ecological diversity. To conserve or restore a diverse physical template it will be important to recognize the ecologically important differences in physical characteristics and processes among streams or watersheds that we might attempt to mimic in management or represent in conservation or restoration reserves.

Integrative Therapies and Pediatric Inflammatory Bowel Disease: The Current Evidence.

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Misra, Sanghamitra M

2014-08-25

Inflammatory bowel disease (IBD) primarily describes two distinct chronic conditions with unknown etiology, ulcerative colitis (UC) and Crohn's disease (CD). UC is limited to the colon, while CD may involve any portion of the gastrointestinal tract from mouth to anus. These diseases exhibit a pattern of relapse and remission, and the disease processes are often painful and debilitating. Due to the chronic nature of IBD and the negative side effects of many of the conventional therapies, many patients and their families turn to complementary and alternative medicine (CAM) for symptom relief. This article focuses on the current available evidence behind CAM/integrative therapies for IBD.

Value-Based Medicine and Integration of Tumor Biology.

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Brooks, Gabriel A; Bosserman, Linda D; Mambetsariev, Isa; Salgia, Ravi

2017-01-01

Clinical oncology is in the midst of a genomic revolution, as molecular insights redefine our understanding of cancer biology. Greater awareness of the distinct aberrations that drive carcinogenesis is also contributing to a growing armamentarium of genomically targeted therapies. Although much work remains to better understand how to combine and sequence these therapies, improved outcomes for patients are becoming manifest. As we welcome this genomic revolution in cancer care, oncologists also must grapple with a number of practical problems. Costs of cancer care continue to grow, with targeted therapies responsible for an increasing proportion of spending. Rising costs are bringing the concept of value into sharper focus and challenging the oncology community with implementation of value-based cancer care. This article explores the ways that the genomic revolution is transforming cancer care, describes various frameworks for considering the value of genomically targeted therapies, and outlines key challenges for delivering on the promise of personalized cancer care. It highlights practical solutions for the implementation of value-based care, including investment in biomarker development and clinical trials to improve the efficacy of targeted therapy, the use of evidence-based clinical pathways, team-based care, computerized clinical decision support, and value-based payment approaches.

Promoting convergence: The integrated graduate program in physical and engineering biology at Yale University, a new model for graduate education.

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Noble, Dorottya B; Mochrie, Simon G J; O'Hern, Corey S; Pollard, Thomas D; Regan, Lynne

2016-11-12

In 2008, we established the Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) at Yale University. Our goal was to create a comprehensive graduate program to train a new generation of scientists who possess a sophisticated understanding of biology and who are capable of applying physical and quantitative methodologies to solve biological problems. Here we describe the framework of the training program, report on its effectiveness, and also share the insights we gained during its development and implementation. The program features co-teaching by faculty with complementary specializations, student peer learning, and novel hands-on courses that facilitate the seamless blending of interdisciplinary research and teaching. It also incorporates enrichment activities to improve communication skills, engage students in science outreach, and foster a cohesive program cohort, all of which promote the development of transferable skills applicable in a variety of careers. The curriculum of the graduate program is integrated with the curricular requirements of several Ph.D.-granting home programs in the physical, engineering, and biological sciences. Moreover, the wide-ranging recruiting activities of the IGPPEB serve to enhance the quality and diversity of students entering graduate school at Yale. We also discuss some of the challenges we encountered in establishing and optimizing the program, and describe the institution-level changes that were catalyzed by the introduction of the new graduate program. The goal of this article is to serve as both an inspiration and as a practical "how to" manual for those who seek to establish similar programs at their own institutions. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):537-549, 2016. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

Clarification of the Use of Biological Data and Information in the 2002 Integrated Water Quality Monitoring and Assessment Report Guidance

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The memorandum modifies the 2002 Integrated Water Quality Monitoring and Assessment Report Guidance to provide clarity and promote consistency in the manner in which states use biological data and information in developing their 2002 submissions.

Adaptation of sensor morphology: an integrative view of perception from biologically inspired robotics perspective

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Nurzaman, Surya G.

2016-01-01

Sensor morphology, the morphology of a sensing mechanism which plays a role of shaping the desired response from physical stimuli from surroundings to generate signals usable as sensory information, is one of the key common aspects of sensing processes. This paper presents a structured review of researches on bioinspired sensor morphology implemented in robotic systems, and discusses the fundamental design principles. Based on literature review, we propose two key arguments: first, owing to its synthetic nature, biologically inspired robotics approach is a unique and powerful methodology to understand the role of sensor morphology and how it can evolve and adapt to its task and environment. Second, a consideration of an integrative view of perception by looking into multidisciplinary and overarching mechanisms of sensor morphology adaptation across biology and engineering enables us to extract relevant design principles that are important to extend our understanding of the unfinished concepts in sensing and perception. PMID:27499843

Water as Life, Death, and Power: Building an Integrated Interdisciplinary Course Combining Perspectives from Anthropology, Biology, and Chemistry

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Willermet, Cathy; Mueller, Anja; Juris, Stephen J.; Drake, Eron; Upadhaya, Samik; Chhetri, Pratik

2013-01-01

In response to a request from a campus student organization, faculty from three fields came together to develop and teach an integrated interdisciplinary course on water issues and social activism. This course, "Water as Life, Death, and Power", brought together topics from the fields of anthropology, biology and chemistry to explore…

Removal of Furfural From Wastewater Using Integrated Catalytic Ozonation and Biological Approaches

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Mostafa Leili

2014-12-01

Full Text Available Furfural with a chemical formula of C5H4O2 is a toxic compound which has several health problems for both humans and environment. It has a few exposure routes for entering the human body such as oral, dermal or nasal. In the present study, the efficacies of an integrated catalytic ozonation process (COP and novel cyclic biological reactor (CBR were explored for the removal of furfural from aqueous solutions. Activated carbon was purchased from Merck Company. It had a Brunauer, Emmett, and Teller (BET specific surface area of 1100 m2/g, with an average micropore volume and size of 0.385 cm3/g and 595 µm, respectively. The results indicated that 30% pretreatment with COP could increase furfural and chemical oxygen demand (COD removal efficiency with CBR 5.56% and 27.01%, respectively. With 70% pretreatment by COP, 98.57% furfural and 95.34% COD removal efficiencies happen in CBR. Generally, batch and continuous experiments showed that the integrated COP/CBR could be efficient in eliminating furfural from wastewater and thus may be a promising technique for treating furfural-containing wastewater.

Integration of systems biology with organs-on-chips to humanize therapeutic development

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Edington, Collin D.; Cirit, Murat; Chen, Wen Li Kelly; Clark, Amanda M.; Wells, Alan; Trumper, David L.; Griffith, Linda G.

2017-02-01

"Mice are not little people" - a refrain becoming louder as the gaps between animal models and human disease become more apparent. At the same time, three emerging approaches are headed toward integration: powerful systems biology analysis of cell-cell and intracellular signaling networks in patient-derived samples; 3D tissue engineered models of human organ systems, often made from stem cells; and micro-fluidic and meso-fluidic devices that enable living systems to be sustained, perturbed and analyzed for weeks in culture. Integration of these rapidly moving fields has the potential to revolutionize development of therapeutics for complex, chronic diseases, including those that have weak genetic bases and substantial contributions from gene-environment interactions. Technical challenges in modeling complex diseases with "organs on chips" approaches include the need for relatively large tissue masses and organ-organ cross talk to capture systemic effects, such that current microfluidic formats often fail to capture the required scale and complexity for interconnected systems. These constraints drive development of new strategies for designing in vitro models, including perfusing organ models, as well as "mesofluidic" pumping and circulation in platforms connecting several organ systems, to achieve the appropriate physiological relevance.

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

Science.gov (United States)

2010-01-01

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

Assessing Cross-disciplinary Efficiency of Soil Amendments for Agro-biologically, Economically, and Ecologically Integrated Soil Health Management

Science.gov (United States)

2010-01-01

Preventive and/or manipulative practices will be needed to maintain soil's biological, physiochemical, nutritional, and structural health in natural, managed, and disturbed ecosystems as a foundation for food security and global ecosystem sustainability. While there is a substantial body of interdisciplinary science on understanding function and structure of soil ecosystems, key gaps must be bridged in assessing integrated agro-biological, ecological, economical, and environmental efficiency of soil manipulation practices in time and space across ecosystems. This presentation discusses the application of a fertilizer use efficiency (FUE) model for assessing agronomic, economic, ecological, environmental, and nematode (pest) management efficiency of soil amendments. FUE is defined as increase in host productivity and/or decrease in plant-parasitic nematode population density in response to a given fertilizer treatment. Using the effects of nutrient amendment on Heterodera glycines population density and normalized difference vegetative index (indicator of physiological activities) of a soybean cultivar ‘CX 252’, how the FUE model recognizes variable responses and separates nutrient deficiency and toxicity from nematode parasitism as well as suitability of treatments designed to achieve desired biological and physiochemical soil health conditions is demonstrated. As part of bridging gaps between agricultural and ecological approaches to integrated understanding and management of soil health, modifications of the FUE model for analyzing the relationships amongst nematode community structure, soil parameters (eg. pH, nutrients, %OM), and plant response to soil amendment is discussed. PMID:22736840

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

Science.gov (United States)

Feser, Jason; Vasaly, Helen; Herrera, Jose

2013-01-01

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

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

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Calvo-Dmgz D.

2012-12-01

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

Treatment of high strength distillery wastewater (cherry stillage) by integrated aerobic biological oxidation and ozonation.

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Beltrán, F J; Alvarez, P M; Rodríguez, E M; García-Araya, J F; Rivas, J

2001-01-01

The performance of integrated aerobic digestion and ozonation for the treatment of high strength distillery wastewater (i.e., cherry stillage) is reported. Experiments were conducted in laboratory batch systems operating in draw and fill mode. For the biological step, activated sludge from a municipal wastewater treatment facility was used as inoculum, showing a high degree of activity to distillery wastewater. Thus, BOD and COD overall conversions of 95% and 82% were achieved, respectively. However, polyphenol content and absorbance at 254 nm (A(254)) could not be reduced more than 35% and 15%, respectively, by means of single biological oxidation. By considering COD as substrate, the aerobic digestion process followed a Contois' model kinetics, from which the maximum specific growth rate of microorganisms (mu(max)) and the inhibition factor, beta, were then evaluated at different conditions of temperature and pH. In the combined process, the effect of a post-ozonation stage was studied. The main goals achieved by the ozonation step were the removal of polyphenols and A(254). Therefore, ozonation was shown to be an appropriate technology to aid aerobic biological oxidation in the treatment of cherry stillage.

Wireless Biological Electronic Sensors.

Science.gov (United States)

Cui, Yue

2017-10-09

The development of wireless biological electronic sensors could open up significant advances for both fundamental studies and practical applications in a variety of areas, including medical diagnosis, environmental monitoring, and defense applications. One of the major challenges in the development of wireless bioelectronic sensors is the successful integration of biosensing units and wireless signal transducers. In recent years, there are a few types of wireless communication systems that have been integrated with biosensing systems to construct wireless bioelectronic sensors. To successfully construct wireless biological electronic sensors, there are several interesting questions: What types of biosensing transducers can be used in wireless bioelectronic sensors? What types of wireless systems can be integrated with biosensing transducers to construct wireless bioelectronic sensors? How are the electrical sensing signals generated and transmitted? This review will highlight the early attempts to address these questions in the development of wireless biological electronic sensors.

Integration of Plant Defense Traits with Biological Control of Arthropod Pests: Challenges and Opportunities.

Science.gov (United States)

Peterson, Julie A; Ode, Paul J; Oliveira-Hofman, Camila; Harwood, James D

2016-01-01

Crop plants exhibit a wide diversity of defensive traits and strategies to protect themselves from damage by herbivorous pests and disease. These defensive traits may be naturally occurring or artificially selected through crop breeding, including introduction via genetic engineering. While these traits can have obvious and direct impacts on herbivorous pests, many have profound effects on higher trophic levels, including the natural enemies of herbivores. Multi-trophic effects of host plant resistance have the potential to influence, both positively and negatively, biological control. Plant defense traits can influence both the numerical and functional responses of natural enemies; these interactions can be semiochemically, plant toxin-, plant nutrient-, and/or physically mediated. Case studies involving predators, parasitoids, and pathogens of crop pests will be presented and discussed. These diverse groups of natural enemies may respond differently to crop plant traits based on their own unique biology and the ecological niches they fill. Genetically modified crop plants that have been engineered to express transgenic products affecting herbivorous pests are an additional consideration. For the most part, transgenic plant incorporated protectant (PIP) traits are compatible with biological control due to their selective toxicity to targeted pests and relatively low non-target impacts, although transgenic crops may have indirect effects on higher trophic levels and arthropod communities mediated by lower host or prey number and/or quality. Host plant resistance and biological control are two of the key pillars of integrated pest management; their potential interactions, whether they are synergistic, complementary, or disruptive, are key in understanding and achieving sustainable and effective pest management.

Integration of plant defense traits with biological control of arthropod pests: challenges and opportunities

Directory of Open Access Journals (Sweden)

Julie A Peterson

2016-11-01

Full Text Available Crop plants exhibit a wide diversity of defensive traits and strategies to protect themselves from damage by herbivorous pests and disease. These defensive traits may be naturally occurring or artificially selected through crop breeding, including introduction via genetic engineering. While these traits can have obvious and direct impacts on herbivorous pests, many have profound effects on higher trophic levels, including the natural enemies of herbivores. Multi-trophic effects of host plant resistance have the potential to influence, both positively and negatively, biological control. Plant defense traits can influence both the numerical and functional responses of natural enemies; these interactions can be semiochemically-, plant toxin-, plant nutrient-, and/or physically-mediated. Case studies involving predators, parasitoids, and pathogens of crop pests will be presented and discussed. These diverse groups of natural enemies may respond differently to crop plant traits based on their own unique biology and the ecological niches they fill. Genetically modified crop plants that have been engineered to express transgenic products affecting herbivorous pests are an additional consideration. For the most part, transgenic plant incorporated protectant (PIP traits are compatible with biological control due to their selective toxicity to targeted pests and relatively low non-target impacts, although transgenic crops may have indirect effects on higher trophic levels and arthropod communities mediated by lower host or prey number and/or quality. Host plant resistance and biological control are two of the key pillars of integrated pest management; their potential interactions, whether they are synergistic, complementary, or disruptive, are key in understanding and achieving sustainable and effective pest management.

Structural Molecular Biology 2017 | SSRL

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Highlights Training Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating experimental driver for structural biology research, serving the needs of a large number of academic and — Our Mission The SSRL Structural Molecular Biology program operates as an integrated resource and has

Integrative oncology: an overview.

Science.gov (United States)

Deng, Gary; Cassileth, Barrie

2014-01-01

Integrative oncology, the diagnosis-specific field of integrative medicine, addresses symptom control with nonpharmacologic therapies. Known commonly as "complementary therapies" these are evidence-based adjuncts to mainstream care that effectively control physical and emotional symptoms, enhance physical and emotional strength, and provide patients with skills enabling them to help themselves throughout and following mainstream cancer treatment. Integrative or complementary therapies are rational and noninvasive. They have been subjected to study to determine their value, to document the problems they ameliorate, and to define the circumstances under which such therapies are beneficial. Conversely, "alternative" therapies typically are promoted literally as such; as actual antitumor treatments. They lack biologic plausibility and scientific evidence of safety and efficacy. Many are outright fraudulent. Conflating these two very different categories by use of the convenient acronym "CAM," for "complementary and alternative therapies," confuses the issue and does a substantial disservice to patients and medical professionals. Complementary and integrative modalities have demonstrated safety value and benefits. If the same were true for "alternatives," they would not be "alternatives." Rather, they would become part of mainstream cancer care. This manuscript explores the medical and sociocultural context of interest in integrative oncology as well as in "alternative" therapies, reviews commonly-asked patient questions, summarizes research results in both categories, and offers recommendations to help guide patients and family members through what is often a difficult maze. Combining complementary therapies with mainstream oncology care to address patients' physical, psychologic and spiritual needs constitutes the practice of integrative oncology. By recommending nonpharmacologic modalities that reduce symptom burden and improve quality of life, physicians also enable

Meteorological Integration for the Biological Warning and Incident Characterization (BWIC) System: General Guidance for BWIC Cities

Energy Technology Data Exchange (ETDEWEB)

Shaw, William J.; Wang, Weiguo; Rutz, Frederick C.; Chapman, Elaine G.; Rishel, Jeremy P.; Xie, YuLong; Seiple, Timothy E.; Allwine, K Jerry

2007-02-16

The U.S. Department of Homeland Security (DHS) is responsible for developing systems to detect the release of aerosolized bioagents in urban environments. The system that accomplishes this, known as BioWatch, is a robust first-generation monitoring system. In conjunction with the BioWatch detection network, DHS has also developed a software tool for cities to use to assist in their response when a bioagent is detected. This tool, the Biological Warning and Incident Characterization (BWIC) System, will eventually be deployed to all BioWatch cities to aid in the interpretation of the public health significance of indicators from the BioWatch networks. BWIC consists of a set of integrated modules, including meteorological models, that estimate the effect of a biological agent on a city’s population once it has been detected. For the meteorological models in BWIC to successfully calculate the distribution of biological material, they must have as input accurate meteorological data, and wind fields in particular. The purpose of this document is to provide guidance for cities to use in identifying sources of good-quality local meteorological data that BWIC needs to function properly. This process of finding sources of local meteorological data, evaluating the data quality and gaps in coverage, and getting the data into BWIC, referred to as meteorological integration, is described. The good news for many cities is that meteorological measurement networks are becoming increasingly common. Most of these networks allow their data to be distributed in real time via the internet. Thus, cities will often only need to evaluate the quality of available measurements and perhaps add a modest number of stations where coverage is poor.

Pegasys: software for executing and integrating analyses of biological sequences

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Lett Drew

2004-04-01

Full Text Available Abstract Background We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. Results The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. Conclusions The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.

Evidence-based educational pathway for the integration of first aid training in school curricula.

Science.gov (United States)

De Buck, Emmy; Van Remoortel, Hans; Dieltjens, Tessa; Verstraeten, Hans; Clarysse, Matthieu; Moens, Olaf; Vandekerckhove, Philippe

2015-09-01

"Calling for help, performing first aid and providing Cardiopulmonary Resuscitation (CPR)" is part of the educational goals in secondary schools in Belgium (Flanders). However, for teachers it is not always clear at what age children can be taught which aspects of first aid. In addition, it is not clear what constitutes "performing first aid" and we strongly advocate that the first aid curriculum is broader than CPR training alone. To develop an evidence-based educational pathway to enable the integration of first aid into the school curriculum by defining the goals to be achieved for knowledge, skills and attitudes, for different age groups. Studies were identified through electronic databases research (The Cochrane Library, MEDLINE, Embase). We included studies on first aid education for children and adolescents up to 18 years old. A multidisciplinary expert panel formulated their practice experience and expert opinion and discussed the available evidence. We identified 5822 references and finally retained 30 studies (13 experimental and 17 observational studies), including studies concerning emergency call (7 studies), cardiopulmonary resuscitation (18 studies), AED (Automated External Defibrillator) use (6 studies), recovery position (5 studies), choking (2 studies), injuries (5 studies), and poisoning (2 studies). Recommendations (educational goals) were derived after carefully discussing the currently available evidence in the literature and balancing the skills and attitudes of children of different ages. An evidence-based educational pathway with educational goals concerning learning first aid for each age group was developed. This educational pathway can be used for the integration of first aid training in school curricula. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

The use of aquatic macrophytes in monitoring and in assessment of biological integrity

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Stewart, P.M.; Scribailo, R.W.; Simon, T.P.; Gerhardt, A.

1999-01-01

Aquatic plant species, populations, and communities should be used as indicators of the aquatic environment, allowing detection of ecosystem response to different stressors. Plant tissues bioaccumulate and concentrate toxin levels higher than what is present in the sediments; and this appears to be related to organic matter content, acidification, and buffering capacity. The majority of toxicity studies, most of these with heavy metals, have been done with several Lemna species and Vallisneria americana. Organic chemicals reviewed include pesticides and herbicides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and other industrial contaminants. The use of aquatic plant communities as bioindicators of environmental quality was evaluated for specific characteristics and indices that may assess biological integrity. Indices such as the floristic quality index (FQI) and coefficient of conservatism (C) are pioneering efforts to describe the quality of natural areas and protect native biodiversity. Our case study in the Grand Calumet Lagoons found that 'least-impacted' sites had the greatest aquatic plant species richness, highest FQI and C values, and highest relative abundance. Lastly, we introduce the concepts necessary for the development of a plant index of biotic integrity. Development of reference conditions is essential to understanding aquatic plant community structure, function, individual health, condition, and abundance. Information on guild development and tolerance definition are also integral to the development of a multi-metric index.

Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

Science.gov (United States)

Vallat, Brinda; Webb, Benjamin; Westbrook, John D; Sali, Andrej; Berman, Helen M

2018-04-09

Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain "hybrid" or "integrative" structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms. Here we present the development of data standards and a prototype system for archiving I/H models. The data standards provide the definitions required for representing I/H models that span multiple spatiotemporal scales and conformational states, as well as spatial restraints derived from different experimental techniques. Based on these data definitions, we have built a prototype system called PDB-Dev, which provides the infrastructure necessary to archive I/H structural models. PDB-Dev is now accepting structures and is open to the community for new submissions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder

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Atsushi Takata

2018-01-01

Full Text Available Recent studies have established important roles of de novo mutations (DNMs in autism spectrum disorders (ASDs. Here, we analyze DNMs in 262 ASD probands of Japanese origin and confirm the “de novo paradigm” of ASDs across ethnicities. Based on this consistency, we combine the lists of damaging DNMs in our and published ASD cohorts (total number of trios, 4,244 and perform integrative bioinformatics analyses. Besides replicating the findings of previous studies, our analyses highlight ATP-binding genes and fetal cerebellar/striatal circuits. Analysis of individual genes identified 61 genes enriched for damaging DNMs, including ten genes for which our dataset now contributes to statistical significance. Screening of compounds altering the expression of genes hit by damaging DNMs reveals a global downregulating effect of valproic acid, a known risk factor for ASDs, whereas cardiac glycosides upregulate these genes. Collectively, our integrative approach provides deeper biological and potential medical insights into ASDs.

Why we cannot conclude that sexual orientation is primarily a biological phenomenon.

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Byne, W

1997-01-01

While all mental phenomena must have an ultimate biological substrate, the precise contribution of biological factors to the development of sexual orientation remains to be elucidated. Does biology merely provide the slate of neural circuitry upon which sexual orientation is inscribed by experience? Do biological factors directly wire the brain so that it will support a particular orientation? Or do biological factors influence sexual orientation only indirectly, perhaps by influencing personality variables that in turn influence how one interacts with and shapes the environment as it contributes to the social relationships and experiences that shape sexual orientation as it emerges developmentally? Recent neurostructural and genetic linkage evidence pertaining to sexual orientation must be viewed tentatively until it has been adequately corroborated and integrated with psychological and cultural models. Moreover, even a reliable and robust correlation between a biological marker and sexual orientation would be equally compatible with the second and third possibilities delineated above. Yet if the third possibility more closely approximates reality, the search for predisposing biological factors will result in incomplete and misleading findings until their interactions with environmental factors are taken into account and controlled for in adequate longitudinal studies.

Integrating Radiology and Anatomy Teaching in Medical Education in the UK--The Evidence, Current Trends, and Future Scope.

Science.gov (United States)

Heptonstall, N B; Ali, T; Mankad, K

2016-04-01

This review article presents the current evidence of the importance of integrating radiology and anatomy in medical education in the UK, a recommendation by a number of key anatomy, education, and radiology organizations. Current evidence highlights that on average only 5% of total teaching time in medical education is dedicated to radiology. Often, radiology teaching does not adequately fulfill students' learning needs and potentially leaves them underprepared for medical practice. Benefits of integrating radiology and anatomy include improved clinical application of anatomy, an increase in student's interest in anatomy, and ultimately improved radiological interpretation. Various modalities exist for the integration of radiology and anatomy, facilitated by the vast portability of radiological images. It appears that combining radiological resources with traditional anatomy teaching methodology in a blended approach is most beneficial. Copyright © 2016 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

A Conceptual Framework for Integration of Evidence-Based Design with Lighting Simulation Tools

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Anahita Davoodi

2017-09-01

Full Text Available The use of lighting simulation tools has been growing over the past years which has improved lighting analysis. While computer simulations have proven to be a viable tool for analyzing lighting in physical environments, they have difficulty in assessing the effects of light on occupant’s perception. Evidence-based design (EBD is a design method that is gaining traction in building design due to its strength in providing means to assess the effects of built environments on humans. The aim of this study was to develop a conceptual framework for integrating EBD with lighting simulation tools. Based on a literature review, it was investigated how EBD and lighting simulation can be combined to provide a holistic lighting performance evaluation method. The results show that they can mutually benefit from each other. EBD makes it possible to evaluate and/or improve performance metrics by utilizing user feedback. On the other hand, performance metrics can be used for a better description of evidence, and to analyze the effects of lighting with more details. The results also show that EBD can be used to evaluate light simulations to better understand when and how they should be performed. A framework is presented for integration of lighting simulation and EBD.

Integrating population genetics and conservation biology in the era of genomics.

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Ouborg, N Joop

2010-02-23

As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled 'Integrating Population Genetics and Conservation Biology' was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.

Vertical Integration of Hospitals and Physicians: Economic Theory and Empirical Evidence on Spending and Quality.

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Post, Brady; Buchmueller, Tom; Ryan, Andrew M

2017-08-01

Hospital-physician vertical integration is on the rise. While increased efficiencies may be possible, emerging research raises concerns about anticompetitive behavior, spending increases, and uncertain effects on quality. In this review, we bring together several of the key theories of vertical integration that exist in the neoclassical and institutional economics literatures and apply these theories to the hospital-physician relationship. We also conduct a literature review of the effects of vertical integration on prices, spending, and quality in the growing body of evidence ( n = 15) to evaluate which of these frameworks have the strongest empirical support. We find some support for vertical foreclosure as a framework for explaining the observed results. We suggest a conceptual model and identify directions for future research. Based on our analysis, we conclude that vertical integration poses a threat to the affordability of health services and merits special attention from policymakers and antitrust authorities.

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

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de los Reyes Benildo G

2008-04-01

Full Text Available Abstract Background Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths and depths, while databases contain biological information based on established facts or published data. Integrating these complementary datasets helps infer a mutually consistent transcriptional regulatory network (TRN with strong similarity to the structure of the underlying genetic regulatory modules. Decomposing the TRN into a small set of recurring regulatory patterns, called network motifs (NM, facilitates the inference. Identifying NMs defined by specific transcription factors (TF establishes the framework structure of a TRN and allows the inference of TF-target gene relationship. This paper introduces a computational framework for utilizing data from multiple sources to infer TF-target gene relationships on the basis of NMs. The data include time course gene expression profiles, genome-wide location analysis data, binding sequence data, and gene ontology (GO information. Results The proposed computational framework was tested using gene expression data associated with cell cycle progression in yeast. Among 800 cell cycle related genes, 85 were identified as candidate TFs and classified into four previously defined NMs. The NMs for a subset of TFs are obtained from literature. Support vector machine (SVM classifiers were used to estimate NMs for the remaining TFs. The potential downstream target genes for the TFs were clustered into 34 biologically significant groups. The relationships between TFs and potential target gene clusters were examined by training recurrent neural networks whose topologies mimic the NMs to which the TFs are classified. The identified relationships between TFs and gene clusters were evaluated using the following biological validation and statistical analyses: (1 Gene set enrichment

Adjuvant Biological Therapies in Chronic Leg Ulcers

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Natalia Burgos-Alonso

2017-11-01

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

Anticipation: Beyond synthetic biology and cognitive robotics.

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Nasuto, Slawomir J; Hayashi, Yoshikatsu

2016-10-01

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

Modeling the integration of bacterial rRNA fragments into the human cancer genome.

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Sieber, Karsten B; Gajer, Pawel; Dunning Hotopp, Julie C

2016-03-21

Cancer is a disease driven by the accumulation of genomic alterations, including the integration of exogenous DNA into the human somatic genome. We previously identified in silico evidence of DNA fragments from a Pseudomonas-like bacteria integrating into the 5'-UTR of four proto-oncogenes in stomach cancer sequencing data. The functional and biological consequences of these bacterial DNA integrations remain unknown. Modeling of these integrations suggests that the previously identified sequences cover most of the sequence flanking the junction between the bacterial and human DNA. Further examination of these reads reveals that these integrations are rich in guanine nucleotides and the integrated bacterial DNA may have complex transcript secondary structures. The models presented here lay the foundation for future experiments to test if bacterial DNA integrations alter the transcription of the human genes.

Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

Science.gov (United States)

Roever, Stefan

2012-01-01

A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

Environmental hazards from natural hydrocarbons seepage: Integrated classification of risk from sediment chemistry, bioavailability and biomarkers responses in sentinel species

International Nuclear Information System (INIS)

Benedetti, Maura; Gorbi, Stefania; Fattorini, Daniele; D'Errico, Giuseppe; Piva, Francesco; Pacitti, Davide; Regoli, Francesco

2014-01-01

Potential effects of natural emissions of hydrocarbons in the marine environment have been poorly investigated. In this study, a multidisciplinary weight of evidence (WOE) study was carried out on a shallow seepage, integrating sediment chemistry with bioavailability and onset of subcellular responses (biomarkers) in caged eels and mussels. Results from different lines of evidence (LOEs) were elaborated within a quantitative WOE model which, based on logical flowcharts, provide synthetic indices of hazard for each LOE, before their integration in a quantitative risk assessment. Evaluations of different LOEs were not always in accordance and their overall elaboration summarized as Moderate the risk in the seepage area. This study provided first evidence of biological effects in organisms exposed to natural hydrocarbon emissions, confirming the limit of chemical characterization as stand-alone criteria for environmental quality assessment and the utility of multidisciplinary investigations to determine the good environmental status as required by Environmental Directives. -- Highlights: • Hazards from natural seepage were evaluated through a multidisciplinary WOE study. • Caged eels and mussels were chosen as bioindicator organisms. • Evaluations obtained from various LOEs were not always in accordance. • Biological effects of natural hydrocarbons release were demonstrated. • WOE approach could discriminate different levels of hazard in low impacted conditions. -- A multidisciplinary WOE study in a shallow coastal seepage summarized a Moderate level of risk based on integration of sediment chemistry with biological effects in caged organisms

World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia. Part 3

DEFF Research Database (Denmark)

Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas

2015-01-01

These updated guidelines are based on the first edition of the World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia published in the years 2005 and 2006. For this 2015 revision, all available publications pertaining to the biological...... treatment of schizophrenia were reviewed systematically to allow for an evidence-based update. These guidelines provide evidence-based practice recommendations which are clinically and scientifically relevant. They are intended to be used by all physicians diagnosing and treating patients with schizophrenia...

Evidence from dynamic integrated proctography to redefine anismus.

Science.gov (United States)

Roberts, J P; Womack, N R; Hallan, R I; Thorpe, A C; Williams, N S

1992-11-01

The role of anismus in the aetiology of defective rectal evacuation was investigated by dynamic integrated proctography in 20 controls and 71 constipated patients. Normal parameters were defined and compared between 21 constipated patients with poor evacuation during proctography ( 90 per cent of contrast evacuated; group 2). Nine patients in group 1 failed to evacuate. Radiological abnormalities of the rectum were recorded in all groups but obstructed evacuation was not observed. Anismus (defined as a recruitment of puborectalis electromyogram (EMG) activity of > 50 per cent) was significantly more common in group 1 than group 2 patients (14 of 21 versus 12 of 50, P 50 cmH2O compared with two in group 2 (P anismus and inability to raise intrarectal pressure, which may combine to cause defective evacuation. EMG recruitment alone is insufficient to diagnose anismus. Definition should be based on three criteria: demonstration of puborectalis EMG recruitment of > 50 per cent; evidence of an adequate level of intrarectal pressure (> 50 cmH2O) on straining; and presence of defective evacuation.

IntegromeDB: an integrated system and biological search engine.

Science.gov (United States)

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

2012-01-19

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

Evaluating the effect of integrated microfinance and health interventions: an updated review of the evidence.

Science.gov (United States)

Lorenzetti, Lara M J; Leatherman, Sheila; Flax, Valerie L

2017-06-01

Solutions delivered within firm sectoral boundaries are inadequate in achieving income security and better health for poor populations. Integrated microfinance and health interventions leverage networks of women to promote financial inclusion, build livelihoods, and safeguard against high cost illnesses. Our understanding of the effect of integrated interventions has been limited by variability in intervention, outcome, design, and methodological rigour. This systematic review synthesises the literature through 2015 to understand the effect of integrated microfinance and health programs. We searched PubMed, Scopus, Embase, EconLit, and Global Health databases and sourced bibliographies, identifying 964 articles exclusive of duplicates. Title, abstract, and full text review yielded 35 articles. Articles evaluated the effect of intentionally integrated microfinance and health programs on client outcomes. We rated the quality of evidence for each article. Most interventions combined microfinance with health education, which demonstrated positive effects on health knowledge and behaviours, though not health status. Among programs that integrated microfinance with other health components ( i.e. health micro-insurance, linkages to health providers, and access to health products), results were generally positive but mixed due to the smaller number and quality of studies. Interventions combining multiple health components in a given study demonstrated positive effects, though it was unclear which component was driving the effect. Most articles (57%) were moderate in quality. Integrated microfinance and health education programs were effective, though longer intervention periods are necessary to measure more complex pathways to health status. The effect of microfinance combined with other health components was less clear. Stronger randomized research designs with multiple study arms are required to improve evidence and disentangle the effects of multiple component

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

Directory of Open Access Journals (Sweden)

Ghisalberti Giorgio

2010-12-01

different biological databases and integrated in the GFINDer data warehouse. By doing so, we identified in these data a variety of different types of errors and inconsistencies; this enables us to ensure good quality of the data in the GFINDer data warehouse. We reported all identified data errors and inconsistencies to the curators of the original databases from where the data were retrieved, who mainly corrected them in subsequent updating of the original database. This contributed to improve the quality of the data available, in the original databases, to the whole scientific community.

A monograph assignment as an integrative application of evidence-based medicine and pharmacoeconomic principles.

Science.gov (United States)

Law, Anandi V; Jackevicius, Cynthia A; Bounthavong, Mark

2011-02-10

To describe the development and assessment of monographs as an assignment to incorporate evidence-based medicine (EBM) and pharmacoeconomic principles into a third-year pharmacoeconomic course. Eight newly FDA-approved drugs were assigned to 16 teams of students, where each drug was assigned to 2 teams. Teams had to research their drug, write a professional monograph, deliver an oral presentation, and answer questions posed by faculty judges. One team was asked to present evidence for inclusion of the drug into a formulary, while another team presented evidence against inclusion. The teams' average score on the written report was 99.1%; on the oral presentation, 92.5%, and on the online quiz given at the end of the presentations, 77%. Monographs are a successful method of incorporating and integrating learning across different concepts, as well as increasing relevance of pharmacoeconomics in the PharmD curriculum.

Integrated, multi-scale, spatial-temporal cell biology--A next step in the post genomic era.

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Horwitz, Rick

2016-03-01

New microscopic approaches, high-throughput imaging, and gene editing promise major new insights into cellular behaviors. When coupled with genomic and other 'omic information and "mined" for correlations and associations, a new breed of powerful and useful cellular models should emerge. These top down, coarse-grained, and statistical models, in turn, can be used to form hypotheses merging with fine-grained, bottom up mechanistic studies and models that are the back bone of cell biology. The goal of the Allen Institute for Cell Science is to develop the top down approach by developing a high throughput microscopy pipeline that is integrated with modeling, using gene edited hiPS cell lines in various physiological and pathological contexts. The output of these experiments and models will be an "animated" cell, capable of integrating and analyzing image data generated from experiments and models. Copyright © 2015 Elsevier Inc. All rights reserved.

Fostering synergy between cell biology and systems biology.

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

2015-08-01

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

Systems biology integration of proteomic data in rodent models of depression reveals involvement of the immune response and glutamatergic signaling.

Science.gov (United States)

Carboni, Lucia; Nguyen, Thanh-Phuong; Caberlotto, Laura

2016-12-01

The pathophysiological basis of major depression is incompletely understood. Recently, numerous proteomic studies have been performed in rodent models of depression to investigate the molecular underpinnings of depressive-like behaviours with an unbiased approach. The objective of the study is to integrate the results of these proteomic studies in depression models to shed light on the most relevant molecular pathways involved in the disease. Network analysis is performed integrating preexisting proteomic data from rodent models of depression. The IntAct mouse and the HRPD are used as reference protein-protein interaction databases. The functionality analyses of the networks are then performed by testing overrepresented GO biological process terms and pathways. Functional enrichment analyses of the networks revealed an association with molecular processes related to depression in humans, such as those involved in the immune response. Pathways impacted by clinically effective antidepressants are modulated, including glutamatergic signaling and neurotrophic responses. Moreover, dysregulations of proteins regulating energy metabolism and circadian rhythms are implicated. The comparison with protein pathways modulated in depressive patients revealed significant overlapping. This systems biology study supports the notion that animal models can contribute to the research into the biology and therapeutics of depression. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fuzzy method of recognition of high molecular substances in evidence-based biology

Science.gov (United States)

Olevskyi, V. I.; Smetanin, V. T.; Olevska, Yu. B.

2017-10-01

Nowadays modern requirements to achieving reliable results along with high quality of researches put mathematical analysis methods of results at the forefront. Because of this, evidence-based methods of processing experimental data have become increasingly popular in the biological sciences and medicine. Their basis is meta-analysis, a method of quantitative generalization of a large number of randomized trails contributing to a same special problem, which are often contradictory and performed by different authors. It allows identifying the most important trends and quantitative indicators of the data, verification of advanced hypotheses and discovering new effects in the population genotype. The existing methods of recognizing high molecular substances by gel electrophoresis of proteins under denaturing conditions are based on approximate methods for comparing the contrast of electrophoregrams with a standard solution of known substances. We propose a fuzzy method for modeling experimental data to increase the accuracy and validity of the findings of the detection of new proteins.

Quantum mechanics formalism for biological evolution

International Nuclear Information System (INIS)

Bianconi, Ginestra; Rahmede, Christoph

2012-01-01

Highlights: ► Biological evolution is an off-equilibrium process described by path integrals over phylogenies. ► The phylogenies are sums of linear lineages for asexual populations. ► For sexual populations, each lineage is a tree and the path integral is given by a sum over these trees. ► Quantum statistics describe the stationary state of biological populations in simple cases. - Abstract: We study the evolution of sexual and asexual populations in fitness landscapes compatible with epistatic interactions. We find intriguing relations between the mathematics of biological evolution and quantum mechanics formalism. We give the general structure of the evolution of sexual and asexual populations which is in general an off-equilibrium process that can be expressed by path integrals over phylogenies. These phylogenies are the sum of linear lineages for asexual populations. For sexual populations, instead, each lineage is a tree of branching ratio two and the path integral describing the evolving population is given by a sum over these trees. Finally we show that the Bose–Einstein and the Fermi–Dirac distributions describe the stationary state of biological populations in simple cases.

Enhanced degradation of phenolic compounds in coal gasification wastewater by a novel integration of micro-electrolysis with biological reactor (MEBR) under the micro-oxygen condition.

Science.gov (United States)

Ma, Weiwei; Han, Yuxing; Xu, Chunyan; Han, Hongjun; Ma, Wencheng; Zhu, Hao; Li, Kun; Wang, Dexin

2018-03-01

The aim of this work was to study an integration of micro-electrolysis with biological reactor (MEBR) for strengthening removal of phenolic compounds in coal gasification wastewater (CGW). The results indicated MEBR achieved high efficiencies in removal of COD and phenolic compounds as well as improvement of biodegradability of CGW under the micro-oxygen condition. The integrated MEBR process was more favorable to improvement of the structural stability of activated sludge and biodiversity of specific functional microbial communities. Especially, Shewanella and Pseudomonas were enriched to accelerate the extracellular electron transfer, finally facilitating the degradation of phenolic compounds. Moreover, MEBR process effectively relieved passivation of Fe-C filler surface and prolonged lifespan of Fe-C filler. Accordingly, the synergetic effect between iron-carbon micro-electrolysis (ICME) and biological action played a significant role in performance of the integrated process. Therefore, the integrated MEBR was a promising practical process for enhancing CGW treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Collinear facilitation and contour integration in autism: evidence for atypical visual integration.

Science.gov (United States)

Jachim, Stephen; Warren, Paul A; McLoughlin, Niall; Gowen, Emma

2015-01-01

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social interaction, atypical communication and a restricted repertoire of interests and activities. Altered sensory and perceptual experiences are also common, and a notable perceptual difference between individuals with ASD and controls is their superior performance in visual tasks where it may be beneficial to ignore global context. This superiority may be the result of atypical integrative processing. To explore this claim we investigated visual integration in adults with ASD (diagnosed with Asperger's Syndrome) using two psychophysical tasks thought to rely on integrative processing-collinear facilitation and contour integration. We measured collinear facilitation at different flanker orientation offsets and contour integration for both open and closed contours. Our results indicate that compared to matched controls, ASD participants show (i) reduced collinear facilitation, despite equivalent performance without flankers; and (ii) less benefit from closed contours in contour integration. These results indicate weaker visuospatial integration in adults with ASD and suggest that further studies using these types of paradigms would provide knowledge on how contextual processing is altered in ASD.

Collinear facilitation and contour integration in autism: evidence for atypical visual integration

Directory of Open Access Journals (Sweden)

Stephen eJachim

2015-03-01

Full Text Available Autism spectrum disorder (ASD is a neurodevelopmental disorder characterized by impaired social interaction, atypical communication and a restricted repertoire of interests and activities. Altered sensory and perceptual experiences are also common, and a notable perceptual difference between individuals with ASD and controls is their superior performance in visual tasks where it may be beneficial to ignore global context. This superiority may be the result of atypical integrative processing. To explore this claim we investigated visual integration in adults with ASD (diagnosed with Asperger’s Syndrome using two psychophysical tasks thought to rely on integrative processing - collinear facilitation and contour integration. We measured collinear facilitation at different flanker orientation offsets and contour integration for both open and closed contours. Our results indicate that compared to matched controls, ASD participants show (i reduced collinear facilitation, despite equivalent performance without flankers and (ii less benefit from closed contours in contour integration. These results indicate weaker visuospatial integration in adults with ASD and suggest that further studies using these types of paradigms would provide knowledge on how contextual processing is altered in ASD.

Development of a flexible microfluidic system integrating magnetic micro-actuators for trapping biological species

International Nuclear Information System (INIS)

Fulcrand, R; Jugieu, D; Escriba, C; Bancaud, A; Bourrier, D; Boukabache, A; Gué, A M

2009-01-01

A flexible microfluidic system embedding microelectromagnets has been designed, modeled and fabricated by using a photosensitive resin as structural material. The fabrication process involves the integration of micro-coils in a multilayer SU-8 microfluidic system by combining standard electroplating and dry films lamination. This technique offers numerous advantages in terms of integration, biocompatibility and chemical resistance. Various designs of micro-coils, including spiral, square or serpentine wires, have been simulated and experimentally tested. It has been established that thermal dissipation in micro-coils depends strongly on the number of turns and current density but remains compatible with biological applications. Real-time experimentations show that these micro-actuators are efficient in trapping magnetic micro-beads without any external field source or a permanent magnet and highlight that the size of microfluidic channels has been adequately designed for optimal trapping. Moreover, we trap magnetic beads in less than 2 s and release them instantaneously into the micro-channel. The actuation solely relies on electric fields, which are easier to control than standard magneto-fluidic modules

Development of a flexible microfluidic system integrating magnetic micro-actuators for trapping biological species

Science.gov (United States)

Fulcrand, R.; Jugieu, D.; Escriba, C.; Bancaud, A.; Bourrier, D.; Boukabache, A.; Gué, A. M.

2009-10-01

A flexible microfluidic system embedding microelectromagnets has been designed, modeled and fabricated by using a photosensitive resin as structural material. The fabrication process involves the integration of micro-coils in a multilayer SU-8 microfluidic system by combining standard electroplating and dry films lamination. This technique offers numerous advantages in terms of integration, biocompatibility and chemical resistance. Various designs of micro-coils, including spiral, square or serpentine wires, have been simulated and experimentally tested. It has been established that thermal dissipation in micro-coils depends strongly on the number of turns and current density but remains compatible with biological applications. Real-time experimentations show that these micro-actuators are efficient in trapping magnetic micro-beads without any external field source or a permanent magnet and highlight that the size of microfluidic channels has been adequately designed for optimal trapping. Moreover, we trap magnetic beads in less than 2 s and release them instantaneously into the micro-channel. The actuation solely relies on electric fields, which are easier to control than standard magneto-fluidic modules.

The SCIDOTS Project: Evidence of benefits of an integrated tobacco cessation intervention in tuberculosis care on treatment outcomes

Directory of Open Access Journals (Sweden)

Syed Sulaiman Syed Azhar

2011-09-01

Full Text Available Abstract Background There is substantial evidence to support the association between tuberculosis (TB and tobacco smoking and that the smoking-related immunological abnormalities in TB are reversible within six weeks of cessation. Therefore, connecting TB and tobacco cessation interventions may produce significant benefits and positively impact TB treatment outcomes. However, no study has extensively documented the evidence of benefits of such integration. SCIDOTS Project is a study from the context of a developing nation aimed to determine this. Methods An integrated TB-tobacco intervention was provided by trained TB directly observed therapy short-course (DOTS providers at five chest clinics in Malaysia. The study was a prospective non-randomized controlled intervention using quasi-experimental design. Using Transtheoretical Model approach, 120 eligible participants who were current smokers at the time of TB diagnosis were assigned to either of two treatment groups: conventional TB DOTS plus smoking cessation intervention (integrated intervention or SCIDOTS group or conventional TB DOTS alone (comparison or DOTS group. At baseline, newly diagnosed TB patients considering quitting smoking within the next 30 days were placed in the integrated intervention group, while those who were contemplating quitting were assigned to the comparison group. Eleven sessions of individualized cognitive behavioral therapy with or without nicotine replacement therapy were provided to each participant in the integrated intervention group. The impacts of the novel approach on biochemically validated smoking cessation and TB treatment outcomes were measured periodically as appropriate. Results A linear effect on both 7-day point prevalence abstinence and continuous abstinence was observed over time in the intervention group. At the end of 6 months, patients who received the integrated intervention had significantly higher rate of success in quitting smoking when

How experimental biology and ecology can support evidence-based decision-making in conservation: avoiding pitfalls and enabling application.

Science.gov (United States)

Cooke, Steven J; Birnie-Gauvin, Kim; Lennox, Robert J; Taylor, Jessica J; Rytwinski, Trina; Rummer, Jodie L; Franklin, Craig E; Bennett, Joseph R; Haddaway, Neal R

2017-01-01

Policy development and management decisions should be based upon the best available evidence. In recent years, approaches to evidence synthesis, originating in the medical realm (such as systematic reviews), have been applied to conservation to promote evidence-based conservation and environmental management. Systematic reviews involve a critical appraisal of evidence, but studies that lack the necessary rigour (e.g. experimental, technical and analytical aspects) to justify their conclusions are typically excluded from systematic reviews or down-weighted in terms of their influence. One of the strengths of conservation physiology is the reliance on experimental approaches that help to more clearly establish cause-and-effect relationships. Indeed, experimental biology and ecology have much to offer in terms of building the evidence base that is needed to inform policy and management options related to pressing issues such as enacting endangered species recovery plans or evaluating the effectiveness of conservation interventions. Here, we identify a number of pitfalls that can prevent experimental findings from being relevant to conservation or would lead to their exclusion or down-weighting during critical appraisal in a systematic review. We conclude that conservation physiology is well positioned to support evidence-based conservation, provided that experimental designs are robust and that conservation physiologists understand the nuances associated with informing decision-making processes so that they can be more relevant.

Extraction of DNA from Forensic Biological Samples for Genotyping.

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Stray, J E; Liu, J Y; Brevnov, M G; Shewale, J G

2010-07-01

Biological forensic samples constitute evidence with probative organic matter. Evidence believed to contain DNA is typically processed for extraction and purification of its nucleic acid content. Forensic DNA samples are composed of two things, a tissue and the substrate it resides on. Compositionally, a sample may contain almost anything and for each, the type, integrity, and content of both tissue and substrate will vary, as will the contaminant levels. This fact makes the success of extraction one of the most unpredictable steps in genotypic analysis. The development of robust genotyping systems and analysis platforms for short tandem repeat (STR) and mitochondrial DNA sequencing and the acceptance of results generated by these methods in the court system, resulted in a high demand for DNA testing. The increasing variety of sample submissions created a need to isolate DNA from forensic samples that may be compromised or contain low levels of biological material. In the past decade, several robust chemistries and isolation methods have been developed to safely and reliably recover DNA from a wide array of sample types in high yield and free of PCR inhibitors. In addition, high-throughput automated workflows have been developed to meet the demand for processing increasing numbers of samples. This review summarizes a number of the most widely adopted methods and the best practices for DNA isolation from forensic biological samples, including manual, semiautomated, and fully automated platforms. Copyright © 2010 Central Police University.

Biological preconcentrator

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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.

Integrative Chemical-Biological Read-Across Approach for Chemical Hazard Classification

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Low, Yen; Sedykh, Alexander; Fourches, Denis; Golbraikh, Alexander; Whelan, Maurice; Rusyn, Ivan; Tropsha, Alexander

2013-01-01

Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays (”biological” similarity). The Chemical-Biological Read-Across (CBRA) approach infers each compound's toxicity from those of both chemical and biological analogs whose similarities are determined by the Tanimoto coefficient. Classification accuracy of CBRA was compared to that of classical RA and other methods using chemical descriptors alone, or in combination with biological data. Different types of adverse effects (hepatotoxicity, hepatocarcinogenicity, mutagenicity, and acute lethality) were classified using several biological data types (gene expression profiling and cytotoxicity screening). CBRA-based hazard classification exhibited consistently high external classification accuracy and applicability to diverse chemicals. Transparency of the CBRA approach is aided by the use of radial plots that show the relative contribution of analogous chemical and biological neighbors. Identification of both chemical and biological features that give rise to the high accuracy of CBRA-based toxicity prediction facilitates mechanistic interpretation of the models. PMID:23848138

In search of integrated specificity: comment on Denson, Spanovic, and Miller (2009).

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Miller, Gregory E

2009-11-01

Psychologists have long been interested in the integrated specificity hypothesis, which maintains that stressors elicit fairly distinct behavioral, emotional, and biological responses that are molded by selective pressures to meet specific demands from the environment. This issue of Psychological Bulletin features a meta-analytic review of the evidence for this proposition by T. F. Denson, M. Spanovic, and N. Miller. Their review concluded that the meta-analytic findings support the "core concept behind the integrated specificity model" (p. 845) and reveal that "within the context of a stressful event, organisms produce an integrated and coordinated response at multiple levels (i.e., cognitive, emotional, physiological)" (p. 845). I argue that conclusions such as this are unwarranted, given the data. Aside from some effects for cortisol, little evidence of specificity was presented, and most of the significant findings reported would be expected by chance alone. I also contend that Denson et al. failed to consider some important sources of evidence bearing on the specificity hypothesis, particularly how appraisals and emotions couple with autonomic nervous system endpoints and functional indices of immune response. If selective pressures did give rise to an integrated stress response, such pathways almost certainly would have been involved. By omitting such outcomes from the meta-analysis, Denson et al. overlooked what are probably the most definitive tests of the specificity hypothesis. As a result, the field is back where it started: with a lot of affection for the concept of integrated specificity but little in the way of definitive evidence to refute or accept it.

International lessons in new methods for grading and integrating cost effectiveness evidence into clinical practice guidelines.

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Antioch, Kathryn M; Drummond, Michael F; Niessen, Louis W; Vondeling, Hindrik

2017-01-01

Economic evidence is influential in health technology assessment world-wide. Clinical Practice Guidelines (CPG) can enable economists to include economic information on health care provision. Application of economic evidence in CPGs, and its integration into clinical practice and national decision making is hampered by objections from professions, paucity of economic evidence or lack of policy commitment. The use of state-of-art economic methodologies will improve this. Economic evidence can be graded by 'checklists' to establish the best evidence for decision making given methodological rigor. New economic evaluation checklists, Multi-Criteria Decision Analyses (MCDA) and other decision criteria enable health economists to impact on decision making world-wide. We analyse the methodologies for integrating economic evidence into CPG agencies globally, including the Agency of Health Research and Quality (AHRQ) in the USA, National Health and Medical Research Council (NHMRC) and Australian political reforms. The Guidelines and Economists Network International (GENI) Board members from Australia, UK, Canada and Denmark presented the findings at the conference of the International Health Economists Association (IHEA) and we report conclusions and developments since. The Consolidated Guidelines for the Reporting of Economic Evaluations (CHEERS) 24 item check list can be used by AHRQ, NHMRC, other CPG and health organisations, in conjunction with the Drummond ten-point check list and a questionnaire that scores that checklist for grading studies, when assessing economic evidence. Cost-effectiveness Analysis (CEA) thresholds, opportunity cost and willingness-to-pay (WTP) are crucial issues for decision rules in CEA generally, including end-of-life therapies. Limitations of inter-rater reliability in checklists can be addressed by including more than one assessor to reach a consensus, especially when impacting on treatment decisions. We identify priority areas to generate

Add-On Complementary Medicine in Cancer Care: Evidence in Literature and Experiences of Integration.

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Rossi, Elio; Di Stefano, Mariella; Firenzuoli, Fabio; Monechi, Maria Valeria; Baccetti, Sonia

2017-01-24

Background : According to the literature an increasing number of cancer patients demand for complementary therapies during their disease. Research has demonstrated that some of these therapies are effective and safe as adjunctive treatments in specific symptoms of these patients. Methods : The aims of the paper are to review the main and recent papers of international literature on the effectiveness of complementary medicine (CM) therapies on side effects of anti-cancer protocols and improvement in the quality of life of oncological patients, and to describe the integration of evidence-based acupuncture, herbal medicine and homeopathy treatments in Public Cancer Network of the region of Tuscany. Results : After the review of literature and the approval of a Regional Resolution, some CM will be introduced in Cancer Departments in Tuscany to additionally treat cancer-related symptoms and side effects of conventional cancer therapy: acupuncture for nausea and post-chemotherapy and post-surgery vomiting, pain, hot flashes of iatrogenic menopause, xerostomia; homeopathy for hot flashes of iatrogenic menopause and the side effects of radiotherapy; herbal medicine for cancer-related fatigue, nausea and vomiting, pain, mucositis, anxiety, and depression. Conclusions : The integration of evidence-based complementary treatments allows for an effective response to the demand coming from cancer patients and combines safety and equity of access in public health systems.

Innovations in Undergraduate Chemical Biology Education.

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Van Dyke, Aaron R; Gatazka, Daniel H; Hanania, Mariah M

2018-01-19

Chemical biology derives intellectual vitality from its scientific interface: applying chemical strategies and perspectives to biological questions. There is a growing need for chemical biologists to synergistically integrate their research programs with their educational activities to become holistic teacher-scholars. This review examines how course-based undergraduate research experiences (CUREs) are an innovative method to achieve this integration. Because CUREs are course-based, the review first offers strategies for creating a student-centered learning environment, which can improve students' outcomes. Exemplars of CUREs in chemical biology are then presented and organized to illustrate the five defining characteristics of CUREs: significance, scientific practices, discovery, collaboration, and iteration. Finally, strategies to overcome common barriers in CUREs are considered as well as future innovations in chemical biology education.

Workshop on Biological Integrity of Coral Reefs August 21-22, 2012, Caribbean Coral Reef Institute, Isla Magueyes, La Parguera, Puerto Rico.

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This report summarizes an EPA-sponsored workshop on coral reef biological integrity held at the Caribbean Coral Reef Institute in La Parguera, Puerto Rico on August 21-22, 2012. The goals of this workshop were to:• Identify key qualitative and quantitative ecological characterist...

Human evolution. Evolution of early Homo: an integrated biological perspective.

Science.gov (United States)

Antón, Susan C; Potts, Richard; Aiello, Leslie C

2014-07-04

Integration of evidence over the past decade has revised understandings about the major adaptations underlying the origin and early evolution of the genus Homo. Many features associated with Homo sapiens, including our large linear bodies, elongated hind limbs, large energy-expensive brains, reduced sexual dimorphism, increased carnivory, and unique life history traits, were once thought to have evolved near the origin of the genus in response to heightened aridity and open habitats in Africa. However, recent analyses of fossil, archaeological, and environmental data indicate that such traits did not arise as a single package. Instead, some arose substantially earlier and some later than previously thought. From ~2.5 to 1.5 million years ago, three lineages of early Homo evolved in a context of habitat instability and fragmentation on seasonal, intergenerational, and evolutionary time scales. These contexts gave a selective advantage to traits, such as dietary flexibility and larger body size, that facilitated survival in shifting environments. Copyright © 2014, American Association for the Advancement of Science.

Uncharted waters: Bivalves of midway atoll and integrating mathematics into biology education

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McCully, Kristin M.

To protect and conserve the Earth's biodiversity and ecosystem services, it is important not only to understand and conserve species and ecosystems, but also to instill an understanding and appreciation for biodiversity and ecosystem services in the next generations of both scientists and citizens. Thus, this dissertation combines research into the ecology and identity of large bivalves at Midway Atoll in the Northwestern Hawaiian Islands (NWHI) with research on pedagogical strategies for integrating mathematics into undergraduate biology education. The NWHI is one of the few remaining large, mainly intact, predator-dominated coral reef ecosystems and one of the world's largest marine protected areas. Previous bivalve studies focused on the black-lipped pearl oyster, Pinctada margaritifera, which was heavily harvested in the late 1920s, has not recovered, and is now a candidate species for restoration. First, I combined remote sensing, geographic information systems, SCUBA, and mathematical modeling to quantify the abundance, spatial distributions, and filtration capacity of large epifaunal bivalves at Midway Atoll. These bivalves are most abundant on the forereef outside the atoll, but densities are much lower than reported on other reefs, and Midway's bivalves are unlikely to affect plankton abundance and productivity inside the lagoon. Second, I used molecular techniques and phylogenetic reconstructions to identify pearl oysters (Pinctada) from Midway Atoll as P. maculata , a species not previously reported in Hawaii. As a small morphologically cryptic species, P. maculata may be a native species that has not been collected previously, a native species that has been identified incorrectly as the morphologically similar P. radiata, or it may be a recent introduction or natural range extension from the western Pacific. Finally, I review science education literature integrating mathematics into undergraduate biology curricula, and then present and evaluate a

Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

2006-06-08

With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

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.

Smectite clays in Mars soil - Evidence for their presence and role in Viking biology experimental results

Science.gov (United States)

Banin, A.; Rishpon, J.

1979-01-01

Evidence for the presence of smectite clays in Martian soils is reviewed and results of experiments with certain active clays simulating the Viking biology experiments are reported. Analyses of Martian soil composition by means of X-ray fluorescence spectrometry and dust storm spectroscopy and Martian geological history strongly suggest the presence of a mixture of weathered ferro-silicate minerals, mainly nontronite and montmorillonite, accompanied by soluble sulphate salts, as major constituents. Samples of montmorillonite and nontronite incubated with (C-14)-formate or the radioactive nutrient medium solution used in the Viking Labeled Release experiment, were found to produce patterns of release of radioactive gas very similar to those observed in the Viking experiments, indicating the iron-catalyzed decomposition of formate as the reaction responsible for the Viking results. The experimental results of Hubbard (1979) simulating the results of the Viking Pyrolytic Release experiment using iron montmorillonites are pointed out, and it is concluded that many of the results of the Viking biology experiments can be explained in terms of the surface activity of smectite clays in catalysis and adsorption.

Models for integrated pest control and their biological implications.

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Tang, Sanyi; Cheke, Robert A

2008-09-01

Successful integrated pest management (IPM) control programmes depend on many factors which include host-parasitoid ratios, starting densities, timings of parasitoid releases, dosages and timings of insecticide applications and levels of host-feeding and parasitism. Mathematical models can help us to clarify and predict the effects of such factors on the stability of host-parasitoid systems, which we illustrate here by extending the classical continuous and discrete host-parasitoid models to include an IPM control programme. The results indicate that one of three control methods can maintain the host level below the economic threshold (ET) in relation to different ET levels, initial densities of host and parasitoid populations and host-parasitoid ratios. The effects of host intrinsic growth rate and parasitoid searching efficiency on host mean outbreak period can be calculated numerically from the models presented. The instantaneous pest killing rate of an insecticide application is also estimated from the models. The results imply that the modelling methods described can help in the design of appropriate control strategies and assist management decision-making. The results also indicate that a high initial density of parasitoids (such as in inundative releases) and high parasitoid inter-generational survival rates will lead to more frequent host outbreaks and, therefore, greater economic damage. The biological implications of this counter intuitive result are discussed.

Integrated self-powered microchip biosensor for endogenous biological cyanide.

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Deng, Liu; Chen, Chaogui; Zhou, Ming; Guo, Shaojun; Wang, Erkang; Dong, Shaojun

2010-05-15

In this work we developed a fully integrated biofuel cell on a microchip, which consisted of glucose dehydrogenase supported (carbon nanotubes/thionine/gold nanoparticles)(8) multilayer as the anode, and the (carbon nanotubes/polylysine/laccase)(15) multilayer as the cathode. The as-obtained biofuel cell produced open circuit potential 620 mV and power density 302 microW cm(-2), showing great potential as a small power resource of portable electronics. Most importantly, for the first time we demonstrated the feasibility of developing a self-powered biosensor based on the inhibitive effect on microchip enzyme biofuel cell. With cyanide employed as the model analyte, this method showed a linear range of 3.0 x 10(-7) to 5.0 x 10(-4) M and a detection limit with 1.0 x 10(-7) M under the optimal conditions. The detection limit was lower than the acceptable cyanide concentration in drinking water (1.9 x 10(-6) M) according to the World Health Organization (WHO). This self-powered sensor was successfully used to detect the cyanide concentration in a real sample, cassava, which is the main carbohydrate resource in South America and Africa. This presented biosensor combined with a resistor and a multimeter demonstrated the general applicability as a fast and simple detection method in the determination of endogenous biological cyanide.

Sparse canonical methods for biological data integration: application to a cross-platform study

Directory of Open Access Journals (Sweden)

Robert-Granié Christèle

2009-01-01

Full Text Available Abstract Background In the context of systems biology, few sparse approaches have been proposed so far to integrate several data sets. It is however an important and fundamental issue that will be widely encountered in post genomic studies, when simultaneously analyzing transcriptomics, proteomics and metabolomics data using different platforms, so as to understand the mutual interactions between the different data sets. In this high dimensional setting, variable selection is crucial to give interpretable results. We focus on a sparse Partial Least Squares approach (sPLS to handle two-block data sets, where the relationship between the two types of variables is known to be symmetric. Sparse PLS has been developed either for a regression or a canonical correlation framework and includes a built-in procedure to select variables while integrating data. To illustrate the canonical mode approach, we analyzed the NCI60 data sets, where two different platforms (cDNA and Affymetrix chips were used to study the transcriptome of sixty cancer cell lines. Results We compare the results obtained with two other sparse or related canonical correlation approaches: CCA with Elastic Net penalization (CCA-EN and Co-Inertia Analysis (CIA. The latter does not include a built-in procedure for variable selection and requires a two-step analysis. We stress the lack of statistical criteria to evaluate canonical correlation methods, which makes biological interpretation absolutely necessary to compare the different gene selections. We also propose comprehensive graphical representations of both samples and variables to facilitate the interpretation of the results. Conclusion sPLS and CCA-EN selected highly relevant genes and complementary findings from the two data sets, which enabled a detailed understanding of the molecular characteristics of several groups of cell lines. These two approaches were found to bring similar results, although they highlighted the same

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

OpenAIRE

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

2008-01-01

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

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

Science.gov (United States)

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

2017-10-01

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

Shaping Biological Knowledge: Applications in Proteomics

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R. Appel

2006-04-01

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

Shaping biological knowledge: applications in proteomics.

Science.gov (United States)

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

2004-01-01

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

Ruminant Metabolic Systems Biology: Reconstruction and Integration of Transcriptome Dynamics Underlying Functional Responses of Tissues to Nutrition and Physiological Statea

Science.gov (United States)

Bionaz, Massimo; Loor, Juan J.

2012-01-01

High-throughput ‘omics’ data analysis via bioinformatics is one key component of the systems biology approach. The systems approach is particularly well-suited for the study of the interactions between nutrition and physiological state with tissue metabolism and functions during key life stages of organisms such as the transition from pregnancy to lactation in mammals, ie, the peripartal period. In modern dairy cows with an unprecedented genetic potential for milk synthesis, the nature of the physiologic and metabolic adaptations during the peripartal period is multifaceted and involves key tissues such as liver, adipose, and mammary. In order to understand such adaptation, we have reviewed several works performed in our and other labs. In addition, we have used a novel bioinformatics approach, Dynamic Impact Approach (DIA), in combination with partly previously published data to help interpret longitudinal biological adaptations of bovine liver, adipose, and mammary tissue to lactation using transcriptomics datasets. Use of DIA with transcriptomic data from those tissues during normal physiological adaptations and in animals fed different levels of energy prepartum allowed visualization and integration of most-impacted metabolic pathways around the time of parturition. The DIA is a suitable tool for applying the integrative systems biology approach. The ultimate goal is to visualize the complexity of the systems at study and uncover key molecular players involved in the tissue’s adaptations to physiological state or nutrition. PMID:22807626

Trophic gradients of two minnow species with similar eco-type and their relations to water chemistry and multimetric biological integrity

Directory of Open Access Journals (Sweden)

Seoyun Choi

2017-09-01

Full Text Available The objectives of this study were to determine tolerance ranges and trophic gradients of two fish populations of Zacco koreanus (Zk and Zacco platypus (Zp in relation to chemical water quality and ecological stream health, based on the biological integrity metric (BIM model. Seventy-six streams and rivers were sampled for the analysis. The population of Zk had a narrow chemical tolerance with a low phosphorus limit (< 300 μg/L as total phosphorus, whereas the Zp population occurred within a high limit (up to 1,100 μg/L. Similar patterns in the two populations were shown in nitrogen, biological oxygen demand, suspended solids, and other parameters. The population of Zp had significantly (t=5.25, p<0.001 greater chemical tolerance than the population of Zk. The population of Zk had a positive functional relation (R2=0.43, p<0.001 with insectivore species, but the Zp population had negative linear function (R2=0.50, p<0.001, indicating a trophic difference in the food chain of two populations. Application of the biological integrity model indicated that the values of BIM, as an index of ecological health, were significantly greater (t=13.67, p<0.001 in the population of Zk than the population of Zp.

Integrative Analysis of Omics Big Data.

Science.gov (United States)

Yu, Xiang-Tian; Zeng, Tao

2018-01-01

The diversity and huge omics data take biology and biomedicine research and application into a big data era, just like that popular in human society a decade ago. They are opening a new challenge from horizontal data ensemble (e.g., the similar types of data collected from different labs or companies) to vertical data ensemble (e.g., the different types of data collected for a group of person with match information), which requires the integrative analysis in biology and biomedicine and also asks for emergent development of data integration to address the great changes from previous population-guided to newly individual-guided investigations.Data integration is an effective concept to solve the complex problem or understand the complicate system. Several benchmark studies have revealed the heterogeneity and trade-off that existed in the analysis of omics data. Integrative analysis can combine and investigate many datasets in a cost-effective reproducible way. Current integration approaches on biological data have two modes: one is "bottom-up integration" mode with follow-up manual integration, and the other one is "top-down integration" mode with follow-up in silico integration.This paper will firstly summarize the combinatory analysis approaches to give candidate protocol on biological experiment design for effectively integrative study on genomics and then survey the data fusion approaches to give helpful instruction on computational model development for biological significance detection, which have also provided newly data resources and analysis tools to support the precision medicine dependent on the big biomedical data. Finally, the problems and future directions are highlighted for integrative analysis of omics big data.

Actin Immobilization on Chitin for Purifying Myosin II: A Laboratory Exercise That Integrates Concepts of Molecular Cell Biology and Protein Chemistry

Science.gov (United States)

de Souza, Marcelle Gomes; Grossi, Andre Luiz; Pereira, Elisangela Lima Bastos; da Cruz, Carolina Oliveira; Mendes, Fernanda Machado; Cameron, Luiz Claudio; Paiva, Carmen Lucia Antao

2008-01-01

This article presents our experience on teaching biochemical sciences through an innovative approach that integrates concepts of molecular cell biology and protein chemistry. This original laboratory exercise is based on the preparation of an affinity chromatography column containing F-actin molecules immobilized on chitin particles for purifying…

Towards Logical Designs In Biology

Indian Academy of Sciences (India)

Administrator

thetic biology that envisions integrating designed circuits into living ... research student in the .... integrating an odd number of NOT gates in a circular fashion such that the .... end is rational design where the targeting of gene mutations to.

Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications.

Science.gov (United States)

Hughes, Stephen R; Butt, Tauseef R; Bartolett, Scott; Riedmuller, Steven B; Farrelly, Philip

2011-08-01

The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. High-throughput integrated robotic molecular biology platforms that have the capacity to rapidly clone and express heterologous gene open reading frames in bacteria and yeast and to screen large numbers of expressed proteins for optimized function are an important technology for improving microbial strains for biofuel production. The process involves the production of full-length complementary DNA libraries as a source of plasmid-based clones to express the desired proteins in active form for determination of their functions. Proteins that were identified by high-throughput screening as having desired characteristics are overexpressed in microbes to enable them to perform functions that will allow more cost-effective and sustainable production of biofuels. Because the plasmid libraries are composed of several thousand unique genes, automation of the process is essential. This review describes the design and implementation of an automated integrated programmable robotic workcell capable of producing complementary DNA libraries, colony picking, isolating plasmid DNA, transforming yeast and bacteria, expressing protein, and performing appropriate functional assays. These operations will allow tailoring microbial strains to use renewable feedstocks for production of biofuels, bioderived chemicals, fertilizers, and other coproducts for profitable and sustainable biorefineries. Published by Elsevier Inc.

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

Science.gov (United States)

Smith, Richard N; Aleksic, Jelena; Butano, Daniela; Carr, Adrian; Contrino, Sergio; Hu, Fengyuan; Lyne, Mike; Lyne, Rachel; Kalderimis, Alex; Rutherford, Kim; Stepan, Radek; Sullivan, Julie; Wakeling, Matthew; Watkins, Xavier; Micklem, Gos

2012-12-01

InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. Freely available from http://www.intermine.org under the LGPL license. g.micklem@gen.cam.ac.uk Supplementary data are available at Bioinformatics online.

Integrative Systems Biology Applied to Toxicology

DEFF Research Database (Denmark)

Kongsbak, Kristine Grønning

associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three...... of a system thereby suggesting new ways of thinking specific toxicological endpoints. Furthermore, computational methods can serve as valuable input for the hypothesis generating phase of the preparations of a research project....

A multidisciplinary weight of evidence approach for environmental risk assessment at the Costa Concordia wreck: Integrative indices from Mussel Watch.

Science.gov (United States)

Regoli, Francesco; Pellegrini, David; Cicero, Anna Maria; Nigro, Marco; Benedetti, Maura; Gorbi, Stefania; Fattorini, Daniele; D'Errico, Giuseppe; Di Carlo, Marta; Nardi, Alessandro; Gaion, Andrea; Scuderi, Alice; Giuliani, Silvia; Romanelli, Giulia; Berto, Daniela; Trabucco, Benedetta; Guidi, Patrizia; Bernardeschi, Margherita; Scarcelli, Vittoria; Frenzilli, Giada

2014-05-01

A complex framework of chemical, biological and oceanographic activities was immediately activated after the Costa Concordia shipwreck, to assess possible contamination events and the environmental impact during both emergency and wreck removal operations. In the present paper, we describe the results obtained with caged mussels, Mytilus galloprovincialis, chosen as bioindicator organisms to detect variations of bioavailability and the early onset of molecular and cellular effects (biomarkers). Seven translocation experiments were carried out during the first year from the incident, with organisms deployed at 2 depths in 3 different sites. After 4-6 weeks, tissue concentrations were measured for the main classes of potentially released chemicals (trace metals, polycyclic aromatic hydrocarbons, volatile and aliphatic hydrocarbons, polychlorinated biphenyls, halogenated pesticides, organotin compounds, brominated flame retardants, anionic surfactants); a wide battery of biomarkers covered responses indicative of exposure, detoxification, oxidative stress, cell damage and genotoxic effects. Results excluded serious contamination events or a consistent increase of environmental pollution although some episodic spills with reversible effects were detected. Data were elaborated within a quantitative weight of evidence (WOE) model which provided synthetic hazard indices for each typology of data, before their overall integration in an environmental risk index, which generally ranged from slight to moderate. The proposed WOE model was confirmed a useful tool to summarize large datasets of complex data in integrative indices, and to simplify the interpretation for stakeholders and decision makers, thus supporting a more comprehensive process of "site-oriented" management decisions. Copyright © 2013 Elsevier Ltd. All rights reserved.

International lessons in new methods for grading and integrating cost effectiveness evidence into clinical practice guidelines

DEFF Research Database (Denmark)

Antioch, Kathryn M; Drummond, Michael F; Niessen, Louis W

2017-01-01

Economic evidence is influential in health technology assessment world-wide. Clinical Practice Guidelines (CPG) can enable economists to include economic information on health care provision. Application of economic evidence in CPGs, and its integration into clinical practice and national decisio......-of-life, budget impact, cost-effective ratios, net benefits and disparities in access and outcomes. Priority setting remains essential and trade-off decisions between policy criteria can be based on MCDA, both in evidence based clinical medicine and in health planning....... that scores that checklist for grading studies, when assessing economic evidence. Cost-effectiveness Analysis (CEA) thresholds, opportunity cost and willingness-to-pay (WTP) are crucial issues for decision rules in CEA generally, including end-of-life therapies. Limitations of inter-rater reliability......, logistics, innovation price, price sensitivity, substitutes and complements, WTP, absenteeism and presentism. Supply issues may include economies of scale, efficiency changes, and return on investment. Involved equity and efficiency measures may include cost-of-illness, disease burden, quality...

SEEK: a systems biology data and model management platform.

NARCIS (Netherlands)

Wolstencroft, K.J.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N.J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J.L.; Mueller, W.; Goble, C.

2015-01-01

Background: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems

The Desire for Amputation or Paralyzation: Evidence for Structural Brain Anomalies in Body Integrity Identity Disorder (BIID)

NARCIS (Netherlands)

Blom, Rianne M.; van Wingen, Guido A.; van der Wal, Sija J.; Luigjes, Judy; van Dijk, Milenna T.; Scholte, H. Steven; Denys, Damiaan

2016-01-01

Body Integrity Identity Disorder (BIID) is a condition in which individuals perceive a mismatch between their internal body scheme and physical body shape, resulting in an absolute desire to be either amputated or paralyzed. The condition is hypothesized to be of congenital nature, but evidence for

An "Evidence-Based" Professional Development Program for Physics Teachers Focusing on Knowledge Integration

Science.gov (United States)

Berger, Hana

This dissertation is concerned with the design and study of an evidence-based approach to the professional development of high-school physics teachers responding to the need to develop effective continuing professional development programs (CPD) in domains that require genuine changes in teachers' views, knowledge, and practice. The goals of the thesis were to design an evidence-based model for the CPD program, to implement it with teachers, and to study its influence on teachers' knowledge, views, and practice, as well as its impact on students' learning. The program was developed in three consecutive versions: a pilot, first, and second versions. Based on the pilot version (that was not part of this study), we developed the first version of the program in which we studied difficulties in employing the evidence-based and blended-learning approaches. According to our findings, we modified the strategies for enacting these approaches in the second version of the program. The influence of the program on the teachers and students was studied during the enactment of the second version of the program. The model implemented in the second version of the program was characterized by four main design principles: 1. The KI and evidence aspects are acquired simultaneously in an integrated manner. 2. The guidance of the teachers follows the principles of cognitive apprenticeship both in the evidence and the KI aspects. 3. The teachers experience the innovative activities as learners. 4. The program promotes continuity of teachers' learning through a structured "blended learning" approach. The results of our study show that this version of the program achieved its goals; throughout the program the teachers progressed in their knowledge, views, and practice concerning the knowledge integration, and in the evidence and learner-centered aspects. The results also indicated that students improved their knowledge of physics and knowledge integration skills that were developed

Which coordinate system for modelling path integration?

Science.gov (United States)

Vickerstaff, Robert J; Cheung, Allen

2010-03-21

Path integration is a navigation strategy widely observed in nature where an animal maintains a running estimate, called the home vector, of its location during an excursion. Evidence suggests it is both ancient and ubiquitous in nature, and has been studied for over a century. In that time, canonical and neural network models have flourished, based on a wide range of assumptions, justifications and supporting data. Despite the importance of the phenomenon, consensus and unifying principles appear lacking. A fundamental issue is the neural representation of space needed for biological path integration. This paper presents a scheme to classify path integration systems on the basis of the way the home vector records and updates the spatial relationship between the animal and its home location. Four extended classes of coordinate systems are used to unify and review both canonical and neural network models of path integration, from the arthropod and mammalian literature. This scheme demonstrates analytical equivalence between models which may otherwise appear unrelated, and distinguishes between models which may superficially appear similar. A thorough analysis is carried out of the equational forms of important facets of path integration including updating, steering, searching and systematic errors, using each of the four coordinate systems. The type of available directional cue, namely allothetic or idiothetic, is also considered. It is shown that on balance, the class of home vectors which includes the geocentric Cartesian coordinate system, appears to be the most robust for biological systems. A key conclusion is that deducing computational structure from behavioural data alone will be difficult or impossible, at least in the absence of an analysis of random errors. Consequently it is likely that further theoretical insights into path integration will require an in-depth study of the effect of noise on the four classes of home vectors. Copyright 2009 Elsevier Ltd

Evidence-based dentistry.

Science.gov (United States)

Chambers, David W

2010-01-01

Both panegyric and criticism of evidence-based dentistry tend to be clumsy because the concept is poorly defined. This analysis identifies several contributions to the profession that have been made under the EBD banner. Although the concept of clinicians integrating clinical epidemiology, the wisdom of their practices, and patients' values is powerful, its implementation has been distorted by a too heavy emphasis of computerized searches for research findings that meet the standards of academics. Although EBD advocates enjoy sharing anecdotal accounts of mistakes others have made, faulting others is not proof that one's own position is correct. There is no systematic, high-quality evidence that EBD is effective. The metaphor of a three-legged stool (evidence, experience, values, and integration) is used as an organizing principle. "Best evidence" has become a preoccupation among EBD enthusiasts. That overlong but thinly developed leg of the stool is critiqued from the perspectives of the criteria for evidence, the difference between internal and external validity, the relationship between evidence and decision making, the ambiguous meaning of "best," and the role of reasonable doubt. The strongest leg of the stool is clinical experience. Although bias exists in all observations (including searches for evidence), there are simple procedures that can be employed in practice to increase useful and objective evidence there, and there are dangers in delegating policy regarding allowable treatments to external groups. Patient and practitioner values are the shortest leg of the stool. As they are so little recognized, their integration in EBD is problematic and ethical tensions exist where paternalism privileges science over patient's self-determined best interests. Four potential approaches to integration are suggested, recognizing that there is virtually no literature on how the "seat" of the three-legged stool works or should work. It is likely that most dentists

CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models.

Science.gov (United States)

Chen, Yuhui; Lawless, Conor; Gillespie, Colin S; Wu, Jake; Boys, Richard J; Wilkinson, Darren J

2010-05-01

Dynamic simulation modelling of complex biological processes forms the backbone of systems biology. Discrete stochastic models are particularly appropriate for describing sub-cellular molecular interactions, especially when critical molecular species are thought to be present at low copy-numbers. For example, these stochastic effects play an important role in models of human ageing, where ageing results from the long-term accumulation of random damage at various biological scales. Unfortunately, realistic stochastic simulation of discrete biological processes is highly computationally intensive, requiring specialist hardware, and can benefit greatly from parallel and distributed approaches to computation and analysis. For these reasons, we have developed the BASIS system for the simulation and storage of stochastic SBML models together with associated simulation results. This system is exposed as a set of web services to allow users to incorporate its simulation tools into their workflows. Parameter inference for stochastic models is also difficult and computationally expensive. The CaliBayes system provides a set of web services (together with an R package for consuming these and formatting data) which addresses this problem for SBML models. It uses a sequential Bayesian MCMC method, which is powerful and flexible, providing very rich information. However this approach is exceptionally computationally intensive and requires the use of a carefully designed architecture. Again, these tools are exposed as web services to allow users to take advantage of this system. In this article, we describe these two systems and demonstrate their integrated use with an example workflow to estimate the parameters of a simple model of Saccharomyces cerevisiae growth on agar plates.

Area-wide integration of lepidopteran F1 sterility and augmentative biological control

International Nuclear Information System (INIS)

Carpenter, James E.

2000-01-01

Area-wide pest management (APM) and integrated pest management (IPM) originated from two different efforts to combine two or more control techniques into programmes in which each method could synergise the effectiveness of others and thus create a level of pest control that was greater than that of a single technique (Perkins 1982). Since then, the concept of APM has evolved to include many aspects of IPM and often is now referred to as area-wide IPM. Still, the element of total population management is central to this approach of insect pest management. In support of APM, Knipling (1998) stated that of the insect pests that were of major concern to agriculture before the newer classes of insecticides were available, most are still pests today, the major exceptions being the screw-worm fly and the boll weevil in the southeastern US cotton growing region. Knipling also noted that both of these pest species were subjected to area-wide suppression programmes. In response to the USDA IPM Initiative (USDA 1993, 1994) which seeks to achieve the national goal of having 75% of the crop acres under IPM by the year 2000, the Agricultural Research Service developed an Area-wide IPM Programme. This programme combines environmentally-sound pest control techniques with the advantages of APM and develops partnerships with other federal, state, local and private sector entities. Technologies such as the integration of lepidopteran F 1 sterility and augmentative biological control may be considered for future programmes

A Paradigm Shift in Low Dose Radiation Biology

Directory of Open Access Journals (Sweden)

Z. Alatas

2015-08-01

Full Text Available When ionizing radiation traverses biological material, some energy depositions occur and ionize directly deoxyribonucleic acid (DNA molecules, the critical target. A classical paradigm in radiobiology is that the deposition of energy in the cell nucleus and the resulting damage to DNA are responsible for the detrimental biological effects of radiation. It is presumed that no radiation effect would be expected in cells that receive no direct radiation exposure through nucleus. The risks of exposure to low dose ionizing radiation are estimated by extrapolating from data obtained after exposure to high dose radiation. However, the validity of using this dose-response model is controversial because evidence accumulated over the past decade has indicated that living organisms, including humans, respond differently to low dose radiation than they do to high dose radiation. Moreover, recent experimental evidences from many laboratories reveal the fact that radiation effects also occur in cells that were not exposed to radiation and in the progeny of irradiated cells at delayed times after radiation exposure where cells do not encounter direct DNA damage. Recently, the classical paradigm in radiobiology has been shifted from the nucleus, specifically the DNA, as the principal target for the biological effects of radiation to cells. The universality of target theory has been challenged by phenomena of radiation-induced genomic instability, bystander effect and adaptive response. The new radiation biology paradigm would cover both targeted and non-targeted effects of ionizing radiation. The mechanisms underlying these responses involve biochemical/molecular signals that respond to targeted and non-targeted events. These results brought in understanding that the biological response to low dose radiation at tissue or organism level is a complex process of integrated response of cellular targets as well as extra-cellular factors. Biological understanding of

Add-On Complementary Medicine in Cancer Care: Evidence in Literature and Experiences of Integration

Directory of Open Access Journals (Sweden)

Elio Rossi

2017-01-01

Full Text Available Background: According to the literature an increasing number of cancer patients demand for complementary therapies during their disease. Research has demonstrated that some of these therapies are effective and safe as adjunctive treatments in specific symptoms of these patients. Methods: The aims of the paper are to review the main and recent papers of international literature on the effectiveness of complementary medicine (CM therapies on side effects of anti-cancer protocols and improvement in the quality of life of oncological patients, and to describe the integration of evidence-based acupuncture, herbal medicine and homeopathy treatments in Public Cancer Network of the region of Tuscany. Results: After the review of literature and the approval of a Regional Resolution, some CM will be introduced in Cancer Departments in Tuscany to additionally treat cancer-related symptoms and side effects of conventional cancer therapy: acupuncture for nausea and post-chemotherapy and post-surgery vomiting, pain, hot flashes of iatrogenic menopause, xerostomia; homeopathy for hot flashes of iatrogenic menopause and the side effects of radiotherapy; herbal medicine for cancer-related fatigue, nausea and vomiting, pain, mucositis, anxiety, and depression. Conclusions: The integration of evidence-based complementary treatments allows for an effective response to the demand coming from cancer patients and combines safety and equity of access in public health systems.

The effectiveness of a clinically integrated e-learning course in evidence-based medicine: A cluster randomised controlled trial

NARCIS (Netherlands)

Kulier, Regina; Coppus, Sjors F. P. J.; Zamora, Javier; Hadley, Julie; Malick, Sadia; Das, Kausik; Weinbrenner, Susanne; Meyerrose, Berrit; Decsi, Tamas; Horvath, Andrea R.; Nagy, Eva; Emparanza, Jose I.; Arvanitis, Theodoros N.; Burls, Amanda; Cabello, Juan B.; Kaczor, Marcin; Zanrei, Gianni; Pierer, Karen; Stawiarz, Katarzyna; Kunz, Regina; Mol, Ben W. J.; Khan, Khalid S.

2009-01-01

ABSTRACT: BACKGROUND: To evaluate the educational effects of a clinically integrated e-learning course for teaching basic evidence-based medicine (EBM) among postgraduates compared to a traditional lecture-based course of equivalent content. METHODS: We conducted a cluster randomised controlled

Quantum biological information theory

CERN Document Server

Djordjevic, Ivan B

2016-01-01

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

Neurological and biological foundations of children's social and emotional development: an integrated literature review.

Science.gov (United States)

Nelson, Helen Jean; Kendall, Garth Edward; Shields, Linda

2014-08-01

This article provides an integrated review of the expert literature on developmental processes that combine social, biological, and neurological pathways, and the mechanisms through which these pathways may influence school success and health. It begins with a historical overview of the current understanding of how attachment relationships and social environments influence brain development and plasticity and are, therefore, central to the physical and mental health of individuals and populations. It then expands on the effect of plasticity in relation to behavior and learning at school. This article concludes with a discussion of the role the school nurse may play in supporting health and learning by recognizing signs of relational stress and by advocating for prevention strategies. © The Author(s) 2013.

Integrative systems and synthetic biology of cell-matrix adhesion sites.

Science.gov (United States)

Zamir, Eli

2016-09-02

The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.

Assessing environmental quality status by integrating chemical and biological effect data: The Cartagena coastal zone as a case.

Science.gov (United States)

Martínez-Gómez, Concepción; Fernández, Beatriz; Robinson, Craig D; Campillo, J Antonio; León, Víctor M; Benedicto, José; Hylland, Ketil; Vethaak, A Dick

2017-03-01

Cartagena coastal zone (W Mediterranean) was chosen for a practical case study to investigate the suitability of an integrated indicator framework for marine monitoring and assessment of chemicals and their effects, which was developed by ICES and OSPAR. Red mullet (Mullus barbatus) and the Mediterranean mussel (Mytilus galloprovincialis) were selected as target species. Concentrations of contaminants in sediment and biota, and contaminant-related biomarkers were analysed. To assess environmental quality in the Cartagena coastal zone with respect to chemical pollution, data were assessed using available assessment criteria, and then integrated for different environmental matrices. A qualitative scoring method was used to rank the overall assessments into selected categories and to evaluate the confidence level of the final integrated assessment. The ICES/OSPAR integrated assessment framework, originally designed for the North Atlantic, was found to be applicable for Mediterranean species and environmental matrices. Further development of assessment criteria of chemical and biological parameters in sediments and target species from the Mediterranean will, however, be required before this framework can be fully applied for determining Good Environmental Status (GES) of the Marine Strategy Framework Directive in these regions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information

Directory of Open Access Journals (Sweden)

Lemke Ney

2009-09-01

Full Text Available Abstract Background The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design. However, the experimental techniques for essential genes discovery are labor-intensive and time-consuming. Considering these experimental constraints, a computational approach capable of accurately predicting essential genes would be of great value. We therefore present here a machine learning-based computational approach relying on network topological features, cellular localization and biological process information for prediction of essential genes. Results We constructed a decision tree-based meta-classifier and trained it on datasets with individual and grouped attributes-network topological features, cellular compartments and biological processes-to generate various predictors of essential genes. We showed that the predictors with better performances are those generated by datasets with integrated attributes. Using the predictor with all attributes, i.e., network topological features, cellular compartments and biological processes, we obtained the best predictor of essential genes that was then used to classify yeast genes with unknown essentiality status. Finally, we generated decision trees by training the J48 algorithm on datasets with all network topological features, cellular localization and biological process information to discover cellular rules for essentiality. We found that the number of protein physical interactions, the nuclear localization of proteins and the number of regulating transcription factors are the most important factors determining gene essentiality. Conclusion We were able to demonstrate that network topological features, cellular localization and biological process information are reliable predictors of essential genes. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing

OWL Reasoning Framework over Big Biological Knowledge Network

Science.gov (United States)

Chen, Huajun; Chen, Xi; Gu, Peiqin; Wu, Zhaohui; Yu, Tong

2014-01-01

Recently, huge amounts of data are generated in the domain of biology. Embedded with domain knowledge from different disciplines, the isolated biological resources are implicitly connected. Thus it has shaped a big network of versatile biological knowledge. Faced with such massive, disparate, and interlinked biological data, providing an efficient way to model, integrate, and analyze the big biological network becomes a challenge. In this paper, we present a general OWL (web ontology language) reasoning framework to study the implicit relationships among biological entities. A comprehensive biological ontology across traditional Chinese medicine (TCM) and western medicine (WM) is used to create a conceptual model for the biological network. Then corresponding biological data is integrated into a biological knowledge network as the data model. Based on the conceptual model and data model, a scalable OWL reasoning method is utilized to infer the potential associations between biological entities from the biological network. In our experiment, we focus on the association discovery between TCM and WM. The derived associations are quite useful for biologists to promote the development of novel drugs and TCM modernization. The experimental results show that the system achieves high efficiency, accuracy, scalability, and effectivity. PMID:24877076

Integration of multiple biological features yields high confidence human protein interactome.

Science.gov (United States)

Karagoz, Kubra; Sevimoglu, Tuba; Arga, Kazim Yalcin

2016-08-21

The biological function of a protein is usually determined by its physical interaction with other proteins. Protein-protein interactions (PPIs) are identified through various experimental methods and are stored in curated databases. The noisiness of the existing PPI data is evident, and it is essential that a more reliable data is generated. Furthermore, the selection of a set of PPIs at different confidence levels might be necessary for many studies. Although different methodologies were introduced to evaluate the confidence scores for binary interactions, a highly reliable, almost complete PPI network of Homo sapiens is not proposed yet. The quality and coverage of human protein interactome need to be improved to be used in various disciplines, especially in biomedicine. In the present work, we propose an unsupervised statistical approach to assign confidence scores to PPIs of H. sapiens. To achieve this goal PPI data from six different databases were collected and a total of 295,288 non-redundant interactions between 15,950 proteins were acquired. The present scoring system included the context information that was assigned to PPIs derived from eight biological attributes. A high confidence network, which included 147,923 binary interactions between 13,213 proteins, had scores greater than the cutoff value of 0.80, for which sensitivity, specificity, and coverage were 94.5%, 80.9%, and 82.8%, respectively. We compared the present scoring method with others for evaluation. Reducing the noise inherent in experimental PPIs via our scoring scheme increased the accuracy significantly. As it was demonstrated through the assessment of process and cancer subnetworks, this study allows researchers to construct and analyze context-specific networks via valid PPI sets and one can easily achieve subnetworks around proteins of interest at a specified confidence level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electrophysiological evidence for speech-specific audiovisual integration

NARCIS (Netherlands)

Baart, M.; Stekelenburg, J.J.; Vroomen, J.

2014-01-01

Lip-read speech is integrated with heard speech at various neural levels. Here, we investigated the extent to which lip-read induced modulations of the auditory N1 and P2 (measured with EEG) are indicative of speech-specific audiovisual integration, and we explored to what extent the ERPs were

Degradation of polyethylene glycol by the integration of chemical and biological treatment; Degradacion de polietilenglicos 10.000 mediante tratamiento integrado quimico-biologico

Energy Technology Data Exchange (ETDEWEB)

Otal, E.; Mantzavinos, D.; Lebrato, J. [Universidad de Sevilla (Spain)

2001-07-01

Biodegradation of polyethylene glycol 10.000 molecular weight or higher presented problems, therefore suggesting that integration of chemical and biological treatments, to achieve complete degradation from these sizes of polyethylene glycol may be advisable. Integration of wet air oxidation and aerobic biological treatments of polyethylene glycol 10.000 was investigated. The organic compound, used as the sole carbon and energy source, was partially oxidized in a high pressure reactor achieving a 7% of total organic carbon removal. Enhanced biodegradability was assessed by comparing total organic carbon removal using an Aerobic Continuous-flow Stirred Reactor fed with untreated original organic or previously oxidized samples. the reactor operated at steady-state at loading rates of total organic carbon of 69 mg L-1 d-1 for untreated polyethylene glycol 10.000, and 520 mg L-1 d-1 for wet air oxidation-treated polyethylene glycol 10.000, reaching yields of 68 % and 82% of total organic carbon removal, respective. Even using a retention time 8-fold shorter, total organic carbon removal from the wet air oxidation-treated sample was higher than that from the untreated one. therefore, previous wet air oxidation treatment may improve efficiency of conventional biological treatment of industrial wastewaters containing this organic compound. (Author) 18 refs.

Towards a Unified Approach to Information Integration - A review paper on data/information fusion

Energy Technology Data Exchange (ETDEWEB)

Whitney, Paul D.; Posse, Christian; Lei, Xingye C.

2005-10-14

Information or data fusion of data from different sources are ubiquitous in many applications, from epidemiology, medical, biological, political, and intelligence to military applications. Data fusion involves integration of spectral, imaging, text, and many other sensor data. For example, in epidemiology, information is often obtained based on many studies conducted by different researchers at different regions with different protocols. In the medical field, the diagnosis of a disease is often based on imaging (MRI, X-Ray, CT), clinical examination, and lab results. In the biological field, information is obtained based on studies conducted on many different species. In military field, information is obtained based on data from radar sensors, text messages, chemical biological sensor, acoustic sensor, optical warning and many other sources. Many methodologies are used in the data integration process, from classical, Bayesian, to evidence based expert systems. The implementation of the data integration ranges from pure software design to a mixture of software and hardware. In this review we summarize the methodologies and implementations of data fusion process, and illustrate in more detail the methodologies involved in three examples. We propose a unified multi-stage and multi-path mapping approach to the data fusion process, and point out future prospects and challenges.

Computational aspects of systematic biology.

Science.gov (United States)

Lilburn, Timothy G; Harrison, Scott H; Cole, James R; Garrity, George M

2006-06-01

We review the resources available to systematic biologists who wish to use computers to build classifications. Algorithm development is in an early stage, and only a few examples of integrated applications for systematic biology are available. The availability of data is crucial if systematic biology is to enter the computer age.

'More than two': integrating biological control and sterile insects, from factory to field, and the possibility of its implementation in Argentina

International Nuclear Information System (INIS)

Cladera, Jorge L.; Viscarret, Mariana M.; Carabajal Paladino, Leonela Z.; Pietrek, Alejandro; Soria, M. Alejandra; Ovruski, Sergio M.

2006-01-01

No single control measure is able to provide full control of a pest. Integration of techniques like the sterile insect (SIT) with biological control practices (BC) should be intensively sough for. This possibility is revised here in connection with the fruit fly pest problems in Argentina. Theoretical reasons as well as practical conveniences for this integration are reviewed in this paper, the intention of which is to promote a discussion on how to approach the experimental study of the SIT+CB integration problem, i.e. how to measure the effects of each separate control measure as well as that of both acting together, in a repeatable manner. Arguments are advanced in favor of the joint production and releases of sterile fruit flies and parasitoids. (author)

"Keeping on track"-Hospital nurses' struggles with maintaining workflow while seeking to integrate evidence-based practice into their daily work: A grounded theory study.

Science.gov (United States)

Renolen, Åste; Høye, Sevald; Hjälmhult, Esther; Danbolt, Lars Johan; Kirkevold, Marit

2018-01-01

Evidence-based practice is considered a foundation for the provision of quality care and one way to integrate scientific knowledge into clinical problem-solving. Despite the extensive amount of research that has been conducted to evaluate evidence-based practice implementation and research utilization, these practices have not been sufficiently incorporated into nursing practice. Thus, additional research regarding the challenges clinical nurses face when integrating evidence-based practice into their daily work and the manner in which these challenges are approached is needed. The aim of this study was to generate a theory about the general patterns of behaviour that are discovered when clinical nurses attempt to integrate evidence-based practice into their daily work. We used Glaser's classical grounded theory methodology to generate a substantive theory. The study was conducted in two different medical wards in a large Norwegian hospital. In one ward, nurses and nursing assistants were developing and implementing new evidence-based procedures, and in the other ward, evidence-based huddle boards for risk assessment were being implemented. A total of 54 registered nurses and 9 assistant nurses were observed during their patient care and daily activities. Of these individuals, thirteen registered nurses and five assistant nurses participated in focus groups. These participants were selected through theoretical sampling. Data were collected during 90h of observation and 4 focus groups conducted from 2014 to 2015. Each focus group session included four to five participants and lasted between 55 and 65min. Data collection and analysis were performed concurrently, and the data were analysed using the constant comparative method. "Keeping on track" emerged as an explanatory theory for the processes through which the nurses handled their main concern: the risk of losing the workflow. The following three strategies were used by nurses when attempting to integrate evidence

Evidence-based guidelines of the spanish psoriasis group on the use of biologic therapy in patients with psoriasis in difficult-to-treat sites (nails, scalp, palms, and soles).

Science.gov (United States)

Sánchez-Regaña, M; Aldunce Soto, M J; Belinchón Romero, I; Ribera Pibernat, M; Lafuente-Urrez, R F; Carrascosa Carrillo, J M; Ferrándiz Foraster, C; Puig Sanz, L; Daudén Tello, E; Vidal Sarró, D; Ruiz-Villaverde, R; Fonseca Capdevila, E; Rodríguez Cerdeira, M C; Alsina Gibert, M M; Herrera Acosta, E; Marrón Moya, S E

2014-12-01

Psoriatic lesions affecting the scalp, nails, palms, and the soles of the feet are described as difficult-to-treat psoriasis and require specific management. Involvement of these sites often has a significant physical and emotional impact on the patient and the lesions are difficult to control with topical treatments owing to inadequate penetration of active ingredients and the poor cosmetic characteristics of the vehicles used. Consequently, when difficult-to-treat sites are involved, psoriasis can be considered severe even though the lesions are not extensive. Scant information is available about the use of biologic therapy in this setting, and published data generally comes from clinical trials of patients who also had moderate to severe extensive lesions or from small case series and isolated case reports. In this article we review the quality of the scientific evidence for the 4 biologic agents currently available in Spain (infliximab, etanercept, adalimumab, and ustekinumab) and report level i evidence for the use of biologics to treat nail psoriasis (level of recommendation A) and a somewhat lower level of evidence in the case of scalp involvement and palmoplantar psoriasis. Copyright © 2013 Elsevier España, S.L.U. y AEDV. All rights reserved.

Towards a heterarchical approach to biology and cognition

DEFF Research Database (Denmark)

Bruni, Luis Emilio; Giorgi, Franco

2015-01-01

to the different scientific disciplines working towards a multilevel integrative perspective of biological and cognitive processes, such as systems and integrative biology and neuroscience, social and cultural neuroscience, social signal transduction and psychoneuroimmunology, for instance. We argue...... that structures and substrates are by necessity organized hierarchically, while communication processes – and their embeddedness – are rather organized heterarchically. Before getting into the implications of the heterarchical approach and its congeniality with the semiotic perspective to biology and cognition...... complementarity of bottom-up and top-down causal links. This should contribute to account for the integration, interpretation and response to complex aggregates of information at different levels of organization in a developmental context. We illustrate the dialectical nature of embedded heterarchical processes...

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.

ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

Science.gov (United States)

Fucile, Geoffrey; Di Biase, David; Nahal, Hardeep; La, Garon; Khodabandeh, Shokoufeh; Chen, Yani; Easley, Kante; Christendat, Dinesh; Kelley, Lawrence; Provart, Nicholas J

2011-01-10

Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org).

Discovering and validating biological hypotheses from coherent patterns in functional genomics data

Energy Technology Data Exchange (ETDEWEB)

Joachimiak, Marcin Pawel

2008-08-12

The area of transcriptomics analysis is among the more established in computational biology, having evolved in both technology and experimental design. Transcriptomics has a strong impetus to develop sophisticated computational methods due to the large amounts of available whole-genome datasets for many species and because of powerful applications in regulatory network reconstruction as well as elucidation and modeling of cellular transcriptional responses. While gene expression microarray data can be noisy and comparisons across experiments challenging, there are a number of sophisticated methods that aid in arriving at statistically and biologically significant conclusions. As such, computational transcriptomics analysis can provide guidance for analysis of results from newer experimental technologies. More recently, search methods have been developed to identify modules of genes, which exhibit coherent expression patterns in only a subset of experimental conditions. The latest advances in these methods allow to integrate multiple data types anddatasets, both experimental and computational, within a single statistical framework accounting for data confidence and relevance to specific biological questions. Such frameworks provide a unified environment for the exploration of specific biological hypothesis and for the discovery of coherent data patterns along with the evidence supporting them.

Integrating Individual-Based Indices of Contaminant Effects

Directory of Open Access Journals (Sweden)

Christopher L. Rowe

2001-01-01

Full Text Available Habitat contamination can alter numerous biological processes in individual organisms. Examining multiple individual-level responses in an integrative fashion is necessary to understand how individual health or fitness reflects environmental contamination. Here we provide an example of such an integrated perspective based upon recent studies of an amphibian (the bullfrog, Rana catesbeiana that experiences several, disparate changes when larval development occurs in a trace element�contaminated habitat. First, we present an overview of studies focused on specific responses of individuals collected from, or transplanted into, a habitat contaminated by coal combustion residues (CCR. These studies have reported morphological, behavioral, and physiological modifications to individuals chronically interacting with sediments in the CCR-contaminated site. Morphological abnormalities in the oral and tail regions in contaminant-exposed individuals influenced other properties such as grazing, growth, and swimming performance. Behavioral changes in swimming activities and responses to stimuli appear to influence predation risk in the contaminant-exposed population. Significant changes in bioenergetics in the contaminated habitat, evident as abnormally high energetic expenditures for survival (maintenance costs, may ultimately influence production pathways (growth, energy storage in individuals. We then present a conceptual model to examine how interactions among the affected systems (morphological, behavioral, physiological may ultimately bring about more severe effects than would be predicted if the responses were considered in isolation. A complex interplay among simultaneously occurring biological changes emerges in which multiple, sublethal effects ultimately can translate into reductions in larval or juvenile survival, and thus reduced recruitment of juveniles into the population. In systems where individuals are exposed to low concentrations of

Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

Science.gov (United States)

De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

2010-03-01

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

Analyzing the Biology on the System Level

OpenAIRE

Tong, Wei

2016-01-01

Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells.

Science.gov (United States)

Angelici, Bartolomeo; Mailand, Erik; Haefliger, Benjamin; Benenson, Yaakov

2016-08-30

One of the goals of synthetic biology is to develop programmable artificial gene networks that can transduce multiple endogenous molecular cues to precisely control cell behavior. Realizing this vision requires interfacing natural molecular inputs with synthetic components that generate functional molecular outputs. Interfacing synthetic circuits with endogenous mammalian transcription factors has been particularly difficult. Here, we describe a systematic approach that enables integration and transduction of multiple mammalian transcription factor inputs by a synthetic network. The approach is facilitated by a proportional amplifier sensor based on synergistic positive autoregulation. The circuits efficiently transduce endogenous transcription factor levels into RNAi, transcriptional transactivation, and site-specific recombination. They also enable AND logic between pairs of arbitrary transcription factors. The results establish a framework for developing synthetic gene networks that interface with cellular processes through transcriptional regulators. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Is Reintroduction Biology an Effective Applied Science?

Science.gov (United States)

Taylor, Gemma; Canessa, Stefano; Clarke, Rohan H; Ingwersen, Dean; Armstrong, Doug P; Seddon, Philip J; Ewen, John G

2017-11-01

Reintroduction biology is a field of scientific research that aims to inform translocations of endangered species. We review two decades of published literature to evaluate whether reintroduction science is evolving in its decision-support role, as called for by advocates of evidence-based conservation. Reintroduction research increasingly addresses a priori hypotheses, but remains largely focused on short-term population establishment. Similarly, studies that directly assist decisions by explicitly comparing alternative management actions remain a minority. A small set of case studies demonstrate full integration of research in the reintroduction decision process. We encourage the use of tools that embed research in decision-making, particularly the explicit consideration of multiple management alternatives because this is the crux of any management decisions. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Monitoring sterile and wild insects in area-wide integrated pest management programmes

International Nuclear Information System (INIS)

Vreysen, M.J.B.

2005-01-01

Insect pest control programmes, which integrate the release of sterile insects, can be efficient only if the released insects have an optimal biological quality. Frequent monitoring of the quality of reared insects after being released in the field is an important but often neglected component of area-wide integrated pest management (AW-IPM) programmes that integrate the sterile insect technique (SIT). Parameters of sterile insects, which should be monitored regularly, are sexual competitiveness of the released insects, and related components, e.g. survival, mobility, dispersal characteristics, and spatial occupation of the habitat. A well-balanced monitoring programme will, at any given time, provide essential feedback on the progress being made. This information is prerequisite to efficient implementation of the release and cost-efficient use of sterile insects. The type of monitoring to be done will be determined largely by the particular biology of the target insect species. The most important parameter in relation to the release of sterile insects is the rate of sterility induced in the wild insect pest population; it will provide the best evidence that any observed changes, e.g. in the density of the target insect, are caused by the release of sterile insects. (author)

Processes that Drove the Transition from Chemistry to Biology: Concepts and Evidence

Science.gov (United States)

Pohorille, Andrew

2012-01-01

Two properties are particularly germane to the transition from chemistry to biology. One is the emergence of complex molecules (polymers) capable of performing non-trivial functions, such as catalysis, energy transduction or transport across cell walls. The other is the ability of several functions to work in concert to provide reproductive advantage to systems hosting these functions. Biological systems exhibit these properties at remarkable levels of efficiency and accuracy in a way that appears effortless. However, dissection of these properties reveals great complexities that are involved. This opens a question: how a simple, ancestral system could have acquired the required properties? Other questions follow. What are the chances that a functional polymer emerges at random? What is the minimum structural complexity of a polymer to carry out a function at a reasonable level of efficiency? Can we identify concrete, protobiologically plausible mechanisms that yield advantageous coupling between different functions? These and similar questions are at the core of the main topic of this session: how soulless chemistry became life? Clearly, we do not have complete answers to any of these questions. However, in recent years a number of new and sometimes unexpected clues have been brought to light. Of particular interest are proteins because they are the main functional polymers in contemporary cells. The emergence of protein functions is a puzzle. It is widely accepted that a well ]defined, compact structure (fold) is a prerequisite for function. It is equally widely accepted that compact folds are rare among random amino acid polymers. Then, how did protein functionality start? According to one hypothesis well folded were preceded by their poorly folded, yet still functional ancestors. Only recently, however, experimental evidence supporting this hypothesis has been presented. In particular, a small enzyme capable of ligating two RNA fragments with the rate of 106

Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

Science.gov (United States)

Reinhold, William C

2015-12-10

There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

The Construction of Biology Lessons: A Meta-Paradigmatic Approach.

Science.gov (United States)

Sanchez, Jaime

1991-01-01

The views of Piaget, Ausubel, and Bruner have been used to present an integrated view of biology lesson construction and to assist teachers in the design and development of tools and strategies to improve their teaching. The structure of an integrated model for biology lesson construction and an example of a biolesson using the metaparadigmatic…

S100A4 and its role in metastasis – computational integration of data on biological networks.

Science.gov (United States)

Buetti-Dinh, Antoine; Pivkin, Igor V; Friedman, Ran

2015-08-01

Characterising signal transduction networks is fundamental to our understanding of biology. However, redundancy and different types of feedback mechanisms make it difficult to understand how variations of the network components contribute to a biological process. In silico modelling of signalling interactions therefore becomes increasingly useful for the development of successful therapeutic approaches. Unfortunately, quantitative information cannot be obtained for all of the proteins or complexes that comprise the network, which limits the usability of computational models. We developed a flexible computational framework for the analysis of biological signalling networks. We demonstrate our approach by studying the mechanism of metastasis promotion by the S100A4 protein, and suggest therapeutic strategies. The advantage of the proposed method is that only limited information (interaction type between species) is required to set up a steady-state network model. This permits a straightforward integration of experimental information where the lack of details are compensated by efficient sampling of the parameter space. We investigated regulatory properties of the S100A4 network and the role of different key components. The results show that S100A4 enhances the activity of matrix metalloproteinases (MMPs), causing higher cell dissociation. Moreover, it leads to an increased stability of the pathological state. Thus, avoiding metastasis in S100A4-expressing tumours requires multiple target inhibition. Moreover, the analysis could explain the previous failure of MMP inhibitors in clinical trials. Finally, our method is applicable to a wide range of biological questions that can be represented as directional networks.

GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

Science.gov (United States)

Tran, P. B.; Berrios, D. C.; Gurram, M. M.; Hashim, J. C. M.; Raghunandan, S.; Lin, S. Y.; Le, T. Q.; Heher, D. M.; Thai, H. T.; Welch, J. D.;

Use of a virtual human performance laboratory to improve integration of mathematics and biology in sports science curricula in Sweden and the United States.

Science.gov (United States)

Garza, D; Besier, T; Johnston, T; Rolston, B; Schorsch, A; Matheson, G; Annerstedt, C; Lindh, J; Rydmark, M

2007-01-01

New fields such as bioengineering are exploring the role of the physical sciences in traditional biological approaches to problems, with exciting results in device innovation, medicine, and research biology. The integration of mathematics, biomechanics, and material sciences into the undergraduate biology curriculum will better prepare students for these opportunities and enhance cooperation among faculty and students at the university level. We propose the study of sports science as the basis for introduction of this interdisciplinary program. This novel integrated approach will require a virtual human performance laboratory dual-hosted in Sweden and the United States. We have designed a course model that involves cooperative learning between students at Göteborg University and Stanford University, utilizes new technologies, encourages development of original research and will rely on frequent self-assessment and reflective learning. We will compare outcomes between this course and a more traditional didactic format as well as assess the effectiveness of multiple web-hosted virtual environments. We anticipate the grant will result in a network of original faculty and student research in exercise science and pedagogy as well as provide the opportunity for implementation of the model in more advance training levels and K-12 programs.

Nanoplasmonic and Microfluidic Devices for Biological Sensing

KAUST Repository

Perozziello, G.; Giugni, Andrea; Allione, Marco; Torre, Bruno; Das, Gobind; Coluccio, M. L.; Marini, Monica; Tirinato, Luca; Moretti, Manola; Limongi, Tania; Candeloro, P.; Di Fabrizio, Enzo M.

2017-01-01

In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

Nanoplasmonic and Microfluidic Devices for Biological Sensing

KAUST Repository

Perozziello, G.

2017-02-16

In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

Suppressed visual looming stimuli are not integrated with auditory looming signals: Evidence from continuous flash suppression.

Science.gov (United States)

Moors, Pieter; Huygelier, Hanne; Wagemans, Johan; de-Wit, Lee; van Ee, Raymond

2015-01-01

Previous studies using binocular rivalry have shown that signals in a modality other than the visual can bias dominance durations depending on their congruency with the rivaling stimuli. More recently, studies using continuous flash suppression (CFS) have reported that multisensory integration influences how long visual stimuli remain suppressed. In this study, using CFS, we examined whether the contrast thresholds for detecting visual looming stimuli are influenced by a congruent auditory stimulus. In Experiment 1, we show that a looming visual stimulus can result in lower detection thresholds compared to a static concentric grating, but that auditory tone pips congruent with the looming stimulus did not lower suppression thresholds any further. In Experiments 2, 3, and 4, we again observed no advantage for congruent multisensory stimuli. These results add to our understanding of the conditions under which multisensory integration is possible, and suggest that certain forms of multisensory integration are not evident when the visual stimulus is suppressed from awareness using CFS.

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

Directory of Open Access Journals (Sweden)

Tilton Susan C

2012-11-01

Full Text Available Abstract Background MicroRNAs (miRNAs are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

Science.gov (United States)

2012-01-01

Background MicroRNAs (miRNAs) are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP) miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM) v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf) results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p<0.05) gene targets in BRM indicates that nicotine exposure disrupts genes involved in neurogenesis, possibly through misregulation of nicotine-sensitive miRNAs. Conclusions BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis

A quantitative approach for integrating multiple lines of evidence for the evaluation of environmental health risks

Directory of Open Access Journals (Sweden)

Jerome J. Schleier III

2015-01-01

Full Text Available Decision analysis often considers multiple lines of evidence during the decision making process. Researchers and government agencies have advocated for quantitative weight-of-evidence approaches in which multiple lines of evidence can be considered when estimating risk. Therefore, we utilized Bayesian Markov Chain Monte Carlo to integrate several human-health risk assessment, biomonitoring, and epidemiology studies that have been conducted for two common insecticides (malathion and permethrin used for adult mosquito management to generate an overall estimate of risk quotient (RQ. The utility of the Bayesian inference for risk management is that the estimated risk represents a probability distribution from which the probability of exceeding a threshold can be estimated. The mean RQs after all studies were incorporated were 0.4386, with a variance of 0.0163 for malathion and 0.3281 with a variance of 0.0083 for permethrin. After taking into account all of the evidence available on the risks of ULV insecticides, the probability that malathion or permethrin would exceed a level of concern was less than 0.0001. Bayesian estimates can substantially improve decisions by allowing decision makers to estimate the probability that a risk will exceed a level of concern by considering seemingly disparate lines of evidence.

'Integrative Physiology 2.0': Integration of systems biology into physiology and its application to cardiovascular homeostasis

NARCIS (Netherlands)

D.W.D. Kuster (Diederik); D. Merkus (Daphne); J. van der Velden (Jolanda); A.J.M. Verhoeven (Adrie); D.J.G.M. Duncker (Dirk)

2011-01-01

textabstractSince the completion of the Human Genome Project and the advent of the large scaled unbiased '-omics' techniques, the field of systems biology has emerged. Systems biology aims to move away from the traditional reductionist molecular approach, which focused on understanding the role of

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

Science.gov (United States)

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

2002-01-01

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

Use of Graph Database for the Integration of Heterogeneous Biological Data.

Science.gov (United States)

Yoon, Byoung-Ha; Kim, Seon-Kyu; Kim, Seon-Young

2017-03-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

Evolving Evidence for the Value of Neuroimaging Methods and Biological Markers in Subjects Categorized with Subjective Cognitive Decline.

Science.gov (United States)

Lista, Simone; Molinuevo, Jose L; Cavedo, Enrica; Rami, Lorena; Amouyel, Philippe; Teipel, Stefan J; Garaci, Francesco; Toschi, Nicola; Habert, Marie-Odile; Blennow, Kaj; Zetterberg, Henrik; O'Bryant, Sid E; Johnson, Leigh; Galluzzi, Samantha; Bokde, Arun L W; Broich, Karl; Herholz, Karl; Bakardjian, Hovagim; Dubois, Bruno; Jessen, Frank; Carrillo, Maria C; Aisen, Paul S; Hampel, Harald

2015-09-24

There is evolving evidence that individuals categorized with subjective cognitive decline (SCD) are potentially at higher risk for developing objective and progressive cognitive impairment compared to cognitively healthy individuals without apparent subjective complaints. Interestingly, SCD, during advancing preclinical Alzheimer's disease (AD), may denote very early, subtle cognitive decline that cannot be identified using established standardized tests of cognitive performance. The substantial heterogeneity of existing SCD-related research data has led the Subjective Cognitive Decline Initiative (SCD-I) to accomplish an international consensus on the definition of a conceptual research framework on SCD in preclinical AD. In the area of biological markers, the cerebrospinal fluid signature of AD has been reported to be more prevalent in subjects with SCD compared to healthy controls; moreover, there is a pronounced atrophy, as demonstrated by magnetic resonance imaging, and an increased hypometabolism, as revealed by positron emission tomography, in characteristic brain regions affected by AD. In addition, SCD individuals carrying an apolipoprotein ɛ4 allele are more likely to display AD-phenotypic alterations. The urgent requirement to detect and diagnose AD as early as possible has led to the critical examination of the diagnostic power of biological markers, neurophysiology, and neuroimaging methods for AD-related risk and clinical progression in individuals defined with SCD. Observational studies on the predictive value of SCD for developing AD may potentially be of practical value, and an evidence-based, validated, qualified, and fully operationalized concept may inform clinical diagnostic practice and guide earlier designs in future therapy trials.

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

Science.gov (United States)

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

2017-03-01

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

Network Reconstruction of Dynamic Biological Systems

OpenAIRE

Asadi, Behrang

2013-01-01

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

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

Science.gov (United States)

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

2012-12-01

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

A roadmap for the integration of culture into developmental psychopathology.

Science.gov (United States)

Causadias, José M

2013-11-01

In this paper, I propose a roadmap for the integration of culture in developmental psychopathology. This integration is pressing because culture continues to be somewhat disconnected from theory, research, training, and interventions in developmental psychopathology, thus limiting our understanding of the epigenesis of mental health. I argue that in order to successfully integrate culture into developmental psychopathology, it is crucial to (a) study cultural development, (b) consider both individual-level and social-level cultural processes, (c) examine the interplay between culture and biology, and (d) promote improved and direct cultural assessment. I provide evidence in support of each of these guidelines, present alternative conceptual frameworks, and suggest new lines of research. Hopefully, that these directions will contribute to the emerging field of cultural development and psychopathology, which focuses on the elucidation of the cultural processes that initiate, maintain, or derail trajectories of normal and abnormal behavior.

A Conceptual Model and Clinical Framework for Integrating Mindfulness into Family Therapy with Adolescents.

Science.gov (United States)

Brody, Janet L; Scherer, David G; Turner, Charles W; Annett, Robert D; Dalen, Jeanne

2017-06-07

Individual and group-based psychotherapeutic interventions increasingly incorporate mindfulness-based principles and practices. These practices include a versatile set of skills such as labeling and attending to present-moment experiences, acting with awareness, and avoiding automatic reactivity. A primary motivation for integrating mindfulness into these therapies is compelling evidence that it enhances emotion regulation. Research also demonstrates that family relationships have a profound influence on emotion regulation capacities, which are central to family functioning and prosocial behavior more broadly. Despite this evidence, no framework exists to describe how mindfulness might integrate into family therapy. This paper describes the benefits of mindfulness-based interventions, highlighting how and why informal mindfulness practices might enhance emotion regulation when integrated with family therapy. We provide a clinical framework for integrating mindfulness into family therapy, particularly as it applies to families with adolescents. A brief case example details sample methods showing how incorporating mindfulness practices into family therapy may enhance treatment outcomes. A range of assessment modalities from biological to behavioral demonstrates the breadth with which the benefits of a family-based mindfulness intervention might be evaluated. © 2017 The Authors. Family Process published by Wiley Periodicals, Inc. on behalf of Family Process Institute.

Manipulation of biological samples using micro and nano techniques.

Science.gov (United States)

Castillo, Jaime; Dimaki, Maria; Svendsen, Winnie Edith

2009-01-01

The constant interest in handling, integrating and understanding biological systems of interest for the biomedical field, the pharmaceutical industry and the biomaterial researchers demand the use of techniques that allow the manipulation of biological samples causing minimal or no damage to their natural structure. Thanks to the advances in micro- and nanofabrication during the last decades several manipulation techniques offer us the possibility to image, characterize and manipulate biological material in a controlled way. Using these techniques the integration of biomaterials with remarkable properties with physical transducers has been possible, giving rise to new and highly sensitive biosensing devices. This article reviews the different techniques available to manipulate and integrate biological materials in a controlled manner either by sliding them along a surface (2-D manipulation), by grapping them and moving them to a new position (3-D manipulation), or by manipulating and relocating them applying external forces. The advantages and drawbacks are mentioned together with examples that reflect the state of the art of manipulation techniques for biological samples (171 references).

EVALUATING THE ECOLOGICAL RESILIENT DRIVEN PERFORMANCE OF A TROPICAL WASTE STABILIZATION POND SYSTEM USING ECOLOGICAL SIGNATURE OF BIOLOGICAL INTEGRITY

OpenAIRE

Susmita Lahiri Ganguly; Dipanwita Sarkar Paria; B. B. Jana

2015-01-01

Using ecological signature of biological integrity as a measure of performance, the reclamation efficiency of waste stabilization ponds was evaluated over a period of four years in a tropical sewage treatment plant – cum fish culture consisting of two anaerobic, two facultative and four maturation ponds located serially across the sewage effluent gradient. The four maturation ponds were used for batch culture of fish. Samples of surface and bottom water as well as surface sediment were collec...

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

Science.gov (United States)

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research. PMID:20150964

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

Directory of Open Access Journals (Sweden)

Eric Young

2010-01-01

Full Text Available The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1 the process units and associated streams of the central dogma, (2 the intrinsic regulatory mechanisms, and (3 the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Synthetic biology: tools to design, build, and optimize cellular processes.

Science.gov (United States)

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Innovative use of the integrative review to evaluate evidence of technology transformation in healthcare.

Science.gov (United States)

Phillips, Andrew B; Merrill, Jacqueline A

2015-12-01

Healthcare is in a period significant transformational activity through the accelerated adoption of healthcare technologies, new reimbursement systems that emphasize shared savings and care coordination, and the common place use of mobile technologies by patients, providers, and others. The complexity of healthcare creates barriers to transformational activity and has the potential to inhibit the desired paths toward change envisioned by policymakers. Methods for understanding how change is occurring within this complex environment are important to the evaluation of delivery system reform and the role of technology in healthcare transformation. This study examines the use on an integrative review methodology to evaluate the healthcare literature for evidence of technology transformation in healthcare. The methodology integrates the evaluation of a broad set of literature with an established evaluative framework to develop a more complete understanding of a particular topic. We applied this methodology and the framework of punctuated equilibrium (PEq) to the analysis of the healthcare literature from 2004 to 2012 for evidence of technology transformation, a time during which technology was at the forefront of healthcare policy. The analysis demonstrated that the established PEq framework applied to the literature showed considerable potential for evaluating the progress of policies that encourage healthcare transformation. Significant inhibitors to change were identified through the integrative review and categorized into ten themes that describe the resistant structure of healthcare delivery: variations in the environment; market complexity; regulations; flawed risks and rewards; change theories; barriers; ethical considerations; competition and sustainability; environmental elements, and internal elements. We hypothesize that the resistant nature of the healthcare system described by this study creates barriers to the direct consumer involvement and engagement

The Interaction Between Pubertal Timing and Peer Popularity for Boys and Girls: An Integration of Biological and Interpersonal Perspectives on Adolescent Depression.

Science.gov (United States)

Teunissen, Hanneke A; Adelman, Caroline B; Prinstein, Mitchell J; Spijkerman, Renske; Poelen, Evelien A P; Engels, Rutger C M E; Scholte, Ron H J

2011-04-01

The transition to adolescence marks a time of sharply increased vulnerability to the development of depression, particularly among girls. Past research has examined isolated risk factors from individual theoretical models (e.g., biological, interpersonal, and cognitive) of depression, but few have examined integrative models. This study investigated the conjoint effects of early pubertal timing and popularity in the longitudinal prediction of depressive symptoms. A total of 319 girls and 294 boys (ages 11-14) provided information on their pubertal status, depressive symptoms, and the social status (i.e., popularity) of their peers. Adolescents completed a second measure of depressive symptoms 11 months after the initial time point. Findings supported an integrated biological-interpersonal model in explaining the development of depressive symptoms during adolescence. Early pubertal development was associated with increase in depressive symptoms only when accompanied by low levels of popularity. High levels of popularity buffered the association between early pubertal development and later depressive symptoms. Unexpectedly, these results were significant both for girls and boys. Results are discussed in terms of dynamic systems theories.

CoreFlow: A computational platform for integration, analysis and modeling of complex biological data

DEFF Research Database (Denmark)

Pasculescu, Adrian; Schoof, Erwin; Creixell, Pau

2014-01-01

between data generation, analysis and manuscript writing. CoreFlow is being released to the scientific community as an open-sourced software package complete with proteomics-specific examples, which include corrections for incomplete isotopic labeling of peptides (SILAC) or arginine-to-proline conversion......A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which...... provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Python, or Perl for processing, correcting and modeling this data. CoreFlow organizes these scripts...

Introductory biology students' conceptual models and explanations of the origin of variation.

Science.gov (United States)

Speth, Elena Bray; Shaw, Neil; Momsen, Jennifer; Reinagel, Adam; Le, Paul; Taqieddin, Ranya; Long, Tammy

2014-01-01

Mutation is the key molecular mechanism generating phenotypic variation, which is the basis for evolution. In an introductory biology course, we used a model-based pedagogy that enabled students to integrate their understanding of genetics and evolution within multiple case studies. We used student-generated conceptual models to assess understanding of the origin of variation. By midterm, only a small percentage of students articulated complete and accurate representations of the origin of variation in their models. Targeted feedback was offered through activities requiring students to critically evaluate peers' models. At semester's end, a substantial proportion of students significantly improved their representation of how variation arises (though one-third still did not include mutation in their models). Students' written explanations of the origin of variation were mostly consistent with their models, although less effective than models in conveying mechanistic reasoning. This study contributes evidence that articulating the genetic origin of variation is particularly challenging for learners and may require multiple cycles of instruction, assessment, and feedback. To support meaningful learning of the origin of variation, we advocate instruction that explicitly integrates multiple scales of biological organization, assessment that promotes and reveals mechanistic and causal reasoning, and practice with explanatory models with formative feedback. © 2014 E. Bray Speth et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

[Biologic therapy in idiopathic inflammatory myopathy].

Science.gov (United States)

Selva-O'Callaghan, Albert; Ramos Casals, Manel; Grau Junyent, Josep M

2014-09-15

The aim of this article is to study the evidence-based knowledge related to the use of biological therapies in patients diagnosed with idiopathic inflammatory myopathy (dermatomyositis, polymyositis and inclusion body myositis). In this review the leading published studies related to the use of biological therapy in patients with myositis are analysed; mainly those with high methodological standards, that means randomized and controlled studies. Methodological drawbacks due to the rarity and heterogeneity of these complex diseases are also addressed. Up to now is not possible to ascertain the biologics as a recommended therapy in patients with myositis, at least based in the current evidence-based knowledge, although it can not be neglected as a therapeutic option in some clinical situations, taking into account the scarce of effective treatments in those patients, especially in refractory myositis. Future studies probably will help to better define the role of biological therapies in patients with idiopathic inflammatory myopathy. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

Neurosurgery clinical registry data collection utilizing Informatics for Integrating Biology and the Bedside and electronic health records at the University of Rochester.

Science.gov (United States)

Pittman, Christine A; Miranpuri, Amrendra S

2015-12-01

In a population health-driven health care system, data collection through the use of clinical registries is becoming imperative to continue to drive effective and efficient patient care. Clinical registries rely on a department's ability to collect high-quality and accurate data. Currently, however, data are collected manually with a high risk for error. The University of Rochester's Department of Neurosurgery in conjunction with the university's Clinical and Translational Science Institute has implemented the integrated use of the Informatics for Integrating Biology and the Bedside (i2b2) informatics framework with the Research Electronic Data Capture (REDCap) databases.

Successfully integrating aged care services: A review of the evidence and tools emerging from a long-term care program

Directory of Open Access Journals (Sweden)

Michael J. Stewart

2013-02-01

Full Text Available Background: Providing efficient and effective aged care services is one of the greatest public policy concerns currently facing governments. Increasing the integration of care services has the potential to provide many benefits including increased access, promoting greater efficiency, and improving care outcomes. There is little research, however, investigating how integrated aged care can be successfully achieved. The PRISMA (Program of Research to Integrate Services for the Maintenance of Autonomy project, from Quebec, Canada, is one of the most systematic and sustained bodies of research investigating the translation and outcomes of an integrated care policy into practice.  The PRISMA research program has run since 1988, yet there has been no independent systematic review of this work to draw out the lessons learnt. Methods: Narrative review of all literature emanating from the PRISMA project between 1988 and 2012. Researchers accessed an online list of all published papers from the program website. The reference lists of papers were hand searched to identify additional literature. Finally, Medline, Pubmed, EMBASE and Google Scholar indexing databases were searched using key terms and author names. Results were extracted into specially designed spread sheets for analysis. Results: 45 journal articles and two books authored or co-authored by the PRISMA team were identified. Research was primarily concerned with: the design, development and validation of screening and assessment tools; and results generated from their application. Both quasi-experimental and cross sectional analytic designs were used extensively. Contextually appropriate expert opinion was obtained using variations on the Delphi Method. Literature analysis revealed the structures, processes and outcomes which underpinned the implementation. PRISMA provides evidence that integrating care for older persons is beneficial to individuals through reducing incidence of functional

Successfully integrating aged care services: A review of the evidence and tools emerging from a long-term care program

Directory of Open Access Journals (Sweden)

Michael J. Stewart

2013-02-01

Full Text Available Background: Providing efficient and effective aged care services is one of the greatest public policy concerns currently facing governments. Increasing the integration of care services has the potential to provide many benefits including increased access, promoting greater efficiency, and improving care outcomes. There is little research, however, investigating how integrated aged care can be successfully achieved. The PRISMA (Program of Research to Integrate Services for the Maintenance of Autonomy project, from Quebec, Canada, is one of the most systematic and sustained bodies of research investigating the translation and outcomes of an integrated care policy into practice.  The PRISMA research program has run since 1988, yet there has been no independent systematic review of this work to draw out the lessons learnt.Methods: Narrative review of all literature emanating from the PRISMA project between 1988 and 2012. Researchers accessed an online list of all published papers from the program website. The reference lists of papers were hand searched to identify additional literature. Finally, Medline, Pubmed, EMBASE and Google Scholar indexing databases were searched using key terms and author names. Results were extracted into specially designed spread sheets for analysis.Results: 45 journal articles and two books authored or co-authored by the PRISMA team were identified. Research was primarily concerned with: the design, development and validation of screening and assessment tools; and results generated from their application. Both quasi-experimental and cross sectional analytic designs were used extensively. Contextually appropriate expert opinion was obtained using variations on the Delphi Method. Literature analysis revealed the structures, processes and outcomes which underpinned the implementation. PRISMA provides evidence that integrating care for older persons is beneficial to individuals through reducing incidence of functional

The Chernobyl Tissue Bank — A Repository for Biomaterial and Data Used in Integrative and Systems Biology Modeling the Human Response to Radiation

Science.gov (United States)

Thomas, Geraldine; Unger, Kristian; Krznaric, Marko; Galpine, Angela; Bethel, Jackie; Tomlinson, Christopher; Woodbridge, Mark; Butcher, Sarah

2012-01-01

The only unequivocal radiological effect of the Chernobyl accident on human health is the increase in thyroid cancer in those exposed in childhood or early adolescence. In response to the scientific interest in studying the molecular biology of thyroid cancer post Chernobyl, the Chernobyl Tissue Bank (CTB: www.chernobyltissuebank.com) was established in 1998. Thus far it is has collected biological samples from 3,861 individuals, and provided 27 research projects with 11,254 samples. The CTB was designed from its outset as a resource to promote the integration of research and clinical data to facilitate a systems biology approach to radiation related thyroid cancer. The project has therefore developed as a multidisciplinary collaboration between clinicians, dosimetrists, molecular biologists and bioinformaticians and serves as a paradigm for tissue banking in the omics era. PMID:24704918

The 'third wave' of HIV prevention: filling gaps in integrated interventions, knowledge, and funding.

Science.gov (United States)

Sepúlveda, Jaime

2012-07-01

There is growing optimism in the global health community that the HIV epidemic can be halted. After decades of relying primarily on behavior change to prevent HIV transmission, a second generation of prevention efforts based on medical or biological interventions such as male circumcision and preexposure prophylaxis--the use of antiretroviral drugs to protect uninfected, at-risk individuals--has shown promising results. This article calls for a third generation of HIV prevention efforts that would integrate behavioral, biological, and structural interventions focused on the social, political, and environmental underpinnings of the epidemic, making use of local epidemiological evidence to target affected populations. In this third wave, global programs should deliver HIV prevention services together with cost-effective interventions for reproductive health and for tuberculosis, malaria, and other diseases. Additionally, new efforts are needed to address gaps in HIV prevention research, evaluation, and implementation. Increased and sustained funding, along with evidence-based allocation of funds, will be necessary to accelerate the decline in new HIV infections.

The SCIDOTS Project: evidence of benefits of an integrated tobacco cessation intervention in tuberculosis care on treatment outcomes.

Science.gov (United States)

Awaisu, Ahmed; Nik Mohamed, Mohamad Haniki; Mohamad Noordin, Noorliza; Abd Aziz, Noorizan; Syed Sulaiman, Syed Azhar; Muttalif, Abdul Razak; Ahmad Mahayiddin, Aziah

2011-09-23

There is substantial evidence to support the association between tuberculosis (TB) and tobacco smoking and that the smoking-related immunological abnormalities in TB are reversible within six weeks of cessation. Therefore, connecting TB and tobacco cessation interventions may produce significant benefits and positively impact TB treatment outcomes. However, no study has extensively documented the evidence of benefits of such integration. SCIDOTS Project is a study from the context of a developing nation aimed to determine this. An integrated TB-tobacco intervention was provided by trained TB directly observed therapy short-course (DOTS) providers at five chest clinics in Malaysia. The study was a prospective non-randomized controlled intervention using quasi-experimental design. Using Transtheoretical Model approach, 120 eligible participants who were current smokers at the time of TB diagnosis were assigned to either of two treatment groups: conventional TB DOTS plus smoking cessation intervention (integrated intervention or SCIDOTS group) or conventional TB DOTS alone (comparison or DOTS group). At baseline, newly diagnosed TB patients considering quitting smoking within the next 30 days were placed in the integrated intervention group, while those who were contemplating quitting were assigned to the comparison group. Eleven sessions of individualized cognitive behavioral therapy with or without nicotine replacement therapy were provided to each participant in the integrated intervention group. The impacts of the novel approach on biochemically validated smoking cessation and TB treatment outcomes were measured periodically as appropriate. A linear effect on both 7-day point prevalence abstinence and continuous abstinence was observed over time in the intervention group. At the end of 6 months, patients who received the integrated intervention had significantly higher rate of success in quitting smoking when compared with those who received the conventional TB

Teaching Biology for a Sustainable Future

Science.gov (United States)

Musante, Susan

2011-01-01

Students at Calvin College in Grand Rapids, Michigan, can now take an innovative biology course in which an integrated, interdisciplinary, problem-based approach is used--one that the scientific community itself is promoting. The first course in a four-semester sequence, Biology 123--The Living World: Concepts and Connections--explores real-world…

Crossing Boundaries in Undergraduate Biology Education

Science.gov (United States)

Vanderklein, Dirk; Munakata, Mika; McManus, Jason

2016-01-01

In an effort to make mathematics relevant to biology students, the authors developed two modules that sought to integrate mathematics and ecology instruction to differing degrees. The modules were developed by a team of biology and mathematics educators and were implemented in an ecology course using three different instructional methods for three…

An integrated assessment of pollution and biological effects in flounder, mussels and sediment in the southern Baltic Sea coastal area.

Science.gov (United States)

Dabrowska, Henryka; Kopko, Orest; Lehtonen, Kari K; Lang, Thomas; Waszak, Ilona; Balode, Maija; Strode, Evita

2017-02-01

Organic and metal contaminants and biological effects were investigated in flounder, mussels, and sediments in the southern Baltic Sea coastal area in order to assess environmental quality status in that area. Four sites were selected, including two within the Gulf of Gdańsk (GoG). In biota and sediment at each site, DDTs dominated over PCBs and PBDEs were the least abundant among organic contaminants. Their concentrations decreased progressively outward from GoG. Among metal contaminants, the levels of Hg, Pb, and Cd were elevated in GoG. Biomarkers in flounder, EROD activity and DNA SB, showed moderate positive correlations with organic and metal contaminants. In flounder, the integrated biomarker index (IBR/n) presented a spatial trend coherent with chemical pollution index (CPI), but there was no clear spatial correspondence between IBR/n and CPI in mussels nor between sediment toxicity index (STI) and sediment CPI. The integrated assessment of contaminant and biological effect data against available assessment criteria indicated that in biota, the contaminant assessment thresholds were most often exceeded by CB-118, heptachlor, PBDE, and Hg (in the GoG sediments by p,p'-DDT, Hg and Cd), while of the biological determinants, the threshold was breeched by AChE activity in mussels in GoG. Applying the ICES/OSPAR traffic-light approach showed that of the 50 parameters assessed at each site, there were 18% of determinants in the red color category in the two GoG sites and 8% of determinants in the two sites outside GoG, which indicated that none of the four investigated sites attained good environmental status (GES).

Biological indication in aquatic ecosystems. Biological indication in limnic and coastal ecosystems - fundamentals, techniques, methodology

International Nuclear Information System (INIS)

Gunkel, G.

1994-01-01

Biological methods of water quality evaluation today form an integral part of environmental monitoring and permit to continuously monitor the condition of aquatic ecosystems. They indicate both improvements in water quality following redevelopment measures, and the sometimes insidious deterioration of water quality. This book on biological indication in aquatic ecosystems is a compendium of measurement and evaluation techniques for limnic systems by means of biological parameters. At present, however, an intense discussion of biological evaluation techniques is going on, for one thing as a consequence of the German reunification and the need to unify evaluation techniques, and for another because of harmonizations within the European Community. (orig./EF) [de

Biological intrusion of low-level-waste trench covers

Science.gov (United States)

Hakonson, T. E.; Gladney, E. S.

The long-term integrity of low-level waste shallow land burialsites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. The need to consider biological processes as being potentially important in reducing the integrity of waste burial site cover treatment is demonstrated. One approach to limiting biological intrusion through the waste cover is to apply a barrier within the profile to limit root and animal penetration with depth. Experiments in the Los Alamos Experimental Engineered Test Facility were initiated to develop and evaluate biological barriers that are effective in minimizing intrusion into waste trenches. The experiments that are described employ four different candidate barrier materials of geologic origin. Experimental variables that will be evaluated, in addition to barrier type, are barrier depth and sil overburden depth.

The Integration of Cognitive Remediation Therapy into the Whole Psychosocial Rehabilitation Process: An Evidence-Based and Person-Centered Approach

Directory of Open Access Journals (Sweden)

Rafael Penadés

2012-01-01

Full Text Available Cognitive remediation therapies seem to ameliorate cognitive impairments in patients with schizophrenia. Interestingly, some improvement in daily functioning can also be expected as a result. However, to achieve these results it is necessary that cognitive remediation is carried out in the context of broader psychosocial rehabilitation involving the learning of other communication, social, and self-control skills. Unfortunately, little is known about how to integrate these different rehabilitation tools in broader rehabilitation programs. Based on both the neurocognitive behavioral approach and the action theory framework, a hierarchical flowchart is represented in this paper to integrate CRT with other evidence-based psychological therapies in outpatient settings. Finally, some evidence is provided in which cognitive abilities need to be targeted in remediation programs to improve functioning. In summary, to improve daily functioning, according to these studies, cognitive remediation needs to include the teaching of some cognitive strategies that target executive skills.

Assessment of radiation damage - the need for a multi-parametric and integrative approach with the help of both clinical and biological dosimetry

International Nuclear Information System (INIS)

Meineke, Viktor

2008-01-01

provide the best basis for triage and planning and providing of medical treatment after accidental radiation exposure always different and independent diagnostic procedures integrating all clinical aspects as well as different biological indicators have to be applied. Up to now this multi parametric approach is missing in medical radiation accident management. A new integrative concept is shown and discussed. (author)

The Evolution of Consciousness as a Planetary Imperative: An Integration of Integral Views

Directory of Open Access Journals (Sweden)

Jennifer Gidley

2007-12-01

contemporary academic literature, culminating in a substantial consideration of research that identifies and/or enacts new stage(s or movements of consciousness. In particular, I highlight the extensive adult developmental psychology research that identifies several stages of postformal thinking, and recent critical, ecological and philosophical literature that identifies an emerging planetary consciousness. In summary, my research reveals an interpretation of scientific and other evidence that points beyond the formal, modernist worldview to an emerging postformal-integral-planetary consciousness. I posit that a broader academic consideration of such an integration of integral theoretic narratives could potentially broaden the general evolution discourse beyond its current biological bias. The article concludes with a rewinding of narrative threads, reflecting on the narrators, the journey, and the language of the discourse. Appendixes A and B explore the theoretical implications of the emergence of postformal-integral-planetary consciousness for a reframing of modernist conceptions of time and space. Appendix C holds an aesthetic lens to the evolution of consciousness through examples from the genealogy of writing.

Palm oil mill effluent treatment using a two-stage microbial fuel cells system integrated with immobilized biological aerated filters.

Science.gov (United States)

Cheng, Jia; Zhu, Xiuping; Ni, Jinren; Borthwick, Alistair

2010-04-01

An integrated system of two-stage microbial fuel cells (MFCs) and immobilized biological aerated filters (I-BAFs) was used to treat palm oil mill effluent (POME) at laboratory scale. By replacing the conventional two-stage up-flow anaerobic sludge blanket (UASB) with a newly proposed upflow membrane-less microbial fuel cell (UML-MFC) in the integrated system, significant improvements on NH(3)-N removal were observed and direct electricity generation implemented in both MFC1 and MFC2. Moreover, the coupled iron-carbon micro-electrolysis in the cathode of MFC2 further enhanced treatment efficiency of organic compounds. The I-BAFs played a major role in further removal of NH(3)-N and COD. For influent COD and NH(3)-N of 10,000 and 125 mg/L, respectively, the final effluents COD and NH(3)-N were below 350 and 8 mg/L, with removal rates higher than 96.5% and 93.6%. The GC-MS analysis indicated that most of the contaminants were satisfactorily biodegraded by the integrated system. Copyright 2009 Elsevier Ltd. All rights reserved.

Integrating nutrition and child development interventions: scientific basis, evidence of impact, and implementation considerations.

Science.gov (United States)

Black, Maureen M; Pérez-Escamilla, Rafael; Rao, Sylvia Fernandez

2015-11-01

The Millennium Development Goals (MDGs) have contributed to unprecedented reductions in poverty and improvement in the lives of millions of men, women, and children in low- and middle-income countries. Yet, hundreds of millions of children under 5 y of age are not reaching their developmental potential. This article reviews the scientific basis for early childhood nutrition and child development interventions, the impact of integrated interventions on children's linear growth and cognitive development, and implementation strategies for integrated nutrition and child development programs. Advances in brain science have documented that the origins of adult health and well-being are grounded in early childhood, from conception through age 24 mo (first 1000 d) and extending to age 5 y (second 1000 d). Young children with adequate nutrition, nurturant caregiving, and opportunities for early learning have the best chances of thriving. Evidence from adoption, experimental, and quasi-experimental studies has shown that stunting prevention is sensitive during the first 1000 d, and sensitivity to child development interventions extends through the second 1000 d. Cognitive development responds to interventions post–1000 d with effect sizes that are inversely associated with initial age and length of program exposure. Integrated interventions need governance structures that support integrated policies and programming, with attention to training, supervision, and monitoring. The MDGs have been replaced by the Sustainable Development Goals (SDGs), with targets for the next 15 y. Achievement of the SDGs depends on children receiving adequate nutrition, nurturant caregiving, and learning opportunities from conception through age 5.

Conservation Physiology and Conservation Pathogens: White-Nose Syndrome and Integrative Biology for Host-Pathogen Systems.

Science.gov (United States)

Willis, Craig K R

2015-10-01

Conservation physiology aims to apply an understanding of physiological mechanisms to management of imperiled species, populations, or ecosystems. One challenge for physiologists hoping to apply their expertise to conservation is connecting the mechanisms we study, often in the laboratory, with the vital rates of populations in the wild. There is growing appreciation that infectious pathogens can threaten populations and species, and represent an important issue for conservation. Conservation physiology has much to offer in terms of addressing the threat posed to some host species by infectious pathogens. At the same time, the well-developed theoretical framework of disease ecology could provide a model to help advance the application of physiology to a range of other conservation issues. Here, I use white-nose syndrome (WNS) in hibernating North American bats as an example of a conservation problem for which integrative physiological research has been a critical part of research and management. The response to WNS highlights the importance of a well-developed theoretical framework for the application of conservation physiology to a particular threat. I review what is known about physiological mechanisms associated with mortality from WNS and emphasize the value of combining a strong theoretical background with integrative physiological studies in order to connect physiological mechanisms with population processes and thereby maximize the potential benefits of conservation physiology. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

A functional overview of conservation biological control

DEFF Research Database (Denmark)

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

2017-01-01

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

XML-based approaches for the integration of heterogeneous bio-molecular data.

Science.gov (United States)

Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

2009-10-15

The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

Introductory Biology Students’ Conceptual Models and Explanations of the Origin of Variation

Science.gov (United States)

Shaw, Neil; Momsen, Jennifer; Reinagel, Adam; Le, Paul; Taqieddin, Ranya; Long, Tammy

2014-01-01

Mutation is the key molecular mechanism generating phenotypic variation, which is the basis for evolution. In an introductory biology course, we used a model-based pedagogy that enabled students to integrate their understanding of genetics and evolution within multiple case studies. We used student-generated conceptual models to assess understanding of the origin of variation. By midterm, only a small percentage of students articulated complete and accurate representations of the origin of variation in their models. Targeted feedback was offered through activities requiring students to critically evaluate peers’ models. At semester's end, a substantial proportion of students significantly improved their representation of how variation arises (though one-third still did not include mutation in their models). Students’ written explanations of the origin of variation were mostly consistent with their models, although less effective than models in conveying mechanistic reasoning. This study contributes evidence that articulating the genetic origin of variation is particularly challenging for learners and may require multiple cycles of instruction, assessment, and feedback. To support meaningful learning of the origin of variation, we advocate instruction that explicitly integrates multiple scales of biological organization, assessment that promotes and reveals mechanistic and causal reasoning, and practice with explanatory models with formative feedback. PMID:25185235

Biological evidence of low ionizing radiation doses; Biologischer Nachweis niedriger Dosen ionisierender Strahlung

Energy Technology Data Exchange (ETDEWEB)

Mirsch, Johanna

2017-03-17

Throughout life, every person is constantly exposed to different types of ionising radiation, without even noticing the exposure. The mean radiation exposure for people living in Germany amounts to approximately 4 mSv per year and encompasses the exposure from natural and man-made sources. The risks associated with exposure to low doses of radiation are still the subject of intense and highly controversial discussions, emphasizing the social relevance of studies investigating the effects of low radiation doses. In this thesis, DNA double-strand breaks (DSBs) were analyzed within three projects covering different aspects. DSBs are among the most hazardous DNA lesions induced by ionizing radiation, because this type of damage can easily lead to the loss of genetic information. Consequently, the DSB presents a high risk for the genetic integrity of the cell. In the first project, extensive results uncovered the track structure of charged particles in a biological model tissue. This provided the first biological data that could be used for comparison with data that were measured or predicted using theoretical physical dosimetry methods and mathematical simulations. Charged particles contribute significantly to the natural radiation exposure and are used increasingly in cancer radiotherapy because they are more efficient in tumor cell killing than X- or γ-rays. The difference in the biological effects of high energy charged particles compared with X- or γ-rays is largely determined by the spatial distribution of their energy deposition and the track structure inducing a three-dimensional damage pattern in living cells. This damage pattern consists of cells directly hit by the particle receiving a high dose and neighboring cells not directly hit by primary particles but exposed to far-reaching secondary electrons (δ-electrons). These cells receive a much lower dose deposition in the order of a few mGy. The radial dose distribution of single particle tracks was

On the integration of financial markets: How strong is the evidence from five international stock markets?

Science.gov (United States)

Bentes, Sónia R.

2015-07-01

This paper examines the integration of financial markets using data from five international stock markets in the context of globalization. The theoretical basis of this study relies on the price theory and the Law of One Price, which was adjusted to the framework of financial markets. When price levels are nonstationary, cointegration and the error correction model constitute a powerful tool for the empirical examination of market integration. The error correction model provides a fully dynamic framework that allows to separating the long and the short run effects of the integration process. A dataset encompassing the daily stock price series of the PSI 20 (Portugal), IBEX 35 (Spain), FTSE 100 (UK), NIKKEI 225 (Japan) and SP 500 (US) indices from January 4th 1999 to September 19th 2014 is employed. The results highlight that these five stock markets are linked together by just one long-run relationship, although short-run movements are also present, which causes distinct deviations from the long-run equilibrium relationship. Endogeneity prevails in the system as a whole. While market integration in the sense of the Law of One Price holds, pairwise full price transmission has limited evidence. The results therefore show that stock market price movements are highly nonlinear and complex.

'More than two': integrating biological control and sterile insects, from factory to field, and the possibility of its implementation in Argentina

Energy Technology Data Exchange (ETDEWEB)

Cladera, Jorge L.; Viscarret, Mariana M.; Carabajal Paladino, Leonela Z.; Pietrek, Alejandro [Instituto de Tecnologia Agropecuaria (INTA), Castelar (Argentina). Inst. de Genetica; Soria, M. Alejandra; Ovruski, Sergio M. [Consejo Nacional de Investigaciones Cientificas y Tecnicas (PROIMI/CONICET), Tucuman (Argentina). Planta Piloto de Procesos Industrials Microbiolo

2006-07-01

No single control measure is able to provide full control of a pest. Integration of techniques like the sterile insect (SIT) with biological control practices (BC) should be intensively sough for. This possibility is revised here in connection with the fruit fly pest problems in Argentina. Theoretical reasons as well as practical conveniences for this integration are reviewed in this paper, the intention of which is to promote a discussion on how to approach the experimental study of the SIT+CB integration problem, i.e. how to measure the effects of each separate control measure as well as that of both acting together, in a repeatable manner. Arguments are advanced in favor of the joint production and releases of sterile fruit flies and parasitoids. (author)

Electrophysiological evidence for speech-specific audiovisual integration.

Science.gov (United States)

Baart, Martijn; Stekelenburg, Jeroen J; Vroomen, Jean

2014-01-01

Lip-read speech is integrated with heard speech at various neural levels. Here, we investigated the extent to which lip-read induced modulations of the auditory N1 and P2 (measured with EEG) are indicative of speech-specific audiovisual integration, and we explored to what extent the ERPs were modulated by phonetic audiovisual congruency. In order to disentangle speech-specific (phonetic) integration from non-speech integration, we used Sine-Wave Speech (SWS) that was perceived as speech by half of the participants (they were in speech-mode), while the other half was in non-speech mode. Results showed that the N1 obtained with audiovisual stimuli peaked earlier than the N1 evoked by auditory-only stimuli. This lip-read induced speeding up of the N1 occurred for listeners in speech and non-speech mode. In contrast, if listeners were in speech-mode, lip-read speech also modulated the auditory P2, but not if listeners were in non-speech mode, thus revealing speech-specific audiovisual binding. Comparing ERPs for phonetically congruent audiovisual stimuli with ERPs for incongruent stimuli revealed an effect of phonetic stimulus congruency that started at ~200 ms after (in)congruence became apparent. Critically, akin to the P2 suppression, congruency effects were only observed if listeners were in speech mode, and not if they were in non-speech mode. Using identical stimuli, we thus confirm that audiovisual binding involves (partially) different neural mechanisms for sound processing in speech and non-speech mode. © 2013 Published by Elsevier Ltd.

Integration of evidence-based and experience-based design: contributions from a study in a health care service

Directory of Open Access Journals (Sweden)

Mirela S. da Rosa

2015-06-01

Full Text Available The purpose this paper is to present an integrated study of Service Design and the Mechanism of the Production Function (MPF for redesigning the health care services to improve the perceived value of the patient and increase the productivity of hospital operations by eliminating wastes. The method used was action research and applied in an ICU of a private hospital in southern Brazil. The techniques of participant observation, interviews, archival research and meetings co-creation with a team of the hospital were used to collect data. Data were analyzed through content analysis of the interviews and the Design Service and Production Engineering tools. Evidence based approaches tends to contribute to the replication of the project outcomes in future cases. The MPF can support project development in the field of Design, as well the integrated approach developed in the healthcare sector, helped to devote more time to the phases of diagnosis and implementation. The findings are useful to demonstrate that can use simultaneously approaches the Service Design and MPF for the development of more robust solutions in health care environment. Further research could be done in other private or public hospitals as well as in other hospital units besides the ICUs. Limitations include the work done in a single hospital and service unit, data collected from a small group of people in the hospital. Integrating Evidence-Based Design, Experience-Based Design and the MPF can produce a more robust way to justify and define the focus of improvements in health care services.

Using Active Learning to Teach Concepts and Methods in Quantitative Biology.

Science.gov (United States)

Waldrop, Lindsay D; Adolph, Stephen C; Diniz Behn, Cecilia G; Braley, Emily; Drew, Joshua A; Full, Robert J; Gross, Louis J; Jungck, John A; Kohler, Brynja; Prairie, Jennifer C; Shtylla, Blerta; Miller, Laura A

2015-11-01

This article provides a summary of the ideas discussed at the 2015 Annual Meeting of the Society for Integrative and Comparative Biology society-wide symposium on Leading Students and Faculty to Quantitative Biology through Active Learning. It also includes a brief review of the recent advancements in incorporating active learning approaches into quantitative biology classrooms. We begin with an overview of recent literature that shows that active learning can improve students' outcomes in Science, Technology, Engineering and Math Education disciplines. We then discuss how this approach can be particularly useful when teaching topics in quantitative biology. Next, we describe some of the recent initiatives to develop hands-on activities in quantitative biology at both the graduate and the undergraduate levels. Throughout the article we provide resources for educators who wish to integrate active learning and technology into their classrooms. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Developing an integrated evidence-based medicine curriculum for family medicine residency at the University of Alberta.

Science.gov (United States)

Allan, G Michael; Korownyk, Christina; Tan, Amy; Hindle, Hugh; Kung, Lina; Manca, Donna

2008-06-01

There is general consensus in the academic community that evidence-based medicine (EBM) teaching is essential. Unfortunately, many postgraduate programs have significant weakness in their EBM programs. The Family Medicine Residency committee at the University of Alberta felt their EBM curriculum would benefit from critical review and revision. An EBM Curriculum Committee was created to evaluate previous components and develop new strategies as needed. Input from stakeholders including faculty and residents was sought, and evidence regarding the teaching and practical application of EBM was gathered. The committee drafted goals and objectives, the primary of which were to assist residents to (1) become competent self-directed, lifelong learners with skills to effectively and efficiently keep up to date, and 2) develop EBM skills to solve problems encountered in daily practice. New curriculum components, each evidence based, were introduced in 2005 and include a family medicine EBM workshop to establish basic EBM knowledge; a Web-based Family Medicine Desktop promoting easier access to evidence-based Internet resources; a brief evidence-based assessment of the research project enhancing integration of EBM into daily practice; and a journal club to support peer learning and growth of rapid appraisal skills. Issues including time use, costs, and change management are discussed. Ongoing evaluation of the curriculum and its components is a principal factor of the design, allowing critical review and adaptation of the curriculum. The first two years of the curriculum have yielded positive feedback from faculty and statistically significant improvement in multiple areas of residents' opinions of the curriculum and comfort with evidence-based practice.

Incorporating biological control into IPM decision making

Science.gov (United States)

Of the many ways biological control can be incorporated into Integrated Pest Management (IPM) programs, natural enemy thresholds are arguably most easily adopted by stakeholders. Integration of natural enemy thresholds into IPM programs requires ecological and cost/benefit crop production data, thr...

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.

Science.gov (United States)

Barbosa-Silva, A; Pafilis, E; Ortega, J M; Schneider, R

2007-12-11

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

Biologic interventions for fatigue in rheumatoid arthritis

DEFF Research Database (Denmark)

Almeida, Celia; Choy, Ernest H S; Hewlett, Sarah

2016-01-01

BACKGROUND: Fatigue is a common and potentially distressing symptom for patients with rheumatoid arthritis (RA), with no accepted evidence-based management guidelines. Evidence suggests that biologic interventions improve symptoms and signs in RA as well as reducing joint damage. OBJECTIVES......: To evaluate the effect of biologic interventions on fatigue in rheumatoid arthritis. SEARCH METHODS: We searched the following electronic databases up to 1 April 2014: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, Current Controlled Trials...... and contacted key authors. SELECTION CRITERIA: We included randomised controlled trials if they evaluated a biologic intervention in people with rheumatoid arthritis and had self reported fatigue as an outcome measure. DATA COLLECTION AND ANALYSIS: Two reviewers selected relevant trials, assessed methodological...

Atomic force microscope with integrated optical microscope for biological applications

OpenAIRE

Putman, Constant A.J.; Putman, C.A.J.; van der Werf, Kees; de Grooth, B.G.; van Hulst, N.F.; Segerink, Franciscus B.; Greve, Jan

1992-01-01

Since atomic force microscopy (AFM) is capable of imaging nonconducting surfaces, the technique holds great promises for high‐resolution imaging of biological specimens. A disadvantage of most AFMs is the fact that the relatively large sample surface has to be scanned multiple times to pinpoint a specific biological object of interest. Here an AFM is presented which has an incorporated inverted optical microscope. The optical image from the optical microscope is not obscured by the cantilever...

Biological soil crusts as an integral component of desert environments

Science.gov (United States)

Belnap, Jayne; Weber, Bettina

2013-01-01

The biology and ecology of biological soil crusts, a soil surface community of mosses, lichens, cyanobacteria, green algae, fungi, and bacteria, have only recently been a topic of research. Most efforts began in the western U.S. (Cameron, Harper, Rushforth, and St. Clair), Australia (Rogers), and Israel (Friedmann, Evenari, and Lange) in the late 1960s and 1970s (e.g., Friedmann et al. 1967; Evenari 1985reviewed in Harper and Marble 1988). However, these groups worked independently of each other and, in fact, were often not aware of each other’s work. In addition, biological soil crust communities were seen as more a novelty than a critical component of dryland ecosystems. Since then, researchers have investigated many different aspects of these communities and have shown that although small to microscopic, biological soil crusts are critical in many ecological processes of deserts. They often cover most of desert soil surfaces and substantially mediate inputs and outputs from desert soils (Belnap et al. 2003). They can be a large source of biodiversity for deserts, as they can contain more species than the surrounding vascular plant community (Rosentreter 1986). These communities are important in reducing soil erosion and increasing soil fertility through the capture of dust and the fixation of atmospheric nitrogen and carbon into forms available to other life forms (Elbert et al. 2012). Because of their many effects on soil characteristics, such as external and internal morphological characteristics, aggregate stability, soil moisture, and permeability, they also affect seed germination and establishment and local hydrological cycles. Covering up to 70% of the surface area in many arid and semi-arid regions around the world (Belnap and Lange 2003), biological soil crusts are a key component within desert environments.

Evolution of natural history information in the 21st century – developing an integrated framework for biological and geographical data

Science.gov (United States)

Reusser, Deborah A.; Lee, Henry

2011-01-01

Threats to marine and estuarine species operate over many spatial scales, from nutrient enrichment at the watershed/estuarine scale to invasive species and climate change at regional and global scales. To help address research questions across these scales, we provide here a standardized framework for a biogeographical information system containing queriable biological data that allows extraction of information on multiple species, across a variety of spatial scales based on species distributions, natural history attributes and habitat requirements. As scientists shift from research on localized impacts on individual species to regional and global scale threats, macroecological approaches of studying multiple species over broad geographical areas are becoming increasingly important. The standardized framework described here for capturing and integrating biological and geographical data is a critical first step towards addressing these macroecological questions and we urge organizations capturing biogeoinformatics data to consider adopting this framework.

Systems Biology — the Broader Perspective

Directory of Open Access Journals (Sweden)

Jonathan Bard

2013-06-01

Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

Fuzzy Decision-Making Fuser (FDMF for Integrating Human-Machine Autonomous (HMA Systems with Adaptive Evidence Sources