Guided interaction exploration in artifact-centric process models

NARCIS (Netherlands)

van Eck, M.L.; Sidorova, N.; van der Aalst, W.M.P.

2017-01-01

Artifact-centric process models aim to describe complex processes as a collection of interacting artifacts. Recent development in process mining allow for the discovery of such models. However, the focus is often on the representation of the individual artifacts rather than their interactions. Based

Architecture design in global and model-centric software development

NARCIS (Netherlands)

Heijstek, Werner

2012-01-01

This doctoral dissertation describes a series of empirical investigations into representation, dissemination and coordination of software architecture design in the context of global software development. A particular focus is placed on model-centric and model-driven software development.

Being or Becoming: Toward an Open-System, Process-Centric Model of Personality.

Science.gov (United States)

Giordano, Peter J

2015-12-01

Mainstream personality psychology in the West neglects the investigation of intra-individual process and variation, because it favors a Being over a Becoming ontology. A Being ontology privileges a structural (e.g., traits or selves) conception of personality. Structure-centric models in turn suggest nomothetic research strategies and the investigation of individual and group differences. This article argues for an open-system, process-centric understanding of personality anchored in an ontology of Becoming. A classical Confucian model of personality is offered as an example of a process-centric approach for investigating and appreciating within-person personality process and variation. Both quantitative and qualitative idiographic strategies can be used as methods of scientific inquiry, particularly the exploration of the Confucian exemplar of psychological health and well-being.

I-centric Communications

CERN Document Server

Arbanowski, S; Steglich, S; Popescu-Zeletin, R

2001-01-01

During the last years, a variety of concepts for service integration and corresponding systems have gained momentum. On the one hand, they aim for the interworking and integration of classical telecommunications and data communications services. On the other hand, they are focusing on universal service access from a variety of end user systems. Looking at humans' communication behavior and communication space, it is obvious that human beings interact frequently in a set of contexts in their environment (communication space). Following this view, we want to build communication systems on the analysis of the individual communication spaces. The results are communication systems adapted to the specific demands of each individual. The authors introduce I-centric Communication Systems, an approach to design communication systems which adapt to the individual communication space and individual environment and situation. In this context "I" means I, or individual, "Centric" means adaptable to I requirements and a ce...

Integrative Health Coach Training: A Model for Shifting the Paradigm Toward Patient-centricity and Meeting New National Prevention Goals.

Science.gov (United States)

Smith, Linda L; Lake, Noelle H; Simmons, Leigh Ann; Perlman, Adam; Wroth, Shelley; Wolever, Ruth Q

2013-05-01

To describe the evolution, training, and results of an emerging allied health profession skilled in eliciting sustainable health-related behavior change and charged with improving patient engagement. Through techniques sourced from humanistic and positive psychology, solution-focused and mindfulness-based therapies, and leadership coaching, Integrative Health Coaching (IHC) provides a mechanism to empower patients through various stages of learning and change. IHC also provides a method for the creation and implementation of forward-focused personalized health plans. Clinical studies employing Duke University Integrative Medicine's model of IHC have demonstrated improvements in measures of diabetes and diabetes risk, weight management, and risk for cardiovascular disease and stroke. By supporting and enabling individuals in making major lifestyle changes for the improvement of their health, IHC carries the potential to reduce rates and morbidity of chronic disease and impact myriad aspects of healthcare. As a model of educational and clinical innovation aimed at patient empowerment and lifestyle modification, IHC is aligned well with the tenets and goals of recently sanctioned federal healthcare reform, specifically the creation of the first National Prevention and Health Promotion Strategy. IHC may allow greater patient-centricity while targeting the lifestyle-related chronic disease that lies at the heart of the current healthcare crisis.

Interactive Model-Centric Systems Engineering (IMCSE) Phase 5

Science.gov (United States)

2018-02-28

Interactive Model-Centric Systems Engineering (IMCSE) Phase 5 Technical Report SERC-2018-TR-104 Feb 28, 2018 Principal Investigator...Date February 28, 2018 Copyright © 2018 Stevens Institute of Technology, Systems Engineering ...Research Center The Systems Engineering Research Center (SERC) is a federally funded University Affiliated Research Center managed by Stevens

Task and Interruption Management in Activity-Centric Computing

DEFF Research Database (Denmark)

Jeuris, Steven

to address these not in isolation, but by fundamentally reevaluating the current computing paradigm. To this end, activity-centric computing has been brought forward as an alternative computing paradigm, addressing the increasing strain put on modern-day computing systems. Activity-centric computing follows...... the scalability and intelligibility of current research prototypes. In this dissertation, I postulate that such issues arise due to a lack of support for the full set of practices which make up activity management. Most notably, although task and interruption management are an integral part of personal...... information management, they have thus far been neglected in prior activity-centric computing systems. Advancing the research agenda of activity-centric computing, I (1) implement and evaluate an activity-centric desktop computing system, incorporating support for interruptions and long-term task management...

Transforming Systems Engineering through Model Centric Engineering

Science.gov (United States)

2017-08-08

Contract No. HQ0034-13-D-0004 Report No. SERC-2017-TR-110 Date: August 8, 2017 Transforming Systems Engineering through Model-Centric... Engineering Technical Report SERC-2017-TR-110 Update: August 8, 2017 Principal Investigator: Mark Blackburn, Stevens Institute of Technology Co...Evangelista Sponsor: U.S. Army Armament Research, Development and Engineering Center (ARDEC), Office of the Deputy Assistant Secretary of Defense for

Transforming Systems Engineering through Model-Centric Engineering

Science.gov (United States)

2018-02-28

Contract No. HQ0034-13-D-0004 Research Tasks: 48, 118, 141, 157, 170 Report No. SERC-2018-TR-103 Transforming Systems Engineering through...Model-Centric Engineering Technical Report SERC-2018-TR-103 February 28, 2018 Principal Investigator Dr. Mark Blackburn, Stevens Institute of...Systems Engineering Research Center This material is based upon work supported, in whole or in part, by the U.S. Department of Defense through the

Future consumer mobile phone security: A case study using the data-centric security model

NARCIS (Netherlands)

van Cleeff, A.

Consumer mobile phone security requires more attention, now that their data storage capacity is increasing. At the same time, much effort is spent on data-centric security for large enterprises. In this article we try to apply data-centric security to consumer mobile phones. We show a maturity model

Cognition to Collaboration: User-Centric Approach and Information Behaviour Theories/Models

Directory of Open Access Journals (Sweden)

Alperen M Aydin

2016-12-01

Full Text Available Aim/Purpose: The objective of this paper is to review the vast literature of user-centric in-formation science and inform about the emerging themes in information behaviour science. Background:\tThe paradigmatic shift from system-centric to user-centric approach facilitates research on the cognitive and individual information processing. Various information behaviour theories/models emerged. Methodology: Recent information behaviour theories and models are presented. Features, strengths and weaknesses of the models are discussed through the analysis of the information behaviour literature. Contribution: This paper sheds light onto the weaknesses in earlier information behaviour models and stresses (and advocates the need for research on social information behaviour. Findings: Prominent information behaviour models deal with individual information behaviour. People live in a social world and sort out most of their daily or work problems in groups. However, only seven papers discuss social information behaviour (Scopus search. Recommendations for Practitioners\t: ICT tools used for inter-organisational sharing should be redesigned for effective information-sharing during disaster/emergency times. Recommendation for Researchers: There are scarce sources on social side of the information behaviour, however, most of the work tasks are carried out in groups/teams. Impact on Society: In dynamic work contexts like disaster management and health care settings, collaborative information-sharing may result in decreasing the losses. Future Research: A fieldwork will be conducted in disaster management context investigating the inter-organisational information-sharing.

An Approach to Modelling the Effects of Network Centricity in Maritime Warfare

National Research Council Canada - National Science Library

Fewell, Matthew; Grivell, Ian

2003-01-01

Partial context: TTCP MAR AG-1 Quantitative modelling of NCW, Outline, TACSITS and hypotheses, Maritime interception a coastline of recent interest, Platform-Centric Case Interceptors have an area of responsibility...

Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data.

Science.gov (United States)

Fu, Changhe; Deng, Su; Jin, Guangxu; Wang, Xinxin; Yu, Zu-Guo

2017-09-21

Molecular interaction data at proteomic and genetic levels provide physical and functional insights into a molecular biosystem and are helpful for the construction of pathway structures complementarily. Despite advances in inferring biological pathways using genetic interaction data, there still exists weakness in developed models, such as, activity pathway networks (APN), when integrating the data from proteomic and genetic levels. It is necessary to develop new methods to infer pathway structure by both of interaction data. We utilized probabilistic graphical model to develop a new method that integrates genetic interaction and protein interaction data and infers exquisitely detailed pathway structure. We modeled the pathway network as Bayesian network and applied this model to infer pathways for the coherent subsets of the global genetic interaction profiles, and the available data set of endoplasmic reticulum genes. The protein interaction data were derived from the BioGRID database. Our method can accurately reconstruct known cellular pathway structures, including SWR complex, ER-Associated Degradation (ERAD) pathway, N-Glycan biosynthesis pathway, Elongator complex, Retromer complex, and Urmylation pathway. By comparing N-Glycan biosynthesis pathway and Urmylation pathway identified from our approach with that from APN, we found that our method is able to overcome its weakness (certain edges are inexplicable). According to underlying protein interaction network, we defined a simple scoring function that only adopts genetic interaction information to avoid the balance difficulty in the APN. Using the effective stochastic simulation algorithm, the performance of our proposed method is significantly high. We developed a new method based on Bayesian network to infer detailed pathway structures from interaction data at proteomic and genetic levels. The results indicate that the developed method performs better in predicting signaling pathways than previously

A modeling ontology for integrating vulnerabilities into security requirements conceptual foundations

NARCIS (Netherlands)

Elahi, G.; Yu, E.; Zannone, N.; Laender, A.H.F.; Castano, S.; Dayal, U.; Casati, F.; Palazzo Moreira de Oliveira, J.

2009-01-01

Vulnerabilities are weaknesses in the requirements, design, and implementation, which attackers exploit to compromise the system. This paper proposes a vulnerability-centric modeling ontology, which aims to integrate empirical knowledge of vulnerabilities into the system development process. In

A product feature-based user-centric product search model

OpenAIRE

Ben Jabeur, Lamjed; Soulier, Laure; Tamine, Lynda; Mousset, Paul

2016-01-01

During the online shopping process, users would search for interesting products and quickly access those that fit with their needs among a long tail of similar or closely related products. Our contribution addresses head queries that are frequently submitted on e-commerce Web sites. Head queries usually target featured products with several variations, accessories, and complementary products. We present in this paper a product feature-based user-centric model for product search involving in a...

Ontology-centric integration and navigation of the dengue literature.

Science.gov (United States)

Rajapakse, Menaka; Kanagasabai, Rajaraman; Ang, Wee Tiong; Veeramani, Anitha; Schreiber, Mark J; Baker, Christopher J O

2008-10-01

Uninhibited access to the unstructured information distributed across the web and in scientific literature databases continues to be beyond the reach of scientists and health professionals. To address this challenge we have developed a literature driven, ontology-centric navigation infrastructure consisting of a content acquisition engine, a domain-specific ontology (in OWL-DL) and an ontology instantiation pipeline delivering sentences derived by domain-specific text mining. A visual query tool for reasoning over A-box instances in the populated ontology is presented and used to build conceptual queries that can be issued to the knowledgebase. We have deployed this generic infrastructure to facilitate data integration and knowledge sharing in the domain of dengue, which is one of the most prevalent viral diseases that continue to infect millions of people in the tropical and subtropical regions annually. Using our unique methodology we illustrate simplified search and discovery on dengue information derived from distributed resources and aggregated according to dengue ontology. Furthermore we apply data mining to the instantiated ontology to elucidate trends in the mentions of dengue serotypes in scientific abstracts since 1974.

Ontology for customer centric digital services and analytics

Science.gov (United States)

Keat, Ng Wai; Shahrir, Mohammad Shazri

2017-11-01

In computer science research, ontologies are commonly utilised to create a unified abstract across many rich and different fields. In this paper, we apply the concept to the customer centric domain of digital services analytics and present an analytics solution ontology. The essence is based from traditional Entity Relationship Diagram (ERD), which then was abstracted out to cover wider areas on customer centric digital services. The ontology we developed covers both static aspects (customer identifiers) and dynamic aspects (customer's temporal interactions). The structure of the customer scape is modeled with classes that represent different types of customer touch points, ranging from digital and digital-stamps which represent physical analogies. The dynamic aspects of customer centric digital service are modeled with a set of classes, with the importance is represented in different associations involving establishment and termination of the target interaction. The realized ontology can be used in development of frameworks for customer centric applications, and for specification of common data format used by cooperating digital service applications.

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

Science.gov (United States)

Zhou, Hufeng; Jin, Jingjing; Zhang, Haojun; Yi, Bo; Wozniak, Michal; Wong, Limsoon

2012-01-01

Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and

A design perspective on aligning process-centric and technology-centric approaches

DEFF Research Database (Denmark)

Siurdyban, Artur Henryk; Svejvig, Per; Møller, Charles

2012-01-01

Enterprise systems management (ESM) and business process management (BPM), although highly correlated, have evolved as alternative approaches to operational transformation. As a result, companies struggle to find the right balance when prioritizing technology and processes as change drivers....... The purpose of this paper is to propose a direction towards aligning the process-centric and technology-centric approaches. Using the case study method, we gain insight into two implementation projects: one of an information technology (IT) system and one of a process. We compare them using design thinking...... and strategic alignment theories. Based on the discussion, we assess the shortcomings of the process-centric and technology-centric approaches and argue that a conjoint design approach is required to achieve alignment between processes and technology. From a theoretical stance, this paper offers design-informed...

Agile IT: Thinking in User-Centric Models

Science.gov (United States)

Margaria, Tiziana; Steffen, Bernhard

We advocate a new teaching direction for modern CS curricula: extreme model-driven development (XMDD), a new development paradigm designed to continuously involve the customer/application expert throughout the whole systems' life cycle. Based on the `One-Thing Approach', which works by successively enriching and refining one single artifact, system development becomes in essence a user-centric orchestration of intuitive service functionality. XMDD differs radically from classical software development, which, in our opinion is no longer adequate for the bulk of application programming - in particular when it comes to heterogeneous, cross organizational systems which must adapt to rapidly changing market requirements. Thus there is a need for new curricula addressing this model-driven, lightweight, and cooperative development paradigm that puts the user process in the center of the development and the application expert in control of the process evolution.

The perspective matters! Multisensory integration in ego-centric reference frames determines full body ownership

Directory of Open Access Journals (Sweden)

Valeria Ivanova Petkova

2011-03-01

Full Text Available Recent advances in experimental science have made it possible to investigate the perceptual processes involved in generating a sense of owning an entire body. This is achieved by full-body ownership illusions which make use of specific patterns of visual and somatic stimuli integration. Here we investigate the fundamental question of the reference frames used in the process of attributing an entire body to the self. We quantified the strength of the body-swap illusion in conditions where the participants were observing this artificial body from the perspective of the first or third person. Consistent results from subjective reports and physiological recordings show that the first person visual perspective is critical for the induction of this full-body ownership illusion. This demonstrates that the multisensory integration processes producing the sense of corporeal self operates in an ego-centric reference frame.

The Perspective Matters! Multisensory Integration in Ego-Centric Reference Frames Determines Full-Body Ownership

Science.gov (United States)

Petkova, Valeria I.; Khoshnevis, Mehrnoush; Ehrsson, H. Henrik

2011-01-01

Recent advances in experimental science have made it possible to investigate the perceptual processes involved in generating a sense of owning an entire body. This is achieved by full-body ownership illusions which make use of specific patterns of visual and somatic stimuli integration. Here we investigate the fundamental question of the reference frames used in the process of attributing an entire body to the self. We quantified the strength of the body-swap illusion in conditions where the participants were observing this artificial body from the perspective of the first or third person. Consistent results from subjective reports and physiological recordings show that the first person visual perspective is critical for the induction of this full-body ownership illusion. This demonstrates that the multisensory integration processes producing the sense of corporeal self operates in an ego-centric reference frame. PMID:21687436

Group Centric Networking: Large Scale Over the Air Testing of Group Centric Networking

Science.gov (United States)

2016-11-01

Large Scale Over-the-Air Testing of Group Centric Networking Logan Mercer, Greg Kuperman, Andrew Hunter, Brian Proulx MIT Lincoln Laboratory...performance of Group Centric Networking (GCN), a networking protocol developed for robust and scalable communications in lossy networks where users are...devices, and the ad-hoc nature of the network . Group Centric Networking (GCN) is a proposed networking protocol that addresses challenges specific to

An OAI repository centric peer-review model

CERN Multimedia

CERN. Geneva

2005-01-01

Pre-print repositories have seen a significant increase in use over the past fifteen years across multiple research domains. Researchers are beginning to develop applications capable of using these repositories to assist the scientific community above and beyond the pure dissemination of information. The contributions set forth by this paper emphasize a deconstructed publication model where in which the peer-review certification phase of a pre-print is mediated by an OAI-compliant peer-review service. This peer-review service uses a social-network algorithm for determining potential reviewers for a submitted manuscript and for weighting the influence of each participating reviewer’s evaluations. The paper also provides a set of peer-review specific metadata tags that can accompany a pre-prints existing metadata record. The combinations of these contributions provide a unique repository-centric peer-review model within the framework of the current OAI standards existing today.

From unified messaging towards I-centric Services for the virtual home environment

CERN Document Server

van der Meer, S

2001-01-01

The vision of user centric information and an architecture for the realization of user centric services was discussed. The illustrated framework shows that these ideas can be assembled to set up an environment where services that allow users to interact with their environment are possible. The technologies integrated into the system were platform localization capabilities, environment awareness, communication capabilities and information storage capabilities. (Edited abstract)

Penalized differential pathway analysis of integrative oncogenomics studies.

Science.gov (United States)

van Wieringen, Wessel N; van de Wiel, Mark A

2014-04-01

Through integration of genomic data from multiple sources, we may obtain a more accurate and complete picture of the molecular mechanisms underlying tumorigenesis. We discuss the integration of DNA copy number and mRNA gene expression data from an observational integrative genomics study involving cancer patients. The two molecular levels involved are linked through the central dogma of molecular biology. DNA copy number aberrations abound in the cancer cell. Here we investigate how these aberrations affect gene expression levels within a pathway using observational integrative genomics data of cancer patients. In particular, we aim to identify differential edges between regulatory networks of two groups involving these molecular levels. Motivated by the rate equations, the regulatory mechanism between DNA copy number aberrations and gene expression levels within a pathway is modeled by a simultaneous-equations model, for the one- and two-group case. The latter facilitates the identification of differential interactions between the two groups. Model parameters are estimated by penalized least squares using the lasso (L1) penalty to obtain a sparse pathway topology. Simulations show that the inclusion of DNA copy number data benefits the discovery of gene-gene interactions. In addition, the simulations reveal that cis-effects tend to be over-estimated in a univariate (single gene) analysis. In the application to real data from integrative oncogenomic studies we show that inclusion of prior information on the regulatory network architecture benefits the reproducibility of all edges. Furthermore, analyses of the TP53 and TGFb signaling pathways between ER+ and ER- samples from an integrative genomics breast cancer study identify reproducible differential regulatory patterns that corroborate with existing literature.

Introducing the religio-centric positional advantage to Indonesian small businesses

Directory of Open Access Journals (Sweden)

Hendar Hendar

2017-03-01

Full Text Available With a focus on small religion-based businesses in Indonesia, this research examines whether marketing innovativeness, customers responsiveness and competitors′ responsiveness can improve marketing performance. A conceptual model on the correlation of these three variables with religio-centric positional advantage and marketing performance is examined by using structural equation model. For this purpose 335 small businesses of Islamic Fashion had been studied using purposive sampling from 11 regencies/cities in Central Java (Indonesia. The results showed that (1 small companies in these market segments based on religion is likely to have better marketing performance when they have the Religio-centric positional advantage, (2 The increase in marketing innovativeness, CuR and CoR is required to improve and maintain religio-centric positional advantage, and (3 religio-centric positional advantage is definitely a mediator in the correlation of marketing innovativeness, customer responsiveness and competitors responsiveness with marketing performance.

Grid Service for User-Centric Job

Energy Technology Data Exchange (ETDEWEB)

Lauret, Jerome

2009-07-31

The User Centric Monitoring (UCM) project was aimed at developing a toolkit that provides the Virtual Organization (VO) with tools to build systems that serve a rich set of intuitive job and application monitoring information to the VO’s scientists so that they can be more productive. The tools help collect and serve the status and error information through a Web interface. The proposed UCM toolkit is composed of a set of library functions, a database schema, and a Web portal that will collect and filter available job monitoring information from various resources and present it to users in a user-centric view rather than and administrative-centric point of view. The goal is to create a set of tools that can be used to augment grid job scheduling systems, meta-schedulers, applications, and script sets in order to provide the UCM information. The system provides various levels of an application programming interface that is useful through out the Grid environment and at the application level for logging messages, which are combined with the other user-centric monitoring information in a abstracted “data store”. A planned monitoring portal will also dynamically present the information to users in their web browser in a secure manor, which is also easily integrated into any JSR-compliant portal deployment that a VO might employ. The UCM is meant to be flexible and modular in the ways that it can be adopted to give the VO many choices to build a solution that works for them with special attention to the smaller VOs that do not have the resources to implement home-grown solutions.

GoFFish: A Sub-Graph Centric Framework for Large-Scale Graph Analytics1

Energy Technology Data Exchange (ETDEWEB)

Simmhan, Yogesh; Kumbhare, Alok; Wickramaarachchi, Charith; Nagarkar, Soonil; Ravi, Santosh; Raghavendra, Cauligi; Prasanna, Viktor

2014-08-25

Large scale graph processing is a major research area for Big Data exploration. Vertex centric programming models like Pregel are gaining traction due to their simple abstraction that allows for scalable execution on distributed systems naturally. However, there are limitations to this approach which cause vertex centric algorithms to under-perform due to poor compute to communication overhead ratio and slow convergence of iterative superstep. In this paper we introduce GoFFish a scalable sub-graph centric framework co-designed with a distributed persistent graph storage for large scale graph analytics on commodity clusters. We introduce a sub-graph centric programming abstraction that combines the scalability of a vertex centric approach with the flexibility of shared memory sub-graph computation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation.

Model-centric approaches for the development of health information systems.

Science.gov (United States)

Tuomainen, Mika; Mykkänen, Juha; Luostarinen, Heli; Pöyhölä, Assi; Paakkanen, Esa

2007-01-01

Modeling is used increasingly in healthcare to increase shared knowledge, to improve the processes, and to document the requirements of the solutions related to health information systems (HIS). There are numerous modeling approaches which aim to support these aims, but a careful assessment of their strengths, weaknesses and deficiencies is needed. In this paper, we compare three model-centric approaches in the context of HIS development: the Model-Driven Architecture, Business Process Modeling with BPMN and BPEL and the HL7 Development Framework. The comparison reveals that all these approaches are viable candidates for the development of HIS. However, they have distinct strengths and abstraction levels, they require local and project-specific adaptation and offer varying levels of automation. In addition, illustration of the solutions to the end users must be improved.

Concept of „long centric"

Directory of Open Access Journals (Sweden)

Martinović Željko

2004-01-01

Full Text Available The objective of this paper was to show the historical perspective of the „long centric" occlusal concept and its importance in the modern dentistry, especially from the gnathological aspect. The „long centric" concept represents therapeutic modality used in modern dentistry and occlusal adjustment in all patients showing differences in strong and weak closure of the lower jaw starting from the position of physiological rest/long centric" concept is applied only for anterior teeth and occlusal movements from rather than toward the center. Whenever the „long centric" parameters are not adequate, occlusal disturbance, resulting from the „wedge" effect during the initial closure of the lower jaw, is present. Different degrees of abrasion or hypermobility of the teeth are often the result of the above-mentioned occlusal disturbances and can potentially trigger bruxism and malfunction. Modus procedendi should be the regular approach of every dentist to any occlusion, because only the built-in „long centric" efficiently contributes to the occlusal stability of the anterior portion of the dentition. All occlusions should be routinely tested regarding their need for „long centric", especially when the extensive therapeutic interventions (conservative, prosthetics of the occlusal complex are required.

Human-centric decision-making models for social sciences

CERN Document Server

Pedrycz, Witold

2014-01-01

The volume delivers a wealth of effective methods to deal with various types of uncertainty inherently existing in human-centric decision problems. It elaborates on  comprehensive decision frameworks to handle different decision scenarios, which help use effectively the explicit and tacit knowledge and intuition, model perceptions and preferences in a more human-oriented style. The book presents original approaches and delivers new results on fundamentals and applications related to human-centered decision making approaches to business, economics and social systems. Individual chapters cover multi-criteria (multiattribute) decision making, decision making with prospect theory, decision making with incomplete probabilistic information, granular models of decision making and decision making realized with the use of non-additive measures. New emerging decision theories being presented as along with a wide spectrum of ongoing research make the book valuable to all interested in the field of advanced decision-mak...

Concept of „long centric"

OpenAIRE

Martinović Željko; Obradović-Đuričić Kosovka; Teodorović Nevenka S.; Živković Rade

2004-01-01

The objective of this paper was to show the historical perspective of the „long centric" occlusal concept and its importance in the modern dentistry, especially from the gnathological aspect. The „long centric" concept represents therapeutic modality used in modern dentistry and occlusal adjustment in all patients showing differences in strong and weak closure of the lower jaw starting from the position of physiological rest/long centric" concept is applied only for anterior teeth and occlusa...

Predicting Biological Information Flow in a Model Oxygen Minimum Zone

Science.gov (United States)

Louca, S.; Hawley, A. K.; Katsev, S.; Beltran, M. T.; Bhatia, M. P.; Michiels, C.; Capelle, D.; Lavik, G.; Doebeli, M.; Crowe, S.; Hallam, S. J.

2016-02-01

Microbial activity drives marine biochemical fluxes and nutrient cycling at global scales. Geochemical measurements as well as molecular techniques such as metagenomics, metatranscriptomics and metaproteomics provide great insight into microbial activity. However, an integration of molecular and geochemical data into mechanistic biogeochemical models is still lacking. Recent work suggests that microbial metabolic pathways are, at the ecosystem level, strongly shaped by stoichiometric and energetic constraints. Hence, models rooted in fluxes of matter and energy may yield a holistic understanding of biogeochemistry. Furthermore, such pathway-centric models would allow a direct consolidation with meta'omic data. Here we present a pathway-centric biogeochemical model for the seasonal oxygen minimum zone in Saanich Inlet, a fjord off the coast of Vancouver Island. The model considers key dissimilatory nitrogen and sulfur fluxes, as well as the population dynamics of the genes that mediate them. By assuming a direct translation of biocatalyzed energy fluxes to biosynthesis rates, we make predictions about the distribution and activity of the corresponding genes. A comparison of the model to molecular measurements indicates that the model explains observed DNA, RNA, protein and cell depth profiles. This suggests that microbial activity in marine ecosystems such as oxygen minimum zones is well described by DNA abundance, which, in conjunction with geochemical constraints, determines pathway expression and process rates. Our work further demonstrates how meta'omic data can be mechanistically linked to environmental redox conditions and biogeochemical processes.

User-centric networking future perspectives

CERN Document Server

Aldini, Alessandro

2014-01-01

This work represents a milestone for the? 'ULOOP User-centric Wireless Local Loop' project funded by the EU IST Seventh Framework Programme.ULOOP is focused on the robust, secure, and autonomic deployment of user-centric wireless networks. Contributions by ULOOP partners as well as invited tutorials by international experts in the field. The expected impact is to increase awareness to user-centric networking in terms, e.g., of business opportunities and quality of experience, and to present adequate technology to sustain the growth of user-friendly wireless architectures.Throughout the last 3

Application of the critical pathway and integrated case teaching method to nursing orientation.

Science.gov (United States)

Goodman, D

1997-01-01

Nursing staff development programs must be responsive to current changes in healthcare. New nursing staff must be prepared to manage continuous change and to function competently in clinical practice. The orientation pathway, based on a case management model, is used as a structure for the orientation phase of staff development. The integrated case is incorporated as a teaching strategy in orientation. The integrated case method is based on discussion and analysis of patient situations with emphasis on role modeling and integration of theory and skill. The orientation pathway and integrated case teaching method provide a useful framework for orientation of new staff. Educators, preceptors and orientees find the structure provided by the orientation pathway very useful. Orientation that is developed, implemented and evaluated based on a case management model with the use of an orientation pathway and incorporation of an integrated case teaching method provides a standardized structure for orientation of new staff. This approach is designed for the adult learner, promotes conceptual reasoning, and encourages the social and contextual basis for continued learning.

A Liver-Centric Multiscale Modeling Framework for Xenobiotics.

Directory of Open Access Journals (Sweden)

James P Sluka

Full Text Available We describe a multi-scale, liver-centric in silico modeling framework for acetaminophen pharmacology and metabolism. We focus on a computational model to characterize whole body uptake and clearance, liver transport and phase I and phase II metabolism. We do this by incorporating sub-models that span three scales; Physiologically Based Pharmacokinetic (PBPK modeling of acetaminophen uptake and distribution at the whole body level, cell and blood flow modeling at the tissue/organ level and metabolism at the sub-cellular level. We have used standard modeling modalities at each of the three scales. In particular, we have used the Systems Biology Markup Language (SBML to create both the whole-body and sub-cellular scales. Our modeling approach allows us to run the individual sub-models separately and allows us to easily exchange models at a particular scale without the need to extensively rework the sub-models at other scales. In addition, the use of SBML greatly facilitates the inclusion of biological annotations directly in the model code. The model was calibrated using human in vivo data for acetaminophen and its sulfate and glucuronate metabolites. We then carried out extensive parameter sensitivity studies including the pairwise interaction of parameters. We also simulated population variation of exposure and sensitivity to acetaminophen. Our modeling framework can be extended to the prediction of liver toxicity following acetaminophen overdose, or used as a general purpose pharmacokinetic model for xenobiotics.

User-Centric Multi-Criteria Information Retrieval

Science.gov (United States)

Wolfe, Shawn R.; Zhang, Yi

2009-01-01

Information retrieval models usually represent content only, and not other considerations, such as authority, cost, and recency. How could multiple criteria be utilized in information retrieval, and how would it affect the results? In our experiments, using multiple user-centric criteria always produced better results than a single criteria.

Data Centric Sensor Stream Reduction for Real-Time Applications in Wireless Sensor Networks

Science.gov (United States)

Aquino, Andre Luiz Lins; Nakamura, Eduardo Freire

2009-01-01

This work presents a data-centric strategy to meet deadlines in soft real-time applications in wireless sensor networks. This strategy considers three main aspects: (i) The design of real-time application to obtain the minimum deadlines; (ii) An analytic model to estimate the ideal sample size used by data-reduction algorithms; and (iii) Two data-centric stream-based sampling algorithms to perform data reduction whenever necessary. Simulation results show that our data-centric strategies meet deadlines without loosing data representativeness. PMID:22303145

Graph Theoretical Analysis of Network Centric Operations Using Multi-Layer Models

National Research Council Canada - National Science Library

Wong-Jiru, Ann

2006-01-01

.... The research incorporates the importance of understanding network topology for evaluating an environment for net-centricity and using network characteristics to help commanders assess the effects...

Large scale network-centric distributed systems

CERN Document Server

Sarbazi-Azad, Hamid

2014-01-01

A highly accessible reference offering a broad range of topics and insights on large scale network-centric distributed systems Evolving from the fields of high-performance computing and networking, large scale network-centric distributed systems continues to grow as one of the most important topics in computing and communication and many interdisciplinary areas. Dealing with both wired and wireless networks, this book focuses on the design and performance issues of such systems. Large Scale Network-Centric Distributed Systems provides in-depth coverage ranging from ground-level hardware issu

Challenges in horizontal model integration.

Science.gov (United States)

Kolczyk, Katrin; Conradi, Carsten

2016-03-11

Systems Biology has motivated dynamic models of important intracellular processes at the pathway level, for example, in signal transduction and cell cycle control. To answer important biomedical questions, however, one has to go beyond the study of isolated pathways towards the joint study of interacting signaling pathways or the joint study of signal transduction and cell cycle control. Thereby the reuse of established models is preferable, as it will generally reduce the modeling effort and increase the acceptance of the combined model in the field. Obtaining a combined model can be challenging, especially if the submodels are large and/or come from different working groups (as is generally the case, when models stored in established repositories are used). To support this task, we describe a semi-automatic workflow based on established software tools. In particular, two frequent challenges are described: identification of the overlap and subsequent (re)parameterization of the integrated model. The reparameterization step is crucial, if the goal is to obtain a model that can reproduce the data explained by the individual models. For demonstration purposes we apply our workflow to integrate two signaling pathways (EGF and NGF) from the BioModels Database.

Information Integration Platform for Patient-Centric Healthcare Services: Design, Prototype and Dependability Aspects

Directory of Open Access Journals (Sweden)

Yohanes Baptista Dafferianto Trinugroho

2014-03-01

Full Text Available Technology innovations have pushed today’s healthcare sector to an unprecedented new level. Various portable and wearable medical and fitness devices are being sold in the consumer market to provide the self-empowerment of a healthier lifestyle to society. Many vendors provide additional cloud-based services for devices they manufacture, enabling the users to visualize, store and share the gathered information through the Internet. However, most of these services are integrated with the devices in a closed “silo” manner, where the devices can only be used with the provided services. To tackle this issue, an information integration platform (IIP has been developed to support communications between devices and Internet-based services in an event-driven fashion by adopting service-oriented architecture (SOA principles and a publish/subscribe messaging pattern. It follows the “Internet of Things” (IoT idea of connecting everyday objects to various networks and to enable the dissemination of the gathered information to the global information space through the Internet. A patient-centric healthcare service environment is chosen as the target scenario for the deployment of the platform, as this is a domain where IoT can have a direct positive impact on quality of life enhancement. This paper describes the developed platform, with emphasis on dependability aspects, including availability, scalability and security.

Theorizing Network-Centric Activity in Education

Science.gov (United States)

HaLevi, Andrew

2011-01-01

Networks and network-centric activity are increasingly prevalent in schools and school districts. In addition to ubiquitous social network tools like Facebook and Twitter, educational leaders deal with a wide variety of network organizational forms that include professional development, advocacy, informational networks and network-centric reforms.…

A Web Service-Based Framework Model for People-Centric Sensing Applications Applied to Social Networking

Directory of Open Access Journals (Sweden)

Jorge Sá Silva

2012-02-01

Full Text Available As the Internet evolved, social networks (such as Facebook have bloomed and brought together an astonishing number of users. Mashing up mobile phones and sensors with these social environments enables the creation of people-centric sensing systems which have great potential for expanding our current social networking usage. However, such systems also have many associated technical challenges, such as privacy concerns, activity detection mechanisms or intermittent connectivity, as well as limitations due to the heterogeneity of sensor nodes and networks. Considering the openness of the Web 2.0, good technical solutions for these cases consist of frameworks that expose sensing data and functionalities as common Web-Services. This paper presents our RESTful Web Service-based model for people-centric sensing frameworks, which uses sensors and mobile phones to detect users’ activities and locations, sharing this information amongst the user’s friends within a social networking site. We also present some screenshot results of our experimental prototype.

A Web Service-based framework model for people-centric sensing applications applied to social networking.

Science.gov (United States)

Nunes, David; Tran, Thanh-Dien; Raposo, Duarte; Pinto, André; Gomes, André; Silva, Jorge Sá

2012-01-01

As the Internet evolved, social networks (such as Facebook) have bloomed and brought together an astonishing number of users. Mashing up mobile phones and sensors with these social environments enables the creation of people-centric sensing systems which have great potential for expanding our current social networking usage. However, such systems also have many associated technical challenges, such as privacy concerns, activity detection mechanisms or intermittent connectivity, as well as limitations due to the heterogeneity of sensor nodes and networks. Considering the openness of the Web 2.0, good technical solutions for these cases consist of frameworks that expose sensing data and functionalities as common Web-Services. This paper presents our RESTful Web Service-based model for people-centric sensing frameworks, which uses sensors and mobile phones to detect users' activities and locations, sharing this information amongst the user's friends within a social networking site. We also present some screenshot results of our experimental prototype.

PathText: a text mining integrator for biological pathway visualizations

Science.gov (United States)

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

DMPD: Signal integration between IFNgamma and TLR signalling pathways in macrophages. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 16920490 Signal integration between IFNgamma and TLR signalling pathways in macroph...tml) (.csml) Show Signal integration between IFNgamma and TLR signalling pathways in macrophages. PubmedID 16920490 Title Signal inte...gration between IFNgamma and TLR signalling pathways in

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution.

Science.gov (United States)

Ou, Yang; Shi, Wenjing; Smith, Steven J; Ledna, Catherine M; West, J Jason; Nolte, Christopher G; Loughlin, Daniel H

2018-04-15

There are many technological pathways that can lead to reduced carbon dioxide emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessment model with state-level resolution of the energy system to compare environmental impacts of alternative low-carbon pathways for the United States. One set of pathways emphasizes nuclear energy and carbon capture and storage, while another set emphasizes renewable energy, including wind, solar, geothermal power, and bioenergy. These are compared with pathways in which all technologies are available. Air pollutant emissions, mortality costs attributable to particulate matter smaller than 2.5 μm in diameter, and energy-related water demands are evaluated for 50% and 80% carbon dioxide reduction targets in 2050. The renewable low-carbon pathways require less water withdrawal and consumption than the nuclear and carbon capture pathways. However, the renewable low-carbon pathways modeled in this study produce higher particulate matter-related mortality costs due to greater use of biomass in residential heating. Environmental co-benefits differ among states because of factors such as existing technology stock, resource availability, and environmental and energy policies.

2012 International Conference on Human-centric Computing

CERN Document Server

Jin, Qun; Yeo, Martin; Hu, Bin; Human Centric Technology and Service in Smart Space, HumanCom 2012

2012-01-01

The theme of HumanCom is focused on the various aspects of human-centric computing for advances in computer science and its applications and provides an opportunity for academic and industry professionals to discuss the latest issues and progress in the area of human-centric computing. In addition, the conference will publish high quality papers which are closely related to the various theories and practical applications in human-centric computing. Furthermore, we expect that the conference and its publications will be a trigger for further related research and technology improvements in this important subject.

Evaluation of additional biogeochemical impacts on mitigation pathways in an energy sytem integrated assessment model.

Science.gov (United States)

Dessens, O.

2017-12-01

Within the last IPCC AR5 a large and systematic sensitivity study around available technologies and timing of policies applied in IAMs to achieve the 2°C target has been conducted. However the simple climate representations included in IAMs are generally tuned to the results of ensemble means. This may result in hiding within the ensemble mean results possible challenging mitigation pathways for the economy or the technology future scenarios. This work provides new insights on the sensitivity of the socio-economic response to different climate factors under a 2°C climate change target in order to help guide future efforts to reduce uncertainty in the climate mitigation decisions. The main objective is to understand and bring new insights on how future global warming will affect the natural biochemical feedbacks on the climate system and what could be the consequences of these feedbacks on the anthropogenic emission pathways with a specific focus on the energy-economy system. It specifically focuses on three issues of the climate representation affecting the energy system transformation and GHG emissions pathways: 1- Impacts of the climate sensitivity (or TCR); 2- Impacts of warming on the radiative forcing (cloudiness,...); 3- Impacts of warming on the carbon cycle (carbon cycle feedback). We use the integrated assessment model TIAM-UCL to examine the mitigation pathways compatible with the 2C target depending on assumptions regarding the 3 issues of the climate representation introduced above. The following key conclusions drawn from this study are that mitigation to 2°C is still possible under strong climate sensitivity (TCR), strong carbon cycle amplification or positive radiative forcing feedback. However, this level of climate mitigation will require a significant transformation in the way we produce and consume energy. Carbon capture and sequestration on electricity generation, industry and biomass is part of the technology pool needed to achieve this

Device-Centric Monitoring for Mobile Device Management

Directory of Open Access Journals (Sweden)

Luke Chircop

2016-03-01

Full Text Available The ubiquity of computing devices has led to an increased need to ensure not only that the applications deployed on them are correct with respect to their specifications, but also that the devices are used in an appropriate manner, especially in situations where the device is provided by a party other than the actual user. Much work which has been done on runtime verification for mobile devices and operating systems is mostly application-centric, resulting in global, device-centric properties (e.g. the user may not send more than 100 messages per day across all applications being difficult or impossible to verify. In this paper we present a device-centric approach to runtime verify the device behaviour against a device policy with the different applications acting as independent components contributing to the overall behaviour of the device. We also present an implementation for Android devices, and evaluate it on a number of device-centric policies, reporting the empirical results obtained.

A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment

Science.gov (United States)

Kibria, Muhammad Golam; Fattah, Sheik Mohammad Mostakim; Jeong, Kwanghyeon; Chong, Ilyoung; Jeong, Youn-Kwae

2015-01-01

User-centric service features in a Web of Object-enabled Internet of Things environment can be provided by using a semantic ontology that classifies and integrates objects on the World Wide Web as well as shares and merges context-aware information and accumulated knowledge. The semantic ontology is applied on a Web of Object platform to virtualize the real world physical devices and information to form virtual objects that represent the features and capabilities of devices in the virtual world. Detailed information and functionalities of multiple virtual objects are combined with service rules to form composite virtual objects that offer context-aware knowledge-based services, where context awareness plays an important role in enabling automatic modification of the system to reconfigure the services based on the context. Converting the raw data into meaningful information and connecting the information to form the knowledge and storing and reusing the objects in the knowledge base can both be expressed by semantic ontology. In this paper, a knowledge creation model that synchronizes a service logistic model and a virtual world knowledge model on a Web of Object platform has been proposed. To realize the context-aware knowledge-based service creation and execution, a conceptual semantic ontology model has been developed and a prototype has been implemented for a use case scenario of emergency service. PMID:26393609

A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment

Directory of Open Access Journals (Sweden)

Muhammad Golam Kibria

2015-09-01

Full Text Available User-centric service features in a Web of Object-enabled Internet of Things environment can be provided by using a semantic ontology that classifies and integrates objects on the World Wide Web as well as shares and merges context-aware information and accumulated knowledge. The semantic ontology is applied on a Web of Object platform to virtualize the real world physical devices and information to form virtual objects that represent the features and capabilities of devices in the virtual world. Detailed information and functionalities of multiple virtual objects are combined with service rules to form composite virtual objects that offer context-aware knowledge-based services, where context awareness plays an important role in enabling automatic modification of the system to reconfigure the services based on the context. Converting the raw data into meaningful information and connecting the information to form the knowledge and storing and reusing the objects in the knowledge base can both be expressed by semantic ontology. In this paper, a knowledge creation model that synchronizes a service logistic model and a virtual world knowledge model on a Web of Object platform has been proposed. To realize the context-aware knowledge-based service creation and execution, a conceptual semantic ontology model has been developed and a prototype has been implemented for a use case scenario of emergency service.

A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment.

Science.gov (United States)

Kibria, Muhammad Golam; Fattah, Sheik Mohammad Mostakim; Jeong, Kwanghyeon; Chong, Ilyoung; Jeong, Youn-Kwae

2015-09-18

User-centric service features in a Web of Object-enabled Internet of Things environment can be provided by using a semantic ontology that classifies and integrates objects on the World Wide Web as well as shares and merges context-aware information and accumulated knowledge. The semantic ontology is applied on a Web of Object platform to virtualize the real world physical devices and information to form virtual objects that represent the features and capabilities of devices in the virtual world. Detailed information and functionalities of multiple virtual objects are combined with service rules to form composite virtual objects that offer context-aware knowledge-based services, where context awareness plays an important role in enabling automatic modification of the system to reconfigure the services based on the context. Converting the raw data into meaningful information and connecting the information to form the knowledge and storing and reusing the objects in the knowledge base can both be expressed by semantic ontology. In this paper, a knowledge creation model that synchronizes a service logistic model and a virtual world knowledge model on a Web of Object platform has been proposed. To realize the context-aware knowledge-based service creation and execution, a conceptual semantic ontology model has been developed and a prototype has been implemented for a use case scenario of emergency service.

Integration of the Dynamic Model of Situated Cognition in the Design of Edge Organizations

OpenAIRE

Miller, Gregory A.; Kujawski, Edouard

2008-01-01

13th International Command and Control Research and Technology Symposium (ICCRTS), June 17-19, 2008, Seattle, WA. Much of the R&D in Network Centric Warfare has been on technology. Improvements in connectivity and processing speed challenge the integration of technological and human elements into a single C2 framework. The Dynamic Model of Situated Cognition (DMSC) was developed as an analysis method explicitly representing the human- technology relationships. It takes into account that se...

Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time.

Science.gov (United States)

van Dijk, Aalt D J; Molenaar, Jaap

2017-01-01

The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral pathway integrator genes. At a quantitative level, it is currently unclear how the impact of genetic variation in signaling pathways on flowering time is mediated by floral pathway integrator genes. Here, using datasets available from literature, we connect Arabidopsis thaliana flowering time in genetic backgrounds varying in upstream signalling components with the expression levels of floral pathway integrator genes in these genetic backgrounds. Our modelling results indicate that flowering time depends in a quite linear way on expression levels of floral pathway integrator genes. This gradual, proportional response of flowering time to upstream changes enables a gradual adaptation to changing environmental factors such as temperature and light.

Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time

Directory of Open Access Journals (Sweden)

Aalt D.J. van Dijk

2017-04-01

Full Text Available The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral pathway integrator genes. At a quantitative level, it is currently unclear how the impact of genetic variation in signaling pathways on flowering time is mediated by floral pathway integrator genes. Here, using datasets available from literature, we connect Arabidopsis thaliana flowering time in genetic backgrounds varying in upstream signalling components with the expression levels of floral pathway integrator genes in these genetic backgrounds. Our modelling results indicate that flowering time depends in a quite linear way on expression levels of floral pathway integrator genes. This gradual, proportional response of flowering time to upstream changes enables a gradual adaptation to changing environmental factors such as temperature and light.

Defining Patient Centric Pharmaceutical Drug Product Design.

Science.gov (United States)

Stegemann, Sven; Ternik, Robert L; Onder, Graziano; Khan, Mansoor A; van Riet-Nales, Diana A

2016-09-01

The term "patient centered," "patient centric," or "patient centricity" is increasingly used in the scientific literature in a wide variety of contexts. Generally, patient centric medicines are recognized as an essential contributor to healthy aging and the overall patient's quality of life and life expectancy. Besides the selection of the appropriate type of drug substance and strength for a particular indication in a particular patient, due attention must be paid that the pharmaceutical drug product design is also adequately addressing the particular patient's needs, i.e., assuring adequate patient adherence and the anticipate drug safety and effectiveness. Relevant pharmaceutical design aspects may e.g., involve the selection of the route of administration, the tablet size and shape, the ease of opening the package, the ability to read the user instruction, or the ability to follow the recommended (in-use) storage conditions. Currently, a harmonized definition on patient centric drug development/design has not yet been established. To stimulate scientific research and discussions and the consistent interpretation of test results, it is essential that such a definition is established. We have developed a first draft definition through various rounds of discussions within an interdisciplinary AAPS focus group of experts. This publication summarizes the outcomes and is intended to stimulate further discussions with all stakeholders towards a common definition of patient centric pharmaceutical drug product design that is useable across all disciplines involved.

A change navigation-based, scenario planning process within a developing world context from an Afro-centric leadership perspective

Directory of Open Access Journals (Sweden)

Chris A. Geldenhuys

2011-02-01

Research purpose: This study aimed to investigate how scenario-based planning (a strictly cognitive management tool can be combined with organisational change navigation (a practice addressing the emotionality of change and how this integrated process should be aligned with the prerequisites imposed by a developing country context and an Afro-centric leadership perspective in order to make the process more context relevant and aligned. Motivation for the study: The integration of organisational change navigation with conventional scenario based planning, as well as the incorporation of the perquisites of a developing countries and an Afro-centric leadership perspective, will give organisations a more robust, holistic strategic management tool that will add significantly more value within a rapidly, radically and unpredictably changing world. Research design, approach and method: The adopted research approach comprised a combination of the sourcing of the latest thinking in the literature (the ‘theory’ as well as the views of seasoned practitioners of scenario planning (the ‘practice’ through an iterative research process, moving between theory and practice, back to practice and finally returning to theory in order to arrive at a validated expanded and enhanced scenario-based planning process which is both theory and practice ‘proof’. Main findings: A management tool incorporating the change navigation and the unique features of developing countries and Afro-centric leadership was formulated and empirically validated. This management tool is referred to as a change navigation based, scenario planning process (CNBSPP. Practical/managerial implications: CNBSPP is available for use by organisations wishing to apply a strategic planning tool that fits within a developing country context and an Afro-centric leadership approach. Contribution/value add: The research makes a unique contribution to the current level of knowledge by integrating two disciplines

Pathview Web: user friendly pathway visualization and data integration.

Science.gov (United States)

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data.

Science.gov (United States)

Beltrame, Luca; Bianco, Luca; Fontana, Paolo; Cavalieri, Duccio

2013-07-15

Pathway Processor 2.0 is a web application designed to analyze high-throughput datasets, including but not limited to microarray and next-generation sequencing, using a pathway centric logic. In addition to well-established methods such as the Fisher's test and impact analysis, Pathway Processor 2.0 offers innovative methods that convert gene expression into pathway expression, leading to the identification of differentially regulated pathways in a dataset of choice. Pathway Processor 2.0 is available as a web service at http://compbiotoolbox.fmach.it/pathwayProcessor/. Sample datasets to test the functionality can be used directly from the application. duccio.cavalieri@fmach.it Supplementary data are available at Bioinformatics online.

A Model of an Integrated Immune System Pathway in Homo sapiens and Its Interaction with Superantigen Producing Expression Regulatory Pathway in Staphylococcus aureus: Comparing Behavior of Pathogen Perturbed and Unperturbed Pathway

Science.gov (United States)

Tomar, Namrata; De, Rajat K.

2013-01-01

Response of an immune system to a pathogen attack depends on the balance between the host immune defense and the virulence of the pathogen. Investigation of molecular interactions between the proteins of a host and a pathogen helps in identifying the pathogenic proteins. It is necessary to understand the dynamics of a normally behaved host system to evaluate the capacity of its immune system upon pathogen attack. In this study, we have compared the behavior of an unperturbed and pathogen perturbed host system. Moreover, we have developed a formalism under Flux Balance Analysis (FBA) for the optimization of conflicting objective functions. We have constructed an integrated pathway system, which includes Staphylococcal Superantigen (SAg) expression regulatory pathway and TCR signaling pathway of Homo sapiens. We have implemented the method on this pathway system and observed the behavior of host signaling molecules upon pathogen attack. The entire study has been divided into six different cases, based on the perturbed/unperturbed conditions. In other words, we have investigated unperturbed and pathogen perturbed human TCR signaling pathway, with different combinations of optimization of concentrations of regulatory and signaling molecules. One of these cases has aimed at finding out whether minimization of the toxin production in a pathogen leads to the change in the concentration levels of the proteins coded by TCR signaling pathway genes in the infected host. Based on the computed results, we have hypothesized that the balance between TCR signaling inhibitory and stimulatory molecules can keep TCR signaling system into resting/stimulating state, depending upon the perturbation. The proposed integrated host-pathogen interaction pathway model has accurately reflected the experimental evidences, which we have used for validation purpose. The significance of this kind of investigation lies in revealing the susceptible interaction points that can take back the

kpath: integration of metabolic pathway linked data.

Science.gov (United States)

Navas-Delgado, Ismael; García-Godoy, María Jesús; López-Camacho, Esteban; Rybinski, Maciej; Reyes-Palomares, Armando; Medina, Miguel Ángel; Aldana-Montes, José F

2015-01-01

In the last few years, the Life Sciences domain has experienced a rapid growth in the amount of available biological databases. The heterogeneity of these databases makes data integration a challenging issue. Some integration challenges are locating resources, relationships, data formats, synonyms or ambiguity. The Linked Data approach partially solves the heterogeneity problems by introducing a uniform data representation model. Linked Data refers to a set of best practices for publishing and connecting structured data on the Web. This article introduces kpath, a database that integrates information related to metabolic pathways. kpath also provides a navigational interface that enables not only the browsing, but also the deep use of the integrated data to build metabolic networks based on existing disperse knowledge. This user interface has been used to showcase relationships that can be inferred from the information available in several public databases. © The Author(s) 2015. Published by Oxford University Press.

An Extended Petri-Net Based Approach for Supply Chain Process Enactment in Resource-Centric Web Service Environment

Science.gov (United States)

Wang, Xiaodong; Zhang, Xiaoyu; Cai, Hongming; Xu, Boyi

Enacting a supply-chain process involves variant partners and different IT systems. REST receives increasing attention for distributed systems with loosely coupled resources. Nevertheless, resource model incompatibilities and conflicts prevent effective process modeling and deployment in resource-centric Web service environment. In this paper, a Petri-net based framework for supply-chain process integration is proposed. A resource meta-model is constructed to represent the basic information of resources. Then based on resource meta-model, XML schemas and documents are derived, which represent resources and their states in Petri-net. Thereafter, XML-net, a high level Petri-net, is employed for modeling control and data flow of process. From process model in XML-net, RESTful services and choreography descriptions are deduced. Therefore, unified resource representation and RESTful services description are proposed for cross-system integration in a more effective way. A case study is given to illustrate the approach and the desirable features of the approach are discussed.

Variability of centric relation position in TMD patients.

NARCIS (Netherlands)

Zonnenberg, A.J.J.; Mulder, J.

2006-01-01

Reproducibility of the centric relation position for patients with temporomandibular disorders (TMD) is not documented in the current literature. It was the objective of this study to assess clinical variability of the centric relation position for TMD patients with a muscle-determined technique by

Integrative Analysis of Gene Expression Data Including an Assessment of Pathway Enrichment for Predicting Prostate Cancer

Directory of Open Access Journals (Sweden)

Pingzhao Hu

2006-01-01

Full Text Available Background: Microarray technology has been previously used to identify genes that are differentially expressed between tumour and normal samples in a single study, as well as in syntheses involving multiple studies. When integrating results from several Affymetrix microarray datasets, previous studies summarized probeset-level data, which may potentially lead to a loss of information available at the probe-level. In this paper, we present an approach for integrating results across studies while taking probe-level data into account. Additionally, we follow a new direction in the analysis of microarray expression data, namely to focus on the variation of expression phenotypes in predefined gene sets, such as pathways. This targeted approach can be helpful for revealing information that is not easily visible from the changes in the individual genes. Results: We used a recently developed method to integrate Affymetrix expression data across studies. The idea is based on a probe-level based test statistic developed for testing for differentially expressed genes in individual studies. We incorporated this test statistic into a classic random-effects model for integrating data across studies. Subsequently, we used a gene set enrichment test to evaluate the significance of enriched biological pathways in the differentially expressed genes identified from the integrative analysis. We compared statistical and biological significance of the prognostic gene expression signatures and pathways identified in the probe-level model (PLM with those in the probeset-level model (PSLM. Our integrative analysis of Affymetrix microarray data from 110 prostate cancer samples obtained from three studies reveals thousands of genes significantly correlated with tumour cell differentiation. The bioinformatics analysis, mapping these genes to the publicly available KEGG database, reveals evidence that tumour cell differentiation is significantly associated with many

Using declarative workflow languages to develop process-centric web applications

NARCIS (Netherlands)

Bernardi, M.L.; Cimitile, M.; Di Lucca, G.A.; Maggi, F.M.

2012-01-01

Nowadays, process-centric Web Applications (WAs) are extensively used in contexts where multi-user, coordinated work is required. Recently, Model Driven Engineering (MDE) techniques have been investigated for the development of this kind of applications. However, there are still some open issues.

On Lifecycle Constraints of Artifact-Centric Workflows

Science.gov (United States)

Kucukoguz, Esra; Su, Jianwen

Data plays a fundamental role in modeling and management of business processes and workflows. Among the recent "data-aware" workflow models, artifact-centric models are particularly interesting. (Business) artifacts are the key data entities that are used in workflows and can reflect both the business logic and the execution states of a running workflow. The notion of artifacts succinctly captures the fluidity aspect of data during workflow executions. However, much of the technical dimension concerning artifacts in workflows is not well understood. In this paper, we study a key concept of an artifact "lifecycle". In particular, we allow declarative specifications/constraints of artifact lifecycle in the spirit of DecSerFlow, and formulate the notion of lifecycle as the set of all possible paths an artifact can navigate through. We investigate two technical problems: (Compliance) does a given workflow (schema) contain only lifecycle allowed by a constraint? And (automated construction) from a given lifecycle specification (constraint), is it possible to construct a "compliant" workflow? The study is based on a new formal variant of artifact-centric workflow model called "ArtiNets" and two classes of lifecycle constraints named "regular" and "counting" constraints. We present a range of technical results concerning compliance and automated construction, including: (1) compliance is decidable when workflow is atomic or constraints are regular, (2) for each constraint, we can always construct a workflow that satisfies the constraint, and (3) sufficient conditions where atomic workflows can be constructed.

Revisiting video game ratings: Shift from content-centric to parent-centric approach

Directory of Open Access Journals (Sweden)

Jiow Hee Jhee

2017-01-01

Full Text Available The rapid adoption of video gaming among children has placed tremendous strain on parents’ ability to manage their children’s consumption. While parents refer online to video games ratings (VGR information to support their mediation efforts, there are many difficulties associated with such practice. This paper explores the popular VGR sites, and highlights the inadequacies of VGRs to capture the parents’ concerns, such as time displacement, social interactions, financial spending and various video game effects, beyond the widespread panics over content issues, that is subjective, ever-changing and irrelevant. As such, this paper argues for a shift from content-centric to a parent-centric approach in VGRs, that captures the evolving nature of video gaming, and support parents, the main users of VGRs, in their management of their young video gaming children. This paper proposes a Video Games Repository for Parents to represent that shift.

Individual Syllabus for Personalized Learner-Centric E-Courses in E-Learning and M-Learning

OpenAIRE

Khaled Nasser ElSayed

2014-01-01

Most of e-learning and m-learning systems are course-centric. These systems provided services that concentrated on course material and pedagogical. They did not take into account varieties of student levels, skills, interests or preferences. This paper provides a design of an approach for personalized and self-adapted agent-based learning systems for enhancing e-learning and mobile learning (m-learning) services to be learner-centric. It presents a modeling of goals of different learners of a...

A Cloud Computing Based Patient Centric Medical Information System

Science.gov (United States)

Agarwal, Ankur; Henehan, Nathan; Somashekarappa, Vivek; Pandya, A. S.; Kalva, Hari; Furht, Borko

This chapter discusses an emerging concept of a cloud computing based Patient Centric Medical Information System framework that will allow various authorized users to securely access patient records from various Care Delivery Organizations (CDOs) such as hospitals, urgent care centers, doctors, laboratories, imaging centers among others, from any location. Such a system must seamlessly integrate all patient records including images such as CT-SCANS and MRI'S which can easily be accessed from any location and reviewed by any authorized user. In such a scenario the storage and transmission of medical records will have be conducted in a totally secure and safe environment with a very high standard of data integrity, protecting patient privacy and complying with all Health Insurance Portability and Accountability Act (HIPAA) regulations.

Modeling IoT-Based Solutions Using Human-Centric Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Álvaro Monares

2014-08-01

Full Text Available The Internet of Things (IoT has inspired solutions that are already available for addressing problems in various application scenarios, such as healthcare, security, emergency support and tourism. However, there is no clear approach to modeling these systems and envisioning their capabilities at the design time. Therefore, the process of designing these systems is ad hoc and its real impact is evaluated once the solution is already implemented, which is risky and expensive. This paper proposes a modeling approach that uses human-centric wireless sensor networks to specify and evaluate models of IoT-based systems at the time of design, avoiding the need to spend time and effort on early implementations of immature designs. It allows designers to focus on the system design, leaving the implementation decisions for a next phase. The article illustrates the usefulness of this proposal through a running example, showing the design of an IoT-based solution to support the first responses during medium-sized or large urban incidents. The case study used in the proposal evaluation is based on a real train crash. The proposed modeling approach can be used to design IoT-based systems for other application scenarios, e.g., to support security operatives or monitor chronic patients in their homes.

Modeling IoT-based solutions using human-centric wireless sensor networks.

Science.gov (United States)

Monares, Álvaro; Ochoa, Sergio F; Santos, Rodrigo; Orozco, Javier; Meseguer, Roc

2014-08-25

The Internet of Things (IoT) has inspired solutions that are already available for addressing problems in various application scenarios, such as healthcare, security, emergency support and tourism. However, there is no clear approach to modeling these systems and envisioning their capabilities at the design time. Therefore, the process of designing these systems is ad hoc and its real impact is evaluated once the solution is already implemented, which is risky and expensive. This paper proposes a modeling approach that uses human-centric wireless sensor networks to specify and evaluate models of IoT-based systems at the time of design, avoiding the need to spend time and effort on early implementations of immature designs. It allows designers to focus on the system design, leaving the implementation decisions for a next phase. The article illustrates the usefulness of this proposal through a running example, showing the design of an IoT-based solution to support the first responses during medium-sized or large urban incidents. The case study used in the proposal evaluation is based on a real train crash. The proposed modeling approach can be used to design IoT-based systems for other application scenarios, e.g., to support security operatives or monitor chronic patients in their homes.

A Study on Intelligent User-Centric Logistics Service Model Using Ontology

Directory of Open Access Journals (Sweden)

Saraswathi Sivamani

2014-01-01

Full Text Available Much research has been undergone in the smart logistics environment for the prompt delivery of the product in the right place at the right time. Most of the services were based on time management, routing technique, and location based services. The services in the recent logistics environment aim for situation based logistics service centered around the user by utilizing various information technologies such as mobile devices, computer systems, and GPS. This paper proposes a smart logistics service model for providing user-centric intelligent logistics service by utilizing smartphones in a smart environment. We also develop an OWL based ontology model for the smart logistics for the better understanding among the context information. In addition to basic delivery information, the proposed service model makes use of the location and situation information of the delivery vehicle and user, to draw the route information according to the user’s requirement. With the increase of internet usage, the real-time situations are received which helps to create a more reliable relationship, owing to the Internet of Things. Through this service model, it is possible to engage in the development of various IT and logistics convergence services based on situation information between the deliverer and user which occurs in real time.

Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy.

Directory of Open Access Journals (Sweden)

Michael Volpers

thermodynamic favorable under conditions analysed. However, the most important challenge identified for improving photo-electro-autotrophic growth is increasing the proton-pumping rate of the rhodopsin photosystems, allowing for higher ATP regeneration. Alternatively, other designs of autotrophy may be considered, therefore the herein presented integrated modeling approach allows synthetic biologists to evaluate and compare complex pathway designs before experimental implementation.

Implications of Network Centric Warfare

National Research Council Canada - National Science Library

Bailey, Alvin

2004-01-01

.... These areas of dependence also provide numerous vulnerabilities. This paper will focus specifically on Network Centric Warfare's vulnerabilities in terms of sensors cyberterrorism/ Electro-Magnetic Pulse (EMP...

Peering Strategic Game Models for Interdependent ISPs in Content Centric Internet

Directory of Open Access Journals (Sweden)

Jia Zhao

2013-01-01

Full Text Available Emergent content-oriented networks prompt Internet service providers (ISPs to evolve and take major responsibility for content delivery. Numerous content items and varying content popularities motivate interdependence between peering ISPs to elaborate their content caching and sharing strategies. In this paper, we propose the concept of peering for content exchange between interdependent ISPs in content centric Internet to minimize content delivery cost by a proper peering strategy. We model four peering strategic games to formulate four types of peering relationships between ISPs who are characterized by varying degrees of cooperative willingness from egoism to altruism and interconnected as profit-individuals or profit-coalition. Simulation results show the price of anarchy (PoA and communication cost in the four games to validate that ISPs should decide their peering strategies by balancing intradomain content demand and interdomain peering relations for an optimal cost of content delivery.

Peering Strategic Game Models for Interdependent ISPs in Content Centric Internet

Science.gov (United States)

Guan, Jianfeng; Xu, Changqiao; Su, Wei; Zhang, Hongke

2013-01-01

Emergent content-oriented networks prompt Internet service providers (ISPs) to evolve and take major responsibility for content delivery. Numerous content items and varying content popularities motivate interdependence between peering ISPs to elaborate their content caching and sharing strategies. In this paper, we propose the concept of peering for content exchange between interdependent ISPs in content centric Internet to minimize content delivery cost by a proper peering strategy. We model four peering strategic games to formulate four types of peering relationships between ISPs who are characterized by varying degrees of cooperative willingness from egoism to altruism and interconnected as profit-individuals or profit-coalition. Simulation results show the price of anarchy (PoA) and communication cost in the four games to validate that ISPs should decide their peering strategies by balancing intradomain content demand and interdomain peering relations for an optimal cost of content delivery. PMID:24381517

Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR

DEFF Research Database (Denmark)

Jakočiūnas, Tadas; Jensen, Emil D.; Jensen, Michael Krogh

2018-01-01

and marker-free integration of the carotenoid pathway from 15 exogenously supplied DNA parts into three targeted genomic loci. As a second proof-of-principle, a total of ten DNA parts were assembled and integrated in two genomic loci to construct a tyrosine production strain, and at the same time knocking......Genome integration is a vital step for implementing large biochemical pathways to build a stable microbial cell factory. Although traditional strain construction strategies are well established for the model organism Saccharomyces cerevisiae, recent advances in CRISPR/Cas9-mediated genome...... engineering allow much higher throughput and robustness in terms of strain construction. In this chapter, we describe CasEMBLR, a highly efficient and marker-free genome engineering method for one-step integration of in vivo assembled expression cassettes in multiple genomic sites simultaneously. Cas...

Application of remote debugging techniques in user-centric job monitoring

International Nuclear Information System (INIS)

Dos Santos, T; Mättig, P; Harenberg, T; Volkmer, F; Beermann, T; Kalinin, S; Ahrens, R; Wulff, N

2012-01-01

With the Job Execution Monitor, a user-centric job monitoring software developed at the University of Wuppertal and integrated into the job brokerage systems of the WLCG, job progress and grid worker node health can be supervised in real time. Imminent error conditions can thus be detected early by the submitter and countermeasures can be taken. Grid site admins can access aggregated data of all monitored jobs to infer the site status and to detect job misbehaviour. To remove the last 'blind spot' from this monitoring, a remote debugging technique based on the GNU C compiler suite was developed and integrated into the software; its design concept and architecture is described in this paper and its application discussed.

The Influence of Local Ethnic Diversity on Group-Centric Crime Attitudes

DEFF Research Database (Denmark)

Hjorth, Frederik

2017-01-01

Several studies provide evidence of group-centric policy attitudes, that is, citizens evaluating policies based on linkages with visible social groups. The existing literature generally points to the role of media imagery, rhetoric and prominent political sponsors in driving group-centric attitudes......-down’ influence on group-centric attitudes by elite actors is complemented by ‘bottom-up’ local processes of experiential learning about group–policy linkages....

Featureous: infrastructure for feature-centric analysis of object-oriented software

DEFF Research Database (Denmark)

Olszak, Andrzej; Jørgensen, Bo Nørregaard

2010-01-01

The decentralized nature of collaborations between objects in object-oriented software makes it difficult to understand how user-observable program features are implemented and how their implementations relate to each other. It is worthwhile to improve this situation, since feature-centric program...... understanding and modification are essential during software evolution and maintenance. In this paper, we present an infrastructure built on top of the NetBeans IDE called Featureous that allows for rapid construction of tools for feature-centric analysis of object-oriented software. Our infrastructure...... encompasses a lightweight feature location mechanism, a number of analytical views and an API allowing for addition of third-party extensions. To form a common conceptual framework for future feature-centric extensions, we propose to structure feature centric analysis along three dimensions: perspective...

Wound care clinical pathway: a conceptual model.

Science.gov (United States)

Barr, J E; Cuzzell, J

1996-08-01

A clinical pathway is a written sequence of clinical processes or events that guides a patient with a defined problem toward an expected outcome. Clinical pathways are tools to assist with the cost-effective management of clinical outcomes related to specific problems or disease processes. The primary obstacles to developing clinical pathways for wound care are the chronic natures of some wounds and the many variables that can delay healing. The pathway introduced in this article was modeled upon the three phases of tissue repair: inflammatory, proliferative, and maturation. This physiology-based model allows clinicians to identify and monitor outcomes based on observable and measurable clinical parameters. The pathway design, which also includes educational and behavioral outcomes, allows the clinician to individualize the expected timeframe for outcome achievement based on individual patient criteria and expert judgement. Integral to the pathway are the "4P's" which help standardize the clinical processes by wound type: Protocols, Policies, Procedures, and Patient education tools. Four categories into which variances are categorized based on the cause of the deviation from the norm are patient, process/system, practitioner, and planning/discharge. Additional research is warranted to support the value of this clinical pathway in the clinical arena.

EVALUATING A CUSTOMER-CENTRIC APPROACH

Directory of Open Access Journals (Sweden)

Luigi-Nicolae DUMITRESCU

2007-01-01

Full Text Available Customer focus is, at best, only one element of the relationship between a company and its customers. At worst it is a board-room buzzworld, witch makes every board member feel a little more secure. Not unlike the phrase “working towards equal opportunities”, it is showing an awareness of a need but is not addressing the issues. Customer focus must lead to something meaningful, will probably require sacrifices and is just one of the steps necessary to become truly customer-centric. A customer focus puts your customers high on your list of priorities. When you put your customers into the heart of your business, make customers part of the culture, then you to become customer-centric.

An engineering approach to an integrated value proposition design framework

Directory of Open Access Journals (Sweden)

Van Der Merwe, Carmen

2015-05-01

Full Text Available Numerous problems with product quality and time-to-market launches can be traced back to how the product lifecycle process is managed within the organisation. This article provides insight into how an integrated value proposition design framework shifts product lifecycle management from a product-centric view to a customer-centric view, through the use of good engineering practices as found in the systems engineering discipline. Combining this with methods and tools such as the Refined Kano model, Blue Ocean strategy, and the Generalised Bass model enables the organisation to enhance product and service quality while reducing the time-to-market for new value proposition launches.

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.

Data Centric Development Methodology

Science.gov (United States)

Khoury, Fadi E.

2012-01-01

Data centric applications, an important effort of software development in large organizations, have been mostly adopting a software methodology, such as a waterfall or Rational Unified Process, as the framework for its development. These methodologies could work on structural, procedural, or object oriented based applications, but fails to capture…

Re-Structuring Preservice Teacher Education: Introducing the School-Community Integrated Learning (SCIL) Pathway

Science.gov (United States)

Hudson, Sue; Hudson, Peter

2013-01-01

Reviews into teacher education call for new models that develop preservice teachers' practical knowledge and skills. The study involved 9 mentor teachers and 14 mentees (final-year preservice teachers) working in a new teacher education model, the School-Community Integrated Learning (SCIL) pathway, and analysed data from a Likert survey with…

Integrated care pathways for airway diseases (AIRWAYS-ICPs)

NARCIS (Netherlands)

Bousquet, J.; Addis, A.; Adcock, I.; Agache, I.; Agusti, A.; Alonso, A.; Annesi-Maesano, I.; Anto, J. M.; Bachert, C.; Baena-Cagnani, C. E.; Bai, C.; Baigenzhin, A.; Barbara, C.; Barnes, P. J.; Bateman, E. D.; Beck, L.; Bedbrook, A.; Bel, E. H.; Benezet, O.; Bennoor, K. S.; Benson, M.; Bernabeu-Wittel, M.; Bewick, M.; Bindslev-Jensen, C.; Blain, H.; Blasi, F.; Bonini, M.; Bonini, S.; Boulet, L. P.; Bourdin, A.; Bourret, R.; Bousquet, P. J.; Brightling, C. E.; Briggs, A.; Brozek, J.; Buhl, R.; Bush, A.; Caimmi, D.; Calderon, M.; Calverley, P.; Camargos, P. A.; Camuzat, T.; Canonica, G. W.; Carlsen, K. H.; Casale, T. B.; Cazzola, M.; Cepeda Sarabia, A. M.; Cesario, A.; Chen, Y. Z.; Chkhartishvili, E.; Chavannes, N. H.; Chiron, R.; Chuchalin, A.; Chung, K. F.; Cox, L.; Crooks, G.; Crooks, M. G.; Cruz, A. A.; Custovic, A.; Dahl, R.; Dahlen, S. E.; de Blay, F.; Dedeu, T.; Deleanu, D.; Demoly, P.; Devillier, P.; Didier, A.; Dinh-Xuan, A. T.; Djukanovic, R.; Dokic, D.; Douagui, H.; Dubakiene, R.; Eglin, S.; Elliot, F.; Emuzyte, R.; Fabbri, L.; Fink Wagner, A.; Fletcher, M.; Fokkens, W. J.; Fonseca, J.; Franco, A.; Frith, P.; Furber, A.; Gaga, M.; Garcés, J.; Garcia-Aymerich, J.; Gamkrelidze, A.; Gonzales-Diaz, S.; Gouzi, F.; Guzmán, M. A.; Haahtela, T.; Harrison, D.; Hayot, M.; Heaney, L. G.; Heinrich, J.; Hellings, P. W.; Hooper, J.; Humbert, M.; Hyland, M.; Iaccarino, G.; Jakovenko, D.; Jardim, J. R.; Jeandel, C.; Jenkins, C.; Johnston, S. L.; Jonquet, O.; Joos, G.; Jung, K. S.; Kalayci, O.; Karunanithi, S.; Keil, T.; Khaltaev, N.; Kolek, V.; Kowalski, M. L.; Kull, I.; Kuna, P.; Kvedariene, V.; Le, L. T.; Lodrup Carlsen, K. C.; Louis, R.; MacNee, W.; Mair, A.; Majer, I.; Manning, P.; de Manuel Keenoy, E.; Masjedi, M. R.; Melen, E.; Melo-Gomes, E.; Menzies-Gow, A.; Mercier, G.; Mercier, J.; Michel, J. P.; Miculinic, N.; Mihaltan, F.; Milenkovic, B.; Molimard, M.; Momas, I.; Montilla-Santana, A.; Morais-Almeida, M.; Morgan, M.; N'Diaye, M.; Nafti, S.; Nekam, K.; Neou, A.; Nicod, L.; O'Hehir, R.; Ohta, K.; Paggiaro, P.; Palkonen, S.; Palmer, S.; Papadopoulos, N. G.; Papi, A.; Passalacqua, G.; Pavord, I.; Pigearias, B.; Plavec, D.; Postma, D. S.; Price, D.; Rabe, K. F.; Radier Pontal, F.; Redon, J.; Rennard, S.; Roberts, J.; Robine, J. M.; Roca, J.; Roche, N.; Rodenas, F.; Roggeri, A.; Rolland, C.; Rosado-Pinto, J.; Ryan, D.; Samolinski, B.; Sanchez-Borges, M.; Schünemann, H. J.; Sheikh, A.; Shields, M.; Siafakas, N.; Sibille, Y.; Similowski, T.; Small, I.; Sola-Morales, O.; Sooronbaev, T.; Stelmach, R.; Sterk, P. J.; Stiris, T.; Sud, P.; Tellier, V.; To, T.; Todo-Bom, A.; Triggiani, M.; Valenta, R.; Valero, A. L.; Valiulis, A.; Valovirta, E.; van Ganse, E.; Vandenplas, O.; Vasankari, T.; Vestbo, J.; Vezzani, G.; Viegi, G.; Visier, L.; Vogelmeier, C.; Vontetsianos, T.; Wagstaff, R.; Wahn, U.; Wallaert, B.; Whalley, B.; Wickman, M.; Williams, D. M.; Wilson, N.; Yawn, B. P.; Yiallouros, P. K.; Yorgancioglu, A.; Yusuf, O. M.; Zar, H. J.; Zhong, N.; Zidarn, M.; Zuberbier, T.

2014-01-01

The objective of Integrated Care Pathways for Airway Diseases (AIRWAYS-ICPs) is to launch a collaboration to develop multi-sectoral care pathways for chronic respiratory diseases in European countries and regions. AIRWAYS-ICPs has strategic relevance to the European Union Health Strategy and will

Integrated care pathways for airway diseases (AIRWAYS-ICPs)

NARCIS (Netherlands)

Bousquet, J.; Addis, A.; Adcock, I.; Agache, I.; Agusti, A.; Alonso, A.; Annesi-Maesano, I.; Anto, J. M.; Bachert, C.; Baena-Cagnani, C. E.; Bai, C.; Baigenzhin, A.; Barbara, C.; Barnes, P. J.; Bateman, E. D.; Beck, L.; Bedbrook, A.; Bel, E. H.; Benezet, O.; Bennoor, K. S.; Benson, M.; Bernabeu-Wittel, M.; Bewick, M.; Bindslev-Jensen, C.; Blain, H.; Blasi, F.; Bonini, M.; Bonini, S.; Boulet, L. P.; Bourdin, A.; Bourret, R.; Bousquet, P. J.; Brightling, C. E.; Briggs, A.; Brozek, J.; Buh, R.; Bush, A.; Caimmi, D.; Calderon, M.; Calverley, P.; Camargos, P. A.; Camuzat, T.; Canonica, G. W.; Carlsen, K. H.; Casale, T. B.; Cazzola, M.; Sarabia, A. M. Cepeda; Cesario, A.; Chen, Y. Z.; Chkhartishvili, E.; Chavannes, N. H.; Chiron, R.; Chuchalin, A.; Chung, K. F.; Cox, L.; Crooks, G.; Crooks, M. G.; Cruz, A. A.; Custovic, A.; Dahl, R.; Dahlen, S. E.; De Blay, F.; Dedeu, T.; Deleanu, D.; Demoly, P.; Devillier, P.; Didier, A.; Dinh-Xuan, A. T.; Djukanovic, R.; Dokic, D.; Douagui, H.; Dubakiene, R.; Eglin, S.; Elliot, F.; Emuzyte, R.; Fabbri, L.; Wagner, A. Fink; Fletcher, M.; Fokkens, W. J.; Fonseca, J.; Franco, A.; Frith, P.; Furber, A.; Gaga, M.; Garces, J.; Garcia-Aymerich, J.; Gamkrelidze, A.; Gonzales-Diaz, S.; Gouzi, F.; Guzman, M. A.; Haahtela, T.; Harrison, D.; Hayot, M.; Heaney, L. G.; Heinrich, J.; Hellings, P. W.; Hooper, J.; Humbert, M.; Hyland, M.; Iaccarino, G.; Jakovenko, D.; Jardim, J. R.; Jeandel, C.; Jenkins, C.; Johnston, S. L.; Jonquet, O.; Joos, G.; Jung, K. S.; Kalayci, O.; Karunanithi, S.; Keil, T.; Khaltaev, N.; Kolek, V.; Kowalski, M. L.; Kull, I.; Kuna, P.; Kvedariene, V.; Le, L. T.; Carlsen, K. C. Lodrup; Louis, R.; MacNee, W.; Mair, A.; Majer, I.; Manning, P.; Keenoy, E. de Manuel; Masjedi, M. R.; Meten, E.; Melo-Gomes, E.; Menzies-Gow, A.; Mercier, G.; Mercier, J.; Michel, J. P.; Miculinic, N.; Mihaltan, F.; Milenkovic, B.; Molimard, M.; Mamas, I.; Montilla-Santana, A.; Morais-Almeida, M.; Morgan, M.; N'Diaye, M.; Nafti, S.; Nekam, K.; Neou, A.; Nicod, L.; O'Hehir, R.; Ohta, K.; Paggiaro, P.; Palkonen, S.; Palmer, S.; Papadopoulos, N. G.; Papi, A.; Passalacqua, G.; Pavord, I.; Pigearias, B.; Plavec, D.; Postma, D. S.; Price, D.; Rabe, K. F.; Pontal, F. Radier; Redon, J.; Rennard, S.; Roberts, J.; Robine, J. M.; Roca, J.; Roche, N.; Rodenas, F.; Roggeri, A.; Rolland, C.; Rosado-Pinto, J.; Ryan, D.; Samolinski, B.; Sanchez-Borges, M.; Schunemann, H. J.; Sheikh, A.; Shields, M.; Siafakas, N.; Sibille, Y.; Similowski, T.; Small, I.; Sola-Morales, O.; Sooronbaev, T.; Stelmach, R.; Sterk, P. J.; Stiris, T.; Sud, P.; Tellier, V.; To, T.; Todo-Bom, A.; Triggiani, M.; Valenta, R.; Valero, A. L.; Valiulis, A.; Valovirta, E.; Van Ganse, E.; Vandenplas, O.; Vasankari, T.; Vestbo, J.; Vezzani, G.; Viegi, G.; Visier, L.; Vogelmeier, C.; Vontetsianos, T.; Wagstaff, R.; Wahn, U.; Wallaert, B.; Whalley, B.; Wickman, M.; Williams, D. M.; Wilson, N.; Yawn, B. P.; Yiallouros, P. K.; Yorgancioglu, A.; Yusuf, O. M.; Zar, H. J.; Zhong, N.; Zidarn, M.; Zuberbier, T.

The objective of Integrated Care Pathways for Airway Diseases (AIRWAYS-ICPs) is to launch a collaboration to develop multi-sectoral care pathways for chronic respiratory diseases in European countries and regions. AIRWAYS-ICPs has strategic relevance to the European Union Health Strategy and will

An Efficient and Secure m-IPS Scheme of Mobile Devices for Human-Centric Computing

Directory of Open Access Journals (Sweden)

Young-Sik Jeong

2014-01-01

Full Text Available Recent rapid developments in wireless and mobile IT technologies have led to their application in many real-life areas, such as disasters, home networks, mobile social networks, medical services, industry, schools, and the military. Business/work environments have become wire/wireless, integrated with wireless networks. Although the increase in the use of mobile devices that can use wireless networks increases work efficiency and provides greater convenience, wireless access to networks represents a security threat. Currently, wireless intrusion prevention systems (IPSs are used to prevent wireless security threats. However, these are not an ideal security measure for businesses that utilize mobile devices because they do not take account of temporal-spatial and role information factors. Therefore, in this paper, an efficient and secure mobile-IPS (m-IPS is proposed for businesses utilizing mobile devices in mobile environments for human-centric computing. The m-IPS system incorporates temporal-spatial awareness in human-centric computing with various mobile devices and checks users’ temporal spatial information, profiles, and role information to provide precise access control. And it also can extend application of m-IPS to the Internet of things (IoT, which is one of the important advanced technologies for supporting human-centric computing environment completely, for real ubiquitous field with mobile devices.

Laboratory informatics tools integration strategies for drug discovery: integration of LIMS, ELN, CDS, and SDMS.

Science.gov (United States)

Machina, Hari K; Wild, David J

2013-04-01

There are technologies on the horizon that could dramatically change how informatics organizations design, develop, deliver, and support applications and data infrastructures to deliver maximum value to drug discovery organizations. Effective integration of data and laboratory informatics tools promises the ability of organizations to make better informed decisions about resource allocation during the drug discovery and development process and for more informed decisions to be made with respect to the market opportunity for compounds. We propose in this article a new integration model called ELN-centric laboratory informatics tools integration.

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

Science.gov (United States)

Uyar, Bora; Yusuf, Dilmurat; Wurmus, Ricardo; Rajewsky, Nikolaus; Ohler, Uwe; Akalin, Altuna

2017-06-02

In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies. The design of RCAS is modular, which enables flexible usage and convenient integration with other bioinformatics workflows. RCAS is an R/Bioconductor package but we also created graphical user interfaces including a Galaxy wrapper and a stand-alone web service. The application of RCAS on published datasets shows that RCAS is not only able to reproduce published findings but also helps generate novel knowledge and hypotheses. The meta-gene profiles, gene-centric annotation, motif analysis and gene-set analysis provided by RCAS provide contextual knowledge which is necessary for understanding the functional aspects of different biological events that involve RNAs. In addition, the array of different interfaces and deployment options adds the convenience of use for different levels of users. RCAS is available at http://bioconductor.org/packages/release/bioc/html/RCAS.html and http://rcas.mdc-berlin.de. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Metrics for measuring net-centric data strategy implementation

Science.gov (United States)

Kroculick, Joseph B.

2010-04-01

An enterprise data strategy outlines an organization's vision and objectives for improved collection and use of data. We propose generic metrics and quantifiable measures for each of the DoD Net-Centric Data Strategy (NCDS) data goals. Data strategy metrics can be adapted to the business processes of an enterprise and the needs of stakeholders in leveraging the organization's data assets to provide for more effective decision making. Generic metrics are applied to a specific application where logistics supply and transportation data is integrated across multiple functional groups. A dashboard presents a multidimensional view of the current progress to a state where logistics data shared in a timely and seamless manner among users, applications, and systems.

Process-centric IT in Practice

DEFF Research Database (Denmark)

Siurdyban, Artur; Nielsen, Peter Axel

2012-01-01

, they should find governance structures which ensure that there is a fruitful collaboration between the corporate IT department and the local business units. This collaboration should also include different competences with both IT and process management and competences differing because they are centralized......This case illustrates and discusses the issues and challenges at Kerrtec Corporation in their effort to establish process-centric IT management. The case describes how a local business unit in Kerrtec managed their business processes and how that created a necessity for IT to be managed to match...... the business processes. It also describes how the central IT department at corporate headquarters responded to requests rooted in business processes. In discussing the challenges for Kerrtec, it is clear that they will have to map out the needed competences for process-centric IT management. In particular...

Advanced Technologies, Embedded and Multimedia for Human-Centric Computing

CERN Document Server

Chao, Han-Chieh; Deng, Der-Jiunn; Park, James; HumanCom and EMC 2013

2014-01-01

The theme of HumanCom and EMC are focused on the various aspects of human-centric computing for advances in computer science and its applications, embedded and multimedia computing and provides an opportunity for academic and industry professionals to discuss the latest issues and progress in the area of human-centric computing. And the theme of EMC (Advanced in Embedded and Multimedia Computing) is focused on the various aspects of embedded system, smart grid, cloud and multimedia computing, and it provides an opportunity for academic, industry professionals to discuss the latest issues and progress in the area of embedded and multimedia computing. Therefore this book will be include the various theories and practical applications in human-centric computing and embedded and multimedia computing.

A Privacy-Preserving Platform for User-Centric Quantitative Benchmarking

Science.gov (United States)

Herrmann, Dominik; Scheuer, Florian; Feustel, Philipp; Nowey, Thomas; Federrath, Hannes

We propose a centralised platform for quantitative benchmarking of key performance indicators (KPI) among mutually distrustful organisations. Our platform offers users the opportunity to request an ad-hoc benchmarking for a specific KPI within a peer group of their choice. Architecture and protocol are designed to provide anonymity to its users and to hide the sensitive KPI values from other clients and the central server. To this end, we integrate user-centric peer group formation, exchangeable secure multi-party computation protocols, short-lived ephemeral key pairs as pseudonyms, and attribute certificates. We show by empirical evaluation of a prototype that the performance is acceptable for reasonably sized peer groups.

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution

Energy Technology Data Exchange (ETDEWEB)

Ou, Yang; Shi, Wenjing; Smith, Steven J.; Ledna, Catherine M.; West, J. Jason; Nolte, Christopher G.; Loughlin, Daniel H.

2018-04-01

There are many technological pathways that can lead to reduced carbon dioxide (CO₂) emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessment model with state-level resolution of the U.S. energy system to compare environmental impacts of alternative low-carbon pathways. One set of pathways emphasizes nuclear energy and carbon capture and storage (NUC/CCS), while another set emphasizes renewable energy (RE). These are compared with pathways in which all technologies are available. Air pollutant emissions, mortality costs attributable to particulate matter less than 2.5 microns in diameter (PM2.5), and energy-related water demands are evaluated for 50% and 80% CO₂ reduction targets in the U.S. in 2050. The RE low-carbon pathways require less water withdrawal and consumption than the NUC/CCS pathways because of the large cooling demands of nuclear power and CCS. However, the NUC/CCS low-carbon pathways produce greater health benefits, mainly because the NUC/CCS assumptions result in less primary PM2.5 emissions from residential wood combustion. Environmental co-benefits differ among states because of factors such as existing technology stock, resource availability, and environmental and energy policies. An important finding is that biomass in the building sector can offset some of the health co-benefits of the low-carbon pathways even though it plays only a minor role in reducing CO₂ emissions.

Modeling of nitrous oxide production by autotrophic ammonia-oxidizing bacteria with multiple production pathways.

Science.gov (United States)

Ni, Bing-Jie; Peng, Lai; Law, Yingyu; Guo, Jianhua; Yuan, Zhiguo

2014-04-01

Autotrophic ammonia oxidizing bacteria (AOB) have been recognized as a major contributor to N2O production in wastewater treatment systems. However, so far N2O models have been proposed based on a single N2O production pathway by AOB, and there is still a lack of effective approach for the integration of these models. In this work, an integrated mathematical model that considers multiple production pathways is developed to describe N2O production by AOB. The pathways considered include the nitrifier denitrification pathway (N2O as the final product of AOB denitrification with NO2(-) as the terminal electron acceptor) and the hydroxylamine (NH2OH) pathway (N2O as a byproduct of incomplete oxidation of NH2OH to NO2(-)). In this model, the oxidation and reduction processes are modeled separately, with intracellular electron carriers introduced to link the two types of processes. The model is calibrated and validated using experimental data obtained with two independent nitrifying cultures. The model satisfactorily describes the N2O data from both systems. The model also predicts shifts of the dominating pathway at various dissolved oxygen (DO) and nitrite levels, consistent with previous hypotheses. This unified model is expected to enhance our ability to predict N2O production by AOB in wastewater treatment systems under varying operational conditions.

Environmental impact assessment for energy pathways: an integrated methodology

International Nuclear Information System (INIS)

Sommereux-Blanc, Isabelle

2010-01-01

This document presents the synthesis of my research work contributing to the development of an integrated methodology of environmental impact assessment for energy pathways. In the context of world globalization, environmental impact assessments issues are highly linked with the following questioning: Which environmental impacts? for which demand? at which location? at which temporal scale? My work is built upon the definition of a conceptual framework able to handle these issues and upon its progressive implementation. The integration of the spatial and temporal issues within the methodology are key elements. Fundamental cornerstones of this framework are presented along the DPSIR concept (Driving forces, Pressures, State, Impacts, Responses). They cover a comprehensive analysis of the limits and the relevance of life cycle analysis and the development of a geo-spatialized environmental performance approach for an electrical production pathway. Perspectives linked with the development of this integrated methodology are detailed for energy pathways. (author)

Fostering development of nursing practices to support integrated care when implementing integrated care pathways: what levers to use?

Science.gov (United States)

Longpré, Caroline; Dubois, Carl-Ardy

2017-11-29

Care integration has been the focus of recent health system reforms. Given their functions at all levels of the care continuum, nurses have a substantial and primordial role to play in such integration processes. The aim of this study was to identify levers and strategies that organizations can use to support the development of a nursing practice aligned with the requirements of care integration in a health and social services centre (HSSC) in Quebec. The research design was a cross-sectional descriptive qualitative study based on a single case study with nested levels of analysis. The case was a public, multi-disciplinary HSSC in a semi-urban region of Quebec. Semi-structured interviews with 37 persons (nurses, professionals, managers, administrators) allowed for data saturation and ensured theoretical representation by covering four care pathways constituting different care integration contexts. Analysis involved four steps: preparing a predetermined list of codes based on the reference framework developed by Minkman (2011); coding transcript content; developing general and summary matrices to group observations for each care pathway; and creating a general model showing the overall results for the four pathways. The organization's capacity for response with regard to developing an integrated system of services resulted in two types of complementary interventions. The first involved investing in key resources and renewing organizational structures; the second involved deploying a series of organizational and clinical-administrative processes. In resource terms, integration efforts resulted in setting up new strategic services, re-arranging physical infrastructures, and deploying new technological resources. Organizational and clinical-administrative processes to promote integration involved renewing governance, improving the flow of care pathways, fostering continuous quality improvement, developing new roles, promoting clinician collaboration, and strengthening

Cooperative Human-Centric Sensing Cooperation

DEFF Research Database (Denmark)

Mihovska, Albena

Human-Centric Sensing (HCS) is a new concept relevant to Internet of Things (IoT). HCS connectivity, referred to as “smart connectivity” enables applications that are highly personalized and often time-critical. In a typical HCS scenario, there may be many hundreds of sensor streams connections...

'How Much is a Pound of C4ISR Worth?' An Assessment methodology to Evolve Network Centric Measures and Metrics for Application to FORCEnet

National Research Council Canada - National Science Library

Poirier, John A; Bates, Edgar; Tempestilli, Mark

2003-01-01

... centric outcomes including work being done in support of the Office of Force Transformation and the office of the Assistant Secretary of Defense for Networks, and Information Integration (ASD (NI2...

Preface for the book: Antennas And Propagation for Body-Centric Wireless Communications

DEFF Research Database (Denmark)

Frederiksen, Flemming Bjerge; Prasad, Ramjee

2006-01-01

The book address the following subjects: Body Centric Wireless Communications possibilities, Electromagnetic properties of the body, On-body Communication Channels at high and low frequency bands, Body Centric UWB Communications, Wearable Antennas for cellular and WLAN communications, Body...

Integrative analyses of miRNA and proteomics identify potential biological pathways associated with onset of pulmonary fibrosis in the bleomycin rat model

International Nuclear Information System (INIS)

Fukunaga, Satoki; Kakehashi, Anna; Sumida, Kayo; Kushida, Masahiko; Asano, Hiroyuki; Gi, Min; Wanibuchi, Hideki

2015-01-01

To determine miRNAs and their predicted target proteins regulatory networks which are potentially involved in onset of pulmonary fibrosis in the bleomycin rat model, we conducted integrative miRNA microarray and iTRAQ-coupled LC-MS/MS proteomic analyses, and evaluated the significance of altered biological functions and pathways. We observed that alterations of miRNAs and proteins are associated with the early phase of bleomycin-induced pulmonary fibrosis, and identified potential target pairs by using ingenuity pathway analysis. Using the data set of these alterations, it was demonstrated that those miRNAs, in association with their predicted target proteins, are potentially involved in canonical pathways reflective of initial epithelial injury and fibrogenic processes, and biofunctions related to induction of cellular development, movement, growth, and proliferation. Prediction of activated functions suggested that lung cells acquire proliferative, migratory, and invasive capabilities, and resistance to cell death especially in the very early phase of bleomycin-induced pulmonary fibrosis. The present study will provide new insights for understanding the molecular pathogenesis of idiopathic pulmonary fibrosis. - Highlights: • We analyzed bleomycin-induced pulmonary fibrosis in the rat. • Integrative analyses of miRNA microarray and proteomics were conducted. • We determined the alterations of miRNAs and their potential target proteins. • The alterations may control biological functions and pathways in pulmonary fibrosis. • Our result may provide new insights of pulmonary fibrosis

Integrative analyses of miRNA and proteomics identify potential biological pathways associated with onset of pulmonary fibrosis in the bleomycin rat model

Energy Technology Data Exchange (ETDEWEB)

Fukunaga, Satoki [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugade-Naka, Konohana-ku, Osaka 554-8558 (Japan); Kakehashi, Anna [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Sumida, Kayo; Kushida, Masahiko; Asano, Hiroyuki [Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugade-Naka, Konohana-ku, Osaka 554-8558 (Japan); Gi, Min [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan); Wanibuchi, Hideki, E-mail: wani@med.osaka-cu.ac.jp [Department of Molecular Pathology, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585 (Japan)

2015-08-01

To determine miRNAs and their predicted target proteins regulatory networks which are potentially involved in onset of pulmonary fibrosis in the bleomycin rat model, we conducted integrative miRNA microarray and iTRAQ-coupled LC-MS/MS proteomic analyses, and evaluated the significance of altered biological functions and pathways. We observed that alterations of miRNAs and proteins are associated with the early phase of bleomycin-induced pulmonary fibrosis, and identified potential target pairs by using ingenuity pathway analysis. Using the data set of these alterations, it was demonstrated that those miRNAs, in association with their predicted target proteins, are potentially involved in canonical pathways reflective of initial epithelial injury and fibrogenic processes, and biofunctions related to induction of cellular development, movement, growth, and proliferation. Prediction of activated functions suggested that lung cells acquire proliferative, migratory, and invasive capabilities, and resistance to cell death especially in the very early phase of bleomycin-induced pulmonary fibrosis. The present study will provide new insights for understanding the molecular pathogenesis of idiopathic pulmonary fibrosis. - Highlights: • We analyzed bleomycin-induced pulmonary fibrosis in the rat. • Integrative analyses of miRNA microarray and proteomics were conducted. • We determined the alterations of miRNAs and their potential target proteins. • The alterations may control biological functions and pathways in pulmonary fibrosis. • Our result may provide new insights of pulmonary fibrosis.

SDN Based User-Centric Framework for Heterogeneous Wireless Networks

Directory of Open Access Journals (Sweden)

Zhaoming Lu

2016-01-01

Full Text Available Due to the rapid growth of mobile data traffic, more and more basestations and access points (APs have been densely deployed to provide users with ubiquitous network access, which make current wireless network a complex heterogeneous network (HetNet. However, traditional wireless networks are designed with network-centric approaches where different networks have different quality of service (QoS strategies and cannot easily cooperate with each other to serve network users. Massive network infrastructures could not assure users perceived network and service quality, which is an indisputable fact. To address this issue, we design a new framework for heterogeneous wireless networks with the principle of user-centricity, refactoring the network from users’ perspective to suffice their requirements and preferences. Different from network-centric approaches, the proposed framework takes advantage of Software Defined Networking (SDN and virtualization technology, which will bring better perceived services quality for wireless network users. In the proposed user-centric framework, control plane and data plane are decoupled to manage the HetNets in a flexible and coadjutant way, and resource virtualization technology is introduced to abstract physical resources of HetNets into unified virtualized resources. Hence, ubiquitous and undifferentiated network connectivity and QoE (quality of experience driven fine-grained resource management could be achieved for wireless network users.

Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes

DEFF Research Database (Denmark)

Fontana, Alessandra; Campanaro, Stefano; Treu, Laura

2018-01-01

-depth characterization of the microbial community structure using genome-centric metagenomics. Both reactor configurations showed acidification problems under the tested organic loading rates (OLRs) of 3.6 and 2.4 g COD/L-reactor day and the hydraulic retention time (HRT) of 15 days. However, the two-stage design...... of the main population genomes highlighted specific metabolic pathways responsible for the AD process and the mechanisms of main intermediates production. Particularly, the acetate accumulation experienced by the single stage configuration was mainly correlated to the low abundant syntrophic acetate oxidizer...

Single, Integrated, Service-Centric Model of Military Health System Governance

Science.gov (United States)

of the research is to establish what the model of governance of the Military Health System should be. That, with other recommendations, should be the...foundation for the impending transformation. The research found that the model of governance should be a single service model with regional health...commands that support the geographic combatant commander (GCC). With an organization based on the presented model of governance , the Military Health

Hierarchical Brokering with Feedback Control Framework in Mobile Device-Centric Clouds

Directory of Open Access Journals (Sweden)

Chao-Lieh Chen

2016-01-01

Full Text Available We propose a hierarchical brokering architecture (HiBA and Mobile Multicloud Networking (MMCN feedback control framework for mobile device-centric cloud (MDC2 computing. Exploiting the MMCN framework and RESTful web-based interconnection, each tier broker probes resource state of its federation for control and management. Real-time and seamless services were developed. Case studies including intrafederation energy-aware balancing based on fuzzy feedback control and higher tier load balancing are further demonstrated to show how HiBA with MMCN relieves the embedding of algorithms when developing services. Theoretical performance model and real-world experiments both show that an MDC2 based on HiBA features better quality in terms of resource availability and network latency if it federates devices with enough resources distributed in lower tier hierarchy. The proposed HiBA realizes a development platform for MDC2 computing which is a feasible solution to User-Centric Networks (UCNs.

A Commander in Chief's Network-Centric Odyssey

National Research Council Canada - National Science Library

Copley, E

2002-01-01

.... Each Armed Service has begun training and equipping its force using the tenets of Network-Centric Operations, but those forces come together for the first time under the combatant Commander-in-Chief...

Network Centric Information Structure - Crisis Information Management

National Research Council Canada - National Science Library

Aarholt, Eldar; Berg, Olav

2004-01-01

This paper presents a generic Network Centric Information Structure (NCIS) that can be used by civilian, military and public sectors, and that supports information handling applied to crises management and emergency response...

Integrated QSAR study for inhibitors of Hedgehog Signal Pathway against multiple cell lines:a collaborative filtering method.

Science.gov (United States)

Gao, Jun; Che, Dongsheng; Zheng, Vincent W; Zhu, Ruixin; Liu, Qi

2012-07-31

The Hedgehog Signaling Pathway is one of signaling pathways that are very important to embryonic development. The participation of inhibitors in the Hedgehog Signal Pathway can control cell growth and death, and searching novel inhibitors to the functioning of the pathway are in a great demand. As the matter of fact, effective inhibitors could provide efficient therapies for a wide range of malignancies, and targeting such pathway in cells represents a promising new paradigm for cell growth and death control. Current research mainly focuses on the syntheses of the inhibitors of cyclopamine derivatives, which bind specifically to the Smo protein, and can be used for cancer therapy. While quantitatively structure-activity relationship (QSAR) studies have been performed for these compounds among different cell lines, none of them have achieved acceptable results in the prediction of activity values of new compounds. In this study, we proposed a novel collaborative QSAR model for inhibitors of the Hedgehog Signaling Pathway by integration the information from multiple cell lines. Such a model is expected to substantially improve the QSAR ability from single cell lines, and provide useful clues in developing clinically effective inhibitors and modifications of parent lead compounds for target on the Hedgehog Signaling Pathway. In this study, we have presented: (1) a collaborative QSAR model, which is used to integrate information among multiple cell lines to boost the QSAR results, rather than only a single cell line QSAR modeling. Our experiments have shown that the performance of our model is significantly better than single cell line QSAR methods; and (2) an efficient feature selection strategy under such collaborative environment, which can derive the commonly important features related to the entire given cell lines, while simultaneously showing their specific contributions to a specific cell-line. Based on feature selection results, we have proposed several

SPARTex: A Vertex-Centric Framework for RDF Data Analytics

KAUST Repository

Abdelaziz, Ibrahim

2015-08-31

A growing number of applications require combining SPARQL queries with generic graph search on RDF data. However, the lack of procedural capabilities in SPARQL makes it inappropriate for graph analytics. Moreover, RDF engines focus on SPARQL query evaluation whereas graph management frameworks perform only generic graph computations. In this work, we bridge the gap by introducing SPARTex, an RDF analytics framework based on the vertex-centric computation model. In SPARTex, user-defined vertex centric programs can be invoked from SPARQL as stored procedures. SPARTex allows the execution of a pipeline of graph algorithms without the need for multiple reads/writes of input data and intermediate results. We use a cost-based optimizer for minimizing the communication cost. SPARTex evaluates queries that combine SPARQL and generic graph computations orders of magnitude faster than existing RDF engines. We demonstrate a real system prototype of SPARTex running on a local cluster using real and synthetic datasets. SPARTex has a real-time graphical user interface that allows the participants to write regular SPARQL queries, use our proposed SPARQL extension to declaratively invoke graph algorithms or combine/pipeline both SPARQL querying and generic graph analytics.

Modeling biological pathway dynamics with timed automata.

Science.gov (United States)

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

2014-05-01

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

Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR.

Science.gov (United States)

Jakočiūnas, Tadas; Jensen, Emil D; Jensen, Michael K; Keasling, Jay D

2018-01-01

Genome integration is a vital step for implementing large biochemical pathways to build a stable microbial cell factory. Although traditional strain construction strategies are well established for the model organism Saccharomyces cerevisiae, recent advances in CRISPR/Cas9-mediated genome engineering allow much higher throughput and robustness in terms of strain construction. In this chapter, we describe CasEMBLR, a highly efficient and marker-free genome engineering method for one-step integration of in vivo assembled expression cassettes in multiple genomic sites simultaneously. CasEMBLR capitalizes on the CRISPR/Cas9 technology to generate double-strand breaks in genomic loci, thus prompting native homologous recombination (HR) machinery to integrate exogenously derived homology templates. As proof-of-principle for microbial cell factory development, CasEMBLR was used for one-step assembly and marker-free integration of the carotenoid pathway from 15 exogenously supplied DNA parts into three targeted genomic loci. As a second proof-of-principle, a total of ten DNA parts were assembled and integrated in two genomic loci to construct a tyrosine production strain, and at the same time knocking out two genes. This new method complements and improves the field of genome engineering in S. cerevisiae by providing a more flexible platform for rapid and precise strain building.

User Centric Job Monitoring – a redesign and novel approach in the STAR experiment

International Nuclear Information System (INIS)

Arkhipkin, D; Lauret, J; Zulkarneeva, Y

2014-01-01

User Centric Monitoring (or UCM) has been a long awaited feature in STAR, whereas programs, workflows and system 'events' could be logged, broadcast and later analyzed. UCM allows to collect and filter available job monitoring information from various resources and present it to users in a user-centric view rather than an administrative-centric point of view. The first attempt and implementation of 'a' UCM approach was made in STAR 2004 using a log4cxx plug-in back-end and then further evolved with an attempt to push toward a scalable database back-end (2006) and finally using a Web-Service approach (2010, CSW4DB SBIR). The latest showed to be incomplete and not addressing the evolving needs of the experiment where streamlined messages for online (data acquisition) purposes as well as the continuous support for the data mining needs and event analysis need to coexists and unified in a seamless approach. The code also revealed to be hardly maintainable. This paper presents the next evolutionary step of the UCM toolkit, a redesign and redirection of our latest attempt acknowledging and integrating recent technologies and a simpler, maintainable and yet scalable manner. The extended version of the job logging package is built upon three-tier approach based on Task, Job and Event, and features a Web-Service based logging API, a responsive AJAX-powered user interface, and a database back-end relying on MongoDB, which is uniquely suited for STAR needs. In addition, we present details of integration of this logging package with the STAR offline and online software frameworks. Leveraging on the reported experience and work from the ATLAS and CMS experience on using the ESPER engine, we discuss and show how such approach has been implemented in STAR for meta-data event triggering stream processing and filtering. An ESPER based solution seems to fit well into the online data acquisition system where many systems are monitored.

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

DEFF Research Database (Denmark)

King, Zachary A.; Lu, Justin; Dräger, Andreas

2016-01-01

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repo...

White matter integrity deficits in prefrontal-amygdala pathways in Williams syndrome.

Science.gov (United States)

Avery, Suzanne N; Thornton-Wells, Tricia A; Anderson, Adam W; Blackford, Jennifer Urbano

2012-01-16

Williams syndrome is a neurodevelopmental disorder associated with significant non-social fears. Consistent with this elevated non-social fear, individuals with Williams syndrome have an abnormally elevated amygdala response when viewing threatening non-social stimuli. In typically-developing individuals, amygdala activity is inhibited through dense, reciprocal white matter connections with the prefrontal cortex. Neuroimaging studies suggest a functional uncoupling of normal prefrontal-amygdala inhibition in individuals with Williams syndrome, which might underlie both the extreme amygdala activity and non-social fears. This functional uncoupling might be caused by structural deficits in underlying white matter pathways; however, prefrontal-amygdala white matter deficits have yet to be explored in Williams syndrome. We used diffusion tensor imaging to investigate prefrontal-amygdala white matter integrity differences in individuals with Williams syndrome and typically-developing controls with high levels of non-social fear. White matter pathways between the amygdala and several prefrontal regions were isolated using probabilistic tractography. Within each pathway, we tested for between-group differences in three measures of white matter integrity: fractional anisotropy (FA), radial diffusivity (RD), and parallel diffusivity (λ(1)). Individuals with Williams syndrome had lower FA, compared to controls, in several of the prefrontal-amygdala pathways investigated, indicating a reduction in white matter integrity. Lower FA in Williams syndrome was explained by significantly higher RD, with no differences in λ(1), suggestive of lower fiber density or axon myelination in prefrontal-amygdala pathways. These results suggest that deficits in the structural integrity of prefrontal-amygdala white matter pathways might underlie the increased amygdala activity and extreme non-social fears observed in Williams syndrome. Copyright © 2011 Elsevier Inc. All rights reserved.

Petroleum migration pathways and charge concentration: A three-dimensional model

Energy Technology Data Exchange (ETDEWEB)

Hindle, A.D. [Anadarko Algeria Corp., Middlesex (United Kingdom)

1997-09-01

Petroleum migration pathways through a basin are determined by the three-dimensional distribution of discontinuous sealing surfaces, which are usually parallel to bedding. The petroleum migrates below the sealing surface, taking the structurally most advantageous route. The three-dimensional distribution of migration pathways within the petroleum system can be modeled on a personal computer using a program based on the parameters discussed in this paper. Application of the model to the Paris and Williston basins demonstrates that a good correlation between predicted pathways and discovered accumulations can be made using simple models. Pathways form a dense network overlying generating areas in the central parts of basins. Toward the basin margins these routes commonly become increasingly focused into discrete pathways by the sealing-surface morphologies. Eventually, these pathways may reach the surface as seepages. It is important to integrate surface outcrops of migration routes (surface seepages) into migration modeling. Deflection of the pathways from the structurally most advantageous route below the sealing surface may be caused by lateral sealing barriers due to faces variation in the carrier rock below the seal, fault juxtaposition, or cross-formational seals such as salt intrusions. Deflection of pathways also occurs where there are hydrodynamic conditions in response to topography-driven groundwater flow. Zones of vertical migration are associated with facies changes along the horizon of the sealing surface into a nonsealing facies, or juxtaposition to nonsealing strata by faults. Vertical migration from either normally or abnormally pressured strata is most likely to occur into normally or lesser pressured strata at intrabasinal highs where hydrocarbons can be stored and transferred at times of temporary seal rupture.

Sustainable BECCS pathways evaluated by an integrated assessment model

Science.gov (United States)

Kato, E.

2017-12-01

Negative emissions technologies, particularly Bioenergy with Carbon Capture and Storage (BECCS), are key components of mitigation strategies in ambitious future socioeconomic scenarios analysed by integrated assessment models. Generally, scenarios aiming to keep mean global temperature rise below 2°C above pre-industrial would require net negative carbon emissions in the end of the 21st century. Also, in the context of Paris agreement which acknowledges "a balance between anthropogenic emissions by sources and removals by sinks of greenhouse gases in the second half of this century", RD&D for the negative emissions technologies in this decade has a crucial role for the possibility of early deployment of the technology. Because of the requirement of potentially extensive use of land and water for producing the bioenergy feedstock to get the anticipated level of gross negative emissions, researches on how to develop sustainable scenarios of BECCS is needed. Here, we present BECCS deployment scenarios that consider economically viable flow of bioenergy system including power generation and conversion process to liquid and gaseous fuels for transportation and heat with consideration of sustainable global biomass use. In the modelling process, detailed bioenergy representations, i.e. various feedstock and conversion technologies with and without CCS, are implemented in an integrated assessment (IA) model GRAPE (Global Relationship Assessment to Protect the Environment). Also, to overcome a general discrepancy about assumed future agricultural yield between 'top-down' IA models and 'bottom-up' estimates, which would crucially affect the land-use pattern, we applied yields change of food and energy crops consistent with process-based biophysical crop models in consideration of changing climate conditions. Using the framework, economically viable strategy for implementing sustainable bioenergy and BECCS flow are evaluated in the scenarios targeting to keep global average

Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

KAUST Repository

Guardiani, Carlo; Marino, Daniele Di; Tramontano, Anna; Chinappi, Mauro; Cecconi, Fabio

2014-01-01

© 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.

Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

KAUST Repository

Guardiani, Carlo

2014-09-09

© 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.

Pathways and impacts of nitrogen in water bodies: establishing a framework for integrated assessment modelling of management benefits

DEFF Research Database (Denmark)

Andersen, Mikael Skou; Kronvang, Brian; Carstensen, Jacob

Monetization of environmental benefits has become relevant as an element of proportionality tests required for justifications under the EU’s Water Framework Directive article 4 (relating to benefits andcosts of measures). This study extends an impact pathway approach to analysis of aquatic...... the study demonstrates how state-of-the-art environmental modelling can be linked with valuation to provide an adequate cross-media assessment framework relevant to integrated water quality management. The results must be regarded as illustrative and more research is required in several areas to consolidate...... relationships relating to exposures. The findings nevertheless suggest the significance of health effects for overall monetary benefits related to ecological quality objectives for water....

Integrated Systems Engineering Framework (ISEF)

Data.gov (United States)

Federal Laboratory Consortium — The ISEF is an integrated SE framework built to create and capture knowledge using a decision-centric method, high-quality data visualizations, intuitive navigation...

Featureous: A Tool for Feature-Centric Analysis of Java Software

DEFF Research Database (Denmark)

Olszak, Andrzej; Jørgensen, Bo Nørregaard

2010-01-01

Feature-centric comprehension of source code is necessary for incorporating user-requested modifications during software evolution and maintenance. However, such comprehension is difficult to achieve in case of large object-oriented programs due to the size, complexity, and implicit character...... of mappings between features and source code. To support programmers in overcoming these difficulties, we present a feature-centric analysis tool, Featureous. Our tool extends the NetBeans IDE with mechanisms for efficient location of feature implementations in legacy source code, and an extensive analysis...

Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example.

Science.gov (United States)

Gunalan, Kabilar; Chaturvedi, Ashutosh; Howell, Bryan; Duchin, Yuval; Lempka, Scott F; Patriat, Remi; Sapiro, Guillermo; Harel, Noam; McIntyre, Cameron C

2017-01-01

Deep brain stimulation (DBS) is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both academic and industrial research, as well as clinical software systems. However, the exact methodology for creating patient-specific DBS models can vary substantially and important technical details are often missing from published reports. Provide a detailed description of the assembly workflow and parameterization of a patient-specific DBS pathway-activation model (PAM) and predict the response of the hyperdirect pathway to clinical stimulation. Integration of multiple software tools (e.g. COMSOL, MATLAB, FSL, NEURON, Python) enables the creation and visualization of a DBS PAM. An example DBS PAM was developed using 7T magnetic resonance imaging data from a single unilaterally implanted patient with Parkinson's disease (PD). This detailed description implements our best computational practices and most elaborate parameterization steps, as defined from over a decade of technical evolution. Pathway recruitment curves and strength-duration relationships highlight the non-linear response of axons to changes in the DBS parameter settings. Parameterization of patient-specific DBS models can be highly detailed and constrained, thereby providing confidence in the simulation predictions, but at the expense of time demanding technical implementation steps. DBS PAMs represent new tools for investigating possible correlations between brain pathway activation patterns and clinical symptom modulation.

Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example.

Directory of Open Access Journals (Sweden)

Kabilar Gunalan

Full Text Available Deep brain stimulation (DBS is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both academic and industrial research, as well as clinical software systems. However, the exact methodology for creating patient-specific DBS models can vary substantially and important technical details are often missing from published reports.Provide a detailed description of the assembly workflow and parameterization of a patient-specific DBS pathway-activation model (PAM and predict the response of the hyperdirect pathway to clinical stimulation.Integration of multiple software tools (e.g. COMSOL, MATLAB, FSL, NEURON, Python enables the creation and visualization of a DBS PAM. An example DBS PAM was developed using 7T magnetic resonance imaging data from a single unilaterally implanted patient with Parkinson's disease (PD. This detailed description implements our best computational practices and most elaborate parameterization steps, as defined from over a decade of technical evolution.Pathway recruitment curves and strength-duration relationships highlight the non-linear response of axons to changes in the DBS parameter settings.Parameterization of patient-specific DBS models can be highly detailed and constrained, thereby providing confidence in the simulation predictions, but at the expense of time demanding technical implementation steps. DBS PAMs represent new tools for investigating possible correlations between brain pathway activation patterns and clinical symptom modulation.

IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis.

Science.gov (United States)

Zhang, Fan; Drabier, Renee

2012-01-01

Next-Generation Sequencing (NGS) technologies and Genome-Wide Association Studies (GWAS) generate millions of reads and hundreds of datasets, and there is an urgent need for a better way to accurately interpret and distill such large amounts of data. Extensive pathway and network analysis allow for the discovery of highly significant pathways from a set of disease vs. healthy samples in the NGS and GWAS. Knowledge of activation of these processes will lead to elucidation of the complex biological pathways affected by drug treatment, to patient stratification studies of new and existing drug treatments, and to understanding the underlying anti-cancer drug effects. There are approximately 141 biological human pathway resources as of Jan 2012 according to the Pathguide database. However, most currently available resources do not contain disease, drug or organ specificity information such as disease-pathway, drug-pathway, and organ-pathway associations. Systematically integrating pathway, disease, drug and organ specificity together becomes increasingly crucial for understanding the interrelationships between signaling, metabolic and regulatory pathway, drug action, disease susceptibility, and organ specificity from high-throughput omics data (genomics, transcriptomics, proteomics and metabolomics). We designed the Integrated Pathway Analysis Database for Systematic Enrichment Analysis (IPAD, http://bioinfo.hsc.unt.edu/ipad), defining inter-association between pathway, disease, drug and organ specificity, based on six criteria: 1) comprehensive pathway coverage; 2) gene/protein to pathway/disease/drug/organ association; 3) inter-association between pathway, disease, drug, and organ; 4) multiple and quantitative measurement of enrichment and inter-association; 5) assessment of enrichment and inter-association analysis with the context of the existing biological knowledge and a "gold standard" constructed from reputable and reliable sources; and 6) cross-linking of

Towards a service centric contextualized vehicular cloud

NARCIS (Netherlands)

Hu, Xiping; Wang, Lei; Sheng, Zhengguo; TalebiFard, Peyman; Zhou, Li; Liu, Jia; Leung, Victor C.M.

2014-01-01

This paper proposes a service-centric contextualized vehicular (SCCV) cloud platform to facilitate the deployment and delivery of cloud-based mobile applications over vehicular networks. SCCV cloud employs a multi-tier architecture that consists of the network, mobile device, and cloud tiers. Based

A comparative evaluation of static and functional methods for recording centric relation and condylar guidance: a clinical study.

Science.gov (United States)

Thakur, Mridul; Jain, Veena; Parkash, Hari; Kumar, Pravesh

2012-09-01

To evaluate and compare the centric relation and horizontal condylar guidance using interocclusal wax and extra oral Gothic arch methods and subjective evaluation of dentures thus fabricated. Centric relation and horizontal condylar guidance was recorded by using interocclusal wax and gothic arch tracing in 28 completely edentulous patients. These records were transferred to the articulator and difference in both values was recorded. After that patients were divided in two groups according to the centric relation and horizontal condylar guidance recording method used to achieve balanced occlusion. Response of the dentures was subjectively evaluated using "Woelfel subjective evaluation criteria". Centric relation recorded by both the methods did coincide in 7.14 % of patients. Centric relation recorded by interocclusal wax was posterior to Gothic centric relation in 21.43 % of patients, and anterior to Gothic centric relation in 71.42 % patients. Gothic arch tracings gave higher mean guidance values on both the sides as compared to protrusive wax record in all the subjects, although the difference was statistically insignificant (P > 0.05). Subjective evaluation showed statistical insignificance for all the parameters in both groups. Gothic arch method records the centric relation at a more posterior position than the Static method, but it does not make any difference in clinical performance of the complete denture. Horizontal condylar guidance angle was approximately similar by both the methods.

A Reference Architecture for Network-Centric Information Systems

National Research Council Canada - National Science Library

Renner, Scott; Schaefer, Ronald

2003-01-01

This paper presents the "C2 Enterprise Reference Architecture" (C2ERA), which is a new technical concept of operations for building information systems better suited to the Network-Centric Warfare (NCW) environment...

Integrated care pathways for airway diseases (AIRWAYS-ICPs)

DEFF Research Database (Denmark)

Bousquet, J; Addis, A; Adcock, I

2014-01-01

The objective of Integrated Care Pathways for Airway Diseases (AIRWAYS-ICPs) is to launch a collaboration to develop multi-sectoral care pathways for chronic respiratory diseases in European countries and regions. AIRWAYS-ICPs has strategic relevance to the European Union Health Strategy...... and will add value to existing public health knowledge by: 1) proposing a common framework of care pathways for chronic respiratory diseases, which will facilitate comparability and trans-national initiatives; 2) informing cost-effective policy development, strengthening in particular those on smoking...... and environmental exposure; 3) aiding risk stratification in chronic disease patients, using a common strategy; 4) having a significant impact on the health of citizens in the short term (reduction of morbidity, improvement of education in children and of work in adults) and in the long-term (healthy ageing); 5...

An optimization model for metabolic pathways.

Science.gov (United States)

Planes, F J; Beasley, J E

2009-10-15

Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner.

Game-centric pedagogy and curriculums in higher education

DEFF Research Database (Denmark)

Nørgård, Rikke Toft; Murray, John; Morgan, James

2017-01-01

This paper examines some recent trends in game-centric education for STEAM (science, technology,engineering, art and mathematics) fields, especially those that explore and promote collaborationamong multiple disciplines. We discuss various multimodal design research activities that draw uponthe...... applications and usage of popular technical hackathons and game design jams in educationalenvironments. The intent of this work is to guide and inform new approaches to the corecomponents of STEAM curriculums.Game-centric methods appear to be well-suited to a variety of education and trainingcircumstances...... a valuable vehicle for enhancing general education andlong-term life skills.We conclude by describing some opportunities to undertake qualitative and quantitative research on teams of participants in popular game development events, such as the multinational Global GameJam (GGJ) series. This process involves...

From school centric to ‘material centric’ education

DEFF Research Database (Denmark)

Christensen, Suna Møller

2015-01-01

as craftsman. A pilot-project in spring 2014 revealed that designing talent education pushed teachers (who all have a personal background in vocational jobs) to challenge a theory based and in this sense school centric curriculum objectifying materials as pre-existing elements or resources in an assignment...... ([1934]2005) in ‘Art as Experience’ draws between art as an object and art as experience, this presentation examines the way in which education for particularly skilled students at vocational education schools in Denmark re-focus teachers attention to materials and student-material relations. Technically......, and re-consider relations with materials as dimensions facilitating the professional development of vocational ‘talent’. The broader topic of school centric versus ‘material centric’ education ties this research into vocational skills and craftsmanship with inquiries into framing and structuring...

Uberon, an integrative multi-species anatomy ontology

Science.gov (United States)

2012-01-01

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org PMID:22293552

Creep and cracking of concrete hinges: insight from centric and eccentric compression experiments.

Science.gov (United States)

Schlappal, Thomas; Schweigler, Michael; Gmainer, Susanne; Peyerl, Martin; Pichler, Bernhard

2017-01-01

Existing design guidelines for concrete hinges consider bending-induced tensile cracking, but the structural behavior is oversimplified to be time-independent. This is the motivation to study creep and bending-induced tensile cracking of initially monolithic concrete hinges systematically. Material tests on plain concrete specimens and structural tests on marginally reinforced concrete hinges are performed. The experiments characterize material and structural creep under centric compression as well as bending-induced tensile cracking and the interaction between creep and cracking of concrete hinges. As for the latter two aims, three nominally identical concrete hinges are subjected to short-term and to longer-term eccentric compression tests. Obtained material and structural creep functions referring to centric compression are found to be very similar. The structural creep activity under eccentric compression is significantly larger because of the interaction between creep and cracking, i.e. bending-induced cracks progressively open and propagate under sustained eccentric loading. As for concrete hinges in frame-like integral bridge construction, it is concluded (i) that realistic simulation of variable loads requires consideration of the here-studied time-dependent behavior and (ii) that permanent compressive normal forces shall be limited by 45% of the ultimate load carrying capacity, in order to avoid damage of concrete hinges under sustained loading.

The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine.

Directory of Open Access Journals (Sweden)

Brett A McKinney

Full Text Available Although many diseases and traits show large heritability, few genetic variants have been found to strongly separate phenotype groups by genotype. Complex regulatory networks of variants and expression of multiple genes lead to small individual-variant effects and difficulty replicating the effect of any single variant in an affected pathway. Interaction network modeling of GWAS identifies effects ignored by univariate models, but population differences may still cause specific genes to not replicate. Integrative network models may help detect indirect effects of variants in the underlying biological pathway. In this study, we used gene-level functional interaction information from the Integrative Multi-species Prediction (IMP tool to reveal important genes associated with a complex phenotype through evidence from epistasis networks and pathway enrichment. We test this method for augmenting variant-based network analyses with functional interactions by applying it to a smallpox vaccine immune response GWAS. The integrative analysis spotlights the role of genes related to retinoid X receptor alpha (RXRA, which has been implicated in a previous epistasis network analysis of smallpox vaccine.

Vibration of a Cylindrical Tunnel under a Centric Point-Source Explosion

Directory of Open Access Journals (Sweden)

Yuetang Zhao

2017-01-01

Full Text Available Underground tunnels are vulnerable to terrorists’ bombing attacks, which calls for studies on tunnel’s response to internal explosive loading. In this paper, the dynamic response of a cylindrical tunnel to an ideal centric point explosion was treated as an axisymmetric 2-dimensional problem, in which the tunnel was modeled with a continuous anisotropic shell, while the ground medium’s effect was accounted for with linear elastic Winkler springs and the explosive loading described by a temporal and spatial function. The governing equation of the motion is a fourth-order partial differential equation, for which a numerical method combining finite difference with the implicit Newmark-β method was adopted. This method avoided complicated integral transform and numerical inverse transformation, thus allowing efficient parameter study. The maximum radial displacement was found on the cricle of the center of explosive, where hoop stress is the maximum principal stress. The anisotropy showed little influence on maximum hoop stress. Within the range of ground medium’s modulus, minor influence on maximum hoop stress was incurred. This research may be helpful to hazard assessment and protective design for some critical subway tunnels.

Evolution of the New Pathway curriculum at Harvard Medical School: the new integrated curriculum.

Science.gov (United States)

Dienstag, Jules L

2011-01-01

In 1985, Harvard Medical School adopted a "New Pathway" curriculum, based on active, adult learning through problem-based, faculty-facilitated small-group tutorials designed to promote lifelong skills of self-directed learning. Despite the successful integration of clinically relevant material in basic science courses, the New Pathway goals were confined primarily to the preclinical years. In addition, the shifting balance in the delivery of health care from inpatient to ambulatory settings limited the richness of clinical education in clinical clerkships, creating obstacles for faculty in their traditional roles as teachers. In 2006, Harvard Medical School adopted a more integrated curriculum based on four principles that emerged after half a decade of self-reflection and planning: (1) integrate the teaching of basic/population science and clinical medicine throughout the entire student experience; (2) reestablish meaningful and intensive faculty-student interactions and reengage the faculty; (3) develop a new model of clinical education that offers longitudinal continuity of patient experience, cross-disciplinary curriculum, faculty mentoring, and student evaluation; and (4) provide opportunities for all students to pursue an in-depth, faculty-mentored scholarly project. These principles of our New Integrated Curriculum reflect our vision for a curriculum that fosters a partnership between students and faculty in the pursuit of scholarship and leadership.

Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration.

Directory of Open Access Journals (Sweden)

Lieven P C Verbeke

Full Text Available The study of cancer, a highly heterogeneous disease with different causes and clinical outcomes, requires a multi-angle approach and the collection of large multi-omics datasets that, ideally, should be analyzed simultaneously. We present a new pathway relevance ranking method that is able to prioritize pathways according to the information contained in any combination of tumor related omics datasets. Key to the method is the conversion of all available data into a single comprehensive network representation containing not only genes but also individual patient samples. Additionally, all data are linked through a network of previously identified molecular interactions. We demonstrate the performance of the new method by applying it to breast and ovarian cancer datasets from The Cancer Genome Atlas. By integrating gene expression, copy number, mutation and methylation data, the method's potential to identify key pathways involved in breast cancer development shared by different molecular subtypes is illustrated. Interestingly, certain pathways were ranked equally important for different subtypes, even when the underlying (epi-genetic disturbances were diverse. Next to prioritizing universally high-scoring pathways, the pathway ranking method was able to identify subtype-specific pathways. Often the score of a pathway could not be motivated by a single mutation, copy number or methylation alteration, but rather by a combination of genetic and epi-genetic disturbances, stressing the need for a network-based data integration approach. The analysis of ovarian tumors, as a function of survival-based subtypes, demonstrated the method's ability to correctly identify key pathways, irrespective of tumor subtype. A differential analysis of survival-based subtypes revealed several pathways with higher importance for the bad-outcome patient group than for the good-outcome patient group. Many of the pathways exhibiting higher importance for the bad

performance evaluation of a pilot paraplegic centricity mobility aid

African Journals Online (AJOL)

eobe

PERFORMANCE EVALUATION OF A PILOT PARAPLEGIC CENTRICITY. MOBILITY AID. MOBILITY ... The result of the test showed a remarkable improvement in. Wilcoxin's signed rank test. .... RESEARCH METHOD. RESEARCH METHOD.

Game-centric pedagogy and curriculums in higher education

DEFF Research Database (Denmark)

Nørgård, Rikke Toft; Murray, John; Morgan, James

2017-01-01

This paper examines some recent trends in game-centric education for STEAM (science, technology,engineering, art and mathematics) fields, especially those that explore and promote collaborationamong multiple disciplines. We discuss various multimodal design research activities that draw uponthe a...

Methods of assessing total doses integrated across pathways

International Nuclear Information System (INIS)

Grzechnik, M.; Camplin, W.; Clyne, F.; Allott, R.; Webbe-Wood, D.

2006-01-01

Calculated doses for comparison with limits resulting from discharges into the environment should be summed across all relevant pathways and food groups to ensure adequate protection. Current methodology for assessments used in the radioactivity in Food and the Environment (R.I.F.E.) reports separate doses from pathways related to liquid discharges of radioactivity to the environment from those due to gaseous releases. Surveys of local inhabitant food consumption and occupancy rates are conducted in the vicinity of nuclear sites. Information has been recorded in an integrated way, such that the data for each individual is recorded for all pathways of interest. These can include consumption of foods, such as fish, crustaceans, molluscs, fruit and vegetables, milk and meats. Occupancy times over beach sediments and time spent in close proximity to the site is also recorded for inclusion of external and inhalation radiation dose pathways. The integrated habits survey data may be combined with monitored environmental radionuclide concentrations to calculate total dose. The criteria for successful adoption of a method for this calculation were: Reproducibility can others easily use the approach and reassess doses? Rigour and realism how good is the match with reality?Transparency a measure of the ease with which others can understand how the calculations are performed and what they mean. Homogeneity is the group receiving the dose relatively homogeneous with respect to age, diet and those aspects that affect the dose received? Five methods of total dose calculation were compared and ranked according to their suitability. Each method was labelled (A to E) and given a short, relevant name for identification. The methods are described below; A) Individual doses to individuals are calculated and critical group selection is dependent on dose received. B) Individual Plus As in A, but consumption and occupancy rates for high dose is used to derive rates for application in

A Probabilistic, Facility-Centric Approach to Lightning Strike Location

Science.gov (United States)

Huddleston, Lisa L.; Roeder, William p.; Merceret, Francis J.

2012-01-01

A new probabilistic facility-centric approach to lightning strike location has been developed. This process uses the bivariate Gaussian distribution of probability density provided by the current lightning location error ellipse for the most likely location of a lightning stroke and integrates it to determine the probability that the stroke is inside any specified radius of any location, even if that location is not centered on or even with the location error ellipse. This technique is adapted from a method of calculating the probability of debris collisionith spacecraft. Such a technique is important in spaceport processing activities because it allows engineers to quantify the risk of induced current damage to critical electronics due to nearby lightning strokes. This technique was tested extensively and is now in use by space launch organizations at Kennedy Space Center and Cape Canaveral Air Force Station. Future applications could include forensic meteorology.

A case study to illustrate the utility of the Aggregate Exposure Pathway and Adverse Outcome Pathway frameworks for integrating human health and ecological data into cumulative risk assessment

Science.gov (United States)

Cumulative risk assessment (CRA) methods, which evaluate the risk of multiple adverse outcomes (AOs) from multiple chemicals, promote the use of a conceptual site model (CSM) to integrate risk from relevant stressors. The Adverse Outcome Pathway (AOP) framework can inform these r...

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

Discourse-Centric Learning Analytics: Mapping the Terrain

Science.gov (United States)

Knight, Simon; Littleton, Karen

2015-01-01

There is an increasing interest in developing learning analytic techniques for the analysis, and support of, high-quality learning discourse. This paper maps the terrain of discourse-centric learning analytics (DCLA), outlining the distinctive contribution of DCLA and outlining a definition for the field moving forwards. It is our claim that DCLA…

A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in MATLAB.

Science.gov (United States)

Sinha, Shriprakash

2016-12-01

Simulation study in systems biology involving computational experiments dealing with Wnt signaling pathways abound in literature but often lack a pedagogical perspective that might ease the understanding of beginner students and researchers in transition, who intend to work on the modeling of the pathway. This paucity might happen due to restrictive business policies which enforce an unwanted embargo on the sharing of important scientific knowledge. A tutorial introduction to computational modeling of Wnt signaling pathway in a human colorectal cancer dataset using static Bayesian network models is provided. The walkthrough might aid biologists/informaticians in understanding the design of computational experiments that is interleaved with exposition of the Matlab code and causal models from Bayesian network toolbox. The manuscript elucidates the coding contents of the advance article by Sinha (Integr. Biol. 6:1034-1048, 2014) and takes the reader in a step-by-step process of how (a) the collection and the transformation of the available biological information from literature is done, (b) the integration of the heterogeneous data and prior biological knowledge in the network is achieved, (c) the simulation study is designed, (d) the hypothesis regarding a biological phenomena is transformed into computational framework, and (e) results and inferences drawn using d -connectivity/separability are reported. The manuscript finally ends with a programming assignment to help the readers get hands-on experience of a perturbation project. Description of Matlab files is made available under GNU GPL v3 license at the Google code project on https://code.google.com/p/static-bn-for-wnt-signaling-pathway and https: //sites.google.com/site/shriprakashsinha/shriprakashsinha/projects/static-bn-for-wnt-signaling-pathway. Latest updates can be found in the latter website.

A Project-Centric Course on Cyberinfrastructure to Support High School STEM Education

Directory of Open Access Journals (Sweden)

Daphne Rainey

2013-06-01

Full Text Available Recent rapid advances in information technology pose new challenges for teachers in the Science, Technology, Engineering, and Mathematics (STEM fields to incorporate the latest knowledge and technical expertise into courses in a way that will be applicable to students as future scientists. A demonstration project was designed, developed, and deployed by university faculty and high school teachers for their students to explore the use of the components of cyberinfrastructure. The project explored the introduction of cyberinfrastructure through the use of bioinformatics and the use of team science. This paper describes the high school course that was deployed at Galileo Magnet High School (GMHS in collaboration with the scientists at Virginia Tech University, and details its overall assessment. Implementation of a project-centric teaching paradigm to engage students in applying the concepts of cyberinfrastructure by integrating the disciplines of biology, computer science, mathematics, and statistics through bioinformatics was an integral part of this study.

New methods for clinical pathways-Business Process Modeling Notation (BPMN) and Tangible Business Process Modeling (t.BPM).

Science.gov (United States)

Scheuerlein, Hubert; Rauchfuss, Falk; Dittmar, Yves; Molle, Rüdiger; Lehmann, Torsten; Pienkos, Nicole; Settmacher, Utz

2012-06-01

Clinical pathways (CP) are nowadays used in numerous institutions, but their real impact is still a matter of debate. The optimal design of a clinical pathway remains unclear and is mainly determined by the expectations of the individual institution. The purpose of the here described pilot project was the development of two CP (colon and rectum carcinoma) according to Business Process Modeling Notation (BPMN) and Tangible Business Process Modeling (t.BPM). BPMN is an established standard for business process modelling in industry and economy. It is, in the broadest sense, a computer programme which enables the description and a relatively easy graphical imaging of complex processes. t.BPM is a modular construction system of the BPMN symbols which enables the creation of an outline or raw model, e.g. by placing the symbols on a spread-out paper sheet. The thus created outline can then be transferred to the computer and further modified as required. CP for the treatment of colon and rectal cancer have been developed with support of an external IT coach. The pathway was developed in an interdisciplinary and interprofessional manner (55 man-days over 15 working days). During this time, necessary interviews with medical, nursing and administrative staffs were conducted as well. Both pathways were developed parallel. Subsequent analysis was focussed on feasibility, expenditure, clarity and suitability for daily clinical practice. The familiarization with BPMN was relatively quick and intuitive. The use of t.BPM enabled the pragmatic, effective and results-directed creation of outlines for the CP. The development of both CP was finished from the diagnostic evaluation to the adjuvant/neoadjuvant therapy and rehabilitation phase. The integration of checklists, guidelines and important medical or other documents is easily accomplished. A direct integration into the hospital computer system is currently not possible for technical reasons. BPMN and t.BPM are sufficiently

On bridging relational and document-centric data stores

NARCIS (Netherlands)

Roijackers, J.; Fletcher, G.H.L.; Gottlob, G.; Grasso, G.; Olteanu, D.; Schallhart, C.

2013-01-01

Big Data scenarios often involve massive collections of nested data objects, typically referred to as "documents." The challenges of document management at web scale have stimulated a recent trend towards the development of document-centric "NoSQL" data stores. Many query tasks naturally involve

A pathway-centric survey of somatic mutations in Chinese patients with colorectal carcinomas.

Directory of Open Access Journals (Sweden)

Chao Ling

Full Text Available Previous genetic studies on colorectal carcinomas (CRC have identified multiple somatic mutations in four candidate pathways (TGF-β, Wnt, P53 and RTK-RAS pathways on populations of European ancestry. However, it is under-studied whether other populations harbor different sets of hot-spot somatic mutations in these pathways and other oncogenes. In this study, to evaluate the mutational spectrum of novel somatic mutations, we assessed 41 pairs of tumor-stroma tissues from Chinese patients with CRC, including 29 colon carcinomas and 12 rectal carcinomas. We designed Illumina Custom Amplicon panel to target 43 genes, including genes in the four candidate pathways, as well as several known oncogenes for other cancers. Candidate mutations were validated by Sanger sequencing, and we further used SIFT and PolyPhen-2 to assess potentially functional mutations. We discovered 3 new somatic mutations in gene APC, TCF7L2, and PIK3CA that had never been reported in the COSMIC or NCI-60 databases. Additionally, we confirmed 6 known somatic mutations in gene SMAD4, APC, FBXW7, BRAF and PTEN in Chinese CRC patients. While most were previously reported in CRC, one mutation in PTEN was reported only in malignant endometrium cancer. Our study confirmed the existence of known somatic mutations in the four candidate pathways for CRC in Chinese patients. We also discovered a number of novel somatic mutations in these pathways, which may have implications for the pathogenesis of CRC.

cMapper: gene-centric connectivity mapper for EBI-RDF platform.

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Shoaib, Muhammad; Ansari, Adnan Ahmad; Ahn, Sung-Min

2017-01-15

In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language. To overcome this practical limitation of the EBI-RDF platform, we developed cMapper, a web-based tool that enables biologists to search the EBI-RDF databases in a gene-centric manner without a thorough knowledge of RDF and SPARQL. cMapper allows biologists to search data entities in the EBI-RDF platform that are connected to genes or small molecules of interest in multiple biological contexts. The input to cMapper consists of a set of genes or small molecules, and the output are data entities in six independent EBI-RDF databases connected with the given genes or small molecules in the user's query. cMapper provides output to users in the form of a graph in which nodes represent data entities and the edges represent connections between data entities and inputted set of genes or small molecules. Furthermore, users can apply filters based on database, taxonomy, organ and pathways in order to focus on a core connectivity graph of their interest. Data entities from multiple databases are differentiated based on background colors. cMapper also enables users to investigate shared connections between genes or small molecules of interest. Users can view the output graph on a web browser or download it in either GraphML or JSON formats. cMapper is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on Tomcat server. We developed the user interface using HTML5, JQuery and the Cytoscape Graph API. cMapper can be accessed at

Regulation of Cell Wall Biogenesis in Saccharomyces cerevisiae: The Cell Wall Integrity Signaling Pathway

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Levin, David E.

2011-01-01

The yeast cell wall is a strong, but elastic, structure that is essential not only for the maintenance of cell shape and integrity, but also for progression through the cell cycle. During growth and morphogenesis, and in response to environmental challenges, the cell wall is remodeled in a highly regulated and polarized manner, a process that is principally under the control of the cell wall integrity (CWI) signaling pathway. This pathway transmits wall stress signals from the cell surface to the Rho1 GTPase, which mobilizes a physiologic response through a variety of effectors. Activation of CWI signaling regulates the production of various carbohydrate polymers of the cell wall, as well as their polarized delivery to the site of cell wall remodeling. This review article centers on CWI signaling in Saccharomyces cerevisiae through the cell cycle and in response to cell wall stress. The interface of this signaling pathway with other pathways that contribute to the maintenance of cell wall integrity is also discussed. PMID:22174182

Refining and validating a conceptual model of Clinical Nurse Leader integrated care delivery.

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Bender, Miriam; Williams, Marjory; Su, Wei; Hites, Lisle

2017-02-01

To empirically validate a conceptual model of Clinical Nurse Leader integrated care delivery. There is limited evidence of frontline care delivery models that consistently achieve quality patient outcomes. Clinical Nurse Leader integrated care delivery is a promising nursing model with a growing record of success. However, theoretical clarity is necessary to generate causal evidence of effectiveness. Sequential mixed methods. A preliminary Clinical Nurse Leader practice model was refined and survey items developed to correspond with model domains, using focus groups and a Delphi process with a multi-professional expert panel. The survey was administered in 2015 to clinicians and administrators involved in Clinical Nurse Leader initiatives. Confirmatory factor analysis and structural equation modelling were used to validate the measurement and model structure. Final sample n = 518. The model incorporates 13 components organized into five conceptual domains: 'Readiness for Clinical Nurse Leader integrated care delivery'; 'Structuring Clinical Nurse Leader integrated care delivery'; 'Clinical Nurse Leader Practice: Continuous Clinical Leadership'; 'Outcomes of Clinical Nurse Leader integrated care delivery'; and 'Value'. Sample data had good fit with specified model and two-level measurement structure. All hypothesized pathways were significant, with strong coefficients suggesting good fit between theorized and observed path relationships. The validated model articulates an explanatory pathway of Clinical Nurse Leader integrated care delivery, including Clinical Nurse Leader practices that result in improved care dynamics and patient outcomes. The validated model provides a basis for testing in practice to generate evidence that can be deployed across the healthcare spectrum. © 2016 John Wiley & Sons Ltd.

Nonassociative learning as gated neural integrator and differentiator in stimulus-response pathways

Directory of Open Access Journals (Sweden)

Young Daniel L

2006-08-01

Full Text Available Abstract Nonassociative learning is a basic neuroadaptive behavior exhibited across animal phyla and sensory modalities but its role in brain intelligence is unclear. Current literature on habituation and sensitization, the classic "dual process" of nonassociative learning, gives highly incongruous accounts between varying experimental paradigms. Here we propose a general theory of nonassociative learning featuring four base modes: habituation/primary sensitization in primary stimulus-response pathways, and desensitization/secondary sensitization in secondary stimulus-response pathways. Primary and secondary modes of nonassociative learning are distinguished by corresponding activity-dependent recall, or nonassociative gating, of neurotransmission memory. From the perspective of brain computation, nonassociative learning is a form of integral-differential calculus whereas nonassociative gating is a form of Boolean logic operator – both dynamically transforming the stimulus-response relationship. From the perspective of sensory integration, nonassociative gating provides temporal filtering whereas nonassociative learning affords low-pass, high-pass or band-pass/band-stop frequency filtering – effectively creating an intelligent sensory firewall that screens all stimuli for attention and resultant internal model adaptation and reaction. This unified framework ties together many salient characteristics of nonassociative learning and nonassociative gating and suggests a common kernel that correlates with a wide variety of sensorimotor integration behaviors such as central resetting and self-organization of sensory inputs, fail-safe sensorimotor compensation, integral-differential and gated modulation of sensorimotor feedbacks, alarm reaction, novelty detection and selective attention, as well as a variety of mental and neurological disorders such as sensorimotor instability, attention deficit hyperactivity, sensory defensiveness, autism

Securing Gateways within Clustered Power Centric Network of Nodes

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Qaisar Javaid

2016-01-01

Full Text Available Knowledge Networks are gaining momentum within cyber world. Knowledge leads to innovation and for this reason organizations focus on research and information gathering in order to gain and improve existing knowledge. This of information era, which is primarily based on world wide web technologies, enables significantly expanded networks of people to communicate and collaborate 'virtually' across teams, across entire organizations and across the world, anytime and anywhere. Innovations in computing and telecommunications have transformed the corporations from structured and manageable types to interwoven network of blurred boundaries such as; ad hoc networks and mobile wireless networks, etc. This study explores knowledge networks in Information Technology and security leaks that are found, as well as measures that are taken to counter this menace which is coming up with optimal Secure Clustered Power Centric node network. The paper concludes these measures, evaluating and integrating them to come up with a secured network design.

The base excision repair pathway is required for efficient lentivirus integration.

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Kristine E Yoder

Full Text Available An siRNA screen has identified several proteins throughout the base excision repair (BER pathway of oxidative DNA damage as important for efficient HIV infection. The proteins identified included early repair factors such as the base damage recognition glycosylases OGG1 and MYH and the late repair factor POLß, implicating the entire BER pathway. Murine cells with deletions of the genes Ogg1, Myh, Neil1 and Polß recapitulate the defect of HIV infection in the absence of BER. Defective infection in the absence of BER proteins was also seen with the lentivirus FIV, but not the gammaretrovirus MMLV. BER proteins do not affect HIV infection through its accessory genes nor the central polypurine tract. HIV reverse transcription and nuclear entry appear unaffected by the absence of BER proteins. However, HIV integration to the host chromosome is reduced in the absence of BER proteins. Pre-integration complexes from BER deficient cell lines show reduced integration activity in vitro. Integration activity is restored by addition of recombinant BER protein POLß. Lentiviral infection and integration efficiency appears to depend on the presence of BER proteins.

Understanding Health Information Seeking from an Actor-Centric Perspective

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Simon Batchelor

2015-07-01

Full Text Available This paper presents a conceptual approach for discussing health information seeking among poor households in Africa and Asia. This approach is part of a larger research endeavor aimed at understanding how health systems are adapting; with possibilities and constraints emerging. These health systems can be found in a context of the changing relationships between states, markets and civil society in low and middle income countries. The paper starts from an understanding of the health sector as a “health knowledge economy”, organized to provide people with access to knowledge and advice. The use of the term “health knowledge economy” draws attention to the ways the health sector is part of a broader knowledge economy changing the way individuals and households obtain and use specialist information. The paper integrates an actor centric approach with the theory of planned behavior. It seeks to identify the actors engaged in the health knowledge economy as a precursor to longer term studies on the uptake of innovations integrating health services with mobile phones, commonly designated as mHealth, contributing to an understanding of the potential vulnerabilities of poor people, and highlighting possible dangers if providers of health information and advice are strongly influenced by interest groups.

Designing User-Centric Patient Portals: Clinician and Patients' Uses and Gratifications.

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Alpert, Jordan M; Krist, Alex H; Aycock, Rebecca A; Kreps, Gary L

2017-03-01

Legislation mandates that clinicians make patients' medical information available digitally. This has resulted in hurriedly installing patient portals that do not fully meet the needs of patients or clinicians. This study examined a specific portal, MyPreventiveCare (MPC), a patient-centered portal designed to promote preventive care to consumers, to elicit recommendations from patients and clinicians about how it could be more beneficial by uncovering their uses and gratifications (U&G). In-depth interviews with 31 patients and two clinician focus groups were conducted. Multiple methods were utilized, such as grounded theory coding to develop themes and content analysis to classify responses according to the U&G framework. Four main categories emerged that users desire to be included in health portals: integration with technology (27%), coordination of care (27%), incorporation of lifestyle (26%), and increased control (20%). Additional analysis revealed that health portals are mainly utilized to fulfill cognitive and affective needs, with over 80% of recommendations related to the U&G categories of cognitive and affective needs. Cognitive (60%), affective (21%), social integrative (10%), personal integrative (9%), and tension release (0%). Portals will continue to evolve and become important health communication tools if they address the user's perspective and are inclusive of new technological advances. Specifically, portals must become more user centric and incorporate aspects of the patients' lifestyle and integrate health information technology.

The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion: The Pathway for Oxygen.

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Bassingthwaighte, James B; Raymond, Gary M; Dash, Ranjan K; Beard, Daniel A; Nolan, Margaret

2016-01-01

The 'Pathway for Oxygen' is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system's basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: (1) a 'one-alveolus lung' with airway resistance, lung volume compliance, (2) bidirectional transport of solute gasses like O2 and CO2, (3) gas exchange between alveolar air and lung capillary blood, (4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and (5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there.

Representative Agricultural Pathways and Scenarios for Regional Integrated Assessment of Climate Change Impacts, Vulnerability, and Adaptation. 5; Chapter

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Valdivia, Roberto O.; Antle, John M.; Rosenzweig, Cynthia; Ruane, Alexander C.; Vervoort, Joost; Ashfaq, Muhammad; Hathie, Ibrahima; Tui, Sabine Homann-Kee; Mulwa, Richard; Nhemachena, Charles;

Revisiting the Robustness of PET-Based Textural Features in the Context of Multi-Centric Trials.

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Bailly, Clément; Bodet-Milin, Caroline; Couespel, Solène; Necib, Hatem; Kraeber-Bodéré, Françoise; Ansquer, Catherine; Carlier, Thomas

2016-01-01

This study aimed to investigate the variability of textural features (TF) as a function of acquisition and reconstruction parameters within the context of multi-centric trials. The robustness of 15 selected TFs were studied as a function of the number of iterations, the post-filtering level, input data noise, the reconstruction algorithm and the matrix size. A combination of several reconstruction and acquisition settings was devised to mimic multi-centric conditions. We retrospectively studied data from 26 patients enrolled in a diagnostic study that aimed to evaluate the performance of PET/CT 68Ga-DOTANOC in gastro-entero-pancreatic neuroendocrine tumors. Forty-one tumors were extracted and served as the database. The coefficient of variation (COV) or the absolute deviation (for the noise study) was derived and compared statistically with SUVmax and SUVmean results. The majority of investigated TFs can be used in a multi-centric context when each parameter is considered individually. The impact of voxel size and noise in the input data were predominant as only 4 TFs presented a high/intermediate robustness against SUV-based metrics (Entropy, Homogeneity, RP and ZP). When combining several reconstruction settings to mimic multi-centric conditions, most of the investigated TFs were robust enough against SUVmax except Correlation, Contrast, LGRE, LGZE and LZLGE. Considering previously published results on either reproducibility or sensitivity against delineation approach and our findings, it is feasible to consider Homogeneity, Entropy, Dissimilarity, HGRE, HGZE and ZP as relevant for being used in multi-centric trials.

Computational Modeling of Fluctuations in Energy and Metabolic Pathways of Methanogenic Archaea

Energy Technology Data Exchange (ETDEWEB)

Luthey-Schulten, Zaida [Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Chemistry; Carl R. Woese Inst. for Genomic Biology

2017-01-04

The methanogenic archaea, anaerobic microbes that convert CO2 and H2 and/or other small organic fermentation products into methane, play an unusually large role in the global carbon cycle. As they perform the final step in the anaerobic breakdown of biomass, methanogens are a biogenic source of an estimated one billion tons methane each year. Depending on the location, produced methane can be considered as either a greenhouse gas (agricultural byproduct), sequestered carbon storage (methane hydrate deposits), or a potential energy source (organic wastewater treatment). These microbes therefore represent an important target for biotechnology applications. Computational models of methanogens with predictive power are useful aids in the adaptation of methanogenic systems, but need to connect processes of wide-ranging time and length scales. In this project, we developed several computational methodologies for modeling the dynamic behavior of entire cells that connects stochastic reaction-diffusion dynamics of individual biochemical pathways with genome-scale modeling of metabolic networks. While each of these techniques were in the realm of well-defined computational methods, here we integrated them to develop several entirely new approaches to systems biology. The first scientific aim of the project was to model how noise in a biochemical pathway propagates into cellular phenotypes. Genetic circuits have been optimized by evolution to regulate molecular processes despite stochastic noise, but the effect of such noise on a cellular biochemical networks is currently unknown. An integrated stochastic/systems model of Escherichia coli species was created to analyze how noise in protein expression gives—and therefore noise in metabolic fluxes—gives rise to multiple cellular phenotype in isogenic population. After the initial work developing and validating methods that allow characterization of the heterogeneity in the model organism E. coli, the project shifted toward

Expression profiling on soybean leaves reveals integration of ER- and osmotic-stress pathways

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Dewey Ralph E

2007-11-01

Full Text Available Abstract Background Despite the potential of the endoplasmic reticulum (ER stress response to accommodate adaptive pathways, its integration with other environmental-induced responses is poorly understood in plants. We have previously demonstrated that the ER-stress sensor binding protein (BiP from soybean exhibits an unusual response to drought. The members of the soybean BiP gene family are differentially regulated by osmotic stress and soybean BiP confers tolerance to drought. While these results may reflect crosstalk between the osmotic and ER-stress signaling pathways, the lack of mutants, transcriptional response profiles to stresses and genome sequence information of this relevant crop has limited our attempts to identify integrated networks between osmotic and ER stress-induced adaptive responses. As a fundamental step towards this goal, we performed global expression profiling on soybean leaves exposed to polyethylene glycol treatment (osmotic stress or to ER stress inducers. Results The up-regulated stress-specific changes unmasked the major branches of the ER-stress response, which include enhancing protein folding and degradation in the ER, as well as specific osmotically regulated changes linked to cellular responses induced by dehydration. However, a small proportion (5.5% of total up-regulated genes represented a shared response that seemed to integrate the two signaling pathways. These co-regulated genes were considered downstream targets based on similar induction kinetics and a synergistic response to the combination of osmotic- and ER-stress-inducing treatments. Genes in this integrated pathway with the strongest synergistic induction encoded proteins with diverse roles, such as plant-specific development and cell death (DCD domain-containing proteins, an ubiquitin-associated (UBA protein homolog and NAC domain-containing proteins. This integrated pathway diverged further from characterized specific branches of ER-stress as

Integrated modelling of ecosystem services and energy systems research

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Agarwala, Matthew; Lovett, Andrew; Bateman, Ian; Day, Brett; Agnolucci, Paolo; Ziv, Guy

2016-04-01

The UK Government is formally committed to reducing carbon emissions and protecting and improving natural capital and the environment. However, actually delivering on these objectives requires an integrated approach to addressing two parallel challenges: de-carbonising future energy system pathways; and safeguarding natural capital to ensure the continued flow of ecosystem services. Although both emphasise benefiting from natural resources, efforts to connect natural capital and energy systems research have been limited, meaning opportunities to improve management of natural resources and meet society's energy needs could be missed. The ecosystem services paradigm provides a consistent conceptual framework that applies in multiple disciplines across the natural and economic sciences, and facilitates collaboration between them. At the forefront of the field, integrated ecosystem service - economy models have guided public- and private-sector decision making at all levels. Models vary in sophistication from simple spreadsheet tools to complex software packages integrating biophysical, GIS and economic models and draw upon many fields, including ecology, hydrology, geography, systems theory, economics and the social sciences. They also differ in their ability to value changes in natural capital and ecosystem services at various spatial and temporal scales. Despite these differences, current models share a common feature: their treatment of energy systems is superficial at best. In contrast, energy systems research has no widely adopted, unifying conceptual framework that organises thinking about key system components and interactions. Instead, the literature is organised around modelling approaches, including life cycle analyses, econometric investigations, linear programming and computable general equilibrium models. However, some consistencies do emerge. First, often contain a linear set of steps, from exploration to resource supply, fuel processing, conversion

Integration of deep geothermal energy and woody biomass conversion pathways in urban systems

International Nuclear Information System (INIS)

Moret, Stefano; Peduzzi, Emanuela; Gerber, Léda; Maréchal, François

2016-01-01

Highlights: • Novel optimization-based methodology to integrate renewable energy systems in cities. • Multiperiod model including storage, heat integration and Life Cycle Assessment. • Case study: systematic assessment of deep geothermal and wood conversion pathways. • Identification of novel wood-geothermal hybrid systems leading to higher efficiencies. • Extensive Supplementary Material to ensure full reproducibility of the work. - Abstract: Urban systems account for about two-thirds of global primary energy consumption and energy-related greenhouse gas emissions, with a projected increasing trend. Deep geothermal energy and woody biomass can be used for the production of heat, electricity and biofuels, thus constituting a renewable alternative to fossil fuels for all end-uses in cities: heating, cooling, electricity and mobility. This paper presents a methodology to assess the potential for integrating deep geothermal energy and woody biomass in an urban energy system. The city is modeled in its entirety as a multiperiod optimization problem with the total annual cost as an objective, assessing as well the environmental impact with a Life Cycle Assessment approach. For geothermal energy, deep aquifers and Enhanced Geothermal Systems are considered for stand-alone production of heat and electricity, and for cogeneration. For biomass, besides direct combustion and cogeneration, conversion to biofuels by a set of alternative processes (pyrolysis, Fischer-Tropsch synthesis and synthetic natural gas production) is studied. With a scenario-based approach, all pathways are first individually evaluated. Secondly, all possible combinations between geothermal and biomass options are systematically compared, taking into account the possibility of hybrid systems. Results show that integrating these two resources generates configurations featuring both lower costs and environmental impacts. In particular, synergies are found in innovative hybrid systems using

Pain management: a review of organisation models with integrated processes for the management of pain in adult cancer patients.

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Brink-Huis, Anita; van Achterberg, Theo; Schoonhoven, Lisette

2008-08-01

This paper reports a review of the literature conducted to identify organisation models in cancer pain management that contain integrated care processes and describe their effectiveness. Pain is experienced by 30-50% of cancer patients receiving treatment and by 70-90% of those with advanced disease. Efforts to improve pain management have been made through the development and dissemination of clinical guidelines. Early improvements in pain management were focussed on just one or two single processes such as pain assessment and patient education. Little is known about organisational models with multiple integrated processes throughout the course of the disease trajectory and concerning all stages of the care process. Systematic review. The review involved a systematic search of the literature, published between 1986-2006. Subject-specific keywords used to describe patients, disease, pain management interventions and integrated care processes, relevant for this review were selected using the thesaurus of the databases. Institutional models, clinical pathways and consultation services are three alternative models for the integration of care processes in cancer pain management. A clinical pathway is a comprehensive institutionalisation model, whereas a pain consultation service is a 'stand-alone' model that can be integrated in a clinical pathway. Positive patient and process outcomes have been described for all three models, although the level of evidence is generally low. Evaluation of the quality of pain management must involve standardised measurements of both patient and process outcomes. We recommend the development of policies for referrals to a pain consultation service. These policies can be integrated within a clinical pathway. To evaluate the effectiveness of pain management models standardised outcome measures are needed.

Human-Centric Interfaces for Ambient Intelligence

CERN Document Server

Aghajan, Hamid; Delgado, Ramon Lopez-Cozar

2009-01-01

To create truly effective human-centric ambient intelligence systems both engineering and computing methods are needed. This is the first book to bridge data processing and intelligent reasoning methods for the creation of human-centered ambient intelligence systems. Interdisciplinary in nature, the book covers topics such as multi-modal interfaces, human-computer interaction, smart environments and pervasive computing, addressing principles, paradigms, methods and applications. This book will be an ideal reference for university researchers, R&D engineers, computer engineers, and graduate s

PathwayAccess: CellDesigner plugins for pathway databases.

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Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

Revisiting the Robustness of PET-Based Textural Features in the Context of Multi-Centric Trials.

Directory of Open Access Journals (Sweden)

Clément Bailly

Full Text Available This study aimed to investigate the variability of textural features (TF as a function of acquisition and reconstruction parameters within the context of multi-centric trials.The robustness of 15 selected TFs were studied as a function of the number of iterations, the post-filtering level, input data noise, the reconstruction algorithm and the matrix size. A combination of several reconstruction and acquisition settings was devised to mimic multi-centric conditions. We retrospectively studied data from 26 patients enrolled in a diagnostic study that aimed to evaluate the performance of PET/CT 68Ga-DOTANOC in gastro-entero-pancreatic neuroendocrine tumors. Forty-one tumors were extracted and served as the database. The coefficient of variation (COV or the absolute deviation (for the noise study was derived and compared statistically with SUVmax and SUVmean results.The majority of investigated TFs can be used in a multi-centric context when each parameter is considered individually. The impact of voxel size and noise in the input data were predominant as only 4 TFs presented a high/intermediate robustness against SUV-based metrics (Entropy, Homogeneity, RP and ZP. When combining several reconstruction settings to mimic multi-centric conditions, most of the investigated TFs were robust enough against SUVmax except Correlation, Contrast, LGRE, LGZE and LZLGE.Considering previously published results on either reproducibility or sensitivity against delineation approach and our findings, it is feasible to consider Homogeneity, Entropy, Dissimilarity, HGRE, HGZE and ZP as relevant for being used in multi-centric trials.

An evaluation of the implementation of maternal obesity pathways of care: a mixed methods study with data integration.

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Nicola Heslehurst

Full Text Available Maternal obesity has multiple associated risks and requires substantial intervention. This research evaluated the implementation of maternal obesity care pathways from multiple stakeholder perspectives.A simultaneous mixed methods model with data integration was used. Three component studies were given equal priority. 1: Semi-structured qualitative interviews explored obese pregnant women's experiences of being on the pathways. 2: A quantitative and qualitative postal survey explored healthcare professionals' experiences of delivering the pathways. 3: A case note audit quantitatively assessed pathway compliance. Data were integrated using following a thread and convergence coding matrix methods to search for agreement and disagreement between studies.Study 1: Four themes were identified: women's overall (positive and negative views of the pathways; knowledge and understanding of the pathways; views on clinical and weight management advice and support; and views on the information leaflet. Key results included positive views of receiving additional clinical care, negative experiences of risk communication, and weight management support was considered a priority. Study 2: Healthcare professionals felt the pathways were worthwhile, facilitated good practice, and increased confidence. Training was consistently identified as being required. Healthcare professionals predominantly focussed on women's response to sensitive obesity communication. Study 3: There was good compliance with antenatal clinical interventions. However, there was poor compliance with public health and postnatal interventions. There were some strong areas of agreement between component studies which can inform future development of the pathways. However, disagreement between studies included a lack of shared priorities between healthcare professionals and women, different perspectives on communication issues, and different perspectives on women's prioritisation of weight

An Evaluation of the Implementation of Maternal Obesity Pathways of Care: A Mixed Methods Study with Data Integration

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Heslehurst, Nicola; Dinsdale, Sarah; Sedgewick, Gillian; Simpson, Helen; Sen, Seema; Summerbell, Carolyn Dawn; Rankin, Judith

2015-01-01

Objectives Maternal obesity has multiple associated risks and requires substantial intervention. This research evaluated the implementation of maternal obesity care pathways from multiple stakeholder perspectives. Study Design A simultaneous mixed methods model with data integration was used. Three component studies were given equal priority. 1: Semi-structured qualitative interviews explored obese pregnant women’s experiences of being on the pathways. 2: A quantitative and qualitative postal survey explored healthcare professionals’ experiences of delivering the pathways. 3: A case note audit quantitatively assessed pathway compliance. Data were integrated using following a thread and convergence coding matrix methods to search for agreement and disagreement between studies. Results Study 1: Four themes were identified: women’s overall (positive and negative) views of the pathways; knowledge and understanding of the pathways; views on clinical and weight management advice and support; and views on the information leaflet. Key results included positive views of receiving additional clinical care, negative experiences of risk communication, and weight management support was considered a priority. Study 2: Healthcare professionals felt the pathways were worthwhile, facilitated good practice, and increased confidence. Training was consistently identified as being required. Healthcare professionals predominantly focussed on women’s response to sensitive obesity communication. Study 3: There was good compliance with antenatal clinical interventions. However, there was poor compliance with public health and postnatal interventions. There were some strong areas of agreement between component studies which can inform future development of the pathways. However, disagreement between studies included a lack of shared priorities between healthcare professionals and women, different perspectives on communication issues, and different perspectives on women�

Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models.

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Hakime Öztürk

Full Text Available β-lactamase mediated antibiotic resistance is an important health issue and the discovery of new β-lactam type antibiotics or β-lactamase inhibitors is an area of intense research. Today, there are about a thousand β-lactamases due to the evolutionary pressure exerted by these ligands. While β-lactamases hydrolyse the β-lactam ring of antibiotics, rendering them ineffective, Penicillin-Binding Proteins (PBPs, which share high structural similarity with β-lactamases, also confer antibiotic resistance to their host organism by acquiring mutations that allow them to continue their participation in cell wall biosynthesis. In this paper, we propose a novel approach to include ligand sharing information for classifying and clustering β-lactamases and PBPs in an effort to elucidate the ligand induced evolution of these β-lactam binding proteins. We first present a detailed summary of the β-lactamase and PBP families in the Protein Data Bank, as well as the compounds they bind to. Then, we build two different types of networks in which the proteins are represented as nodes, and two proteins are connected by an edge with a weight that depends on the number of shared identical or similar ligands. These models are analyzed under three different edge weight settings, namely unweighted, weighted, and normalized weighted. A detailed comparison of these six networks showed that the use of ligand sharing information to cluster proteins resulted in modules comprising proteins with not only sequence similarity but also functional similarity. Consideration of ligand similarity highlighted some interactions that were not detected in the identical ligand network. Analysing the β-lactamases and PBPs using ligand-centric network models enabled the identification of novel relationships, suggesting that these models can be used to examine other protein families to obtain information on their ligand induced evolutionary paths.

Protesters as "passionate economists" : A dynamic dual pathway model of approach coping with collective disadvantage

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van Zomeren, Martijn; Leach, Colin Wayne; Spears, Russell

To explain the psychology behind individuals' motivation to participate in collective action against collective disadvantage (e.g., protest marches), the authors introduce a dynamic dual pathway model of approach coping that integrates many common explanations of collective action (i.e., group

Designing User-Centric Patient Portals: Clinician and Patients' Uses and Gratifications

Science.gov (United States)

Krist, Alex H.; Aycock, Rebecca A.; Kreps, Gary L.

2017-01-01

Abstract Background: Legislation mandates that clinicians make patients' medical information available digitally. This has resulted in hurriedly installing patient portals that do not fully meet the needs of patients or clinicians. This study examined a specific portal, MyPreventiveCare (MPC), a patient-centered portal designed to promote preventive care to consumers, to elicit recommendations from patients and clinicians about how it could be more beneficial by uncovering their uses and gratifications (U&G). Materials and Methods: In-depth interviews with 31 patients and two clinician focus groups were conducted. Multiple methods were utilized, such as grounded theory coding to develop themes and content analysis to classify responses according to the U&G framework. Results: Four main categories emerged that users desire to be included in health portals: integration with technology (27%), coordination of care (27%), incorporation of lifestyle (26%), and increased control (20%). Additional analysis revealed that health portals are mainly utilized to fulfill cognitive and affective needs, with over 80% of recommendations related to the U&G categories of cognitive and affective needs. Cognitive (60%), affective (21%), social integrative (10%), personal integrative (9%), and tension release (0%). Conclusions: Portals will continue to evolve and become important health communication tools if they address the user's perspective and are inclusive of new technological advances. Specifically, portals must become more user centric and incorporate aspects of the patients' lifestyle and integrate health information technology. PMID:27333468

Ontology modeling for generation of clinical pathways

Directory of Open Access Journals (Sweden)

Jasmine Tehrani

2012-12-01

Full Text Available Purpose: Increasing costs of health care, fuelled by demand for high quality, cost-effective healthcare has drove hospitals to streamline their patient care delivery systems. One such systematic approach is the adaptation of Clinical Pathways (CP as a tool to increase the quality of healthcare delivery. However, most organizations still rely on are paper-based pathway guidelines or specifications, which have limitations in process management and as a result can influence patient safety outcomes. In this paper, we present a method for generating clinical pathways based on organizational semiotics by capturing knowledge from syntactic, semantic and pragmatic to social level. Design/methodology/approach: The proposed modeling approach to generation of CPs adopts organizational semiotics and enables the generation of semantically rich representation of CP knowledge. Semantic Analysis Method (SAM is applied to explicitly represent the semantics of the concepts, their relationships and patterns of behavior in terms of an ontology chart. Norm Analysis Method (NAM is adopted to identify and formally specify patterns of behavior and rules that govern the actions identified on the ontology chart. Information collected during semantic and norm analysis is integrated to guide the generation of CPs using best practice represented in BPMN thus enabling the automation of CP. Findings: This research confirms the necessity of taking into consideration social aspects in designing information systems and automating CP. The complexity of healthcare processes can be best tackled by analyzing stakeholders, which we treat as social agents, their goals and patterns of action within the agent network. Originality/value: The current modeling methods describe CPs from a structural aspect comprising activities, properties and interrelationships. However, these methods lack a mechanism to describe possible patterns of human behavior and the conditions under which the

Psychotherapy, psychopathology, research and practice: pathways of connections and integration.

Science.gov (United States)

Castonguay, Louis G

2011-03-01

This paper describes three pathways of connections between different communities of knowledge seekers: integration of psychotherapeutic approaches, integration of psychotherapy and psychopathology, and integration of science and practice. Some of the issues discussed involve the delineation and investigation of common factors (e.g., principles of change), improvement of major forms of psychotherapy, clinical implications of psychopathology research, as well as current and future directions related to practice-research networks. The aim of this paper is to suggest that building bridges across theoretical orientations, scientific fields, professional experiences, and epistemological views may be a fruitful strategy to improve our understanding and the impact of psychotherapy.

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.

Advancing coupled human-earth system models: The integrated Earth System Model Project

Science.gov (United States)

Thomson, A. M.; Edmonds, J. A.; Collins, W.; Thornton, P. E.; Hurtt, G. C.; Janetos, A. C.; Jones, A.; Mao, J.; Chini, L. P.; Calvin, K. V.; Bond-Lamberty, B. P.; Shi, X.

2012-12-01

As human and biogeophysical models develop, opportunities for connections between them evolve and can be used to advance our understanding of human-earth systems interaction in the context of a changing climate. One such integration is taking place with the Community Earth System Model (CESM) and the Global Change Assessment Model (GCAM). A multi-disciplinary, multi-institution team has succeeded in integrating the GCAM integrated assessment model of human activity into CESM to dynamically represent the feedbacks between changing climate and human decision making, in the context of greenhouse gas mitigation policies. The first applications of this capability have focused on the feedbacks between climate change impacts on terrestrial ecosystem productivity and human decisions affecting future land use change, which are in turn connected to human decisions about energy systems and bioenergy production. These experiments have been conducted in the context of the RCP4.5 scenario, one of four pathways of future radiative forcing being used in CMIP5, which constrains future human-induced greenhouse gas emissions from energy and land activities to stabilize radiative forcing at 4.5 W/m2 (~650 ppm CO2 -eq) by 2100. When this pathway is run in GCAM with the climate feedback on terrestrial productivity from CESM, there are implications for both the land use and energy system changes required for stabilization. Early findings indicate that traditional definitions of radiative forcing used in scenario development are missing a critical component of the biogeophysical consequences of land use change and their contribution to effective radiative forcing. Initial full coupling of the two global models has important implications for how climate impacts on terrestrial ecosystems changes the dynamics of future land use change for agriculture and forestry, particularly in the context of a climate mitigation policy designed to reduce emissions from land use as well as energy systems

Content-centric networks an overview, applications and research challenges

CERN Document Server

Ahmed, Syed Hassan; Kim, Dongkyun

2016-01-01

This book introduces Content-Centric Networking (CCN), a networking paradigm that provides a simple and effective solution to the challenging demands of future wired and wireless communications. It provides an overview of the recent developments in the area of future internet technologies, bringing together the advancements that have been made in Information-Centric Networking (ICN) in general, with a focus on CCN. It begins with an introduction to the basics of CCN is followed by an overview of the current internet paradigm and its challenges. Next, an application perspective has been included, where the authors encompass the selected applications for CCN with recent refereed research and developments. These applications include Internet of Things (IoT), Smart Grid, Vehicular Ad hoc Networks (VANETs), and Wireless Sensor Networks (WSNs). The book is a useful reference source for practising researchers, and can be used as supporting material for undergraduate and graduate level courses in computer science and...

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.

Science.gov (United States)

Papatheodorou, Irene; Ziehm, Matthias; Wieser, Daniela; Alic, Nazif; Partridge, Linda; Thornton, Janet M

2012-01-01

A challenge of systems biology is to integrate incomplete knowledge on pathways with existing experimental data sets and relate these to measured phenotypes. Research on ageing often generates such incomplete data, creating difficulties in integrating RNA expression with information about biological processes and the phenotypes of ageing, including longevity. Here, we develop a logic-based method that employs Answer Set Programming, and use it to infer signalling effects of genetic perturbations, based on a model of the insulin signalling pathway. We apply our method to RNA expression data from Drosophila mutants in the insulin pathway that alter lifespan, in a foxo dependent fashion. We use this information to deduce how the pathway influences lifespan in the mutant animals. We also develop a method for inferring the largest common sub-paths within each of our signalling predictions. Our comparisons reveal consistent homeostatic mechanisms across both long- and short-lived mutants. The transcriptional changes observed in each mutation usually provide negative feedback to signalling predicted for that mutation. We also identify an S6K-mediated feedback in two long-lived mutants that suggests a crosstalk between these pathways in mutants of the insulin pathway, in vivo. By formulating the problem as a logic-based theory in a qualitative fashion, we are able to use the efficient search facilities of Answer Set Programming, allowing us to explore larger pathways, combine molecular changes with pathways and phenotype and infer effects on signalling in in vivo, whole-organism, mutants, where direct signalling stimulation assays are difficult to perform. Our methods are available in the web-service NetEffects: http://www.ebi.ac.uk/thornton-srv/software/NetEffects.

Manned/Unmanned Common Architecture Program (MCAP) net centric flight tests

Science.gov (United States)

Johnson, Dale

2009-04-01

Properly architected avionics systems can reduce the costs of periodic functional improvements, maintenance, and obsolescence. With this in mind, the U.S. Army Aviation Applied Technology Directorate (AATD) initiated the Manned/Unmanned Common Architecture Program (MCAP) in 2003 to develop an affordable, high-performance embedded mission processing architecture for potential application to multiple aviation platforms. MCAP analyzed Army helicopter and unmanned air vehicle (UAV) missions, identified supporting subsystems, surveyed advanced hardware and software technologies, and defined computational infrastructure technical requirements. The project selected a set of modular open systems standards and market-driven commercial-off-theshelf (COTS) electronics and software, and, developed experimental mission processors, network architectures, and software infrastructures supporting the integration of new capabilities, interoperability, and life cycle cost reductions. MCAP integrated the new mission processing architecture into an AH-64D Apache Longbow and participated in Future Combat Systems (FCS) network-centric operations field experiments in 2006 and 2007 at White Sands Missile Range (WSMR), New Mexico and at the Nevada Test and Training Range (NTTR) in 2008. The MCAP Apache also participated in PM C4ISR On-the-Move (OTM) Capstone Experiments 2007 (E07) and 2008 (E08) at Ft. Dix, NJ and conducted Mesa, Arizona local area flight tests in December 2005, February 2006, and June 2008.

Laboring for integration

DEFF Research Database (Denmark)

Fogelman, Tatiana

Over the past fifteen years the district of Berlin-Marzahn became home to the largest concentration of post-Soviet migrants of German ancestry in the former East Germany. Drawing on my research in the district, including two of its integration projects for middle-aged, unemployed migrants, I...... examine these projects’ failed attempts to create spaces of encounter between the migrants and district’s long-term residents. In this presentation I focus specifically on the structural position of integration work (Integrationsarbeit) that creates first and foremost conditions of possibility for its...... temporal imaginaries underpinning the ideas of integration through encounter, as well as integration more broadly, I argue for reflexivity-centric public reformulations of both integration and encounter....

Functional Assessment of the Stomatognathic System, after the Treatment of Edentulous Patients, with Different Methods of Establishing the Centric Relation.

Science.gov (United States)

Nitecka-Buchta, Aleksandra; Proba, Thomas; Proba, Paulina; Stefański, Kamil; Baron, Stefan

2018-01-01

The study compares subjective experiences of patients, wearing complete dentures. Two different methods of determining a centric relation were performed: the traditional method using wax occlusal rims and the Gerber method, based on gothic arch tracings. The success rate of establishing a centric relation in both methods was evaluated (rentgenodiagnostics). The influence of the method used to obtain the centric relation on patients' stomatognathic system (condyle centralization, pain) was also evaluated. Better results were achieved in gothic arch tracing method. Before every prosthetic treatment of edentulous patients, a functional analysis of the TMJ is necessary. The lack of centric relation, in a long term adaptation patients, does not lead to TMD symptoms. This trial is registered with NCT03343015.

User centric monitoring (UCM) information service for the next generation of Grid-enabled scientists

International Nuclear Information System (INIS)

Alexander, D A; Li, C; Lauret, J; Fine, V

2008-01-01

Nuclear and high-energy physicists routinely execute data processing and data analysis jobs on a Grid and need to be able to easily and remotely monitor the execution of these jobs. Existing Grid monitoring tools provide abundant information about the whole system, but are geared towards production jobs and well suited for Grid administrators, while the information tailored towards an individual user is not readily available in a user-friendly and user-centric way. Such User Centric information includes monitoring information such as the status of the submitted job, queue position, time of the start/finish, percentage of being done, error messages, standard output, and reasons for failure. We proposed to develop a framework based on Grid service technology that allows scientists to track and monitor their jobs easily from a user-centric view. The proposed framework aims to be flexible so that it can be applied by any Grid Virtual Organization (VO) with various ways of collecting the user-centric job monitoring information built into the framework. Furthermore, the framework provides a rich and reusable set of methods of presenting the information to the user from within a Web browser and other clients. In this presentation, we will give an architectural overview of the UCM service, show an example implementation in the RHIC/STAR experiment context and discuss limitations and future collaborative work

User centric monitoring (UCM) information service for the next generation of Grid-enabled scientists

Energy Technology Data Exchange (ETDEWEB)

Alexander, D A; Li, C [Tech-X Corporation, 5621 Arapahoe Avenue Suite A, Boulder, CO 80303 (United States); Lauret, J; Fine, V [Physics Department, Brookhaven National Laboratory, Upton, NY 11973 (United States)], E-mail: alexanda@txcorp.com

2008-07-15

Nuclear and high-energy physicists routinely execute data processing and data analysis jobs on a Grid and need to be able to easily and remotely monitor the execution of these jobs. Existing Grid monitoring tools provide abundant information about the whole system, but are geared towards production jobs and well suited for Grid administrators, while the information tailored towards an individual user is not readily available in a user-friendly and user-centric way. Such User Centric information includes monitoring information such as the status of the submitted job, queue position, time of the start/finish, percentage of being done, error messages, standard output, and reasons for failure. We proposed to develop a framework based on Grid service technology that allows scientists to track and monitor their jobs easily from a user-centric view. The proposed framework aims to be flexible so that it can be applied by any Grid Virtual Organization (VO) with various ways of collecting the user-centric job monitoring information built into the framework. Furthermore, the framework provides a rich and reusable set of methods of presenting the information to the user from within a Web browser and other clients. In this presentation, we will give an architectural overview of the UCM service, show an example implementation in the RHIC/STAR experiment context and discuss limitations and future collaborative work.

Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease.

Science.gov (United States)

Zhang, Yan; Liu, Dianming; Wang, Lihong; Wang, Shuyuan; Yu, Xuexin; Dai, Enyu; Liu, Xinyi; Luo, Shanshun; Jiang, Wei

2015-12-01

Coronary artery disease (CAD) is the most common type of heart disease. However, the molecular mechanisms of CAD remain elusive. Regulatory pathways are known to play crucial roles in many pathogenic processes. Thus, inferring risk regulatory pathways is an important step toward elucidating the mechanisms underlying CAD. With advances in high-throughput data, we developed an integrated systems approach to identify CAD risk regulatory pathways and key regulators. Firstly, a CAD-related core subnetwork was identified from a curated transcription factor (TF) and microRNA (miRNA) regulatory network based on a random walk algorithm. Secondly, candidate risk regulatory pathways were extracted from the subnetwork by applying a breadth-first search (BFS) algorithm. Then, risk regulatory pathways were prioritized based on multiple CAD-associated data sources. Finally, we also proposed a new measure to prioritize upstream regulators. We inferred that phosphatase and tensin homolog (PTEN) may be a key regulator in the dysregulation of risk regulatory pathways. This study takes a closer step than the identification of disease subnetworks or modules. From the risk regulatory pathways, we could understand the flow of regulatory information in the initiation and progression of the disease. Our approach helps to uncover its potential etiology. We developed an integrated systems approach to identify risk regulatory pathways. We proposed a new measure to prioritize the key regulators in CAD. PTEN may be a key regulator in dysregulation of the risk regulatory pathways.

Using big data for customer centric marketing

OpenAIRE

Camilleri, Mark Anthony; Evans, Chris

2016-01-01

This chapter deliberates on “big data” and provides a short overview of business intelligence and emerging analytics. It underlines the importance of data for customer-centricity in marketing. This contribution contends that businesses ought to engage in marketing automation tools and apply them to create relevant, targeted customer experiences. Today’s business increasingly rely on digital media and mobile technologies as on-demand, real-time marketing has become more personalised than ever....

Sensitivity and uncertainty analysis of the PATHWAY radionuclide transport model

International Nuclear Information System (INIS)

Otis, M.D.

1983-01-01

Procedures were developed for the uncertainty and sensitivity analysis of a dynamic model of radionuclide transport through human food chains. Uncertainty in model predictions was estimated by propagation of parameter uncertainties using a Monte Carlo simulation technique. Sensitivity of model predictions to individual parameters was investigated using the partial correlation coefficient of each parameter with model output. Random values produced for the uncertainty analysis were used in the correlation analysis for sensitivity. These procedures were applied to the PATHWAY model which predicts concentrations of radionuclides in foods grown in Nevada and Utah and exposed to fallout during the period of atmospheric nuclear weapons testing in Nevada. Concentrations and time-integrated concentrations of iodine-131, cesium-136, and cesium-137 in milk and other foods were investigated. 9 figs., 13 tabs

Integrative structure modeling with the Integrative Modeling Platform.

Science.gov (United States)

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.

Modeling of non-steroidal anti-inflammatory drug effect within signaling pathways and miRNA-regulation pathways.

Directory of Open Access Journals (Sweden)

Jian Li

Full Text Available To date, it is widely recognized that Non-Steroidal Anti-Inflammatory Drugs (NSAIDs can exert considerable anti-tumor effects regarding many types of cancers. The prolonged use of NSAIDs is highly associated with diverse side effects. Therefore, tailoring down the NSAID application onto individual patients has become a necessary and relevant step towards personalized medicine. This study conducts the systemsbiological approach to construct a molecular model (NSAID model containing a cyclooxygenase (COX-pathway and its related signaling pathways. Four cancer hallmarks are integrated into the model to reflect different developmental aspects of tumorigenesis. In addition, a Flux-Comparative-Analysis (FCA based on Petri net is developed to transfer the dynamic properties (including drug responsiveness of individual cellular system into the model. The gene expression profiles of different tumor-types with available drug-response information are applied to validate the predictive ability of the NSAID model. Moreover, two therapeutic developmental strategies, synthetic lethality and microRNA (miRNA biomarker discovery, are investigated based on the COX-pathway. In conclusion, the result of this study demonstrates that the NSAID model involving gene expression, gene regulation, signal transduction, protein interaction and other cellular processes, is able to predict the individual cellular responses for different therapeutic interventions (such as NS-398 and COX-2 specific siRNA inhibition. This strongly indicates that this type of model is able to reflect the physiological, developmental and pathological processes of an individual. The approach of miRNA biomarker discovery is demonstrated for identifying miRNAs with oncogenic and tumor suppressive functions for individual cell lines of breast-, colon- and lung-tumor. The achieved results are in line with different independent studies that investigated miRNA biomarker related to diagnostics of cancer

Towards integrating extracellular matrix and immunological pathways.

Science.gov (United States)

Boyd, David F; Thomas, Paul G

2017-10-01

The extracellular matrix (ECM) is a complex and dynamic structure made up of an estimated 300 different proteins. The ECM is also a rich source of cytokines and growth factors in addition to numerous bioactive ECM degradation products that influence cell migration, proliferation, and differentiation. The ECM is constantly being remodeled during homeostasis and in a wide range of pathological contexts. Changes in the ECM modulate immune responses, which in turn regulate repair and regeneration of tissues. Here, we review the many components of the ECM, enzymes involved in ECM remodeling, and the signals that feed into immunological pathways in the context of a dynamic ECM. We highlight studies that have taken an integrative approach to studying immune responses in the context of the ECM and studies that use novel proteomic strategies. Finally, we discuss research challenges relevant to the integration of immune and ECM networks and propose experimental and translational approaches to resolve these issues. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functional Assessment of the Stomatognathic System, after the Treatment of Edentulous Patients, with Different Methods of Establishing the Centric Relation

Directory of Open Access Journals (Sweden)

Aleksandra Nitecka-Buchta

2018-01-01

Full Text Available The study compares subjective experiences of patients, wearing complete dentures. Two different methods of determining a centric relation were performed: the traditional method using wax occlusal rims and the Gerber method, based on gothic arch tracings. The success rate of establishing a centric relation in both methods was evaluated (rentgenodiagnostics. The influence of the method used to obtain the centric relation on patients’ stomatognathic system (condyle centralization, pain was also evaluated. Better results were achieved in gothic arch tracing method. Before every prosthetic treatment of edentulous patients, a functional analysis of the TMJ is necessary. The lack of centric relation, in a long term adaptation patients, does not lead to TMD symptoms. This trial is registered with NCT03343015.

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Directory of Open Access Journals (Sweden)

Zhongqi Ge

2018-04-01

Full Text Available Summary: Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations. Ubiquitin pathway genes tend to be upregulated in cancer mediated by diverse mechanisms. By integrating pan-cancer multiomic data, we identify a group of tumor samples that exhibit worse prognosis. These samples are consistently associated with the upregulation of cell-cycle and DNA repair pathways, characterized by mutated TP53, MYC/TERT amplification, and APC/PTEN deletion. Our analysis highlights the importance of the ubiquitin pathway in cancer development and lays a foundation for developing relevant therapeutic strategies. : Ge et al. analyze a cohort of 9,125 TCGA samples across 33 cancer types to provide a comprehensive characterization of the ubiquitin pathway. They detect somatic driver candidates in the ubiquitin pathway and identify a cluster of patients with poor survival, highlighting the importance of this pathway in cancer development. Keywords: ubiquitin pathway, pan-cancer analysis, The Cancer Genome Atlas, tumor subtype, cancer prognosis, therapeutic targets, biomarker, FBXW7

An Audience-Centric Approach for Museums Sustainability

Directory of Open Access Journals (Sweden)

Laura Di Pietro

2014-08-01

Full Text Available The main purpose of this study is to propose a visitor centric perspective that can support museums towards sustainability. The main premise of this study is due to a concept of economic and social sustainability of museums, defined as the possession of sufficient resources to maintain the existence of an organization, and achieve their goals in the future, ensuring a certain flow of visitors. A great number of museums are characterized by a low number of visits; therefore, in order to become sustainable, museums should pay attention to audience and its internal diversity. In this way, a cultural site can plan tailored strategies to increase the number of visits and re-visits and to achieve community support. For this reason it is necessary to understand the cultural needs of visitors, acquiring appropriate monitoring tools, such as qualitative and quantitative ones. Generally, quantitative analyses are more reliable and complete, even if they require a considerable number of observations for the reliability of the results. Moreover, qualitative analysis provides more in depth information, even if their data do not allow us to make generalizations. The qualitative and quantitative methods for the detection of satisfaction are usually used separately, but their integration may bring significant added value in terms of the wealth of information. This study follows the analysis of the potential of the integration of qualitative and quantitative analysis techniques customized with respect to different types of targets. The results of the experimentation performed on ethnographic museums shows a consistency of the results obtained by the two different tools that increase the capacity information of survey instruments.

Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis

DEFF Research Database (Denmark)

Huang, Sijia; Chong, Nicole; Lewis, Nathan

2016-01-01

diagnosis. We applied this method to predict breast cancer occurrence, in combination with correlation feature selection (CFS) and classification methods. Results: The resulting all-stage and early-stage diagnosis models are highly accurate in two sets of testing blood samples, with average AUCs (Area Under.......993. Moreover, important metabolic pathways, such as taurine and hypotaurine metabolism and the alanine, aspartate, and glutamate pathway, are revealed as critical biological pathways for early diagnosis of breast cancer. Conclusions: We have successfully developed a new type of pathway-based model to study...... metabolomics data for disease diagnosis. Applying this method to blood-based breast cancer metabolomics data, we have discovered crucial metabolic pathway signatures for breast cancer diagnosis, especially early diagnosis. Further, this modeling approach may be generalized to other omics data types for disease...

Value-centric design architecture based on analysis of space system characteristics

Science.gov (United States)

Xu, Q.; Hollingsworth, P.; Smith, K.

2018-03-01

Emerging design concepts such as miniaturisation, modularity, and standardisation, have contributed to the rapid development of small and inexpensive platforms, particularly cubesats. This has been stimulating an upcoming revolution in space design and development, leading satellites into the era of "smaller, faster, and cheaper". However, the current requirement-centric design philosophy, focused on bespoke monolithic systems, along with the associated development and production process does not inherently fit with the innovative modular, standardised, and mass-produced technologies. This paper presents a new categorisation, characterisation, and value-centric design architecture to address this need for both traditional and novel system designs. Based on the categorisation of system configurations, a characterisation of space systems, comprised of duplication, fractionation, and derivation, is proposed to capture the overall system configuration characteristics and promote potential hybrid designs. Complying with the definitions of the system characterisation, mathematical mapping relations between the system characterisation and the system properties are described to establish the mathematical foundation of the proposed value-centric design methodology. To illustrate the methodology, subsystem reliability relationships are therefore analysed to explore potential system configurations in the design space. The results of the applications of system characteristic analysis clearly show that the effects of different configuration characteristics on the system properties can be effectively analysed and evaluated, enabling the optimization of system configurations.

Physical Training Strategies for Military Women's Performance Optimization in Combat-Centric Occupations.

Science.gov (United States)

Nindl, Bradley C

2015-11-01

The physiological differences, particularly of upper-body strength and power, between women and men, and the rigors of combat-centric occupational demands would seem to place women at a significant disadvantage, as the U.S. military opens up previously closed combat-arms military occupational specialties (MOSs) to women. This inherent disadvantage can be significantly mitigated by implementing effective and comprehensive physical training (PT) regimens for women targeting those fitness components most critical for those tasks considered most essential for solider warfighting duties (i.e., strength and power). Regrettably, the military historical and legacy overemphasis on aerobic fitness and on "field expediency" as the major criteria for implementing training have limited the extent to which the military has fully operationalized state-of-the-science PT policies. This continued legacy approach could be problematic regarding fully enhancing women's abilities to perform physically demanding combat-centric occupations and could place the successful integration of women into ground combat MOSs at significant risk. Seminal studies from the literature indicate that (a) a minimum of 6 months of periodized combined resistance/endurance training preparedness is recommended for untrained women considering entering combat-arms MOS training; (b) any comprehensive PT program should incorporate and emphasize progressive load carriage training; (c) a greater emphasis on upper body on strength/power development in military women is needed; (d) heavy resistance training in the range of 3-8 repetition maximum sets should be incorporated into training programs to target type II motor units and muscle fibers (those fibers that produce the most force and have the greatest capacity to hypertrophy); (e) low-volume, high-intensity interval training should be considered as a time-efficient training method to improve aerobic fitness while protecting against lower-body musculoskeletal

Understanding "Understanding" Flow for Network-Centric Warfare: Military Knowledge-Flow Mechanics

National Research Council Canada - National Science Library

Nissen, Mark

2002-01-01

Network-centric warfare (NCW) emphasizes information superiority for battlespace efficacy, but it is clear that the mechanics of how knowledge flows are just as important as those pertaining to the networks and communication...

User-centric Query Refinement and Processing Using Granularity Based Strategies

NARCIS (Netherlands)

Zeng, Y.; Zhong, N.; Wang, Y.; Qin, Y.; Huang, Z.; Zhou, H; Yao, Y; van Harmelen, F.A.H.

2011-01-01

Under the context of large-scale scientific literatures, this paper provides a user-centric approach for refining and processing incomplete or vague query based on cognitive- and granularity-based strategies. From the viewpoints of user interests retention and granular information processing, we

Efficient Asymmetric Index Encapsulation Scheme for Anonymous Content Centric Networking

Directory of Open Access Journals (Sweden)

Rong Ma

2017-01-01

Full Text Available Content Centric Networking (CCN is an effective communication paradigm that well matches the features of wireless environments. To be considered a viable candidate in the emerging wireless networks, despite the clear benefits of location-independent security, CCN must at least have parity with existing solutions for confidential and anonymous communication. This paper designs a new cryptographic scheme, called Asymmetric Index Encapsulation (AIE, that enables the router to test whether an encapsulated header matches the token without learning anything else about both of them. We suggest using the AIE as the core protocol of anonymous Content Centric Networking. A construction of AIE which strikes a balance between efficiency and security is given. The scheme is proved to be secure based on the DBDH assumption in the random oracle with tight reduction, while the encapsulated header and the token in our system consist of only three elements.

Device-Centric Monitoring for Mobile Device Management

OpenAIRE

Chircop, Luke; Colombo, Christian; Pace, Gordon J.

2016-01-01

The ubiquity of computing devices has led to an increased need to ensure not only that the applications deployed on them are correct with respect to their specifications, but also that the devices are used in an appropriate manner, especially in situations where the device is provided by a party other than the actual user. Much work which has been done on runtime verification for mobile devices and operating systems is mostly application-centric, resulting in global, device-centri...

Precise generation of systems biology models from KEGG pathways.

Science.gov (United States)

Wrzodek, Clemens; Büchel, Finja; Ruff, Manuel; Dräger, Andreas; Zell, Andreas

2013-02-21

The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, the pathways can be extended with an enormous amount of information and provide a foundation for initial structural modeling approaches. As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and often omit important details for the sake of a clear arrangement of its entries. Thus, a direct conversion into systems biology models would produce incomplete and erroneous models. Here, we present a precise method for processing and converting KEGG pathways into initial metabolic and signaling models encoded in the standardized community pathway formats SBML (Levels 2 and 3) and BioPAX (Levels 2 and 3). This method involves correcting invalid or incomplete KGML content, creating complete and valid stoichiometric reactions, translating relations to signaling models and augmenting the pathway content with various information, such as cross-references to Entrez Gene, OMIM, UniProt ChEBI, and many more.Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG to BioPAX does not involve a loss of information, whilst lossless translations to SBML can only be performed using SBML Level 3, including its recently proposed qualitative models and groups extension packages. Building correct BioPAX and SBML signaling models from the KEGG database is a unique characteristic of the proposed method. Further, there is no other approach that is able to appropriately construct metabolic models from KEGG pathways, including correct reactions with stoichiometry. The resulting initial models, which contain valid and comprehensive SBML or BioPAX code and a multitude of cross-references, lay the foundation to facilitate further modeling steps.

Manage customer-centric innovation--systematically.

Science.gov (United States)

Selden, Larry; MacMillan, Ian C

2006-04-01

No matter how hard companies try, their approaches to innovation often don't grow the top line in the sustained, profitable way investors expect. For many companies, there's a huge difference between what's in their business plans and the market's expectations for growth (as reflected in firms' share prices, market capitalizations, and P/E ratios). This growth gap springs from the fact that companies are pouring money into their insular R&D labs instead of working to understand what the customer wants and using that understanding to drive innovation. As a result, even companies that spend the most on R&D remain starved for both customer innovation and market-capitalization growth. In this article, the authors spell out a systematic approach to innovation that continuously fuels sustained, profitable growth. They call this approach customer-centric innovation, or CCI. At the heart of CCI is a rigorous customer R&D process that helps companies to continually improve their understanding of who their customers are and what they need. By so doing, they consistently create or improve their customer value proposition. Customer R&D also focuses on better ways of communicating value propositions and delivering the complete experience to real customers. Since so much of the learning about customers and so much of the experimentation with different segmentations, value propositions, and delivery mechanisms involve the people who regularly deal with customers, it is absolutely essential for frontline employees to be at the center of the CCI process. Simply put, customer R&D propels the innovation effort away from headquarters and the traditional R&D lab out to those closest to the customer. Using the example of the luggage manufacturer Tumi, the authors provide a step-by-step approach for achieving true customer-centric innovation.

DCOS, a Real-Time Light-weight Data Centric Operating System

NARCIS (Netherlands)

Hofmeijer, T.J.; Dulman, S.O.; Jansen, P.G.; Havinga, Paul J.M.; Sahni, S.

2004-01-01

DCOS is a Data Centric lightweight Operating System for embedded devices. Despite limited energy and hardware resources, it supports a data driven architecture with provisions for dynamic loadable Modules. It combines these with Real-Time provisions based on Earliest Deadline First with a simple but

DCOS, a real-time light-weight Data Centric Operating System

NARCIS (Netherlands)

Hofmeijer, T.J.; Dulman, S.O.; Jansen, P.G.; Havinga, Paul J.M.

2004-01-01

DCOS is a Data Centric lightweight Operating System for embedded devices. Despite limited energy and hardware resources, it supports a data driven architecture with provisions for dynamic loadable Modules. It combines these with Real-Time provisions based on Earliest Deadline First with a simple but

User-centric incentive design for participatory mobile phone sensing

Science.gov (United States)

Gao, Wei; Lu, Haoyang

2014-05-01

Mobile phone sensing is a critical underpinning of pervasive mobile computing, and is one of the key factors for improving people's quality of life in modern society via collective utilization of the on-board sensing capabilities of people's smartphones. The increasing demands for sensing services and ambient awareness in mobile environments highlight the necessity of active participation of individual mobile users in sensing tasks. User incentives for such participation have been continuously offered from an application-centric perspective, i.e., as payments from the sensing server, to compensate users' sensing costs. These payments, however, are manipulated to maximize the benefits of the sensing server, ignoring the runtime flexibility and benefits of participating users. This paper presents a novel framework of user-centric incentive design, and develops a universal sensing platform which translates heterogenous sensing tasks to a generic sensing plan specifying the task-independent requirements of sensing performance. We use this sensing plan as input to reduce three categories of sensing costs, which together cover the possible sources hindering users' participation in sensing.

Transport fuel demand responses to fuel price and income projections : Comparison of integrated assessment models

NARCIS (Netherlands)

Edelenbosch, O. Y.; van Vuuren, Detlef; Bertram, C.; Carrara, S.; Emmerling, J.; Daly, H.; Kitous, A.; McCollum, D. L.; Saadi Failali, N.

Income and fuel price pathways are key determinants in projections of the energy system in integrated assessment models. In recent years, more details have been added to the transport sector representation in these models. To better understand the model dynamics, this manuscript analyses transport

A NEW PARADIGM FOR INDIAN SUPERMARKET RETAILERS BASED ON CUSTOMER-CENTRIC STRATEGIC APPROACH

Directory of Open Access Journals (Sweden)

Seema S. Shenoy

2011-12-01

Full Text Available Supermarket retailers in India admist fierce competition and the only way out is through the attainment of competitive advantage. Strategy is the route to attain competitive advantage that could facilitate firms attain superior performance. The objective of this paper is to develop a conceptual framework on customer-centric retail strategy, to facilitate supermarket retailers in India attain competitive advantage. The paper draws heavily from existing literature on retail strategies and competitive advantage in order to ascertain the most effective customer-centric strategies. Adding strength to the research is the result derived from interviews of supermarket managers and customers; and also the results of pilot study .The work involves identification of constructs and research hypothesis for the proposed framework. The framework contributes to literature by emphasizing on not just effective customer-centric strategies but also, on specific performance outcomes that supermarket retailers could be enjoying riding on these strategies. A new dimension to attainment of competitive advantage and superior performance has definitely been recognized by this research effort. Supermarket retailers in India can be certain of attaining competitive advantage by riding on the proposed strategies.

Combining Vertex-centric Graph Processing with SPARQL for Large-scale RDF Data Analytics

KAUST Repository

Abdelaziz, Ibrahim

2017-06-27

Modern applications, such as drug repositioning, require sophisticated analytics on RDF graphs that combine structural queries with generic graph computations. Existing systems support either declarative SPARQL queries, or generic graph processing, but not both. We bridge the gap by introducing Spartex, a versatile framework for complex RDF analytics. Spartex extends SPARQL to support programs that combine seamlessly generic graph algorithms (e.g., PageRank, Shortest Paths, etc.) with SPARQL queries. Spartex builds on existing vertex-centric graph processing frameworks, such as Graphlab or Pregel. It implements a generic SPARQL operator as a vertex-centric program that interprets SPARQL queries and executes them efficiently using a built-in optimizer. In addition, any graph algorithm implemented in the underlying vertex-centric framework, can be executed in Spartex. We present various scenarios where our framework simplifies significantly the implementation of complex RDF data analytics programs. We demonstrate that Spartex scales to datasets with billions of edges, and show that our core SPARQL engine is at least as fast as the state-of-the-art specialized RDF engines. For complex analytical tasks that combine generic graph processing with SPARQL, Spartex is at least an order of magnitude faster than existing alternatives.

Integrating nitric oxide into salicylic acid and jasmonic acid/ ethylene plant defense pathways.

Science.gov (United States)

Mur, Luis A J; Prats, Elena; Pierre, Sandra; Hall, Michael A; Hebelstrup, Kim H

2013-01-01

Plant defense against pests and pathogens is known to be conferred by either salicylic acid (SA) or jasmonic acid (JA)/ethylene (ET) pathways, depending on infection or herbivore-grazing strategy. It is well attested that SA and JA/ET pathways are mutually antagonistic allowing defense responses to be tailored to particular biotic stresses. Nitric oxide (NO) has emerged as a major signal influencing resistance mediated by both signaling pathways but no attempt has been made to integrate NO into established SA/JA/ET interactions. NO has been shown to act as an inducer or suppressor of signaling along each pathway. NO will initiate SA biosynthesis and nitrosylate key cysteines on TGA-class transcription factors to aid in the initiation of SA-dependent gene expression. Against this, S-nitrosylation of NONEXPRESSOR OF PATHOGENESIS-RELATED PROTEINS1 (NPR1) will promote the NPR1 oligomerization within the cytoplasm to reduce TGA activation. In JA biosynthesis, NO will initiate the expression of JA biosynthetic enzymes, presumably to over-come any antagonistic effects of SA on JA-mediated transcription. NO will also initiate the expression of ET biosynthetic genes but a suppressive role is also observed in the S-nitrosylation and inhibition of S-adenosylmethionine transferases which provides methyl groups for ET production. Based on these data a model for NO action is proposed but we have also highlighted the need to understand when and how inductive and suppressive steps are used.

User Location Identification for Cooperative Human-Centric Sensing (HCS) Scenario

DEFF Research Database (Denmark)

Mihovska, Albena Dimitrova

– Human-Centric Sensing (HCS) is a newly emerged concept in the context of the Internet of Things (IoT) and the active and assisted living (AAL) scenario. HCS connectivity, also referred to as “smart connectivity” enables applications that are highly personalized and often time...

Identification of mutated driver pathways in cancer using a multi-objective optimization model.

Science.gov (United States)

Zheng, Chun-Hou; Yang, Wu; Chong, Yan-Wen; Xia, Jun-Feng

2016-05-01

New-generation high-throughput technologies, including next-generation sequencing technology, have been extensively applied to solve biological problems. As a result, large cancer genomics projects such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium are producing large amount of rich and diverse data in multiple cancer types. The identification of mutated driver genes and driver pathways from these data is a significant challenge. Genome aberrations in cancer cells can be divided into two types: random 'passenger mutation' and functional 'driver mutation'. In this paper, we introduced a Multi-objective Optimization model based on a Genetic Algorithm (MOGA) to solve the maximum weight submatrix problem, which can be employed to identify driver genes and driver pathways promoting cancer proliferation. The maximum weight submatrix problem defined to find mutated driver pathways is based on two specific properties, i.e., high coverage and high exclusivity. The multi-objective optimization model can adjust the trade-off between high coverage and high exclusivity. We proposed an integrative model by combining gene expression data and mutation data to improve the performance of the MOGA algorithm in a biological context. Copyright © 2016 Elsevier Ltd. All rights reserved.

Applied data-centric social sciences concepts, data, computation, and theory

CERN Document Server

Sato, Aki-Hiro

2014-01-01

Applied data-centric social sciences aim to develop both methodology and practical applications of various fields of social sciences and businesses with rich data. Specifically, in the social sciences, a vast amount of data on human activities may be useful for understanding collective human nature. In this book, the author introduces several mathematical techniques for handling a huge volume of data and analysing collective human behaviour. The book is constructed from data-oriented investigation, with mathematical methods and expressions used for dealing with data for several specific problems. The fundamental philosophy underlying the book is that both mathematical and physical concepts are determined by the purposes of data analysis. This philosophy is shown throughout exemplar studies of several fields in socio-economic systems. From a data-centric point of view, the author proposes a concept that may change people’s minds and cause them to start thinking from the basis of data. Several goals underlie ...

Internet-centric collaborative design in a distributed environment

International Nuclear Information System (INIS)

Kim, Hyun; Kim, Hyoung Sun; Do, Nam Chul; Lee, Jae Yeol; Lee, Joo Haeng; Myong, Jae Hyong

2001-01-01

Recently, advanced information technologies including internet-related technology and distributed object technology have opened new possibilities for collaborative designs. In this paper, we discuss computer supports for collaborative design in a distributed environment. The proposed system is the internet-centric system composed of an engineering framework, collaborative virtual workspace and engineering service. It allows the distributed designers to more efficiently and collaboratively work their engineering tasks throughout the design process

Evaluating mobile centric readiness of students: A case of computer science students in open-distance learning

CSIR Research Space (South Africa)

Chipangura, B

2015-07-01

Full Text Available and Education]: Distance learning Keywords Mobile centric services, mobile information access, mobile readiness 1. INTRODUCTION As the mobile phone market matures in terms of penetration rate, subscription rate, handsets functionality and mobile centric..., this reflects a ratio of one mobile phone per person. High mobile phone penetration has made it possible for digitally alienated communities in developing countries to have improved access to business, health, education and social services. Indeed, this has...

Problem-centric Process for Research-based Learning

Directory of Open Access Journals (Sweden)

Khaled Shaban

2015-05-01

Full Text Available Research-based Learning (RbL extends Inquiry and Project-based Learning by facilitating an early stage exposure and training for future scientists through authentic research activities. In this paper, an iterative problem-centric RbL process is introduced, and its activities and management aspects are described. The process helps implement course-integrated research systematically and practically. Furthermore, the novel process follows constructivist methods in incorporating inquiry, scaffolding, open-ended projects, as well as a goal oriented learning approach. The RbL process is adopted in two advanced computing courses, at two different universities: a leading comprehensive Western university and a new university in a developing country. The paper summarizes new lessons learned in these rewarding experiences. In particular, the instructor should help students start their projects, by providing them with previous work or data and pre-approving the papers to review by students. He should also maintain a continuous feedback to and from students to keep the students motivated and help the instructor refine and adapt the RBL process. We note that research collaborators can help students in identifying the research topics early. The paper also shows how to alleviate difficulties that may be encountered by students who find the novel approach demanding, and consequently it also helps the instructors better manage the course contents.

Greening the Grid: Pathways to Integrate 175 Gigawatts of Renewable Energy into India's Electric Grid, Vol. II - Regional Study

Energy Technology Data Exchange (ETDEWEB)

Cochran, Jaquelin M. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Palchak, Joseph D [National Renewable Energy Lab. (NREL), Golden, CO (United States); McBennett, Brendan [National Renewable Energy Lab. (NREL), Golden, CO (United States); Milligan, Michael [National Renewable Energy Lab. (NREL), Golden, CO (United States); Ehlen, Ali [National Renewable Energy Lab. (NREL), Golden, CO (United States); Deshmukh, Ranjit [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Abhyankar, Nikit [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Soonee, Sushil Kumar [Power System Operation Corporation Limited (POSOCO), New Delhi (India); Narasimhan, S. R. [Power System Operation Corporation Limited (POSOCO), New Delhi (India); Joshi, Mohit [Power System Operation Corporation Limited (POSOCO), New Delhi (India); Sreedharan, Priya [U.S. Agency for International Development (USAID), Washington, DC (United States)

2017-10-27

The higher-spatial-resolution model of 'Greening the Grid: Pathways to Integrate 175 Gigawatts of Renewable Energy into India's Electric Grid, Vol. II - Regional Study' (the Regional Study), which better represents the impact of congestion on least-cost scheduling and dispatch, provides a deeper understanding of the relationship among renewable energy (RE) location, transmission, and system flexibility with regard to RE integration, compared to 'Greening the Grid: Pathways to Integrate 175 Gigawatts of Renewable Energy into India's Electric Grid, Vol. I - National Study.' The Regional Study validates the relative value of mitigation strategies demonstrated in the National Study - namely, coordinated operations among states reduce production costs, and reducing coal minimum generation levels reduces RE curtailment. Significantly, the Regional Study also highlights a potential barrier to realizing the value of these mitigation strategies: when locations of RE development are planned independently of state-level transmission, intrastate congestion can result in undesirable levels of RE curtailment. Therefore a key objective of this study is to illustrate to state-level power system planners and operators, in particular, how a higher-resolution model, inclusive of intrastate granularity, can be used as a planning tool for two primary purposes: -To better anticipate, understand, and mitigate system constraints that could affect RE integration; and - To provide a modeling framework that can be used as part of future transmission studies and planning efforts. The Regional Study is not intended to predict precisely how RE will affect state-level operations. There is considerable uncertainty regarding the locations of the RE development, as well as how contract terms can affect access to the inherent physical flexibility of the system. But the scenarios analyzed identify the types of issues that can arise under various RE and transmission

Enhancing the Internet with the CONVERGENCE system an information-centric network coupled with a standard middleware

CERN Document Server

Andrade, Maria; Melazzi, Nicola; Walker, Richard; Hussmann, Heinrich; Venieris, Iakovos

2014-01-01

Convergence proposes the enhancement of the Internet with a novel, content-centric, publish–subscribe service model based on the versatile digital item (VDI): a common container for all kinds of digital content, including digital representations of real-world resources. VDIs will serve the needs of the future Internet, providing a homogeneous method for handling structured information, incorporating security and privacy mechanisms. CONVERGENCE subsumes the following areas of research: ·         definition of the VDI as a new fundamental unit of distribution and transaction; ·         content-centric networking functionality to complement or replace IP-address-based routing; ·         security and privacy protection mechanisms; ·         open-source middleware, including a community dictionary service to enable rich semantic searches; ·         applications, tested under real-life conditions. This book shows how CONVERGENCE allows publishing, searching and subscri...

The Human - Nature Relationship i n t he Context o f Theo - Centric Environmental Ethics

Directory of Open Access Journals (Sweden)

Gülşen YAYLI

2015-07-01

Full Text Available The environmental problems are one of the issues that intensively occupy the agenda of humankind. This fact mainly derives from the ambiguity of the s pan and the content of the issue. The concept of environmental problems can not be confined to th e soil, air and water pollution for the reason that it covers a scope wider than a classical pollution issues. Initially the form of the relations hip between h uman and nature has been relying on the “consumption at the level of content” which stands for a level that is enough to sustain the living. The perception of the nature used to be described with the metaphor of mother while natural environment was defined as the “mother earth”. However subsequent to natural environment definition of the Cartesian philosophy with its approach to the human nature relationship, the core metaphor to describe the natural environment has changed from the metaphor of “mother” to the “slave” which should serve by any means. The human - nature relationship within the context of ethics, both the parties an d their respective statues bear an importance. In terms of ethics of human - nature relationship, it is possible to mention three main approaches. First one is the anthropo - centric approach. Within the scope of historical process, human - nature relationship is addressed according to anthropo - centric ethics comprehension so human has remained at the center of discussion. Following the change of the perception regarding the issue of environment, new approaches have emerged that give emphasis not only on human beings but also others; on li ving and non - living beings with in the eco - system. In principle, this represents a departure from an anthropo - centric ethics to a new ethic approach which fall s into two categories, bio centric and eco - centric. The theo - centric ethics should also be included to these ethics approaches that are shaped within the sphere of positive sciences. The Abrahamic

Preventing Network Centric Overload (End State Education for the Operational Commander/Staff)

National Research Council Canada - National Science Library

Beck, John

2001-01-01

.... An end state education system must be devised that prepares our senior leaders to operate a newly formed network centric task force with equipment, organizations and theory of use that most likely...

Integrating nitric oxide into salicylic acid and jasmonic acid/ethylene plant defense pathways

DEFF Research Database (Denmark)

Mur, Luis A J; Prats, Elena; Pierre, Sandra

2013-01-01

to be tailored to particular biotic stresses. Nitric oxide (NO) has emerged as a major signal influencing resistance mediated by both signalling pathways but no attempt has been made to integrate NO into established SA/JA/ET interactions. NO has been shown to act as an inducer or suppressor of signalling along......Plant defence against pests and pathogens is known to be conferred by either salicylic acid (SA) or jasmonic acid (JA)/ethylene (ET) pathways, depending on infection or herbivore-grazing strategy. It is well attested that SA and JA/ET pathways are mutually antagonistic allowing defence responses...

A Monte Carlo approach to the ship-centric Markov decision process for analyzing decisions over converting a containership to LNG power

NARCIS (Netherlands)

Kana, A.A.; Harrison, B.M.

2017-01-01

A Monte Carlo approach to the ship-centric Markov decision process (SC-MDP) is presented for analyzing whether a container ship should convert to LNG power in the face of evolving Emission Control Area regulations. The SC-MDP model was originally developed as a means to analyze uncertain,

Comprehensive School Mental Health: An Integrated "School-Based Pathway to Care" Model for Canadian Secondary Schools

Science.gov (United States)

Wei, Yifeng; Kutcher, Stan; Szumilas, Magdalena

2011-01-01

Adolescence is a critical period for the promotion of mental health and the treatment of mental disorders. Schools are well-positioned to address adolescent mental health. This paper describes a school mental health model, "School-Based Pathway to Care," for Canadian secondary schools that links schools with primary care providers and…

OptiCentric lathe centering machine

Science.gov (United States)

Buß, C.; Heinisch, J.

2013-09-01

High precision optics depend on precisely aligned lenses. The shift and tilt of individual lenses as well as the air gap between elements require accuracies in the single micron regime. These accuracies are hard to meet with traditional assembly methods. Instead, lathe centering can be used to machine the mount with respect to the optical axis. Using a diamond turning process, all relevant errors of single mounted lenses can be corrected in one post-machining step. Building on the OptiCentric® and OptiSurf® measurement systems, Trioptics has developed their first lathe centering machines. The machine and specific design elements of the setup will be shown. For example, the machine can be used to turn optics for i-line steppers with highest precision.

Evaluating between-pathway models with expression data.

Science.gov (United States)

Hescott, B J; Leiserson, M D M; Cowen, L J; Slonim, D K

2010-03-01

Between-pathway models (BPMs) are network motifs consisting of pairs of putative redundant pathways. In this article, we show how adding another source of high-throughput data--microarray gene expression data from knockout experiments--allows us to identify a compensatory functional relationship between genes from the two BPM pathways. We evaluate the quality of the BPMs from four different studies, and we describe how our methods might be extended to refine pathways.

Does Mobile Technology Matter? A Student Centric Perspective

OpenAIRE

Chen, Wenshin

2010-01-01

Based on a student-centric perspective, this study seeks to understand how mobile technology influences students’ learning experiences. Our research motivation is driven by the increasing attention paid to mobile technology in the research and business community. Set in a public university setting, our investigation seeks to shed light on how teaching and learning could be reshaped by mobile technology, most specifically, emerging tablet PCs. The findings, based on two MIS (Management Informa...

PumpKin: A tool to find principal pathways in plasma chemical models

Science.gov (United States)

Markosyan, A. H.; Luque, A.; Gordillo-Vázquez, F. J.; Ebert, U.

2014-10-01

PumpKin is a software package to find all principal pathways, i.e. the dominant reaction sequences, in chemical reaction systems. Although many tools are available to integrate numerically arbitrarily complex chemical reaction systems, few tools exist in order to analyze the results and interpret them in relatively simple terms. In particular, due to the large disparity in the lifetimes of the interacting components, it is often useful to group reactions into pathways that recycle the fastest species. This allows a researcher to focus on the slow chemical dynamics, eliminating the shortest timescales. Based on the algorithm described by Lehmann (2004), PumpKin automates the process of finding such pathways, allowing the user to analyze complex kinetics and to understand the consumption and production of a certain species of interest. We designed PumpKin with an emphasis on plasma chemical systems but it can also be applied to atmospheric modeling and to industrial applications such as plasma medicine and plasma-assisted combustion.

Can Cultural Behavior Have a Negative Impact on the Development of Visual Integration Pathways?

Science.gov (United States)

Pretorius, E.; Naude, H.; van Vuuren, C. J.

2002-01-01

Contends that cultural practices such as carrying the baby on the mother's back for prolonged periods can impact negatively on development of visual integration during the sensorimotor stage pathways by preventing adequate or enough crawling. Maintains that crawling is essential for cross- modality integration and that higher mental functions may…

Version control of pathway models using XML patches.

Science.gov (United States)

Saffrey, Peter; Orton, Richard

2009-03-17

Computational modelling has become an important tool in understanding biological systems such as signalling pathways. With an increase in size complexity of models comes a need for techniques to manage model versions and their relationship to one another. Model version control for pathway models shares some of the features of software version control but has a number of differences that warrant a specific solution. We present a model version control method, along with a prototype implementation, based on XML patches. We show its application to the EGF/RAS/RAF pathway. Our method allows quick and convenient storage of a wide range of model variations and enables a thorough explanation of these variations. Trying to produce these results without such methods results in slow and cumbersome development that is prone to frustration and human error.

Got risk? risk-centric perspective for spacecraft technology decision-making

Science.gov (United States)

Feather, Martin S.; Cornford, Steven L.; Moran, Kelly

2004-01-01

A risk-based decision-making methodology conceived and developed at JPL and NASA has been used to aid in decision making for spacecraft technology assessment, adoption, development and operation. It takes a risk-centric perspective, through which risks are used as a reasoning step to interpose between mission objectives and risk mitigation measures.

A distributed name resolution system in information centric networks

Science.gov (United States)

Elbreiki, Walid; Arlimatti, Shivaleela; Hassan, Suhaidi; Habbal, Adib; Elshaikh, Mohamed

2016-08-01

Information Centric Networks (ICN) is the new paradigm that envisages to shift the Internet away from its existing Point-to-Point architecture to a data centric, where communication is based on named hosts rather than the information stored on these hosts. Name Resolution is the center of attraction for ICN, where Named Data Objects (NDO) are used for identifying the information and guiding for routing or forwarding inside ICN. Recently, several researches use distributed NRS to overcome the problem of interest flooding, congestion and overloading. Yet the distribution of NRS is based on random distribution. How to distribute the NRS is still an important and challenging problem. In this work, we address the problem of distribution of NRS by proposing a new mechanism called Distributed Name Resolution System (DNRS), by considering the time of publishing the NDOs in the NRS. This mechanism partitions the network to distribute the workload among NRSs by increasing storage capacity. In addition, partitioning the network increases flexibility and scalability of NRS. We evaluate the effectiveness of our proposed mechanism, which achieves lesser end-to-end delay with more average throughputs compared to random distribution of NRS without disturbing the underlying routing or forwarding strategies.

Integrated Pathway-Based Approach Identifies Association between Genomic Regions at CTCF and CACNB2 and Schizophrenia

NARCIS (Netherlands)

Juraeva, Dilafruz; Haenisch, Britta; Zapatka, Marc; Frank, Josef; Witt, Stephanie H.; Mühleisen, Thomas W.; Treutlein, Jens; Strohmaier, Jana; Meier, Sandra; Degenhardt, Franziska; Giegling, Ina; Ripke, Stephan; Leber, Markus; Lange, Christoph; Schulze, Thomas G.; Mössner, Rainald; Nenadic, Igor; Sauer, Heinrich; Rujescu, Dan; Maier, Wolfgang; Børglum, Anders; Ophoff, Roel; Cichon, Sven; Nöthen, Markus M.; Rietschel, Marcella; Mattheisen, Manuel; Brors, Benedikt; Kahn, René S.; Cahn, Wiepke; Linszen, Don H.; de Haan, Lieuwe; van Os, Jim; Krabbendam, Lydia; Myin-Germeys, Inez; Wiersma, Durk; Bruggeman, Richard; Mors, O.; Børglum, A. D.; Mortensen, P. B.; Pedersen, C. B.; Demontis, D.; Grove, J.; Mattheisen, M.; Hougaard, D. M.

2014-01-01

In the present study, an integrated hierarchical approach was applied to: (1) identify pathways associated with susceptibility to schizophrenia; (2) detect genes that may be potentially affected in these pathways since they contain an associated polymorphism; and (3) annotate the functional

The effect of a customer-centric approach towards doctors in a private hospital / Mario van der Westhuizen

OpenAIRE

Van der Westhuizen, Mario

2014-01-01

Globally, trade and industry has shifted its focus from the traditional service delivery approaches to various alternative practices to be more successful, cost efficient, customer orientated, flexible and innovative. This shift in focus has lead to organisations applying a customer centric approach in their business. In order to understand customer centricity, it is necessary to be familiar with the term customer service. Customer service is the offering of services to customers before, d...

A Framework for Architecture-Based Planning and Assessment to Support Modeling and Simulation of Network-Centric Command and Control

Science.gov (United States)

2006-02-17

included system-unique specifications derived to counter these threats. But the international security environment has changed --- and it will continue... Netowrk -Centric Command and Control 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK...contains color images. 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 20 19a. NAME

Customer-­Centric Business Models for Smart Grid Development

OpenAIRE

Schabram, Sarah

2013-01-01

The digitalization of the electricity grid can provide politicians and different kinds of companies with solid benefits in terms of efficiency, renewable integration and control. However, some part of the deployment of smart grids is only possible with the engagement of consumers who are required to change their behavior significantly. This behavioral change can be induced if energy companies (incumbents and new players) adopt business models that do not sell a technology but use technology t...

Defence Adademies and Colleges 2009 International Conference. Network Centric Learning: Towards Authentic ePractices, 25 - 27 March 2009

Science.gov (United States)

2009-03-27

Keywords/phrases: Network-Centric Learning; Network-Centric Warfare& Security; student ICT skills; student engagement ; first year experience; faculty...learning policies supportive of strategies that scaffold staff and student engagement in TELT is also critical in an already stressful new environment...Generation ‘Y’ stereotyping for deploying VLE is likely to be problematic in terms of effective student engagement and the targeting of staff development. The

Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk.

Science.gov (United States)

Kar, Siddhartha P; Tyrer, Jonathan P; Li, Qiyuan; Lawrenson, Kate; Aben, Katja K H; Anton-Culver, Hoda; Antonenkova, Natalia; Chenevix-Trench, Georgia; Baker, Helen; Bandera, Elisa V; Bean, Yukie T; Beckmann, Matthias W; Berchuck, Andrew; Bisogna, Maria; Bjørge, Line; Bogdanova, Natalia; Brinton, Louise; Brooks-Wilson, Angela; Butzow, Ralf; Campbell, Ian; Carty, Karen; Chang-Claude, Jenny; Chen, Yian Ann; Chen, Zhihua; Cook, Linda S; Cramer, Daniel; Cunningham, Julie M; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; Dennis, Joe; Dicks, Ed; Doherty, Jennifer A; Dörk, Thilo; du Bois, Andreas; Dürst, Matthias; Eccles, Diana; Easton, Douglas F; Edwards, Robert P; Ekici, Arif B; Fasching, Peter A; Fridley, Brooke L; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G; Glasspool, Rosalind; Goode, Ellen L; Goodman, Marc T; Grownwald, Jacek; Harrington, Patricia; Harter, Philipp; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A T; Hillemanns, Peter; Hogdall, Estrid; Hogdall, Claus K; Hosono, Satoyo; Iversen, Edwin S; Jakubowska, Anna; Paul, James; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y; Kjaer, Susanne K; Kelemen, Linda E; Kellar, Melissa; Kelley, Joseph; Kiemeney, Lambertus A; Krakstad, Camilla; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D; Lee, Alice W; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A; Liang, Dong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R; McNeish, Iain A; Menon, Usha; Modugno, Francesmary; Moysich, Kirsten B; Narod, Steven A; Nedergaard, Lotte; Ness, Roberta B; Nevanlinna, Heli; Odunsi, Kunle; Olson, Sara H; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Pearce, Celeste Leigh; Pejovic, Tanja; Pelttari, Liisa M; Permuth-Wey, Jennifer; Phelan, Catherine M; Pike, Malcolm C; Poole, Elizabeth M; Ramus, Susan J; Risch, Harvey A; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H; Rudolph, Anja; Runnebaum, Ingo B; Rzepecka, Iwona K; Salvesen, Helga B; Schildkraut, Joellen M; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C; Sucheston-Campbell, Lara E; Tangen, Ingvild L; Teo, Soo-Hwang; Terry, Kathryn L; Thompson, Pamela J; Timorek, Agnieszka; Tsai, Ya-Yu; Tworoger, Shelley S; van Altena, Anne M; Van Nieuwenhuysen, Els; Vergote, Ignace; Vierkant, Robert A; Wang-Gohrke, Shan; Walsh, Christine; Wentzensen, Nicolas; Whittemore, Alice S; Wicklund, Kristine G; Wilkens, Lynne R; Woo, Yin-Ling; Wu, Xifeng; Wu, Anna; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Sellers, Thomas A; Monteiro, Alvaro N A; Freedman, Matthew L; Gayther, Simon A; Pharoah, Paul D P

2015-10-01

Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified by coexpression may also be enriched for additional EOC risk associations. We selected TF genes within 1 Mb of the top signal at the 12 genome-wide significant risk loci. Mutual information, a form of correlation, was used to build networks of genes strongly coexpressed with each selected TF gene in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls). Gene set enrichment analysis identified six networks centered on TF genes (HOXB2, HOXB5, HOXB6, HOXB7 at 17q21.32 and HOXD1, HOXD3 at 2q31) that were significantly enriched for genes from the risk-associated end of the ranked list (P < 0.05 and FDR < 0.05). These results were replicated (P < 0.05) using an independent association study (7,035 cases/21,693 controls). Genes underlying enrichment in the six networks were pooled into a combined network. We identified a HOX-centric network associated with serous EOC risk containing several genes with known or emerging roles in serous EOC development. Network analysis integrating large, context-specific datasets has the potential to offer mechanistic insights into cancer susceptibility and prioritize genes for experimental characterization. ©2015 American Association for Cancer Research.

Model integration and a theory of models

OpenAIRE

Dolk, Daniel R.; Kottemann, Jeffrey E.

1993-01-01

Model integration extends the scope of model management to include the dimension of manipulation as well. This invariably leads to comparisons with database theory. Model integration is viewed from four perspectives: Organizational, definitional, procedural, and implementational. Strategic modeling is discussed as the organizational motivation for model integration. Schema and process integration are examined as the logical and manipulation counterparts of model integr...

Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants

Directory of Open Access Journals (Sweden)

Subhasis eSamanta

2015-09-01

Full Text Available Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either increase or decrease the rate of transcription. Mediator complex is one such cofactor, and recently has drawn a lot of interest because of its integrative power to converge different signaling pathways before channelling the transcription instructions to the RNA polymerase II machinery. Like yeast and metazoans, plants do possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Genetic and molecular analyses have unravelled important regulatory roles of Mediator subunits at every stage of plant life cycle starting from flowering to embryo and organ development, to even size determination. It also contributes immensely to the survival of plants against different environmental vagaries by the timely activation of its resistance mechanisms. Here, we have provided an overview of plant Mediator complex starting from its discovery to regulation of stoichiometry of its subunits. We have also reviewed involvement of different Mediator subunits in different processes and pathways including defense response pathways evoked by diverse biotic cues. Wherever possible, attempts have been made to provide mechanistic insight of Mediator’s involvement in these processes.

Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants.

Science.gov (United States)

Samanta, Subhasis; Thakur, Jitendra K

2015-01-01

Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either increase or decrease the rate of transcription. Mediator complex is one such cofactor, and recently has drawn a lot of interest because of its integrative power to converge different signaling pathways before channeling the transcription instructions to the RNA polymerase II machinery. Like yeast and metazoans, plants do possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Genetic, and molecular analyses have unraveled important regulatory roles of Mediator subunits at every stage of plant life cycle starting from flowering to embryo and organ development, to even size determination. It also contributes immensely to the survival of plants against different environmental vagaries by the timely activation of its resistance mechanisms. Here, we have provided an overview of plant Mediator complex starting from its discovery to regulation of stoichiometry of its subunits. We have also reviewed involvement of different Mediator subunits in different processes and pathways including defense response pathways evoked by diverse biotic cues. Wherever possible, attempts have been made to provide mechanistic insight of Mediator's involvement in these processes.

Anonysense: privacy-aware people-centric sensing

DEFF Research Database (Denmark)

Triandopoulos, Nikolaos; Cornelius, Cory; Kapadia, Apu

2008-01-01

applications. For example, users' mobile phones may contribute data to community-oriented information services, from city-wide pollution monitoring to enterprise-wide detection of unauthorized Wi-Fi access points. This people-centric mobile-sensing model introduces a new security challenge in the design...... of mobile systems: protecting the privacy of participants while allowing their devices to reliably contribute high-quality data to these large-scale applications. We describe AnonySense, a privacy-aware architecture for realizing pervasive applications based on collaborative, opportunistic sensing...... by personal mobile devices. AnonySense allows applications to submit sensing tasks that will be distributed across anonymous participating mobile devices, later receiving verified, yet anonymized, sensor data reports back from the field, thus providing the first secure implementation of this participatory...

Supporting Elementary Education in-Service Teachers' Proficiency in Planning STEM-Centric Lessons

Science.gov (United States)

Bowers, Sharon W.

The purpose of this study was to explore the McDaniel College Elementary STEM Instructional Leader (ESIL) pilot cohort's ability to proficiently plan lessons that incorporated the Maryland State STEM Standards of Practice (SOP), targeting integration of STEM content, inquiry learning, students' abilities to collaborate as a STEM team and students' strategic application of technology. Data collection, in the form of reviewing and analyzing study participants' lesson plans and self-reflections, was completed by three independent assessors. The researcher examined the interrater reliability among the three assessors using the Fleiss' kappa statistic. A 0.91 proportion of agreement consensus was documented among the three assessors. A test of hypothetical value was conducted using the nonparametric Wilcoxonsigned- rank Test. Interpretation of the Wilcoxon-signed-rank Test results suggest that the sample population demonstrated proficient planning abilities for the four targeted Maryland State STEM SOP. Findings from this research add to the field's knowledge of elements in the promotion of graduate coursework that leads to elementary in-service teachers' proficiency in planning STEM-centric lessons, however the findings also have broader implications for teacher education at large. The McDaniel College ESIL model could frame K-12 teacher education for both preservice and in-service teachers. The pragmatic, hybrid experience maximizes flexibility, promotes analytical thinking and self-reflection and builds communication skills. The introduction and development of inquiry and design-based learning through the 7E Learning Cycle develops the teachers' understanding of practices promoted not only within the Maryland State STEM SOP, but also within the Next Generation Science Standards. The McDaniel College ESIL model also builds upon the collective efforts of academia, a non-profit STEM research facility, and local school divisions to align efforts that may lead to

Implementing an Interdisciplinary Student Centric Approach to Work-Integrated Learning

Science.gov (United States)

Marchioro, Gary; Ryan, Maria M.; Perkins, Tim

2014-01-01

This paper describes the implementation of an innovative approach to work-integrated learning using interdisciplinary projects within a university Faculty of Business. Further, it discusses the implementation of integrated and authentic assessments involving academic units in the marketing, urban planning and business communication disciplines.…

Cultural Competence and the Operational Commander: Moving Beyond Cultural Awareness into Culture-Centric Warfare

National Research Council Canada - National Science Library

Karcanes, James A

2007-01-01

.... Understanding the different levels of cultural awareness -- cultural consideration, cultural understanding, and cultural competence -- will help usher in a new focus on culture-centric warfare...

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.

Updates to the Corn Ethanol Pathway and Development of an Integrated Corn and Corn Stover Ethanol Pathway in the GREET™ Model

Energy Technology Data Exchange (ETDEWEB)

Wang, Zhichao [Argonne National Lab. (ANL), Argonne, IL (United States). Energy Systems Division; Dunn, Jennifer B. [Argonne National Lab. (ANL), Argonne, IL (United States). Energy Systems Division; Wang, Michael Q. [Argonne National Lab. (ANL), Argonne, IL (United States). Energy Systems Division

2014-09-01

Corn ethanol, a first-generation biofuel, is the predominant biofuel in the United States. In 2013, the total U.S. ethanol fuel production was 13.3 billion gallons, over 95% of which was produced from corn (RFA, 2014). The 2013 total renewable fuel mandate was 16.6 billion gallons according to the Energy Independence and Security Act (EISA) (U.S. Congress, 2007). Furthermore, until 2020, corn ethanol will make up a large portion of the renewable fuel volume mandated by Renewable Fuels Standard (RFS2). For the GREET1_2014 release, the corn ethanol pathway was subject to updates reflecting changes in corn agriculture and at corn ethanol plants. In the latter case, we especially focused on the incorporation of corn oil as a corn ethanol plant co-product. Section 2 covers these updates. In addition, GREET now includes options to integrate corn grain and corn stover ethanol production on the field and at the biorefinery. These changes are the focus of Section 3.

2005 Net Centric Operations, Interoperability and Systems Integration Conference - Facilitating Net Centric Operations and Warfare

Science.gov (United States)

2005-03-24

QoS to “the edge” – High bandwidth tactical ad-hoc mobile communications – Laser communications and high bandwidth RF relays – QoS management...Information Management Information Assurance Director, Information Assurance Cross- Cutting & Inter-Dependent Domains ASD(NII)/CIO leads Intelligence...Layer Common ServicesDCGS Integration Backbone (DIB) Data level – J2EE and the Metadata Framework ( MDF ) Application level – J2EE and the workflow engine

Solution of fractional kinetic equation by a class of integral transform of pathway type

Science.gov (United States)

Kumar, Dilip

2013-04-01

Solutions of fractional kinetic equations are obtained through an integral transform named Pα-transform introduced in this paper. The Pα-transform is a binomial type transform containing many class of transforms including the well known Laplace transform. The paper is motivated by the idea of pathway model introduced by Mathai [Linear Algebra Appl. 396, 317-328 (2005), 10.1016/j.laa.2004.09.022]. The composition of the transform with differential and integral operators are proved along with convolution theorem. As an illustration of applications to the general theory of differential equations, a simple differential equation is solved by the new transform. Being a new transform, the Pα-transform of some elementary functions as well as some generalized special functions such as H-function, G-function, Wright generalized hypergeometric function, generalized hypergeometric function, and Mittag-Leffler function are also obtained. The results for the classical Laplace transform is retrieved by letting α → 1.

Radiation protection of the environment: anthropocentric and eco-centric principles

International Nuclear Information System (INIS)

Alexakhin, R.M.; Fesenko, S.V.

2004-01-01

The second half of the 20. century was dominated in the field of radiation protection by the anthropocentric concept stated by the International Commission on Radiological Protection (ICRP). According to this concept 'if radiation standards protect man then biota are also adequately protected from ionizing radiation'. At the end of the 20. beginning of the 21. centuries in the area of radiation protection of nature an eco-centric strategy is beginning to develop where emphasis has swung to the protection of biota in their environment. Inadequacy of ICRP's anthropocentric concept is reported. Issues are discussed such as ecological dosimetry, non-equi-dose irradiation of man and biota, criteria for estimating radiation induced changes in biota and man, as well as the need to harmonize permissible exposure doses to man and biota. An urgent need is stressed to develop a single (synthetic) concept of radiation protection which simultaneously ensures protection of human health and biota well-being in their environment. This concept is to be based on the recognition of the integrity of socio-natural ecosystems where man and biota are considered as a unity. (author)

Bridging the Gap in Port Security; Network Centric Theory Applied to Public/Private Collaboration

National Research Council Canada - National Science Library

Wright, Candice L

2007-01-01

...." Admiral Thad Allen, 2007 The application of Network Centric Warfare theory enables all port stakeholders to better prepare for a disaster through increased information sharing and collaboration...

On a User-Centric Base Station Cooperation Scheme for Reliable Communications

DEFF Research Database (Denmark)

Kim, Dong Min; Thomsen, Henning; Popovski, Petar

2017-01-01

In this paper, we describe CoMP2flex, a user-centric base station (BS) cooperation scheme that provides improvements in reliability of both uplink (UL) and downlink (DL) communications of wireless cellular networks. CoMP2flex supports not only cooperation of two BSs with same direction of traffic...

Weather-centric rangeland revegetation planning

Science.gov (United States)

Hardegree, Stuart P.; Abatzoglou, John T.; Brunson, Mark W.; Germino, Matthew; Hegewisch, Katherine C.; Moffet, Corey A.; Pilliod, David S.; Roundy, Bruce A.; Boehm, Alex R.; Meredith, Gwendwr R.

2018-01-01

Invasive annual weeds negatively impact ecosystem services and pose a major conservation threat on semiarid rangelands throughout the western United States. Rehabilitation of these rangelands is challenging due to interannual climate and subseasonal weather variability that impacts seed germination, seedling survival and establishment, annual weed dynamics, wildfire frequency, and soil stability. Rehabilitation and restoration outcomes could be improved by adopting a weather-centric approach that uses the full spectrum of available site-specific weather information from historical observations, seasonal climate forecasts, and climate-change projections. Climate data can be used retrospectively to interpret success or failure of past seedings by describing seasonal and longer-term patterns of environmental variability subsequent to planting. A more detailed evaluation of weather impacts on site conditions may yield more flexible adaptive-management strategies for rangeland restoration and rehabilitation, as well as provide estimates of transition probabilities between desirable and undesirable vegetation states. Skillful seasonal climate forecasts could greatly improve the cost efficiency of management treatments by limiting revegetation activities to time periods where forecasts suggest higher probabilities of successful seedling establishment. Climate-change projections are key to the application of current environmental models for development of mitigation and adaptation strategies and for management practices that require a multidecadal planning horizon. Adoption of new weather technology will require collaboration between land managers and revegetation specialists and modifications to the way we currently plan and conduct rangeland rehabilitation and restoration in the Intermountain West.

Comparative evaluation of the efficacy of occlusal splints fabricated in centric relation or maximum intercuspation in temporomandibular disorders patients

OpenAIRE

Hamata,Marcelo Matida; Zuim,Paulo Renato Junqueira; Garcia,Alicio Rosalino

2009-01-01

Fabrication of occlusal splints in centric relation for temporomandibular disorders (TMD) patients is arguable, since this position has been defined for asymptomatic stomatognathic system. Thus, maximum intercuspation might be employed in patients with occlusal stability, eliminating the need for interocclusal records. This study compared occlusal splints fabricated in centric relation and maximum intercuspation in muscle pain reduction of TMD patients. Twenty patients with TMD of myogenous o...

Application of process monitoring to anomaly detection in nuclear material processing systems via system-centric event interpretation of data from multiple sensors of varying reliability

International Nuclear Information System (INIS)

Garcia, Humberto E.; Simpson, Michael F.; Lin, Wen-Chiao; Carlson, Reed B.; Yoo, Tae-Sic

2017-01-01

Highlights: • Process monitoring can strengthen nuclear safeguards and material accountancy. • Assessment is conducted at a system-centric level to improve safeguards effectiveness. • Anomaly detection is improved by integrating process and operation relationships. • Decision making is benefited from using sensor and event sequence information. • Formal framework enables optimization of sensor and data processing resources. - Abstract: In this paper, we apply an advanced safeguards approach and associated methods for process monitoring to a hypothetical nuclear material processing system. The assessment regarding the state of the processing facility is conducted at a system-centric level formulated in a hybrid framework. This utilizes architecture for integrating both time- and event-driven data and analysis for decision making. While the time-driven layers of the proposed architecture encompass more traditional process monitoring methods based on time series data and analysis, the event-driven layers encompass operation monitoring methods based on discrete event data and analysis. By integrating process- and operation-related information and methodologies within a unified framework, the task of anomaly detection is greatly improved. This is because decision-making can benefit from not only known time-series relationships among measured signals but also from known event sequence relationships among generated events. This available knowledge at both time series and discrete event layers can then be effectively used to synthesize observation solutions that optimally balance sensor and data processing requirements. The application of the proposed approach is then implemented on an illustrative monitored system based on pyroprocessing and results are discussed.

The Norrtaelje model: a unique model for integrated health and social care in Sweden.

Science.gov (United States)

Bäck, Monica Andersson; Calltorp, Johan

2015-01-01

Many countries organise and fund health and social care separately. The Norrtaelje model is a Swedish initiative that transformed the funding and organisation of health and social care in order to better integrate care for older people with complex needs. In Norrtaelje model, this transformation made it possible to bringing the team together, to transfer responsibility to different providers, to use care coordinators, and to develop integrated pathways and plans around transitions in and out of hospital and from nursing homes to hospital. The Norrtaelje model operates in the context of the Swedish commitment to universal coverage and public programmes based on tax-funded resources that are pooled and redistributed to citizens on the basis of need. The experience of Norrtaelje model suggests that one way to promote integration of health and social care is to start with a transformation that aligns these two sectors in terms of high level organisation and funding. This transformation then enables the changes in operations and management that can be translated into changes in care delivery. This "top-down" approach must be in-line with national priorities and policies but ultimately is successful only if the culture, resource allocation and management are changed throughout the local system.

Position-specific isotope modeling of organic micropollutants transformations through different reaction pathways

Science.gov (United States)

Jin, Biao; Rolle, Massimo

2016-04-01

Organic compounds are produced in vast quantities for industrial and agricultural use, as well as for human and animal healthcare [1]. These chemicals and their metabolites are frequently detected at trace levels in fresh water environments where they undergo degradation via different reaction pathways. Compound specific stable isotope analysis (CSIA) is a valuable tool to identify such degradation pathways in different environmental systems. Recent advances in analytical techniques have promoted the fast development and implementation of multi-element CSIA. However, quantitative frameworks to evaluate multi-element stable isotope data and incorporating mechanistic information on the degradation processes [2,3] are still lacking. In this study we propose a mechanism-based modeling approach to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. We validate the proposed approach with the concentration and multi-element isotope data of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model precisely captures the dual element isotope trends characteristic of different reaction pathways and their range of variation consistent with observed multi-element (C, N) bulk isotope fractionation. The proposed approach can also be used as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. [1] Schwarzenbach, R.P., Egli, T., Hofstetter, T.B., von Gunten, U., Wehrli, B., 2010. Global Water Pollution and Human Health. Annu. Rev. Environ. Resour. doi:10.1146/annurev-environ-100809-125342. [2] Jin, B., Haderlein, S.B., Rolle, M

Bridging the Gap Between the Social and the Technical: The Enrolment of Socio-Technical Information Architects to Cope with the Two-Level Model of EPR Systems.

Science.gov (United States)

Pedersen, Rune

2017-01-01

This is a project proposal derived from an urge to re-define the governance of ICT in healthcare towards regional and national standardization of the patient pathways. The focus is on a two-levelled approach for governing EPR systems where the clinicians' model structured variables and patient pathways. The overall goal is a patient centric EPR portfolio. This paper define and enlighten the need for establishing the socio- technical architect role necessary to obtain the capabilities of a modern structured EPR system. Clinicians are not capable to moderate between the technical and the clinical.

A Computational Model of a Descending Mechanosensory Pathway Involved in Active Tactile Sensing.

Directory of Open Access Journals (Sweden)

Jan M Ache

2015-07-01

Full Text Available Many animals, including humans, rely on active tactile sensing to explore the environment and negotiate obstacles, especially in the dark. Here, we model a descending neural pathway that mediates short-latency proprioceptive information from a tactile sensor on the head to thoracic neural networks. We studied the nocturnal stick insect Carausius morosus, a model organism for the study of adaptive locomotion, including tactually mediated reaching movements. Like mammals, insects need to move their tactile sensors for probing the environment. Cues about sensor position and motion are therefore crucial for the spatial localization of tactile contacts and the coordination of fast, adaptive motor responses. Our model explains how proprioceptive information about motion and position of the antennae, the main tactile sensors in insects, can be encoded by a single type of mechanosensory afferents. Moreover, it explains how this information is integrated and mediated to thoracic neural networks by a diverse population of descending interneurons (DINs. First, we quantified responses of a DIN population to changes in antennal position, motion and direction of movement. Using principal component (PC analysis, we find that only two PCs account for a large fraction of the variance in the DIN response properties. We call the two-dimensional space spanned by these PCs 'coding-space' because it captures essential features of the entire DIN population. Second, we model the mechanoreceptive input elements of this descending pathway, a population of proprioceptive mechanosensory hairs monitoring deflection of the antennal joints. Finally, we propose a computational framework that can model the response properties of all important DIN types, using the hair field model as its only input. This DIN model is validated by comparison of tuning characteristics, and by mapping the modelled neurons into the two-dimensional coding-space of the real DIN population. This

Comparison of Perturbed Pathways in Two Different Cell Models for Parkinson's Disease with Structural Equation Model.

Science.gov (United States)

Pepe, Daniele; Do, Jin Hwan

2015-12-16

Increasing evidence indicates that different morphological types of cell death coexist in the brain of patients with Parkinson's disease (PD), but the molecular explanation for this is still under investigation. In this study, we identified perturbed pathways in two different cell models for PD through the following procedures: (1) enrichment pathway analysis with differentially expressed genes and the Reactome pathway database, and (2) construction of the shortest path model for the enriched pathway and detection of significant shortest path model with fitting time-course microarray data of each PD cell model to structural equation model. Two PD cell models constructed by the same neurotoxin showed different perturbed pathways. That is, one showed perturbation of three Reactome pathways, including cellular senescence, chromatin modifying enzymes, and chromatin organization, while six modules within metabolism pathway represented perturbation in the other. This suggests that the activation of common upstream cell death pathways in PD may result in various down-stream processes, which might be associated with different morphological types of cell death. In addition, our results might provide molecular clues for coexistence of different morphological types of cell death in PD patients.

Enhancing network centric operations doctrine to support civil military cooperation in disaster management

NARCIS (Netherlands)

Wolbers, J.J.; Beeres, R.; Bakx, G.; de Waard, E.; Rietjens, S.

2016-01-01

Network Centric Operations is a promising command doctrine in both military operations and during civil disaster management. As both sectors started intensifying their joint operational capacity through civil-military collaboration, it becomes increasingly relevant to address the different command

An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization.

Science.gov (United States)

Halper, Sean M; Cetnar, Daniel P; Salis, Howard M

2018-01-01

Engineering many-enzyme metabolic pathways suffers from the design curse of dimensionality. There are an astronomical number of synonymous DNA sequence choices, though relatively few will express an evolutionary robust, maximally productive pathway without metabolic bottlenecks. To solve this challenge, we have developed an integrated, automated computational-experimental pipeline that identifies a pathway's optimal DNA sequence without high-throughput screening or many cycles of design-build-test. The first step applies our Operon Calculator algorithm to design a host-specific evolutionary robust bacterial operon sequence with maximally tunable enzyme expression levels. The second step applies our RBS Library Calculator algorithm to systematically vary enzyme expression levels with the smallest-sized library. After characterizing a small number of constructed pathway variants, measurements are supplied to our Pathway Map Calculator algorithm, which then parameterizes a kinetic metabolic model that ultimately predicts the pathway's optimal enzyme expression levels and DNA sequences. Altogether, our algorithms provide the ability to efficiently map the pathway's sequence-expression-activity space and predict DNA sequences with desired metabolic fluxes. Here, we provide a step-by-step guide to applying the Pathway Optimization Pipeline on a desired multi-enzyme pathway in a bacterial host.

Integrating computational methods to retrofit enzymes to synthetic pathways.

Science.gov (United States)

Brunk, Elizabeth; Neri, Marilisa; Tavernelli, Ivano; Hatzimanikatis, Vassily; Rothlisberger, Ursula

2012-02-01

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target compounds with high yields and turnover rates. We use integrated computational methods to generate and quantify the performance of novel biosynthetic routes that contain highly optimized catalysts. Engineering a novel reaction pathway entails addressing feasibility on multiple levels, which involves handling the complexity of large-scale biochemical networks while respecting the critical chemical phenomena at the atomistic scale. To pursue this multi-layer challenge, our strategy merges knowledge-based metabolic engineering methods with computational chemistry methods. By bridging multiple disciplines, we provide an integral computational framework that could accelerate the discovery and implementation of novel biosynthetic production routes. Using this approach, we have identified and optimized a novel biosynthetic route for the production of 3HP from pyruvate. Copyright © 2011 Wiley Periodicals, Inc.

Representative Agricultural Pathways: A Trans-Disciplinary Approach to Agricultural Model Inter-comparison, Improvement, Climate Impact Assessment and Stakeholder Engagement

Science.gov (United States)

Antle, J. M.; Valdivia, R. O.; Claessens, L.; Nelson, G. C.; Rosenzweig, C.; Ruane, A. C.; Vervoort, J.

2013-12-01

The global change research community has recognized that new pathway and scenario concepts are needed to implement impact and vulnerability assessment that is logically consistent across local, regional and global scales. For impact and vulnerability assessment, new socio-economic pathway and scenario concepts are being developed. Representative Agricultural Pathways (RAPs) are designed to extend global pathways to provide the detail needed for global and regional assessment of agricultural systems. In addition, research by the Agricultural Model Inter-comparison and Improvement Project (AgMIP) shows that RAPs provide a powerful way to engage stakeholders in climate-related research throughout the research process and in communication of research results. RAPs are based on the integrated assessment framework developed by AgMIP. This framework shows that both bio-physical and socio-economic drivers are essential components of agricultural pathways and logically precede the definition of adaptation and mitigation scenarios that embody associated capabilities and challenges. This approach is based on a trans-disciplinary process for designing pathways and then translating them into parameter sets for bio-physical and economic models that are components of agricultural integrated assessments of climate impact, adaptation and mitigation. RAPs must be designed to be part of a logically consistent set of drivers and outcomes from global to regional and local. Global RAPs are designed to be consistent with higher-level global socio-economic pathways, but add key agricultural drivers such as agricultural growth trends that are not specified in more general pathways, as illustrated in a recent inter-comparison of global agricultural models. To create pathways at regional or local scales, further detail is needed. At this level, teams of scientists and other experts with knowledge of the agricultural systems and regions work together through a step-wise process. Experiences

Testing an integral conceptual model of frailty.

Science.gov (United States)

Gobbens, Robbert J; van Assen, Marcel A; Luijkx, Katrien G; Schols, Jos M

2012-09-01

This paper is a report of a study conducted to test three hypotheses derived from an integral conceptual model of frailty.   The integral model of frailty describes the pathway from life-course determinants to frailty to adverse outcomes. The model assumes that life-course determinants and the three domains of frailty (physical, psychological, social) affect adverse outcomes, the effect of disease(s) on adverse outcomes is mediated by frailty, and the effect of frailty on adverse outcomes depends on the life-course determinants. In June 2008 a questionnaire was sent to a sample of community-dwelling people, aged 75 years and older (n = 213). Life-course determinants and frailty were assessed using the Tilburg frailty indicator. Adverse outcomes were measured using the Groningen activity restriction scale, the WHOQOL-BREF and questions regarding healthcare utilization. The effect of seven self-reported chronic diseases was examined. Life-course determinants, chronic disease(s), and frailty together explain a moderate to large part of the variance of the seven continuous adverse outcomes (26-57%). All these predictors together explained a significant part of each of the five dichotomous adverse outcomes. The effect of chronic disease(s) on all 12 adverse outcomes was mediated at least partly by frailty. The effect of frailty domains on adverse outcomes did not depend on life-course determinants. Our finding that the adverse outcomes are differently and uniquely affected by the three domains of frailty (physical, psychological, social), and life-course determinants and disease(s), emphasizes the importance of an integral conceptual model of frailty. © 2011 Blackwell Publishing Ltd.

Designing a Care Pathway Model - A Case Study of the Outpatient Total Hip Arthroplasty Care Pathway.

Science.gov (United States)

Oosterholt, Robin I; Simonse, Lianne Wl; Boess, Stella U; Vehmeijer, Stephan Bw

2017-03-09

Although the clinical attributes of total hip arthroplasty (THA) care pathways have been thoroughly researched, a detailed understanding of the equally important organisational attributes is still lacking. The aim of this article is to contribute with a model of the outpatient THA care pathway that depicts how the care team should be organised to enable patient discharge on the day of surgery. The outpatient THA care pathway enables patients to be discharged on the day of surgery, shortening the length of stay and intensifying the provision and organisation of care. We utilise visual care modelling to construct a visual design of the organisation of the care pathway. An embedded case study was conducted of the outpatient THA care pathway at a teaching hospital in the Netherlands. The data were collected using a visual care modelling toolkit in 16 semi-structured interviews. Problems and inefficiencies in the care pathway were identified and addressed in the iterative design process. The results are two visual models of the most critical phases of the outpatient THA care pathway: diagnosis & preparation (1) and mobilisation & discharge (4). The results show the care team composition, critical value exchanges, and sequence that enable patient discharge on the day of surgery. The design addressed existing problems and is an optimisation of the case hospital's pathway. The network of actors consists of the patient (1), radiologist (1), anaesthetist (1), nurse specialist (1), pharmacist (1), orthopaedic surgeon (1,4), physiotherapist (1,4), nurse (4), doctor (4) and patient application (1,4). The critical value exchanges include patient preparation (mental and practical), patient education, aligned care team, efficient sequence of value exchanges, early patient mobilisation, flexible availability of the physiotherapist, functional discharge criteria, joint decision making and availability of the care team.

The Dangers of Test Preparation: What Students Learn (And Don't Learn) about Reading Comprehension from Test-Centric Literacy Instruction

Science.gov (United States)

Davis, Dennis S.; Vehabovic, Nermin

2018-01-01

The authors offer guidance on recognizing and resisting test-centric instruction in reading comprehension. They posit that five practices indicate a test-centric view of comprehension: when the tested content is privileged, when the test becomes the text, when annotation requirements replace strategic thinking, when test items frame how students…

Constructing disease-centric knowledge graphs : A case study for depression (short version)

NARCIS (Netherlands)

Huang, Zhisheng; Yang, Jie; van Harmelen, Frank; Hu, Qing

2017-01-01

In this paper we show how we used multiple large knowledge sources to construct a much smaller knowledge graph that is focussed on single disease (in our case major depression disorder). Such a disease-centric knowledge-graph makes it more convenient for doctors (in our case psychiatric doctors) to

Building executable biological pathway models automatically from BioPAX

NARCIS (Netherlands)

Willemsen, Timo; Feenstra, Anton; Groth, Paul

2013-01-01

The amount of biological data exposed in semantic formats is steadily increasing. In particular, pathway information (a model of how molecules interact within a cell) from databases such as KEGG and WikiPathways are available in a standard RDF-based format BioPAX. However, these models are

Bringing service design to manufacturing companies: integrating PSS and service design approaches

DEFF Research Database (Denmark)

Costa, Nina; Patrício, Lia; Morelli, Nicola

2018-01-01

in a manufacturing industry. This paper details how the application supports the design of product–service system solutions from the exploration to the implementation stages, highlighting the physical evidence of service, and contributes to advance design research at the intersection of PSS and Service Design.......Manufacturing companies increasingly try to innovate in their offers to consumers by creating more complete solutions that combine product and service components. However, shifting from a product-centric perspective to a solution-oriented perspective is challenging. The present study adopted...... a design research methodology and built on Service-Dominant logic, integrating the human-oriented perspective of Service Design with an organizational network-oriented perspective of Product–Service System. It creates a new Integrative PSS approach, evolves design models, and provides an application...

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.

LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models.

Science.gov (United States)

Soto, Axel J; Zerva, Chrysoula; Batista-Navarro, Riza; Ananiadou, Sophia

2018-04-15

Pathway models are valuable resources that help us understand the various mechanisms underpinning complex biological processes. Their curation is typically carried out through manual inspection of published scientific literature to find information relevant to a model, which is a laborious and knowledge-intensive task. Furthermore, models curated manually cannot be easily updated and maintained with new evidence extracted from the literature without automated support. We have developed LitPathExplorer, a visual text analytics tool that integrates advanced text mining, semi-supervised learning and interactive visualization, to facilitate the exploration and analysis of pathway models using statements (i.e. events) extracted automatically from the literature and organized according to levels of confidence. LitPathExplorer supports pathway modellers and curators alike by: (i) extracting events from the literature that corroborate existing models with evidence; (ii) discovering new events which can update models; and (iii) providing a confidence value for each event that is automatically computed based on linguistic features and article metadata. Our evaluation of event extraction showed a precision of 89% and a recall of 71%. Evaluation of our confidence measure, when used for ranking sampled events, showed an average precision ranging between 61 and 73%, which can be improved to 95% when the user is involved in the semi-supervised learning process. Qualitative evaluation using pair analytics based on the feedback of three domain experts confirmed the utility of our tool within the context of pathway model exploration. LitPathExplorer is available at http://nactem.ac.uk/LitPathExplorer_BI/. sophia.ananiadou@manchester.ac.uk. Supplementary data are available at Bioinformatics online.

A method of demand-driven and data-centric Web service configuration for flexible business process implementation

Science.gov (United States)

Xu, Boyi; Xu, Li Da; Fei, Xiang; Jiang, Lihong; Cai, Hongming; Wang, Shuai

2017-08-01

Facing the rapidly changing business environments, implementation of flexible business process is crucial, but difficult especially in data-intensive application areas. This study aims to provide scalable and easily accessible information resources to leverage business process management. In this article, with a resource-oriented approach, enterprise data resources are represented as data-centric Web services, grouped on-demand of business requirement and configured dynamically to adapt to changing business processes. First, a configurable architecture CIRPA involving information resource pool is proposed to act as a scalable and dynamic platform to virtualise enterprise information resources as data-centric Web services. By exposing data-centric resources as REST services in larger granularities, tenant-isolated information resources could be accessed in business process execution. Second, dynamic information resource pool is designed to fulfil configurable and on-demand data accessing in business process execution. CIRPA also isolates transaction data from business process while supporting diverse business processes composition. Finally, a case study of using our method in logistics application shows that CIRPA provides an enhanced performance both in static service encapsulation and dynamic service execution in cloud computing environment.

Not para-, not peri-, but centric inversion of chromosome 12

DEFF Research Database (Denmark)

Silahtaroglu, A N; Hacihanefioglu, S; Güven, G S

1998-01-01

a break in the alphoid repeats followed by an inversion within the short arm, resulting in a pseudodicentric chromosome. Further FISH analyses using telomeric and subtelomeric probes showed that the other breakpoint was in the subtelomeric region of the short arm. The karyotype is designated 47,XXY,inv(12......)(p10p13.3). To our knowledge this is the first report of a case of "centric inversion"....

Modeling energy-economy interactions using integrated models

International Nuclear Information System (INIS)

Uyterlinde, M.A.

1994-06-01

Integrated models are defined as economic energy models that consist of several submodels, either coupled by an interface module, or embedded in one large model. These models can be used for energy policy analysis. Using integrated models yields the following benefits. They provide a framework in which energy-economy interactions can be better analyzed than in stand-alone models. Integrated models can represent both energy sector technological details, as well as the behaviour of the market and the role of prices. Furthermore, the combination of modeling methodologies in one model can compensate weaknesses of one approach with strengths of another. These advantages motivated this survey of the class of integrated models. The purpose of this literature survey therefore was to collect and to present information on integrated models. To carry out this task, several goals were identified. The first goal was to give an overview of what is reported on these models in general. The second one was to find and describe examples of such models. Other goals were to find out what kinds of models were used as component models, and to examine the linkage methodology. Solution methods and their convergence properties were also a subject of interest. The report has the following structure. In chapter 2, a 'conceptual framework' is given. In chapter 3 a number of integrated models is described. In a table, a complete overview is presented of all described models. Finally, in chapter 4, the report is summarized, and conclusions are drawn regarding the advantages and drawbacks of integrated models. 8 figs., 29 refs

40-Gb/s all-optical processing systems using hybrid photonic integration technology

DEFF Research Database (Denmark)

Kehayas, E.; Tsiokos, D.I.; Bakopoulos, P.

2006-01-01

the potential that all-optical technology can find application in future data-centric networks with efficient and dynamic bandwidth utilization. This paper also reports on the latest photonic integration breakthroughs as a potential migration path for reducing fabrication cost by developing photonic systems...

Mathematical modeling of the Phoenix Rising pathway.

Directory of Open Access Journals (Sweden)

Chad Liu

2014-02-01

Full Text Available Apoptosis is a tightly controlled process in mammalian cells. It is important for embryogenesis, tissue homoeostasis, and cancer treatment. Apoptosis not only induces cell death, but also leads to the release of signals that promote rapid proliferation of surrounding cells through the Phoenix Rising (PR pathway. To quantitatively understand the kinetics of interactions of different molecules in this pathway, we developed a mathematical model to simulate the effects of various changes in the PR pathway on the secretion of prostaglandin E2 (PGE2, a key factor for promoting cell proliferation. These changes include activation of caspase 3 (C3, caspase 7 (C7, and nuclear factor κB (NFκB. In addition, we simulated the effects of cyclooxygenase-2 (COX2 inhibition and C3 knockout on the level of secreted PGE2. The model predictions on PGE2 in MEF and 4T1 cells at 48 hours after 10-Gray radiation were quantitatively consistent with the experimental data in the literature. Compared to C7, the model predicted that C3 activation was more critical for PGE2 production. The model also predicted that PGE2 production could be significantly reduced when COX2 expression was blocked via either NFκB inactivation or treatment of cells with exogenous COX2 inhibitors, which led to a decrease in the rate of conversion from arachidonic acid to prostaglandin H2 in the PR pathway. In conclusion, the mathematical model developed in this study yielded new insights into the process of tissue regrowth stimulated by signals from apoptotic cells. In future studies, the model can be used for experimental data analysis and assisting development of novel strategies/drugs for improving cancer treatment or normal tissue regeneration.

Hydroacoustic Studies Using HydroCAM - Station-centric Integration of Models and Observations Quarterly Report No.4 July 2003 - September 2003

International Nuclear Information System (INIS)

Upton, Zachary M.; Pulli, Jay J.

2003-01-01

OAK B272 Quarterly technical report summarizing BBN's efforts to improve DOE's hydroacoustic modeling and analysis capability for nuclear explosion monitoring. BBN's work during the third quarter of 2003 was focused on preparations for and participation in the 2003 Seismic Research Review Meeting, unit testing and bug fixes to HydroCAM 4.1, data collection and analysis, and procuring high-resolution bathymetric data. In an attempt to save money, BBN scaled back its labor in the third quarter, delaying some deliverables but saving contract funding in case our next increment is delayed. We have succeeded in finding the correct Naval contact that can help us procure high-resolution bathymetry data. Although these data may require the release of a classified version of HydroCAM, we are optimistic that we will be able to acquire and integrate high-resolution bathymetric data near the Indian Ocean IMS stations. HydroCAM 4.1, which includes the ability to make blockage predictions using varying resolution bathymetric data, has completed unit testing and is now under integration (release) testing. We hope to deliver that functionality to DOE and AFTAC in November. BBN improved its database of hydroacoustic events in the Indian Ocean by including meta-data for associated arrivals. For each earthquake event, BBN is now picking the direct arrival at each station (Diego Garcia North and South, and Cape Leeuwin) and associating that arrival with the origin information that we are compiling. The data for 2001, 2002 and 2003 (to date) will be delivered to LLNL for integration into the Knowledge Base during the fourth quarter of 2003

Modelling and Analysis of Biochemical Signalling Pathway Cross-talk

Directory of Open Access Journals (Sweden)

Robin Donaldson

2010-02-01

Full Text Available Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical in producing the correct signal-response relationship. Formal models of signalling pathways and cross-talk in particular can aid understanding and drive experimentation. We define an approach to modelling based on the concept that a pathway is the (synchronising parallel composition of instances of generic modules (with internal and external labels. Pathways are then composed by (synchronising parallel composition and renaming; different types of cross-talk result from different combinations of synchronisation and renaming. We define a number of generic modules in PRISM and five types of cross-talk: signal flow, substrate availability, receptor function, gene expression and intracellular communication. We show that Continuous Stochastic Logic properties can both detect and distinguish the types of cross-talk. The approach is illustrated with small examples and an analysis of the cross-talk between the TGF-b/BMP, WNT and MAPK pathways.

Integrated Assessment of Shallow-Aquifer Vulnerability to Multiple Contaminants and Drinking-Water Exposure Pathways in Holliston, Massachusetts

Directory of Open Access Journals (Sweden)

Birgit Claus Henn

2017-12-01

Full Text Available Half of U.S. drinking water comes from aquifers, and very shallow ones (<20 feet to water table are especially vulnerable to anthropogenic contamination. We present the case of Holliston, a Boston, Massachusetts suburb that draws its drinking water from very shallow aquifers, and where metals and solvents have been reported in groundwater. Community concerns focus on water discolored by naturally occurring manganese (Mn, despite reports stating regulatory aesthetic compliance. Epidemiologic studies suggest Mn is a potentially toxic element (PTE for children exposed by the drinking-water pathway at levels near the regulatory aesthetic level. We designed an integrated, community-based project: five sites were profiled for contaminant releases; service areas for wells were modeled; and the capture zone for one vulnerable well was estimated. Manganese, mercury, and trichloroethylene are among 20 contaminants of interest. Findings show that past and/or current exposures to multiple contaminants in drinking water are plausible, satisfying the criteria for complete exposure pathways. This case questions the adequacy of aquifer protection and monitoring regulations, and highlights the need for integrated assessment of multiple contaminants, associated exposures and health risks. It posits that community-researcher partnerships are essential for understanding and solving complex problems.

A Quest for Missing Proteins : update 2015 on Chromosome-Centric Human Proteome Project

NARCIS (Netherlands)

Horvatovich, Péter; Lundberg, Emma K; Chen, Yu-Ju; Sung, Ting-Yi; He, Fuchu; Nice, Edouard C; Goode, Robert J A; Yu, Simon; Ranganathan, Shoba; Baker, Mark S; Domont, Gilberto B; Velasquez, Erika; Li, Dong; Liu, Siqi; Wang, Quanhui; He, Qing-Yu; Menon, Rajasree; Guan, Yuanfang; Corrales, Fernando Jose; Segura, Victor; Casal, José Ignacio; Pascual-Montano, Alberto; Albar, Juan Pablo; Fuentes, Manuel; Gonzalez-Gonzalez, Maria; Diez, Paula; Ibarrola, Nieves; Degano, Rosa M; Mohammed, Yassene; Borchers, Christoph H; Urbani, Andrea; Soggiu, Alessio; Yamamoto, Tadashi; Archakov, Alexander I; Ponomarenko, Elena; Lisitsa, Andrey V; Lichti, Cheryl F; Mostovenko, Ekaterina; Kroes, Roger A; Rezeli, Melinda; Vegvari, Akos; Fehniger, Thomas E; Bischoff, Rainer; Vizcaíno, Juan Antonio; Deutsch, Eric W; Lane, Lydie; Nilsson, Carol L; Marko-Varga, György; Omenn, Gilbert S; Jeong, Seul-Ki; Cho, Jin-Young; Paik, Young-Ki; Hancock, William S

2015-01-01

This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level

User Interface Requirements for Web-Based Integrated Care Pathways: Evidence from the Evaluation of an Online Care Pathway Investigation Tool.

Science.gov (United States)

Balatsoukas, Panos; Williams, Richard; Davies, Colin; Ainsworth, John; Buchan, Iain

2015-11-01

Integrated care pathways (ICPs) define a chronological sequence of steps, most commonly diagnostic or treatment, to be followed in providing care for patients. Care pathways help to ensure quality standards are met and to reduce variation in practice. Although research on the computerisation of ICP progresses, there is still little knowledge on what are the requirements for designing user-friendly and usable electronic care pathways, or how users (normally health care professionals) interact with interfaces that support design, analysis and visualisation of ICPs. The purpose of the study reported in this paper was to address this gap by evaluating the usability of a novel web-based tool called COCPIT (Collaborative Online Care Pathway Investigation Tool). COCPIT supports the design, analysis and visualisation of ICPs at the population level. In order to address the aim of this study, an evaluation methodology was designed based on heuristic evaluations and a mixed method usability test. The results showed that modular visualisation and direct manipulation of information related to the design and analysis of ICPs is useful for engaging and stimulating users. However, designers should pay attention to issues related to the visibility of the system status and the match between the system and the real world, especially in relation to the display of statistical information about care pathways and the editing of clinical information within a care pathway. The paper concludes with recommendations for interface design.

Integrative pathway knowledge bases as a tool for systems molecular medicine.

Science.gov (United States)

Liang, Mingyu

2007-08-20

There exists a sense of urgency to begin to generate a cohesive assembly of biomedical knowledge as the pace of knowledge accumulation accelerates. The urgency is in part driven by the emergence of systems molecular medicine that emphasizes the combination of systems analysis and molecular dissection in the future of medical practice and research. A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.

Exploring Bim for Operational Integrated Asset Management - a Preliminary Study Utilising Real-World Infrastructure Data

Science.gov (United States)

Boyes, G. A.; Ellul, C.; Irwin, D.

2017-10-01

The use of 3D information models within collaborative working environments and the practice of Building Information Modelling (BIM) are becoming more commonplace within infrastructure projects. Currently used predominantly during the design and construction phase, the use of BIM is capable in theory of providing the information at handover that will satisfy the Asset Information Requirements (AIRs) of the future Infrastructure Manager (IM). One particular challenge is establishing a link between existing construction-centric information and the asset-centric information needed for future operations. Crossrail, a project to build a new high-frequency railway underneath London, is handling many such challenges as they prepare to handover their digital information to the future operator, in particular the need to provide a two-way link between a federated 3D CAD model and an object-relational Asset Information Management System (AIMS). This paper focusses on the potential for improved Asset Management (AM) by integrating BIM and GIS systems and practices, and makes a preliminary report on how 3D spatial queries can be used to establish a two-way relational link between two information systems (3D geometry and asset lists), as well as the challenges being overcome to transform the data to be suitable for AM.

People-centric sensing in assistive healthcare

DEFF Research Database (Denmark)

Giannetsos, Thanassis; Dimitriou, Tassos; Prasad, Neeli R.

2011-01-01

, we discuss the latest advances in security and privacy protection strategies that hold promise in this new exciting paradigm. We hope this work will better highlight the need for privacy in people-centric sensing applications and spawn further research in this area. Copyright © 2011 John Wiley & Sons......As the domains of pervasive computing and sensor networking are expanding, there is an ongoing trend towards assistive living and healthcare support environments that can effectively assimilate these technologies according to human needs. Most of the existing research in assistive healthcare...... follows a more passive approach and has focused on collecting and processing data using a static-topology and an application-aware infrastructure. However, with the technological advances in sensing, computation, storage, and communications, a new era is about to emerge changing the traditional view...

Modeled aerosol nitrate formation pathways during wintertime in the Great Lakes region of North America

Science.gov (United States)

Kim, Yoo Jung; Spak, Scott N.; Carmichael, Gregory R.; Riemer, Nicole; Stanier, Charles O.

2014-11-01

Episodic wintertime particle pollution by ammonium nitrate is an important air quality concern across the Midwest U.S. Understanding and accurately forecasting PM2.5 episodes are complicated by multiple pathways for aerosol nitrate formation, each with uncertain rate parameters. Here, the Community Multiscale Air Quality model (CMAQ) simulated regional atmospheric nitrate budgets during the 2009 LADCO Winter Nitrate Study, using integrated process rate (IPR) and integrated reaction rate (IRR) tools to quantify relevant processes. Total nitrate production contributing to PM2.5 episodes is a regional phenomenon, with peak production over the Ohio River Valley and southern Great Lakes. Total nitrate production in the lower troposphere is attributed to three pathways, with 57% from heterogeneous conversion of N2O5, 28% from the reaction of OH and NO2, and 15% from homogeneous conversion of N2O5. TNO3 formation rates varied day-to-day and on synoptic timescales. Rate-limited production does not follow urban-rural gradients and NOx emissions due, to counterbalancing of urban enhancement in daytime HNO3 production with nocturnal reductions. Concentrations of HNO3 and N2O5 and nighttime TNO3 formation rates have maxima aloft (100-500 m), leading to net total nitrate vertical flux during episodes, with substantial vertical gradients in nitrate partitioning. Uncertainties in all three pathways are relevant to wintertime aerosol modeling and highlight the importance of interacting transport and chemistry processes during ammonium nitrate episodes, as well as the need for additional constraint on the system through field and laboratory experiments.

Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows

DEFF Research Database (Denmark)

Andersen, Jakob L.; Flamm, Christoph; Merkle, Daniel

2018-01-01

analysis are discussed in detail. To demonstrate the applicability of the mathematical framework to real-life problems we first explore the design space of possible non-oxidative glycolysis pathways and show that recent manually designed pathways can be further optimised. We then use a model of sugar...... chemistry to investigate pathways in the autocatalytic formose process. A graph transformation-based approach is used to automatically generate the reaction networks of interest....

Standard guidelines for the chromosome-centric human proteome project.

Science.gov (United States)

Paik, Young-Ki; Omenn, Gilbert S; Uhlen, Mathias; Hanash, Samir; Marko-Varga, György; Aebersold, Ruedi; Bairoch, Amos; Yamamoto, Tadashi; Legrain, Pierre; Lee, Hyoung-Joo; Na, Keun; Jeong, Seul-Ki; He, Fuchu; Binz, Pierre-Alain; Nishimura, Toshihide; Keown, Paul; Baker, Mark S; Yoo, Jong Shin; Garin, Jerome; Archakov, Alexander; Bergeron, John; Salekdeh, Ghasem Hosseini; Hancock, William S

2012-04-06

The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-HPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, introduce topics associated with experimental approaches, data production, quality control, treatment, and transparency of data, governance of the consortium, and collaborative benefits. A companion approach for the Biology and Disease-Driven HPP (B/D-HPP) component of the Human Proteome Project is currently being organized, building upon the Human Proteome Organization's organ-based and biofluid-based initiatives (www.hupo.org/research). The common application of these guidelines in the participating laboratories is expected to facilitate the goal of a comprehensive analysis of the human proteome.

Pathway cross-talk network analysis identifies critical pathways in neonatal sepsis.

Science.gov (United States)

Meng, Yu-Xiu; Liu, Quan-Hong; Chen, Deng-Hong; Meng, Ying

2017-06-01

Despite advances in neonatal care, sepsis remains a major cause of morbidity and mortality in neonates worldwide. Pathway cross-talk analysis might contribute to the inference of the driving forces in bacterial sepsis and facilitate a better understanding of underlying pathogenesis of neonatal sepsis. This study aimed to explore the critical pathways associated with the progression of neonatal sepsis by the pathway cross-talk analysis. By integrating neonatal transcriptome data with known pathway data and protein-protein interaction data, we systematically uncovered the disease pathway cross-talks and constructed a disease pathway cross-talk network for neonatal sepsis. Then, attract method was employed to explore the dysregulated pathways associated with neonatal sepsis. To determine the critical pathways in neonatal sepsis, rank product (RP) algorithm, centrality analysis and impact factor (IF) were introduced sequentially, which synthetically considered the differential expression of genes and pathways, pathways cross-talks and pathway parameters in the network. The dysregulated pathways with the highest IF values as well as RPpathways in neonatal sepsis. By integrating three kinds of data, only 6919 common genes were included to perform the pathway cross-talk analysis. By statistic analysis, a total of 1249 significant pathway cross-talks were selected to construct the pathway cross-talk network. Moreover, 47 dys-regulated pathways were identified via attract method, 20 pathways were identified under RPpathways with the highest IF were also screened from the pathway cross-talk network. Among them, we selected 8 common pathways, i.e. critical pathways. In this study, we systematically tracked 8 critical pathways involved in neonatal sepsis by integrating attract method and pathway cross-talk network. These pathways might be responsible for the host response in infection, and of great value for advancing diagnosis and therapy of neonatal sepsis. Copyright © 2017

MODA A Framework for Memory Centric Performance Characterization

Energy Technology Data Exchange (ETDEWEB)

Shrestha, Sunil; Su, Chun-Yi; White, Amanda M.; Manzano Franco, Joseph B.; Marquez, Andres; Feo, John T.

2012-06-29

In the age of massive parallelism, the focus of performance analysis has switched from the processor and related structures to the memory and I/O resources. Adapting to this new reality, a performance analysis tool has to provide a way to analyze resource usage to pinpoint existing and potential problems in a given application. This paper provides an overview of the Memory Observant Data Analysis (MODA) tool, a memory-centric tool first implemented on the Cray XMT supercomputer. Throughout the paper, MODA's capabilities have been showcased with experiments done on matrix multiply and Graph-500 application codes.

Electronic patient information systems and care pathways: the organisational challenges of implementation and integration.

Science.gov (United States)

Dent, Mike; Tutt, Dylan

2014-09-01

Our interest here is with the 'marriage' of e-patient information systems with care pathways in order to deliver integrated care. We report on the development and implementation of four such pathways within two National Health Service primary care trusts in England: (a) frail elderly care, (b) stroke care, (c) diabetic retinopathy screening and (d) intermediate care. The pathways were selected because each represents a different type of information and data 'couplings', in terms of task interdependency with some pathways/systems reflecting more complex coordinating patterns than others. Our aim here is identify and explain how health professionals and information specialists in two organisational National Health Service primary care trusts organisationally construct and use such systems and, in particular, the implications this has for issues of professional and managerial control and autonomy. The article is informed by an institutionalist analysis. © The Author(s) 2013.

Towards integrated solutions for water, energy, and land using an integrated nexus modeling framework

Science.gov (United States)

Wada, Y.

2017-12-01

Humanity has already reached or even exceeded the Earth's carrying capacity. Growing needs for food, energy and water will only exacerbate existing challenges over the next decades. Consequently, the acceptance of "business as usual" is eroding and we are being challenged to adopt new, more integrated, and more inclusive development pathways that avoid dangerous interference with the local environment and global planetary boundaries. This challenge is embodied in the United Nation's Sustainable Development Goals (SDGs), which endeavor to set a global agenda for moving towards more sustainable development strategies. To improve and sustain human welfare, it is critical that access to modern, reliable, and affordable water, energy, and food is expanded and maintained. The Integrated Solutions for Water, Energy, and Land (IS-WEL) project has been launched by IIASA, together with the Global Environment Facility (GEF) and the United Nations Industrial Development Organization (UNIDO). This project focuses on the water-energy-land nexus in the context of other major global challenges such as urbanization, environmental degradation, and equitable and sustainable futures. It develops a consistent framework for looking at the water-energy-land nexus and identify strategies for achieving the needed transformational outcomes through an advanced assessment framework. A multi-scalar approach are being developed that aims to combine global and regional integrated assessment tools with local stakeholder knowledge in order to identify robust solutions to energy, water, food, and ecosystem security in selected regions of the world. These are regions facing multiple energy, water and land use challenges and rapid demographic and economic changes, and are hardest hit by increasing climate variability and change. This project combines the global integrated assessment model (MESSAGE) with the global land (GLOBIOM) and water (Community Water Model) model respectively, and the integrated

Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer

Directory of Open Access Journals (Sweden)

Chung Jae

2009-06-01

Full Text Available Abstract Background Cisplatin and carboplatin are the primary first-line therapies for the treatment of ovarian cancer. However, resistance to these platinum-based drugs occurs in the large majority of initially responsive tumors, resulting in fully chemoresistant, fatal disease. Although the precise mechanism(s underlying the development of platinum resistance in late-stage ovarian cancer patients currently remains unknown, CpG-island (CGI methylation, a phenomenon strongly associated with aberrant gene silencing and ovarian tumorigenesis, may contribute to this devastating condition. Methods To model the onset of drug resistance, and investigate DNA methylation and gene expression alterations associated with platinum resistance, we treated clonally derived, drug-sensitive A2780 epithelial ovarian cancer cells with increasing concentrations of cisplatin. After several cycles of drug selection, the isogenic drug-sensitive and -resistant pairs were subjected to global CGI methylation and mRNA expression microarray analyses. To identify chemoresistance-associated, biological pathways likely impacted by DNA methylation, promoter CGI methylation and mRNA expression profiles were integrated and subjected to pathway enrichment analysis. Results Promoter CGI methylation revealed a positive association (Spearman correlation of 0.99 between the total number of hypermethylated CGIs and GI50 values (i.e., increased drug resistance following successive cisplatin treatment cycles. In accord with that result, chemoresistance was reversible by DNA methylation inhibitors. Pathway enrichment analysis revealed hypermethylation-mediated repression of cell adhesion and tight junction pathways and hypomethylation-mediated activation of the cell growth-promoting pathways PI3K/Akt, TGF-beta, and cell cycle progression, which may contribute to the onset of chemoresistance in ovarian cancer cells. Conclusion Selective epigenetic disruption of distinct biological

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.

An overview of bioinformatics methods for modeling biological pathways in yeast.

Science.gov (United States)

Hou, Jie; Acharya, Lipi; Zhu, Dongxiao; Cheng, Jianlin

2016-03-01

The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein-protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae In particular, discovery of biological pathways in yeast has become an important forefront in systems biology, which aims to understand the interactions among molecules within a cell leading to certain cellular processes in response to a specific environment. While the existing theoretical and experimental approaches enable the investigation of well-known pathways involved in metabolism, gene regulation and signal transduction, bioinformatics methods offer new insights into computational modeling of biological pathways. A wide range of computational approaches has been proposed in the past for reconstructing biological pathways from high-throughput datasets. Here we review selected bioinformatics approaches for modeling biological pathways inS. cerevisiae, including metabolic pathways, gene-regulatory pathways and signaling pathways. We start with reviewing the research on biological pathways followed by discussing key biological databases. In addition, several representative computational approaches for modeling biological pathways in yeast are discussed. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Critical assessment of human metabolic pathway databases: a stepping stone for future integration

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Stobbe Miranda D

2011-10-01

Full Text Available Abstract Background Multiple pathway databases are available that describe the human metabolic network and have proven their usefulness in many applications, ranging from the analysis and interpretation of high-throughput data to their use as a reference repository. However, so far the various human metabolic networks described by these databases have not been systematically compared and contrasted, nor has the extent to which they differ been quantified. For a researcher using these databases for particular analyses of human metabolism, it is crucial to know the extent of the differences in content and their underlying causes. Moreover, the outcomes of such a comparison are important for ongoing integration efforts. Results We compared the genes, EC numbers and reactions of five frequently used human metabolic pathway databases. The overlap is surprisingly low, especially on reaction level, where the databases agree on 3% of the 6968 reactions they have combined. Even for the well-established tricarboxylic acid cycle the databases agree on only 5 out of the 30 reactions in total. We identified the main causes for the lack of overlap. Importantly, the databases are partly complementary. Other explanations include the number of steps a conversion is described in and the number of possible alternative substrates listed. Missing metabolite identifiers and ambiguous names for metabolites also affect the comparison. Conclusions Our results show that each of the five networks compared provides us with a valuable piece of the puzzle of the complete reconstruction of the human metabolic network. To enable integration of the networks, next to a need for standardizing the metabolite names and identifiers, the conceptual differences between the databases should be resolved. Considerable manual intervention is required to reach the ultimate goal of a unified and biologically accurate model for studying the systems biology of human metabolism. Our comparison

EXPLORING BIM FOR OPERATIONAL INTEGRATED ASSET MANAGEMENT – A PRELIMINARY STUDY UTILISING REAL-WORLD INFRASTRUCTURE DATA

Directory of Open Access Journals (Sweden)

G. A. Boyes

2017-10-01

Full Text Available The use of 3D information models within collaborative working environments and the practice of Building Information Modelling (BIM are becoming more commonplace within infrastructure projects. Currently used predominantly during the design and construction phase, the use of BIM is capable in theory of providing the information at handover that will satisfy the Asset Information Requirements (AIRs of the future Infrastructure Manager (IM. One particular challenge is establishing a link between existing construction-centric information and the asset-centric information needed for future operations. Crossrail, a project to build a new high-frequency railway underneath London, is handling many such challenges as they prepare to handover their digital information to the future operator, in particular the need to provide a two-way link between a federated 3D CAD model and an object-relational Asset Information Management System (AIMS. This paper focusses on the potential for improved Asset Management (AM by integrating BIM and GIS systems and practices, and makes a preliminary report on how 3D spatial queries can be used to establish a two-way relational link between two information systems (3D geometry and asset lists, as well as the challenges being overcome to transform the data to be suitable for AM.

Designing a Care Pathway Model – A Case Study of the Outpatient Total Hip Arthroplasty Care Pathway

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Robin I. Oosterholt

2017-03-01

Full Text Available Introduction: Although the clinical attributes of total hip arthroplasty (THA care pathways have been thoroughly researched, a detailed understanding of the equally important organisational attributes is still lacking. The aim of this article is to contribute with a model of the outpatient THA care pathway that depicts how the care team should be organised to enable patient discharge on the day of surgery. Theory: The outpatient THA care pathway enables patients to be discharged on the day of surgery, short- ening the length of stay and intensifying the provision and organisation of care. We utilise visual care modelling to construct a visual design of the organisation of the care pathway. Methods: An embedded case study was conducted of the outpatient THA care pathway at a teaching hospital in the Netherlands. The data were collected using a visual care modelling toolkit in 16 semi- structured interviews. Problems and inefficiencies in the care pathway were identified and addressed in the iterative design process. Results: The results are two visual models of the most critical phases of the outpatient THA care pathway: diagnosis & preparation (1 and mobilisation & discharge (4. The results show the care team composition, critical value exchanges, and sequence that enable patient discharge on the day of surgery. Conclusion: The design addressed existing problems and is an optimisation of the case hospital’s pathway. The network of actors consists of the patient (1, radiologist (1, anaesthetist (1, nurse specialist (1, pharmacist (1, orthopaedic surgeon (1,4, physiotherapist (1,4, nurse (4, doctor (4 and patient applica- tion (1,4. The critical value exchanges include patient preparation (mental and practical, patient education, aligned care team, efficient sequence of value exchanges, early patient mobilisation, flexible availability of the physiotherapist, functional discharge criteria, joint decision making and availability of the care team.

Model of the Russian Federation Construction Innovation System: An Integrated Participatory Systems Approach

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Emiliya Suprun

2016-08-01

Full Text Available This research integrates systemic and participatory techniques to model the Russian Federation construction innovation system. Understanding this complex construction innovation system and determining the best levers for enhancing it require the dynamic modelling of a number of factors, such as flows of resources and activities, policies, uncertainty and time. To build the foundations for such a dynamic model, the employed study method utilised an integrated stakeholder-based participatory approach coupled with structural analysis (MICMAC—Matrice d'Impacts Croisés Multiplication Appliquée à un Classement Cross-Impact Matrix. This method identified the key factors of the Russian Federation construction innovation system, their causal relationship (i.e., influence/dependence map and, ultimately, a causal loop diagram. The generated model reveals pathways to improving construction innovation in the Russian Federation and underpins the future development of an operationalised system dynamics model.

Baldrige Theory into Practice: A Generic Model

Science.gov (United States)

Arif, Mohammed

2007-01-01

Purpose: The education system globally has moved from a push-based or producer-centric system to a pull-based or customer centric system. Malcolm Baldrige Quality Award (MBQA) model happens to be one of the latest additions to the pull based models. The purpose of this paper is to develop a generic framework for MBQA that can be used by…

Aulacoseira kruegeriana (Bacillariophyta, Coscinodiscophyceae): a new centric diatom from high-elevation Andean streams of Bolivia

Czech Academy of Sciences Publication Activity Database

Morales, E. A.; Rivera, S. F.; Rubin, S. D. C.; Vis, M. L.; Houk, Václav

2015-01-01

Roč. 30, č. 3 (2015), s. 269-277 ISSN 0269-249X Institutional support: RVO:67985939 Keywords : centric diatoms * taxonomy * valve ultrastructure Subject RIV: EF - Botanics Impact factor: 1.868, year: 2015

Network Centric Warfare Case Study: U.S. V Corps and 3rd Infantry Division (Mechanized) During Operation Iraqi Freedom Combat Operations (Mar-Apr 2003). Volume 3. Network Centric Warfare Insights

Science.gov (United States)

2003-01-01

OPSEC), military deception, psychological operations (PSYOPS), special information operations (IO), information assurance, physical security...nonlethal effects, such as operational 8 Network Centric Warfare Case Study security (OPSEC), military deception, psychological operations (PSYOP...Support Operations Group ASR Alternate Supply Route; or, Ammunition Supply Rate ATACMS Army Tactical Missile System ATARS Advanced

Integration of Robotic Resources into FORCEnet

National Research Council Canada - National Science Library

Nguyen, Chinh; Carroll, Daniel; Nguyen, Hoa

2006-01-01

.... publish-and-subscribe methodology. and software reuse. The paper defines the goals and boundaries for NISR with focus on the system architecture, including the design tradeoffs necessary for unmanned systems in a net-centric model...

An efficient tool for metabolic pathway construction and gene integration for Aspergillus niger.

Science.gov (United States)

Sarkari, Parveen; Marx, Hans; Blumhoff, Marzena L; Mattanovich, Diethard; Sauer, Michael; Steiger, Matthias G

2017-12-01

Metabolic engineering requires functional genetic tools for easy and quick generation of multiple pathway variants. A genetic engineering toolbox for A. niger is presented, which facilitates the generation of strains carrying heterologous expression cassettes at a defined genetic locus. The system is compatible with Golden Gate cloning, which facilitates the DNA construction process and provides high design flexibility. The integration process is mediated by a CRISPR/Cas9 strategy involving the cutting of both the genetic integration locus (pyrG) as well as the integrating plasmid. Only a transient expression of Cas9 is necessary and the carrying plasmid is readily lost using a size-reduced AMA1 variant. A high integration efficiency into the fungal genome of up to 100% can be achieved, thus reducing the screening process significantly. The feasibility of the approach was demonstrated by the integration of an expression cassette enabling the production of aconitic acid in A. niger. Copyright © 2017 Elsevier Ltd. All rights reserved.

Identification of differentially expressed genes and signaling pathways in ovarian cancer by integrated bioinformatics analysis

Directory of Open Access Journals (Sweden)

Yang X

2018-03-01

Full Text Available Xiao Yang,1 Shaoming Zhu,2 Li Li,3 Li Zhang,1 Shu Xian,1 Yanqing Wang,1 Yanxiang Cheng1 1Department of Obstetrics and Gynecology, 2Department of Urology, Renmin Hospital of Wuhan University, 3Department of Pharmacology, Wuhan University Health Science Center, Wuhan, Hubei, People’s Republic of China Background: The mortality rate associated with ovarian cancer ranks the highest among gynecological malignancies. However, the cause and underlying molecular events of ovarian cancer are not clear. Here, we applied integrated bioinformatics to identify key pathogenic genes involved in ovarian cancer and reveal potential molecular mechanisms. Results: The expression profiles of GDS3592, GSE54388, and GSE66957 were downloaded from the Gene Expression Omnibus (GEO database, which contained 115 samples, including 85 cases of ovarian cancer samples and 30 cases of normal ovarian samples. The three microarray datasets were integrated to obtain differentially expressed genes (DEGs and were deeply analyzed by bioinformatics methods. The gene ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG pathway enrichments of DEGs were performed by DAVID and KOBAS online analyses, respectively. The protein–protein interaction (PPI networks of the DEGs were constructed from the STRING database. A total of 190 DEGs were identified in the three GEO datasets, of which 99 genes were upregulated and 91 genes were downregulated. GO analysis showed that the biological functions of DEGs focused primarily on regulating cell proliferation, adhesion, and differentiation and intracellular signal cascades. The main cellular components include cell membranes, exosomes, the cytoskeleton, and the extracellular matrix. The molecular functions include growth factor activity, protein kinase regulation, DNA binding, and oxygen transport activity. KEGG pathway analysis showed that these DEGs were mainly involved in the Wnt signaling pathway, amino acid metabolism, and the

Integrative Functional Genomics for Systems Genetics in GeneWeaver.org.

Science.gov (United States)

Bubier, Jason A; Langston, Michael A; Baker, Erich J; Chesler, Elissa J

2017-01-01

The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data. GeneWeaver contains curated experimental data together with resource-level data such as GO annotations, MP annotations, and KEGG pathways, along with persistent stores of user entered data sets. These can be entered directly into GeneWeaver or transferred from widely used resources such as GeneNetwork.org. Data are analyzed using statistical tools and advanced graph algorithms to discover new relations, prioritize candidate genes, and generate function hypotheses. Here we use GeneWeaver to find genes common to multiple gene sets, prioritize candidate genes from a quantitative trait locus, and characterize a set of differentially expressed genes. Coupling a large multispecies repository curated and empirical functional genomics data to fast computational tools allows for the rapid integrative analysis of heterogeneous data for interpreting and extrapolating systems genetics results.

Elastic LiDAR Fusion: Dense Map-Centric Continuous-Time SLAM

OpenAIRE

Park, Chanoh; Moghadam, Peyman; Kim, Soohwan; Elfes, Alberto; Fookes, Clinton; Sridharan, Sridha

2017-01-01

The concept of continuous-time trajectory representation has brought increased accuracy and efficiency to multi-modal sensor fusion in modern SLAM. However, regardless of these advantages, its offline property caused by the requirement of global batch optimization is critically hindering its relevance for real-time and life-long applications. In this paper, we present a dense map-centric SLAM method based on a continuous-time trajectory to cope with this problem. The proposed system locally f...

How Effective Are Clinical Pathways With and Without Online Peer-Review? An Analysis of Bone Metastases Pathway in a Large, Integrated National Cancer Institute-Designated Comprehensive Cancer Center Network

Energy Technology Data Exchange (ETDEWEB)

Beriwal, Sushil, E-mail: beriwals@upmc.edu [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); Rajagopalan, Malolan S.; Flickinger, John C.; Rakfal, Susan M. [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); Rodgers, Edwin [Via Oncology, Pittsburgh, PA (United States); Heron, Dwight E. [Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States)

2012-07-15

Purpose: Clinical pathways are an important tool used to manage the quality in health care by standardizing processes. This study evaluated the impact of the implementation of a peer-reviewed clinical pathway in a large, integrated National Cancer Institute-Designated Comprehensive Cancer Center Network. Methods: In 2003, we implemented a clinical pathway for the management of bone metastases with palliative radiation therapy. In 2009, we required the entry of management decisions into an online tool that records pathway choices. The pathway specified 1 or 5 fractions for symptomatic bone metastases with the option of 10-14 fractions for certain clinical situations. The data were obtained from 13 integrated sites (3 central academic, 10 community locations) from 2003 through 2010. Results: In this study, 7905 sites were treated with 64% of courses delivered in community practice and 36% in academic locations. Academic practices were more likely than community practices to treat with 1-5 fractions (63% vs. 23%; p < 0.0001). The number of delivered fractions decreased gradually from 2003 to 2010 for both academic and community practices (p < 0.0001); however, greater numbers of fractions were selected more often in community practices (p < 0.0001). Using multivariate logistic regression, we found that a significantly greater selection of 1-5 fractions developed after implementation online pathway monitoring (2009) with an odds ratio of 1.2 (confidence interval, 1.1-1.4) for community and 1.3 (confidence interval, 1.1-1.6) for academic practices. The mean number of fractions also decreased after online peer review from 6.3 to 6.0 for academic (p = 0.07) and 9.4 to 9.0 for community practices (p < 0.0001). Conclusion: This is one of the first studies to examine the efficacy of a clinical pathway for radiation oncology in an integrated cancer network. Clinical pathway implementation appears to be effective in changing patterns of care, particularly with online clinical

How Effective Are Clinical Pathways With and Without Online Peer-Review? An Analysis of Bone Metastases Pathway in a Large, Integrated National Cancer Institute–Designated Comprehensive Cancer Center Network

International Nuclear Information System (INIS)

Beriwal, Sushil; Rajagopalan, Malolan S.; Flickinger, John C.; Rakfal, Susan M.; Rodgers, Edwin; Heron, Dwight E.

2012-01-01

Purpose: Clinical pathways are an important tool used to manage the quality in health care by standardizing processes. This study evaluated the impact of the implementation of a peer-reviewed clinical pathway in a large, integrated National Cancer Institute–Designated Comprehensive Cancer Center Network. Methods: In 2003, we implemented a clinical pathway for the management of bone metastases with palliative radiation therapy. In 2009, we required the entry of management decisions into an online tool that records pathway choices. The pathway specified 1 or 5 fractions for symptomatic bone metastases with the option of 10–14 fractions for certain clinical situations. The data were obtained from 13 integrated sites (3 central academic, 10 community locations) from 2003 through 2010. Results: In this study, 7905 sites were treated with 64% of courses delivered in community practice and 36% in academic locations. Academic practices were more likely than community practices to treat with 1–5 fractions (63% vs. 23%; p < 0.0001). The number of delivered fractions decreased gradually from 2003 to 2010 for both academic and community practices (p < 0.0001); however, greater numbers of fractions were selected more often in community practices (p < 0.0001). Using multivariate logistic regression, we found that a significantly greater selection of 1–5 fractions developed after implementation online pathway monitoring (2009) with an odds ratio of 1.2 (confidence interval, 1.1–1.4) for community and 1.3 (confidence interval, 1.1–1.6) for academic practices. The mean number of fractions also decreased after online peer review from 6.3 to 6.0 for academic (p = 0.07) and 9.4 to 9.0 for community practices (p < 0.0001). Conclusion: This is one of the first studies to examine the efficacy of a clinical pathway for radiation oncology in an integrated cancer network. Clinical pathway implementation appears to be effective in changing patterns of care, particularly with

Pappas and Tepe's Pathways to Knowledge Model.

Science.gov (United States)

Zimmerman, Nancy P.; Pappas, Marjorie L.; Tepe, Ann E.

2002-01-01

Describes the Pathways to Knowledge model for helping students achieve information literacy in library media programs. Discusses the searcher's thinking, information search or seeking, and instructional strategies; information skills; the six stages in the model, including appreciation, presearch, search, interpretation, communication, and…

A kinetic model for the penicillin biosynthetic pathway in

DEFF Research Database (Denmark)

Nielsen, Jens; Jørgensen, Henrik

1996-01-01

A kinetic model for the first two steps in the penicillin biosynthetic pathway, i.e. the ACV synthetase (ACVS) and the isopenicillin N synthetase (IPNS) is proposed. The model is based on Michaelis-Menten type kinetics with non-competitive inhibition of the ACVS by ACV, and competitive inhibition...... of the IPNS by glutathione. The model predicted flux through the pathway corresponds well with the measured rate of penicillin biosynthesis. From the kinetic model the elasticity coefficients and the flux control coefficients are calculated throughout a fed-batch cultivation, and it is found...

Comparative evaluation of the efficacy of occlusal splints fabricated in centric relation or maximum intercuspation in temporomandibular disorders patients

Directory of Open Access Journals (Sweden)

Marcelo Matida Hamata

2009-02-01

Full Text Available Fabrication of occlusal splints in centric relation for temporomandibular disorders (TMD patients is arguable, since this position has been defined for asymptomatic stomatognathic system. Thus, maximum intercuspation might be employed in patients with occlusal stability, eliminating the need for interocclusal records. This study compared occlusal splints fabricated in centric relation and maximum intercuspation in muscle pain reduction of TMD patients. Twenty patients with TMD of myogenous origin and bruxism were divided into 2 groups treated with splints in maximum intercuspation (I or centric relation (II. Clinical, electrognathographic and electromyographic examinations were performed before and 3 months after therapy. Data were analyzed by the Student's t test. Differences at 5% level of probability were considered statistically significant. There was a remarkable reduction in pain symptomatology, without statistically significant differences (p>0.05 between the groups. There was mandibular repositioning during therapy, as demonstrated by the change in occlusal contacts on the splints. Electrognathographic examination demonstrated a significant increase in maximum left lateral movement for group I and right lateral movement for group II (p0.05 in the electromyographic activities at rest after utilization of both splints. In conclusion, both occlusal splints were effective for pain control and presented similar action. The results suggest that maximum intercuspation may be used for fabrication of occlusal splints in patients with occlusal stability without large discrepancies between centric relation and maximum intercuspation. Moreover, this technique is simpler and less expensive.

Comparative evaluation of the efficacy of occlusal splints fabricated in centric relation or maximum intercuspation in temporomandibular disorders patients.

Science.gov (United States)

Hamata, Marcelo Matida; Zuim, Paulo Renato Junqueira; Garcia, Alicio Rosalino

2009-01-01

Fabrication of occlusal splints in centric relation for temporomandibular disorders (TMD) patients is arguable, since this position has been defined for asymptomatic stomatognathic system. Thus, maximum intercuspation might be employed in patients with occlusal stability, eliminating the need for interocclusal records. This study compared occlusal splints fabricated in centric relation and maximum intercuspation in muscle pain reduction of TMD patients. Twenty patients with TMD of myogenous origin and bruxism were divided into 2 groups treated with splints in maximum intercuspation (I) or centric relation (II). Clinical, electrognathographic and electromyographic examinations were performed before and 3 months after therapy. Data were analyzed by the Student's t test. Differences at 5% level of probability were considered statistically significant. There was a remarkable reduction in pain symptomatology, without statistically significant differences (p>0.05) between the groups. There was mandibular repositioning during therapy, as demonstrated by the change in occlusal contacts on the splints. Electrognathographic examination demonstrated a significant increase in maximum left lateral movement for group I and right lateral movement for group II (p0.05) in the electromyographic activities at rest after utilization of both splints. In conclusion, both occlusal splints were effective for pain control and presented similar action. The results suggest that maximum intercuspation may be used for fabrication of occlusal splints in patients with occlusal stability without large discrepancies between centric relation and maximum intercuspation. Moreover, this technique is simpler and less expensive.

A theory of physician-hospital integration: contending institutional and market logics in the health care field.

Science.gov (United States)

Rundall, Thomas G; Shortell, Stephen M; Alexander, Jeffrey A

2004-01-01

This article proposes a theory of physician-hospital integration. The theory is developed by building on three streams of scholarship: "new" institutionalism, "old" institutionalism, and the theory of economic markets. The theory uses several key concepts from these theoretical frameworks, including the notions of environmental demands for legitimacy, market demands for efficiency, and agency. To enhance the predictive power of the theory, two new concepts are introduced: directionality of influence between institutional and market forces at the macro-societal level, and degree of separation of institutional and market domains at the local level--which add important predictive power to the theory. Using these concepts, a number of hypotheses are proposed regarding the ideal types of physician-hospital arrangements that are likely to emerge under different combinations of directionality of influence and institutional and market domain separation. Moreover, the theory generates hypotheses regarding organizational dynamics associated with physician-hospital integration, including the conditions associated with high and low prevalence of physician-hospital integration, the extent to which the integrated organization is physician-centric or hospital-centric, and whether physician-hospital integration is likely to be based on loose contractual arrangements or tight, ownership-based arrangements.

Group Centric Networking: Addressing Information Sharing Requirements at the Tactical Edge

Science.gov (United States)

2016-04-10

Group Centric Networking: Addressing Information Sharing Requirements at the Tactical Edge Bow-Nan Cheng, Greg Kuperman, Patricia Deutsch, Logan...been a large push in the U.S. Department of Defense to move to an all Internet Protocol (IP) infrastructure, particularly on the tactical edge . IP and...lossy links, and scaling to large numbers of users. Unfortunately, these are the exact conditions military tactical edge networks must operate within

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

Science.gov (United States)

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

Cyber-Security Challenges with SMEs in Developing Economies: Issues of Confidentiality, Integrity & Availability (CIA)

DEFF Research Database (Denmark)

Yeboah-Boateng, Ezer Osei

The essence of this study is first to highlight the cyber-security challenges confronting SMEs in developing economies, and to model a framework for safeguarding their assets, to ensure continuous optimal business operations, and to participate and compete securely in the ubiquitous cyber......, to develop customer-centric strategies. While connectivity is indispensable for achieving business success, being connected also implies being exposed to a myriad of cyber-security challenges, such as vulnerabilities of confidentiality, integrity and availability (CIA). As vulnerabilities are exploited...... cognitive map (FCM) approach is also used to show the implications of vulnerabilities amongst SMEs asset disposal policies....

VISIBIOweb: visualization and layout services for BioPAX pathway models

Science.gov (United States)

Dilek, Alptug; Belviranli, Mehmet E.; Dogrusoz, Ugur

2010-01-01

With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org. PMID:20460470

Integrative Network Analysis Unveils Convergent Molecular Pathways in Parkinson's Disease and Diabetes

OpenAIRE

Santiago, Jose A.; Potashkin, Judith A.

2013-01-01

Background Shared dysregulated pathways may contribute to Parkinson's disease and type 2 diabetes, chronic diseases that afflict millions of people worldwide. Despite the evidence provided by epidemiological and gene profiling studies, the molecular and functional networks implicated in both diseases, have not been fully explored. In this study, we used an integrated network approach to investigate the extent to which Parkinson's disease and type 2 diabetes are linked at the molecular level. ...

Boolean network model for cancer pathways: predicting carcinogenesis and targeted therapy outcomes.

Directory of Open Access Journals (Sweden)

Herman F Fumiã

Full Text Available A Boolean dynamical system integrating the main signaling pathways involved in cancer is constructed based on the currently known protein-protein interaction network. This system exhibits stationary protein activation patterns--attractors--dependent on the cell's microenvironment. These dynamical attractors were determined through simulations and their stabilities against mutations were tested. In a higher hierarchical level, it was possible to group the network attractors into distinct cell phenotypes and determine driver mutations that promote phenotypic transitions. We find that driver nodes are not necessarily central in the network topology, but at least they are direct regulators of central components towards which converge or through which crosstalk distinct cancer signaling pathways. The predicted drivers are in agreement with those pointed out by diverse census of cancer genes recently performed for several human cancers. Furthermore, our results demonstrate that cell phenotypes can evolve towards full malignancy through distinct sequences of accumulated mutations. In particular, the network model supports routes of carcinogenesis known for some tumor types. Finally, the Boolean network model is employed to evaluate the outcome of molecularly targeted cancer therapies. The major find is that monotherapies were additive in their effects and that the association of targeted drugs is necessary for cancer eradication.

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi.

OpenAIRE

Feldmesser, Ester; Rosenwasser, Shilo; Vardi, Assaf; Ben-Dor, Shifra

2014-01-01

Background The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly whe...

Diverse methods for integrable models

NARCIS (Netherlands)

Fehér, G.

2017-01-01

This thesis is centered around three topics, sharing integrability as a common theme. This thesis explores different methods in the field of integrable models. The first two chapters are about integrable lattice models in statistical physics. The last chapter describes an integrable quantum chain.

High-resolution modelling of health impacts from air pollution using the integrated model system EVA

Science.gov (United States)

Brandt, Jørgen; Andersen, Mikael S.; Bønløkke, Jakob; Christensen, Jesper H.; Geels, Camilla; Hansen, Kaj M.; Jensen, Steen S.; Ketzel, Matthias; Plejdrup, Marlene S.; Sigsgaard, Torben; Silver, Jeremy D.

2014-05-01

A high-resolution assessment of health impacts from air pollution and related external cost has been conducted for Denmark using the integrated EVA model system. The EVA system has been further developed by implementing an air quality model with a 1 km x 1 km resolution covering the whole of Denmark. New developments of the integrated model system will be presented as well as results for health impacts and related external costs over several decades. Furthermore, the sensitivity of health impacts to model resolution will be studied. We have developed an integrated model system EVA (Economic Valuation of Air pollution), based on the impact-pathway chain, to assess the health impacts and health-related economic externalities of air pollution resulting from specific emission sources or sectors. The system is used to support policymaking with respect to emission control. In Brandt et al. (2013a; 2013b), the EVA system was used to assess the impacts in Europe and Denmark from the past, present and future total air pollution levels as well as the contribution from the major anthropogenic emission sectors. The EVA system was applied using the hemispheric chemistry-transport model, the Danish Eulerian Hemispheric Model (DEHM), with nesting capability for higher resolution over Europe (50 km x 50 km) and Northern Europe (16.7 km x 16.7 km). In this study an Urban Background Model (UBM) has been further developed to cover the whole of Denmark with a 1 km x 1 km resolution and the model has been implemented as a part of the integrated model system, EVA. The EVA system is based on the impact-pathway methodology. The site-specific emissions will result (via atmospheric transport and chemistry) in a concentration distribution, which together with detailed population data, are used to estimate the population-level exposure. Using exposure-response functions and economic valuations, the exposure is transformed into impacts on human health and related external costs. In this study

Teaching Customer-Centric Operations Management--Evidence from an Experiential Learning-Oriented Mass Customisation Class

Science.gov (United States)

Medini, Khaled

2018-01-01

The increase of individualised customer demands and tough competition in the manufacturing sector gave rise to more customer-centric operations management such as products and services (mass) customisation. Mass customisation (MC), which inherits the "economy of scale" from mass production (MP), aims to meet specific customer demands…

Sustaining Innovative Success: A Case Study on Consumer-Centric Innovation in the ICT Industry

Directory of Open Access Journals (Sweden)

Minkyung Choy

2016-09-01

Full Text Available The phenomenon of innovation growing rapidly and having a shorter lifespan is a structural change due to the development of ICT (Information and Communications Technology, diverse investment methods, and reduced pattern of innovation adoption. For ICT companies to survive and maintain their success in this ever-changing environment, they need to succeed in fulfilling both productivity and accuracy of innovation. To sustain their innovative success, ICT companies should consistently maintain the direction of innovation towards consumers. The present study analyzes various cases of ICT companies which succeeded or failed to maintain their prior innovative success, and suggests consumer-centric innovation as a solution. To create consumer-centric innovations, companies have to (1 predict the dynamically evolving demand of consumers and continuously transform; (2 proactively employ observation method and big data analysis to discover hidden demands; and (3 identify hassles such as wastes, inconveniences, and anxieties, and put effort in solving these hassles.

Overview on Patient Centricity in Cancer Care

Directory of Open Access Journals (Sweden)

Šarunas Narbutas

2017-10-01

Full Text Available Successful implementation of treatment in cancer care partially depends on how patients' perspectives are taken into account, as preferences of health care professionals and patients may differ. Objectives of this exploratory research were (I to identify patient preferences and values (PPVs in cancer care as indicated by patient organizations (POs, (II to determine how these PPVs are captured in cancer care guidelines and (III to review how guidelines take into account these PPVs. Based on a survey developed and completed by 19 POs, a literature review was conducted to analyse how patient perspectives are incorporated in oncology treatment guidelines. Based on survey results traditional health technology assessment value propositions of oncology care, such as extended life, treatment-free remission and pain reduction, were also highly rated by POs. However, the heterogeneity of cancer PPVs were clearly reflected in the survey results. PPVs in cancer care guidelines were mostly limited to those micro-level aspects that are strictly related to health care provision, such as side-effects and comorbidities. Patient experience, emotional support and convenience of care were relatively neglected fields in the reviewed guidelines. Patient engagement was rarely presented in the guideline development phase. POs believe that patients should be encouraged to take an active role in their own care due to the heterogeneity of cancer patients and PPVs. Even if patient-centricity is a leading paradigm in cancer policy, based on our research it is not yet standard practice to include patients or POs at all appropriate levels of decision-making processes that are related to their health and well-being. Patient engagement should be an integral part of cancer care decision-making. This complexity must be reflected throughout policy making, avoiding a population level “one-size-fits-all” solution.

A Longitudinal Empirical Investigation of the Pathways Model of Problem Gambling.

Science.gov (United States)

Allami, Youssef; Vitaro, Frank; Brendgen, Mara; Carbonneau, René; Lacourse, Éric; Tremblay, Richard E

2017-12-01

The pathways model of problem gambling suggests the existence of three developmental pathways to problem gambling, each differentiated by a set of predisposing biopsychosocial characteristics: behaviorally conditioned (BC), emotionally vulnerable (EV), and biologically vulnerable (BV) gamblers. This study examined the empirical validity of the Pathways Model among adolescents followed up to early adulthood. A prospective-longitudinal design was used, thus overcoming limitations of past studies that used concurrent or retrospective designs. Two samples were used: (1) a population sample of French-speaking adolescents (N = 1033) living in low socio-economic status (SES) neighborhoods from the Greater Region of Montreal (Quebec, Canada), and (2) a population sample of adolescents (N = 3017), representative of French-speaking students in Quebec. Only participants with at-risk or problem gambling by mid-adolescence or early adulthood were included in the main analysis (n = 180). Latent Profile Analyses were conducted to identify the optimal number of profiles, in accordance with participants' scores on a set of variables prescribed by the Pathways Model and measured during early adolescence: depression, anxiety, impulsivity, hyperactivity, antisocial/aggressive behavior, and drug problems. A four-profile model fit the data best. Three profiles differed from each other in ways consistent with the Pathways Model (i.e., BC, EV, and BV gamblers). A fourth profile emerged, resembling a combination of EV and BV gamblers. Four profiles of at-risk and problem gamblers were identified. Three of these profiles closely resemble those suggested by the Pathways Model.

Modelling and Decision Support of Clinical Pathways

Science.gov (United States)

Gabriel, Roland; Lux, Thomas

The German health care market is under a rapid rate of change, forcing especially hospitals to provide high-quality services at low costs. Appropriate measures for more effective and efficient service provision are process orientation and decision support by information technology of clinical pathway of a patient. The essential requirements are adequate modelling of clinical pathways as well as usage of adequate systems, which are capable of assisting the complete path of a patient within a hospital, and preferably also outside of it, in a digital way. To fulfil these specifications the authors present a suitable concept, which meets the challenges of well-structured clinical pathways as well as rather poorly structured diagnostic and therapeutic decisions, by interplay of process-oriented and knowledge-based hospital information systems.

Architecture-Centric Evolution : New Issues and Trends. Report on the Workshop ACE at ECOOP’06

NARCIS (Netherlands)

Avgeriou, Paris; Zdun, Uwe; Borne, Isabelle

2006-01-01

Software evolution has largely been focused on low-level implementation artefacts through refactoring techniques rather than the architectural level. However code-centric evolution techniques have not managed to effectively solve the problems that software evolution entails. Instead a paradigm shift

Transforming System Engineering through Model-Centric Engineering

Science.gov (United States)

2015-11-18

infrastructure). In addition, the set-based design concept originally attributed to Toyota described how the design and manufacturing processes work...related domains. History suggests that there is limited success in exposing cross-domain issues until a physical integration is developed to enabling

Computational Modeling of Biological Systems From Molecules to Pathways

CERN Document Server

2012-01-01

Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

Multi-Device to Multi-Device (MD2MD Content-Centric Networking Based on Multi-RAT Device

Directory of Open Access Journals (Sweden)

Cheolhoon Kim

2017-11-01

Full Text Available This paper proposes a method whereby a device can transmit and receive information using a beacon, and also describes application scenarios for the proposed method. In a multi-device to multi-device (MD2MD content-centric networking (CCN environment, the main issue involves searching for and connecting to nearby devices. However, if a device can’t find another device that satisfies its requirements, the connection is delayed due to the repetition of processes. It is possible to rapidly connect to a device without repetition through the selection of the optimal device using the proposed method. Consequently, the proposed method and scenarios are advantageous in that they enable efficient content identification and delivery in a content-centric Internet of Things (IoT environment, in which multiple mobile devices coexist.

Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles.

Science.gov (United States)

Kibinge, Nelson; Ono, Naoaki; Horie, Masafumi; Sato, Tetsuo; Sugiura, Tadao; Altaf-Ul-Amin, Md; Saito, Akira; Kanaya, Shigehiko

2016-06-01

Conventionally, workflows examining transcription regulation networks from gene expression data involve distinct analytical steps. There is a need for pipelines that unify data mining and inference deduction into a singular framework to enhance interpretation and hypotheses generation. We propose a workflow that merges network construction with gene expression data mining focusing on regulation processes in the context of transcription factor driven gene regulation. The pipeline implements pathway-based modularization of expression profiles into functional units to improve biological interpretation. The integrated workflow was implemented as a web application software (TransReguloNet) with functions that enable pathway visualization and comparison of transcription factor activity between sample conditions defined in the experimental design. The pipeline merges differential expression, network construction, pathway-based abstraction, clustering and visualization. The framework was applied in analysis of actual expression datasets related to lung, breast and prostrate cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

Immersive Technology for Human-Centric Cyberphysical Systems in Complex Manufacturing Processes: A Comprehensive Overview of the Global Patent Profile Using Collective Intelligence

Directory of Open Access Journals (Sweden)

Usharani Hareesh Govindarajan

2018-01-01

Full Text Available Immersive technology for human-centric cyberphysical systems includes broad concepts that enable users in the physical world to connect with the cyberworld with a sense of immersion. Complex systems such as virtual reality, augmented reality, brain-computer interfaces, and brain-machine interfaces are emerging as immersive technologies that have the potential for improving manufacturing systems. Industry 4.0 includes all technologies, standards, and frameworks for the fourth industrial revolution to facilitate intelligent manufacturing. Industrial immersive technologies will be used for smart manufacturing innovation in the context of Industry 4.0’s human machine interfaces. This research provides a thorough review of the literature, construction of a domain ontology, presentation of patent metatrend statistical analysis, and data mining analysis using a technology function matrix and highlights technical and functional development trends using latent Dirichlet allocation (LDA models. A total of 179 references from the IEEE and IET databases and 2,672 patents are systematically analyzed to identify current trends. The paper establishes an essential foundation for the development of advanced human-centric cyberphysical systems in complex manufacturing processes.

Developing Integrated Care: Towards a development model for integrated care

NARCIS (Netherlands)

M.M.N. Minkman (Mirella)

2012-01-01

textabstractThe thesis adresses the phenomenon of integrated care. The implementation of integrated care for patients with a stroke or dementia is studied. Because a generic quality management model for integrated care is lacking, the study works towards building a development model for integrated

Training courses on integrated safety assessment modelling for waste repositories

International Nuclear Information System (INIS)

Mallants, D.

2007-01-01

Near-surface or deep repositories of radioactive waste are being developed and evaluated all over the world. Also, existing repositories for low- and intermediate-level waste often need to be re-evaluated to extend their license or to obtain permission for final closure. The evaluation encompasses both a technical feasibility as well as a safety analysis. The long term safety is usually demonstrated by means of performance or safety assessment. For this purpose computer models are used that calculate the migration of radionuclides from the conditioned radioactive waste, through engineered barriers to the environment (groundwater, surface water, and biosphere). Integrated safety assessment modelling addresses all relevant radionuclide pathways from source to receptor (man), using in combination various computer codes in which the most relevant physical, chemical, mechanical, or even microbiological processes are mathematically described. SCK-CEN organizes training courses in Integrated safety assessment modelling that are intended for individuals who have either a controlling or supervising role within the national radwaste agencies or regulating authorities, or for technical experts that carry out the actual post-closure safety assessment for an existing or new repository. Courses are organised by the Department of Waste and Disposal

Integrating knowledge seeking into knowledge management models and frameworks

Directory of Open Access Journals (Sweden)

Francois Lottering

2012-09-01

Objectives: This article investigates the theoretical status of the knowledge-seeking process in extant KM models and frameworks. It also statistically describes knowledge seeking and knowledge sharing practices in a sample of South African companies. Using this data, it proposes a KM model based on knowledge seeking. Method: Knowledge seeking is traced in a number of KM models and frameworks with a specific focus on Han Lai and Margaret Graham’s adapted KM cycle model, which separates knowledge seeking from knowledge sharing. This empirical investigation used a questionnaire to examine knowledge seeking and knowledge sharing practices in a sample of South African companies. Results: This article critiqued and elaborated on the adapted KM cycle model of Lai and Graham. It identified some of the key features of knowledge seeking practices in the workplace. It showed that knowledge seeking and sharing are human-centric actions and that seeking knowledge uses trust and loyalty as its basis. It also showed that one cannot separate knowledge seeking from knowledge sharing. Conclusion: The knowledge seeking-based KM model elaborates on Lai and Graham’s model. It provides insight into how and where people seek and share knowledge in the workplace. The article concludes that it is necessary to cement the place of knowledge seeking in KM models as well as frameworks and suggests that organisations should apply its findings to improving their knowledge management strategies.

Experiences with a researcher-centric ELN.

Science.gov (United States)

Badiola, Katrina A; Bird, Colin; Brocklesby, William S; Casson, John; Chapman, Richard T; Coles, Simon J; Cronshaw, James R; Fisher, Adam; Frey, Jeremy G; Gloria, Danmar; Grossel, Martin C; Hibbert, D Brynn; Knight, Nicola; Mapp, Lucy K; Marazzi, Luke; Matthews, Brian; Milsted, Andy; Minns, Russell S; Mueller, Karl T; Murphy, Kelly; Parkinson, Tim; Quinnell, Rosanne; Robinson, John S; Robertson, Murray N; Robins, Michael; Springate, Emma; Tizzard, Graham; Todd, Matthew H; Williamson, Alice E; Willoughby, Cerys; Yang, Erica; Ylioja, Paul M

2015-03-01

Electronic Laboratory Notebooks (ELNs) are progressively replacing traditional paper books in both commercial research establishments and academic institutions. University researchers require specific features from ELNs, given the need to promote cross-institutional collaborative working, to enable the sharing of procedures and results, and to facilitate publication. The LabTrove ELN, which we use as our exemplar, was designed to be researcher-centric ( i.e. , not only aimed at the individual researcher's basic needs rather than to a specific institutional or subject or disciplinary agenda, but also able to be tailored because it is open source). LabTrove is being used in a heterogeneous set of academic laboratories, for a range of purposes, including analytical chemistry, X-ray studies, drug discovery and a biomaterials project. Researchers use the ELN for recording experiments, preserving data collected, and for project coordination. This perspective article describes the experiences of those researchers from several viewpoints, demonstrating how a web-based open source electronic notebook can meet the diverse needs of academic researchers.

Unprecedented rates of land-use transformation in modeled climate change mitigation pathways

Science.gov (United States)

Turner, P. A.; Field, C. B.; Lobell, D. B.; Sanchez, D.; Mach, K. J.

2017-12-01

Integrated assessment models (IAMs) generate climate change mitigation scenarios consistent with global temperature targets. To limit warming to 2°, stylized cost-effective mitigation pathways rely on extensive deployments of carbon dioxide (CO2) removal (CDR) technologies, including multi-gigatonne yearly carbon removal from the atmosphere through bioenergy with carbon capture and storage (BECCS) and afforestation/reforestation. These assumed CDR deployments keep ambitious temperature limits in reach, but associated rates of land-use transformation have not been evaluated. For IAM scenarios from the IPCC Fifth Assessment Report, we compare rates of modeled land-use conversion to recent observed commodity crop expansions. In scenarios with a likely chance of limiting warming to 2° in 2100, the rate of energy cropland expansion supporting BECCS exceeds past commodity crop rates by several fold. In some cases, mitigation scenarios include abrupt reversal of deforestation, paired with massive afforestation/reforestation. Specifically, energy cropland in crop. If energy cropland instead increases at rates equal to recent soybean and oil palm expansions, the scale of CO2 removal possible with BECCS is 2.6 to 10-times lower, respectively, than the deployments <2° IAM scenarios rely upon in 2100. IAM mitigation pathways may favor multi-gigatonne biomass-based CDR given undervalued sociopolitical and techno-economic deployment barriers. Heroic modeled rates for land-use transformation imply that large-scale biomass-based CDR is not an easy solution to the climate challenge.

Integrated analysis of breast cancer cell lines reveals unique signaling pathways

Energy Technology Data Exchange (ETDEWEB)

Heiser, Laura M.; Wang, Nicholas J.; Talcott, Carolyn L.; Laderoute, Keith R.; Knapp, Merrill; Guan, Yinghui; Hu, Zhi; Ziyad, Safiyyah; Weber, Barbara L.; Laquerre, Sylvie; Jackson, Jeffrey R.; Wooster, Richard F.; Kuo, Wen-Lin; Gray, Joe W.; Spellman, Paul T.

2009-03-31

Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EGFR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes. We were interested in identifying subnetworks within the EGFR-MAPK pathway that are similarly deregulated across subsets of breast cancers. To that end, we mapped genomic, transcriptional and proteomic profiles for 30 breast cancer cell lines onto a curated Pathway Logic symbolic systems model of EGFR-MEK signaling. This model was comprised of 539 molecular states and 396 rules governing signaling between active states. We analyzed these models and identified several subtype specific subnetworks, including one that suggested PAK1 is particularly important in regulating the MAPK cascade when it is over-expressed. We hypothesized that PAK1 overexpressing cell lines would have increased sensitivity to MEK inhibitors. We tested this experimentally by measuring quantitative responses of 20 breast cancer cell lines to three MEK inhibitors. We found that PAK1 over-expressing luminal breast cancer cell lines are significantly more sensitive to MEK inhibition as compared to those that express PAK1 at low levels. This indicates that PAK1 over-expression may be a useful clinical marker to identify patient populations that may be sensitive to MEK inhibitors. All together, our results support the utility of symbolic system biology models for identification of therapeutic approaches that will be effective against breast cancer subsets.

Integrated analysis of breast cancer cell lines reveals unique signaling pathways.

Science.gov (United States)

Heiser, Laura M; Wang, Nicholas J; Talcott, Carolyn L; Laderoute, Keith R; Knapp, Merrill; Guan, Yinghui; Hu, Zhi; Ziyad, Safiyyah; Weber, Barbara L; Laquerre, Sylvie; Jackson, Jeffrey R; Wooster, Richard F; Kuo, Wen Lin; Gray, Joe W; Spellman, Paul T

2009-01-01

Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EgfR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes. We were interested in identifying subnetworks within the EgfR-MAPK pathway that are similarly deregulated across subsets of breast cancers. To that end, we mapped genomic, transcriptional and proteomic profiles for 30 breast cancer cell lines onto a curated Pathway Logic symbolic systems model of EgfR-MAPK signaling. This model was composed of 539 molecular states and 396 rules governing signaling between active states. We analyzed these models and identified several subtype-specific subnetworks, including one that suggested Pak1 is particularly important in regulating the MAPK cascade when it is over-expressed. We hypothesized that Pak1 over-expressing cell lines would have increased sensitivity to Mek inhibitors. We tested this experimentally by measuring quantitative responses of 20 breast cancer cell lines to three Mek inhibitors. We found that Pak1 over-expressing luminal breast cancer cell lines are significantly more sensitive to Mek inhibition compared to those that express Pak1 at low levels. This indicates that Pak1 over-expression may be a useful clinical marker to identify patient populations that may be sensitive to Mek inhibitors. All together, our results support the utility of symbolic system biology models for identification of therapeutic approaches that will be effective against breast cancer subsets.

Compromised Integrity of Central Visual Pathways in Patients With Macular Degeneration.

Science.gov (United States)

Malania, Maka; Konrad, Julia; Jägle, Herbert; Werner, John S; Greenlee, Mark W

2017-06-01

Macular degeneration (MD) affects the central retina and leads to gradual loss of foveal vision. Although, photoreceptors are primarily affected in MD, the retinal nerve fiber layer (RNFL) and central visual pathways may also be altered subsequent to photoreceptor degeneration. Here we investigate whether retinal damage caused by MD alters microstructural properties of visual pathways using diffusion-weighted magnetic resonance imaging. Six MD patients and six healthy control subjects participated in the study. Retinal images were obtained by spectral-domain optical coherence tomography (SD-OCT). Diffusion tensor images (DTI) and high-resolution T1-weighted structural images were collected for each subject. We used diffusion-based tensor modeling and probabilistic fiber tractography to identify the optic tract (OT) and optic radiations (OR), as well as nonvisual pathways (corticospinal tract and anterior fibers of corpus callosum). Fractional anisotropy (FA) and axial and radial diffusivity values (AD, RD) were calculated along the nonvisual and visual pathways. Measurement of RNFL thickness reveals that the temporal circumpapillary retinal nerve fiber layer was significantly thinner in eyes with macular degeneration than normal. While we did not find significant differences in diffusion properties in nonvisual pathways, patients showed significant changes in diffusion scalars (FA, RD, and AD) both in OT and OR. The results indicate that the RNFL and the white matter of the visual pathways are significantly altered in MD patients. Damage to the photoreceptors in MD leads to atrophy of the ganglion cell axons and to corresponding changes in microstructural properties of central visual pathways.

Cholinergic anti-inflammatory pathway in the non-obese diabetic mouse model

NARCIS (Netherlands)

Koopman, F. A.; Vosters, J. L.; Roescher, N.; Broekstra, N.; Tak, P. P.; Vervoordeldonk, M. J.

2015-01-01

Activation of the cholinergic anti-inflammatory pathway (CAP) has been shown to reduce inflammation in animal models, while abrogation of the pathway increases inflammation. We investigated whether modulation of CAP influences inflammation in the non-obese diabetic (NOD) mouse model for Sjögren's

Patient Portals as a Means of Information and Communication Technology Support to Patient- Centric Care Coordination - the Missing Evidence and the Challenges of Evaluation. A joint contribution of IMIA WG EVAL and EFMI WG EVAL.

Science.gov (United States)

Rigby, M; Georgiou, A; Hyppönen, H; Ammenwerth, E; de Keizer, N; Magrabi, F; Scott, P

2015-08-13

To review the potential contribution of Information and Communication Technology (ICT) to enable patient-centric and coordinated care, and in particular to explore the role of patient portals as a developing ICT tool, to assess the available evidence, and to describe the evaluation challenges. Reviews of IMIA, EFMI, and other initiatives, together with literature reviews. We present the progression from care coordination to care integration, and from patient-centric to person-centric approaches. We describe the different roles of ICT as an enabler of the effective presentation of information as and when needed. We focus on the patient's role as a co-producer of health as well as the focus and purpose of care. We discuss the need for changing organisational processes as well as the current mixed evidence regarding patient portals as a logical tool, and the reasons for this dichotomy, together with the evaluation principles supported by theoretical frameworks so as to yield robust evidence. There is expressed commitment to coordinated care and to putting the patient in the centre. However to achieve this, new interactive patient portals will be needed to enable peer communication by all stakeholders including patients and professionals. Few portals capable of this exist to date. The evaluation of these portals as enablers of system change, rather than as simple windows into electronic records, is at an early stage and novel evaluation approaches are needed.

Cascade of chromosomal rearrangements caused by a heterogeneous T-DNA integration supports the double-stranded break repair model for T-DNA integration.

Science.gov (United States)

Hu, Yufei; Chen, Zhiyu; Zhuang, Chuxiong; Huang, Jilei

2017-06-01

Transferred DNA (T-DNA) from Agrobacterium tumefaciens can be integrated into the plant genome. The double-stranded break repair (DSBR) pathway is a major model for T-DNA integration. From this model, we expect that two ends of a T-DNA molecule would invade into a single DNA double-stranded break (DSB) or independent DSBs in the plant genome. We call the later phenomenon a heterogeneous T-DNA integration, which has never been observed. In this work, we demonstrated it in an Arabidopsis T-DNA insertion mutant seb19. To resolve the chromosomal structural changes caused by T-DNA integration at both the nucleotide and chromosome levels, we performed inverse PCR, genome resequencing, fluorescence in situ hybridization and linkage analysis. We found, in seb19, a single T-DNA connected two different chromosomal loci and caused complex chromosomal rearrangements. The specific break-junction pattern in seb19 is consistent with the result of heterogeneous T-DNA integration but not of recombination between two T-DNA insertions. We demonstrated that, in seb19, heterogeneous T-DNA integration evoked a cascade of incorrect repair of seven DSBs on chromosomes 4 and 5, and then produced translocation, inversion, duplication and deletion. Heterogeneous T-DNA integration supports the DSBR model and suggests that two ends of a T-DNA molecule could be integrated into the plant genome independently. Our results also show a new origin of chromosomal abnormalities. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Operational integration in primary health care: patient encounters and workflows.

Science.gov (United States)

Sifaki-Pistolla, Dimitra; Chatzea, Vasiliki-Eirini; Markaki, Adelais; Kritikos, Kyriakos; Petelos, Elena; Lionis, Christos

2017-11-29

Despite several countrywide attempts to strengthen and standardise the primary healthcare (PHC) system, Greece is still lacking a sustainable, policy-based model of integrated services. The aim of our study was to identify operational integration levels through existing patient care pathways and to recommend an alternative PHC model for optimum integration. The study was part of a large state-funded project, which included 22 randomly selected PHC units located across two health regions of Greece. Dimensions of operational integration in PHC were selected based on the work of Kringos and colleagues. A five-point Likert-type scale, coupled with an algorithm, was used to capture and transform theoretical framework features into measurable attributes. PHC services were grouped under the main categories of chronic care, urgent/acute care, preventive care, and home care. A web-based platform was used to assess patient pathways, evaluate integration levels and propose improvement actions. Analysis relied on a comparison of actual pathways versus optimal, the latter ones having been identified through literature review. Overall integration varied among units. The majority (57%) of units corresponded to a basic level. Integration by type of PHC service ranged as follows: basic (86%) or poor (14%) for chronic care units, poor (78%) or basic (22%) for urgent/acute care units, basic (50%) for preventive care units, and partial or basic (50%) for home care units. The actual pathways across all four categories of PHC services differed from those captured in the optimum integration model. Certain similarities were observed in the operational flows between chronic care management and urgent/acute care management. Such similarities were present at the highest level of abstraction, but also in common steps along the operational flows. Existing patient care pathways were mapped and analysed, and recommendations for an optimum integration PHC model were made. The developed web

An integrated Biophysical CGE model to provide Sustainable Development Goal insights

Science.gov (United States)

Sanchez, Marko; Cicowiez, Martin; Howells, Mark; Zepeda, Eduardo

2016-04-01

Future projected changes in the energy system will inevitably result in changes to the level of appropriation of environmental resources, particularly land and water, and this will have wider implications for environmental sustainability, and may affect other sectors of the economy. An integrated climate, land, energy and water (CLEW) system will provide useful insights, particularly with regard to the environmental sustainability. However, it will require adequate integration with other tools to detect economic impacts and broaden the scope for policy analysis. A computable general equilibrium (CGE) model is a well suited tool to channel impacts, as detected in a CLEW analysis, onto all sectors of the economy, and evaluate trade-offs and synergies, including those of possible policy responses. This paper will show an application of such integration in a single-country CGE model with the following key characteristics. Climate is partly exogenous (as proxied by temperature and rainfall) and partly endogenous (as proxied by emissions generated by different sectors) and has an impact on endogenous variables such as land productivity and labor productivity. Land is a factor of production used in agricultural and forestry activities which can be of various types if land use alternatives (e.g., deforestation) are to be considered. Energy is an input to the production process of all economic sectors and a consumption good for households. Because it is possible to allow for substitution among different energy sources (e.g. renewable vs non-renewable) in the generation of electricity, the production process of energy products can consider the use of natural resources such as oil and water. Water, data permitting, can be considered as an input into the production process of agricultural sectors, which is particularly relevant in case of irrigation. It can also be considered as a determinant of total factor productivity in hydro-power generation. The integration of a CLEW

Risk methodology for geologic disposal of radioactive waste: model description and user manual for Pathways model

International Nuclear Information System (INIS)

Helton, J.C.; Kaestner, P.C.

1981-03-01

A model for the environmental movement and human uptake of radionuclides is presented. This model is designated the Pathways-to-Man Model and was developed as part of a project funded by the Nuclear Regulatory Commission to design a methodology to assess the risk associated with the geologic disposal of high-level radioactive waste. The Pathways-to-Man Model is divided into two submodels. One of these, the Environmental Transport Model, represents the long-term distribution and accumulation of radionuclides in the environment. This model is based on a mixed-cell approach and describes radionuclide movement with a system of linear differential equations. The other, the Transport-to-Man Model, represents the movement of radionuclides from the environment to man. This model is based on concentration ratios. General descriptions of these models are provided in this report. Further, documentation is provided for the computer program which implements the Pathways Model

Simplified life cycle assessment models: methodological framework and applications to energy pathways

International Nuclear Information System (INIS)

Padey, Pierryves

2013-01-01

The energy transition debate is a key issue for today and the coming years. One of the challenges is to limit the environmental impacts of electricity production. Decision support tools, sufficiently accurate, simple to use, accounting for environmental aspects and favoring future energetic choices, must be implemented. However, the environmental assessment of the energy pathways is complex, and it means considering a two levels characterization. The 'energy pathway' is the first level and corresponds to its environmental distribution, to compare overall pathways. The 'system pathway' is the 2. level and compares environmental impacts of systems within each pathway. We have devised a generic methodology covering both necessary characterization levels by estimating the energy pathways environmental profiles while allowing a simple comparison of its systems environmental impacts. This methodology is based on the definition of a parameterized Life Cycle Assessment model and considers, through a Global Sensitivity Analysis, the environmental impacts of a large sample of systems representative of an energy pathway. As a second step, this methodology defines simplified models based on few key parameters identified as inducing the largest variability in the energy pathway environmental impacts. These models assess in a simple way the systems environmental impacts, avoiding any complex LCAs. This reduction methodology has been applied to the onshore wind power energy pathway in Europe and the photovoltaic energy pathway in France. (author)

Integration of Nutrition and Economic Development in Sri Lanka: The Graduation Model

International Nuclear Information System (INIS)

Peiris, Dilka; Fernando, Sisira

2014-01-01

-microfinance (savings clubs), skills/technical/asset transfer and microfinance, depending on the PLSR ranking. Economic development activities include skills transfer, savings clubs and small business development. Progress along the Graduation Pathway is measured by improvements in both economic well-being and child nutritional status. The Graduation Model optimizes development resources through its integrated pathway to economic self-sufficiency and improved nutrition. Families are empowered to improve their living conditions and children’s nutritional status. Future plans include expansion of the Model to new project areas and incorporation of early childhood education and agriculture interventions. World Vision Lanka has achieved significant achievements by integration of economic development and nutrition through the graduation pathway model. 24% of Poorest of the Poor (PoP) families who were identified at the baseline survey were reduced to 19.2% within a two years which is a 4.8% progress. The number of Poor (P) families reduced from 31% to 27.6%; Vulnerable non-poor families reduced from 23% to 19.5% and Small and Medium entrepreneur families increased from 14% to 17%. After two years of implementation in one project area, significant reductions were noted in the prevalence of anaemia (71% to 33%) and underweight (32% to 26%) among children 6-59 months. Changes were seen in wasting (17% to 16%) or stunting (26% to 24%). (author)

Construction and completion of flux balance models from pathway databases.

Science.gov (United States)

Latendresse, Mario; Krummenacker, Markus; Trupp, Miles; Karp, Peter D

2012-02-01

Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models can be time consuming and tedious because of the difficulty in assembling completely accurate descriptions of these sets, and in identifying errors in the composition of these sets. For example, the presence of a single non-producible metabolite in the biomass will make the entire model infeasible. Other difficulties in FBA modeling are that model distributions, and predicted fluxes, can be cryptic and difficult to understand. We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant high-flux loops, solve FBA models once they are generated and model the effects of gene knockouts. MetaFlux has been validated through construction of FBA models for Escherichia coli and Homo sapiens. Pathway Tools with MetaFlux is freely available to academic users, and for a fee to commercial users. Download from: biocyc.org/download.shtml. mario.latendresse@sri.com Supplementary data are available at Bioinformatics online.

Developing a customer-centric digital marketing communication strategy : Commissioner Salusfin Oy

OpenAIRE

Lokteva, Daria

2015-01-01

The present study relates to the field of digital marketing communication. The purpose of the study is to create a customer-centric digital marketing communication strategy for Salusfin, a technological start-up company in need of an effective digital strategy. The key issue of the study is to provide an insight on how digital marketing communication tools can fulfil the needs and benefit the company while adding value for the customers. The research questions addressed in the study are 1. Wh...

Ambient Assisted Living Systems in the Context of Human Centric Sensing and IoT Concept

DEFF Research Database (Denmark)

Zaric, Nicola; Pejanovic-Djurisic, Milica; Mihovska, Albena Dimitrova

2016-01-01

This paper proposes the concept of Human Centric Sensing in the context of Internet of Things and Ambient Assisted Living. The paper uses a case study to present and analyze the proposed idea, and identifies the main challenges and open issues that require research and policy attention....

Pathway Model of the Kinetics of the TGFbeta Antagonist Smad7 and Cross-Talk with the ATM and WNT Pathways

Science.gov (United States)

Carra, Claudio; Wang, Minli; Huff, Janice L.; Hada, Megumi; ONeill, Peter; Cucinotta, Francis A.

2010-01-01

Signal transduction controls cellular and tissue responses to radiation. Transforming growth factor beta (TGFbeta) is an important regulator of cell growth and differentiation and tissue homeostasis, and is often dis-regulated in tumor formation. Mathematical models of signal transduction pathways can be used to elucidate how signal transduction varies with radiation quality, and dose and dose-rate. Furthermore, modeling of tissue specific responses can be considered through mechanistic based modeling. We developed a mathematical model of the negative feedback regulation by Smad7 in TGFbeta-Smad signaling and are exploring possible connections to the WNT/beta -catenin, and ATM/ATF2 signaling pathways. A pathway model of TGFbeta-Smad signaling that includes Smad7 kinetics based on data in the scientific literature is described. Kinetic terms included are TGFbeta/Smad transcriptional regulation of Smad7 through the Smad3-Smad4 complex, Smad7-Smurf1 translocation from nucleus to cytoplasm, and Smad7 negative feedback regulation of the TGFO receptor through direct binding to the TGFO receptor complex. The negative feedback controls operating in this pathway suggests non-linear responses in signal transduction, which are described mathematically. We then explored possibilities for cross-talk mediated by Smad7 between DNA damage responses mediated by ATM, and with the WNT pathway and consider the design of experiments to test model driven hypothesis. Numerical comparisons of the mathematical model to experiments and representative predictions are described.

AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces

Science.gov (United States)

2016-01-01

Inhibition of protein–protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structural characterization of the surface using geometry-based pocket-detection methods. An attractive mapping strategy—that builds on the principles of fragment-based drug discovery (FBDD)—is to detect the fragment-centric modularity at the protein surface and then characterize the large PPI interface as a set of localized, fragment-targetable interaction regions. Here, we introduce AlphaSpace, a computational analysis tool designed for fragment-centric topographical mapping (FCTM) of PPI interfaces. Our approach uses the alpha sphere construct, a geometric feature of a protein’s Voronoi diagram, to map out concave interaction space at the protein surface. We introduce two new features—alpha-atom and alpha-space—and the concept of the alpha-atom/alpha-space pair to rank pockets for fragment-targetability and to facilitate the evaluation of pocket/fragment complementarity. The resulting high-resolution interfacial map of targetable pocket space can be used to guide the rational design and optimization of small molecule or biomimetic PPI inhibitors. PMID:26225450

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

Science.gov (United States)

Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W

2016-09-01

Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Linking the X3D Pathway to Integral Field Spectrographs: YSNR 1E 0102.2-7219 in the SMC as a Case Study

Science.gov (United States)

Vogt, Frédéric P. A.; Seitenzahl, Ivo R.; Dopita, Michael A.; Ruiter, Ashley J.

2017-05-01

The concept of the x3d pathway was introduced by Vogt et al. as a new approach to sharing and publishing three-dimensional structures interactively in online scientific journals. The core characteristics of the x3d pathway are that: (1) it does not rely on specific software, but rather a file format (x3d), (2) it can be implemented using fully open-source tools, and (3) article readers can access the interactive models using most main stream web browsers without the need for any additional plugins. In this article, we further demonstrate the potential of the x3d pathway to visualize data sets from optical integral field spectrographs. We use recent observations of the oxygen-rich young supernova remnant 1E 0102.2-7219 in the Small Magellanic Cloud to implement additional x3dom tools & techniques and expand the range of interactions that can be offered to article readers. In particular, we present a set of javascript functions allowing the creation and interactive handling of clip planes, effectively allowing users to take measurements of distances and angles directly from the interactive model itself.

Athena: Towards Decision-Centric Anticipatory Sensor Information Delivery

Directory of Open Access Journals (Sweden)

Jongdeog Lee

2018-01-01

Full Text Available The paper introduces a new direction in quality-of-service-aware networked sensing that designs communication protocols and scheduling policies for data delivery that are optimized specifically for decision needs. The work complements present decision monitoring and support tools and falls in the larger framework of decision-driven resource management. A hallmark of the new protocols is that they are aware of the inference structure used to arrive at decisions (from logical predicates, as well as the data (and data quality that need to be furnished to successfully evaluate the unknowns on which these decisions are based. Such protocols can therefore anticipate and deliver precisely the right data, at the right level of quality, from the right sources, at the right time, to enable valid and timely decisions at minimum cost to the underlying network. This paper presents the decision model used and the protocol design philosophy, reviews the key recent results and describes a novel system, called Athena, that is the first to embody the aforementioned data delivery paradigm. Evaluation results are presented that compare the performance of decision-centric anticipatory information delivery to several baselines, demonstrating its various advantages in terms of decision timeliness, validity and network resources used. The paper concludes with a discussion of remaining future challenges in this emerging area.

Qualitative Analysis of Integration Adapter Modeling

OpenAIRE

Ritter, Daniel; Holzleitner, Manuel

2015-01-01

Integration Adapters are a fundamental part of an integration system, since they provide (business) applications access to its messaging channel. However, their modeling and configuration remain under-represented. In previous work, the integration control and data flow syntax and semantics have been expressed in the Business Process Model and Notation (BPMN) as a semantic model for message-based integration, while adapter and the related quality of service modeling were left for further studi...

Aquatic pathways model to predict the fate of phenolic compounds

Energy Technology Data Exchange (ETDEWEB)

Aaberg, R.L.; Peloquin, R.A.; Strenge, D.L.; Mellinger, P.J.

1983-04-01

Organic materials released from energy-related activities could affect human health and the environment. To better assess possible impacts, we developed a model to predict the fate of spills or discharges of pollutants into flowing or static bodies of fresh water. A computer code, Aquatic Pathways Model (APM), was written to implement the model. The computer programs use compartmental analysis to simulate aquatic ecosystems. The APM estimates the concentrations of chemicals in fish tissue, water and sediment, and is therefore useful for assessing exposure to humans through aquatic pathways. The APM will consider any aquatic pathway for which the user has transport data. Additionally, APM will estimate transport rates from physical and chemical properties of chemicals between several key compartments. The major pathways considered are biodegradation, fish and sediment uptake, photolysis, and evaporation. The model has been implemented with parameters for distribution of phenols, an important class of compounds found in the water-soluble fractions of coal liquids. Current modeling efforts show that, in comparison with many pesticides and polyaromatic hydrocarbons (PAH), the lighter phenolics (the cresols) are not persistent in the environment. The properties of heavier molecular weight phenolics (indanols, naphthols) are not well enough understood at this time to make similar judgements. For the twelve phenolics studied, biodegradation appears to be the major pathway for elimination from aquatic environments. A pond system simulation (using APM) of a spill of solvent refined coal (SRC-II) materials indicates that phenol, cresols, and other single cyclic phenolics are degraded to 16 to 25 percent of their original concentrations within 30 hours. Adsorption of these compounds into sediments and accumulation by fish was minor.

Hydrological Modeling Reproducibility Through Data Management and Adaptors for Model Interoperability

Science.gov (United States)

Turner, M. A.

2015-12-01

Because of a lack of centralized planning and no widely-adopted standards among hydrological modeling research groups, research communities, and the data management teams meant to support research, there is chaos when it comes to data formats, spatio-temporal resolutions, ontologies, and data availability. All this makes true scientific reproducibility and collaborative integrated modeling impossible without some glue to piece it all together. Our Virtual Watershed Integrated Modeling System provides the tools and modeling framework hydrologists need to accelerate and fortify new scientific investigations by tracking provenance and providing adaptors for integrated, collaborative hydrologic modeling and data management. Under global warming trends where water resources are under increasing stress, reproducible hydrological modeling will be increasingly important to improve transparency and understanding of the scientific facts revealed through modeling. The Virtual Watershed Data Engine is capable of ingesting a wide variety of heterogeneous model inputs, outputs, model configurations, and metadata. We will demonstrate one example, starting from real-time raw weather station data packaged with station metadata. Our integrated modeling system will then create gridded input data via geostatistical methods along with error and uncertainty estimates. These gridded data are then used as input to hydrological models, all of which are available as web services wherever feasible. Models may be integrated in a data-centric way where the outputs too are tracked and used as inputs to "downstream" models. This work is part of an ongoing collaborative Tri-state (New Mexico, Nevada, Idaho) NSF EPSCoR Project, WC-WAVE, comprised of researchers from multiple universities in each of the three states. The tools produced and presented here have been developed collaboratively alongside watershed scientists to address specific modeling problems with an eye on the bigger picture of

Integrability of the Rabi Model

International Nuclear Information System (INIS)

Braak, D.

2011-01-01

The Rabi model is a paradigm for interacting quantum systems. It couples a bosonic mode to the smallest possible quantum model, a two-level system. I present the analytical solution which allows us to consider the question of integrability for quantum systems that do not possess a classical limit. A criterion for quantum integrability is proposed which shows that the Rabi model is integrable due to the presence of a discrete symmetry. Moreover, I introduce a generalization with no symmetries; the generalized Rabi model is the first example of a nonintegrable but exactly solvable system.

Structuring research methods and data with the research object model: genomics workflows as a case study.

Science.gov (United States)

Hettne, Kristina M; Dharuri, Harish; Zhao, Jun; Wolstencroft, Katherine; Belhajjame, Khalid; Soiland-Reyes, Stian; Mina, Eleni; Thompson, Mark; Cruickshank, Don; Verdes-Montenegro, Lourdes; Garrido, Julian; de Roure, David; Corcho, Oscar; Klyne, Graham; van Schouwen, Reinout; 't Hoen, Peter A C; Bechhofer, Sean; Goble, Carole; Roos, Marco

2014-01-01

One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?". Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro.

PATHWAY: a dynamic foodchain model to predict radionuclide ingestion after fallout deposition. Final report, September 17, 1979-December 31, 1985

International Nuclear Information System (INIS)

Whicker, F.W.; Kirchner, T.B.

1986-01-01

This paper describes the structure and basis for parameter values of a computerized foodchain transport model for radionuclides. The model, called ''PATHWAY,'' estimates the time-integrated intake by humans of twenty radionuclides after a single deposition of radioactive material from the atmosphere to the landscape. The model solves a set of differential equations to estimate the inventories and concentrations of radionuclides in three soil layers and numerous types of vegetation, animal tissues and animal products as a function of time following a deposition event. Dynamic processes considered in the model include foliar interception, weathering and absorption; plant growth, uptake, harvest and senescence; soil resuspension, percolation, leaching and tillage; radioactive decay; livestock ingestion, absorption, excretion; and etc. An age- and sex-specific human diet is embodied in the model to permit calculation of time-dependent radionuclide ingestion rates, which are then numerically integrated. 3 figs., 10 tabs

Ferocia gen. nov., a new centric diatom genus (Bacillariophyceae) from the sub-Antarctic region

Czech Academy of Sciences Publication Activity Database

Van de Vijver, B.; Chattová, B.; Lebouvier, M.; Houk, Václav

2017-01-01

Roč. 332, č. 1 (2017), s. 22-30 ISSN 1179-3155 R&D Projects: GA ČR GA205/05/0204 Institutional research plan: CEZ:AV0Z60050516 Institutional support: RVO:67985939 Keywords : centric diatoms * new genus * Melosira * Ferocia * sub-Antarctic Region Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 1.240, year: 2016

Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia.

Science.gov (United States)

Wu, Chong; Pan, Wei

2018-04-01

Many genetic variants affect complex traits through gene expression, which can be exploited to boost statistical power and enhance interpretation in genome-wide association studies (GWASs) as demonstrated by the transcriptome-wide association study (TWAS) approach. Furthermore, due to polygenic inheritance, a complex trait is often affected by multiple genes with similar functions as annotated in gene pathways. Here, we extend TWAS from gene-based analysis to pathway-based analysis: we integrate public pathway collections, expression quantitative trait locus (eQTL) data and GWAS summary association statistics (or GWAS individual-level data) to identify gene pathways associated with complex traits. The basic idea is to weight the SNPs of the genes in a pathway based on their estimated cis-effects on gene expression, then adaptively test for association of the pathway with a GWAS trait by effectively aggregating possibly weak association signals across the genes in the pathway. The P values can be calculated analytically and thus fast. We applied our proposed test with the KEGG and GO pathways to two schizophrenia (SCZ) GWAS summary association data sets, denoted by SCZ1 and SCZ2 with about 20,000 and 150,000 subjects, respectively. Most of the significant pathways identified by analyzing the SCZ1 data were reproduced by the SCZ2 data. Importantly, we identified 15 novel pathways associated with SCZ, such as GABA receptor complex (GO:1902710), which could not be uncovered by the standard single SNP-based analysis or gene-based TWAS. The newly identified pathways may help us gain insights into the biological mechanism underlying SCZ. Our results showcase the power of incorporating gene expression information and gene functional annotations into pathway-based association testing for GWAS. © 2018 WILEY PERIODICALS, INC.

Connecting Social Science and Information Technology through an Interface-Centric Framework of Analysis

Directory of Open Access Journals (Sweden)

Mikael Sundström

2008-06-01

Full Text Available The gathering pace of IT innovation has, or ought to have had notable methodological repercussions for the social-science community (and beyond. Where yesterday the researcher could unhurriedly unlock the social-scientific significance of a chosen medium, secure in the knowledge that his or her work would have bearing for many years, by now there is every reason to confront a fear that the prodded IT implementation may in fact be gone or at least heavily altered by the time such comprehensive research is concluded. This paper will propose a complementing systematic "interface-centric" research model capable of interconnecting a non-finite variety of IT implementations and social science studies in a coherent way. The paper also outlines how users "downstream", whether political actors or technology operators can use the proposed framework to more easily approach and weight academic input when evaluating complex IT effects.

Chiropractic Integrated Care Pathway for Low Back Pain in Veterans: Results of a Delphi Consensus Process.

Science.gov (United States)

Lisi, Anthony J; Salsbury, Stacie A; Hawk, Cheryl; Vining, Robert D; Wallace, Robert B; Branson, Richard; Long, Cynthia R; Burgo-Black, A Lucille; Goertz, Christine M

2018-02-01

The purpose of this study was to develop an integrated care pathway for doctors of chiropractic, primary care providers, and mental health professionals who manage veterans with low back pain, with or without mental health comorbidity, within Department of Veterans Affairs health care facilities. The research method used was a consensus process. A multidisciplinary investigative team reviewed clinical guidelines and Veterans Affairs pain and mental health initiatives to develop seed statements and care algorithms to guide chiropractic management and collaborative care of veterans with low back pain. A 5-member advisory committee approved initial recommendations. Veterans Affairs-based panelists (n = 58) evaluated the pathway via e-mail using a modified RAND/UCLA methodology. Consensus was defined as agreement by 80% of panelists. The modified Delphi process was conducted in July to December 2016. Most (93%) seed statements achieved consensus during the first round, with all statements reaching consensus after 2 rounds. The final care pathway addressed the topics of informed consent, clinical evaluation including history and examination, screening for red flags, documentation, diagnostic imaging, patient-reported outcomes, adverse event reporting, chiropractic treatment frequency and duration standards, tailored approaches to chiropractic care in veteran populations, and clinical presentation of common mental health conditions. Care algorithms outlined chiropractic case management and interprofessional collaboration and referrals between doctors of chiropractic and primary care and mental health providers. This study offers an integrative care pathway that includes chiropractic care for veterans with low back pain. Copyright © 2018. Published by Elsevier Inc.

A document centric metadata registration tool constructing earth environmental data infrastructure

Science.gov (United States)

Ichino, M.; Kinutani, H.; Ono, M.; Shimizu, T.; Yoshikawa, M.; Masuda, K.; Fukuda, K.; Kawamoto, H.

2009-12-01

DIAS (Data Integration and Analysis System) is one of GEOSS activities in Japan. It is also a leading part of the GEOSS task with the same name defined in GEOSS Ten Year Implementation Plan. The main mission of DIAS is to construct data infrastructure that can effectively integrate earth environmental data such as observation data, numerical model outputs, and socio-economic data provided from the fields of climate, water cycle, ecosystem, ocean, biodiversity and agriculture. Some of DIAS's data products are available at the following web site of http://www.jamstec.go.jp/e/medid/dias. Most of earth environmental data commonly have spatial and temporal attributes such as the covering geographic scope or the created date. The metadata standards including these common attributes are published by the geographic information technical committee (TC211) in ISO (the International Organization for Standardization) as specifications of ISO 19115:2003 and 19139:2007. Accordingly, DIAS metadata is developed with basing on ISO/TC211 metadata standards. From the viewpoint of data users, metadata is useful not only for data retrieval and analysis but also for interoperability and information sharing among experts, beginners and nonprofessionals. On the other hand, from the viewpoint of data providers, two problems were pointed out after discussions. One is that data providers prefer to minimize another tasks and spending time for creating metadata. Another is that data providers want to manage and publish documents to explain their data sets more comprehensively. Because of solving these problems, we have been developing a document centric metadata registration tool. The features of our tool are that the generated documents are available instantly and there is no extra cost for data providers to generate metadata. Also, this tool is developed as a Web application. So, this tool does not demand any software for data providers if they have a web-browser. The interface of the tool

Nutrition pathways in consequence modeling

International Nuclear Information System (INIS)

Tveten, U.

1982-01-01

During 1979-1980 calculations of risk from waste transportation by truck (fire following collision) and fire in temporary storage for waste were performed. A modified version of the consequence model of WASH-1400 (CRAC) was used. Two exposure pathways dominated the results: external exposure from material on the ground and exposure via nutrition. Many of the parameters entering into the nutrition calculations will depend upon local conditions, like soil composition, crop yield, etc. It was decided to collect detailed comments upon the CRAC nutritions model and parameter values from radioecologists in the four Nordic countries. Four alternate sets of parameter values were derived from these comments, and new risk calculations were performed

KeyPathwayMinerWeb

DEFF Research Database (Denmark)

List, Markus; Alcaraz, Nicolas; Dissing-Hansen, Martin

2016-01-01

, for instance), KeyPathwayMiner extracts connected sub-networks containing a high number of active or differentially regulated genes (proteins, metabolites) in the molecular profiles. The web interface at (http://keypathwayminer.compbio.sdu.dk) implements all core functionalities of the KeyPathwayMiner tool set......We present KeyPathwayMinerWeb, the first online platform for de novo pathway enrichment analysis directly in the browser. Given a biological interaction network (e.g. protein-protein interactions) and a series of molecular profiles derived from one or multiple OMICS studies (gene expression...... such as data integration, input of background knowledge, batch runs for parameter optimization and visualization of extracted pathways. In addition to an intuitive web interface, we also implemented a RESTful API that now enables other online developers to integrate network enrichment as a web service...

Living in a Patient-Centric Universe.

Science.gov (United States)

Kraus, Dennis H

2016-12-01

Patients with head and neck cancer face a number of challenges in terms of treatment, cure of their underlying malignant condition, and quality of survivorship. This presentation will focus on the patient perception of both the quality of care and the empathy and availability of the head and neck oncology team. It has become evident that the quality of survivorship plays a central role in the patient's decision-making process. The process of decision making by the patient facing head and neck cancer and the impact on treatment choices will be explored. The ability of the patient and her or his support system to navigate through the increasingly complicated health care system will be considered, with an emphasis on strategies for success. Finally, the role of the of the head and neck surgeon, and the need for physician wellness in predicating successful patient outcomes will be considered. The ultimate goal of achieving optimal care, superior patient outcomes, and patient satisfaction is the true objective of the concept of living in a patient-centric universe.

Evaluation of the reproducibility of two techniques used to determine and record centric relation in angle's class I patients

Directory of Open Access Journals (Sweden)

Fernanda Paixão

2007-08-01

Full Text Available The centric relation is a mandibular position that determines a balance relation among the temporomandibular joints, the chew muscles and the occlusion. This position makes possible to the dentist to plan and to execute oral rehabilitation respecting the physiological principles of the stomatognathic system. The aim of this study was to investigate the reproducibility of centric relation records obtained using two techniques: Dawson's Bilateral Manipulation and Gysi's Gothic Arch Tracing. Twenty volunteers (14 females and 6 males with no dental loss, presenting occlusal contacts according to those described in Angle's I classification and without signs and symptoms of temporomandibular disorders were selected. All volunteers were submitted five times with a 1-week interval, always in the same schedule, to the Dawson's Bilateral Manipulation and to the Gysi's Gothic Arch Tracing with aid of an intraoral apparatus. The average standard error of each technique was calculated (Bilateral Manipulation 0.94 and Gothic Arch Tracing 0.27. Shapiro-Wilk test was applied and the results allowed application of Student's t-test (sampling error of 5%. The techniques showed different degrees of variability. The Gysi's Gothic Arch Tracing was found to be more accurate than the Bilateral Manipulation in reproducing the centric relation records.

Resistance against brute-force attacks on stateless forwarding in information centric networking

OpenAIRE

Alzahrani, Bander A.; Reed, Martin J.; Vassilakis, Vassilios G.

2015-01-01

Line Speed Publish/Subscribe Inter-networking (LIPSIN) is one of the proposed forwarding mechanisms in Information Centric Networking (ICN). It is a stateless source-routing approach based on Bloom filters. However, it has been shown that LIPSIN is vulnerable to brute-force attacks which may lead to distributed denial-of-service (DDoS) attacks and unsolicited messages. In this work, we propose a new forwarding approach that maintains the advantages of Bloom filter based forwarding while allow...

Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis.

Science.gov (United States)

Cava, Claudia; Bertoli, Gloria; Colaprico, Antonio; Olsen, Catharina; Bontempi, Gianluca; Castiglioni, Isabella

2018-01-06

Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumourigenesis has yet to be completely understood. Pathways and networks are important tools to explain the role of genes in functional genomic studies. However, few methods consider the functional non-equal roles of genes in pathways and the complex gene-gene interactions in a network. We present a novel method in pan-cancer analysis that identifies de-regulated genes with a functional role by integrating pathway and network data. A pan-cancer analysis of 7158 tumour/normal samples from 16 cancer types identified 895 genes with a central role in pathways and de-regulated in cancer. Comparing our approach with 15 current tools that identify cancer driver genes, we found that 35.6% of the 895 genes identified by our method have been found as cancer driver genes with at least 2/15 tools. Finally, we applied a machine learning algorithm on 16 independent GEO cancer datasets to validate the diagnostic role of cancer driver genes for each cancer. We obtained a list of the top-ten cancer driver genes for each cancer considered in this study. Our analysis 1) confirmed that there are several known cancer driver genes in common among different types of cancer, 2) highlighted that cancer driver genes are able to regulate crucial pathways.

Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

Directory of Open Access Journals (Sweden)

Jason Gunther Lomnitz

2016-07-01

Full Text Available Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1 enumeration of the repertoire of model phenotypes, (2 prediction of values for the parameters for any model phenotype and (3 analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3 and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between 3 stable states by transient stimulation through one of two input channels: a positive channel that increases

Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

Science.gov (United States)

Lomnitz, Jason G.; Savageau, Michael A.

2016-01-01

Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

2016-01-01

Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Science.gov (United States)

Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

2003-11-01

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration.

Science.gov (United States)

Arneson, Douglas; Bhattacharya, Anindya; Shu, Le; Mäkinen, Ville-Petteri; Yang, Xia

2016-09-09

Human diseases are commonly the result of multidimensional changes at molecular, cellular, and systemic levels. Recent advances in genomic technologies have enabled an outpour of omics datasets that capture these changes. However, separate analyses of these various data only provide fragmented understanding and do not capture the holistic view of disease mechanisms. To meet the urgent needs for tools that effectively integrate multiple types of omics data to derive biological insights, we have developed Mergeomics, a computational pipeline that integrates multidimensional disease association data with functional genomics and molecular networks to retrieve biological pathways, gene networks, and central regulators critical for disease development. To make the Mergeomics pipeline available to a wider research community, we have implemented an online, user-friendly web server ( http://mergeomics. idre.ucla.edu/ ). The web server features a modular implementation of the Mergeomics pipeline with detailed tutorials. Additionally, it provides curated genomic resources including tissue-specific expression quantitative trait loci, ENCODE functional annotations, biological pathways, and molecular networks, and offers interactive visualization of analytical results. Multiple computational tools including Marker Dependency Filtering (MDF), Marker Set Enrichment Analysis (MSEA), Meta-MSEA, and Weighted Key Driver Analysis (wKDA) can be used separately or in flexible combinations. User-defined summary-level genomic association datasets (e.g., genetic, transcriptomic, epigenomic) related to a particular disease or phenotype can be uploaded and computed real-time to yield biologically interpretable results, which can be viewed online and downloaded for later use. Our Mergeomics web server offers researchers flexible and user-friendly tools to facilitate integration of multidimensional data into holistic views of disease mechanisms in the form of tissue-specific key regulators

A multi-pathway model for photosynthetic reaction center

International Nuclear Information System (INIS)

Qin, M.; Shen, H. Z.; Yi, X. X.

2016-01-01

Charge separation occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine. Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem II reaction center (PSII RC) to describe the charge separation. Our model mainly considers two charge-separation pathways which is more than that typically considered in the published literature. We explore how these cross-couplings increase the current and power of the charge separation and discuss the effects of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PSII RC and dephasing induced by environments is also explored, and extension from two pathways to multiple pathways is made. These results suggest that noise-induced quantum coherence helps to suppress the influence of acceptor-to-donor charge recombination, and besides, nature-mimicking architectures with engineered multiple pathways for charge separations might be better for artificial solar energy devices considering the influence of environments.

BrahmVE platform for design and test of Large Scale Multi-agent Human-centric Mission Concepts, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — This Phase I proposal seeks support to extend the BrahmsVE architecture to support a multi-agent human-centric simulation of a hypothetical future ISS which is...

Modular and Stochastic Approaches to Molecular Pathway Models of ATM, TGF beta, and WNT Signaling

Science.gov (United States)

Cucinotta, Francis A.; O'Neill, Peter; Ponomarev, Artem; Carra, Claudio; Whalen, Mary; Pluth, Janice M.

2009-01-01

Deterministic pathway models that describe the biochemical interactions of a group of related proteins, their complexes, activation through kinase, etc. are often the basis for many systems biology models. Low dose radiation effects present a unique set of challenges to these models including the importance of stochastic effects due to the nature of radiation tracks and small number of molecules activated, and the search for infrequent events that contribute to cancer risks. We have been studying models of the ATM, TGF -Smad and WNT signaling pathways with the goal of applying pathway models to the investigation of low dose radiation cancer risks. Modeling challenges include introduction of stochastic models of radiation tracks, their relationships to more than one substrate species that perturb pathways, and the identification of a representative set of enzymes that act on the dominant substrates. Because several pathways are activated concurrently by radiation the development of modular pathway approach is of interest.

Topological quantum theories and integrable models

International Nuclear Information System (INIS)

Keski-Vakkuri, E.; Niemi, A.J.; Semenoff, G.; Tirkkonen, O.

1991-01-01

The path-integral generalization of the Duistermaat-Heckman integration formula is investigated for integrable models. It is shown that for models with periodic classical trajectories the path integral reduces to a form similar to the finite-dimensional Duistermaat-Heckman integration formula. This provides a relation between exactness of the stationary-phase approximation and Morse theory. It is also argued that certain integrable models can be related to topological quantum theories. Finally, it is found that in general the stationary-phase approximation presumes that the initial and final configurations are in different polarizations. This is exemplified by the quantization of the SU(2) coadjoint orbit

Business and technology integrated model

OpenAIRE

Noce, Irapuan; Carvalho, João Álvaro

2011-01-01

There is a growing interest in business modeling and architecture in the areas of management and information systems. One of the issues in the area is the lack of integration between the modeling techniques that are employed to support business development and those used for technology modeling. This paper proposes a modeling approach that is capable of integrating the modeling of the business and of the technology. By depicting the business model, the organization structure and the technolog...

Estimating environmental co-benefits of U.S. low-carbon pathways using the GCAM-USA integrated assessment model

Data.gov (United States)

U.S. Environmental Protection Agency — There are many technological pathways that can lead to reduced carbon dioxide (CO2) emissions. However, these pathways can have substantially different impacts on...

Longitudinal and Integrative Tests of Family Stress Model Effects on Mexican-Origin Adolescents

Science.gov (United States)

White, Rebecca M. B.; Liu, Yu; Nair, Rajni L.; Tein, Jenn-Yun

2015-01-01

The family stress model represents a common framework through which to examine the effects of environmental stressors on adolescent adjustment. The model suggests that economic and neighborhood stressors influence youth adjustment via disruptions to parenting. Incorporating integrative developmental theory, we examined the degree to which parents’ cultural value orientations mitigated the effects of stressors on parenting disruptions and the degree to which environmental adversity qualified the effect of parenting on adolescent adjustment. We tested the hypothesized Integrative Family Stress Model longitudinally in a sample of mother-youth dyads (N = 749) and father-youth dyads (N = 467) from Mexican origin families, across three times points spanning early to middle adolescence. Providing the first longitudinal evidence of family stress mediated effects, mothers’ perceptions of economic pressure were associated with increases in adolescent externalizing symptoms five years later via intermediate increases in harsh parenting. The remaining findings supported the notion that integrative developmental theory can inform family stress model hypothesis testing that is culturally and contextually relevant for wide range of diverse families and youth. For example, fathers’ perceptions of economic pressure and neighborhood danger had important implications for adolescent internalizing, via reductions in paternal warmth, but only at certain levels of neighborhood adversity. Mothers’ familism value orientations mitigated the effects of economic pressure on maternal warmth, protecting their adolescents from experiencing developmental costs associated with environmental stressors. Results are discussed in terms of identifying how integrative developmental theory intersects with the family stress model to set diverse youth on different developmental pathways. PMID:25751100

Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA.

Science.gov (United States)

Yang, Xian; Han, Rui; Guo, Yike; Bradley, Jeremy; Cox, Benita; Dickinson, Robert; Kitney, Richard

2012-01-01

Hospitals nowadays have to serve numerous patients with limited medical staff and equipment while maintaining healthcare quality. Clinical pathway informatics is regarded as an efficient way to solve a series of hospital challenges. To date, conventional research lacks a mathematical model to describe clinical pathways. Existing vague descriptions cannot fully capture the complexities accurately in clinical pathways and hinders the effective management and further optimization of clinical pathways. Given this motivation, this paper presents a clinical pathway management platform, the Imperial Clinical Pathway Analyzer (ICPA). By extending the stochastic model performance evaluation process algebra (PEPA), ICPA introduces a clinical-pathway-specific model: clinical pathway PEPA (CPP). ICPA can simulate stochastic behaviours of a clinical pathway by extracting information from public clinical databases and other related documents using CPP. Thus, the performance of this clinical pathway, including its throughput, resource utilisation and passage time can be quantitatively analysed. A typical clinical pathway on stroke extracted from a UK hospital is used to illustrate the effectiveness of ICPA. Three application scenarios are tested using ICPA: 1) redundant resources are identified and removed, thus the number of patients being served is maintained with less cost; 2) the patient passage time is estimated, providing the likelihood that patients can leave hospital within a specific period; 3) the maximum number of input patients are found, helping hospitals to decide whether they can serve more patients with the existing resource allocation. ICPA is an effective platform for clinical pathway management: 1) ICPA can describe a variety of components (state, activity, resource and constraints) in a clinical pathway, thus facilitating the proper understanding of complexities involved in it; 2) ICPA supports the performance analysis of clinical pathway, thereby assisting

Support given to lecturers when providing mobile centric services in teaching and learning: a policy analysis perspective

CSIR Research Space (South Africa)

Chipangura, B

2015-05-01

Full Text Available The objective of this study is to examine the status of Higher Education Institutions (HEIs) policies in supporting lecturers when providing mobile centric services to students. The research was undertaken as a single case study within the Open...

Evaluating mobile-centric readiness of higher education institutions: the case of institutional policies and information systems students

CSIR Research Space (South Africa)

Chipangura, B

2015-12-01

Full Text Available . To investigate this question from a policy perspective, nine policies from the open and distance learning (ODL) university in South Africa were analysed for providing institutional mobile-centric support. Policy document analysis was used to evaluate five...

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

Science.gov (United States)

Mitsos, Alexander; Melas, Ioannis N; Morris, Melody K; Saez-Rodriguez, Julio; Lauffenburger, Douglas A; Alexopoulos, Leonidas G

2012-01-01

Modeling of signal transduction pathways plays a major role in understanding cells' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i) excessive CPU time requirements and ii) loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP) formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms.

Non Linear Programming (NLP formulation for quantitative modeling of protein signal transduction pathways.

Directory of Open Access Journals (Sweden)

Alexander Mitsos

Full Text Available Modeling of signal transduction pathways plays a major role in understanding cells' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i excessive CPU time requirements and ii loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms.

Serpentinization reaction pathways: implications for modeling approach

Energy Technology Data Exchange (ETDEWEB)

Janecky, D.R.

1986-01-01

Experimental seawater-peridotite reaction pathways to form serpentinites at 300/sup 0/C, 500 bars, can be accurately modeled using the EQ3/6 codes in conjunction with thermodynamic and kinetic data from the literature and unpublished compilations. These models provide both confirmation of experimental interpretations and more detailed insight into hydrothermal reaction processes within the oceanic crust. The accuracy of these models depends on careful evaluation of the aqueous speciation model, use of mineral compositions that closely reproduce compositions in the experiments, and definition of realistic reactive components in terms of composition, thermodynamic data, and reaction rates.

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 Patient's Voice in Pharmacovigilance: Pragmatic Approaches to Building a Patient-Centric Drug Safety Organization.

Science.gov (United States)

Smith, Meredith Y; Benattia, Isma

2016-09-01

Patient-centeredness has become an acknowledged hallmark of not only high-quality health care but also high-quality drug development. Biopharmaceutical companies are actively seeking to be more patient-centric in drug research and development by involving patients in identifying target disease conditions, participating in the design of, and recruitment for, clinical trials, and disseminating study results. Drug safety departments within the biopharmaceutical industry are at a similar inflection point. Rising rates of per capita prescription drug use underscore the importance of having robust pharmacovigilance systems in place to detect and assess adverse drug reactions (ADRs). At the same time, the practice of pharmacovigilance is being transformed by a host of recent regulatory guidances and related initiatives which emphasize the importance of the patient's perspective in drug safety. Collectively, these initiatives impact the full range of activities that fall within the remit of pharmacovigilance, including ADR reporting, signal detection and evaluation, risk management, medication error assessment, benefit-risk assessment and risk communication. Examples include the fact that manufacturing authorization holders are now expected to monitor all digital sources under their control for potential reports of ADRs, and the emergence of new methods for collecting, analysing and reporting patient-generated ADR reports for signal detection and evaluation purposes. A drug safety department's ability to transition successfully into a more patient-centric organization will depend on three defining attributes: (1) a patient-centered culture; (2) deployment of a framework to guide patient engagement activities; and (3) demonstrated proficiency in patient-centered competencies, including patient engagement, risk communication and patient preference assessment. Whether, and to what extent, drug safety departments embrace the new patient-centric imperative, and the methods and

INTEGRATED CORPORATE STRATEGY MODEL

Directory of Open Access Journals (Sweden)

CATALINA SORIANA SITNIKOV

2014-02-01

Full Text Available Corporations are at present operating in demanding and highly unsure periods, facing a mixture of increased macroeconomic need, competitive and capital market dangers, and in many cases, the prospect for significant technical and regulative gap. Throughout these demanding and highly unsure times, the corporations must pay particular attention to corporate strategy. In present times, corporate strategy must be perceived and used as a function of various fields, covers, and characters as well as a highly interactive system. For the corporation's strategy to become a competitive advantage is necessary to understand and also to integrate it in a holistic model to ensure sustainable progress of corporation activities under the optimum conditions of profitability. The model proposed in this paper is aimed at integrating the two strategic models, Hoshin Kanri and Integrated Strategy Model, as well as their consolidation with the principles of sound corporate governance set out by the OECD.

DRUG: An Energy-Efficient Data-Centric Routing Protocol for Wireless Sensor Networks

OpenAIRE

Sahoo, B. P. S.; Puthal, Deepak

2014-01-01

In general, sensor nodes are deployed in left unattended area. In such situation feeding energy to the batteries or replacing the batteries is difficult or even sometimes impossible too. Therefore, prolonging the network lifetime is an important optimization goal in this aspect. In this paper, we propose a new Energy-efficient Datacentric RoUtinG protocol called DRUG. In this paper, we propose an adaptive Data centric approach to find an optimal routing path from source to sink when the senso...

Taxonomic studies of centric diatoms (Diatomeae: unusual nanoplanktonic forms and new records for Brazil

Directory of Open Access Journals (Sweden)

Kaoli Pereira Cavalcante

2013-06-01

Full Text Available There have been few taxonomic studies of centric diatoms in lotic freshwater environments in Brazil, especially in terms of those including nanoplanktonic forms, which are often neglected in studies of local floras, because of their small size or confusing taxonomy. This is the first study focusing on centric diatoms in the flora of the state of Bahia, in northeastern Brazil. Plankton and periphyton attached to Eichornia crassipes were collected in the winter of 2009 in the Cachoeira River. The diatoms were analyzed and described under light and electron microscopies. Seventeen infrageneric taxa were identified. Cyclotella was represented by five taxa, and concerning of similarities between diacritical features of species in this genus, their descriptions were thoroughly detailed. This was the first time that Cyclotella atomus var. marina, previously recorded only in coastal areas of Japan and Korea, has been documented in a river in South America. We also identified two diatom taxa previously unrecorded in the flora of Brazil: C. cryptica and C. meduanae. Finally, we present a detailed light, transmission and scanning electron microscopy analysis of Skeletonema potamos, a diatom rarely found in the Brazilian literature.

Mechanistic kinetic models of enzymatic cellulose hydrolysis-A review.

Science.gov (United States)

Jeoh, Tina; Cardona, Maria J; Karuna, Nardrapee; Mudinoor, Akshata R; Nill, Jennifer

2017-07-01

Bioconversion of lignocellulose forms the basis for renewable, advanced biofuels, and bioproducts. Mechanisms of hydrolysis of cellulose by cellulases have been actively studied for nearly 70 years with significant gains in understanding of the cellulolytic enzymes. Yet, a full mechanistic understanding of the hydrolysis reaction has been elusive. We present a review to highlight new insights gained since the most recent comprehensive review of cellulose hydrolysis kinetic models by Bansal et al. (2009) Biotechnol Adv 27:833-848. Recent models have taken a two-pronged approach to tackle the challenge of modeling the complex heterogeneous reaction-an enzyme-centric modeling approach centered on the molecularity of the cellulase-cellulose interactions to examine rate limiting elementary steps and a substrate-centric modeling approach aimed at capturing the limiting property of the insoluble cellulose substrate. Collectively, modeling results suggest that at the molecular-scale, how rapidly cellulases can bind productively (complexation) and release from cellulose (decomplexation) is limiting, while the overall hydrolysis rate is largely insensitive to the catalytic rate constant. The surface area of the insoluble substrate and the degrees of polymerization of the cellulose molecules in the reaction both limit initial hydrolysis rates only. Neither enzyme-centric models nor substrate-centric models can consistently capture hydrolysis time course at extended reaction times. Thus, questions of the true reaction limiting factors at extended reaction times and the role of complexation and decomplexation in rate limitation remain unresolved. Biotechnol. Bioeng. 2017;114: 1369-1385. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.

Science.gov (United States)

Yang, Qian; Wang, Shuyuan; Dai, Enyu; Zhou, Shunheng; Liu, Dianming; Liu, Haizhou; Meng, Qianqian; Jiang, Bin; Jiang, Wei

2017-08-16

Pathway enrichment analysis has been widely used to identify cancer risk pathways, and contributes to elucidating the mechanism of tumorigenesis. However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway. Here, we first reviewed the existing widely used pathway enrichment analysis approaches briefly, and then, we proposed a novel topology-based pathway enrichment analysis (TPEA) method, which integrated topological properties and global upstream/downstream positions of genes in pathways. We compared TPEA with four widely used pathway enrichment analysis tools, including database for annotation, visualization and integrated discovery (DAVID), gene set enrichment analysis (GSEA), centrality-based pathway enrichment (CePa) and signaling pathway impact analysis (SPIA), through analyzing six gene expression profiles of three tumor types (colorectal cancer, thyroid cancer and endometrial cancer). As a result, we identified several well-known cancer risk pathways that could not be obtained by the existing tools, and the results of TPEA were more stable than that of the other tools in analyzing different data sets of the same cancer. Ultimately, we developed an R package to implement TPEA, which could online update KEGG pathway information and is available at the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/TPEA/. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence.

Science.gov (United States)

Sahoo, Satya S; Bodenreider, Olivier; Rutter, Joni L; Skinner, Karen J; Sheth, Amit P

2008-10-01

This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. RESOURCE PAGE: http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/

Development of an Innovation Model Based on a Service-Oriented Product Service System (PSS

Directory of Open Access Journals (Sweden)

Seungkyum Kim

2015-10-01

Full Text Available Recently, there have been many attempts to cope with increasingly-diversified and ever-changing customer needs by combining products and services that are critical components of innovation models. Although not only manufacturers, but also service providers, try to integrate products and services, most of the previous studies on Product Service System (PSS development deal with how to effectively integrate services into products from the product-centric point of view. Services provided by manufacturers’ PSSes, such as delivery services, training services, disposal services, and so on, offer customers ancillary value, whereas products of service providers’ PSSes enrich core value by enhancing the functionality and quality of the service. Thus, designing an effective PSS development process from the service-centric point of view is an important research topic. Accordingly, the purpose of this paper is to propose a service-oriented PSS development process, which consists of four stages: (1 strategic planning; (2 idea generation and selection; (3 service design; and (4 product development. In the proposed approach, the PSS development project is initiated and led by a service provider from a service-centric point of view. From the perspective of methodology, customer needs are converted into product functions according to Quality Function Deployment (QFD, while Analytic Hierarchy Process (AHP is employed to prioritize the functions. Additionally, this paper illustrates a service-oriented PSS development that demonstrates the application of the proposed process. The proposed process and illustration are expected to serve as a foundation for research on service-oriented PSS development and as a useful guideline for service providers who are considering the development of a service-oriented PSS.

2050 pathway to an active renewable energy scenario for Jiangsu province

International Nuclear Information System (INIS)

Hong, Lixuan; Lund, Henrik; Mathiesen, Brian Vad; Möller, Bernd

2013-01-01

In 2009, Jiangsu province of China supplied 99.6 percent of its total energy consumption with fossil fuels, of which 82 percent was imported from other provinces and countries. With rising energy demand, frequent energy shortages, and increasing pollution, it is essential for Jiangsu to put more emphasis on improving its energy efficiency and utilizing its renewable resources in the future. This paper presents the integrated energy pathway for Jiangsu during its social and economic transformation until 2050. EnergyPLAN is the chosen energy system analysis tool, since it accounts for all sectors of the energy system that needs to be considered when integrating large-scale renewable energy. A current policy scenario (CPS) based on current energy policies and an ambitious policy scenario (APS) based on large-scale integration of renewable energy and ambitious measures of energy efficiency improvement are proposed. The two energy pathways are modeled and compared in terms of technology combination, non-fossil fuel shares of primary energy supply, socioeconomic costs, and CO 2 emissions. The insights from these pathways can provide valuable input for Jiangsu's future energy policies. - Highlights: ► An integrated energy pathway is designed for Jiangsu province by 2050. ► A current policy scenario and an ambitious policy scenario are modeled and assessed. ► The ambitious policy scenario can help stabilize CO 2 emissions and achieve better economy. ► The next 5–10 years would be a key period for Jiangsu's energy system transition. ► Several policy suggestions have been proposed.

"Could I return to my life?" Integrated Narrative Nursing Model in Education (INNE).

Science.gov (United States)

Artioli, Giovanna; Foà, Chiara; Cosentino, Chiara; Sulla, Francesco; Sollami, Alfonso; Taffurelli, Chiara

2018-03-28

The Integrated Narrative Nursing Model (INNM) is an approach that integrates the qualitative methodology typical of the human sciences, with the quantitative methodology more often associated with the natural sciences. This complex model, which combines a focus on narrative with quantitative measures, has recently been effectively applied to the assessment of chronic patients. In this study, the model is applied to the planning phase of education (Integrated Narrative Nursing Education, INNE), and proves to be a valid instrument for the promotion of the current educational paradigm that is centered on the engagement of both the patient and the caregiver in their own path of care. The aim of this study is therefore to describe the nurse's strategy in the planning of an educational intervention by using the INNE model. The case of a 70-year-old woman with pulmonary neoplasm is described at her first admission to Hospice. Each step conducted by the reference nurse, who uses INNE to record the nurse-patient narrative and collect subsequent questionnaires in order to create a shared educational plan, is also described. The information collected was submitted, starting from a grounded methodology to the following four levels of analysis: I. Needs Assessment, II. Narrative Diagnosis, III. Quantitative Outcome, IV. Integrated Outcome. Step IV, which is derived from the integration of all levels of analysis, allows a nurse to define, even graphically, the conceptual map of a patient's needs, resources and perspectives, in a completely tailored manner. The INNE model offers a valid methodological support for the professional who intends to educate the patient through an inter-subjective and engaged pathway, between the professional, their patient and the socio-relational context. It is a matter of adopting a complex vision that combines processes and methods that require a steady scientific basis and advanced methodological expertise with active listening and empathy

Separations and safeguards model integration.

Energy Technology Data Exchange (ETDEWEB)

Cipiti, Benjamin B.; Zinaman, Owen

2010-09-01

Research and development of advanced reprocessing plant designs can greatly benefit from the development of a reprocessing plant model capable of transient solvent extraction chemistry. This type of model can be used to optimize the operations of a plant as well as the designs for safeguards, security, and safety. Previous work has integrated a transient solvent extraction simulation module, based on the Solvent Extraction Process Having Interaction Solutes (SEPHIS) code developed at Oak Ridge National Laboratory, with the Separations and Safeguards Performance Model (SSPM) developed at Sandia National Laboratory, as a first step toward creating a more versatile design and evaluation tool. The goal of this work was to strengthen the integration by linking more variables between the two codes. The results from this integrated model show expected operational performance through plant transients. Additionally, ORIGEN source term files were integrated into the SSPM to provide concentrations, radioactivity, neutron emission rate, and thermal power data for various spent fuels. This data was used to generate measurement blocks that can determine the radioactivity, neutron emission rate, or thermal power of any stream or vessel in the plant model. This work examined how the code could be expanded to integrate other separation steps and benchmark the results to other data. Recommendations for future work will be presented.

IT-supported integrated care pathways for diabetes: A compilation and review of good practices.

Science.gov (United States)

Vrijhoef, Hubertus Jm; de Belvis, Antonio Giulio; de la Calle, Matias; de Sabata, Maria Stella; Hauck, Bastian; Montante, Sabrina; Moritz, Annette; Pelizzola, Dario; Saraheimo, Markku; Guldemond, Nick A

2017-06-01

Integrated Care Pathways (ICPs) are a method for the mutual decision-making and organization of care for a well-defined group of patients during a well-defined period. The aim of a care pathway is to enhance the quality of care by improving patient outcomes, promoting patient safety, increasing patient satisfaction, and optimizing the use of resources. To describe this concept, different names are used, e.g. care pathways and integrated care pathways. Modern information technologies (IT) can support ICPs by enabling patient empowerment, better management, and the monitoring of care provided by multidisciplinary teams. This study analyses ICPs across Europe, identifying commonalities and success factors to establish good practices for IT-supported ICPs in diabetes care. A mixed-method approach was applied, combining desk research on 24 projects from the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA) with follow-up interviews of project participants, and a non-systematic literature review. We applied a Delphi technique to select process and outcome indicators, derived from different literature sources which were compiled and applied for the identification of successful good practices. Desk research identified sixteen projects featuring IT-supported ICPs, mostly derived from the EIP on AHA, as good practices based on our criteria. Follow-up interviews were then conducted with representatives from 9 of the 16 projects to gather information not publicly available and understand how these projects were meeting the identified criteria. In parallel, the non-systematic literature review of 434 PubMed search results revealed a total of eight relevant projects. On the basis of the selected EIP on AHA project data and non-systematic literature review, no commonalities with regard to defined process or outcome indicators could be identified through our approach. Conversely, the research produced a heterogeneous picture in all aspects of the projects

Integration of Advanced Probabilistic Analysis Techniques with Multi-Physics Models

Energy Technology Data Exchange (ETDEWEB)

Cetiner, Mustafa Sacit; none,; Flanagan, George F. [ORNL; Poore III, Willis P. [ORNL; Muhlheim, Michael David [ORNL

2014-07-30

An integrated simulation platform that couples probabilistic analysis-based tools with model-based simulation tools can provide valuable insights for reactive and proactive responses to plant operating conditions. The objective of this work is to demonstrate the benefits of a partial implementation of the Small Modular Reactor (SMR) Probabilistic Risk Assessment (PRA) Detailed Framework Specification through the coupling of advanced PRA capabilities and accurate multi-physics plant models. Coupling a probabilistic model with a multi-physics model will aid in design, operations, and safety by providing a more accurate understanding of plant behavior. This represents the first attempt at actually integrating these two types of analyses for a control system used for operations, on a faster than real-time basis. This report documents the development of the basic communication capability to exchange data with the probabilistic model using Reliability Workbench (RWB) and the multi-physics model using Dymola. The communication pathways from injecting a fault (i.e., failing a component) to the probabilistic and multi-physics models were successfully completed. This first version was tested with prototypic models represented in both RWB and Modelica. First, a simple event tree/fault tree (ET/FT) model was created to develop the software code to implement the communication capabilities between the dynamic-link library (dll) and RWB. A program, written in C#, successfully communicates faults to the probabilistic model through the dll. A systems model of the Advanced Liquid-Metal Reactor–Power Reactor Inherently Safe Module (ALMR-PRISM) design developed under another DOE project was upgraded using Dymola to include proper interfaces to allow data exchange with the control application (ConApp). A program, written in C+, successfully communicates faults to the multi-physics model. The results of the example simulation were successfully plotted.