| 1. |
- Franke, Ulrik, et al.
(author)
-
A formal method for cost and accuracy trade-off analysis in software assessment measures
- 2009
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In: RCIS 2009. - NEW YORK : IEEE. - 9781424428649 ; , s. 295-302
-
Conference paper (peer-reviewed)abstract
- Creating accurate models of information systems is an important but challenging task. It is generally well understood that such modeling encompasses general scientific issues, but the monetary aspects of the modeling of software systems are not equally well acknowledged. The present paper describes a method using Bayesian networks for optimizing modeling strategies, perceived as a trade-off between these two aspects. Using GeNIe, a graphical tool with the proper Bayesian algorithms implemented, decision support can thus be provided to the modeling process. Specifically, an informed trade-off can be made, based on the modeler's prior knowledge of the predictive power of certain models, combined with his projection of their costs. It is argued that this method might enhance modeling of large and complex software systems in two principal ways: Firstly, by enforcing rigor and making hidden assumptions explicit. Secondly, by enforcing cost awareness even in the early phases of modeling. The method should be used primarily when the choice of modeling can have great economic repercussions.
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| 2. |
- Franke, Ulrik, et al.
(author)
-
A Method for Choosing Software Assessment Measures using Bayesian Networks and Diagnosis : CSMR 2009, PROCEEDINGS
- 2009
-
In: 13TH EUROPEAN CONFERENCE ON SOFTWARE MAINTENANCE AND REENGINEERING: CSMR 2009, PROCEEDINGS. - LOS ALAMITOS, CA. : IEEE COMPUTER SOC.. - 9780769535890 ; , s. 241-245
-
Conference paper (peer-reviewed)abstract
- Creating accurate models of information systems is an important but challenging task. While the scienti c aspects of such modeling are generally acknowledged, the monetary aspects of the modeling of software systems are not. The present paper describes a Bayesian method for optimizing modeling strategies, perceived as a trade-off between these two aspects. Speci cally, an informed trade-off can be made, based on the modeler's prior knowledge of the predictive power of certain models, combined with her projection of the costs. It is argued that this method enhances modeling of large and complex software systems in two principal ways: Firstly, by enforcing rigor and making hidden assumptions explicit. Secondly, by enforcing cost awareness even in the early phases of modeling. The method should be used primarily when the choice of modeling can have great economic repercussions.
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| 3. |
- Franke, Ulrik, et al.
(author)
-
EAF(2) - A Framework for Categorizing Enterprise Architecture Frameworks
- 2009
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In: SNPD 2009. - LOS ALAMITOS : IEEE COMPUTER SOC. ; , s. 327-332
-
Conference paper (peer-reviewed)abstract
- What constitutes an enterprise architecture framework is a contested subject. The contents of present enterprise architecture frameworks thus differ substantially. This paper aims to alleviate the confusion regarding which framework contains what by proposing a meta framework for enterprise architecture frameworks. By using this meta framework, decision makers are able to express their requirements on what their enterprise architecture framework must contain and also to evaluate whether the existing frameworks meets these requirements. An example classification of common EA frameworks illustrates the approach.
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| 4. |
- Ahlin, Gustav, 1977-
(author)
-
In vitro and in silico prediction of drug-drug interactions with transport proteins
- 2009
-
Doctoral thesis (other academic/artistic)abstract
- Drug transport across cells and cell membranes in the human body is crucial for the pharmacological effect of drugs. Active transport governed by transport proteins plays an important role in this process. A vast number of transport proteins with a wide tissue distribution have been identified during the last 15 years. Several important examples of their role in drug disposition and drug-drug interactions have been described to date. Investigation of drug-drug interactions at the transport protein level are therefore of increasing interest to the academic, industrial and regulatory research communities. The gene expression of transport proteins involved in drug transport was investigated in the jejunum, liver, kidney and colon to better understand their influence on the ADMET properties of drugs. In addition, the gene and protein expression of transport proteins in cell lines, widely used for predictions of drug transport and metabolism, was examined. The substrate and inhibitor heterogeneity of many transport proteins makes it difficult to foresee whether the transport proteins will cause drug-drug interactions. Therefore, in vitro assays for OCT1 and OATP1B1, among the highest expressed transport proteins in human liver, were developed to allow investigation of the inhibitory patterns of these proteins. These assays were used to investigate two data sets, consisting of 191 and 135 registered drugs and drug-like molecules for the inhibition of OCT1 and OATP1B1, respectively. Numerous new inhibitors of the transport proteins were identified in the data sets and the properties governing inhibition were determined. Further, antidepressant drugs and statins displayed strong inhibition of OCT1 and OATP1B1, respectively. The inhibition data was used to develop predictive in silico models for each of the two transport proteins. The highly polymorphic nature of some transport proteins has been shown to affect drug response and may lead to an increased risk of drug-drug interactions, and therefore, the OCT1 in vitro assay was used to study the effect of common genetic variants of OCT1 on drug inhibition and drug-drug interactions. The results indicated that OCT1 variants with reduced function were more susceptible to inhibition. Further, a drug-drug interaction of potential clinical significance in the genetic OCT1 variant M420del was proposed. In summary, gene expression of transport proteins was investigated in human tissues and cell lines. In vitro assays for two of the highest expressed liver transport proteins were used to identify previously unknown SLC transport protein inhibitors and to develop predictive in silico models, which may detect previously known drug-drug interactions and enable new ones to be identified at the transport protein level. In addition, the effect of genetic variation on inhibition of the OCT1 was investigated.
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| 5. |
- Botling, Johan, et al.
(author)
-
Biomarker Discovery in Non-Small Cell Lung Cancer : Integrating Gene Expression Profiling, Meta-analysis, and Tissue Microarray Validation
- 2013
-
In: Clinical Cancer Research. - 1078-0432 .- 1557-3265. ; 19:1, s. 194-204
-
Journal article (peer-reviewed)abstract
- Purpose: Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the published signatures virtually do not overlap.Experimental Design: Here, we describe a novel single institute cohort, including 196 non-small lung cancers (NSCLC) with clinical information and long-term follow-up. Gene expression array data were used as a training set to screen for single genes with prognostic impact. The top 450 probe sets identified using a univariate Cox regression model (significance level P < 0.01) were tested in a meta-analysis including five publicly available independent lung cancer cohorts (n = 860).Results: The meta-analysis revealed 14 genes that were significantly associated with survival (P < 0.001) with a false discovery rate < 1%. The prognostic impact of one of these genes, the cell adhesion molecule 1 (CADM1), was confirmed by use of immunohistochemistry on tissue microarrays from 2 independent NSCLC cohorts, altogether including 617 NSCLC samples. Low CADM1 protein expression was significantly associated with shorter survival, with particular influence in the adenocarcinoma patient subgroup.Conclusions: Using a novel NSCLC cohort together with a meta-analysis validation approach, we have identified a set of single genes with independent prognostic impact. One of these genes, CADM1, was further established as an immunohistochemical marker with a potential application in clinical diagnostics. Clin Cancer Res; 19(1); 194-204. (c) 2012 AACR.
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| 6. |
- Franke, Ulrik, 1981-, et al.
(author)
-
An architecture framework for enterprise IT service availability analysis
- 2014
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In: Software and Systems Modeling. - : Springer Berlin/Heidelberg. - 1619-1366 .- 1619-1374. ; 13:4, s. 1417-1445
-
Journal article (peer-reviewed)abstract
- This paper presents an integrated enterprise architecture framework for qualitative and quantitative modeling and assessment of enterprise IT service availability. While most previous work has either focused on formal availability methods such as fault trees or qualitative methods such as maturity models, this framework offers a combination. First, a modeling and assessment framework is described. In addition to metamodel classes, relationships and attributes suitable for availability modeling, the framework also features a formal computational model written in a probabilistic version of the object constraint language. The model is based on 14 systemic factors impacting service availability and also accounts for the structural features of the service architecture. Second, the framework is empirically tested in nine enterprise information system case studies. Based on an initial availability baseline and the annual evolution of the 14 factors of the model, annual availability predictions are made and compared with the actual outcomes as reported in SLA reports and system logs. The practical usefulness of the method is discussed based on the outcomes of a workshop conducted with the participating enterprises, and some directions for future research are offered.
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| 7. |
- Franke, Ulrik, et al.
(author)
-
Availability of enterprise IT systems : an expert-based Bayesian model
- 2010
-
In: Proc. Fourth International Workshop on Software Quality and Maintainability.
-
Conference paper (peer-reviewed)abstract
- Ensuring the availability of enterprise IT systems is a challenging task. The factors that can bring systems down are numerous, and their impact on various system architectures is difficult to predict. At the same time, maintaining high availability is crucial in many applications, ranging from control systems in the electric power grid, over electronic trading systems on the stock market to specialized command and control systems for military and civilian purposes. The present paper desccribes a Bayesian decision support model, designed to help enterprise IT systems decision makers evaluate the consequences of their decisions by analyzing various scenarios. The model is based on expert elicitation from 50 academic experts on IT systems availability, obtained through an electronic survey. The Bayesian model uses a leaky Noisy-OR method to weigh together the expert opinions on 16 factors affecting systems availability. Using this model, the effect of changes to a system can be estimated beforehand, providing decision support for improvement of enterprise IT systems availability.
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| 8. |
- Franke, Ulrik, et al.
(author)
-
Availability of enterprise IT systems : an expert-based Bayesian framework
- 2012
-
In: Software quality journal. - : Springer Science and Business Media LLC. - 0963-9314 .- 1573-1367. ; 20:2, s. 369-394
-
Journal article (peer-reviewed)abstract
- Ensuring the availability of enterprise IT systems is a challenging task. The factors that can bring systems down are numerous, and their impact on various system architectures is difficult to predict. At the same time, maintaining high availability is crucial in many applications, ranging from control systems in the electric power grid, over electronic trading systems on the stock market to specialized command and control systems for military and civilian purposes. This paper describes a Bayesian decision support model, designed to help enterprise IT systems decision makers evaluate the consequences of their decisions by analyzing various scenarios. The model is based on expert elicitation from 50 experts on IT systems availability, obtained through an electronic survey. The Bayesian model uses a leaky Noisy-OR method to weigh together the expert opinions on 16 factors affecting systems availability. Using this model, the effect of changes to a system can be estimated beforehand, providing decision support for improvement of enterprise IT systems availability. The Bayesian model thus obtained is then integrated within a standard, reliability block diagram-style, mathematical model for assessing availability on the architecture level. In this model, the IT systems play the role of building blocks. The overall assessment framework thus addresses measures to ensure high availability both on the level of individual systems and on the level of the entire enterprise architecture. Examples are presented to illustrate how the framework can be used by practitioners aiming to ensure high availability.
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| 9. |
- Franke, Ulrik, et al.
(author)
-
The Distribution of Time to Recovery of Enterprise IT Services
- 2014
-
In: IEEE Transactions on Reliability. - 0018-9529 .- 1558-1721. ; 63:4, s. 858-867
-
Journal article (peer-reviewed)abstract
- The context of this article is the availability of enterprise IT services, a key concern for many enterprises. While there is a plethora of literature concerned with service availability, there is no previous systematic empirical study on IT service time to recovery following outages. The existing literature typically assumes a distribution, or builds on analogies to related areas such as software engineering. Therefore, our objective is to find the statistical distribution of IT service time to recovery. Method-wise, this investigation is based on logs of more than 1 800 incidents in a large Nordic bank, corresponding to more than 11 000 hours of recorded downtime. Five possible distributions of time to recovery from the literature were investigated using the Akaike Information Criterion to find the distribution offering the best fit. The results show that the log-normal distribution outperformed the others for all tested service channels (collections of IT services). It is concluded that the log-normal distribution offers the best fit of IT service time to recovery. Using this distribution in simulation and decision-support tools offers the prospect of better predictions of downtime and downtime costs to the practitioner community.
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| 10. |
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| 11. |
- Holster, Savanne, et al.
(author)
-
Faecal microbiota transfer in patients with microscopic colitis : a pilot study in collagenous colitis
- 2020
-
In: Scandinavian Journal of Gastroenterology. - : Taylor & Francis. - 0036-5521 .- 1502-7708. ; 55:12, s. 1454-1466
-
Journal article (peer-reviewed)abstract
- Objectives: Faecal microbiota transfer (FMT) consists of the infusion of donor faecal material into the intestine of patients with the aim to restore a disturbed gut microbiota. Methods: In this pilot study (NCT03275467), the effect of three repeated FMTs (day 0, two weeks, four weeks) was studied and followed up for six months in nine collagenous colitis (CC) patients, using two stool donors. Results: Five patients had an active disease at the time of baseline sampling. The primary endpoint (remission at six weeks, defined as <3 stools whereof <1 watery stool per day) was achieved by two of these patients, and by one at eight weeks. Overall, in all nine patients, FMT did not result in a significant reduction of watery stools, assessed by daily diary. However, diarrhoea (assessed by gastrointestinal symptom rating scale) was significantly improved at four (p = .038) and eight weeks (p = .038), indigestion at eight (p = .045) and 12 weeks (p = .006), disease-related worries at four (p = .027) and eight weeks (p = .027), and quality of life at six months (p = .009). FMT resulted in an increased number of lamina propria lymphocytes, possibly indicating an initial mucosal immune activation. No serious adverse events, no systemic effects, and no changes in faecal calprotectin and psychological symptoms were observed. Conclusions: FMT is able to improve symptoms in a yet undefined subset of CC patients. Further studies could help to characterise this subset and to understand if these results can be generalised to all microscopic colitis patients.
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| 12. |
- König, Johan, et al.
(author)
-
An Architecture-Based Framework for Reliability Analysis of ICT for Power Systems
- 2011
-
In: Power and Energy Society General Meeting, 2011 IEEE.
-
Conference paper (peer-reviewed)abstract
- This paper presents an architecture based framework for reliability analysis of ICT systems for power system protection, monitoring and control. The analysis framework applies Probabilistic Relational Models (PRMs) - providing a combination of entity-relationship diagrams together with a probabilistic analysis engine of Bayesian networks. Moreover, the framework allows modeling and analysis of the relations between the ICT and the power system, including both physical and logical relations. Three architectural scenarios are presented onto which the analysis framework is applied. By using component failure rates gathered from various sources each scenario is analyzed based on the probability of successful operation. Calculations are preformed using Bayesian networks and contrasted with the application of Reliability Block Diagrams. The outcome verifies the successful use of PRMs for reliability analysis of ICT systems for power system protection, monitoring and control architecture.
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| 13. |
- König, Johan, et al.
(author)
-
An extended framework for reliability analysis of ICT for power systems
- 2011
-
In: 2011 IEEE PES Trondheim PowerTech. - : IEEE. - 9781424484195 ; , s. 6019343-
-
Conference paper (peer-reviewed)abstract
- This paper presents an extended probabilistic framework for reliability analysis of Information and Communication Technology (ICT) for power systems. The framework is based on Probabilistic Relational Models (PRMs) and includes the analysis of both primary equipment and the supporting ICT systems. The framework also separates between the functional structure and the physical infrastructure. To be able to analyze architectural properties, such as redundancy, the framework is extended with logical gates which are based on AND and OR logic. The gates serve and important purpose when integrating the framework into an analysis tool that supports PRMs. The problem without logical gates is the dynamic sizing of the conditional probability tables which depend on the number of parent nodes. This problem is solved by using aggregation functions. The application of the extended framework is demonstrated by applying to an example system-architecture with two types of redundant configurations.
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| 14. |
- König, Johan, 1983-
(author)
-
Analyzing Substation Automation System Reliability using Probabilistic Relational Models and Enterprise Architecture
- 2014
-
Doctoral thesis (other academic/artistic)abstract
- Modern society is unquestionably heavily reliant on supply of electricity. Hence, the power system is one of the important infrastructures for future growth. However, the power system of today was designed for a stable radial flow of electricity from large power plants to the customers and not for the type of changes it is presently being exposed to, like large scale integration of electric vehicles, wind power plants, residential photovoltaic systems etc. One aspect of power system control particular exposed to these changes is the design of power system control and protection functionality. Problems occur when the flow of electricity changes from a unidirectional radial flow to a bidirectional. Such an implication requires redesign of control and protection functionality as well as introduction of new information and communication technology (ICT). To make matters worse, the closer the interaction between the power system and the ICT systems the more complex the matter becomes from a reliability perspective. This problem is inherently cyber-physical, including everything from system software to power cables and transformers, rather than the traditional reliability concern of only focusing on power system components.The contribution of this thesis is a framework for reliability analysis, utilizing system modeling concepts that supports the industrial engineering issues that follow with the imple-mentation of modern substation automation systems. The framework is based on a Bayesian probabilistic analysis engine represented by Probabilistic Relational Models (PRMs) in com-bination with an Enterprise Architecture (EA) modeling formalism. The gradual development of the framework is demonstrated through a number of application scenarios based on substation automation system configurations.This thesis is a composite thesis consisting of seven papers. Paper 1 presents the framework combining EA, PRMs and Fault Tree Analysis (FTA). Paper 2 adds primary substation equipment as part of the framework. Paper 3 presents a mapping between modeling entities from the EA framework ArchiMate and substation automation system configuration objects from the IEC 61850 standard. Paper 4 introduces object definitions and relations in coherence with EA modeling formalism suitable for the purpose of the analysis framework.Paper 5 describes an extension of the analysis framework by adding logical operators to the probabilistic analysis engine. Paper 6 presents enhanced failure rates for software components by studying failure logs and an application of the framework to a utility substation automation system. Finally, Paper 7 describes the ability to utilize domain standards for coherent modeling of functions and their interrelations and an application of the framework utilizing software-tool support.
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| 15. |
- König, Johan, et al.
(author)
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Assessing Impact of ICT System Quality on Operation of Active Distribution Grids
- 2009
-
In: 2009 IEEE BUCHAREST POWERTECH. - NEW YORK : IEEE. - 9781424422340 ; , s. 1977-1984
-
Conference paper (peer-reviewed)abstract
- This position paper presents starting research on assessment of ICT system characteristics and their impact on controllability and observability of future electricity distribution grids. The aspects of controllability and observability for active grids are key factors for guaranteeing safe, efficient and reliable network operation. An assessment framework is proposed for analyzing the impact of ICT system quality on controllability and observability of the power distribution grid. The proposed assessment method is based on architectural models extended with a probabilistic inference analysis engine. For this, a combination between Enterprise Architecture meta-models and extended influence diagrams are proposed. The paper presents how the framework is constructed and the method on applying it for analysis. The paper is concluded with an example providing an instantiation of the assessment framework.
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| 16. |
- König, Johan, et al.
(author)
-
Mapping the Substation Configuration Language of IEC 61850 to ArchiMate
- 2010
-
In: Proceedings - IEEE International Enterprise Distributed Object Computing Workshop, EDOC. - : IEEE. - 9780769541648 ; , s. 60-68
-
Conference paper (peer-reviewed)abstract
- This paper presents a mapping between the Enterprise Architecture framework ArchiMate and the Substation Configuration Language (SCL) of IEC 61850. Enterprise Architecture (EA) is a discipline for managing an enterprise's information system portfolio in relation to the supported business. Metamodels, descriptive models on how to model and one of the core components of EA, can assist stakeholders in many ways, for example in decision-making. Moreover, the power industry is a domain with an augmented reliance on the support of information systems. IEC 61850 is a standard for the design of Substation Automation (SA) systems and provides a vendor independent framework for interoperability by defining communication networks and functions. The SCL is a descriptive language in IEC 61850 on the configuration of substation Intelligent Electronic Devices (IED) which describes the structure together with physical components and their relating functions. By using SCL, which models the architecture of SA systems, and mapping it to ArchiMate, stakeholders are assisted in understanding their SA system and its architecture. The mapping is intended to support the integration of SA systems applying IEC 61850 into the enterprise architecture. The mapping is demonstrated with an example applying the mapping to a SA configuration based on SCL.
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| 17. |
- König, Johan, et al.
(author)
-
Probabilistic Availability Analysis of Control and Automation Systems for Active Distribution Networks
- 2010
-
In: 2010 IEEE PES TRANSMISSION AND DISTRIBUTION CONFERENCE AND EXPOSITION. - NEW YORK : IEEE. - 9781424465477
-
Conference paper (peer-reviewed)abstract
- The future smart electricity grids will exhibit tight integration between control and automation systems and primary power system equipment. Optimal and safe operation of the power system will be completely dependent on well functioning information and communication (ICT) systems. Considering this, it is essential that the control and automation systems do not constitute the weak link in ensuring reliable power supply to society. At the same time, studies of reliability when considering complex interdependencies between integrated ICT systems becomes increasingly difficult to perform due to the large amount of integrated entities with varying characteristics involved. To manage this challenge there is a need for structured modeling and analysis methods that accommodate this characteristics and interdependencies. In other fields, the analysis of large interconnected systems is done using models that capture the systems and its context as well as its components and interactions. This paper addresses this issue by combining enterprise architecture methods that utilize these modeling concepts, with fault tree analysis and probabilistic relational models. This novel approach enables a holistic overview thanks to the use of formalized models. It also allows use of rigorous analysis thanks to the adaptation of the models to enable Fault Tree Analysis. The paper is concluded with an example of application of the analysis method on a proposed smart grid function in a distribution network.
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| 18. |
- König, Johan, et al.
(author)
-
Probabilistic Relational Models for assessment of reliability of active distribution management systems
- 2010
-
In: 2010 IEEE 11th International Conference on Probabilistic Methods Applied to Power Systems, PMAPS 2010. - Singapore : IEEE. - 9781424457236 ; , s. 454-459
-
Conference paper (peer-reviewed)abstract
- This paper presents the use of Probabilistic Relational Models (PRM) for reliability analysis of control systems for active distribution grids. The approach is based on two key concepts; first, it addresses both the reliability of primary system components and the supporting secondary, ICT-based systems. Secondly, the use of PRMs enables representation of architecture of the ICT systems, including for instance redundancy of hardware and allocation of software functions to several hardware devices. This later aspect is important, since allocation of software across different hardware platforms is a feature enabled by for instance the IEC 61850 standard. The increasing number of software dependent systems for controlling and supervising the power grid enhances the risk of software-caused failures. Thus, for reliable operation it is of high importance to not only concern primary component, but also the software and hardware of the secondary systems controlling it. A variety of methods exist for reliability analysis of secondary systems, however few address the issue of failing software together with failing primary components. The paper presents the underlying theory for Probabilistic Relational Models, and presents the steps necessary to use the technique. The paper is concluded with an example of application of the approach.
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| 19. |
- König, Johan, 1983-, et al.
(author)
-
Probabilistic Relational Models for Reliability Centered Asset Management of Active Distribution Management Systems
- 2010
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In: CIRED Workshop 2010.
-
Conference paper (other academic/artistic)abstract
- This paper presents an approach for reliability centred asset management of active distribution management systems. The application of Probabilistic Relational Models (PRMs) together with a set of defined components and their attribute allows both the ability to capture system configurations in architectural models and the ability of probabilistic reasoning offered by Bayesian networks. The approach is based on two key concepts; first, it addresses both the reliability of primary system components and the supporting secondary, ICT-based systems. Secondly, it enables representation of architecture of the ICT systems, including for instance redundancy of hardware and allocation of software functions to several hardware devices. The increasing number of software dependent systems for controlling and supervising the power grid enhances the risk of software-caused failures. Thus, for reliable operation it is of high importance to not only concern primary component, but also the software and hardware of the secondary systems controlling it. The approach is demonstrated using an example composing both primary equipment and secondary systems.
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| 20. |
- König, Johan, 1983-, et al.
(author)
-
Reliability Analysis of Substation Automation Functions using PRMs
- 2013
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In: IEEE Transactions on Smart Grid. - : IEEE Press. - 1949-3053 .- 1949-3061. ; 4:1, s. 206-213
-
Journal article (peer-reviewed)abstract
- This paper presents the application of a framework for reliability analysis of substation automation (SA) system functions. The framework is based on probabilistic relational models which combines probabilistic reasoning offered by Bayesian networks together with architecture models in form of entity relationship diagrams. In the analysis, both the physical infrastructure, and the logical structure of the system, is regarded in terms of qualitative modeling and quantitative analysis. Moreover, the framework treats the aspect of failures caused by software. An example is detailed with the framework applied to an IEC 61850-based SA system. The logical structure, including functions and their relations, is modeled in accordance with Pieces of Information for COMmunication (PICOM) defined in the IEC 61850 standard. By applying PICOMs as frame of reference when modeling functions the model instantiation becomes more standardized compared to subjectively defining functions. A quantitative reliability analysis is performed on a function for tipping a circuit breaker in case of mismatch between currents. The result is presented both in terms of a qualitative architecture model and a quantitative result showing the probability of successful operation during a period of one year.
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| 21. |
- König, Johan, et al.
(author)
-
Reliability analysis of substation automation system functions
- 2012
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In: 2012 Proceedings - Annual Reliability and Maintainability Symposium (RAMS). - : IEEE. - 9781457718496
-
Conference paper (peer-reviewed)abstract
- This paper presents a case study applying a framework developed for the analysis of substation automation system function reliability. The analysis framework is based on Probabilistic Relational Models (PRMs) and includes the analysis of both primary equipment and the supporting information and communication (ICT) systems. Furthermore, the reliability analysis also considers the logical structure and its relation to the physical infrastructure. The system components that are composing the physical infrastructure are set with failure probabilities and depending of the logical structure the reliability of the studied functionality is evaluated. Software failures are also accounted for in the analysis. As part of the case study failure rates of modern digital control and protection relays were identified by studying failure logs from a Nordic power utility. According to the failure logs software counts for approximately 35% of causes of failures related to modern control and protection relays. The framework including failure probabilities is applied to a system for voltage control that consists of a voltage transformer with an on-load tap changer and a control system for controlling the tap. The result shows a 96% probability of successful operation over period of one year for the automatic voltage control. A concluding remark is that when analyzing substation automation system business functions it is important to reduce the modeling effort. The expressiveness of the presented modeling framework has shown somewhat cumbersome when modeling a single business function with a small number of components. Instead the analysis framework's full usefulness may expect to arise when a larger number of business functions are evaluated for a system with a high degree of dependency between the components in the physical infrastructure. The identification of accurate failure rates is also a limiting factor for the analysis and is something that is interesting for further work.
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| 22. |
- König, Malin A. E., et al.
(author)
-
Among-Population Variation in Tolerance to Larval Herbivory by Anthocharis cardamines in the Polyploid Herb Cardamine pratensis
- 2014
-
In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:6, s. e99333-
-
Journal article (peer-reviewed)abstract
- Plants have two principal defense mechanisms to decrease fitness losses to herbivory: tolerance, the ability to compensate fitness after damage, and resistance, the ability to avoid damage. Variation in intensity of herbivory among populations should result in variation in plant defense levels if tolerance and resistance are associated with costs. Yet little is known about how levels of tolerance are related to resistance and attack intensity in the field, and about the costs of tolerance. In this study, we used information about tolerance and resistance against larval herbivory by the butterfly Anthocharis cardamines under controlled conditions together with information about damage in the field for a large set of populations of the perennial plant Cardamine pratensis. Plant tolerance was estimated in a common garden experiment where plants were subjected to a combination of larval herbivory and clipping. We found no evidence of that the proportion of damage that was caused by larval feeding vs. clipping influenced plant responses. Damage treatments had a negative effect on the three measured fitness components and also resulted in an earlier flowering in the year after the attack. Tolerance was related to attack intensity in the population of origin, i.e. plants from populations with higher attack intensity were more likely to flower in the year following damage. However, we found no evidence of a relationship between tolerance and resistance. These results indicate that herbivory drives the evolution for increased tolerance, and that changes in tolerance are not linked to changes in resistance. We suggest that the simultaneous study of tolerance, attack intensity in the field and resistance constitutes a powerful tool to understand how plant strategies to avoid negative effects of herbivore damage evolve.
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| 23. |
- König, Malin A. E., et al.
(author)
-
Butterfly oviposition preference is not related to larval performance on a polyploid herb
- 2016
-
In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 6:9, s. 2781-2789
-
Journal article (peer-reviewed)abstract
- The preference-performance hypothesis predicts that female insects maximize their fitness by utilizing host plants which are associated with high larval performance. Still, studies with several insect species have failed to find a positive correlation between oviposition preference and larval performance. In the present study, we experimentally investigated the relationship between oviposition preferences and larval performance in the butterfly Anthocharis cardamines. Preferences were assessed using both cage experiments and field data on the proportion of host plant individuals utilized in natural populations. Larval performance was experimentally investigated using larvae descending from 419 oviposition events by 21 females on plants from 51 populations of two ploidy types of the perennial herb Cardamine pratensis. Neither ploidy type nor population identity influenced egg survival or larval development, but increased plant inflorescence size resulted in a larger final larval size. There was no correlation between female oviposition preference and egg survival or larval development under controlled conditions. Moreover, variation in larval performance among populations under controlled conditions was not correlated with the proportion of host plants utilized in the field. Lastly, first instar larvae added to plants rejected for oviposition by butterfly females during the preference experiment performed equally well as larvae growing on plants chosen for oviposition. The lack of a correlation between larval performance and oviposition preference for A. cardamines under both experimental and natural settings suggests that female host choice does not maximize the fitness of the individual offspring.
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| 24. |
- König, Malin A. E., 1987-
(author)
-
Context dependency of plant – animal interactions
- 2014
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Doctoral thesis (other academic/artistic)abstract
- The strength and direction of interactions between organisms vary spatially across the landscape. Traditionally, the focus has been on how trait variation affects the interactions between species. However, differences in abiotic and biotic environmental factors may also alter the distribution, phenology and behavior of the interacting species. To be able to understand why an interaction varies across the landscape, the effects of trait variation has to be separated from the effects of the environmental context. In this thesis, I try to separate the effects of context and trait differences on plant resistance against herbivory, through experimental and observational studies conducted with two cytotypes of the perennial herb Cardamine pratensis and its main herbivore, Anthocharis cardamines.The results show that differences in plant resistance against oviposition under controlled conditions were mainly mediated by flower size; larger flowers were more attractive to the female butterfly. However, among-populations differences in oviposition under natural conditions were not related to the resistance observed under controlled conditions, or to ploidy type, flowering phenology or plant size. Within populations under natural conditions the oviposition patterns by A. cardamines was affected by the plant traits plant size and flowering phenology.The result of this thesis shows that among-population differences in intensity of plant-herbivore interactions were caused by differences in environmental context rather than by herbivore preferences for any phenotypic plant traits, while host plant selection within population was based on plant traits. This suggests that biotic and biotic context can have important effects on the intensity of plant-herbivore interactions. Although genetic traits influenced the outcome of the interaction within populations, it was the environmental context of the populations that determined largely if the interaction took place or not.
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| 25. |
- König, Malin A. E., et al.
(author)
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Context-dependent resistance against butterfly herbivory in a polyploid herb
- 2014
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In: Oecologia. - : Springer Science and Business Media LLC. - 0029-8549 .- 1432-1939. ; 174:4, s. 1265-1272
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Journal article (peer-reviewed)abstract
- Spatial variation in biotic interactions and natural selection are fundamental parts of natural systems, and can be driven by differences in both trait distributions and the local environmental context of the interaction. Most studies of plant–animal interactions have been performed only in natural settings, making it difficult to disentangle the effects of traits and context. To assess the relative importance of trait differences and environmental context for among-population variation in plant resistance to herbivory, we compared oviposition by the butterfly Anthocharis cardamines on two ploidy types of the herb Cardamine pratensis under experimentally controlled conditions with oviposition in natural populations. Under controlled conditions, plants from octoploid populations were significantly more preferred than plants from tetraploid populations. This difference was largely mediated by differences in flower size. Among natural populations, there was no difference in oviposition rates between the two ploidy types. Our results suggest that differences in oviposition rates among populations of the two cytotypes in the field are caused mainly by differences in environmental context, and that the higher attractiveness of octoploids to herbivores observed under common environmental conditions is balanced by the fact that they occur in habitats which harbor lower densities of butterflies. This illustrates that spatial variation in biotic interactions is the net result of differences in trait distributions of the interacting organisms and differences in environmental context, and that variation in both traits and context are important in understanding species interactions.
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| 26. |
- König, Malin A. E., et al.
(author)
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Timing of flowering and intensity of attack by a butterfly herbivore in a polyploid herb
- 2015
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In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 5:9, s. 1863-1872
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Journal article (peer-reviewed)abstract
- Timing of plant development both determines the abiotic conditions that the plant experiences and strongly influences the intensity of interactions with other organisms. Plants and herbivores differ in their response to environmental cues, and spatial and temporal variation in environmental conditions might influence the synchrony between host plants and herbivores, and the intensity of their interactions. We investigated whether differences in first day of flowering among and within 21 populations of the polyploid herb Cardamine pratensis influenced the frequency of oviposition by the butterfly Anthocharis cardamines during four study years. The proportion of plants that became oviposited upon differed among populations, but these differences were not related to mean flowering phenology within the population in any of the four study years. Attack rates in the field were also not correlated with resistance to oviposition estimated under controlled conditions. Within populations, the frequency of butterfly attack was higher in early-flowering individuals in two of the four study years, while there was no significant relationship in the other 2years. Larger plants were more likely to become oviposited upon in all 4years. The effects of first flowering day and size on the frequency of butterfly attack did not differ among populations. The results suggest that differences in attack intensities among populations are driven mainly by differences in the environmental context of populations while mean differences in plant traits play a minor role. The fact that within populations timing of flowering influenced the frequency of herbivore attack only in some years and suggests that herbivore-mediated selection on plant phenology differs among years, possibly because plants and herbivores respond differently to environmental cues.
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| 27. |
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| 28. |
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| 29. |
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| 30. |
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| 31. |
- Lango Allen, Hana, et al.
(author)
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Hundreds of variants clustered in genomic loci and biological pathways affect human height.
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 467:7317, s. 832-8
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Journal article (peer-reviewed)abstract
- Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
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| 32. |
- Närman, Per, et al.
(author)
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Data accuracy assessment using enterprise architecture
- 2011
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In: Enterprise Information Systems. - : Informa UK Limited. - 1751-7575 .- 1751-7583. ; 5:1, s. 37-58
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Journal article (peer-reviewed)abstract
- Errors in business processes result in poor data accuracy. This article proposes an architecture analysis method which utilises ArchiMate and the Probabilistic Relational Model formalism to model and analyse data accuracy. Since the resources available for architecture analysis are usually quite scarce, the method advocates interviews as the primary data collection technique. A case study demonstrates that the method yields correct data accuracy estimates and is more resource-efficient than a competing sampling-based data accuracy estimation method.
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| 33. |
- Närman, Per, et al.
(author)
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Enterprise Architecture Analysis for Data Accuracy Assessments
- 2009
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In: 2009 IEEE INTERNATIONAL ENTERPRISE DISTRIBUTED OBJECT COMPUTING CONFERENCE. - Los Alamitos, CA : IEEE COMPUTER SOC. - 9780769537856 ; , s. 24-33
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Conference paper (peer-reviewed)abstract
- Poor data in information systems impede the quality of decision-making in many modern organizations. Manual business process activities and application services are never executed flawlessly which results in steadily deteriorating data accuracy, the further away from the source the data gets, the poorer its accuracy becomes. This paper proposes an architecture analysis method based on Bayesian Networks to assess data accuracy deterioration in a quantitative manner. The method is model-based and uses the ArchiMate language to model business processes and the way in which data objects are transformed by various operations. A case study at a Swedish utility demonstrates the approach.
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| 34. |
- Närman, Per, et al.
(author)
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Enterprise Architecture Availability Analysis Using Fault Trees and Stakeholder Interviews
- 2014
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In: Enterprise Information Systems. - : Informa UK Limited. - 1751-7575 .- 1751-7583. ; 8:1, s. 1-25
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Journal article (peer-reviewed)abstract
- The availability of enterprise information systems is a key concern for many organisations. This article describes a method for availability analysis based on Fault Tree Analysis and constructs from the ArchiMate enterprise architecture (EA) language. To test the quality of the method, several case-studies within the banking and electrical utility industries were performed. Input data were collected through stakeholder interviews. The results from the case studies were compared with availability of log data to determine the accuracy of the method's predictions. In the five cases where accurate log data were available, the yearly downtime estimates were within eight hours from the actual downtimes. The cost of performing the analysis was low; no case study required more than 20 man-hours of work, making the method ideal for practitioners with an interest in obtaining rapid availability estimates of their enterprise information systems.
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| 35. |
- Närman, Per, et al.
(author)
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Hybrid Probabilistic Relational Models for System Quality Analysis
- 2010
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In: Proceedings - IEEE International Enterprise Distributed Object Computing Workshop, EDOC. - : KTH Royal Institute of Technology. - 9780769541631 ; , s. 57-66
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Conference paper (peer-reviewed)abstract
- The formalism Probabilistic Relational Models (PRM) couples discrete Bayesian Networks with a modeling formalism similar to UML class diagrams and has been used for architecture analysis previously. PRMs are well-suited to perform architecture analysis with respect to system qualities since they support both modeling and analysis at the same time. A particular strength of PRMs is the ability to perform meaningful analysis of domains where there is a high level of uncertainty, as is often the case when performing system quality analysis. However, the use of discrete Bayesian networks in PRMs complicates the analysis of continuous phenomena. The main contribution of this paper is the Hybrid Probabilistic Relational Models (HPRM) formalism which extends PRMs to enable continuous analysis thus extending the applicability for architecture analysis and especially for trade-off analysis of system qualities. HPRMs use hybrid Bayesian networks which allow combinations of discrete and continuous variables. In addition to presenting the HPRM formalism, the paper contains an example which details the use of HPRMs for architecture trade-off analysis.
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| 36. |
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| 37. |
- Tugues, Sònia, et al.
(author)
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Genetic deficiency in plasma protein HRG enhances tumor growth and metastasis by exacerbating immune escape and vessel abnormalization
- 2012
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In: Cancer Research. - 0008-5472 .- 1538-7445.
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Journal article (peer-reviewed)abstract
- Histidine-rich glycoprotein (HRG) is a 75 kDa heparin-binding plasma protein implicated in the regulation of tumor growth and vascularization. In this study, we show that hrg-/- mice challenged with fibrosarcoma or pancreatic carcinomas grow larger tumors with increased metastatic properties. Compared with wild type mice, fibrosarcomas in hrg-/- mice were more hypoxic, necrotic and less perfused, indicating enhanced vessel abnormalization. HRG-deficiency was associated with a suppressed anti-tumor immune response, with both increased infiltration of M2-marker-expressing macrophages and decreased infiltration of dendritic cells and cytotoxic T cells. Analysis of transcript expression in tumor-associated as well as peritoneal macrophages from hrg-/- mice revealed an increased expression of genes associated with a pro-angiogenic and immunoinhibitory phenotype. In accordance, expression arrays performed on HRG-treated peritoneal macrophages showed induction of genes involved in extracellular matrix biology and immune responsiveness. In conclusion, our findings demonstrate that macrophages are a direct target of HRG. HRG loss influences macrophage gene regulation, leading to excess stimulation of tumor angiogenesis, suppression of tumor immune response, and increased tumor growth and metastatic spread.
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| 38. |
- Zhu, Kun, et al.
(author)
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Analysis of data quality issues in wide area monitoring and control systems
- 2010
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In: 2010 IREP Symposium - Bulk Power System Dynamics and Control - VIII, IREP2010. - Rio de Janeiro. - 9781424474677
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Conference paper (peer-reviewed)abstract
- Synchronized phasor measurement based Wide Area Monitoring and Control (WAMC) system is becoming a reality with international research and development both in academia and industry. Timely and accurate data with high resolutions holds great promise for more responsible and advanced grid control and operation. Currently, most of the research focuses on the different control schemes and applications. A relatively less addressed aspect is the dependency of the WAMC system on the performance of the Information and Communication Technology (ICT) infrastructure, without whose support the projected functionalities of the WAMC systems will not be achieved. Possible input delay brought by the complex data transfer and processing processes in WAMC systems are presented at the beginning of this paper. Thereafter, simulations where delayed phasor measurements are fed to a typical WAMC application - Static Var Compensation (SVC) are conducted iteratively to detect its maximum tolerated delay. Based on this maximum tolerated delay, the consequences of missing certain data in the phaor packets have been studied. Furthermore, data quality requirements to design a reliable SVC function are analyzed based on simulation results. In conjunction with the requirement discussion, the paper is concluded by proposing a robust ICT architecture to mitigate the aforementioned data quality issues.
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| 39. |
- Zhu, Kun, et al.
(author)
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Data quality and reliability aspects of ICT infrastructures for Wide Area Monitoring and Control Systems
- 2010
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In: 2010 5th International Conference on Critical Infrastructure, CRIS 2010. - Beijing. - 9781424480814
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Conference paper (peer-reviewed)abstract
- Synchronized phasor measurement based Wide Area Monitoring and Control (WAMC) system is becoming a reality within international research and development both in academia and industry. Timely and accurate data with high resolutions holds great promise for more responsible and advanced grid control and operation. Currently, most of the research focuses on the different control schemes and applications. A relatively less addressed aspect is the dependency of the WAMC system on the performance of the Information and Communication Technology (ICT) infrastructure, without whose support the projected functionalities of the WAMC systems will be not achieved. Possible delays brought by the complex data transfer and processing processes in WAMC systems are addressed in the first part of this paper. Thereafter, simulations where delayed Phasor measurements are fed to a typical WAMC application - Static Var Compensation (SVC) are conducted iteratively to detect its maximum tolerated delay. Furthermore, performance requirements to design a reliable SVC function are analyzed based on simulation results. In conjunction with the requirement discussion, a robust ICT architecture is proposed to mitigate the data latency and incompleteness issue. The paper is concluded by addressing data quality issues relating to the remote signal based SVC controller system reliability.
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