| 1. |
- Boomsma, Wouter, et al.
(författare)
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PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure.
- 2013
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 34:19, s. 1697-1705
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Tidskriftsartikel (refereegranskat)abstract
- We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fragment and rotamer libraries. Combined with an easily extendible software architecture, this makes PHAISTOS well suited for Bayesian inference of protein structure from sequence and/or experimental data. Currently, two force-fields are available within the framework: PROFASI and OPLS-AA/L, the latter including the generalized Born surface area solvent model. A flexible command-line and configuration-file interface allows users quickly to set up simulations with the desired configuration. PHAISTOS is released under the GNU General Public License v3.0. Source code and documentation are freely available from http://phaistos.sourceforge.net. The software is implemented in C++ and has been tested on Linux and OSX platforms. © 2013 Wiley Periodicals, Inc.
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| 2. |
- Borg, Farhana, Lektor, 1967-, et al.
(författare)
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A whole (pre)school approach to sustainability in eco- and non-eco-certified preschools in Sweden : Principals’ views and attitudes
- 2023
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Ingår i: Konferens i pedagogiskt arbete, 2023. - Linköping : Linköping University Electronic Press. - 9789180752831 - 9789180752848 ; , s. 22-23
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Konferensbidrag (refereegranskat)abstract
- Although a whole school approach (WSA) to sustainability has been described as one of the most meaningful education approaches, the concept of WSA has not yet been widely explored within the context of preschool education, where the play, learning, and care are preconditions for a wholeness in childhood. The concept of the WSA considers raising quality and standard across entire education institution (Henderson & Tilbury, 2004). This approach also emphasizes the needs for (pre)school to engage children, teachers, parents, and the wider community in sustainability (Mogren, Gericke & Scherp, 2019). The principals have important roles to play in reforming and prioritizing preschools activities towards sustainability (Borg & Vinterek, 2020). This paper explores 50 principals’ views and attitudes towards sustainability from a WSA perspective. Using randomized sampling, the principals were selected from 25 eco-certified and 25 non-eco-certified preschools in 25 municipalities in Sweden, out of 290. A questionnaire was utilized to collect demographic information about the preschools, number of children, number of qualified teachers, principals’ attitudes towards preschool’s activities with sustainability, and also an open-ended question about how the principals themselves integrate sustainability in their planning of preschool activities and what they actually do. The qualitative data was analyzed by using Wals and Mathie’s (2022) six component Whole School Approach Flower Model. The components are: 1. Vision, ethos, leadership and coordination; 2. Institutional practices; 3. Pedagogy and learning; 4. Curriculum; 5. Community connections; and 6. Capacity building. The components were adapted and operationalized within a preschool context. The quantitative data was analyzed by principal component analysis (PCA) in the SIMCA statistical software (Umetrics 2020). This study is a part of a project, “Eco-certified preschools and children’s learning for sustainability: Researching holistic outcomes of preschool education for sustainability (HOPES)” (Swedish Research Council, Dnr. 2018-04445). The analyses will be completed by June, 2023. ReferencesBorg, F., & Vinterek, M. (2020). Principals´ Views on and Descriptions of Preschool Education for Sustainable Development. Journal of Applied Technical and Educational Sciences, 10(2), 18-40. doi:10.24368/jates.v10i2.170Henderson, K., & Tilbury, D. (2004). Whole school approaches to sustainability: An international review of sustainable school programs. Report prepared by Macquarie University for the Australian Government Department of the Environment and Heritage. Sydney.Mogren, A., Gericke, N., & Scherp, H.-Å. (2019). Whole school approaches to education for sustainable development: a model that links to school improvement. Environmental Education Research, 25(4), 508-531. https://doi:10.1080/13504622.2018.1455074 Umetrics. (2020). SIMCA-P+. In (Version 16.0) [Computer software]. Sartorius Stedim Inc. https://www.sartorius.com/en/products/process-analytical-technology/data-analytics-software/mvda-software/simca?gclid=Cj0KCQiAvvKBBhCXARIsACTePW-oD9sm_Ng1dgNBivHH9GFSApdp5wo2G0EDOydryNnzZQ-20Xoj_vIaApIwEALw_wcB
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| 3. |
- Borg, Farhana, Lektor, 1967-, et al.
(författare)
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Methodological and ethical issues when interviewing preschool children : Experiences from a study on sustainability in Sweden
- 2023
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Ingår i: 31st EECERA ANNUAL CONFERENCE. Children’s Curiosity, Agency and Participation: Challenges for Professional Action and Development. ; , s. 135-135
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Konferensbidrag (refereegranskat)abstract
- To contribute to the methodological and ethical discourse on children’sparticipation in research on complex issues, this case-study critically discusses experiences from a large-scale randomized interview study about preschool education for sustainability in Sweden. Young children’s ability to express their views has been subject to debate, resulting in them often being excluded asresearch participants. Hence, age-appropriate methodological approaches are needed to ensure their participation.This study draws from Josefsson and Wall’s(2020) concept of children’s “empowered inclusion” and Lundy’s (2007) model of voice, space, audience, and influence.Employing a qualitative case-studyapproach, methodological approaches and ethical considerations and experiences of a randomized study are scrutinized. A total of 403 children from 50 preschools were interviewed about sustainability using illustrations. An interview instrument was developed and pretested in two iterations. Data were analyzed thematically. The Swedish Ethical Review Authority did not raise any objection to the interview study. Consent to participate was collected from parents and children.They were informed that the children could withdraw at any time if they wanted. The findings demonstrate that research with young children can be undertaken in an ethically acceptable manner. The use of illustrations was helpful in creating a friendly environment and supporting children’s understanding of complex issues. Individual and pair interviews were effective while group interviews were problematic. Children’s attention dropped after 12-15 minutes. These findings suggest that preschool children can express their views on important matters under ethically acceptable and methodologically appropriate conditions.
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| 4. |
- Harder, Tim, et al.
(författare)
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An Efficient Null Model for Conformational Fluctuations in Proteins
- 2012
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Ingår i: Structure. - : Elsevier BV. - 0969-2126. ; 20:6, s. 1028-1039
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Tidskriftsartikel (refereegranskat)abstract
- Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide bridges. The choice of the restraints themselves is heuristic, but the resulting probabilistic model is well-defined and rigorous. Conceptually, TYPHON constitutes a null model of conformational fluctuations under a given set of restraints. We demonstrate that TYPHON can provide information on conformational fluctuations that is in correspondence with experimental measurements. TYPHON provides a flexible, yet computationally efficient, method to explore possible conformational fluctuations in proteins.
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| 5. |
- Lindström, John, et al.
(författare)
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Zero Defect Manufacturing in an Industry 4.0 Context : A Case Study of Requirements for Change and Desired Effects
- 2020
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Ingår i: TESConf 2020 - 9th International Conference on Through-life Engineering Services. - : Elsevier BV.
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Konferensbidrag (refereegranskat)abstract
- The paper addresses, based on a case study comprising six process- and manufacturing industry companies, requirements for change and desired effects from Zero Defect Manufacturing in an Industry 4.0 context. The results outline seven problems and five needs perceived by the companies. Further, the results also outline four desired effects. The results are aligned with existing literature and studies but also bring up new aspects of Zero Defect Manufacturing in terms of problems, needs and desired effects. Noteworthy new desired effects are increased trust for the production process and improved gender equality.
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| 6. |
- Almazidou, Maria, et al.
(författare)
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Maria-mottagningarna i Stockholm, Göteborg och Malmö - Ungdomar i öppenvård år 2013
- 2014
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Trestad2 är en nationell satsning där de tre städerna Stockholm, Göteborg och Malmö samarbetar för att minska användandet av cannabis bland ungdomar. Inom ramen för projektet har det skapats en modell för att identifiera och följa trender i de tre storstäderna vad gäller droganvändning och psykosocial situation för ungdomar som påbörjar behandling för missbruksproblem. Framtagandet av relevanta indikatorer har skett i nära samarbete mellan praktiker och forskare utifrån en sammanvägning av forskningsmässiga, metodologiska och kliniskt betydelsefulla utgångspunkter. Underlaget utgörs av uppgifter om 788 ungdomar som inledde öppenvårdsbehandling vid någon av städernas Maria-mottagningar under år 2013 och har inhämtats med intervjumetoden UngDOK.Sammanställningen av indikatorer visar att flickor utgör cirka en fjärdedel av det totala antalet ungdomar som påbörjar öppenvård för problem med alkohol eller narkotika. Ungdomarnas medianålder när vårdkontakten inleds är 17 år och mer än hälften av ungdomarna har kommit i kontakt med Maria-mottagningarna via eget eller nätverkets initiativ. Nästan två tredjedelar av ungdomarna uppger att de har eller har haft omfattande problem under sin skolgång och cirka en tiondel av ungdomarna varken studerar, arbetar eller praktiserar. Drygt tre fjärdedelar av ungdomarna anger cannabis som sin primära drog, men nästan hälften av dem har även en riskfylld alkoholkonsumtion. Den genomsnittliga debutåldern för den primära drogen är 15 år. Ungefär en fjärdedel av ungdomarna har tidigare fått vård och behandling för alkohol- eller narkotikaproblem. Förekomsten av besvärliga uppväxtvillkor är hög hos ungdomarna och över hälften av dem har erfarenheter av att ha växt upp med våld, psykiska problem och/eller missbruk i familjen. Drygt en tredjedel av samtliga ungdomar har eller har haft kontakt med den psykiatriska vården.Vissa skillnader mellan de tre städernas Maria-mottagningar kan identifieras. Ungdomarna som påbörjar kontakt med mottagningen i Stockholm verkar ha problem av något lindrigare art jämfört med Göteborg och Malmö och utgör mindre andelar både när det gäller komplicerande bakgrundsfaktorer och nuvarande problembeteenden. Det finns även mindre skillnader i åldersstrukturen i de tre städerna, där Stockholm har fler ungdomar under 18 år medan både Göteborg och Malmö har fler som är över 18 år. Det finns även vissa könsskillnader genom att flickorna i samtliga tre städer tycks ha en tyngre problematik i jämförelse med pojkarna. Flickorna saknar i högre grad sysselsättning, anger oftare problem i skolan, har haft svårare uppväxtvillkor och har i större utsträckning haft kontakt med psykiatrin i jämförelse med pojkarna.Att sammanställa och rapportera deskriptiva indikatorer om individer som påbörjar behandling för alkohol- och narkotikaproblem kan ha flera fördelar. En sådan är att informationen kan ligga till grund för en ökad förståelse av ungdomars alkohol- och narkotikaanvändning och dess omfattning. Även om rapportens uppgifter inte är heltäckande, beskriver den en större population av svenska ungdomar med en problematisk användning av alkohol och droger. Föreliggande rapport är således en första ansats till att ge en sammanfattande bild av de ungdomar som påbörjar behandling vid Maria-mottagningarnas öppenvård i Stockholm, Göteborg och Malmö.
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| 7. |
- Birgersson, Martin, et al.
(författare)
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Density-functional theory applied to Rh(111) and CO/Rh(111) systems: Geometries, energies, and chemical shifts
- 2003
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 67:4, s. 1-04502
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Tidskriftsartikel (refereegranskat)abstract
- We present extensive density-functional theory (DFT) based calculations of the clean Rh(111) surface and of CO/Rh(111) overlayer systems. We study both ground-state structural properties and core-level shifts from differences in total energies at different coverages and adsorption sites. Most results are obtained using using norm-conserving or ultrasoft pseudopotentials. The overall reliability of the pseudopotential method is analyzed theoretically, and computationally by way of all-electron calculations. In general, core corrections are required in order to correctly simulate all-electron total energies, although the corrections are rather small for the systems considered here. Overall there is a very good agreement both between the pseudopotential and all-electron results as well as with high-resolution experimental spectra. The obtained agreement between theoretical and experimental core-level energies, however, requires that the correct geometrical parameters are used. For instance, inclusion of bucklings of the first Rh layer in the (2x2)-1CO and (root3x3)R30degrees-1CO overlayers is essential. For the overlayers studied here, different competing adsorption sites give almost the same frozen-lattice adsorption energies. However, the C 1s binding energy shows large differences between CO adsorbed in different sites. Thus calculations of the C 1s shifts allow us to predict the adsorption sites despite the small differences in ground-state energies. We also analyze sources of the shifts in terms of differences in Hartree potential and relaxation at different sites. As the DFT core eigenvalue lies above rather than below the core excitation energy some care is required in order to properly identify a relaxation energy in a DFT framework. In order to clarify the question we relate the DFT approach for core energies to approaches based on self-energies or the Hartree-Fock approximation.
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| 8. |
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| 9. |
- Bolte, S., et al.
(författare)
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The Roots of Autism and ADHD Twin Study in Sweden (RATSS)
- 2014
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Ingår i: Twin Research and Human Genetics. - Stockholm : Cambridge University Press (CUP). - 1832-4274 .- 1839-2628. ; 17:3, s. 164-176
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Tidskriftsartikel (refereegranskat)abstract
- Neurodevelopmental disorders affect a substantial minority of the general population. Their origins are still largely unknown, but a complex interplay of genetic and environmental factors causing disturbances of the central nervous system's maturation and a variety of higher cognitive skills is presumed. Only limited research of rather small sample size and narrow scope has been conducted in neurodevelopmental disorders using a twin-differences design. The Roots of Autism and ADHD Twin Study in Sweden (RATSS) is an ongoing project targeting monozygotic twins discordant for categorical or dimensional autistic and inattentive/hyperactive-impulsive phenotypes as well as other neurodevelopmental disorders, and typically developing twin controls. Included pairs are 9 years of age or older, and comprehensively assessed for psychopathology, medical history, neuropsychology, and dysmorphology, as well as structural, functional, and molecular brain imaging. Specimens are collected for induced pluripotent (iPS) and neuroepithelial stem cells, genetic, gut bacteria, protein-/monoamine, and electron microscopy analyses. RATSS's objective is to generate a launch pad for novel surveys to understand the complexity of genotype-environment-phenotype interactions in autism spectrum disorder and attention-deficit hyperactivity disorder (ADHD). By October 2013, RATSS had collected data from 55 twin pairs, among them 10 monozygotic pairs discordant for autism spectrum disorder, seven for ADHD, and four for other neurodevelopmental disorders. This article describes the design, recruitment, data collection, measures, collected pairs' characteristics, as well as ongoing and planned analyses in RATSS. Potential gains of the study comprise the identification of environmentally mediated biomarkers, the emergence of candidates for drug development, translational modeling, and new leads for prevention of incapacitating outcomes.
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| 10. |
- Borg, Andreas, 1976-, et al.
(författare)
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A Method for Improving the Treatment of Capacity Requirements in Large Telecommunication Systems
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Non-functional requirements crosscut functional models and are more difficult to enforce in system models. This paper describes a long-term research collaboration regarding capacity requirements between Linköping University and Ericsson AB. We describe an industrial case study on non-functional requirements as a background. Succeeding efforts dedicated to capacity include a detailed description of the term, a best practice inventory within Ericsson, and a pragmatic approach for how to annotate UML models with capacity information. The results are also represented as a method plug-in to the OpenUP software process and an anatomy facilitating the possibility to assess and improve an organization’s abilities to develop for capacity. The results combine into a method for how to improve the treatment of capacity requirements in large-scale software systems. Both product and process views are included, with emphasis on the latter.
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