umu.sePublikationer
Ändra sökning
Avgränsa sökresultatet
1234567 151 - 200 av 19822
RefereraExporteraLänk till träfflistan
Permanent länk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Träffar per sida
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Författare A-Ö
  • Författare Ö-A
  • Titel A-Ö
  • Titel Ö-A
  • Publikationstyp A-Ö
  • Publikationstyp Ö-A
  • Äldst först
  • Nyast först
  • Skapad (Äldst först)
  • Skapad (Nyast först)
  • Senast uppdaterad (Äldst först)
  • Senast uppdaterad (Nyast först)
  • Disputationsdatum (tidigaste först)
  • Disputationsdatum (senaste först)
  • Standard (Relevans)
  • Författare A-Ö
  • Författare Ö-A
  • Titel A-Ö
  • Titel Ö-A
  • Publikationstyp A-Ö
  • Publikationstyp Ö-A
  • Äldst först
  • Nyast först
  • Skapad (Äldst först)
  • Skapad (Nyast först)
  • Senast uppdaterad (Äldst först)
  • Senast uppdaterad (Nyast först)
  • Disputationsdatum (tidigaste först)
  • Disputationsdatum (senaste först)
Markera
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 151.
    Ahlm, Kristoffer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Prey specialization and diet of frogs in Borneo2015Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Earlier studies of the diet of frogs indicate that most adult frogs are mainly insectivorous. Overall, frogs are viewed more as generalists than specialists in terms of their diet. However, despite earlier studies, there are still gaps in our knowledge regarding what frogs tend to eat and the degree of specialization. The aim of this study was to investigate the diet choice of frogs in a tropical ecosystem. The present study was conducted in a well-known hotspot for frogs with 66 of the 156 known frog species in Borneo found in a protected area comprising of primary rainforest.

     

    Frogs were caught in the field and their stomachs were flushed. The stomach content was retrieved, sorted to prey categories, and the diet analysed. In addition, the frogs were identified to species level. The frogs belonged to five families: Bufonidae, Dicroglossidae, Megophryidae, Microhylidae and Ranidae. My results show that the most common food source was ants, which constituted 63.7 % of the total food for all studied frog families. Termites, beetles and spiders made up 11.7 %, 4.2 % and 2.8 % of the total prey, respectively. The results from the analysis of Shannon’s diversity index supported two diet specialist families, the Bufonidae and Megophridae, which had a significantly lower mean diversity index compared to the generalist Dicroglossidae. To better reveal differences in frog’s diet in this ecosystem, further studies using larger sample size are needed.

     

     

     

  • 152.
    Ahlqvist, Emil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    Implementing a Resume Database with Online Learning to Rank2015Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Learning to Rank is a research area within Machine Learning. It is mainly used in Information Retrieval and has been applied to, among other systems, web search engines and in computational advertising. The purpose of the Learning to Rank model is to rank a list of items, placing the most relevant at the top of the list, according to the users' requirements. Online Learning to Rank is a type of this model, that learns directly from the users' interactions with the system.

    In this thesis a resume database is implemented, where the search engine applies an Online Learning to Rank algorithm, to rank consultant's resumes, when queries with required skills and competences are issued to the system. The implementation of the Resume Database and the ranking algorithm, as well as an evaluation, is presented in this report. Results from the evaluation indicates that the performance of the search engine, with the Online Learning to Rank algorithm, could be desirable in a production environment.

  • 153.
    Ahlqvist, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Arkitekthögskolan vid Umeå universitet.
    CO-LIVING: Proposal for a collective community in relation to nature2019Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Manifest

    Today we live in a society were we live longer, with access to food,medicine, pure water with all services we could possibly need around the corner. Still we struggle with growing issues that our way of living and planning have affected us. Together we face issues of rising housing prices with a steady progressing marginalized rental market. Causing segregated gentrified areas of high income in comparison to low income. At the same time we contaminate the environment around us without reflecting of how we can alter our way of building and living instead. Previously we had access to pure air, water with tighter relations with our community, living with the nature without being a bystander that have distanced herself from it.

    What have we lost along the way? I will through my project propose an alternative to how we plan our city today, by working from following points.

    -Living in a natural landscape without implementing a generic city plan that do not consider the qualities of the site. I instead intend to take advantage of the natural qualities while combining them with our modern way of living.

    --Living with nature without impeding long lasting harm to nature, this include treatment of wastewater from the housing.

    -Creating a social diverse community by combining housing to prevent the development of a gentrified area of high income elite. As a part of this is to design affordable housing that low income groups can afford to rent or buy.

    -Vivid community life by offering both public and private spaces, with community activities.

  • 154.
    Ahlqvist, Stina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Arkitekthögskolan vid Umeå universitet.
    Charging the Void: (Perception Odd Logic)2017Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    As a concern for how new city developments invest in commercial

    public space of economic activity rather than cultural activity and

    inclusion, part of a global trend and also the case of Umeå’s ambition

    to reach the population growth of 200 000 inhabitants by the year of

    2050. The question to be asked in this regard is what kind of effect

    does this produce on the way we as local inhabitants can take control

    and be part of the creation of our own living environment? Or are

    we just victims of a life consumed by slow decay due to the capital

    dominance?

    In relation to this main concern, the project has been developing

    through the aspect of acknowledging inferior space and abandoned

    objects as a method and typology to analyze alternative ways to

    perceive the city off based the logic of clear function and use, but in

    terms of human interaction and subjective perception of space. The

    point of departure and important key element for this development

    derived from the early stages of research and influential work by

    Robert Smithson’s Monuments of Passaic New Jersey, (1967) with

    a main quote on the description of Smithson’s work and the term of

    monuments, here defined by Ann Reynolds as: “how something plot

    out and charge a space with meaning”

    Learning from memory traces of an abandoned set of futures evoked

    the idea and strive towards creating space not tied to a specific

    use or function, but as a collaboration and juxtaposition between

    form and the viewer’s experience. In add to an understanding of a

    presence which ties together the past and the present as an indirect

    translation of the developed concept for contemporary Ruins, as the

    perception of void. The ruins association to object defined through

    the observer became a guideline towards the aim of designing nonhierarchical

    space, free of us and interpreted by the visitor within the

    city scape.

    Based on this foundation this thesis aims to examine the possibilities

    of architectural structures which can encourage and create conditions

    for new cultural and social meetings. The abstract concept of space

    and deliberate openness to interpretation can allow the visitor to

    take co-authorship of their own living environment based on their

    personal understanding and imagination of that space. The action

    is by deliberate disjunction between form and viewer’s experience

    forced by a superimposition plan as a design strategy for redeveloping

    the current Döbelns Park into a new culture park in the city context

    of Umeå, Västerbotten, Sweden. Fragments of the park will in add

    create a system of integrated monumental sculpture scapes, as a

    network of in-between small scale interventions adapting to specific

    site conditions together with implemented greenery. To secure areas

    within the city scape with access to greenery and social interactive

    meeting points, part of the Urban strategy.

  • 155.
    Ahlstrand, Samuel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Partiformning vid intern materialförsörjning och layoutanpassning av lager: En fallstudie vid GE Healthcare Umeå av två-binge, supermarkets ochmaterialspindlar2014Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    GE Healthcare (GEHC) Umeå har vid sin implementering av Lean genomfört förändringar i lagerstrukturen som är i behov av bättre anpassning. GEHC Umeås nya lagerstruktur innebär öppna supermarkets med förändrade försörjningsrutiner från lager till produktion. Ett två-binge system har implementeras där signalbehållare med material fylls av lageransvariga materialspindlar.

    Det första identifierade problemet och forskningsfrågan utgör två-bingarnas kvantiteter som bestämmer mängden artiklar vid monteringsstationerna. Dessa behöver ses över och en rutin för bestämmande av kvantitet behöver etableras. Som den andra, och oberoende forskningsfrågan, har antalet supermarkets (lager) och dessmaterialspindlar identifieras som är många till antalet och utspridda med begränsad samordning.

    Ett tidigare examensarbete, litteraturstudier, intervjuer samt egna observationer på plats har används för att beskriva nuläget genom både kvalitativa och kvantitativa metoder. På grund av bristen på liknande problem i litteraturen har externa partiformningsmetoder och lagerstyrning används och komplimenterats med simulering för två-binge systemet som del i besvarandet av den första frågeställningen. För den andra frågeställningen har delar ur förenklad systematisk lokalplanläggning används där bland annat olika centraliseringsgrader undersökts med simulering av materialtransporter vid olika artikelplaceringar.

    Idag sätts kvantiteten efter prognoserat användande utifrån personliga erfarenheter. Samordningen mellan materialspindlarna är bristande och nyttjandegraden upplevs ojämn samtidigt som godsmottagningen skulle gynnas av ökad kapacitet. Standardiserade processer i materialhanteringen saknas och produktionsgrupperna har skilda arbetssätt som antaskunna gynnas av en centralisering där gemensamma rutiner lättare kan etableras.

    De historiska transaktionerna visar att det finns utrymme för förbättringar då vissa artiklar genererar långa transportsträckor på grund lagerplats i förhållande till var de används iproduktionen. De nya binge-kvantiteterna från partiformningsmetoderna EOQ, m-EOQ och Kanbanformeln har testats i simulering av påfyllning och materialåtgång via en implementation i Excel VBA.

    Kanbanformeln uppvisar högsta servicenivån 90 %, för lägsta totalkostnaden och minskad kapitalbindning. Kanbankvantiteterna minskar den totala kostnaden med 20 %. Antalet påfyllningar skulle öka med 7 % och antalet artiklar i produktion minskar med 59%. För layoutanpassningen har även simulering av olika orderplock och artikelplaceringen genomförts. Resultatet visar att en centraliseringsgrad är möjlig med en liten ökning avmaterialtransporterna. Det framgår även att artiklar som plockas väldigt sällan är beräknade att ta upp 89 hyllställage av totalt 230 stycken och bör ses över. Detta tillsammans med kravspecifikationen från analys-delen har hjälpt för att generera olika koncept.

    GEHC Umeå bör använda Kanbanformeln i framtiden för bestämmande av kvantiteten i bingarna. Vissa anpassningar för gemensamma artiklar i Comm-lagret och artiklar utan historiska efterfrågan bör ske. För layouten bör GEHC Umeå först och främst flytta artiklarsom idag bidrar med onödiga transporter. På längre sikt bör en ökad grad centralisering avlagren vara möjlig med hänsyn till fördelar vid samordning och informell spridning av arbetsrutiner. Materialspindlarna bör underlätta för godsmottagningen, delta i bristrapportering samt förbättringsarbetet. Utöver detta bör möjligheter till ökat samarbetet mellan materialplaneringen, produktionsplaneringen och materialspindlarna undersökas

  • 156.
    Ahmad, Bayar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Apotekverksamhetens regler i Holland: – skillnader och likheter mellan Sverige och Holland2014Självständigt arbete på grundnivå (yrkesexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 157.
    Ahmad, Bayar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Apotekverksamhetens regler i Holland – skillnader och likheter mellan Sverige och Holland2014Självständigt arbete på grundnivå (yrkesexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 158.
    Ahmad, Farooq
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    Lindgren, Helena
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    Selection of foundational ontology for collaborative knowledge modeling in healthcare domain2010Ingår i: Artificial intelligence: methodology, systems, and applications / [ed] Dicheva, Darina; Dochev, Danail, Springer Berlin/Heidelberg, 2010, s. 261-262Konferensbidrag (Refereegranskat)
    Abstract [en]

    Ontology design is an important process for structuring knowledge to be reused in different projects in the health domain. In this paper, we describe an ontology design for the collaborative knowledge building system ACKTUS to be used for developing personalized knowledge applications for different domains. Different foundational ontologies were compared with respect to selected criteria considered vital for the project, such as modularity and descriptiveness.

  • 159.
    Ahmad, Iftikhar
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Fysiologisk botanik.
    Screening for mutants with delayed leaf senescence in Arabidopsis2009Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Senescence is the last stage of development in plants. During foliar senescence, theleaves experience changes in metabolism, cell structures and gene expression. In thisprocess the limiting nutrients of leaves are relocated from senescing organs to thedeveloping leaves, fruits and buds. The genetic screening to identify senescence mutantsis of utmost importance both for scientific research and for future biotechnology becausethe stay green mutants could increase crop yields.In our experimental setup, the senescence was induced by darkening the individual leavesof Arabidopsis thaliana plants with “mittens” for six days. We have screened 1064Arabidopsis plants for the mutants with delayed senescence phenotypes (stay-green,light-green and slightly light green plants) by measuring chlorophyll content, proteincontent and change in protein levels of the rubisco LSU, COXII, GS1 and GS2 duringdark induced senescence. After senescence induction, the wild type plants had showntypical yellowing and drying of leaves coupled with chlorophyll and protein degradation,while the foliar senescence progresses more slowly in selected stay green mutants. Theselected stay green mutants (19/29, 19/1043 and 19/531) delayed the degradation ofchlorophyll and protein contents even after 6 days of dark treatment. Furthermore, theretention of chloroplast and mitochondrial protein (rubisco LSU and GS2, and COXIIrespectively) and their higher chlorophyll contents may suggest that 19/29, 19/531and19/1043 plants may maintain their photosynthetic and respiratory activities. Thesemutants delay the functional leaf senescence and could be candidates for functional staygreen mutants for upcoming experiments.

  • 160.
    Ahmad, Raghad
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sambandet mellan neuroleptika och det metabola syndromet2014Självständigt arbete på grundnivå (yrkesexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 161.
    Ahmed, Shibbir
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Cadmium sulphide / Zinc sulphide quantum dot decoration of three-dimensional porous graphene2014Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 162.
    Ahmed, Shibbir
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Micro-wave synthesis of co-doped transition metal oxides anchored on reduced graphene oxide and their implementation as catalysts for water oxidation2015Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Abstract: Artificial photosynthesis is a very attractive and a desirable way to solve the rising energy demand. In order to harvest energy directly from sunlight catalyst for oxygen reduction and evolution reaction are at the core of key renewable-energy technologies including fuel cells and water splitting. Herein, tungsten oxide-reduced graphene oxide (WO3-rGO), cobalt oxide-reduced graphene oxide (Co3O4-rGO) and tungsten oxide-cobalt oxide-reduced graphene oxide (WO3-Co3O4-rGO) nano-composites were synthesized via a facile, efficient, one-pot microwave assisted method as an efficient electro-catalyst for water oxidation. The structural and chemical compositions of the produced nano-structures were investigated by Scanning Electron Microscopy (SEM), X-ray Photoelectron Spectroscopy (XPS), Raman Spectroscopy as well as thremogravimetric analysis. Catalytic performances of the engineered nano hybrids for the oxygen evolution reaction (OER) were evaluated using a standard three electrode system in 0.1 M KOH aqueous solution, with a coiled Pt wire as the counter electrode and an Ag/AgCl as the reference electrode. In the produced nano-composites, WO3 and Co3O4 nano-particles are uniformly decorated on the reduced graphene oxide sheets without any agglomeration. The WO3-Co3O4-rGO hybrids afforded current density 1 mA/cm2 at 1.693 V vs RHE and the Co3O4-rGO reached the current density 1 mA/cm2 at 1.769 V vs RHE regarding the catalytic performance for OER in alkaline solution. The over potential was significantly reduced by 76 mV after co-doping of WO3 with Co3O4-rGO nano hybrids. The WO3-Co3O4-rGO gives current density 1 mA/cm2 at 1.658 V vs RHE. We also show that the over potential for oxygen evolution of the WO3-Co3O4-rGO was further reduced by illuminating the catalyst to visible light thus manifesting the photo-catalytic properties of the hybrid catalyst.

  • 163.
    Ahmed, Zina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Poly-ADP ribos polymeras (PARP) inhibitorers effekt på bröstcancer: Poly-ADP ribos polymeras (PARP) inhibitorers effekt på bröstcancer2015Självständigt arbete på grundnivå (yrkesexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 164. Ahn, Ji Hoon
    et al.
    Schmid, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Editorial overview: Growth and development: Change is in the air: how plants modulate development in response to the environment2017Ingår i: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, s. IV-VIArtikel i tidskrift (Refereegranskat)
  • 165.
    Ahonen, Jani
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Can morphologic restoration of hydropower outlet channels create hydraulically suitable spawning and larvae habitats for grayling?: Modelling the effects of environmental measures with HEC-RAS.2018Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The aim of this study was to model if hydraulically suitable habitats for juvenile and spawning grayling could be created by morphological restoration alone in the Bjurfors Övre hydropower outlet channel in the Ume River Basin. The study was done by 2D modelling with HEC-RAS using hourly water flow and level data collected during the period 20160521-20161029. Suitable water depth and velocity values for larvae and spawning grayling were collected from literature. Environmental measures for the Bjurfors Övre outlet channel were designed based on the morphology in outlet channels with documented reproducing grayling populations and large habitat diversities. The outlet channel at present morphology and after morphological modifications were modelled at different flow scenarios (0-369m3/s) and areas of suitable water velocities and depths before and after proposed measures were compared. Results show that suitable velocity areas would increase with a factor of between 1,03-1,81 and the suitable depth areas with a factor of 2,34-19,09 and that suitable depths may be the major limiting factor in current conditions. Results also show that zero-flow events at Bjurfors Övre hydropower plant create unsuitable velocities for larvae and spawning grayling and that the frequency and duration of such events could be more limiting than the mere occurrence of such events. The study indicates that the morphological restoration in hydropeaking outlet channels could improve the availability of habitats with suitability water depth and velocity not only for larvae and spawning grayling, but for other lotic organisms. The study also showed that HEC-RAS modelling is a potential resource effective way to assess to what extent certain proposed environmental measures may create suitable water depths and velocities in hydropeaking outlet channels.

  • 166.
    Ahonen, Jani
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Korttidsregleringsmönster i Ångermanälvens avrinningsområde: Har elmarknadens avreglering påverkat regleringsintensiteten?2013Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The effects of the deregulation of the electricity market 1996 in Sweden on short-term hydropower regulation are unknown. This report investigates patterns in subdaily regulation in the Ångerman River Basin during the period 1993-2011. Differences in subdaily flows and zero flow events between the periods 1993-1995 and 1996-2011 were studied by analyzing hourly data from 8 regulated and 8 unregulated locations with four subdaily flow variation indices. No correlations between the market deregulation and the regulation intensity in the Ångerman River basin were detected. The number of days natural ranges of variability were exceeded and the magnitude of subdaily variation were significantly higher at regulated locations. Zero flow events increased substantially when the periods 1993-2007 and 2008-2011 were compared. Significant correlations were detected in the summer periods between dry years and high magnitudes for the indices that measured variation in volume and low magnitudes for subdaily flow reversals. Zero flow events in the summer periods increased during dry years if the period 2008-2011 were excluded. The major conclusions are that the deregulation of the electricity market has not affected the subdaily regulation of the Ångerman River and that the regulated sites show highly unnatural subdaily variations. Regulation intensity and zero flows events increases during summertime in dry years and the latter also increased substantially after 2007. The current regulation regime is considered harmful for riverine ecosystems and the high and increasing levels of subdaily flow alteration shows the urgent need of national directives for subdaily hydropower operation.

  • 167. Aichroth, Patrick
    et al.
    Weigel, Christian
    Kurz, Thomas
    Stadler, Horst
    Drewes, Frank
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    Björklund, Johanna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    Schlegel, Kai
    Berndl, Emanuel
    Perez, Antonio
    Bowyer, Alex
    Volpini, Andrea
    MICO - MEDIA IN CONTEXT2015Ingår i: 2015 IEEE International Conference on Multimedia & Expo Workshops (ICMEW), 2015Konferensbidrag (Refereegranskat)
    Abstract [en]

    The abundance of digital content requires cost-effective technologies to extract the hidden meaning from media objects. However, current approaches fail to deal with the challenges related to cross-media analysis, metadata publishing, querying and recommendation that are necessary to overcome this challenge. In this paper, we describe the EU project MICO (Media in Context) which aims to provide the necessary technologies based on open-source software (OSS) core components.

  • 168. Aid, T.
    et al.
    Hyvarinen, S.
    Vaher, M.
    Koel, M.
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Laboratory of Industrial Chemistry and Reaction Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Saccharification of lignocellulosic biomasses via ionic liquid pretreatment2016Ingår i: Industrial crops and products (Print), ISSN 0926-6690, E-ISSN 1872-633X, Vol. 92, s. 336-341Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The current work focuses on the pretreatment efficiency of ILs combined with heat for woody biomass consisting of spruce, birch and pine as well as winter wheat straw. The latter was investigated as a comparison and with the aim to enhance its digestibility during enzymatic hydrolysis whereby the influence of IL-treatment to cellulose resistance for hydrolysis was investigated. Considering the wood species, the most common and industrially important wood species in Northern Europe were chosen in the present work and the goal was to obtain fermentable sugars and their degradation product, i.e. 5-hydroxymethylfurfural (5-HMF), which is known valuable platform chemical. Further, the differences in the yields of IL-obtainable carbohydrates between these species were studied. The highest sugar yields were obtained to glucose in the case of spruce and arabinose in the case of pine sapwood, 12.07 and 7.72 mmol/L, respectively. The highest 5-HMF yield was obtained for spruce heartwood (9.18 mmol/L) with longer treatment time, such as 100h. However, regarding woody biomass, the present work was focused more on the study and analysis of the IL-containing liquid part, wood hydrolysate, after IL-treatment aiming to answer the analysis challenges related to this fraction.

  • 169. Aidanpää, Jan - Olov
    et al.
    Lundström, Niklas L.P.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Developments in rotor dynamical modeling of hydropower units2009Konferensbidrag (Refereegranskat)
  • 170.
    Aigner, Harald
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Characterization of FtsH proteases in the annual plant Arabidopsis thaliana2012Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Background FtsH is an ATP-dependent membrane-bound metalloprotease. A. thaliana contains 12 FtsH proteases localized in membranes of chloroplasts and mitochondria where they form homo- or hetero-hexameric complexes. FtsH11 – the main subject of this thesis – is located in the chloroplast envelope.

     

    Methods

    • Field studies with A. thaliana to determine Darwinian fitness. A growth under outdoor conditions often allows discovering of phenotypes that are unascertainable in the controlled environment of growth chambers.
    • Proteomic methods to discover fragments of substrate proteins (limited proteolysis) and changes in the proteome of FtsH protease deficient mutants.

     

    Results ftsh11 has increased amount of: RuBisCO activase, several Calvin cycle enzymes, two enzymes involved in starch synthesis and some chaperons. Some of those enzymes have been identified as possible substrates of FtsH11. Under long photoperiods ftsh11 develops a chlorotic phenotype accompanied by decreasing NADP+/NADPH ratio and increase of ROS damaged proteins. 

  • 171.
    Aigner, Harald
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Comparison of hypothetical 3D-structures of Arabidopsis thaliana FtsH Proteases with the aim to predict FtsH complex formationManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    In Arabidopsis thaliana 12 metallo proteases of the FtsH family are located in the organellar membranes of chloroplasts and mitochondria. While it is known for the Arabidopsis FtsH proteases FtsH1, 2, 5 and 8 to form a hetero–oligomeric, hexameric complex in the chloroplast thylakoid membrane and for FtsH3 and 10 in the inner membrane of mitochondria, no data are available for the remaining (low abundant) FtsH proteases . We compared the sequence identity of amino acids predicted to be relevant in complex formation of FtsH proteases in order to predict additional hetero-oligomeric FtsH complexes. Focus was set on FtsH11 and FtsH4, two subunits that might form a complex in mitochondria. 

  • 172.
    Aigner, Harald
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Searching for substrates of the metallo protease FtsH11 of Arabidopsis thaliana using N-terminal proteomics2012Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    FtsH11 is a membrane-bound metalloprotease localized in mitochondria and in the chloroplast envelope of Arabidopsis thaliana. An ftsh11 knock-out mutant has been shown to develop a chlorotic phenotype in prolonged photoperiods. The proteome of the ftsh11 chloroplast revealed increased abundance of several Calvin cycle enzymes, chaperones and some other proteins, however, none of those proteins could be verified to be an FtsH11 substrate (Harald Aigner, Raik Wagner, Lars L.E. Sjögren, Holger Eubel, A. Harvey Millar, Adrian K. Clarke, Christiane Funk, 2012, manuscript submitted). Here, we have used positional proteomics to identify peptides that report FtsH11 processing events. In this work we were able to identify seven chloroplast-localized proteins that are processed in wild type, but not in ftsh11.  

  • 173.
    Aigner, Harald
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wagner, Raik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sjögren, Lars
    Eubel, Holger
    Millar, Harvey
    Clarke, Adrian
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    FtsH11 protease is required for Arabidopsis thaliana to adapt to gtowth in continuous lightManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Continuous light can increase greenhouse food production; however, some of the most important greenhouse horticulture crops are not able to adapt to long photoperiods. Here, we provide evidence that knock-out of the FtsH11 protease causes molecular differences that prevent Arabidopsis thaliana to adapt to prolonged photoperiods. Previously this protease had been shown to be critical for thermotolerance (Chen et al. 2006). We demonstrate that knock-out mutants deficient of FtsH11 develop chlorosis when shifted to continuous light. When grown under normal growth conditions and short days, ftsh11 displayed changes in protein amount of chloroplast proteins involved in the photosynthetic light reaction and the Calvin cycle as well as of the FtsH12 protease. The proteomic changes are accompanied by reduced non-photochemical quenching and faster state transition. A shift to continuous light further enhanced these effects and induced morphological changes of the chloroplast and chlorosis. No changes in the mitochondrial proteome were observed between wild type and ftsh11.

  • 174.
    Aili, Margareta
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Role of YopE and LcrH in effector translocation, HeLa cell cytotoxicity and virulence2005Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    In order to establish an extra-cellular infection the gram-negative bacteria Yersinia pseudotuberculosis uses a type III secretion system (T3SS) to translocate a set of anti-host effectors into eukaryotic cells. The toxins disrupt signalling pathways important for phagocytosis, cytokine production and cell survival. Secretion and translocation via this T3SS is strictly regulated on several levels. In this context, the function of YopE and LcrH during Yersinia infections has been analysed.

    YopE is an essential translocated effector that disrupts the actin cytoskeleton of infected eukaryotic cells, by inactivating small GTPases through its GTPase activating protein (GAP) activity. However, cytotoxicity can be uncoupled from in vitro GAP activity towards the RhoA, Rac1 and Cdc42 GTPases. Furthermore, in vivo studies of the YopE GAP activity revealed that only RhoA and Rac1 are targeted, but this is not a pre-requisite for Yersinia virulence. Hence, YopE must target one or more additional GTPases to cause disease in mice.

    YopE was the only Yersinia effector that blocks LDH release from infected cells. Moreover, translocated YopE could regulate the level of subsequent effector translocation by a mechanism that involved the YopE GAP function and another T3S component, YopK. Loss of translocation control elevated total T3S gene expression in the presence of eukaryotic cells. This indicated the existence of a regulatory loop for feedback control of T3S gene expression in the bacteria that originates from the interior of the eukaryotic cell after effector translocation is completed. This might represent the true virulence function of YopE.

    Exoenzyme S (ExoS) of Pseudomonas aeruginosa has a YopE-like GAP domain with similar activity towards RhoA, Rac1 and Cdc42. However, ExoS is unable to complement hyper-translocation resulting from loss of YopE. This indicates a unique function for YopE in translocation control in Yersinia that might be dependent on correct intracellular localisation. It follows that the Membrane Localisation Domain in YopE was important for translocation control, but dispensable for cytotoxicity and blockage of LDH release.

    YopD and its cognate chaperone LcrH are negative regulatory elements of the T3S regulon and together with YopB, are involved in the effector translocation process. Randomly generated point mutants in LcrH specifically effected stability and secretion of both the YopB and YopD substrates in vitro and prevented their apparent insertion as translocon pores in the membranes of infected cells. Yet, these mutants still produced stable substrates in the presence of eukaryotic cells and most could mediate at least partial effector translocation. Thus, only minimal amounts of the YopB and YopD translocator proteins are needed for translocation and the LcrH chaperone may regulate this process from inside the bacteria.

  • 175. Aili, Margareta
    et al.
    Hallberg, Bengt
    Wolf-Watz, Hans
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Rosqvist, Roland
    GAP activity of Yersinia YopE2002Ingår i: Methods in Enzymology, ISSN 0076-6879, E-ISSN 1557-7988, Vol. 358, s. 359-70Artikel i tidskrift (Refereegranskat)
  • 176.
    Aili, Margareta
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Isaksson, Elin L
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Carlsson, Sara E
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Wolf-Watz, Hans
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    Rosqvist, Roland
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Francis, Matthew S
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Regulation of Yersinia Yop-effector delivery by translocated YopE2008Ingår i: International Journal of Medical Microbiology, ISSN 1438-4221, E-ISSN 1618-0607, Vol. 298, nr 3-4, s. 183-192Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The bacterial pathogen Yersinia pseudotuberculosis uses a type III secretion (T3S) system to translocate Yop effectors into eukaryotic cells. Effectors are thought to gain access to the cytosol via pores formed in the host cell plasma membrane. Translocated YopE can modulate this pore formation through its GTPase-activating protein (GAP) activity. In this study, we analysed the role of translocated YopE and all the other known Yop effectors in the regulation of effector translocation. Elevated levels of Yop effector translocation into HeLa cells occurred by YopE-defective strains, but not those defective for other Yop effectors. Only Yersinia devoid of YopK exhibits a similar hyper-translocation phenotype. Since both yopK and yopE mutants also failed to down-regulate Yop synthesis in the presence of eukaryotic cells, these data imply that translocated YopE specifically regulates subsequent effector translocation by Yersinia through at least one mechanism that involves YopK. We suggest that the GAP activity of YopE might be working as an intra-cellular probe measuring the amount of protein translocated by Yersinia during infection. This may be a general feature of T3S-associated GAP proteins, since two homologues from Pseudomonas aeruginosa, exoenzyme S (ExoS) and exoenzyme T (ExoT), can complement the hyper-translocation phenotypes of the yopE GAP mutant.

  • 177.
    Aili, Margareta
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Isaksson, Elin L
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Hallberg, Bengt
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi.
    Wolf-Watz, Hans
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Rosqvist, Roland
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Functional analysis of the YopE GTPase-activating protein (GAP) activity of Yersinia pseudotuberculosis2006Ingår i: Cellular Microbiology, ISSN 1462-5814, E-ISSN 1462-5822, Vol. 8, nr 6, s. 1020-1033Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    YopE of Yersinia pseudotuberculosis inactivates three members of the small RhoGTPase family (RhoA, Rac1 and Cdc42) in vitro and mutation of a critical arginine abolishes both in vitro GTPase-activating protein (GAP) activity and cytotoxicity towards HeLa cells, and renders the pathogen avirulent in a mouse model. To understand the functional role of YopE, in vivo studies of the GAP activity in infected eukaryotic cells were conducted. Wild-type YopE inactivated Rac1 as early as 5 min after infection whereas RhoA was down regulated about 30 min after infection. No effect of YopE was found on the activation state of Cdc42 in Yersinia-infected cells. Single-amino-acid substitution mutants of YopE revealed two different phenotypes: (i) mutants with significantly lowered in vivo GAP activity towards RhoA and Rac1 displaying full virulence in mice, and (ii) avirulent mutants with wild-type in vivo GAP activity towards RhoA and Rac1. Our results show that Cdc42 is not an in vivo target for YopE and that YopE interacts preferentially with Rac1, and to a lesser extent with RhoA, during in vivo conditions. Surprisingly, we present results suggesting that these interactions are not a prerequisite to establish infection in mice. Finally, we show that avirulent yopE mutants translocate YopE in about sixfold higher amount compared with wild type. This raises the question whether YopE's primary function is to sense the level of translocation rather than being directly involved in downregulation of the host defence.

  • 178.
    Aili, Margareta
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Telepnev, Max
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet). Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Hallberg, Bengt
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Wolf-Watz, Hans
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Rosqvist, Roland
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    In vitro GAP activity towards RhoA, Rac1 and Cdc42 is not a prerequisite for YopE induced HeLa cell cytotoxicity2003Ingår i: Microbial Pathogenesis, ISSN 0882-4010, E-ISSN 1096-1208, Vol. 34, nr 6, s. 297-308Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The YopE cytotoxin of Yersinia is an essential virulence determinant that is translocated into the eukaryotic target cell via a plasmid-encoded type III secretion system. YopE possess a GTPase activating protein activity that in vitro has been shown to down regulate RhoA, Rac1, and Cdc42. Translocated YopE induces de-polymerisation of the actin microfilament structure in the eukaryotic cell which results in a rounding up of infected cells described as a cytotoxic effect. Here, we have investigated the importance of different regions of YopE for induction of cytotoxicity and in vitro GAP activity. Sequential removal of the N- and C-terminus of YopE identified the region between amino acids 90 and 215 to be necessary for induction of cytotoxicity. Internal deletions containing the essential arginine at position 144 resulted in a total loss of cytotoxic response. In-frame deletions flanking the arginine finger defined a region important for the cytotoxic effect to amino acids 166–183. Four triple-alanine substitution mutants in this region, YopE166-8A, 169-71A, 175-7A and 178-80A were still able to induce cytotoxicity on HeLa cells although they did not show any in vitro GAP activity towards RhoA, Rac1 or Cdc42. A substitution mutant in position 206-8A showed the same phenotype, ability to induce cytotoxic response but no in vitro GAP activity. We speculate that YopE may have additional unidentified targets within the eukaryotic cell.

  • 179.
    Aimaiti, Nuerrennisahan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    A Comparison of Rotation Parameterisations for Bundle Adjustment2015Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Bundle Adjustment is an iterative process where 3D information is estimated from 2D image measurements. Typically, the position of object points are estimated simultaneously with the position and orientation of the cameras. While the object points and camera positions have a straightforward "natural" parameterisation, several possibilities exist for the rotation. In this thesis, seven parameterisation of the rotation were investigated; Euler angles (two variants), the Rodriguez representation, the axis-and-angle representation, unit quaternions, and two variants of the direction cosine matrix (DCM). The Euler and Rodriguez parameterisation are common in photogrammetry and each has three parameters. The other parameterisations have more parameters and one or more constraint between them.

    The parameterisations were analyzed with respect to singularities, i.e. well-defined rotations that do not have any bounded and/or unique set of parameters. Four bundle adjustment experiments were setup, each corresponding to a singularity for one or more parameterisations. A fitth, singularity-free, experiment was also added. The experiments were perturbation studies that investigated the convergence properties of each parameterisation. The unconstrained parameterisations were solved by a damped and undamped Gauss-Newton algorithm, whereas the parameterisations with constraints were solved using damped and undamped algorithms based on the Gauss-Helmert estimation model.

    As expected, the parameterisations corresponding to the constructed singularity had higher failure rates and required more iterations and execution time than the others when it did converge. Excluding their singular cases, the Euler xyz and Rodriguez representations were the fastest with about 37% of the dcm. Of the singularity-free parameterisation, the unit quaternion was the fastest with 79% of the dcm.

    Surprisingly, the undamped bundle algorithms converged more often and faster than the damped bundle algorithms, even close to singularities. However, the undamped convergence was to a higher degree associated with numerical warnings and convergence toward angular values outside the nominal 2 range.

    The results suggest that if singularities are not expected, the Euler xyz and Rodriguez representations are the best of the tested parameterisations. Otherwise, the unit quaternion is the best. As an alternative to the latter case, the switching algorithm by Singla may be used, at the expense of a more complex algorithm.

  • 180.
    Aimaiti, Nuerrennisahan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap.
    Yan, Xu
    Umeå universitet, Samhällsvetenskapliga fakulteten, Institutionen för informatik.
    Gestire-based Interaction and Implication for the Future2011Självständigt arbete på avancerad nivå (magisterexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Currently there exists an advanced and natural form of interaction, named gesture-based interaction. It has been applied in some fields successfully, especially in the form of game applications. Although people are filled with wonder at the new interaction, it has not replaced the traditional interaction, like keyboard and mouse. From the user experience point of view, gesture-based interaction has advantages which traditional interactive form cannot offer, but also shortcomings which people seem dissatisfied with. This thesis focuses on expressing user experience of gesture-based interaction by conducting interview method. Finally, this paper presents a new design and tries to find implications for its practical usage in the future.

  • 181.
    Airey, John
    et al.
    Department of Physics and Astronomy, Uppsala University.
    Berge, Maria
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för naturvetenskapernas och matematikens didaktik.
    Music and physics don't mix!: What the humorous misuse of disciplinary-specific semiotic resources can tell us about disciplinary boundaries2014Konferensbidrag (Refereegranskat)
    Abstract [en]

    Becoming part of an academic discipline has been described both in terms of becoming fluent in a disciplinary discourse (Airey 2009; Airey & Linder 2009; Northedge 2002) and achieving disciplinary literacy (Airey 2011, 2013; Geisler 1994). In this paper we investigate disciplinary boundaries by documenting the responses of academics to a semiotic disciplinary hybrid. The hybrid we use is the Physikalisches Lied, a bogus piece of sheet music into which disciplinary-specific semiotic resources from the realm of physics have been incorporated to humorous effect.

    The piece is presented to three distinct disciplinary focus groups: physicists, musicians and a group of academics who have had little contact with either discipline. In order to elicit disciplinary responses that are free from researcher prompts, each focus group is first asked the simple, open-ended question What do you see here? Once discussion of this question is exhausted the focus groups are asked to identify as many puns as they can - essentially all the disciplinary items that they feel have been misappropriated - and to attempt to explain what this means from a disciplinary standpoint. The differences in the responses of the three groups are presented and analysed.

    We argue that the semiotic resources focused on by each of the three groups and the nature of the explanation offered provide evidence of the degree of integration into the disciplines of physics and music. Our findings shed light on the process of becoming a disciplinary insider and the semiotic work involved in this process.

  • 182.
    Airey, John
    et al.
    Uppsala University.
    Berge, Maria
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för naturvetenskapernas och matematikens didaktik.
    That’s funny!: The humorous effect of misappropriating disciplinary-specific semiotic resources2014Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    The socialization of disciplinary outsiders into an academic discipline has been described both in terms of becoming fluent in a disciplinary discourse (Airey, 2009; Airey & Linder, 2009; Northedge, 2002) and achieving disciplinary literacy (Airey, 2011, 2013; Geisler, 1994). In this paper we investigate disciplinary boundaries by documenting the responses of academics to a semiotic disciplinary hybrid. The hybrid we use is the Physikalisches Lied, a bogus piece of sheet music into which disciplinary-specific semiotic resources from the realm of physics have been incorporated to humorous effect.

    The piece is presented to three distinct disciplinary focus groups: physicists, musicians and a group of academics who have had little contact with either discipline. In order to elicit disciplinary responses that are free from researcher prompts, each focus group is first asked the simple, open-ended question What do you see here? Once discussion of this question is exhausted the focus groups are asked to identify as many puns as they can—essentially all the disciplinary items that they feel have been misappropriated—and to attempt to explain what this means from a disciplinary standpoint. The differences in the responses of the three groups are presented and analysed.

    We argue that semiotic material focused on by each of the three groups and the nature of the explanation offered, provide evidence of the degree of integration into the disciplines of physics and music. Our findings shed light on the process of becoming a disciplinary insider and the semiotic work involved in this process.

     

    References

    Airey, J. (2009). Science, Language and Literacy. Case Studies of Learning in Swedish University Physics. Acta Universitatis Upsaliensis. Uppsala Dissertations from the Faculty of Science and Technology 81. Uppsala Retrieved 2009-04-27, from http://publications.uu.se/theses/abstract.xsql?dbid=9547

    Airey, J. (2011). The Disciplinary Literacy Discussion Matrix: A Heuristic Tool for Initiating Collaboration in Higher Education. Across the disciplines, 8(3).

    Airey, J. (2013). Disciplinary Literacy. In E. Lundqvist, L. Östman & R. Säljö (eds.), Scientific literacy – teori och praktik (pp. 41-58): Gleerups.

    Airey, J., & Linder, C. (2009). A disciplinary discourse perspective on university science learning: Achieving fluency in a critical constellation of modes. Journal of Research in Science Teaching, 46(1), 27-49.

    Geisler, C. (1994). Academic literacy and the nature of expertise: Reading, writing, and knowing in academic philosophy. Hillsdale, NJ: Erlbaum.

    Northedge, A. (2002). Organizing excursions into specialist discourse communities: A sociocultural account of university teaching. In G. Wells & G. Claxton (eds.), Learning for life in the 21st century. Sociocultural perspectives on the future of education (pp. 252-264). Oxford: Blackwell Publishers.

  • 183.
    Aisenbrey, Christopher
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Bechinger, Burkhard
    Gröbner, Gerhard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Macromolecular Crowding at Membrane Interfaces: Adsorption and Alignment of Membrane Peptides2008Ingår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 375, s. 376-385Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Association of proteins to cellular membranes is involved in various biological processes. Various theoretical models have been developed to describe this adsorption mechanism, commonly implying the concept of an ideal solution. However, due to the two-dimensional character of membrane surfaces intermolecular interactions between the adsorbed molecules become important. Therefore previously adsorbed molecules can influence the adsorption behavior of additional protein molecules and their membrane-associated structure. Using the model peptide LAH4, which upon membrane-adsorption can adopt a transmembrane as well as an in-planar configuration, we carried out a systematic study of the correlation between the peptide concentration in the membrane and the topology of this membrane-associated polypeptide. We could describe the observed binding behavior by establishing a concept, which includes intermolecular interactions in terms of a scaled particle theory.

    High surface concentration of the peptide shifts the molecules from an in-planar into a transmembrane conformation, a process driven by the reduction of occupied surface area per molecule. In a cellular context, the crowding-dependent alignment might provide a molecular switch for a cell to sense and control its membrane occupancy. Furthermore, crowding might have pronounced effects on biological events, such as the cooperative behavior of antimicrobial peptides and the membrane triggered aggregation of amyloidogenic peptides.

  • 184.
    Aisenbrey, Christopher
    et al.
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Bertani, Philippe
    Henklein, Peter
    Bechinger, Burkhard
    Structure, dynamics and topology of membrane polypeptides by oriented 2H solid-state NMR spectroscopy2007Ingår i: European Biophysics Journal, ISSN 0175-7571 (Print) 1432-1017 (Online), Vol. 36, nr 4-5, s. 451-60Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Knowledge of the structure, dynamics and interactions of polypeptides when associated with phospholipid bilayers is key to understanding the functional mechanisms of channels, antibiotics, signal- or translocation peptides. Solid-state NMR spectroscopy on samples uniaxially aligned relative to the magnetic field direction offers means to determine the alignment of polypeptide bonds and domains relative to the bilayer normal. Using this approach the 15N chemical shift of amide bonds provides a direct indicator of the approximate helical tilt, whereas the 2H solid-state NMR spectra acquired from peptides labelled with 3,3,3-2H3-alanines contain valuable complimentary information for a more accurate analysis of tilt and rotation pitch angles. The deuterium NMR line shapes are highly sensitive to small variations in the alignment of the Cα–Cβ bond relative to the magnetic field direction and, therefore, also the orientational distribution of helices relative to the membrane normal. When the oriented membrane samples are investigated with their normal perpendicular to the magnetic field direction, the rate of rotational diffusion can be determined in a semi-quantitative manner and thereby the aggregation state of the peptides can be analysed. Here the deuterium NMR approach is first introduced showing results from model amphipathic helices. Thereafter investigations of the viral channel peptides Vpu1–27 and Influenza A M222–46 are shown. Whereas the 15N chemical shift data confirm the transmembrane helix alignments of these hydrophobic sequences, the deuterium spectra indicate considerable mosaic spread in the helix orientations. At least two peptide populations with differing rotational correlation times are apparent in the deuterium spectra of the viral channels suggesting an equilibrium between monomeric peptides and oligomeric channel configurations under conditions where solid-state NMR structural studies of these peptides have previously been performed.

  • 185.
    Aisenbrey, Christopher
    et al.
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Borowik, Tomasz
    Byström, Roberth
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Bokvist, Marcus
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Lindström, Fredrick
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Misiak, Hanna
    Sani, Marc-Antoine
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Gröbner, Gerhard
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    How is protein aggregation in amyloidogenic diseases modulated by biological membranes?2008Ingår i: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, European Biophysics Journal, ISSN 1432-1017 (Online), Vol. 37, nr 3, s. 247-55Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The fate of proteins with amyloidogenic properties depends critically on their immediate biochemical environment. However, the role of biological interfaces such as membrane surfaces, as promoters of pathological aggregation of amyloidogenic proteins, is rarely studied and only established for the amyloid-β protein (Aβ) involved in Alzheimer’s disease, and α-synuclein in Parkinsonism. The occurrence of binding and misfolding of these proteins on membrane surfaces, is poorly understood, not at least due to the two-dimensional character of this event. Clearly, the nature of the folding pathway for Aβ protein adsorbed upon two-dimensional aggregation templates, must be fundamentally different from the three-dimensional situation in solution. Here, we summarize the current research and focus on the function of membrane interfaces as aggregation templates for amyloidogenic proteins (and even prionic ones). One major aspect will be the relationship between membrane properties and protein association and the consequences for amyloidogenic products. The other focus will be on a general understanding of protein folding pathways on two-dimensional templates on a molecular level. Finally, we will demonstrate the potential importance of membrane-mediated aggregation for non-amphiphatic soluble amyloidogenic proteins, by using the SOD1 protein involved in the amyotrophic lateral sclerosis syndrome.

  • 186.
    Aisenbrey, Christopher
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Byström, Roberth
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Oliveberg, Mikael
    Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
    Gröbner, Gerhard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    SOD1 associates to membranes in its folded apo-stateManuskript (preprint) (Övrig (populärvetenskap, debatt, mm))
    Abstract [en]

    Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease accompanied by misfolding and intracellular deposition of superoxide dismutase 1 (SOD1). Although the molecular details behind this misfolding process are yet poorly understood, increasing evidence suggest that SOD1 is most susceptible to misfolding in its metal-free and relatively unstable apo-state. Here, we addressed the question, if misfolding and aggregation of SOD1 involves erroneous interactions with membranes as has been implicated for the Aβ peptide in Alzheimers disease. To examine this possibility we subjected various apo SOD1 variants to the presence of different membrane systems. The results reveal that wild type apoSOD1 but to less extent destabilized ALS mutations interact with charged vesicles under physiologically relevant conditions, thereby acquiring pronounced helical structural features. As the data further show, the protein binds to the membranes by an electrostatically driven mechanism, which requires a folded apo-state conformation and a negative membrane surface potential. Unfolded SOD1 molecules show no appreciable affinity to the membrane surfaces yielding a correlation between increased stability, i. e. occupancy of folded molecules and extend of membrane association. Since this trend opposes the correlation between decreased SOD1 stability and progression of neural damage, the results suggest that membrane association is not part of the ALS mechanism. An explanation could be that the observed membrane association of apo SOD1 is reversible and does not ‘bleed out’ in irreversible aggregation as observed for other precursors of protein-misfolding diseases.

  • 187.
    Aisenbrey, Christopher
    et al.
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Sizun, Christina
    Koch, Joachim
    Herget, Meike
    Abele, Rupert
    Bechinger, Burkhard
    Tampé, Robert
    Structure and dynamics of membrane-associated ICP47, a viral inhibitor of the MHC I antigen-processing machinery2006Ingår i: The Journal of Biological Chemistry, ISSN 0021-9258, Vol. 281, nr 41, s. 30365-72Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To evade the host's immune response, herpes simplex virus employs the immediate early gene product ICP47 (IE12) to suppress antigen presentation to cytotoxic T-lymphocytes by inhibition of the ATP-binding cassette transporter associated with antigen processing (TAP). ICP47 is a membrane-associated protein adopting an alpha-helical conformation. Its active domain was mapped to residues 3-34 and shown to encode all functional properties of the full-length protein. The active domain of ICP47 was reconstituted into oriented phospholipid bilayers and studied by proton-decoupled 15N and 2H solid-state NMR spectroscopy. In phospholipid bilayers, the protein adopts a helix-loop-helix structure, where the average tilt angle of the helices relative to the membrane surface is approximately 15 degrees (+/- 7 degrees ). The alignment of both structured domains exhibits a mosaic spread of approximately 10 degrees . A flexible dynamic loop encompassing residues 17 and 18 separates the two helices. Refinement of the experimental data indicates that helix 1 inserts more deeply into the membrane. These novel insights into the structure of ICP47 represent an important step toward a molecular understanding of the immune evasion mechanism of herpes simplex virus and are instrumental for the design of new therapeutics.

  • 188.
    Aisenbrey, Christopher
    et al.
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Kemi.
    Sudheendra, U. S.
    Ridley, Helen
    Bertani, Philippe
    Marquette, Arnaud
    Nedelkina, Svetlana
    Lakey, Jeremy H.
    Bechinger, Burkhard
    Helix orientations in membrane-associated Bcl-XL determined by 15N-solid-state NMR spectroscopy2007Ingår i: European Biophysics Journal, ISSN 0175-7571 (Print) 1432-1017 (Online), Vol. 37, nr 1, s. 71-80Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Controlled cell death is fundamental to tissue hemostasis and apoptosis malfunctions can lead to a wide range of diseases. Bcl-xL is an anti-apoptotic protein the function of which is linked to its reversible interaction with mitochondrial outer membranes. Its interfacial and intermittent bilayer association makes prediction of its bound structure difficult without using methods able to extract data from dynamic systems. Here we investigate Bcl-xL associated with oriented lipid bilayers at physiological pH using solid-state NMR spectroscopy. The data are consistent with a C-terminal transmembrane anchoring sequence and an average alignment of the remaining helices, i.e. including helices 5 and 6, approximately parallel to the membrane surface. Data from several biophysical approaches confirm that after removal of the C-terminus from Bcl-xL its membrane interactions are weak. In the presence of membranes Bcl-xL can still interact with a Bak BH3 domain peptide suggesting a model where the hydrophobic C-terminus of the protein unfolds and inserts into the membrane. During this conformational change the Bcl-xL hydrophobic binding pocket becomes accessible for protein–protein interactions whilst the structure of the N-terminal region remains intact.

  • 189.
    Ajaikumar, Samikannu
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ahlkvist, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Larsson, William
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Boström, Dan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för tillämpad fysik och elektronik, Energiteknik och termisk processkemi.
    Kordas, K
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Highly active and selective bimetallic catalysts supported on transition metal oxides for the oxidation of α-pinene using molecular oxygen2010Konferensbidrag (Övrigt vetenskapligt)
  • 190.
    Ajaikumar, Samikannu
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ahlkvist, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Larsson, William
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Boström, Dan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för tillämpad fysik och elektronik.
    Kordas, K
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Synthesis and characterization of Cu and Cu-M (M=Co, Ni, Au and Zn) bimetallic catalysts supported on TiO2 modified SBA-152010Konferensbidrag (Övrigt vetenskapligt)
  • 191.
    Ajaikumar, Samikannu
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ahlkvist, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Larsson, William
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Shchukarev, Andrey
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kordas, K
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Piispankatu 8, FIN-20500, Turku/Åbo, Finland.
    Oxidation of α-pinene over gold containing bimetallic nanoparticles supported on reducible TiO2 by DPU method2011Ingår i: Applied Catalysis A: General, ISSN 0926-860X, E-ISSN 1873-3875, Vol. 392, nr 1-2, s. 11-18Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A series of bimetallic catalysts Au–M (where M = Cu, Co and Ru) were supported on a reducible TiO2 oxide via deposition-precipitation (DP) method with a slow decomposition of urea as the precipitating agent. The characteristic structural features of the prepared materials were characterized by various physico-chemical techniques such as X-ray photoelectron spectroscopy (XPS), and transmission electron microscopy (TEM). XPS results indicated the formation of alloyed bimetallic particles on the TiO2 support. TEM results confirmed the fine dispersion of metal nanoparticles on the support with an average particle size in the range of 3–5 nm. An industrially important process, oxy-functionalization of α-pinene was carried out over the prepared bimetallic heterogeneous catalysts under liquid phase conditions. Reaction parameters such as the reaction time, temperature, and the effect of solvent were studied for optimal conversion of α-pinene into verbenone. The major products obtained were verbenone, verbenol, α-pinene oxide and alkyl-pinene peroxide. The activity of the catalysts followed the order; AuCu/TiO2 > AuCo/TiO2 > Cu/TiO2 > Au/TiO2 > AuRu/TiO2. Upon comparison of the various catalysts, AuCu/TiO2 was found to be an active and selective catalyst towards the formation of verbenone. The temperature, nature of the catalysts and the choice of solvents greatly influenced the reaction rate.

  • 192.
    Ajaikumar, Samikannu
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Department of Chemistry, Anna University, Guindy, Chennai, India.
    Backiaraj, Muthaiah
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Laboratory of Industrial Chemistry and Reaction Engineering, Process Chemistry Centre, Åbo Akademi University, Turku/Åbo, Finland.
    Pandurangan, Arumugam
    Transesterification of diethyl malonate with n-butanol over HPWA/MCM-41 molecular sieves2013Ingår i: Journal of porous materials, ISSN 1380-2224, E-ISSN 1573-4854, Vol. 20, nr 4, s. 951-959Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Mesoporous Si-MCM-41 and Al-MCM-41 (Si/Al = 100) materials were synthesized via a hydrothermal method. Three different ratios (10, 20 and 30 wt%) of heteropoly tungstic acid (HPWA) was loaded on Si-MCM-41 by wet impregnation techniques. The characteristic structural features of the prepared materials were studied by various physico-chemical techniques such as X-ray diffraction (XRD), Nitrogen physisorption (BET), temperature programmed desorption of ammonia (TPD) and transmission electron microscopy (TEM). Transesterification of diethyl malonate (DEM) with n-butanol under autogeneous conditions in a temperature range from 50 to 125 °C was selected as the test reaction for the as synthesized materials. The reactants were fed with various mole ratios in order to determine the optimal feed composition leading to maximum yields of transesterified products. The results indicated that the conversion of diethylmalonate depends on the HPWA concentration on the support, temperature, reaction time and mole ratio of the reactants. Further, the catalytic efficiency of HPWA/MCM-41 was compared with that of Al-MCM-41. The solid acid HPWA/MCM-41 catalysts have several advantages in comparison to conventional mineral acid catalysts which are heterogeneous, eco-friendly, highly active and selective in the formation of transesters.

  • 193.
    Ajdinovic, Dzejla
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Resonemang och problemlösning i Matematik 1b: En uppgiftsanalys av två läroböcker2018Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Studien undersökte möjligheten att utveckla problemlösnings- och resonemangsförmåga i svenska läroböcker. Under studiens gång genomfördes en läromedelsanalys av två läroböcker för gymnasiekursen Matematik 1b, Matematik 5000 och Matematik Origo. Analysen tog hänsyn till olika aspekter av förmågorna, olika svårighetsgrader på uppgifterna samt olika centralt innehåll i ämnesplanen. Av 2223 uppgifter i Matematik 5000 kunde problemlösningsförmågan utvecklas i 5% och resonemangsförmågan i 6%. Motsvarande andelar i 1747 uppgifter i Matematik Origo var 7% respektive 10%. Analysen visade också att större andel av uppgifterna på de två högre svårighetsnivåerna gav möjlighet att utveckla förmågorna än de på den lägsta nivån i båda böckerna. Det framkom även att inte alla aspekter av förmågorna fick lika stort utrymme att utvecklas. I båda böckerna var det geometri-kapitlet som fokuserade på dessa förmågor i störst andel av uppgifterna.

  • 194. Ajuria, Jon
    et al.
    Arnaiz, Maria
    Botas, Cristina
    Carriazo, Daniel
    Mysyk, Roman
    Rojo, Teofilo
    Talyzin, Alexandr V.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Goikolea, Eider
    Graphene-based lithium ion capacitor with high gravimetric energy and power densities2017Ingår i: Journal of Power Sources, ISSN 0378-7753, E-ISSN 1873-2755, Vol. 363, s. 422-427Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Hybrid capacitor configurations are now of increasing interest to overcome the current energy limitations of supercapacitors. In this work, we report a lithium ion capacitor (LIC) entirely based on graphene. On the one hand, the negative-battery-type- electrode consists of a self-standing, binder-free 3D macroporous foam formed by reduced graphene oxide and decorated with tin oxide nanoparticles (SnO2-rGO). On the other hand, the positive-capacitor-type- electrode is based on a thermally expanded and physically activated reduced graphene oxide (a-TEGO). For comparison purposes, a symmetric electrical double layer capacitor (EDLC) using the same activated graphene in 1.5 M Et4NBE4/ACN electrolyte is also assembled. Built in 1 M LiPF6 EC:DMC, the graphene-based LIC shows an outstanding, 10-fold increase in energy density with respect to its EDLC counterpart at low discharge rates (up to 200 Wh kg(-1)). Furthermore, it is still capable to deliver double the energy in the high power region, within a discharge time of few seconds.

  • 195. Akbari, Saieed
    et al.
    Friedland, Shmuel
    Markström, Klas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Zare, Sanaz
    On 1-sum flows in undirected graphs2016Ingår i: The Electronic Journal of Linear Algebra, ISSN 1537-9582, E-ISSN 1081-3810, Vol. 31, s. 646-665Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Let G = (V, E) be a simple undirected graph. For a given set L subset of R, a function omega: E -> L is called an L-flow. Given a vector gamma is an element of R-V , omega is a gamma-L-flow if for each v is an element of V, the sum of the values on the edges incident to v is gamma(v). If gamma(v) = c, for all v is an element of V, then the gamma-L-flow is called a c-sum L-flow. In this paper, the existence of gamma-L-flows for various choices of sets L of real numbers is studied, with an emphasis on 1-sum flows. Let L be a subset of real numbers containing 0 and denote L* := L \ {0}. Answering a question from [S. Akbari, M. Kano, and S. Zare. A generalization of 0-sum flows in graphs. Linear Algebra Appl., 438:3629-3634, 2013.], the bipartite graphs which admit a 1-sum R* -flow or a 1-sum Z* -flow are characterized. It is also shown that every k-regular graph, with k either odd or congruent to 2 modulo 4, admits a 1-sum {-1, 0, 1}-flow.

  • 196.
    Akhatova, Elena
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Do clinical pharmacy servicesimprove outcomes for patientswith heart failure (HF)?: Do clinical pharmacy servicesimprove outcomes for patientswith heart failure (HF)?2015Självständigt arbete på grundnivå (yrkesexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 197.
    Akhtari, Mohammad Mehdi
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik. Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper.
    3D Structural similarity check between CT and SCT2014Självständigt arbete på avancerad nivå (masterexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The aim of the current work was to develop and test a method for comparing the geometrical representation of a patient using computed tomography (CT), and CT like images derived from magnetic resonance images (MRI). It would be beneficial to use MRI alone for both target delineation and treatment planning to save time and costs. This was first investigated in Umea university Hospital by introducing substitute computed tomography (SCT) obtained from MRI images and which can be used as CT equivalent information. The data that is used in this report are from five patients with intracranial tumors; A MATLAB code has been developed to compare DDRs based on s-CT data with CT based DRR’s for these five patients.

  • 198.
    Akhtari, Mohammad Mehdi
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Accuracy of inverse treatment planning on computed tomography like images derived from magnetic resonance data2013Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Treatment planning for radiotherapy involves different types of imaging to delineate target volume precisely. The most suitable sources to get 3D information of the patient are the computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET)/CT modalities. CT is a modern medical imaging technique that allows three-dimensional treatment planning and conformal treatment techniques. By combining CT images with efficient dosimetry software, accurate patient positioning methods and verification and quality assurance good results can be achieved. The CT images show how the radiation interacts with the material based on each tissue has a different attenuation coefficient, so the data can be used for dose calculations in treatment planning.

    Radiation oncology is therapeutic modality, in which irradiating cancer cells as target is the main goal while always try to limit the dose to healthy tissues and organs. CT images have good potentials because they can provide high geometrical accuracy and electron density information. Having said that, however, using CT images alone for planning does not provide enough information in order to delineate the target volume accurately because the attenuation in soft tissue is fairly constant therefore the soft tissue contrast is poor. Here, (MR) imaging can be very useful since it has superior soft tissue contrast especially in conditions such as prostate cancer, brain lesions, and head and neck tumors. It should be noted that MR images cannot provide electron density information that is required for dose calculations.

    It has been hypothesized that since MRI images have certain benefits in comparison with CT images such as its superior soft tissue contrast which improves contrast resolution between different types of tissues, it would be beneficial to use MRI alone for both target delineation and treatment planning to save time and costs. This was investigated by introducing substitute computed tomography (SCT) which can be interpreted as CT equivalent information obtained by MRI images.

    We used data from five patients with intracranial tumors, and reviewed their initial dosimetric treatment plans that were based solely on CT images, that data was also used to evaluate the dosimetric accuracy of our research treatment plans. Optimization plans that are based on CT images and substitute CT (SCT) was compared with each other in the first step. On the second step the treatment plan that was based on SCT images was transferred to the CT images without any changes and comparisons between the dose calculations on both data sets were made. The delivered dose to planning target volume (PTV) and risk organs was compared.

    Gamma index results between SCT and transferred plan showed no difference in the dose distribution map in PTV. The maximum difference was in the outer contour to the skull. The average and median dose delivered to PTV was within 0.35% difference studying in all patients.

    In conclusion for patients with intracranial tumors the dosimetric accuracy of treatment plans based on SCT and MR images were very accurate, and we demonstrated that it was possible to reach the same dose volume histograms by SCT compared to CT with minimal differences, which were not significant. 

  • 199. Akhter, Shirin
    et al.
    Kretzschmar, Warren W.
    Nordal, Veronika
    Delhomme, Nicolas
    Street, Nathaniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Nilsson, Ove
    Emanuelsson, Olof
    Sundström, Jens F.
    Integrative analysis of three RNA sequencing methods identifies mutually exclusive exons of MADS-box isoforms during early bud development in Picea abies2018Ingår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, artikel-id 1625Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister Glade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this subclade, the conifer gene DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.

  • 200.
    Akkerman, V'yacheslav
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Fysik.
    Turbulent burning, flame acceleration, explosion triggering2007Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The present thesis considers several important problems of combustion theory, which are closely related to each other: turbulent burning, flame interaction with walls in different geometries, flame acceleration and detonation triggering.

    The theory of turbulent burning is developed within the renormalization approach. The theory takes into account realistic thermal expansion of burning matter. Unlike previous renormalization models of turbulent burning, the theory includes flame interaction with vortices aligned both perpendicular and parallel to average direction of flame propagation. The perpendicular vortices distort a flame front due to kinematical drift; the parallel vortices modify the flame shape because of the centrifugal force. A corrugated flame front consumes more fuel mixture per unit of time and propagates much faster. The Darrieus-Landau instability is also included in the theory. The instability becomes especially important when the characteristic length scale of the flow is large.

    Flame interaction with non-slip walls is another large-scale effect, which influences the flame shape and the turbulent burning rate. This interaction is investigated in the thesis in different geometries of tubes with open / closed ends. When the tube ends are open, then flame interaction with non-slip walls leads to an oscillating regime of burning. Flame oscillations are investigated for different flame parameters and tube widths. The average increase in the burning rate in the oscillations is found.

    Then, propagating from a closed tube end, a flame accelerates according to the Shelkin mechanism. In the theses, an analytical theory of laminar flame acceleration is developed. The theory predicts the acceleration rate, the flame shape and the velocity profile in the flow pushed by the flame. The theory is validated by extensive numerical simulations. An alternative mechanism of flame acceleration is also considered, which is possible at the initial stages of burning in tubes. The mechanism is investigated using the analytical theory and direct numerical simulations. The analytical and numerical results are in very good agreement with previous experiments on “tulip” flames.

    The analytical theory of explosion triggering by an accelerating flame is developed. The theory describes heating of the fuel mixture by a compression wave pushed by an accelerating flame. As a result, the fuel mixture may explode ahead of the flame front. The explosion time is calculated. The theory shows good agreement with previous numerical simulations on deflagration-to-detonation transition in laminar flows.

    Flame interaction with sound waves is studied in the geometry of a flame propagating to a closed tube end. It is demonstrated numerically that intrinsic flame oscillations coming into resonance with acoustic waves may lead to violent folding of the flame front with a drastic increase in the burning rate. The flame folding is related to the Rayleigh-Taylor instability developing at the flame front in the oscillating acceleration field of the acoustic wave.

1234567 151 - 200 av 19822
RefereraExporteraLänk till träfflistan
Permanent länk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf