| 1. |
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| 2. |
- Ahlford, Marianne, et al.
(author)
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Uppsala Underdogs - A Robot Soccer Project
- 2006
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Reports (pop. science, debate, etc.)abstract
- In this paper, we describe the four-legged soccer team Uppsala Underdogs developed by a group of 4th year computer science students at Uppsala University during the fall of 2004. The project is based on the experience from two similar previous projects. This year the emphasis of the project has been on distribution of data and on support for evaluation and reconfiguration of strategies. To support data distribution, a middleware has been developed, which implements a replication algorithm and provides a clean interface for the other software modules (or behaviors). To enable easy reconfiguration of strategies, an automata-based graphical description language has been developed, which can be compiled into code that uses the database and the lower level modules, such as tactics and positioning, to make decisions and control the robot. In addition, a graphical simulator has been developed in which the strategies can be evaluated.
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| 3. |
- Andersson, David C., 1978-, et al.
(author)
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A multivariate approach to investigate docking parameters' effects on docking performance
- 2007
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In: Journal of chemical information and modeling. - : American Chemical Society Publications. - 1549-9596 .- 1549-960X. ; 47:4, s. 1673-1687
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Journal article (peer-reviewed)abstract
- Increasingly powerful docking programs for analyzing and estimating the strength of protein-ligand interactions have been developed in recent decades, and they are now valuable tools in drug discovery. Software used to perform dockings relies on a number of parameters that affect various steps in the docking procedure. However, identifying the best choices of the settings for these parameters is often challenging. Therefore, the settings of the parameters are quite often left at their default values, even though scientists with long experience with a specific docking tool know that modifying certain parameters can improve the results. In the study presented here, we have used statistical experimental design and subsequent regression based on root-mean-square deviation values using partial least-square projections to latent structures (PLS) to scrutinize the effects of different parameters on the docking performance of two software packages: FRED and GOLD. Protein-ligand complexes with a high level of ligand diversity were selected from the PDBbind database for the study, using principal component analysis based on 1D and 2D descriptors, and space-filling design. The PLS models showed quantitative relationships between the docking parameters and the ability of the programs to reproduce the ligand crystallographic conformation. The PLS models also revealed which of the parameters and what parameter settings were important for the docking performance of the two programs. Furthermore, the variation in docking results obtained with specific parameter settings for different protein-ligand complexes in the diverse set examined indicates that there is great potential for optimizing the parameter settings for selected sets of proteins.
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| 4. |
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| 5. |
- Ekblad, Anton, 1986, et al.
(author)
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A seamless, client-centric programming model for type safe web applications
- 2014
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In: ACM SIGPLAN Notices. - New York, NY, USA : ACM. - 1523-2867. ; 49:12, s. 79-89
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Journal article (peer-reviewed)abstract
- We propose a new programming model for web applications which is (1) seamless; one program and one language is used to produce code for both client and server, (2) client-centric; the programmer takes the viewpoint of the client that runs code on the server rather than the other way around, (3) functional and type-safe, and (4) portable; everything is implemented as a Haskell library that implicitly takes care of all networking code. Our aim is to improve the painful and error-prone experience of today's standard development methods, in which clients and servers are coded in different languages and communicate with each other using ad-hoc protocols. We present the design of our library called Haste.App, an example web application that uses it, and discuss the implementation and the compiler technology on which it depends.
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| 6. |
- Kapoor, Pooja Middha, et al.
(author)
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Combined associations of a polygenic risk score and classical risk factors with breast cancer risk
- 2021
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 113:3, s. 329-337
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Journal article (peer-reviewed)abstract
- We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer.
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| 7. |
- Landgren, Anton J., 1989, et al.
(author)
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Incidence of and risk factors for nephrolithiasis in patients with gout and the general population, a cohort study
- 2017
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In: Arthritis Research & Therapy. - : Springer Science and Business Media LLC. - 1478-6354 .- 1478-6362. ; 19
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Journal article (peer-reviewed)abstract
- Background: Nephrolithiasis (NL) is known to be associated with gout, although there are few comparative studies on risk and risk factors for NL in gout compared to population cohorts. In this cohort study we investigated: (1) overall incidence of NL in gout (cases) and general population controls; (2) risk and risk factors (common comorbidities and medications) for first-time NL in cases and controls separately. Methods: Cases (n = 29,968) and age-matched and sex-matched controls (n = 138,678) were identified from the regional healthcare database in western Sweden (VEGA). The analyzed risk factors (comorbidities and current medication use) for first-time NL, and socioeconomic factors were retrieved from VEGA and other national Swedish registers. For cases, follow up began on 1 January 2006 or on the first diagnosis of gout if this occurred later, and for controls on their index patient's first diagnosis of gout. Follow up ended on death, emigration or 31 December 2012. Incidence rates (IR) per 1000 person-years and hazard ratios (HR) were calculated. The incidence calculations were performed for cases (regardless of prior NL) and their controls. HRs with first occurrence of NL as outcome were calculated only in those without previous NL. Results: In cases there were 678 NL events (IR: 6.16 events per 1000 person-years (95% CI: 5.70-6.64) and in controls 2125 NL events (IR 3.85 events per 1000 person-years (95% CI: 3.69-4.02), resulting in an age-sex-adjusted incidence rate ratio of 1.60 (95% CI: 1.47-1.74). Point estimates for predictive factors were similar in cases and controls, except for a significant interaction for losartan which increased the risk of NL only in controls (HR = 1.49 (95% CI: 1.03-2.14). Loop diuretics significantly decreased the risk of NL by 30-34% in both cases and controls. Further significant predictors of NL in gout cases were male sex, diabetes and obesity and in controls male sex and kidney disease. Conclusions: The risk (age and sex adjusted) of NL was increased by 60% in cases compared to controls. None of the commonly used medications increased the risk of NL in gout patients.
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| 8. |
- Lindström, Anton, 1976-
(author)
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A multivariate approach to characterization of drug-like molecules, proteins and the interactions between them
- 2008
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Doctoral thesis (other academic/artistic)abstract
- En sjukdom kan många gånger härledas till en kaskadereaktion mellan proteiner, co-faktorer och substrat. Denna kaskadreaktion blir många gånger målet för att behandla sjukdomen med läkemedel. För att designa nya läkemedelsmoleyler används vanligen datorbaserade verktyg. Denna design av läkemedelsmolekyler drar stor nytta av att målproteinet är känt och då framförallt dess tredimensionella (3D) struktur. Är 3D-strukturen känd kan man utföra så kallad struktur- och datorbaserad molekyldesign, 3D-geometrin (f.f.a. för inbindningsplatsen) blir en vägledning för designen av en ny molekyl. Många faktorer avgör interaktionen mellan en molekyl och bindningsplatsen, till exempel fysikalisk-kemiska egenskaper hos molekylen och bindningsplatsen, flexibiliteten i molekylen och målproteinet, och det omgivande lösningsmedlet. För att strukturbaserad molekyldesign ska fungera väl måste två viktiga steg utföras: i) 3D anpassning av molekyler till bindningsplatsen i ett målprotein (s.k. dockning) och ii) prediktion av molekylers affinitet för bindningsplatsen. Huvudsyftena med arbetet i denna avhandling var som följer: i) skapa modeler för att prediktera affiniteten mellan en molekyl och bindningsplatsen i ett målprotein; ii) förfina molekyl-protein-geometrin som skapas vid 3D-anpassning mellan en molekyl och bindningsplatsen i ett målprotein (s.k. dockning); iii) karaktärisera proteiner och framför allt deras sekundärstruktur; iv) bedöma effekten av olika matematiska beskrivningar av lösningsmedlet för förfining av 3D molekyl-protein-geometrin skapad vid dockning och prediktion av molekylers affinitet för proteiners bindningsfickor. Ett övergripande syfte var att använda kemometriska metoder för modellering och dataanalys på de ovan nämnda punkterna. För att sammanfatta så presenterar denna avhandling metoder och resultat som är användbara för strukturbaserad molekyldesign. De rapporterade resultaten visar att det är möjligt att skapa kemometriska modeler för prediktion av molekylers affinitet för bindningsplatsen i ett protein och att dessa presterade lika bra som andra vanliga metoder. Dessutom kunde kemometriska modeller skapas för att beskriva effekten av hur inställningarna för olika parametrar i dockningsprogram påverkade den 3D molekyl-protein-geometrin som dockingsprogram skapade. Vidare kunde kemometriska modeller andvändas för att öka förståelsen för deskriptorer som beskrev sekundärstrukturen i proteiner. Förfining av molekyl-protein-geometrin skapad genom dockning gav liknande och ickesignifikanta resultat oberoende av vilken matematisk modell för lösningsmedlet som användes, förutom för ett fåtal (sex av 30) fall. Däremot visade det sig att användandet av en förfinad geometri var värdefullt för prediktion av molekylers affinitet för bindningsplatsen i ett protein. Förbättringen av prediktion av affintitet var markant då en Poisson-Boltzmann beskrivning av lösningsmedlet användes; jämfört med prediktionerna gjorda med ett dockningsprogram förbättrades korrelationen mellan beräknad affintiet och uppmätt affinitet med 0,7 (R2).
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| 9. |
- Lindström, Anton, et al.
(author)
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Bone contrast optimization in magnetic resonance imaging using experimental design of ultra-short echo-time parameters
- 2013
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In: Chemometrics and Intelligent Laboratory Systems. - : Elsevier Science. - 0169-7439 .- 1873-3239. ; 125, s. 33-39
-
Journal article (peer-reviewed)abstract
- For the purpose of improved planning and treatment by radiation of tumours, we present work exploring the effect of controllable ultra-short echo-time (UTE) sequence settings on the bone contrast in magnetic resonance (MR) imaging, using design of experiments (DoE). Images were collected using UTE sequences from MR imaging and from standard computed tomography (CT). CT was used for determining the spatial position of the bony structures in an animal sample and co-registered with the MR images. The effect of the UTE sequence parameter flip angle (Flip), repetition time (T-R), echo time (T-E), image matrix size (Vox) and number of radial sampling spokes (Samp) were studied. The parameters were also investigated in a healthy voluntary and it was determined that the optimal UTE settings for high bone contrast in a clinically relevant set up were: Flip similar to 9 degrees and T-E = 0.07 ms, while T-R was kept at 8 ms, Vox at 192 and Samp at 30,000. The use of response surface maps, describing the modelled relation between bone contrast and UTE settings, founded in the DoE, may provide information and be a tool to more appropriately select suitable UTE sequence settings.
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| 10. |
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