| 1. |
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| 2. |
- Berglund, Lisa, et al.
(författare)
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Glucose-Dependent Insulinotropic Polypeptide (GIP) Stimulates Osteopontin Expression in the Vasculature via Endothelin-1 and CREB.
- 2016
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Ingår i: Diabetes. - : American Diabetes Association. - 1939-327X .- 0012-1797. ; 65:1, s. 239-254
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Tidskriftsartikel (refereegranskat)abstract
- Glucose-dependent insulinotropic polypeptide (GIP) is an incretin hormone with extrapancreatic effects beyond glycemic control. Here we demonstrate unexpected effects of GIP signaling in the vasculature. GIP induces the expression of the pro-atherogenic cytokine osteopontin (OPN) in mouse arteries, via local release of endothelin-1 (ET-1) and activation of cAMP response element binding protein (CREB). Infusion of GIP increases plasma OPN levels in healthy individuals. Plasma ET-1 and OPN levels are positively correlated in patients with critical limb ischemia. Fasting GIP levels are higher in individuals with a history of cardiovascular disease (myocardial infarction, stroke) when compared to controls. GIP receptor (GIPR) and OPN mRNA levels are higher in carotid endarterectomies from patients with symptoms (stroke, transient ischemic attacks, amaurosis fugax) than in asymptomatic patients; and expression associates to parameters characteristic of unstable and inflammatory plaques (increased lipid accumulation, macrophage infiltration and reduced smooth muscle cell content). While GIPR expression is predominantly endothelial in healthy arteries from human, mouse, rat and pig; remarkable up-regulation is observed in endothelial and smooth muscle cells upon culture conditions yielding a "vascular disease-like" phenotype. Moreover, a common variant rs10423928 in the GIPR gene associated with increased risk of stroke in type 2 diabetes patients.
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| 3. |
- Boethius, Adam, et al.
(författare)
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Huseby Klev and the Quest for Pioneer Subsistence Strategies : Diversification of a Maritime Lifestyle
- 2018
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Ingår i: The Ecology of Early Settlement in Northern Europe : Conditions for Subsistence and Survival - Conditions for Subsistence and Survival. - 9781781795156 - 9781781796030 ; 1, s. 99-128
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Bokkapitel (refereegranskat)abstract
- The bone material from three archaeological occupation phases at Huseby Klev provides the best source of evidence currently available about the subsistence strategies of pioneer settlers in Northern Europe. The results from Huseby Klev indicate that the pioneer settlers initially relied heavily on marine mammals for their sustenance. This subsistence strategy changed during the second and third occupation phases of the site, during which fishing became the most important part of the diet. These changes in subsistence strategy are interpreted as arising from different factors. A highly nutritious ocean on the west coast of Scandinavia at the end of the last ice age resulted in large numbers of available marine mammals in the ocean, which supported a large human population able to base its economy on them. As the ocean became less nutritious withthe cessation of freshwater mixing, the marine mammals suffered a natural population decline, while humans still relied upon them heavily, resulting in a marine-mammal collapse. This forced the human populations to change their subsistence strategy, and fish became dominant in the diet. The bone material from Huseby Klev implies a good knowledge of fishing methods and seafaring, in addition to which it highlights the ocean as the main source of sustenance during the time from the Preboreal–Boreal transition to the mid Atlantic chronozone. The hunting of terrestrial mammals, also found on the site, is interpreted as mainly being undertaken to supply raw material. Finds of reindeer imply the presence of reindeer in Mesolithic western Scandinavia, but they were not prioritized in the diet, possibly only being exploited during yearly migrations. Birds are common in the bone material, and a large number of bird species with a low number of identified fragments from each species implies opportunistic hunting of all but auks, which were hunted in large numbers. The bone material from Huseby Klev is the oldest and best-preserved Atlantic coastal material in Europe, and the results indicate an advanced knowledge of utilizing aquatic resources and suggest a boom in aquatic reliance that is earlier and more widespread than previously known.
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| 4. |
- Boethius, Adam, et al.
(författare)
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The Use of Aquatic Resources by Early Mesolithic Foragers in Southern Scandinavia
- 2018
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Ingår i: The Ecology of Early Settlement in Northern Europe : Conditions for Subsistence and Survival - Conditions for Subsistence and Survival. - 9781781795156 - 9781781796030 ; 1, s. 311-334
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Bokkapitel (refereegranskat)abstract
- A long tradition in research on prehistoric southern Scandinavia recognizes full use of aquatic resources in the Late Mesolithic Ertebølle Culture (5500–4000 cal BC): coastal sites are frequently found containing well-preserved fish bones, and isotope values from human collagen indicate a high dietary intake of marine resources. However, recent finds and new methodologies suggest that the view of a terrestrially focused diet in the Early Mesolithic period (9500–6800 cal BC) can be reinterpreted, and the use of freshwater resources is found to be more important than previously known. Aquatic resources can therefore be seen to be a major source of sustenance for foraging societies in Scandinavia much earlier than has been realized previously. At Norje Sunnansund, an Early Mesolithic site located in Blekinge, south-eastern Sweden, large amounts of fish bones have been found, and these have been used to estimate the amount of fish beingcaught at the site, by analyzing different rates of taphonomic loss. The results from the excavated part of the settlement suggest that at least 48 tonnes of fish were caught. The large amount of caught fish and the evidence of the means of preparing and storing them provides the earliest example of a large-scale fishing society, and the knowledge required to catch and prepare this volume of fish has further implications at a more structural societal level. A structured society is a prerequisite for the development of sedentism and enables large groups of people to gather during an extended time period. Conservative dietary estimates from the recovered fish bone material suggest that enough fish was caught to sustain 100 adults living solely on fish for over three years.
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| 5. |
- Borg, Markus, et al.
(författare)
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The More the Merrier: Leveraging on the Bug Inflow to Guide Software Maintenance
- 2015
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Ingår i: Tiny Transactions on Computer Science. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Issue management, a central part of software maintenance, requires much effort for complex software systems. The continuous inflow of issue reports makes it hard for developers to stay on top of the situation, and the threatening information overload makes activities such as duplicate management, Issue Assignment (IA), and Change Impact Analysis (CIA) tedious and error-prone. Still, most practitioners work with tools that act as little more than issue containers. Machine Learning encompasses approaches that identify patterns or make predictions based on empirical data. While humans have limited ability to work with big data, ML instead tends to improve the more training data that is available. Consequently, we argue that the challenge of information overload in issue management appears to be particularly suitable for ML-based tool support. While others have initially explored the area, we develop two ML-based tools, and evaluate them in proprietary software engineering contexts. We replicated [1] for five projects in two companies, and our automated IA obtains an accuracy matching the current manual processes. Thus, as our solution delivers instantaneous IA, an organization can potentially save considerable analysis effort. Moreover, for the most comprehensive of the five projects, we implemented automated CIA in the tool ImpRec [3]. We evaluated the tool in a longitudinal in situ study, i.e., deployment in two development teams in industry. Based on log analysis and complementary interviews using the QUPER model [2] for utility assessment, we conclude that ImpRec offered helpful support in the CIA task.
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| 6. |
- Fredman, David, et al.
(författare)
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Objective classification and comparison of OHCA and AED locations using geographic information systems
- 2015
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Ingår i: Resuscitation. - : Elsevier BV. - 0300-9572 .- 1873-1570. ; 96, s. 21-21
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Tidskriftsartikel (refereegranskat)abstract
- The Utstein registry template stress recording of out-of-hospital cardiac arrest (OHCA) location and suggest eight data options with additional subcategories. The subjectivity in categorization of OHCA locations by emergency medical services (EMS) makes objective regional and international comparisons hard.
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| 7. |
- Fredman, David, et al.
(författare)
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Use of a geographic information system to identify differences in automated external defibrillator installation in urban areas with similar incidence of public out-of-hospital cardiac arrest : A retrospective registry-based study
- 2017
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Ingår i: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 7:5
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Tidskriftsartikel (refereegranskat)abstract
- Objectives Early defibrillation in out-of-hospital cardiac arrest (OHCA) is of importance to improve survival. In many countries the number of automated external defibrillators (AEDs) is increasing, but the use is low. Guidelines suggest that AEDs should be installed in densely populated areas and in locations with many visitors. Attempts have been made to identify optimal AED locations based on the incidence of OHCA using geographical information systems (GIS), but often on small datasets and the studies are seldom reproduced. The aim of this paper is to investigate if the distribution of public AEDs follows the incident locations of public OHCAs in urban areas of Stockholm County, Sweden. Method OHCA data were obtained from the Swedish Register for Cardiopulmonary Resuscitation and AED data were obtained from the Swedish AED Register. Urban areas in Stockholm County were objectively classified according to the pan-European digital mapping tool, Urban Atlas (UA). Furthermore, we reclassified and divided the UA land cover data into three classes (residential, non-residential and other areas). GIS software was used to spatially join and relate public AED and OHCA data and perform computations on relations and distance. Results Between 1 January 2012 and 31 December 2014 a total of 804 OHCAs occurred in public locations in Stockholm County and by December 2013 there were 1828 AEDs available. The incidence of public OHCAs was similar in residential (47.3%) and non-residential areas (43.4%). Fewer AEDs were present in residential areas than in non-residential areas (29.4% vs 68.8%). In residential areas the median distance between OHCAs and AEDs was significantly greater than in non-residential areas (288 m vs 188 m, p<0.001). Conclusion The majority of public OHCAs occurred in areas classified in UA as 'residential areas' with limited AED accessibility. These areas need to be targeted for AED installation and international guidelines need to take geographical location into account when suggesting locations for AED installation.
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| 8. |
- Gaulton, Kyle J, et al.
(författare)
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Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:12, s. 1415-1415
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Tidskriftsartikel (refereegranskat)abstract
- We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.
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| 9. |
- Gullström, Charlie
(författare)
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High-fidelity Mock-up Report : Public deliverable D.2.4 from COMPEIT, EU FP7 project
- 2015
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- COMPEIT is a 3-year EU 7th framework project and focuses on a web-based system for highly interactive, personalised, shared media experiences by developing technologies that A) enrich social connections, B) improve the feeling of being together in one shared space and C) enhance collaboration whilst being separated in time or space. COMPEIT takes the view that Internet-based distribution will transform traditional broadcasting towards higher levels of interactivity and integration with virtual and augmented reality, enabled by advanced web technologies and the proliferation of tangible devices. The project addresses Quality of Experience as a key variable in the experience of media production and consumption systems.A first mock-up of the COMPEIT system has been put together. It illustrates technical components from WP 4 (Mediated Presence Components); services from WP 5 (New Media Services); and D3.2 Initial System Specification. It informs further research towards D3.4 First Prototype.
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| 10. |
- Gullström, Charlie
(författare)
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Immersive Spaces 1.0 : WP4 Mediated Presence Components
- 2016
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- COMPEIT creates a web-based system for highly interactive, personalised, shared media experiences. The new technologies will improve the feeling of being together in a shared mediated space and support interaction and collaboration between people who are separated in time or space.Immersive spaces 1.0 is a software component for the COMPEIT presence system with a feature set that allows users to interact and perform shared actions in virtual spaces, simply using their web browser. The main features are called SharedSpace, a virtual 3D environment which users can redesign and populate by scaling and rearranging their avatar-like live videostream representations; and PixelPresence which is an overlay technique that offers a pixelated view of a livestream, hereby adding an ambient and discrete presence filter, which indicates movement and subtly prompts users to enter a mediated interaction. The COMPEIT presence system supports individuals and distributed groups who want to stay close with one another on a regular basis, ready to spontaneously interact in mediated and virtual space. Feedback from users and user requirements in WP2 showed that people want to be subtly aware of what others are doing, and if they are at a particular place at a given time – which, of course, is quite different to keeping a videolink open 24/7. Whether the context is professional or social, ambient forms of presence are thus called for, in order to support gradation and, perhaps more importantly, to prompt users to join a shared virtual space.
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| 11. |
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| 12. |
- Hasselqvist-Ax, Ingela, et al.
(författare)
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Dispatch of Firefighters and Police Officers in Out-of-Hospital Cardiac Arrest : A Nationwide Prospective Cohort Trial Using Propensity Score Analysis.
- 2017
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Ingår i: Journal of the American Heart Association. - 2047-9980. ; 6:10
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Dispatch of basic life support-trained first responders equipped with automated external defibrillators in addition to advanced life support-trained emergency medical services personnel in out-of-hospital cardiac arrest (OHCA) has, in some minor cohort studies, been associated with improved survival. The aim of this study was to evaluate the association between basic life support plus advanced life support response and survival in OHCA at a national level.METHODS AND RESULTS: This prospective cohort study was conducted from January 1, 2012, to December 31, 2014. People who experienced OHCA in 9 Swedish counties covered by basic life support plus advanced life support response were compared with a propensity-matched contemporary control group of people who experienced OHCA in 12 counties where only emergency medical services was dispatched, providing advanced life support. Primary outcome was survival to 30 days. The analytic sample consisted of 2786 pairs (n=5572) derived from the total cohort of 7308 complete cases. The median time from emergency call to arrival of emergency medical services or first responder was 9 minutes in the intervention group versus 10 minutes in the controls (P<0.001). The proportion of patients admitted alive to the hospital after resuscitation was 31.4% (875/2786) in the intervention group versus 24.9% (694/2786) in the controls (conditional odds ratio, 1.40; 95% confidence interval, 1.24-1.57). Thirty-day survival was 9.5% (266/2786) in the intervention group versus 7.7% (214/2786) in the controls (conditional odds ratio, 1.27; 95% confidence interval, 1.05-1.54).CONCLUSIONS: In this nationwide interventional trial, using propensity score matching, dispatch of first responders in addition to emergency medical services in OHCA was associated with a moderate, but significant, increase in 30-day survival.CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov. Unique identifier: NCT02184468.
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| 13. |
- Hasselqvist-Ax, Ingela, et al.
(författare)
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Early cardiopulmonary resuscitation in out-of-hospital cardiac arrest.
- 2015
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Ingår i: The New England journal of medicine. - 1533-4406 .- 0028-4793. ; 372:24, s. 2307-15
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Tidskriftsartikel (refereegranskat)abstract
- Three million people in Sweden are trained in cardiopulmonary resuscitation (CPR). Whether this training increases the frequency of bystander CPR or the survival rate among persons who have out-of-hospital cardiac arrests has been questioned.
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| 14. |
- Johnsson, Martin, et al.
(författare)
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Genetic Regulation of Bone Metabolism in the Chicken : Similarities and Differences to Mammalian Systems
- 2015
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Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- Birds have a unique bone physiology, due to the demands placed on them through egg production. In particular their medullary bone serves as a source of calcium for eggshell production during lay and undergoes continuous and rapid remodelling. We take advantage of the fact that bone traits have diverged massively during chicken domestication to map the genetic basis of bone metabolism in the chicken. We performed a quantitative trait locus (QTL) and expression QTL (eQTL) mapping study in an advanced intercross based on Red Junglefowl (the wild progenitor of the modern domestic chicken) and White Leghorn chickens. We measured femoral bone traits in 456 chickens by peripheral computerised tomography and femoral gene expression in a subset of 125 females from the cross with microarrays. This resulted in 25 loci for female bone traits, 26 loci for male bone traits and 6318 local eQTL loci. We then overlapped bone and gene expression loci, before checking for an association between gene expression and trait values to identify candidate quantitative trait genes for bone traits. A handful of our candidates have been previously associated with bone traits in mice, but our results also implicate unexpected and largely unknown genes in bone metabolism. In summary, by utilising the unique bone metabolism of an avian species, we have identified a number of candidate genes affecting bone allocation and metabolism. These findings can have ramifications not only for the understanding of bone metabolism genetics in general, but could also be used as a potential model for osteoporosis as well as revealing new aspects of vertebrate bone regulation or features that distinguish avian and mammalian bone.
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| 15. |
- Johnsson, Martin, et al.
(författare)
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Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken
- 2016
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Ingår i: G3. - Bethesda, MD, United States : Oxford University Press (OUP). - 2160-1836. ; 6:2, s. 311-319
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Tidskriftsartikel (refereegranskat)abstract
- Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait-gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.
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| 16. |
- Jonsson, Leif, et al.
(författare)
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Automated Bug Assignment: Ensemble-based Machine Learning in Large Scale Industrial Contexts
- 2015
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Ingår i: Empirical Software Engineering. - : Springer Science and Business Media LLC. - 1573-7616 .- 1382-3256. ; 21:4
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Tidskriftsartikel (refereegranskat)abstract
- Bug report assignment is an important part of software maintenance. In particular, incorrect assignments of bug reports to development teams can be very expensive in large software development projects. Several studies propose automating bug assignment techniques using machine learning in open source software contexts, but no study exists for large-scale proprietary projects in industry. The goal of this study is to evaluate automated bug assignment techniques that are based on machine learning classification. In particular, we study the state-of-the-art ensemble learner Stacked Generalization (SG) that combines several classifiers. We collect more than 50,000 bug reports from five development projects from two companies in different domains. We implement automated bug assignment and evaluate the performance in a set of controlled experiments. We show that SG scales to large scale industrial application and that it outperforms the use of individual classifiers for bug assignment, reaching prediction accuracies from 50 % to 89 % when large training sets are used. In addition, we show how old training data can decrease the prediction accuracy of bug assignment. We advice industry to use SG for bug assignment in proprietary contexts, using at least 2,000 bug reports for training. Finally, we highlight the importance of not solely relying on results from cross-validation when evaluating automated bug assignment.
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| 17. |
- Jonsson, Leif, et al.
(författare)
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Automatic Localization of Bugs to Faulty Components in Large Scale Software Systems using Bayesian Classification
- 2016
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Ingår i: 2016 IEEE INTERNATIONAL CONFERENCE ON SOFTWARE QUALITY, RELIABILITY AND SECURITY (QRS 2016). - : IEEE. - 9781509041275 ; , s. 425-432
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Konferensbidrag (refereegranskat)abstract
- We suggest a Bayesian approach to the problem of reducing bug turnaround time in large software development organizations. Our approach is to use classification to predict where bugs are located in components. This classification is a form of automatic fault localization (AFL) at the component level. The approach only relies on historical bug reports and does not require detailed analysis of source code or detailed test runs. Our approach addresses two problems identified in user studies of AFL tools. The first problem concerns the trust in which the user can put in the results of the tool. The second problem concerns understanding how the results were computed. The proposed model quantifies the uncertainty in its predictions and all estimated model parameters. Additionally, the output of the model explains why a result was suggested. We evaluate the approach on more than 50000 bugs.
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| 18. |
- Jonsson, Leif J., et al.
(författare)
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Pretreatment of lignocellulose : Formation of inhibitory by-products and strategies for minimizing their effects
- 2016
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Ingår i: Bioresource Technology. - : Elsevier BV. - 0960-8524 .- 1873-2976. ; 199, s. 103-112
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Forskningsöversikt (refereegranskat)abstract
- Biochemical conversion of lignocellulosic feedstocks to advanced biofuels and other commodities through a sugar-platform process involves a pretreatment step enhancing the susceptibility of the cellulose to enzymatic hydrolysis. A side effect of pretreatment is formation of lignocellulose-derived by-products that inhibit microbial and enzymatic biocatalysts. This review provides an overview of the formation of inhibitory by-products from lignocellulosic feedstocks as a consequence of using different pretreatment methods and feedstocks as well as an overview of different strategies used to alleviate problems with inhibitors. As technologies for biorefining of lignocellulose become mature and are transferred from laboratory environments to industrial contexts, the importance of management of inhibition problems is envisaged to increase as issues that become increasingly relevant will include the possibility to use recalcitrant feedstocks, obtaining high product yields and high productivity, minimizing the charges of enzymes and microorganisms, and using high solids loadings to obtain high product titers.
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| 19. |
- Jonsson, Leif, 1973-
(författare)
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Machine Learning-Based Bug Handling in Large-Scale Software Development
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis investigates the possibilities of automating parts of the bug handling process in large-scale software development organizations. The bug handling process is a large part of the mostly manual, and very costly, maintenance of software systems. Automating parts of this time consuming and very laborious process could save large amounts of time and effort wasted on dealing with bug reports. In this thesis we focus on two aspects of the bug handling process, bug assignment and fault localization. Bug assignment is the process of assigning a newly registered bug report to a design team or developer. Fault localization is the process of finding where in a software architecture the fault causing the bug report should be solved. The main reason these tasks are not automated is that they are considered hard to automate, requiring human expertise and creativity. This thesis examines the possi- bility of using machine learning techniques for automating at least parts of these processes. We call these automated techniques Automated Bug Assignment (ABA) and Automatic Fault Localization (AFL), respectively. We treat both of these problems as classification problems. In ABA, the classes are the design teams in the development organization. In AFL, the classes consist of the software components in the software architecture. We focus on a high level fault localization that it is suitable to integrate into the initial support flow of large software development organizations.The thesis consists of six papers that investigate different aspects of the AFL and ABA problems. The first two papers are empirical and exploratory in nature, examining the ABA problem using existing machine learning techniques but introducing ensembles into the ABA context. In the first paper we show that, like in many other contexts, ensembles such as the stacked generalizer (or stacking) improves classification accuracy compared to individual classifiers when evaluated using cross fold validation. The second paper thor- oughly explore many aspects such as training set size, age of bug reports and different types of evaluation of the ABA problem in the context of stacking. The second paper also expands upon the first paper in that the number of industry bug reports, roughly 50,000, from two large-scale industry software development contexts. It is still as far as we are aware, the largest study on real industry data on this topic to this date. The third and sixth papers, are theoretical, improving inference in a now classic machine learning tech- nique for topic modeling called Latent Dirichlet Allocation (LDA). We show that, unlike the currently dominating approximate approaches, we can do parallel inference in the LDA model with a mathematically correct algorithm, without sacrificing efficiency or speed. The approaches are evaluated on standard research datasets, measuring various aspects such as sampling efficiency and execution time. Paper four, also theoretical, then builds upon the LDA model and introduces a novel supervised Bayesian classification model that we call DOLDA. The DOLDA model deals with both textual content and, structured numeric, and nominal inputs in the same model. The approach is evaluated on a new data set extracted from IMDb which have the structure of containing both nominal and textual data. The model is evaluated using two approaches. First, by accuracy, using cross fold validation. Second, by comparing the simplicity of the final model with that of other approaches. In paper five we empirically study the performance, in terms of prediction accuracy, of the DOLDA model applied to the AFL problem. The DOLDA model was designed with the AFL problem in mind, since it has the exact structure of a mix of nominal and numeric inputs in combination with unstructured text. We show that our DOLDA model exhibits many nice properties, among others, interpretability, that the research community has iden- tified as missing in current models for AFL.
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| 20. |
- Jonsson, Peter, et al.
(författare)
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Geofysiker, drönare och geologer ger tillsammans en bättre bild av berget
- 2019
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Ingår i: Bygg & teknik. - 0281-658X. ; :1/19, s. 52-55
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- Teknisk geologi vid Lunds tekniska högskola har i ett nyligen slutfört projekt, finansierat av Stiftelsen Bergteknisk Forskning (BeFo), undersökt om geofysiska mätningar med DCIP (kombinerade resistivitets- och IP-mätningar) kan ge bättre information om bergmassan i samband med planeringen av tunnlar och andra bergarbeten samt berguttag i bergtäkter. Resultaten bekräftar att DCIP i den undersökta miljön kan användas för att indikera lervittrade zoner, svaghetsstrukturer och uppkrossade zoner. Detta visar på att det går att underlätta och förbättra prognosarbetet, genom att ännu en möjlighet ges att bedöma bergmassans kvalitet innan byggfasen inleds.
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| 21. |
- Jonsson, Peter, et al.
(författare)
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Tredimensionell bergundersökning med geoelektriska och geologiska metoder
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this project is to enhance the understanding of how geoelectrical investigations in a heterogeneous rock mass can image geological structures in order to develop and adapt future rock assessment methods.A "good" rock quality forecast provides better opportunities for reduced risk level in the design and procurement phases of a construction project. Conversely, uncertainties in a forecast, in terms of rock quality, can entail large costs. The additional information obtained using non-destructive surveys will is therefore of large interest in this context. It has repeatedly (e.g. in connection with the construction of the Hallandsås tunnel) been shown that variations in, for example, the electrical properties, can be linked to factors such as fracture zones, clay weathering or the presence of certain mineral types in the rock mass. .The basic idea is to perform a three-dimensional measurement with simultaneous determination of DC resistivity and induced polarization, (DCIP), in a rock volume in a quarry. The examined rock volume is then removed by bench blasting as part of the normal quarry activities. The vertical benches that occur after each blast are documented with photogrammetric methods, geological sampling and by detailed studies with a sweep electron microscope (SEM). Furthermore, photographic methods such as panoramic photography and 3D computer models created with the help of unmanned aerial vehicles, drones, have been used.The result is another three-dimensional model, with detailed geological information. This creates an opportunity to compare results and interpretations from the geoelectrical methods with geological information throughout the examined volume. For example, the three-dimensional distribution of fracture zones or dolerite dikes can be identified in the geological model and compared to the geophysical.The measuring object in the project was a quarry in Dalby, 10 km East of Lund, Sweden and operated by Sydsten. The site is well investigated from both geological and geophysical viewpoints. The rock consists mainly of three different types: Granitic gneiss, dolerite and amphibolite, but smaller units of other rocks occur. The structures are complex with folding and formation of lenses, mainly in the amphibolite. Due to large-scale tectonic processes, the rock has been subjected to extensive deformation on several occasions. Brecciated and crushed zones occur as well as clay alteration zones.The geophysical method used in the project is resistivity measurement with simultaneous measurement of induced polarization, DCIP. The resistivity method is based on the basic assumption that properties in the ground such as porosity, the actual rock matrix and the conductivity of the pore fluid are reflected in changes in the conductivity. The IP effects rely heavily on the internal composition of the geo-materials, filling in the pores, and structures in micro-scale and upwards.The report initially describes the background and purpose, then the measurements and methodologies in the sections 2 and 3. In section 4 the collected measurement results and input data are described, including recommendations and experiences for panorama- and UAV photography, as well as the results of the geological mapping (visual inspection and SEM) and the geophysics.One of the main objectives of project was to investigate how well geoelectrical measurements in a heterogeneous bedrock can depict geological structures. The ability to document the rock mass in the Dalby Quarry has given an opportunity to compare geological reality with results from DCIP measurements.A comparison in section 5 between the geological and geophysical measurements confirms that the DCIP in the test environment can be used to indicate clay weathering zones, weakness zones and crushed rock. This can be used to distinguish rock mass with zones of clay weathering with potentially high fine material content from other rock, providing an opportunity to assess the quality before the fragmentation of the rock.Further, it is noted that the ability to depict geological structures depends on the design of the geophysical investigation, the inversion process, and the obtained data quality. The data quality can to some extent be affected at the time of measurement, i.e. already during the planning of the assessment, while other factors cannot be affected using available measurement methodology.One example is that dipping geological structures do not show up as clearly as vertical in the geophysical results. The reason for this is unclear. One explanation may be that the petrophysical contrast between, for example, gneiss and amphibolite is too small to be detected by geoelectrical methods, another that the numerical inversion process has difficulties representing these structures correctly.It is also clear that visual geological attributes are not fully sufficient to explain all anomalies appearing in the geophysical model, in particular regarding the IP results. More detailed studies aimed at quantifying these complex effects are needed to understand these complex phenomena. The resistivity anomalies are better explained by the visual observations made. This is because resistivity to a greater extent depends on the composition of the rock mass and macro structures such as fractures, but also here a need to quantify and study correlations in laboratory scale exists.The spatial resolution can be improved by modifying the measurement procedure. One way forward is to install electrodes in a borehole, in addition to the surface electrodes used today. This implies practical difficulties but has a great development potential for the future. Although modern instruments have been used in the project, instruments can be developed towards even more effective measurements, for example by using more channels for the potential measure-ment, dynamic measurement protocols, and adaptive current transmission that adjusts the measurement to the actual conditions on the site.
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| 22. |
- Lind, Ulrika, et al.
(författare)
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Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:7
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Tidskriftsartikel (refereegranskat)abstract
- Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms. The knowledge of the function of aquaporins in crustaceans is, however, limited and nothing is known about them in barnacles. We here present the repertoire of aquaporins from a thecostracan crustacean, the barnacle B. improvisus, based on genome and transcriptome sequencing. Our analyses reveal that B. improvisus contains eight genes for aquaporins. Phylogenetic analysis showed that they represented members of the classical water aquaporins (Aqp1, Aqp2), the aquaglyceroporins (Glp1, Glp2), the unorthodox aquaporin (Aqp12) and the arthropod-specific big brain aquaporin (Bib). Interestingly, we also found two big brain-like proteins (BibL1 and BibL2) constituting a new group of aquaporins not yet described in arthropods. In addition, we found that the two water-specific aquaporins were expressed as C-terminal splice variants. Heterologous expression of some of the aquaporins followed by functional characterization showed that Aqp1 transported water and Glp2 water and glycerol, agreeing with the predictions of substrate specificity based on 3D modeling and phylogeny. To investigate a possible role for the B. improvisus aquaporins in osmoregulation, mRNA expression changes in adult barnacles were analysed after long-term acclimation to different salinities. The most pronounced expression difference was seen for AQP1 with a substantial (>100-fold) decrease in the mantle tissue in low salinity (3 PSU) compared to high salinity (33 PSU). Our study provides a base for future mechanistic studies on the role of aquaporins in osmoregulation. © 2017 Lind et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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| 23. |
- Lindgren, Erik, et al.
(författare)
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Gender differences in utilization of coronary angiography and angiographic findings after out-of-hospital cardiac arrest : A registry study
- 2019
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Ingår i: Resuscitation. - : Elsevier BV. - 0300-9572 .- 1873-1570. ; 143, s. 189-195
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: We investigated the impact of gender in performance and findings of early coronary angiography (CAG) and percutaneous coronary intervention (PCI), comorbidity and outcome in a large population of out-of-hospital cardiac arrest (OHCA) patients with an initially shockable rhythm.Methods: Retrospective cohort study. Data retrieved 2008-2013 from the Swedish Register for Cardio-Pulmonary Resuscitation, Swedeheart Registry and National Patient Register.Results: We identified 1498 patients of whom 78% were men. Men and women had the same pathology on the first registered electrocardiogram (ECG): 30% vs. 29% had ST-elevation and 10% vs. 9% had left bundle branch block (LBBB) (P=0.97). Proportions of performed CAG did not differ between genders. Among patients without ST-elevation/LBBB men more often had at least one significant stenosis, 78% vs. 54% (P= 0.001), more multi-vessel disease (P= 0.01), had normal coronary angiography less often, 22% vs. 46% and PCI more often, 59% vs. 42% (P= 0.03). Among patients without STelevation/LBBB on the initial ECG, more men had previously known ischaemic heart disease, 27% vs. 19% (P=0.02) and a presumed cardiac origin of the cardiac arrest, 86% vs. 72% (P< 0.001). Multivariable analysis showed no association between gender and evaluation by early CAG. In men and women, 1-year survival was 56% vs. 50% (P= 0.22) in patients with ST-elevation/LBBB and 48% vs. 51% (P= 0.50) in patients without.Conclusion: Despite no gender differences in ECG findings indicating an early CAG, men had more severe coronary artery disease while women more frequently had normal coronary angiography. However, this did not influence 1-year survival.
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| 24. |
- Liu, Hailong
(författare)
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A Study of the Particle Transport Behavior in Enclosed Environments
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The main purpose of the present work is to increase the fundamental understanding of the particle transport behavior in an enclosed environment and to provide knowledge to the estimate and measure the particle emission from pellets during a steel production process.A laboratory study focused on the effect of the high sliding velocity on the particle generation from dry sliding wheel-rail contacts has been conducted. The particle concentration and the size distribution were acquired online by using particle number counters during the tests. After the completion of each test, the characteristics of pin worn surfaces and collected particles were analyzed with the aid of SEM (scanning electron microscopy) combined with EDS (energy disperse X-ray analysis). The results show that the amount of the particle generation increases significantly as the sliding velocity increases from 0.1 to 3.4 m/s. Moreover, the particle size distribution results indicate that the majority of the generated particles are submicron (ultrafine and fine) particles in the case of a high sliding velocity (1.2 and 3.4 m/s). The observations of iron oxide layers within the pin worn surface and the collected iron-oxide containing particles reveal that these substantial small particles can be attributed to an oxidative wear between the dry sliding wheel-rail contacts under high sliding velocities.The effect of the particle transport behavior with respect to submicron particles in the test chamber on the measurements taken at the outlet was studied by a three dimensional mathematical model. With the assistance of CFD (computational fluid dynamics) simulations, the airflow pattern was found to have a major effect on the particle transport during the tests. By estimating the particle loss rate, 30% of generated particles failed to be captured at the outlet. The reason for that could be a temporary suspension and a deposition onto the surfaces. It should be noted that the particles were assumed to follow the air stream as a result of the small particle size. In addition, the Lagrangian tracking results reveal that the limiting size for particles to become airborne during tests is around 10 µm. However, the computational cost is found to be significant high when the Lagrangian method is adopted.To consider the measurements of micron particles and to reduce the computational time, a coupled drift flux and Eulerian deposition model was developed. In this model, the effects of the gravitational sedimentation and deposition on the particle dispersion were included. The simulation results are in a good agreement with the available experimental data. The value of APD (average percentage deviation) is in the range of 7.7% to 21.2%. Therefore, a set of simulation cases have been carried out to investigate the influential factors (particle size, wall roughness, source location and duration). The results show that the homogeneity of the particle concentration distribution in the model room declines with an increased particle size (0.01 to 10 µm). An almost uniform particle concentration field is formed for submicron particles (0.01 and 0.1 µm) and for fine particles (1 and 2 µm). However, a clear concentration gradient is obtained for coarse particles (4, 6, 8 and 10 µm). This is due to that the gravitational settling dominates the motion of coarse particles. As a result, a large deposited amount and a high deposition fraction was predicted for coarse particles. Moreover, the surface roughness was found to enhance the deposition of submicron particles (0.1 and 0.01 µm) for a given friction velocity. On the contrary, the deposition of micron particles is much less sensitive to the variation of the surface roughness. For a case of an internal source in the room, where a release over a long duration is considered, the particle dispersion strongly depends on the release location. However, this is not the case for a short release time.The dispersions and depositions of micron particles were explored in a laboratory test focused on the particle emission from the wear between the pellets. The simulation results were compared to the measured data with respect to the particle flux at the outlet. A good agreement (4.92% < APD < 12.02%) is obtained. In addition, the influence of the air flow rate at the inlet and the particle size on the sampling results at the outlet was investigated carefully. The results show that a stronger air supply at the inlet can push more particles to the outlet for any given particle sizes. However, the resulted increase of the measurable fraction is more significant for 4, 6, 8 10 µm particles compared to 1, 2 and 20 µm particles. Moreover, it is apparent that 20 µm particles are unable to be measured in such a measurement system.
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| 25. |
- Magnusson, Måns, 1981-, et al.
(författare)
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Sparse Partially Collapsed MCMC for Parallel Inference in Topic Models
- 2018
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Ingår i: Journal of Computational And Graphical Statistics. - : American Statistical Association. - 1061-8600 .- 1537-2715. ; 27:2, s. 449-463
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Tidskriftsartikel (refereegranskat)abstract
- Topic models, and more specifically the class of latent Dirichlet allocation (LDA), are widely used for probabilistic modeling of text. Markov chain Monte Carlo (MCMC) sampling from the posterior distribution is typically performed using a collapsed Gibbs sampler. We propose a parallel sparse partially collapsed Gibbs sampler and compare its speed and efficiency to state-of-the-art samplers for topic models on five well-known text corpora of differing sizes and properties. In particular, we propose and compare two different strategies for sampling the parameter block with latent topic indicators. The experiments show that the increase in statistical inefficiency from only partial collapsing is smaller than commonly assumed, and can be more than compensated by the speedup from parallelization and sparsity on larger corpora. We also prove that the partially collapsed samplers scale well with the size of the corpus. The proposed algorithm is fast, efficient, exact, and can be used in more modeling situations than the ordinary collapsed sampler. Supplementary materials for this article are available online.
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| 26. |
- Mohan Pawar, Prashant, et al.
(författare)
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Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification
- 2017
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Ingår i: New Phytologist. - : Wiley-Blackwell Publishing Inc.. - 0028-646X .- 1469-8137. ; 214:4, s. 1491-1505
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Tidskriftsartikel (refereegranskat)abstract
- High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter:: GUS lines in hybrid aspen (Populus tremula x tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.
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| 27. |
- Nilsson, Björn, et al.
(författare)
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Seascapes of stability and change: the archaeological and ecological potential of the early mesolithic seascapes with examples from Haväng in SE Baltic, Sweden
- 2018
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Ingår i: Ecology of Early Settlement in Northern Europe Conditions for Subsistence and Survival The Early Settlement of Northern Europe, Volume 1. - 9781781795156 - 9781781796030 ; 1, s. 335-352
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Bokkapitel (refereegranskat)abstract
- The sea level low stand period during the Early Mesolithic in SE Baltic (c. 9,500-6,500 BC) has resulted in vast inundated areas. Some of the sites have yielded extensive remains of lagoonal and riverine sediments, as well as areas with trees preserved in situ. Investigations at one of the sites - Haväng in eastern Scania - have resulted in archaeological findings from the entire period. The preservation of organic materials are very good, and gives new insights in material culture and fishing technologies. Extensive surveying and hydro-acoustic mapping gives possibilities to draw some conclusion of the possible timing of the introduction of stationary fishing and how this relates to cultural and natural changes. The paper proposes that riverine stationary fisheries in the southern Baltic were introduced during the Boreal period (7000 BC or earlier). The Maglemose fisheries are proposed as indirect evidence of early seascape territorialisation, which must be understood in a cultural and ecological context.
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| 28. |
- Olsson, Per-Ivar, et al.
(författare)
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BeFo 382 - Detailed Comparison Study of 3D-characterized Rock Mass and Geophysical Models
- 2017
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Ingår i: Near Surface Geoscience 2017 - 23rd European Meeting of Environmental and Engineering Geophysics. - Netherlands : EAGE Publications BV.
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Konferensbidrag (refereegranskat)abstract
- This paper presents a study where resistivity and integral chargeability three-dimensional (3D) models, representing a volume in the vicinity of a rock quarry is compared to a quasi-3D characterization of rock mass volume. By repeating geological mapping, i.e. with unmanned aerial vehicles, ground based high resolution photography and sampling, as the quarry operation reaches further into the rock volume mapped with geophysics, we retrieve a semi-continuous geological characterization of the same rock mass volume characterized by the geophysical investigations. This enables a detailed comparison between geophysical results and rock volume, where factors such as fracture and weathering zones or rock type is being considered.
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| 29. |
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| 30. |
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| 31. |
- Terenin, Alexander, et al.
(författare)
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Polya Urn Latent Dirichlet Allocation: A Doubly Sparse Massively Parallel Sampler
- 2019
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Ingår i: IEEE Transactions on Pattern Analysis and Machine Intelligence. - : IEEE COMPUTER SOC. - 0162-8828 .- 1939-3539. ; 41:7, s. 1709-1719
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Tidskriftsartikel (refereegranskat)abstract
- Latent Dirichlet Allocation (LDA) is a topic model widely used in natural language processing and machine learning. Most approaches to training the model rely on iterative algorithms, which makes it difficult to run LDA on big corpora that are best analyzed in parallel and distributed computational environments. Indeed, current approaches to parallel inference either dont converge to the correct posterior or require storage of large dense matrices in memory. We present a novel sampler that overcomes both problems, and we show that this sampler is faster, both empirically and theoretically, than previous Gibbs samplers for LDA. We do so by employing a novel Polya-urn-based approximation in the sparse partially collapsed sampler for LDA. We prove that the approximation error vanishes with data size, making our algorithm asymptotically exact, a property of importance for large-scale topic models. In addition, we show, via an explicit example, that-contrary to popular belief in the topic modeling literature-partially collapsed samplers can be more efficient than fully collapsed samplers. We conclude by comparing the performance of our algorithm with that of other approaches on well-known corpora.
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