| 31. |
- de Weerd, Hendrik A., et al.
(författare)
-
MODalyseR—a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL data
- 2022
-
Ingår i: Bioinformatics Advances. - : Oxford University Press. - 2635-0041. ; 2:1
-
Tidskriftsartikel (refereegranskat)abstract
- MotivationNetwork-based disease modules have proven to be a powerful concept for extracting knowledge about disease mechanisms, predicting for example disease risk factors and side effects of treatments. Plenty of tools exist for the purpose of module inference, but less effort has been put on simultaneously utilizing knowledge about regulatory mechanisms for predicting disease module hub regulators.ResultsWe developed MODalyseR, a novel software for identifying disease module regulators and reducing modules to the most disease-associated genes. This pipeline integrates and extends previously published software packages MODifieR and ComHub and hereby provides a user-friendly network medicine framework combining the concepts of disease modules and hub regulators for precise disease gene identification from transcriptomics data. To demonstrate the usability of the tool, we designed a case study for multiple sclerosis that revealed IKZF1 as a promising hub regulator, which was supported by independent ChIP-seq data.Availability and implementationMODalyseR is available as a Docker image at https://hub.docker.com/r/ddeweerd/modalyser with user guide and installation instructions found at https://gustafsson-lab.gitlab.io/MODalyseR/.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
|
|
| 32. |
- de Weerd, Hendrik A., et al.
(författare)
-
MODifieR : an ensemble R package for inference of disease modules from transcriptomics networks
- 2020
-
Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811 .- 1460-2059. ; 36:12, s. 3918-3919
-
Tidskriftsartikel (refereegranskat)abstract
- MOTIVATION: Complex diseases are due to the dense interactions of many disease-associated factors that dysregulate genes that in turn form so-called disease modules, which have shown to be a powerful concept for understanding pathological mechanisms. There exist many disease module inference methods that rely on somewhat different assumptions, but there is still no gold standard or best performing method. Hence, there is a need for combining these methods to generate robust disease modules.RESULTS: We developed MODule IdentiFIER (MODifieR), an ensemble R package of nine disease module inference methods from transcriptomics networks. MODifieR uses standardized input and output allowing the possibility to combine individual modules generated from these methods into more robust disease-specific modules, contributing to a better understanding of complex diseases.AVAILABILITY: MODifieR is available under the GNU GPL license and can be freely downloaded from https://gitlab.com/Gustafsson-lab/MODifieR and as a Docker image from https://hub.docker.com/r/ddeweerd/modifier.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
|
|
| 33. |
- Diaz Cruz, Maria Araceli, et al.
(författare)
-
Characterization of methylation patterns associated with lifestyle factors and vitamin D supplementation in a healthy elderly cohort from Southwest Sweden
- 2022
-
Ingår i: Scientific Reports. - : Nature Portfolio. - 2045-2322. ; 12:1
-
Tidskriftsartikel (refereegranskat)abstract
- Numerous studies have shown that lifestyle factors, such as regular physical activity and vitamin D intake, may remarkably improve overall health and mental wellbeing. This is especially important in older adults whose vitamin D deficiency occurs with a high prevalence. This study aimed to examine the influence of lifestyle and vitamin D on global DNA methylation patterns in an elderly cohort in Southwest of Sweden. We also sought to examine the methylation levels of specific genes involved in vitamin D's molecular and metabolic activated pathways. We performed a genome wide methylation analysis, using Illumina Infinium DNA Methylation EPIC 850kBeadChip array, on 277 healthy individuals from Southwest Sweden at the age of 70-95. The study participants also answered queries on lifestyle, vitamin intake, heart medication, and estimated health. Vitamin D intake did not in general affect methylation patterns, which is in concert with other studies. However, when comparing the group of individuals taking vitamin supplements, including vitamin D, with those not taking supplements, a difference in methylation in the solute carrier family 25 (SCL25A24) gene was found. This confirms a previous finding, where changes in expression of SLC25A24 were associated with vitamin D treatment in human monocytes. The combination of vitamin D intake and high physical activity increased methylation of genes linked to regulation of vitamin D receptor pathway, the Wnt pathway and general cancer processes. To our knowledge, this is the first study detecting epigenetic markers associated with the combined effects of vitamin D supplementation and high physical activity. These results deserve to be further investigated in an extended, interventional study cohort, where also the levels of 25(OH)D3 can be monitored.
|
|
| 34. |
- Dukic, Tania, 1975, et al.
(författare)
-
Effect of drivers' age and push button locations on visual time off road, steering wheel deviation and safety perception
- 2006
-
Ingår i: Ergonomics. - : Taylor & Francis Group. - 0014-0139 .- 1366-5847. ; 49:1, s. 78-92
-
Tidskriftsartikel (refereegranskat)abstract
- The study examined the effects of manual control locations on two groups of randomly selected young and old drivers in relation to visual time off road, steering wheel deviation and safety perception. Measures of visual time off road, steering wheel deviations and safety perception were performed with young and old drivers during real traffic. The results showed an effect of both driver's age and button location on the dependent variables. Older drivers spent longer visual time off road when pushing the buttons and had larger steering wheel deviations. Moreover, the greater the eccentricity between the normal line of sight and the button locations, the longer the visual time off road and the larger the steering wheel deviations. No interaction effect between button location and age was found with regard to visual time off road. Button location had an effect on perceived safety: the further away from the normal line of sight the lower the rating.
|
|
| 35. |
- Dybjer, Elin, et al.
(författare)
-
Type 1 diabetes, cognitive ability and incidence of cardiovascular disease and death over 60 years of follow-up time in men
- 2022
-
Ingår i: Diabetic Medicine. - : Wiley. - 0742-3071 .- 1464-5491. ; 39:8
-
Tidskriftsartikel (refereegranskat)abstract
- Aims There are few cohorts of type 1 diabetes that follow individuals over more than half a century in terms of health outcomes. The aim of this study was to examine associations between type 1 diabetes, diagnosed before age 18, and long-term morbidity and mortality, and to investigate whether cognitive ability plays a role in long-term morbidity and mortality risk. Methods In a Swedish cohort, 120 men with type 1 diabetes and 469 without type 1 diabetes were followed between 18 and 77 years of age as regards morbidity and mortality outcomes, and impact of cognitive ability at military conscription for the outcomes. In Cox regression analyses and Kaplan-Meier analyses with log-rank tests, associations between diabetes and cognitive ability respectively, and outcomes (mortality, cardiovascular morbidity and diabetes complications) were investigated. Results Men with type 1 diabetes suffered from dramatically higher mortality (HR 4.62, 95% CI: 3.56-5.60), cardiovascular mortality (HR 5.60, 95% CI: 3.27-9.57), and cardiovascular events (HR 3.97, 95% CI: 2.79-5.64) compared to men without diabetes. Higher cognitive ability at military conscription was associated with lower mortality in men without diabetes, but was not associated with any outcome in men with diabetes. Conclusions In this historical cohort study with 60 years of follow-up time and a less effective treatment of diabetes than today, mortality rates and cardiovascular outcomes were high for men with type 1 diabetes. Morbidity or mortality did not differ between those that had low to normal or high cognitive ability among men with type 1 diabetes.
|
|
| 36. |
- Ebenman, Bo, 1953-, et al.
(författare)
-
Using community viability analysis to identify fragile systems and keystone species
- 2005
-
Ingår i: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 20:10, s. 568-575
-
Tidskriftsartikel (refereegranskat)abstract
- Owing to interdependences among species in ecological communities, the loss of one species can trigger a cascade of secondary extinctions with potentially dramatic effects on the functioning and stability of the community. It is, therefore, important to assess the risk and likely extent of secondary extinctions. Community viability analysis is a new technique that can be used to accomplish this goal. The analysis can also be used to identify fragile community structures and keystone species and, hence, to provide guidelines for conservation priorities. Here, we describe the principles underlying community viability analysis and review its contributions to our understanding of the response of ecological communities to species loss.
|
|
| 37. |
- Einarsson, Anna, et al.
(författare)
-
Exploring the Multi-Layered Affordances of Composing and Performing Interactive Music with Responsive Technologies
- 2017
-
Ingår i: Frontiers in Psychology. - : Frontiers Media S.A.. - 1664-1078. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- The question motivating the work presented here, starting from a view of music as embodied and situated activity, is how can we account for the complexity of interactive music performance situations. These are situations in which human performers interact with responsive technologies, such as sensor-driven technology or sound synthesis affected by analysis of the performed sound signal. This requires investigating in detail the underlying mechanisms, but also providing a more holistic approach that does not lose track of the complex whole constituted by the interactions and relationships of composers, performers, audience, technologies, etc. The concept of affordances has frequently been invoked in musical research, which has seen a "bodily turn" in recent years, similar to the development of the embodied cognition approach in the cognitive sciences. We therefore begin by broadly delineating its usage in the cognitive sciences in general, and in music research in particular. We argue that what is still missing in the discourse on musical affordances is an encompassing theoretical framework incorporating the sociocultural dimensions that are fundamental to the situatedness and embodiment of interactive music performance and composition. We further argue that the cultural affordances framework, proposed by Rietveld and Kiverstein (2014) and recently articulated further by Ramstead et al. (2016) in this journal, although not previously applied to music, constitutes a promising starting point. It captures and elucidates this complex web of relationships in terms of shared landscapes and individual fields of affordances. We illustrate this with examples foremost from the first author's artistic work as composer and performer of interactive music. This sheds new light on musical composition as a process of construction-and embodied mental simulation-of situations, guiding the performers' and audience's attention in shifting fields of affordances. More generally, we believe that the theoretical perspectives and concrete examples discussed in this paper help to elucidate how situations-and with them affordances-are dynamically constructed through the interactions of various mechanisms as people engage in embodied and situated activity.
|
|
| 38. |
- Ericsson, AnnMarie, 1972-
(författare)
-
Enabling Tool Support for Formal Analysis of ECA Rules
- 2009
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Rule-based systems implemented as event-condition-action (ECA) rules utilize a powerful and flexible paradigm when it comes to specifying systems that need to react to complex situation in their environment. Rules can be specified to react to combinations of events occurring at any time in any order. However, the behavior of a rule based system is notoriously hard to analyze due to the rules ability to interact with each other.Formal methods are not utilized in their full potential for enhancing software quality in practice. We argue that seamless support in a high-level paradigm specific tool is a viable way to provide industrial system designers with powerful verification techniques. This thesis targets the issue of formally verifying that a set of specified rules behaves as indented.The prototype tool REX (Rule and Event eXplorer) is developed as a proof of concept of the results of this thesis. Rules and events are specified in REX which is acting as a rule-based front-end to the existing timed automata CASE tool UPPAAL. The rules, events and requirements of application design are specified in REX. To support formal verification, REX automatically transforms the specified rules to timed automata, queries the requirement properties in the model-checker provided by UPPAAL and returns results to the user of REX in terms of rules and events.The results of this thesis consist of guidelines for modeling and verifying rules in a timed automata model-checker and experiences from using and building a tool implementing the proposed guidelines. Moreover, the result of an industrial case study is presented, validating the ability to model and verify a system of industrial complexity using the proposed approach.
|
|
| 39. |
- Eriksson, Katarina, et al.
(författare)
-
The prevalence of BV in the population on the Åland Islands during a 15-year period
- 2010
-
Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - Malden, USA : John Wiley & Sons. - 0903-4641 .- 1600-0463. ; 118:11, s. 903-908
-
Tidskriftsartikel (refereegranskat)abstract
- The aim of the study was to describe the prevalence and age distribution of bacterial vaginosis (BV) during an observation period of 15 years in a population study with cross-sectional samples of adult women living on the Åland Islands. The Åland Islands form an archipelago in the Baltic Sea and are a province of Finland. Every fifth year, specific age groups in the adult female population are invited to participate in a screening program for early diagnosis of cervical cancer using a papanicolaou (PAP)-stained vaginal smear. Women in the age groups of 20, 25, 30, 35, 40, 45, 50, 55, and 60 years are called each year. BV diagnosis of the PAP-stained smears uses the classification according to Nugent. The PAP-stained smears from the screening program of cervical cancer 1993, 1998, 2003, and 2008 were used in this study. A total of 3456 slides were investigated and 271 women could be followed for the 15-year observation period. The prevalence of BV declined from 15.6% in 1993 to 8.6% in 2008. The highest prevalence occurred among the age groups of 35 and 50 years. Among the 271 women who could be followed for the 15-year observation period, two-third showed normal/intermediate flora and one-third were infected with BV at least once. As this is a cross-sectional population study spanning 15 years, the prevalence of BV in the female adult population of the Åland Islands can be estimated. The prevalence has declined between 1993 and 2008 from 15.6% to 8.6%.
|
|
| 40. |
- Eriksson, Katarina, et al.
(författare)
-
Vaginal retention of locally administered clindamycin
- 2011
-
Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - : John Wiley & Sons. - 0903-4641 .- 1600-0463. ; 119:6, s. 373-376
-
Tidskriftsartikel (refereegranskat)abstract
- Since bacterial vaginosis (BV) is characterized by a lack of, or very few, lactobacilli and high numbers of small, mostly anaerobic bacteria, an obvious treatment modality would be eradication of the BV-associated bacterial flora followed by reintroduction of lactobacilli vaginally. As probiotic treatment with lactobacilli is one tool for improving the cure rate when treating BV, it is necessary to know the length of time after treatment that clindamycin can be found in the vagina and if this could interfere with the growth of the probiotic lactobacilli. We evaluated the vaginal concentration of clindamycin in 12 women for 8 days to obtain data on the concentration of clindamycin in the vagina after intravaginal treatment with the drug. The participants were examined five times between two menstrual periods: before treatment, the day after treatment was finished, and 3, 5 and 8 days post-treatment. The first day post-treatment clindamycin 0.46 x 10-3 to 8.4 x 10-3 g/g vaginal fluid (median 2.87 x 10-3) was found. Thereafter, the concentration of clindamycin decreased rapidly. In 10 patients clindamycin was found after 3 days. A very low concentration was still present 5 days after treatment in four patients. After 8 days no clindamycin was found. Clindamycin is rapidly eliminated from the vagina, within 3-8 days, after local administration. Our results indicate that treatment with probiotic lactobacilli could be problematic if carried out within 5 days after cessation of clindamycin treatment.
|
|
