| 1. |
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| 2. |
- Ahlqvist, Jan, Birger, 1952-, et al.
(author)
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Osseointegrated implants in edentulous jaws: a 2-year longitudinal study.
- 1990
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In: International Journal of Oral & Maxillofacial Implants. - 0882-2786 .- 1942-4434. ; 5:2, s. 155-163
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Journal article (peer-reviewed)abstract
- Osseointegrated implants in 50 edentulous jaws were studied during a 2-year observation period. The implant survival rate was 89% in the maxillae and 97% in the mandibles. The marginal bone loss averaged 1.7 mm in the maxillae and 1.1 mm in the mandibles. Most of this bone loss occurred during the first year. The bone loss was greater in jaws with a preoperatively minor resorption of the alveolar ridge than in those with moderate or advanced resorption. The bone loss was also greater at the medially positioned implants than at those more posterior.
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| 3. |
- Alamidi, Daniel, et al.
(author)
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COPD Patients Have Short Lung Magnetic Resonance T1 Relaxation Time.
- 2016
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In: COPD. - : Informa UK Limited. - 1541-2563 .- 1541-2555. ; 13:2, s. 153-159
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Journal article (peer-reviewed)abstract
- Magnetic resonance imaging (MRI) may provide attractive biomarkers for assessment of pulmonary disease in clinical trials as it is free from ionizing radiation, minimally invasive and allows regional information. The aim of this study was to characterize lung MRI T1 relaxation time as a biomarker of chronic obstructive pulmonary disease (COPD); and specifically its relationship to smoking history, computed tomography (CT), and pulmonary function test (PFT) measurements in comparison to healthy age-matched controls. Lung T1 and inter-quartile range (IQR) of T1 maps from 24 COPD subjects and 12 healthy age-matched non-smokers were retrospectively analyzed from an institutional review board approved study. The subjects underwent PFTs and two separate MR imaging sessions at 1.5 tesla to test T1 repeatability. CT scans were performed on the COPD subjects. T1 repeatability (intraclass correlation coefficient) was 0.72 for repeated scans acquired on two visits. The lung T1 was significantly shorter (p < 0.0001) and T1 IQR was significantly larger (p = 0.0002) for the COPD subjects compared to healthy controls. Lung T1 significantly (p = 0.001) correlated with lung density assessed with CT. Strong significant correlations (p < 0.0001) between lung T1 and all PFT measurements were observed. Cigarette exposure did not correlate with lung T1 in COPD subjects. In conclusion, lung MRI T1 mapping shows potential as a repeatable, radiation free, non-invasive imaging technique in the evaluation of COPD.
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| 4. |
- Beral, V., et al.
(author)
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Ovarian Cancer and Body Size : Individual Participant Meta-Analysis Including 25,157 Women with Ovarian Cancer from 47 Epidemiological Studies
- 2012
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In: PLoS Medicine. - : PUBLIC LIBRARY SCIENCE. - 1549-1277 .- 1549-1676. ; 9:4
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Journal article (peer-reviewed)abstract
- Background: Only about half the studies that have collected information on the relevance of women's height and body mass index to their risk of developing ovarian cancer have published their results, and findings are inconsistent. Here, we bring together the worldwide evidence, published and unpublished, and describe these relationships. Methods and Findings: Individual data on 25,157 women with ovarian cancer and 81,311 women without ovarian cancer from 47 epidemiological studies were collected, checked, and analysed centrally. Adjusted relative risks of ovarian cancer were calculated, by height and by body mass index. Ovarian cancer risk increased significantly with height and with body mass index, except in studies using hospital controls. For other study designs, the relative risk of ovarian cancer per 5 cm increase in height was 1.07 (95% confidence interval [CI], 1.05-1.09; p<0.001); this relationship did not vary significantly by women's age, year of birth, education, age at menarche, parity, menopausal status, smoking, alcohol consumption, having had a hysterectomy, having first degree relatives with ovarian or breast cancer, use of oral contraceptives, or use of menopausal hormone therapy. For body mass index, there was significant heterogeneity (p<0.001) in the findings between ever-users and never-users of menopausal hormone therapy, but not by the 11 other factors listed above. The relative risk for ovarian cancer per 5 kg/m(2) increase in body mass index was 1.10 (95% CI, 1.07-1.13; p<0.001) in never-users and 0.95 (95% CI, 0.92-0.99; p = 0.02) in ever-users of hormone therapy. Conclusions: Ovarian cancer is associated with height and, among never-users of hormone therapy, with body mass index. In high-income countries, both height and body mass index have been increasing in birth cohorts now developing the disease. If all other relevant factors had remained constant, then these increases in height and weight would be associated with a 3% increase in ovarian cancer incidence per decade.
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| 5. |
- Beral, V., et al.
(author)
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Ovarian cancer and smoking: individual participant meta-analysis including 28 114 women with ovarian cancer from 51 epidemiological studies
- 2012
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In: The Lancet Oncology. - 1474-5488. ; 13:9, s. 946-956
-
Journal article (peer-reviewed)abstract
- Background Smoking has been linked to mucinous ovarian cancer, but its effects on other ovarian cancer subtypes and on overall ovarian cancer risk are unclear, and the findings from most studies with relevant data are unpublished. To assess these associations, we review the published and unpublished evidence. Methods Eligible epidemiological studies were identified by electronic searches, review articles, and discussions with colleagues. Individual participant data for 28 114 women with and 94 942 without ovarian cancer from 51 epidemiological studies were analysed centrally, yielding adjusted relative risks (RRs) of ovarian cancer in smokers compared with never smokers. Findings After exclusion of studies with hospital controls, in which smoking could have affected recruitment, overall ovarian cancer incidence was only slightly increased in current smokers compared with women who had never smoked (RR 1.06, 95% CI 1.01-1.11, p=0.01). Of 17 641 epithelial cancers with specified histology, 2314 (13%) were mucinous, 2360 (13%) endometrioid, 969 (5%) clear-cell, and 9086 (52%) serous. Smoking-related risks varied substantially across these subtypes (p(heterogeneity)<0.0001). For mucinous cancers, incidence was increased in current versus never smokers (1.79, 95% CI 1.60-2.00, p<0.0001), but the increase was mainly in borderline malignant rather than in fully malignant tumours (2.25, 95% CI 1.91-2.65 vs 1.49, 1.28-1.73; p(heterogeneity)=0.01; almost half the mucinous tumours were only borderline malignant). Both endometrioid (0.81, 95% CI 0.72-0.92, p=0.001) and clear-cell ovarian cancer risks (0.80, 95% CI 0.65-0.97, p=0.03) were reduced in current smokers, and there was no significant association for serous ovarian cancers (0.99, 95% CI 0.93-1.06, p=0.8). These associations did not vary significantly by 13 sociodemographic and personal characteristics of women including their body-mass index, parity, and use of alcohol, oral contraceptives, and menopausal hormone therapy. Interpretation The excess of mucinous ovarian cancers in smokers, which is mainly of tumours of borderline malignancy, is roughly counterbalanced by the deficit of endometrioid and clear-cell ovarian cancers. The substantial variation in smoking-related risks by tumour subtype is important for understanding ovarian carcinogenesis.
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| 6. |
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| 7. |
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| 8. |
- Cardell, Lars-Olaf, et al.
(author)
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TOTALL: high cost of allergic rhinitis-a national Swedish population-based questionnaire study.
- 2016
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In: NPJ primary care respiratory medicine. - : Springer Science and Business Media LLC. - 2055-1010. ; 26
-
Journal article (peer-reviewed)abstract
- Allergic rhinitis is a global illness with a well-recognised impact on quality of life and work performance. Comparatively little is known about the extent of its economic impact on society. The TOTALL study estimates the total cost of allergic rhinitis using a sample representing the entire Swedish population of working age. A questionnaire focused on allergic rhinitis was mailed out to a random population of Swedish residents, aged 18-65 years. Health-care contacts, medications, absenteeism (absence from work) and presenteeism (reduced working capacity at work) were assessed, and the direct and indirect costs of allergic rhinitis were calculated. Medication use was evaluated in relation to the ARIA guidelines. In all, 3,501 of 8,001 (44%) answered the questionnaire, and 855 (24%) of these reported allergic rhinitis. The mean annual direct and indirect costs because of allergic rhinitis were €210.3 and €750.8, respectively, resulting in a total cost of €961.1 per individual/year. Presenteeism represented 70% of the total cost. Antihistamines appear to be used in excess in relation to topical steroids, and the use of nasal decongestants was alarmingly high. The total cost of allergic rhinitis in Sweden, with a population of 9.5 million, was estimated at €1.3 billion annually. These unexpectedly high costs could be related to the high prevalence of disease, in combination with the previously often underestimated indirect costs. Improved adherence to guidelines might ease the economic burden on society.
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| 9. |
- Chapin, F. Stuart, III, et al.
(author)
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Ecosystem stewardship : sustainability strategies for a rapidly changing planet
- 2010
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In: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 25:4, s. 241-249
-
Research review (peer-reviewed)abstract
- Ecosystem stewardship is an action-oriented framework intended to foster the social ecological sustainability of a rapidly changing planet. Recent developments identify three strategies that make optimal use of current understanding in an environment of inevitable uncertainty and abrupt change: reducing the magnitude of, and exposure and sensitivity to, known stresses; focusing on proactive policies that shape change; and avoiding or escaping unsustainable social ecological traps. As we discuss here, all social ecological systems are vulnerable to recent and projected changes but have sources of adaptive capacity and resilience that can sustain ecosystem services and human well-being through active ecosystem stewardship.
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| 10. |
- Ehnhage, Anders, et al.
(author)
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Treatment of idiopathic rhinitis with kinetic oscillations : a multi-centre randomized controlled study
- 2016
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In: Acta Oto-Laryngologica. - : Informa UK Limited. - 0001-6489 .- 1651-2251. ; 136:8, s. 852-859
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Journal article (peer-reviewed)abstract
- Conclusions: The potential effects of KOS are still uncertain regarding the most effective air pressure to be used as well as the physiological effects on the nasal mucosa. The results of the study do not support a convincing treatment effect by KOS on IR.Objectives: Idiopathic rhinitis (IR) is a common disorder, affecting ∼10-20% of the population. A new method for treating IR, Kinetic Oscillation Stimulation (KOS), has been reported to have beneficial effects on total vasomotor symptom scores (TVRSS). The primary objective with this study was to evaluate if a mean pressure of 65 mbar, pressure amplitude of 100 mbar, and 68Hz treatment with KOS had a positive effect on total vasomotor symptom scores (TVRSS), as compared with a mean pressure of 65 mbar, pressure amplitude of 4 mbar, and 68Hz treatment in patients with idiopathic rhinitis.Methods: Two hundred and seven patients were randomized (Full Analysis Set, FAS) in the study, including five visits and lasting for approximate to 25 weeks. All patients had two treatment episodes, and all patients had at least one treatment, meant as active, with high amplitude pressure for 10min in each nostril. Group 1 had two such treatments, and Group 2 had one treatment with low amplitude pressure, initially meant as placebo, on one occasion. Because of numerical improvements in these two groups, a new control group, Group 3, was introduced. They had one new control treatment where the balloon was inserted into the nose, without any air inflation and without oscillations.Results: KOS treatment with high amplitude pressure did not have significant beneficial effects as compared to low amplitude pressure on TVRSS. Numerical improvements in TVRSS and SNOT 22 were found when comparing high and low amplitude pressure treatments with uninflated balloon treatment. However, this part of the study was initially single-blinded, and these results were secondary objectives.
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| 11. |
- Ericsson, Morgan, et al.
(author)
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A Study of the Effect of Data Normalization on Software and Information Quality Assessment
- 2013
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In: Software Engineering Conference (APSEC, 2013 20th Asia-Pacific). - : IEEE Press. - 9781479921430 ; , s. 55-60
-
Conference paper (peer-reviewed)abstract
- Indirect metrics in quality models define weighted integrations of direct metrics to provide higher-level quality indicators. This paper presents a case study that investigates to what degree quality models depend on statistical assumptions about the distribution of direct metrics values when these are integrated and aggregated. We vary the normalization used by the quality assessment efforts of three companies, while keeping quality models, metrics, metrics implementation and, hence, metrics values constant. We find that normalization has a considerable impact on the ranking of an artifact (such as a class). We also investigate how normalization affects the quality trend and find that normalizations have a considerable effect on quality trends. Based on these findings, we find it questionable to continue to aggregate different metrics in a quality model as we do today.
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| 12. |
- Fazey, Ioan, et al.
(author)
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Transforming knowledge systems for life on Earth : Visions of future systems and how to get there
- 2020
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In: Energy Research & Social Science. - : Elsevier. - 2214-6296 .- 2214-6326. ; 70
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Journal article (peer-reviewed)abstract
- Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent.
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| 13. |
- Figueroa, Jonine D., et al.
(author)
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Genome-wide association study identifies multiple loci associated with bladder cancer risk
- 2014
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In: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 23:5, s. 1387-1398
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Journal article (peer-reviewed)abstract
- andidate gene and genome-wide association studies (GWAS) have identified 11 independent susceptibility loci associated with bladder cancer risk. To discover additional risk variants, we conducted a new GWAS of 2422 bladder cancer cases and 5751 controls, followed by a meta-analysis with two independently published bladder cancer GWAS, resulting in a combined analysis of 6911 cases and 11 814 controls of European descent. TaqMan genotyping of 13 promising single nucleotide polymorphisms with P < 1 × 10−5 was pursued in a follow-up set of 801 cases and 1307 controls. Two new loci achieved genome-wide statistical significance: rs10936599 on 3q26.2 (P = 4.53 × 10−9) and rs907611 on 11p15.5 (P = 4.11 × 10−8). Two notable loci were also identified that approached genome-wide statistical significance: rs6104690 on 20p12.2 (P = 7.13 × 10−7) and rs4510656 on 6p22.3 (P = 6.98 × 10−7); these require further studies for confirmation. In conclusion, our study has identified new susceptibility alleles for bladder cancer risk that require fine-mapping and laboratory investigation, which could further understanding into the biological underpinnings of bladder carcinogenesis.
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| 14. |
- Figueroa, Jonine D., et al.
(author)
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Genome-wide interaction study of smoking and bladder cancer risk
- 2014
-
In: Carcinogenesis. - : Oxford University Press. - 0143-3334 .- 1460-2180. ; 35:8, s. 1737-1744
-
Journal article (peer-reviewed)abstract
- Bladder cancer is a complex disease with known environmental and genetic risk factors. We performed a genome-wide interaction study (GWAS) of smoking and bladder cancer risk based on primary scan data from 3002 cases and 4411 controls from the National Cancer Institute Bladder Cancer GWAS. Alternative methods were used to evaluate both additive and multiplicative interactions between individual single nucleotide polymorphisms (SNPs) and smoking exposure. SNPs with interaction P values < 5 x 10(-5) were evaluated further in an independent dataset of 2422 bladder cancer cases and 5751 controls. We identified 10 SNPs that showed association in a consistent manner with the initial dataset and in the combined dataset, providing evidence of interaction with tobacco use. Further, two of these novel SNPs showed strong evidence of association with bladder cancer in tobacco use subgroups that approached genome-wide significance. Specifically, rs1711973 (FOXF2) on 6p25.3 was a susceptibility SNP for never smokers [combined odds ratio (OR) = 1.34, 95% confidence interval (CI) = 1.20-1.50, P value = 5.18 x 10(-7)]; and rs12216499 (RSPH3-TAGAP-EZR) on 6q25.3 was a susceptibility SNP for ever smokers (combined OR = 0.75, 95% CI = 0.67-0.84, P value = 6.35 x 10-7). In our analysis of smoking and bladder cancer, the tests for multiplicative interaction seemed to more commonly identify susceptibility loci with associations in never smokers, whereas the additive interaction analysis identified more loci with associations among smokers-including the known smoking and NAT2 acetylation interaction. Our findings provide additional evidence of gene-environment interactions for tobacco and bladder cancer.
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| 15. |
- Figueroa, Jonine D., et al.
(author)
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Identification of a novel susceptibility locus at 13q34 and refinement of the 20p12.2 region as a multi-signal locus associated with bladder cancer risk in individuals of European ancestry
- 2016
-
In: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 25:6, s. 1203-1214
-
Journal article (peer-reviewed)abstract
- Candidate gene and genome-wide association studies (GWAS) have identified 15 independent genomic regions associated with bladder cancer risk. In search for additional susceptibility variants, we followed up on four promising single-nucleotide polymorphisms (SNPs) that had not achieved genome-wide significance in 6911 cases and 11 814 controls (rs6104690, rs4510656, rs5003154 and rs4907479, P < 1 × 10−6), using additional data from existing GWAS datasets and targeted genotyping for studies that did not have GWAS data. In a combined analysis, which included data on up to 15 058 cases and 286 270 controls, two SNPs achieved genome-wide statistical significance: rs6104690 in a gene desert at 20p12.2 (P = 2.19 × 10−11) and rs4907479 within the MCF2L gene at 13q34 (P = 3.3 × 10−10). Imputation and fine-mapping analyses were performed in these two regions for a subset of 5551 bladder cancer cases and 10 242 controls. Analyses at the 13q34 region suggest a single signal marked by rs4907479. In contrast, we detected two signals in the 20p12.2 region—the first signal is marked by rs6104690, and the second signal is marked by two moderately correlated SNPs (r2 = 0.53), rs6108803 and the previously reported rs62185668. The second 20p12.2 signal is more strongly associated with the risk of muscle-invasive (T2-T4 stage) compared with non-muscle-invasive (Ta, T1 stage) bladder cancer (case–case P ≤ 0.02 for both rs62185668 and rs6108803). Functional analyses are needed to explore the biological mechanisms underlying these novel genetic associations with risk for bladder cancer.
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| 16. |
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| 17. |
- Fu, Yi-Ping, et al.
(author)
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The 19q12 Bladder Cancer GWAS Signal : Association with Cyclin E Function and Aggressive Disease
- 2014
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In: Cancer Research. - 0008-5472 .- 1538-7445. ; 74:20, s. 5808-5818
-
Journal article (peer-reviewed)abstract
- A genome-wide association study (GWAS) of bladder cancer identified a genetic marker rs8102137 within the 19q12 region as a novel susceptibility variant. This marker is located upstream of the CCNE1 gene, which encodes cyclin E, a cell-cycle protein. We performed genetic fine-mapping analysis of the CCNE1 region using data from two bladder cancer GWAS (5,942 cases and 10,857 controls). We found that the original GWAS marker rs8102137 represents a group of 47 linked SNPs (with r(2) >= 0.7) associated with increased bladder cancer risk. From this group, we selected a functional promoter variant rs7257330, which showed strong allele-specific binding of nuclear proteins in several cell lines. In both GWASs, rs7257330 was associated only with aggressive bladder cancer, with a combined per-allele OR = 1.18 [95% confidence interval (CI), 1.09-1.27, P = 4.67 x 10(-5)] versus OR = 1.01 (95% CI, 0.93-1.10, P = 0.79) for nonaggressive disease, with P = 0.0015 for case-only analysis. Cyclin E protein expression analyzed in 265 bladder tumors was increased in aggressive tumors (P = 0.013) and, independently, with each rs7257330-A risk allele (P-trend = 0.024). Overexpression of recombinant cyclin E in cell lines caused significant acceleration of cell cycle. In conclusion, we defined the 19q12 signal as the first GWAS signal specific for aggressive bladder cancer. Molecular mechanisms of this genetic association may be related to cyclin E overexpression and alteration of cell cycle in carriers of CCNE1 risk variants. In combination with established bladder cancer risk factors and other somatic and germline genetic markers, the CCNE1 variants could be useful for inclusion into bladder cancer risk prediction models.
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| 18. |
- Gapstur, S. M., et al.
(author)
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Menopausal hormone use and ovarian cancer risk: individual participant meta-analysis of 52 epidemiological studies
- 2015
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In: The Lancet. - 1474-547X. ; 385:9980, s. 1835-1842
-
Journal article (peer-reviewed)abstract
- Background Half the epidemiological studies with information about menopausal hormone therapy and ovarian cancer risk remain unpublished, and some retrospective studies could have been biased by selective participation or recall. We aimed to assess with minimal bias the effects of hormone therapy on ovarian cancer risk. Methods Individual participant datasets from 52 epidemiological studies were analysed centrally. The principal analyses involved the prospective studies (with last hormone therapy use extrapolated forwards for up to 4 years). Sensitivity analyses included the retrospective studies. Adjusted Poisson regressions yielded relative risks (RRs) versus never-use. Findings During prospective follow-up, 12 110 postmenopausal women, 55% (6601) of whom had used hormone therapy, developed ovarian cancer. Among women last recorded as current users, risk was increased even with <5 years of use (RR 1.43, 95% CI 1.31-1.56; p<0.0001). Combining current-or-recent use (any duration, but stopped <5 years before diagnosis) resulted in an RR of 1.37 (95% CI 1.29-1.46; p<0.0001); this risk was similar in European and American prospective studies and for oestrogen-only and oestrogen-progestagen preparations, but differed across the four main tumour types (heterogeneity p<0.0001), being definitely increased only for the two most common types, serous (RR 1.53, 95% CI 1.40-1.66; p<0.0001) and endometrioid (1.42, 1.20-1.67; p<0.0001). Risk declined the longer ago use had ceased, although about 10 years after stopping long-duration hormone therapy use there was still an excess of serous or endometrioid tumours (RR 1.25, 95% CI 1.07-1.46, p=0.005). Interpretation The increased risk may well be largely or wholly causal; if it is, women who use hormone therapy for 5 years from around age 50 years have about one extra ovarian cancer per 1000 users and, if its prognosis is typical, about one extra ovarian cancer death per 1700 users.
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| 19. |
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| 20. |
- Johansson, Kristin, 1979, et al.
(author)
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Environmental impact of the EPSPEX system. Part 1: Life cycle assessment of polystyrene insulated district heating systems with PEX fluid pipes
- 2005
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Reports (other academic/artistic)abstract
- The EPSPEX system is a distribution system for district heat with media pipes of cross-linked polyethylene (PEX) insulated by blocks of expanded polystyrene (EPS). In this low-pressure distribution system two pipes are used for a space heating circuit, having layers of EVAL to hinder oxygen diffusion, whereas two pipes without diffusion barrier are used for delivery of hot tap water and warm water circulation. The four pipes are placed in the insulating blocks of EPS. Environmental impacts from production, laying and use of an EPSPEX district heat distribution system have been investigated using life cycle methodology. The distribution system is a secondary system developed specially for areas with low heat density. The case studied is the installation and use of an EPSPEX system in Vråen, Värnamo, Sweden. The environmental impacts are described in four categories:climate change, acidification, eutrophication and use of finite resources. Four weighting methods have also been used in the evaluation: EPS2000, Ecoscarcity, ExternE and EcoIndicator99. While carefully considering the precise circumstances of this study, the findings can be adapted for using the EPSPEX district heat distribution systems in other areas.During this study the question was raised of how this district heat delivery system compares with systems that use conventional district heating pipes. This has beenfurther investigated and is reported in the second part of this report: Miljöbelastning från EPSPEX-systemet. Del 2: Konventionella twinrör eller EPSPEX vad är bäst urmiljösynpunkt. In the second part the environmental impacts from the EPSPEX system have been compared with the impacts from conventional twin pipes (polyurethane insulated steel media pipes) used in a comparable setting. A discussion on the environmental choice between media pipes of PEX and steel can also be found in the second part. It should be noted that the two systems for district heat distribution are not fully comparable in function. The EPSPEX system has stricter limitations regarding pressure and temperature compared with the conventional system. The EPSPEX system is also limited in use for well drained ground conditions above the water table. Conventional district heating pipes do not have this limitation. The most important possibility to decrease the environmental impacts from the EPSPEX system is to increase the insulation, this even though the distribution systemis comparably well insulated to start with. The environmental life cycle impacts of the distribution pipe system production, laying and use are predominated by the extra heat that has to be generated to cover the heat losses from the system. When this report was written, measurements from systems in use to confirm the model calculation of heat losses are still lacking. More fine-tuned results can be achieved when studies of the EPSPEX system in use have been concluded.Among different components in the EPSPEX system the impacts from production and transport of EPS-blocks make the major impact. Thus, it is important to utilize the polystyrene material as efficiently as possible, minimizing spillage, and to ensure that unavoidable spillage is recycled as material. However, the environmental impacts from production of the insulating blocks are well outweighed by the decreased environmental impacts gained by using the insulation. In product development it is thus important to ensure that the insulating capacity of the EPSPEX system is never decreased.Machines used for excavating the pipe trenches combust diesel oil, and the production and use of this diesel oil generates a substantial part of the environmental impacts byseveral of the assessment methods used. If possible, it is desirable to further minimize the excavation work and to use mini excavators and low emitting machines (especially regarding nitrous oxides). The brass swaged coupling used to connect the PEX-pipes, gives a strong impact regarding acidification and the two weighting methods EPS2000 and Ecoscarcity, especially when compared to the very small volume fraction these devices constitute. It would be advisable to study if the devices could be made from other material or from recycled material.
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| 21. |
- Johansson, Kristin, 1979, et al.
(author)
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Environmental impact of the EPSPEX system. Part 2: Traditional twin pipes or EPSPEX for district heat distribution - what is best from an environmental point of view?
- 2005
-
Reports (other academic/artistic)abstract
- In this study the life-cycle environmental impacts from an EPSPEX system for distribution of district heat (a four-pipe system with centrally generated hot tap water) are compared with the environmental impacts of a twin-pipe system with steel media pipes, if installed in the same area. A life cycle assessment of the EPSPEX system constructed in Vråen, Värnamo, Sweden, has been reported in Miljöbelastning från EPSPEX-systemet. Del 1: Livscykelanalys av polystyrenisolerat fjärrvärmesystemmed PEX-mediarör [1]. In that study the question was raised of how the EPSPEX system compares with a conventional twin-pipe system with polyurethane-insulated steel media pipes.In the present study the EPSPEX system in Vråen is compared with a hypothetical construction of a conventional twin pipe system in the same area. Two different fuel mixes for district heat generation have been studied to increase the understanding of the environmental performance of district heat distribution systems; the fuel mix used in Vråen (heat delivered from Värnamo Energi) and Swedish average district heat. How media pipes from the two different materials (PEX and steel) compare is discussed in a separate part. There are technical differences that must be kept in mind when the systems are compared in this way. The EPSPEX system is designed for low-pressure district heat systems and could only be used in such context. It is unadvisable to install the EPSPEX system below the ground water table; this is not a restriction for the twin pipe system. Under the conditions of this study the environmental performance of the EPSPEX system is better than the twin pipe system.The heat loss from the EPSPEX system is approximately 60% of the heat loss for a comparable twin pipe system. This is caused by a combination of thick insulation for the EPSPEX system and the possibility to summertime shut down the district heating circuit for this system and only use the hot tap-water circuit. Note, however, that the heat loss from the EPSPEX system is more uncertain compared to the twin-pipe system. From the characterization methods used, the production of the EPSPEX system gives a higher environmental impact compared to the twin pipe system. This heavily depends on the large amount of insulating material used. However, the environmental impacts from production of the insulation are more then outweighed by the emissionsavoided from heat generation due to lower heat loss. District heating sub centrals generates a notable part of the total environmental impact when using the weighing method EPS2000. Note that sub centrals are not technicallynecessary in low-pressure district heat systems, as the EPSPEX system. The comparison between different fuel mixes for heat generation indicates clearly that the heat generation is an important parameter for environmental performance for all district heating. It is further indicated that also biofuels must be used with sensible andenvironmentally friendly methods. The media pipes of PEX seem to give lower environmental impacts compared withmedia pipes of steel. However, the results differ between assessment methods used.
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| 23. |
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| 24. |
- Kochovska, Slavica, et al.
(author)
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Persisting breathlessness and activities reduced or ceased: a population study in older men
- 2022
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In: BMJ Open Respiratory Research. - : BMJ. - 2052-4439. ; 9:1, s. 1-10
-
Journal article (peer-reviewed)abstract
- Introduction Breathlessness is debilitating and increases in prevalence with age, with people progressively reducing their everyday activities to ‘self-manage’ it. This study aimed to evaluate the impact of breathlessness on function in terms of activities that have been reduced or ceased (‘compromised’) in older men.Methods A cross-sectional postal survey of Swedish 73-year-old man in the VAScular and Chronic Obstructive Lung disease study self-reporting on demographics, breathlessness (modified Medical Research Council (mMRC) scale, Dyspnoea-12, Multidimensional Dyspnea Scale) and its duration, anxiety/depression (Hospital Anxiety and Depression Scale), performance status (WHO Performance Status), everyday activities reduced/ceased and exertion.Results 148/828 (17.9%) respondents reported breathlessness (mMRC >2), of whom 51.9% had reduced/ceased activities compared with 9.6% who did not. Physical activity was the most common activity reduced/ceased (48.0%) followed by sexual activity (41.2%) and social activities (37.8%). Of 16.0% of respondents with mMRC 3–4 talking on the phone was affected compared with only 2.9% of respondents with mMRC 2. Worsening breathlessness was associated with increasingly sedentary lifestyles and more limited function, those reporting reduced/ceased activities had an associated increase in reporting anxiety and depression. In adjusted analyses, breathlessness was associated with increased likelihood of activities being ceased overall as well as physical and sexual activities being affected separately.Conclusion Worsening breathlessness was associated with decreasing levels of self-reported physical activity, sexual activity and function. Overall, the study showed that people with persisting breathlessness modify their lifestyle to avoid it by reducing or ceasing a range of activities, seeking to minimise their exposure to the symptom.
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| 25. |
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| 26. |
- Morgan, Ruth A., et al.
(author)
-
Carbonyl reductase 1 catalyzes 20 beta-reduction of glucocorticoids, modulating receptor activation and metabolic complications of obesity
- 2017
-
In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7
-
Journal article (peer-reviewed)abstract
- Carbonyl Reductase 1 (CBR1) is a ubiquitously expressed cytosolic enzyme important in exogenous drug metabolism but the physiological function of which is unknown. Here, we describe a role for CBR1 in metabolism of glucocorticoids. CBR1 catalyzes the NADPH-dependent production of 20 beta-dihydrocortisol (20 beta-DHF) from cortisol. CBR1 provides the major route of cortisol metabolism in horses and is up-regulated in adipose tissue in obesity in horses, humans and mice. We demonstrate that 20 beta-DHF is a weak endogenous agonist of the human glucocorticoid receptor (GR). Pharmacological inhibition of CBR1 in diet-induced obesity in mice results in more marked glucose intolerance with evidence for enhanced hepatic GR signaling. These findings suggest that CBR1 generating 20 beta-dihydrocortisol is a novel pathway modulating GR activation and providing enzymatic protection against excessive GR activation in obesity.
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| 27. |
- Nordensten, Christina, et al.
(author)
-
Hanteringen av de omfattande naturkatastroferna i Queensland 2011 : Observatörsrapport
- 2012
-
Reports (other academic/artistic)abstract
- En myndighetsgemensam observatörsresa genomfördes våren 2012 för att lära av erfarenheterna av den omfattande naturkatastrofen 2011 i Queensland, Australien. Observatörsresan organiserades av avdelningen för utvärdering och lärande vid Myndigheten för samhällsskydd och beredskap, MSB. Planerade möten hos myndigheter och organisationer ägde rum dels på federal nivå i Canberra, dels i delstaten Queensland med studiebesök i Brisbane och andra orter.Syftet med denna observatörsinsats var sålunda att:–– lära från de erfarenheter Australien gjort med anledning avde stora översvämningar, orsakade av extrema regn och cyklonenYasi, som drabbade delstaten Queensland under periodendecember 2010 - januari 2011.–– studera det australiensiska civila samhällets samlade förmågaatt hantera och återhämta sig efter dessa extrema händelseroch påfrestningar.Observatörsinsatsen initierades via MSB:s samverkansområden. En begäran och önskan riktades till MSB att organisera en observatörsinsats, i enlighet med MSB:s uppdrag att samordna och samverka inom området observatörsverksamhet
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| 28. |
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| 29. |
- Olsson, Petter, et al.
(author)
-
HealthSWEDE : costs with sublingual immunotherapy - a Swedish questionnaire study
- 2021
-
In: Allergy, Asthma & Clinical Immunology. - : BMC. - 1710-1484 .- 1710-1492. ; 17:1
-
Journal article (peer-reviewed)abstract
- Background The aim of this cross-sectional survey was to compare the health-economic consequences for allergic rhinitis (AR) patients treated with sublingual Immunotherapy (SLIT) in terms of direct and indirect costs with a reference population of patients receiving standard of care pharmacological therapy. Methods Primary objective was to analyse the health-economic consequences of SLIT for grass pollen allergy in Sweden vs reference group waiting for subcutaneous immunotherapy (SCIT). A questionnaire was mailed to two groups of AR patients. Results The questionnaire was distributed to 548 patients, 307 with SLIT and 241 in reference group (waiting for SCIT). Response rate was 53.8%. Mean annual costs were higher for reference patients than SLIT group; euro 3907 (SD 4268) vs euro 2084 (SD 1623) p < 0.001. Mean annual direct cost was higher for SLIT-patients, euro 1191 (SD 465) than for reference, euro 751 (SD 589) p < 0.001. Mean annual indirect costs for combined absenteeism and presenteeism were lower for patients treated with SLIT, euro 912 (SD 1530), than for reference, euro 3346 (SD 4120) p < 0.001, with presenteeism as main driver. Conclusions SLIT seems to be a cost-beneficial way to treat seasonal AR. This information might be used to guide future recommendations.
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| 30. |
- Olsson, Tobias, 1974-, et al.
(author)
-
A Preliminary Study on the Use of Key-words for Source Code to Architecture Mappings
- 2021
-
In: Companion Proceedings of the 15th European Conference on Software Architecture. - : CEUR-WS.org.
-
Conference paper (peer-reviewed)abstract
- We implement an automatic mapper that can find the corresponding architectural module for a source code file. The mapperis based on multinomial naive Bayes, and it is trained using custom keywords for each architectural module. For prediction,the mapper uses the path and file name of source code elements. We find that the needed keywords often match the modulenames, but also that ambiguities and discrepancies exist. We evaluate the mapper using nine open-source systems and findthat the mapper can successfully create a mapping with perfect precision, but in most cases, it cannot cover all source codeelements. Other techniques can, however, use the mapping as a foothold and create further mappings.
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| 31. |
- Olsson, Tobias, 1974-, et al.
(author)
-
An exploration and experiment tool suite for code to architecture mapping techniques
- 2019
-
In: ECSA '19 Proceedings of the 13th European Conference on Software Architecture. - New York, NY, USA : ACM Publications. - 9781450371421 ; , s. 26-29
-
Conference paper (peer-reviewed)abstract
- Reflexion modeling can be used to validate that source code conforms to an intended architecture. However, it requires a mapping of source code modules (e.g., classes) to (software) architecture elements. We have developed a tool suite that allows for evaluation and exploration of automatic techniques to map source code modules to architecture elements. The suite includes a reusable core component and tools to define the architecture, define and run experiments with mapping strategies, and explore the results of these experiments. The experiments can be executed locally or in a remote high-performance computing environment.
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| 32. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Evaluation of a static architectural conformance checking method in a line of computer games
- 2014
-
In: QoSA '14 Proceedings of the 10th international ACM Sigsoft conference on Quality of software architectures. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450325769 ; , s. 113-118
-
Conference paper (peer-reviewed)abstract
- We present an evaluation of a simple method to find architectural problems in a product line of computer games. The method uses dependencies (direct, indirect, or no) to automatically classify types in the implementation to high-level components in the product line architecture. We use a commercially available tool to analyse dependencies in the source code. The automatic classification of types is compared to a manual classification by the developer, and all mismatches are reported. To evaluate the method, we inspect the source code and look for a pre-defined set of architectural problems in all types. We compare the set of types that contained problems to the set of types where the manual and automatic classification disagreed to determine precision and recall. We also investigate what changes are needed to correct the found mismatches by either designing and implementing changes in the source code or refining the automatic classification. Our evaluation shows that the simple method is effective at detecting architectural problems in a product line of four games. The method is lightweight, customisable and easy to implement early in the development cycle.
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| 33. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Evaluation of an architectural conformance checking software service
- 2016
-
In: ACM Proccedings of the 10th European Conference on Software Architecture Workshops (ECSA-W). - New York, NY, USA : ACM Press. - 9781450347815
-
Conference paper (peer-reviewed)abstract
- Static architectural conformance checking can be used to find architectural violations, cases where the implementation does not adhere to the architecture, and prevent architectural erosion. We implement a software service for automated conformance checking and investigate the effect this has on the number of architectural violations in software projects. The service is implemented using our heuristic-based approach to static architecture conformance checking of the Model-View-Controller pattern. The service is integrated in the source code management system of each project, so a report is generated every time the source code is modified. The service was evaluated in a field experiment that consisted of eight student projects. We found that the four projects that used the service produced significantly fewer violations compared to those that did not.
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| 34. |
- Olsson, T., et al.
(author)
-
Evolution and Evaluation of the Model-View-Controller Architecture in Games
- 2015
-
In: 2015 IEEE/ACM 4th International Workshop on Games and Software Engineering. - : IEEE. - 9781467370462
-
Conference paper (peer-reviewed)abstract
- In game software it is important to separate game-play code from rendering code to ease transitions to new technologies or different platforms. The architectural pattern Model-View-Controller (MVC) is commonly used to achieve such separation. We investigate how the MVC architectural pattern is implemented in five game projects from a small development studio. We define a metrics-based quality model to assess software quality goals such as portability and rendering engine independence and perform an architectural analysis. The analysis reveals three different evolutions of the pattern. We also assess the quality and find that 1. the evolutions of the architecture differ in quality and 2. an architectural refactoring to a newer version of the architecture increases the software quality.
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| 35. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Evolution and Evaluation of the Model-View-Controller Architecture in Games
- 2015
-
In: Proceedings of the Fourth International Workshop on Games and Software Engineering. - USA : IEEE Press. ; , s. 8-14
-
Conference paper (peer-reviewed)abstract
- In game software it is important to separate game play code from rendering code to ease transitions to new technologies or different platforms. The architectural pattern Model-View-Controller (MVC) is commonly used to achieve such separation. We investigate how the MVC architectural pattern is implemented in five game projects from a small development studio. We define a metrics-based quality model to assess software quality goals such as portability and rendering engine independence and perform an architectural analysis. The analysis reveals three different evolutions of the pattern. We also assess the quality and find that 1. The evolutions of the architecture differ in quality and 2. An architectural refactoring to a newer version of the architecture increases the software quality.
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| 36. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Hard Cases in Source Code to Architecture Mapping using Naive Bayes
- 2021
-
In: Companion Proceedings of the 15th European Conference on Software Architecture. - : CEUR-WS.org.
-
Conference paper (peer-reviewed)abstract
- The automatic mapping of source code entities to architectural modules is a challenging problem that is necessary to solve if we want to increase the use of Static Architecture Conformance Checking in the industry. We apply the state-of-the-art automatic mapping technique to eight open-source systems and find that there are systematic problems in the automatically created mappings. All of these eight systems have small modules that are very hard to map correctly since only a few source code entities are mapped to these. All systems seem to use some naming strategy, mapping source code to modules; however, naming is often ambiguous. We also find differences in ground truth mappings performed by experts, which affect mappings based on these, and that architectural refactoring also affects the mapping performance.
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| 37. |
- Olsson, Tobias, 1974-
(author)
-
Incremental Clustering of Source Code : a Machine Learning Approach
- 2022
-
Doctoral thesis (other academic/artistic)abstract
- Technical debt at the architectural level is a severe threat to software development projects. Uncontrolled technical debt that is allowed to accumulate will undoubtedly hinder speedy development and maintenance, introduce bugs and problems in the software product, and may ultimately result in the abandonment of the source code. It is possible to detect debt accumulation by analyzing the source code and intended modules in the software architecture. However, this is seldom done in practice since it requires a correct and up-to-date mapping from source code to intended modules in the architecture. This mapping requires significant manual effort to create and maintain, something often considered too costly and laborsome. We investigate how to automate the mapping from source code to intended modules. The state-of-the-art considers it an incremental clustering problem, where source code entities should be clustered to the intended modules based on some similarity measure. As the system evolves and source code entities are added or modified, the clustering needs to be updated. The state-of-the-art techniques determine similarity based on either syntactic or semantic features, e.g., dependencies or identifier names. Large sets of parameters modify these features, e.g., weights for various types of dependencies. These parameters have a significant impact on how well the clustering performs. Unfortunately, we have not been able to identify any heuristics to help human experts determine a good set of parameters for a given system. Based on the parameters determined by, e.g., genetic optimization, it seems unlikely that general heuristics exist.Instead, we compute the similarity using a multinomial na\"ive Bayes text classifier trained on tokens from the source code entities. We also include a novel feature that captures dependencies as text to add syntactic features. Our classifier, which relies on significantly fewer parameters, outperforms the state-of-the-art techniques, with their parameters set to near-optimal values.We find that machine learning provides better mapping performance with fewer required parameters. We can successfully combine syntactic information with semantic information without additional parameters. We provide an open-source tool suite with a reference implementation of different techniques and a curated set of systems that can act as a ground truth benchmark.
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| 38. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Mapping Source Code to Modular Architectures Using Keywords
- 2022
-
In: Software Architecture. ECSA 2021. - : Springer. - 9783031151156 - 9783031151163 ; , s. 65-85
-
Conference paper (peer-reviewed)abstract
- We implement an automatic mapper that can find the corresponding architectural module for a source code file. The mapper is based on multinomial naive Bayes, and it is trained using custom keywords for each architectural module. The mapper uses the path and file name of source code elements for prediction. We find that the needed keywords often match the module names; however, ambiguities and discrepancies exist. We evaluate the mapper using ten open-source systems with a mapping to an intended architecture and find that the mapper can successfully create a mapping with perfect precision. Still, it cannot cover all source code elements in most cases. However, other techniques can use the mapping as a foothold and automatically create further mappings. We also apply the approach to two cases where the architecture has been recovered from the implementation and find that the approach currently has limitations of applicability in such architectures.
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| 39. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Motivation and Impact of Modeling Erosion using Static Architecture Conformance Checking
- 2017
-
In: Proceedings - 2017 IEEE International Conference on Software Architecture Workshops, ICSAW 2017. - : IEEE. - 9781509047932 ; , s. 204-209
-
Conference paper (peer-reviewed)abstract
- We motivate and describe why erosion modelingfrom a static architecture conformance checking point of view isimportant as well as the impact we think it can have on industry.Our research goal is to get a better understanding of erosionand develop smarter and simpler methods to assess erosion. Wedescribe preliminary results from a retrospective, longitudinalcase study of an open source software. The software system westudy, JabRef, was created in 2003, and refactored to a layeredstructure to “transition from a spaghetti to a more structuredarchitecture” in 2015. We construct a model from this new,layered architecture, and assess 30 versions of JabRef to findarchitectural conformance violations. Our preliminary resultsshow a significant difference in productivity after refactoring andsuggest that there is a connection between our model of erosionand productivity where more erosion gives lower productivity.
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| 40. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Optimized Dependency Weights in Source Code Clustering
- 2021
-
In: Software Architecture, ECSA 2021. - Cham : Springer. - 9783030860448 - 9783030860431 ; , s. 223-239
-
Conference paper (peer-reviewed)abstract
- Some methods use the dependencies between source code entities to perform clustering to, e.g., automatically map to an intended modular architecture or reconstruct the implemented software architecture. However, there are many different ways that source code entities can depend on each other in an object-oriented system, and it is not likely that all dependencies are equally useful. We investigate how well an optimized set of weights for 14 different types of dependencies perform when automatically mapping source code to modules using an established mapping technique. The optimized weights were found using genetic optimization. We compare the F1 score of precision and recall to uniform weights and weights computed by module relation ratio in eight open-source systems to evaluate performance. Our experiments show that optimized weights significantly outperform the others, especially in systems that seem not to have been designed using the low coupling, high cohesion principle. We also find that dependencies based on method calls are not useful for automatic mapping in any of the eight systems.
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| 41. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Optimized Machine Learning Input for Evolutionary Source Code to Architecture Mapping
- 2023
-
In: Software Architecture. ECSA 2022 Tracks and Workshops. ECSA 2022. - : Springer. - 9783031368882 - 9783031368899 ; , s. 421-435
-
Conference paper (peer-reviewed)abstract
- Automatically mapping source code to architectural modules is an interesting and difficult problem. Mapping can be considered a classification problem, and machine learning approaches have been used to automatically generate mappings. Feature engineering is an essential element of machine learning. We study which source code features are important for an algorithm to function effectively. Additionally, we examine stemming and data cleaning. We systematically evaluate various combinations of features on five datasets created from JabRef, TeamMates, ProM, and two Hadoop subsystems. The systems are open-source with well-established mappings. We find that no single set of features consistently provides the highest performance, and even the subsystems of Hadoop have varied optimal feature combinations. Stemming provided minimal benefit, and cleaning the data is not worth the effort, as it also provided minimal benefit.
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| 42. |
- Olsson, Tobias, 1974-, et al.
(author)
-
s4rdm3x : A Tool Suite to Explore Code to ArchitectureMapping Techniques
- 2021
-
In: Journal of Open Source Software. - : Open journals. - 2475-9066. ; 6:58
-
Journal article (peer-reviewed)abstract
- Architectural drift and erosion, where the implementation starts to deviate from the intended software architecture or the rules set by it, are common problems in long-lived software systems. This can be avoided by using techniques, such as Reflexion modeling, to validate that the implementation conforms to the indented architecture. Unfortunately, such techniques require a mapping from source code modules (e.g., classes) to elements of the architecture, something that is not always available or up to date. This is a known problem when, e.g., companies want to adopt static architecture conformance checking; the effort to manually create or bring this mapping up to date is just too time-consuming and error-prone. The s4rdm3x tool suite is designed for researchers and practitioners to study and evaluate algorithms that perform part of the mapping automatically, such as orphan-adoption clustering or information retrieval techniques. It includes a graphical user interface to define and run experiments with mapping algorithms and their parameters, and visualize and explore the results of these experiments. The experiments can be executed locally or in a remote high-performance computing environment. The tool suite includes reference implementations of state of the art mapping algorithms and a set of Java systems with validated mappings between classes and architecture elements. The tool suite is extensible, so it is easy to add new mapping algorithms and visualizations to explore their performance.
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| 43. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Semi-Automatic Mapping of Source Code Using Naive Bayes
- 2019
-
In: ECSA '19 Proceedings of the 13th European Conference on Software Architecture -. - New York, NY, USA : ACM Publications. - 9781450371421 ; , s. 209-216
-
Conference paper (peer-reviewed)abstract
- The software industry has not adopted continuous use of static architecture conformance checking. One hindrance is the needed mapping from source code elements to elements of the architecture. We present a novel approach of generating and combining dependency and semantic information extracted from an initial set of mapped source code files. We use this to train a Naive Bayes classifier that is then used to map the remainder of the source code files. We compare this approach with the HuGMe technique on six open source projects with known mappings. We find that our approach provides an average performance improvement of 0.22 and an average precision and recall F1-score improvement of 0.26 in comparison to HuGMe.
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| 44. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Studying expert initial set and hard to map cases in automated code-to-architecture mappings
- 2021
-
In: Companion Proceedings of the 15th European Conference on Software Architecture. - : CEUR-WS.
-
Conference paper (peer-reviewed)abstract
- We study the mapping of software source code to architectural modules. Background: To evaluate techniques for performing automatic mapping of code-to-architecture, a ground truth mapping, often provided by an expert, is needed. From this ground truth, techniques use an initial set of mapped source code as a starting point. The size and composition of this set affect the techniques’ performance, and to make comparisons, random sizes and compositions are used. However, while randomness will give a baseline for comparison, it is not likely that a human expert would compose an initial set on random to map source code. We are interested in letting an expert create an initial set based on their experience with the system and study how this affects how a technique performs. Also, previous research has shown that when comparing an automatic mapping with the ground truth mappings, human experts often accept the automated mappings and, if not, point to the need for refactoring the source code. We want to study this phenomenon further. Audience: Researchers and developers of tools in the area of architecture conformance. The system expert can gain valuable insights into where the source code needs to be refactored. Aim: We hypothesize that an initial set assigned by an expert performs better than a random initial set of similar size and that an expert will agree upon or find opportunities for refactoring in a majority of cases where the automatic mapping and expert mapping disagrees. Method: The initial set will be extracted from an interview with the expert. Then the performance (precision and recall f1 score) will be compared to mappings starting from random initial sets and using an automatic technique. We will also use our tool to find the cases where the automatic and human mapping disagrees and then let the expert review these cases. Results: We expect to find a difference when performance is compared. We expect the expert review to reveal source code that should be remapped, source code that needs refactoring (e.g., possible architectural violations), and points where the automatic technique needs to be improved. Limitations: The study will only focus on only a single system, which limits the external validity significantly. The protocol for the interaction with the human expert can also introduce validity problems; for example, a mapping presented by an algorithm could be perceived as more objective and thus more acceptable for a software engineer. Conclusions: We seek to improve our understanding of how a human creates an initial set for automatic mapping and its effect on how well an automated mapping technique performs. By improving the ground truth mappings, we can improve our techniques, tools, and methods for architecture conformance checking.
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| 45. |
- Olsson, Tobias, 1974-, et al.
(author)
-
The relationship of code churn and architectural violations in the open source software JabRef
- 2017
-
In: ECSA '17 Proceedings of the 11th European Conference on Software Architecture. - New York, NY, USA : ACM Publications. - 9781450352178 ; , s. 152-158
-
Conference paper (peer-reviewed)abstract
- The open source application JabRef has existed since 2003. In 2015, the developers decided to make an architectural refactoring as continued development was deemed too demanding. The developers also introduced Static Architecture Conformance Checking (SACC) to prevent violations to the intended architecture. Measurements mined from source code repositories such as code churn and code ownership has been linked to several problems, for example fault proneness, security vulnerabilities, code smells, and degraded maintainability. The root cause of such problems can be architectural. To determine the impact of the refactoring of JabRef, we measure the code churn and code ownership before and after the refactoring and find that large files with violations had a significantly higher code churn than large files without violations before the refactoring. After the refactoring, the files that had violations show a more normal code churn. We find no such effect on code ownership. We conclude that files that contain violations detectable by SACC methods are connected to higher than normal code churn.
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| 46. |
- Olsson, Tobias, 1974-, et al.
(author)
-
To automatically map source code entities to architectural modules with Naive Bayes
- 2022
-
In: Journal of Systems and Software. - : Elsevier. - 0164-1212 .- 1873-1228. ; 183
-
Journal article (peer-reviewed)abstract
- Background: The process of mapping a source code entity onto an architectural module is to a large degree a manual task. Automating this process could increase the use of static architecture conformance checking methods, such as reflexion modeling, in industry. Current techniques rely on user parameterization and a highly cohesive design. A machine learning approach would potentially require fewer parameters and better use of the available information to aid in automatic mapping.Aim: We investigate how a classifier can be trained to map from source code to architecture modules automatically. This classifier is trained with semantic and syntactic dependency information extracted from the source code and from architecture descriptions. The classifier is implemented using multinomial naive Bayes and evaluated.Method: We perform experiments and compare the classifier with three state-of-the-art mapping functions in eight open-source Java systems with known ground-truth-mappings.Results: We find that the classifier outperforms the state-of-the-art in all cases and that it provides a useful baseline for further research in the area of semi-automatic incremental clustering.Conclusions: We conclude that machine learning is a useful approach that performs better and with less need for parameterization compared to other approaches. Future work includes investigating problematic mappings and a more diverse set of subject systems.
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| 47. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Towards Improved Initial Mapping in Semi Automatic Clustering
- 2018
-
In: ECSA 2018. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450364836
-
Conference paper (peer-reviewed)abstract
- An important step in Static Architecture Conformance Checking (SACC) is the mapping of source code entities to entities in the intended architecture. This step is currently relying on manual work, which is one hindrance for more widespread adoption of SACC in industry. Semi-automatic clustering is a promising approach to improve this, and the HuGMe clustering algorithm is an example of such a technique for use in SACC. But HuGMe relies on an initial set of clustered source code elements and algorithm parameters. We investigate the automatic mapping performance of HuGMe in two experiments to gain insight into what influence the starting set has in a medium-sized open source system, JabRef, which contain a relatively large number of architectural violations. Our results show that the highest automatic mapping performance can be achieved with a low number of elements within the initial set. However, the variability of the performance is high. We find a benefit in favoring source code elements with a high fan-out in the initial set.
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| 48. |
- Olsson, Tobias, 1974-
(author)
-
Towards Pattern Based Architectural Conformance Checking
- 2016
-
Licentiate thesis (other academic/artistic)abstract
- Patterns are a source of knowledge when architecting software systems. They provide abstract and time-tested solutions that show how a system should be structured to achieve needed qualities. However, when developing software there is a chance that small mistakes are introduced in the source code. Over time, these mistakes can accumulate and break the structure of the pattern and its qualities are lost. There are methods that can help find such errors, but none of these provide a pattern abstraction. In this work, we describe a method that raises the level of abstraction from checking individual dependencies to checking key dependencies in the pattern. We implement our method, apply it to check the Model-View-Controller pattern. We show that the method can find architectural problems in real source code and examine how removal of detected erosions affects the source code. We conducted an experiment in a software project setting to determine if using the method affects the number of architectural problems. Some project teams were randomly assigned to use a software service that automated our method. It checked how well their implementation conformed to Model-View-Controller every time they updated the source code. The experiment showed that developers that used the tool had significantly fewer detected architectural problems during the course of the project. Our method makes conformance checking easier to use. This might help increase the adoption of conformance checking in industry.
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| 49. |
- Olsson, Tobias, 1974-, et al.
(author)
-
Using Repository Data for Driving Software Architecture
- 2018
-
In: Proceeding of the 40th International Conference on Software Engineering. - New York, NY, USA : ACM Publications. - 9781450356633 ; , s. 197-198
-
Conference paper (peer-reviewed)abstract
- We are in the pursuit of establishing a method for continuous data driven software architecture. We describe the problem with current methods for measuring the impact of refactoring long lived systems at the architectural level and architecture compliance checking. We summarize our studies of code churn, productivity and an automatic tool for compliance checking. We conclude that architecture violations seem to play an important role, but current methods are infeasible for industry practice. Finally we propose to use repository data mining to improve current methods for architecture compliance checking.
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| 50. |
- Sampson, Joshua N., et al.
(author)
-
Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
-
In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Journal article (peer-reviewed)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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