| 1. |
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| 2. |
- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 4. |
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| 5. |
- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 6. |
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| 8. |
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| 9. |
- Thompson, B.A., et al.
(författare)
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Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:2, s. 107-115
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Tidskriftsartikel (refereegranskat)abstract
- The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases. © 2014 Nature America, Inc.
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| 10. |
- Armesto, N., et al.
(författare)
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Heavy-ion collisions at the LHC-Last call for predictions
- 2008
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Ingår i: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 35:5, s. 054001-
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Forskningsöversikt (refereegranskat)abstract
- This writeup is a compilation of the predictions for the forthcoming Heavy Ion Program at the Large Hadron Collider, as presented at the CERN Theory Institute 'Heavy Ion Collisions at the LHC - Last Call for Predictions', held from 14th May to 10th June 2007.
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| 11. |
- Volpe, Giovanni, 1979, et al.
(författare)
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Roadmap for optical tweezers
- 2023
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Ingår i: Journal of Physics-Photonics. - : IOP Publishing. - 2515-7647. ; 5:2
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Tidskriftsartikel (refereegranskat)abstract
- Optical tweezers are tools made of light that enable contactless pushing, trapping, and manipulation of objects, ranging from atoms to space light sails. Since the pioneering work by Arthur Ashkin in the 1970s, optical tweezers have evolved into sophisticated instruments and have been employed in a broad range of applications in the life sciences, physics, and engineering. These include accurate force and torque measurement at the femtonewton level, microrheology of complex fluids, single micro- and nano-particle spectroscopy, single-cell analysis, and statistical-physics experiments. This roadmap provides insights into current investigations involving optical forces and optical tweezers from their theoretical foundations to designs and setups. It also offers perspectives for applications to a wide range of research fields, from biophysics to space exploration.
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| 12. |
- van Vollenhoven, R, et al.
(författare)
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A framework for remission in SLE: consensus findings from a large international task force on definitions of remission in SLE (DORIS)
- 2017
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Ingår i: Annals of the rheumatic diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 76:3, s. 554-561
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Tidskriftsartikel (refereegranskat)abstract
- Treat-to-target recommendations have identified ‘remission’ as a target in systemic lupus erythematosus (SLE), but recognise that there is no universally accepted definition for this. Therefore, we initiated a process to achieve consensus on potential definitions for remission in SLE.MethodsAn international task force of 60 specialists and patient representatives participated in preparatory exercises, a face-to-face meeting and follow-up electronic voting. The level for agreement was set at 90%.ResultsThe task force agreed on eight key statements regarding remission in SLE and three principles to guide the further development of remission definitions:1. Definitions of remission will be worded as follows: remission in SLE is a durable state characterised by …………………. (reference to symptoms, signs, routine labs).2. For defining remission, a validated index must be used, for example, clinical systemic lupus erythematosus disease activity index (SLEDAI)=0, British Isles lupus assessment group (BILAG) 2004 D/E only, clinical European consensus lupus outcome measure (ECLAM)=0; with routine laboratory assessments included, and supplemented with physician's global assessment.3. Distinction is made between remission off and on therapy: remission off therapy requires the patient to be on no other treatment for SLE than maintenance antimalarials; and remission on therapy allows patients to be on stable maintenance antimalarials, low-dose corticosteroids (prednisone ≤5 mg/day), maintenance immunosuppressives and/or maintenance biologics.The task force also agreed that the most appropriate outcomes (dependent variables) for testing the prognostic value (construct validity) of potential remission definitions are: death, damage, flares and measures of health-related quality of life.ConclusionsThe work of this international task force provides a framework for testing different definitions of remission against long-term outcomes.
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| 13. |
- Haycock, Philip C., et al.
(författare)
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Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases A Mendelian Randomization Study
- 2017
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Ingår i: JAMA Oncology. - : American Medical Association. - 2374-2437 .- 2374-2445. ; 3:5, s. 636-651
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE: The causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. OBJECTIVE: To conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases. DATA SOURCES: Genomewide association studies (GWAS) published up to January 15, 2015. STUDY SELECTION: GWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available. DATA EXTRACTION AND SYNTHESIS: Summary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population. MAIN OUTCOMES AND MEASURES: Odds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation. RESULTS: Summary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [ 95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [ 95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [ 95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [ 95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [ 95% CI, 0.05-0.15]). CONCLUSIONS AND RELEVANCE: It is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
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| 14. |
- Lissek, T, et al.
(författare)
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Building Bridges through Science
- 2017
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Ingår i: Neuron. - : Elsevier BV. - 1097-4199 .- 0896-6273. ; 96:4, s. 730-735
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Tidskriftsartikel (refereegranskat)
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| 15. |
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| 16. |
- Andreoli, L, et al.
(författare)
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EULAR recommendations for women's health and the management of family planning, assisted reproduction, pregnancy and menopause in patients with systemic lupus erythematosus and/or antiphospholipid syndrome
- 2017
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Ingår i: Annals of the rheumatic diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 76:3, s. 476-485
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Tidskriftsartikel (refereegranskat)abstract
- Develop recommendations for women's health issues and family planning in systemic lupus erythematosus (SLE) and/or antiphospholipid syndrome (APS).MethodsSystematic review of evidence followed by modified Delphi method to compile questions, elicit expert opinions and reach consensus.ResultsFamily planning should be discussed as early as possible after diagnosis. Most women can have successful pregnancies and measures can be taken to reduce the risks of adverse maternal or fetal outcomes. Risk stratification includes disease activity, autoantibody profile, previous vascular and pregnancy morbidity, hypertension and the use of drugs (emphasis on benefits from hydroxychloroquine and antiplatelets/anticoagulants). Hormonal contraception and menopause replacement therapy can be used in patients with stable/inactive disease and low risk of thrombosis. Fertility preservation with gonadotropin-releasing hormone analogues should be considered prior to the use of alkylating agents. Assisted reproduction techniques can be safely used in patients with stable/inactive disease; patients with positive antiphospholipid antibodies/APS should receive anticoagulation and/or low-dose aspirin. Assessment of disease activity, renal function and serological markers is important for diagnosing disease flares and monitoring for obstetrical adverse outcomes. Fetal monitoring includes Doppler ultrasonography and fetal biometry, particularly in the third trimester, to screen for placental insufficiency and small for gestational age fetuses. Screening for gynaecological malignancies is similar to the general population, with increased vigilance for cervical premalignant lesions if exposed to immunosuppressive drugs. Human papillomavirus immunisation can be used in women with stable/inactive disease.ConclusionsRecommendations for women's health issues in SLE and/or APS were developed using an evidence-based approach followed by expert consensus.
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| 17. |
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| 21. |
- Betz, B, et al.
(författare)
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Quantification of the sensitivity range in neutron dark-field imaging.
- 2015
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 1089-7623 .- 0034-6748. ; 86:12
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Tidskriftsartikel (refereegranskat)abstract
- In neutron grating interferometry, the dark-field image visualizes the scattering properties of samples in the small-angle and ultra-small-angle scattering range. These angles correspond to correlation lengths from several hundred nanometers up to several tens of micrometers. In this article, we present an experimental study that demonstrates the potential of quantitative neutron dark-field imaging. The dark-field signal for scattering from different particle sizes and concentrations of mono-dispersive polystyrene particles in aqueous solution is compared to theoretical predictions and the good agreement between measurements and calculations underlines the quantitative nature of the measured values and reliability of the technique with neutrons.
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| 22. |
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| 26. |
- Conroy, Melanie, et al.
(författare)
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Uncertainty in humanities network visualization
- 2024
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Ingår i: Frontiers in Communication. - : Frontiers Media S.A.. - 2297-900X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Network visualization is one of the most widely used tools in digital humanities research. The idea of uncertain or “fuzzy” data is also a core notion in digital humanities research. Yet network visualizations in digital humanities do not always prominently represent uncertainty. In this article, we present a mathematical and logical model of uncertainty as a range of values which can be used in network visualizations. We review some of the principles for visualizing uncertainty of different kinds, visual variables that can be used for representing uncertainty, and how these variables have been used to represent different data types in visualizations drawn from a range of non-humanities fields like climate science and bioinformatics. We then provide examples of two diagrams: one in which the variables displaying degrees of uncertainty are integrated into the graph and one in which glyphs are added to represent data certainty and uncertainty. Finally, we discuss how probabilistic data and what-if scenarios could be used to expand the representation of uncertainty in humanities network visualizations.
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| 27. |
- Cuddihy, Laury, et al.
(författare)
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Vertebral Body Stapling versus Bracing for Patients with High-Risk Moderate Idiopathic Scoliosis.
- 2015
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Ingår i: BioMed research international. - : Hindawi Limited. - 2314-6141 .- 2314-6133. ; 2015
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Tidskriftsartikel (refereegranskat)abstract
- We report a comparison study of vertebral body stapling (VBS) versus a matched bracing cohort for immature patients with moderate (25 to 44°) idiopathic scoliosis (IS).42 of 49 consecutive patients (86%) with IS were treated with VBS and followed for a minimum of 2 years. They were compared to 121 braced patients meeting identical inclusion criteria. 52 patients (66 curves) were matched according to age at start of treatment (10.6 years versus 11.1 years, resp. [P = 0.07]) and gender.For thoracic curves 25-34°, VBS had a success rate (defined as curve progression <10°) of 81% versus 61% for bracing (P = 0.16). In thoracic curves 35-44°, VBS and bracing both had a poor success rate. For lumbar curves, success rates were similar in both groups for curves measuring 25-34°.In this comparison of two cohorts of patients with high-risk (Risser 0-1) moderate IS (25-44°), in smaller thoracic curves (25-34°) VBS provided better results as a clinical trend as compared to bracing. VBS was found not to be effective for thoracic curves ≥35°. For lumbar curves measuring 25-34°, results appear to be similar for both VBS and bracing, at 80% success.
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| 30. |
- Heldal, Rogardt, 1964, et al.
(författare)
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Sustainability competencies and skills in software engineering: An industry perspective
- 2024
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Ingår i: Journal of Systems and Software. - 0164-1212. ; 211
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Tidskriftsartikel (refereegranskat)abstract
- Context: Achieving the UN Sustainable Development Goals (SDGs) demands a shift by industry, governments, society, and individuals to reach adequate levels of awareness and actions to address sustainability challenges. Software systems will play an important role in moving towards these targets. Sustainability skills are necessary to support the development of software systems and to provide sustainable IT-supported services for citizens. Gap: While there is a growing number of academic bodies including sustainability education in engineering and computer science curricula, there is not yet comprehensive research on the competencies and skills required by IT professionals to develop such systems. Research goal: This study aims to identify the industrial sustainability needs for education and training from software engineers’ perspective. For this, we answer the following questions: (1) what are the interests of organisations with an IT division with respect to sustainability? (2) what do organisations want to achieve with respect to sustainability, and how? and (3) what are the sustainability-related competencies and skills that organisations need to achieve their sustainability goals? Methodology: We conducted a qualitative study with interviews and focus groups with experts from twenty-eight organisations with an IT division from nine countries to understand their interests, goals, and achievements related to sustainability, and the skills and competencies needed to achieve their goals. Results: Our findings show that organisations are interested in sustainability, both idealistically and increasingly for core business reasons. They seek to improve the sustainability of software processes and products but encounter difficulties, like the trade-off between short-term financial profitability and long-term sustainability goals or an unclear understanding of sustainability concepts from a software engineering perspective. To fill these gaps, they have promoted in-house training courses, collaborated with universities, and sent employees to external training. The acquired competencies should support translating environmental and social benefits into economic ones and make sustainability an integral part of software development.
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| 31. |
- Jorgensen, P. M., et al.
(författare)
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Characterisation of the human APC1, the largest subunit of the anaphase-promoting complex
- 2001
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Ingår i: Gene. - 0378-1119 .- 1879-0038. ; 262:02-jan, s. 51-59
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Tidskriftsartikel (refereegranskat)abstract
- Accurate segregation of sister chromatids during mitosis is necessary to avoid the aneuploidy found in many cancers. The spindle checkpoint, which monitors the metaphase to anaphase transition, has been shown to be defective in cancers with chromosomal instability. This checkpoint regulates the anaphase-promoting complex or cyclosome (APC/C), a cell cycle ubiquitin ligase regulating among other things sister chromatid separation. We have previously investigated the mouse Apc1 protein (previously also called Tsg24), the largest subunit of the APC/C. We have now sequenced a full-length human APC1 cDNA, mapped its chromosomal location, and analysed its intron-exon boundaries. We have also investigated the RNA and protein expression of the Apc1 and other APC/C components in normal and cancer cells and the relative occurrence of expressed sequence tugs (ESTs) representing APC subunits from different tissues. The different APC/C subunits are expressed in most tissues and cell types at fairly constant levels relative to each other, suggesting that they perform their functions as part of a complex. A difference from this pattern is however seen for the APC6, which in some cases is more strongly expressed, suggesting a special function for this protein in certain tissues and cell types.
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| 34. |
- Radeva, Nedyalka, et al.
(författare)
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Active Site Mapping of an Aspartic Protease by Multiple Fragment Crystal Structures : Versatile Warheads to Address a Catalytic Dyad
- 2016
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 59:21, s. 9743-9759
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Tidskriftsartikel (refereegranskat)abstract
- Crystallography is frequently used as follow-up method to validate hits identified by biophysical screening cascades. The capacity of crystallography to directly screen fragment libraries is often underestimated, due to its supposed low-throughput and need for high-quality crystals. We applied crystallographic fragment screening to map the protein-binding site of the aspartic protease endothiapepsin by individual soaking experiments. Here, we report on 41 fragments binding to the catalytic dyad and adjacent specificity pockets. The analysis identifies already known warheads but also reveals hydrazide, pyrazole, or carboxylic acid fragments as novel functional groups binding to the dyad. A remarkable swapping of the S1 and S1′ pocket between structurally related fragments is explained by either steric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to tetrahedral geometry of an oxygen functional group in a side chain. Some warheads simultaneously occupying both S1 and S1′ are promising starting points for fragment-growing strategies.
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| 35. |
- Rodriguez-Navas, Guillermo, et al.
(författare)
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Safety vs. sustainability design : Analogies, differences and potential synergies
- 2015
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Ingår i: CEUR Workshop Proceedings. ; , s. 25-34
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Konferensbidrag (refereegranskat)abstract
- The idea that there are important parallels between safety and sustainability and that software engineers might be able to take lessons learned from safety and apply them to sustainability has been voiced and initially explored before. This paper extends the analysis of similarities, differences, and potential synergies between the two concepts, according to four different dimensions of these domains: systemicity, complexity, certification and social perception. Copyright © 2015 for this paper by its authors. Copying permitted for private and academic purposes.
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| 36. |
- Terhal, Paulien A., et al.
(författare)
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A Study of the Clinical and Radiological Features in a Cohort of 93 Patients with a COL2A1 Mutation Causing Spondyloepiphyseal Dysplasia Congenita or a Related Phenotype
- 2015
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Ingår i: American Journal of Medical Genetics. Part A. - : Wiley. - 1552-4825 .- 1552-4833. ; 167A:3, s. 461-475
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Tidskriftsartikel (refereegranskat)abstract
- Type 2 collagen disorders encompass a diverse group of skeletal dysplasias that are commonly associated with orthopedic, ocular, and hearing problems. However, the frequency of many clinical features has never been determined. We retrospectively investigated the clinical, radiological, and genotypic data in a group of 93 patients with molecularly confirmed SEDC or a related disorder. The majority of the patients (80/93) had short stature, with radiological features of SEDC (n=64), others having SEMD (n=5), Kniest dysplasia (n=7), spondyloperipheral dysplasia (n=2), or Torrance-like dysplasia (n=2). The remaining 13 patients had normal stature with mild SED, Stickler-like syndrome or multiple epiphyseal dysplasia. Over 50% of the patients had undergone orthopedic surgery, usually for scoliosis, femoral osteotomy or hip replacement. Odontoid hypoplasia was present in 56% (95% CI 38-74) and a correlation between odontoid hypoplasia and short stature was observed. Atlanto-axial instability, was observed in 5 of the 18 patients (28%, 95% CI 10-54) in whom flexion-extension films of the cervical spine were available; however, it was rarely accompanied by myelopathy. Myopia was found in 45% (95% CI 35-56), and retinal detachment had occurred in 12% (95% CI 6-21; median age 14 years; youngest age 3.5 years). Thirty-two patients complained of hearing loss (37%, 95% CI 27-48) of whom 17 required hearing aids. The ophthalmological features and possibly also hearing loss are often relatively frequent and severe in patients with splicing mutations. Based on clinical findings, age at onset and genotype-phenotype correlations in this cohort, we propose guidelines for the management and follow-up in this group of disorders.
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| 37. |
- Venters, Colin C., et al.
(författare)
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Software Sustainability: Beyond the Tower of Babel
- 2021
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Ingår i: Proceedings - 2021 IEEE/ACM International Workshop on Body of Knowledge for Software Sustainability, BoKSS 2021. ; , s. 3-4
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Konferensbidrag (refereegranskat)
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| 38. |
- Venters, Colin C., et al.
(författare)
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Sustainable software engineering: Reflections on advances in research and practice
- 2023
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Ingår i: Information and Software Technology. - 0950-5849. ; 164
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Tidskriftsartikel (refereegranskat)abstract
- Context: Modern societies are highly dependent on complex, large-scale, software-intensive systems that increasingly operate within an environment of continuous availability, which are challenging to maintain, and evolve in response to changes in stakeholder requirements of the system. Software architectures are the foundation of any software system and provide a mechanism for reasoning about core software quality requirements. Their sustainability – the capacity to endure in changing environments – is a critical concern for software architecture research and practice. Objective: The objective of the paper is to re-examine our previous assumptions and arguments in light of advances in the field. This reflection paper provides an opportunity to obtain new insights into the trends in software sustainability in both academia and industry, from a software architecture perspective specifically and software engineering more broadly. Given advances in research in the field, the increasing introduction of academic courses on different sustainability topics, and the engagement of companies to cope with sustainability goals, we reflect on advances and maturity about the role sustainability in general plays in today's society. More specifically, we revisit the trends, open issues and research challenges identified five years ago in our previous paper on software sustainability research and practice from a software architecture viewpoint, which aimed to provide a foundation and roadmap of emerging research themes in the area of sustainable software architectures in order to consider how this paper influenced and motivated research in the intervening years. Method: The forward snowballing method was used to establish the methodological basis for our reflection on the state of the art. A total of 234 studies were identified between April 2018 and June 2023 and 102 studies were found to be relevant according to the selection criteria. A further subset was mapped to the primary themes of the original paper including definitions and concepts, reference architectures, measures and metrics, and education. Vision: The vision of this reflection paper is to provide a new foundation and road map of emerging research themes in the area of sustainable software engineering highlighting recent trends, and open issues and research challenges.
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| 39. |
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