| 31. |
- Andreasson, U., et al.
(författare)
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An enzyme activity as a potential biomarker for Alzheimer's disease.
- 2010
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Ingår i: Alzheimer's & Dementia. - : Wiley. - 1552-5279 .- 1552-5260. ; 6:4, s. 497-498
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Konferensbidrag (refereegranskat)abstract
- Background: Six different N-terminal amyloid precursor protein (APP) fragments, with molecular weight ∼12 kDa, have previously been identified in human cerebrospinal fluid (CSF). In a pilot study, both the sum of their concentrations, measured by western blot, and the relative abundance pattern, measured by mass spectrometry, were different in Alzheimer's disease (AD) patients compared to healthy controls. To test if these differences were also reflected in protease activities that possibly give rise to the ∼12 kDa fragments an enzymatic assay was developed and the activity in CSF was investigated for its potential as a biomarker for AD. Methods: The substrate in the protease activity assay was a custom made fluorochrome/quencher labeled peptide that covers the cleavage sites in APP (APP118-APP127) corresponding to the C-termini of the six ∼12 kDa APP fragments. The activity was measured in CSF from 55 AD patients and 17 controls. Results: There was a significant increase in the protease activity in CSF from AD patients compared to the controls (p = 0.001). This is in line with previous results which indicate that the sum of the ∼12 kDa fragments are elevated in AD. Results from inhibition studies strongly suggests that the enzyme responsible for the cleavage of the substrate is an aspartic protease since a sub nM IC50 value was recorded for Pepstatin A while no inhibition was observed for the cysteine protease specific inhibitor E64 at concentrations up to100 nM. Conclusions: There exists an enzymatic activity in CSF capable of cleaving a peptide substrate that spans a portion, close to the N-terminal, of APP. In a pilot study the activity is increased in AD patients compared to controls suggesting that it can be used as a biomarker.
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| 32. |
- Aurelius, Oskar, et al.
(författare)
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The Crystal Structure of Thermotoga maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site
- 2015
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides, the building blocks for DNA synthesis, and are found in all but a few organisms. RNRs use radical chemistry to catalyze the reduction reaction. Despite RNR having evolved several mechanisms for generation of different kinds of essential radicals across a large evolutionary time frame, this initial radical is normally always channelled to a strictly conserved cysteine residue directly adjacent to the substrate for initiation of substrate reduction, and this cysteine has been found in the structures of all RNRs solved to date. We present the crystal structure of an anaerobic RNR from the extreme thermophile Thermotoga maritima (tmNrdD), alone and in several complexes, including with the allosteric effector dATP and its cognate substrate CTP. In the crystal structure of the enzyme as purified, tmNrdD lacks a cysteine for radical transfer to the substrate pre-positioned in the active site. Nevertheless activity assays using anaerobic cell extracts from T. maritima demonstrate that the class III RNR is enzymatically active. Other genetic and microbiological evidence is summarized indicating that the enzyme is important for T. maritima. Mutation of either of two cysteine residues in a disordered loop far from the active site results in inactive enzyme. We discuss the possible mechanisms for radical initiation of substrate reduction given the collected evidence from the crystal structure, our activity assays and other published work. Taken together, the results suggest either that initiation of substrate reduction may involve unprecedented conformational changes in the enzyme to bring one of these cysteine residues to the expected position, or that alternative routes for initiation of the RNR reduction reaction may exist. Finally, we present a phylogenetic analysis showing that the structure of tmNrdD is representative of a new RNR subclass IIIh, present in all Thermotoga species plus a wider group of bacteria from the distantly related phyla Firmicutes, Bacteroidetes and Proteobacteria.
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| 33. |
- Ben Henda, N., et al.
(författare)
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OpenSAW : Open security analysis workbench
- 2017
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Ingår i: 20th International Conference on Fundamental Approaches to Software Engineering, FASE 2017 Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2017. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783662544938 ; , s. 321-337
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Konferensbidrag (refereegranskat)abstract
- Software is today often composed of many sourced componets, which potentially contain security vulnerabilities, and therefore require testing before being integrated. Tools for automated test case generation, for example, based on white-box fuzzing, are beneficial for this testing task. Such tools generally explore limitations of the specific underlying techniques for solving problems related to, for example, constraint solving, symbolic execution, search heuristics and execution trace extraction. In this article we describe the design of OpenSAW, a more flexible general-purpose white-box fuzzing framework intended to encourage research on new techniques identifying security problems. In addition, we have formalized two unaddressed technical aspects and devised new algorithms for these. The first relates to generalizing and combining different program exploration strategies, and the second relates to prioritizing execution traces. We have evaluated OpenSAW using both in-house and external programs and identified several bugs.
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| 34. |
- Ben Henda, Noomene, et al.
(författare)
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OpenSAW: Open Security Analysis Workbench
- 2017. - 1
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Ingår i: Fundamental Approaches to Software Engineering : 20th International Conference, FASE 2017, Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2017, Uppsala, Sweden, April 22-29, 2017, Proceedings - 20th International Conference, FASE 2017, Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2017, Uppsala, Sweden, April 22-29, 2017, Proceedings. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783662544938 - 9783662544945 ; 10202, s. 321-337
-
Konferensbidrag (refereegranskat)abstract
- Software is today often composed of many sourced components, which potentially contain security vulnerabilities, and therefore require testing before being integrated. Tools for automated test case generation, for example, based on white-box fuzzing, are beneficial for this testing task. Such tools generally explore limitations of the specific underlying techniques for solving problems related to, for example, constraint solving, symbolic execution, search heuristics and execution trace extraction. In this article we describe the design of OpenSAW, a more flexible general-purpose white-box fuzzing framework intended to encourage research on new techniques identifying security problems. In addition, we have formalized two unaddressed technical aspects and devised new algorithms for these. The first relates to generalizing and combining different program exploration strategies, and the second relates to prioritizing execution traces. We have evaluated OpenSAW using both in-house and external programs and identified several bugs.
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| 35. |
- Bengtsson, Kristofer, 1979, et al.
(författare)
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Emergency department overview - Improving the dynamic capabilities using an event-driven information architecture
- 2016
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Ingår i: IEEE International Conference on Emerging technologies and factory automation (ETFA) 2016.
-
Konferensbidrag (refereegranskat)abstract
- It is challenging to get an overview and understand- ing of what is going on at an emergency department (ED). This is due to the sometimes turbulent work environment and a large variation in patient processes. To increase the dynamic capability and responsiveness of an ED, it is important that the staff and patients have an overview of what is going on and what will happen in the coming hours. This paper presents a smart online support software that shows the current state of the ED as well as a prediction of the coming hours. The software has been developed as a case study of using agile development ideas when developing new systems for hospitals. The result shows that the use of the event-driven information architecture for healthcare (EVAH) enabled a rapid development of a successful running application, helping the nurses getting an overview of current situation and the coming hours.
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| 36. |
- Bergengren, Oskar, et al.
(författare)
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Changes in lifestyle among prostate cancer survivors: A nationwide population-based study
- 2020
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Ingår i: Psycho-Oncology. - : Wiley. - 1057-9249 .- 1099-1611. ; 29:10
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Tidskriftsartikel (refereegranskat)abstract
- Objective Long-term information on lifestyle changes among prostate survivors is lacking. In this nationwide, population-based study we investigated the prevalence of lifestyle changes, factors associated with lifestyle changes and associations between lifestyle changes and general quality of life. Methods All men registered in the National Prostate Cancer Register of Sweden diagnosed in 2008 with low-risk prostate cancer at age 70 years or younger were sent a questionnaire. Logistic regression was used to calculate odds ratios (ORs) with 95% confidence intervals for factors potentially associated with lifestyle change. Results Out of 1288, 1720 men (75%) were responded. A total of 279 (22%) reported a positive lifestyle change regarding diet or exercise. Poor functional outcomes after treatment was associated with exercising less (OR 1.6, 95% CI 1.2-2.1) and less interest in social activities and relationships (OR 1.8, 95% CI 1.5-2.1). Men who exercised more (OR 7.9, 95% CI 4.4-14) and men who had an increased interest in relationships and social activities (OR 5.2, 95% CI 2.1-13) reported higher general quality of life. Conclusions A considerable proportion of men reported making positive lifestyle changes after the prostate cancer diagnosis. The time after diagnosis may be a teachable moment that facilitates lifestyle interventions. Poor functional outcomes after treatment may reduce the willingness to engage in positive lifestyle change, which need be considered when supporting men after treatment. Men who made a positive lifestyle change, regardless of whether it was exercise or regarding relationships and social activities more often reported a high level of general quality of life.
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| 37. |
- Bergengren, Oskar, et al.
(författare)
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Determinants for choosing and adhering to active surveillance for localised prostate cancer: A nationwide population-based study
- 2019
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Ingår i: BMJ Open. - : BMJ. - 2044-6055. ; 9:12
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Tidskriftsartikel (refereegranskat)abstract
- Objective Knowledge about factors influencing choice of and adherence to active surveillance (AS) for prostate cancer (PC) is scarce. We aim to identify which factors most affected choosing and adhering to AS and to quantify their relative importance. Design, setting and participants In 2015, we sent a questionnaire to all Swedish men aged ≤70 years registered in the National Prostate Cancer Register of Sweden who were diagnosed in 2008 with low-risk PC and had undergone prostatectomy, radiotherapy or started on AS. Outcome measurements and statistical analysis Logistic regression was used to calculate ORs with 95% CIs for factors potentially affecting choice and adherence to AS. Results 1288 out of 1720 men (75%) responded, 451 (35%) chose AS and 837 (65%) underwent curative treatment. Of those starting on AS, 238 (53%) diverted to treatment within 7 years. Most men (83%) choose AS because ‘My doctor recommended AS’. Factors associated with choosing AS over treatment were older age (OR 1.81, 95% CI 1.29 to 2.54), a Charlson Comorbidity Index >2 (OR 1.50, 95% CI 1.06 to 2.13), being unaccompanied when notified of the cancer diagnosis (OR 1.45, 95% CI 1.11 to 1.89). Men with a higher prostate-specific antigen (PSA) at the time of diagnosis were less likely to adhere to AS (OR 0.26, 95% CI 0.10 to 0.63). The reason for having treatment after initial AS was ‘the PSA level was rising’ in 55% and biopsy findings in 36%. Conclusions A doctor’s recommendation strongly affects which treatment is chosen for men with low-risk PC. Rising PSA values were the main factor for initiating treatment for men on AS. These findings need be considered by healthcare providers who wish to increase the uptake of and adherence to AS.
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| 38. |
- Bergengren, Oskar, et al.
(författare)
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Satisfaction with Care Among Men with Localised Prostate Cancer: A Nationwide Population-based Study
- 2018
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Ingår i: European Urology Oncology. - : Elsevier BV. - 2588-9311. ; 1:1, s. 37-45
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Tidskriftsartikel (refereegranskat)abstract
- Background: Information about how men with prostate cancer (PC) experience their medical care and factors associated with their overall satisfaction with care (OSC) is limited. Objective: To investigate OSC and factors associated with OSC among men with low-risk PC. Design, setting, and participants: Men registered in the National Prostate Cancer Register of Sweden as diagnosed in 2008 with low-risk PC at the age of ≤70 yr who had undergone radical prostatectomy (RP), radiotherapy (RT), or started on active surveillance (AS) were invited in 2015 to participate in this nationwide population-based survey (n = 1720). Outcome measurements and statistical analysis: OSC data were analysed using ordinal logistic regression. Odds ratios (ORs) were calculated for comparisons between the highest and lowest possible response categories. Results and limitations: A total of 1288 men (74.9%) responded. High OSC was reported by 958 (74.4%). Factors associated with high OSC were high participation in decision-making (OR 4.18, 95% confidence interval [CI] 2.61–6.69), receiving more information (OR 11.1, 95% CI 7.97–15.6), high-quality information (OR 7.85, 95% CI 5.46–11.3), access to a nurse navigator (OR 1.80, 95% CI 1.44–2.26), and better functional outcomes (defined as 25 points higher on the EPIC-26 questionnaire; OR 1.34, 95% CI 1.21–1.48). OSC was not affected by whether a doctor or specialist nurse conducted follow-up (OR 0.84, 95% CI 0.66–1.07). These findings were similar across treatment groups. Men who had undergone RP or RT reported high OSC more often than men on AS (78.2% vs 84.0% vs 72.6%), high participation in decision-making (70.5% vs 64.5% vs 49.2%), and having received more information (40.5% vs 45.8% vs 28.6%), and were less likely to believe they would die from PC (3.8% vs 3.9% vs 8.0%). Limitations include the nonrandomised retrospective design and potential recall bias. Conclusions: Information and participation in decision-making, as well as access to a nurse navigator, are key factors for OSC, regardless of treatment. Men on AS need more information about their treatment and need to participate more in decision-making. OSC was as high among men who had nurse-led follow-up as among men who had doctor-led follow-up. Patient summary: Information about how men with low-risk prostate cancer experience their medical care is limited. In this nationwide population-based study we found that information and participation in decision-making as well as access to a nurse navigator are key factors for satisfaction regardless of treatment. Men who are being closely watched for prostate cancer without immediate curative treatment need more information than they now receive and need to participate more in decision-making than they currently do. Information and participation in decision-making are key factors for satisfaction with care among men with localised prostate cancer. Men under active surveillance need more information about their treatment and need to participate more in decision-making. © 2018 European Association of Urology
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| 39. |
- Bergengren, Oskar, et al.
(författare)
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Satisfaction with Nurse-led Follow-up in Prostate Cancer Patients-A Nationwide Population-based Study
- 2022
-
Ingår i: European Urology Open Science. - : Elsevier. - 2666-1691 .- 2666-1683. ; 38, s. 25-31
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Tidskriftsartikel (refereegranskat)abstract
- Background: Satisfaction with nurse-led follow-up among men with prostate can-cer is high. However, it is unclear whether all men are satisfied or whether there are men who would benefit from being followed by a urologist or a nurse.Objective: To investigate the follow-up distribution between urologists and nurses, and whether the high self-reported satisfaction with nurse-led follow-up is inde-pendent of other factors such as age or comorbidity.Design, setting, and participants: All Swedish men, <= 70 yr of age, with a low-risk prostate cancer diagnosis in 2008, answered a questionnaire 7 yr after diagnosis. The extensive questionnaire included a question on satisfaction with care, answered on a seven-point scale. Participants were divided based on whether they were followed up by a nurse, a urologist, or both.Outcome measurements and statistical analysis: Factors that could influence the level of satisfaction were identified as age, edu-cation, comorbidity, treatment, disease progression, urinary bother, level of infor-mation, and participation in treatment decision. Likelihood ratio tests from ordinal regression were used to test the null hypothesis of similar satisfaction between groups.Results and limitations: Out of 1288 men, 1137 (88%) answered both the question on who performed the follow-up and the question regarding satisfaction. In all, 350 men reported that they were followed up by nurses (31%), 598 (52%) by urologists, and 189 (17%) by both. No differences in satisfaction where seen between the groups. Approximately 50% were satisfied completely, regardless of who performed the follow-up. Results were not affected by age, educational level, comorbidity, treatment, disease progression, urinary bother, information, or participation in treatment decision. Limitations include the nonrandomized, retrospective design and a potential recall bias.Conclusions: Satisfaction with nurse-led follow-up is high, regardless of factors such as age, level of education, comorbidity, and treatment.Patient summary: Men with prostate cancer can be offered nurse-led follow-up on a regular basis and still maintain their satisfaction with health care.
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| 40. |
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