| 1. |
- Ahlford, Annika, et al.
(författare)
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Dried reagents for multiplex genotyping by tag-array minisequencing to be used in microfluidic devices
- 2010
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Ingår i: The Analyst. - : Royal Society of Chemistry (RSC). - 0003-2654 .- 1364-5528. ; 135:9, s. 2377-2385
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Tidskriftsartikel (refereegranskat)abstract
- We present an optimized procedure for freeze-drying and storing reagents for multiplex PCR followed by genotyping using a tag-array minisequencing assay with four color fluorescence detection which is suitable for microfluidic assay formats. A test panel was established for five cancer mutations in three codons (175, 248 and 273) of the tumor protein gene (TP53) and for 13 common single nucleotide polymorphisms (SNPs) in the TP53 gene. The activity of DNA polymerase was preserved for six months of storage after freeze-drying, and the half-life of activities of exonuclease I and shrimp alkaline phosphatase were estimated to 55 and 200 days, respectively. We conducted a systematic genotyping comparison using freeze-dried and liquid reagents. The accuracy of successful genotyping was 99.1% using freeze-dried reagents compared to liquid reagents. As a proof of concept, the genotyping protocol was carried out with freeze-dried reagents stored in reaction chambers fabricated by micromilling in a cyclic olefin copolymer substrate. The results reported in this study are a key step towards the development of an integrated microfluidic device for point-of-care DNA-based diagnostics.
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| 2. |
- Bellec, G., et al.
(författare)
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A social network integrated game experiment to relate tapping to speed perception and explore rhythm reproduction
- 2013
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Ingår i: Proceedings of the Sound and Music Computing Conference 2013. - 9783832534721 ; , s. 19-26
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Konferensbidrag (refereegranskat)abstract
- During recent years, games with a purpose (GWAPs) have become increasingly popular for studying human behaviour [1–4]. However, no standardised method for web-based game experiments has been proposed so far. We present here our approach comprising an extended version of the CaSimIR social game framework [5] for data collection, mini-games for tempo and rhythm tapping, and an initial analysis of the data collected so far. The game presented here is part of the Spot The Odd Song Out game, which is freely available for use on Facebook and on the Web 1 .We present the GWAP method in some detail and a preliminary analysis of data collected. We relate the tapping data to perceptual ratings obtained in previous work. The results suggest that the tapped tempo data collected in a GWAP can be used to predict perceived speed. I toned down the above statement as I understand from the results section that our data are not as good as When averagingthe rhythmic performances of a group of 10 players in the second experiment, the tapping frequency shows a pattern that corresponds to the time signature of the music played. Our experience shows that more effort in design and during runtime is required than in a traditional experiment. Our experiment is still running and available on line.
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| 3. |
- Menkveld, Albert J., et al.
(författare)
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Nonstandard Errors
- 2024
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Ingår i: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Tidskriftsartikel (refereegranskat)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 4. |
- Aranda-Guillén, Maribel, et al.
(författare)
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A polygenic risk score to help discriminate primary adrenal insufficiency of different etiologies.
- 2023
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Ingår i: Journal of internal medicine. - : John Wiley & Sons. - 0954-6820 .- 1365-2796. ; 294:1, s. 96-109
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Tidskriftsartikel (refereegranskat)abstract
- Autoimmune Addison's disease (AAD) is the most common cause of primary adrenal insufficiency (PAI). Despite its exceptionally high heritability, tools to estimate disease susceptibility in individual patients are lacking. We hypothesized that polygenic risk score (PRS) for AAD could help investigate PAI pathogenesis in pediatric patients.We here constructed and evaluated a PRS for AAD in 1223 seropositive cases and 4097 controls. To test its clinical utility, we reevaluated 18 pediatric patients, whose whole genome we also sequenced. We next explored the individual PRS in more than 120 seronegative patients with idiopathic PAI.The genetic susceptibility to AAD-quantified using PRS-was on average 1.5 standard deviations (SD) higher in patients compared with healthy controls (p<2e-16), and 1.2 SD higher in the young patients compared with the old (p=3e-4). Using the novel PRS, we searched for pediatric patients with strikingly low AAD susceptibility and identified cases of monogenic PAI, previously misdiagnosed as AAD. By stratifying seronegative adult patients by autoimmune comorbidities and disease duration we could delineate subgroups of PRS suggesting various disease etiologies.The PRS performed well for case-control differentiation and susceptibility estimation in individual patients. Remarkably, a PRS for AAD holds promise as a means to detect disease etiologies other than autoimmunity.
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| 5. |
- Arnalds, Unnar B., et al.
(författare)
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A new look on the two-dimensional Ising model : thermal artificial spins
- 2016
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- We present a direct experimental investigation of the thermal ordering in an artificial analogue of an asymmetric two-dimensional Ising system composed of a rectangular array of nano-fabricated magnetostatically interacting islands. During fabrication and below a critical thickness of the magnetic material the islands are thermally fluctuating and thus the system is able to explore its phase space. Above the critical thickness the islands freeze-in resulting in an arrested thermalized state for the array. Determining the magnetic state we demonstrate a genuine artificial two-dimensional Ising system which can be analyzed in the context of nearest neighbor interactions.
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| 6. |
- Brantnell, Anders, 1983-, et al.
(författare)
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Barriers and facilitators to the implementation of additive manufacturing in cardiology : A qualitative study
- 2022
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Ingår i: Annals of 3D Printed Medicine. - : Elsevier. - 2666-9641. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Background: Additive manufacturing (AM) is a fast-developing technology with possible applications in car-diology. Existing research has identified two general factors that can influence implementing AM in cardiol-ogy: economics and technology.Objective: In this study we aimed to identify barriers and facilitators to implementing AM in cardiology.Methods: We conducted a multiple case study of two Swedish cardiac surgery departments representingimplementers and non-implementers of AM. We interviewed key stakeholders (n=8) who had been or wereinvolved in implementing AM in cardiology or AM in general at the hospitals: cardiologists, physicians work-ing with AM but not specialized in cardiology such as radiologists, company representatives, and individualsinvolved in the 3D-printing facilities. A combination of an inductive and deductive approach was used to ana-lyze the interviews.Results: Several barriers and facilitators influenced implementing AM in cardiology. Most barriers (n=4) wererelated to innovation factors, whereas most facilitators (n=4) were related to healthcare professionals. No barriers and facilitators were related to patients.Conclusion: Our findings show that AM in cardiology is in its very early phases in both hospitals and mostlythe work of a few individuals. In the two hospitals studied, there were some unique differences in terms ofbarriers that could explain the low level of implementation. These barriers could be important to addresswhen supporting implementation of AM at hospitals where AM use is still low.
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| 7. |
- Bruserud, Oyvind, et al.
(författare)
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A Longitudinal Follow-up of Autoimmune Polyendocrine Syndrome Type 1
- 2016
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Ingår i: Journal of Clinical Endocrinology and Metabolism. - : The Endocrine Society. - 0021-972X .- 1945-7197. ; 101:8, s. 2975-2983
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Tidskriftsartikel (refereegranskat)abstract
- Context: Autoimmune polyendocrine syndrome type 1 (APS1) is a childhood-onset monogenic disease defined by the presence of two of the three major components: hypoparathyroidism, primary adrenocortical insufficiency, and chronic mucocutaneous candidiasis (CMC). Information on longitudinal follow-up of APS1 is sparse. Objective: To describe the phenotypes of APS1 and correlate the clinical features with autoantibody profiles and autoimmune regulator (AIRE) mutations during extended follow-up (1996-2016). Patients: All known Norwegian patients with APS1. Results: Fifty-two patients from 34 families were identified. The majority presented with one of the major disease components during childhood. Enamel hypoplasia, hypoparathyroidism, and CMC were the most frequent components. With age, most patients presented three to five disease manifestations, although some had milder phenotypes diagnosed in adulthood. Fifteen of the patients died during follow-up (median age at death, 34 years) or were deceasedsiblingswithahighprobability of undisclosed APS1. All except three had interferon-omega) autoantibodies, and allhadorgan-specific autoantibodies. The most common AIRE mutation was c.967_979del13, found in homozygosity in 15 patients. A mild phenotype was associated with the splice mutation c.879+1G>A. Primary adrenocortical insufficiency and type 1 diabetes were associated with protective human leucocyte antigen genotypes. Conclusions: Multiple presumable autoimmune manifestations, in particular hypoparathyroidism, CMC, and enamel hypoplasia, should prompt further diagnostic workup using autoantibody analyses (eg, interferon-omega) and AIRE sequencing to reveal APS1, even in adults. Treatment is complicated, and mortality is high. Structured follow-up should be performed in a specialized center.
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| 8. |
- Chulapakorn, Thawatchart, 1988-, et al.
(författare)
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Si-nanoparticle synthesis using ion implantation and MeV ion irradiation
- 2015
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Ingår i: Physica Status Solidi (C) Current Topics in Solid State Physics. - : Wiley-VCH Verlagsgesellschaft. - 1862-6351.
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Tidskriftsartikel (refereegranskat)abstract
- A dielectric matrix with embedded Si-nanoparticles may show strong luminescence depending on nanoparticles size, surface properties, Si-excess concentration and matrix type. Ion implantation of Si ions with energies of a few tens to hundreds of keV in a SiO2 matrix followed by thermal annealing was identified as a powerful method to form such nanoparticles. The aim of the present work is to optimize the synthesis of Si-nanoparticles produced by ion implantation in SiO2 by employing MeV ion irradiation as an additional annealing process. The luminescence properties are measured by spectrally resolved photoluminescence including PL lifetime measurement, while X-ray reflectometry, atomic force microscopy and ion beam analysis are used to characterize the nanoparticle formation process. The results show that the samples implanted at 20%-Si excess atomic concentration display the highest luminescence and that irradiation of 36 MeV 127I ions affects the luminosity in terms of wavelength and intensity. It is also demonstrated that the nanoparticle luminescence lifetime decreases as a function of irradiation fluence.
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| 9. |
- Dave, Vivek Priy, et al.
(författare)
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MicroRNA amplification and detection technologies : opportunities and challenges for point of care diagnostics
- 2018
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Ingår i: Laboratory Investigation. - : Nature Publishing Group. - 0023-6837 .- 1530-0307. ; 99:4, s. 452-469
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Forskningsöversikt (refereegranskat)abstract
- The volume of point of care (POC) testing continues to grow steadily due to the increased availability of easy-to-use devices, thus making it possible to deliver less costly care closer to the patient site in a shorter time relative to the central laboratory services. A novel class of molecules called microRNAs have recently gained attention in healthcare management for their potential as biomarkers for human diseases. The increasing interest of miRNAs in clinical practice has led to an unmet need for assays that can rapidly and accurately measure miRNAs at the POC. However, the most widely used methods for analyzing miRNAs, including Northern blot-based platforms, in situ hybridization, reverse transcription qPCR, microarray, and next-generation sequencing, are still far from being used as ideal POC diagnostic tools, due to considerable time, expertize required for sample preparation, and in terms of miniaturizations making them suitable platforms for centralized labs. In this review, we highlight various existing and upcoming technologies for miRNA amplification and detection with a particular emphasis on the POC testing industries. The review summarizes different miRNA targets and signals amplification-based assays, from conventional methods to alternative technologies, such as isothermal amplification, paper-based, oligonucleotide-templated reaction, nanobead-based, electrochemical signaling-based, and microfluidic chip-based strategies. Based on critical analysis of these technologies, the possibilities and feasibilities for further development of POC testing for miRNA diagnostics are addressed and discussed.
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| 10. |
- Elias Wolff, Federico, et al.
(författare)
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How Levins’ dynamics emerges from a Ricker metapopulation model
- 2016
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Ingår i: Theoretical Ecology. - : Springer Science and Business Media LLC. - 1874-1738 .- 1874-1746. ; 9:2, s. 173-183
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the dynamics of metapopulations close to extinction is of vital importance for management. Levins-like models, in which local patches are treated as either occupied or empty, have been used extensively to explore the extinction dynamics of metapopulations, but they ignore the important role of local population dynamics. In this paper, we consider a stochastic metapopulation model where local populations follow a stochastic, density-dependent dynamics (the Ricker model), and use this framework to investigate the behaviour of the metapopulation on the brink of extinction. We determine under which circumstances the metapopulation follows a time evolution consistent with Levins’ dynamics. We derive analytical expressions for the colonisation and extinction rates (c and e) in Levins-type models in terms of reproduction, survival and dispersal parameters of the local populations, providing an avenue to parameterising Levins-like models from the type of information on local demography that is available for a number of species. To facilitate applying our results, we provide a numerical algorithm for computing c and e.
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