| 1. |
- Asadzadeh, Mohammad, 1952, et al.
(författare)
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Convergence of Finite Volume Scheme for a Three-Dimensional Poisson Equation
- 2014
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Ingår i: Journal of Mathematical Sciences. - : Springer-Verlag New York. - 1072-3374 .- 1573-8795. ; 202:2, s. 130-153
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Tidskriftsartikel (refereegranskat)abstract
- We construct and analyze a finite volume scheme for numerical solution of a three-dimensional Poisson equation. We derive optimal convergence rates in the discrete H1 norm and sub-optimal convergence in the maximum norm, where we use the maximal available regularity of the exact solution and minimal smoothness requirement on the source term. The theoretical results are justified through implementing some canonical examples in 3D.
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| 2. |
- Bartoszek, Krzysztof, et al.
(författare)
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A consistent estimator of the evolutionary rate
- 2015
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 371, s. 69-78
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Tidskriftsartikel (refereegranskat)abstract
- We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate 2, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance sigma(2). In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator 4 of the evolutionary rate rho(2) - sigma(2)/lambda. The estimator R-n(2) is proportional to the sample variance S-n(2) computed from n trait values. We find an approximate formula for the standard error of R-n(2), based on a neat asymptotic relation for the variance of S-n(2). (C) 2015 Elsevier Ltd. All rights reserved.
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| 3. |
- Bartoszek, Krzysztof, 1984, et al.
(författare)
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A phylogenetic comparative method for studying multivariate adaptation
- 2012
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 314, s. 204-215
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic comparative methods have been limited in the way they model adaptation. Although some progress has been made, there are still no methods that can fully account for coadaptation between traits. Based on Ornstein–Uhlenbeck (OU) models of adaptive evolution, we present a method, with R implementation, in which multiple traits evolve both in response to each other and, as in previous OU models, to fixed or randomly evolving predictor variables. We present the interpretation of the model parameters in terms of evolutionary and optimal regressions enabling the study of allometric and adaptive relationships between traits. To illustrate the method we reanalyze a data set of antler and body-size evolution in deer (Cervidae).
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| 4. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Critical case stochastic phylogenetic tree model via the Laplace transform
- 2014
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Ingår i: Demonstratio Matematicae. - : De Gruyter. - 0420-1213 .- 2391-4661. ; 47:2, s. 474-481
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Tidskriftsartikel (refereegranskat)abstract
- Birth-and-death models are now a common mathematical tool to describe branching patterns observed in real-world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth-and-death model that is compatible with phylogenetic trees of both in uenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the death rate. This is a non-trivial situation and to study its asymptotic behaviour we employed the Laplace transform. With this we correct the proof of Liggett and Schinazi (2009) in the critical case.
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| 5. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Phylogenetic confidence intervals for the optimal trait value
- 2015
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Ingår i: Journal of Applied Probability. - : Cambridge University Press (CUP). - 0021-9002 .- 1475-6072. ; 52:4, s. 1115-1132
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Tidskriftsartikel (refereegranskat)abstract
- We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein-Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the sample mean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean is approximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.
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| 6. |
- Bartoszek, Krzysztof
(författare)
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Quantifying the effects of anagenetic and cladogenetic evolution
- 2014
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Ingår i: Mathematical Biosciences. - : Elsevier BV. - 0025-5564 .- 1879-3134. ; 254, s. 42-57
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Tidskriftsartikel (refereegranskat)abstract
- An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.
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| 7. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Time to a single hybridization event in a group of species with unknown ancestral history
- 2013
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 322, s. 1-6
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Tidskriftsartikel (refereegranskat)abstract
- We consider a stochastic process for the generation of species which combines a Yule process with a simple model for hybridization between pairs of co-existent species. We assume that the origin of the process, when there was one species, occurred at an unknown time in the past, and we condition the process on producing n species via the Yule process and a single hybridization event. We prove results about the distribution of the time of the hybridization event. In particular we calculate a formula for all moments, and show that under various conditions, the distribution tends to an exponential with rate twice that of the birth rate for the Yule process.
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| 8. |
- Berman, Anne H., et al.
(författare)
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Clinician experiences of healthy lifestyle promotion and perceptions of digital interventions as complementary tools for lifestyle behavior change in primary care
- 2018
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Ingår i: Bmc Family Practice. - : Springer Science and Business Media LLC. - 1471-2296. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Evidence-based practice for healthy lifestyle promotion in primary health care is supported internationally by national policies and guidelines but implementation in routine primary health care has been slow. Referral to digital interventions could lead to a larger proportion of patients accessing structured interventions for healthy lifestyle promotion, but such referral might have unknown implications for clinicians with patients accessing such interventions. This qualitative study aimed to explore the perceptions of clinicians in primary care on healthy lifestyle promotion with or without digital screening and intervention. Methods: Focus group interviews were conducted at 10 primary care clinics in Sweden with clinicians from different health professions. Transcribed interviews were analyzed using content analysis, with inspiration from a phenomenological-hermeneutic method involving naive understanding, structural analysis and comprehensive understanding. Results: Two major themes captured clinicians' perceptions on healthy lifestyle promotion: 1) the need for structured professional practice and 2) deficient professional practice as a hinder for implementation. Sub-themes in theme 1 were striving towards professionalism, which for participants meant working in a standardized fashion, with replicable routines regardless of clinic, as well as being able to monitor statistics on individual patient and group levels; and embracing the future with critical optimism, meaning expecting to develop professionally but also being concerned about the consequences of integrating digital tools into primary care, particularly regarding the importance of personal interaction between patient and provider. For theme 2, sub-themes were being in an unmanageable situation, meaning not being able to do what is perceived as best for the patient due to lack of time and resources; and following one's perception, meaning working from a gut feeling, which for our participants also meant deviating from clinical routines. Conclusions: In efforts to increase evidence-based practice and lighten the burden of clinicians in primary care, decision-and policy-makers planning the introduction of digital tools for healthy lifestyle promotion will need to explicitly define their role as complements to face-to-face encounters. Our overriding hope is that this study will contribute to maintaining meaningfulness in the patient-clinician encounter, when digital tools are added to facilitate patient behavior change of unhealthy lifestyle behaviors.
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| 9. |
- Fagman, Erika, et al.
(författare)
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High-quality annotations for deep learning enabled plaque analysis in SCAPIS cardiac computed tomography angiography
- 2023
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Ingår i: Heliyon. - : Elsevier BV. - 2405-8440. ; 9:5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Plaque analysis with coronary computed tomography angiography (CCTA) is a promising tool to identify high risk of future coronary events. The analysis process is time-consuming, and requires highly trained readers. Deep learning models have proved to excel at similar tasks, however, training these models requires large sets of expert-annotated training data. The aims of this study were to generate a large, high-quality annotated CCTA dataset derived from Swedish CArdioPulmonary BioImage Study (SCAPIS), report the reproducibility of the annotation core lab and describe the plaque characteristics and their association with established risk factors.Methods and results: The coronary artery tree was manually segmented using semi-automatic software by four primary and one senior secondary reader. A randomly selected sample of 469 subjects, all with coronary plaques and stratified for cardiovascular risk using the Systematic Coronary Risk Evaluation (SCORE), were analyzed. The reproducibility study (n = 78) showed an agreement for plaque detection of 0.91 (0.84-0.97). The mean percentage difference for plaque volumes was-0.6% the mean absolute percentage difference 19.4% (CV 13.7%, ICC 0.94). There was a positive correlation between SCORE and total plaque volume (rho = 0.30, p < 0.001) and total low attenuation plaque volume (rho = 0.29, p < 0.001).Conclusions: We have generated a CCTA dataset with high-quality plaque annotations showing good reproducibility and an expected correlation between plaque features and cardiovascular risk. The stratified data sampling has enriched high-risk plaques making the data well suited as training, validation and test data for a fully automatic analysis tool based on deep learning.
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| 10. |
- Hansen, T. F., et al.
(författare)
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Interpreting the Evolutionary Regression: The Interplay Between Observational and Biological Errors in Phylogenetic Comparative Studies
- 2012
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Ingår i: Systematic Biology. - Oxford : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 61:3, s. 413-425
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Tidskriftsartikel (refereegranskat)abstract
- Regressions of biological variables across species are rarely perfect. Usually, there are residual deviations from the estimated model relationship, and such deviations commonly show a pattern of phylogenetic correlations indicating that they have biological causes. We discuss the origins and effects of phylogenetically correlated biological variation in regression studies. In particular, we discuss the interplay of biological deviations with deviations due to observational or measurement errors, which are also important in comparative studies based on estimated species means. We show how bias in estimated evolutionary regressions can arise from several sources, including phylogenetic inertia and either observational or biological error in the predictor variables. We show how all these biases can be estimated and corrected for in the presence of phylogenetic correlations. We present general formulas for incorporating measurement error in linear models with correlated data. We also show how alternative regression models, such as major axis and reduced major axis regression, which are often recommended when there is error in predictor variables, are strongly biased when there is biological variation in any part of the model. We argue that such methods should never be used to estimate evolutionary or allometric regression slopes.
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