| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
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| 3. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)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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| 4. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 5. |
- Ade, Peter, et al.
(författare)
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The Simons Observatory : science goals and forecasts
- 2019
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :2
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Tidskriftsartikel (refereegranskat)abstract
- The Simons Observatory (SO) is a new cosmic microwave background experiment being built on Cerro Toco in Chile, due to begin observations in the early 2020s. We describe the scientific goals of the experiment, motivate the design, and forecast its performance. SO will measure the temperature and polarization anisotropy of the cosmic microwave background in six frequency bands centered at: 27, 39, 93, 145, 225 and 280 GHz. The initial con figuration of SO will have three small-aperture 0.5-m telescopes and one large-aperture 6-m telescope, with a total of 60,000 cryogenic bolometers. Our key science goals are to characterize the primordial perturbations, measure the number of relativistic species and the mass of neutrinos, test for deviations from a cosmological constant, improve our understanding of galaxy evolution, and constrain the duration of reionization. The small aperture telescopes will target the largest angular scales observable from Chile, mapping approximate to 10% of the sky to a white noise level of 2 mu K-arcmin in combined 93 and 145 GHz bands, to measure the primordial tensor-to-scalar ratio, r, at a target level of sigma(r) = 0.003. The large aperture telescope will map approximate to 40% of the sky at arcminute angular resolution to an expected white noise level of 6 mu K-arcmin in combined 93 and 145 GHz bands, overlapping with the majority of the Large Synoptic Survey Telescope sky region and partially with the Dark Energy Spectroscopic Instrument. With up to an order of magnitude lower polarization noise than maps from the Planck satellite, the high-resolution sky maps will constrain cosmological parameters derived from the damping tail, gravitational lensing of the microwave background, the primordial bispectrum, and the thermal and kinematic Sunyaev-Zel'dovich effects, and will aid in delensing the large-angle polarization signal to measure the tensor-to-scalar ratio. The survey will also provide a legacy catalog of 16,000 galaxy clusters and more than 20,000 extragalactic sources.
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| 6. |
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| 7. |
- Porsbjerg, Celeste M., et al.
(författare)
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Association between pre-biologic T2-biomarker combinations and response to biologics in patients with severe asthma
- 2024
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Ingår i: Frontiers in Immunology. - : Frontiers Media S.A.. - 1664-3224. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: To date, studies investigating the association between pre-biologic biomarker levels and post-biologic outcomes have been limited to single biomarkers and assessment of biologic efficacy from structured clinical trials.Aim: To elucidate the associations of pre-biologic individual biomarker levels or their combinations with pre-to-post biologic changes in asthma outcomes in real-life.Methods: This was a registry-based, cohort study using data from 23 countries, which shared data with the International Severe Asthma Registry (May 2017-February 2023). The investigated biomarkers (highest pre-biologic levels) were immunoglobulin E (IgE), blood eosinophil count (BEC) and fractional exhaled nitric oxide (FeNO). Pre- to approximately 12-month post-biologic change for each of three asthma outcome domains (i.e. exacerbation rate, symptom control and lung function), and the association of this change with pre-biologic biomarkers was investigated for individual and combined biomarkers.Results: Overall, 3751 patients initiated biologics and were included in the analysis. No association was found between pre-biologic BEC and pre-to-post biologic change in exacerbation rate for any biologic class. However, higher pre-biologic BEC and FeNO were both associated with greater post-biologic improvement in FEV1 for both anti-IgE and anti-IL5/5R, with a trend for antiI-IL4R alpha. Mean FEV1 improved by 27-178 mL post-anti-IgE as pre-biologic BEC increased (250 to 1000 cells/mu L), and by 43-216 mL and 129-250 mL post-anti-IL5/5R and - anti- IL4R alpha, respectively along the same BEC gradient. Corresponding improvements along a FeNO gradient (25-100 ppb) were 41-274 mL, 69-207 mL and 148-224 mL for anti-IgE, anti-IL5/5R, and anti-IL4R alpha, respectively. Higher baseline BEC was also associated with lower probability of uncontrolled asthma (OR 0.392; p=0.001) post-biologic for anti-IL5/5R. Pre-biologic IgE was a poor predictor of subsequent pre-to-post-biologic change for all outcomes assessed for all biologics. The combination of BEC + FeNO marginally improved the prediction of post-biologic FEV1 increase (adjusted R-2: 0.751), compared to BEC (adjusted R-2: 0.747) or FeNO alone (adjusted R-2: 0.743) (p=0.005 and <0.001, respectively); however, this prediction was not improved by the addition of IgE.Conclusions: The ability of higher baseline BEC, FeNO and their combination to predict biologic-associated lung function improvement may encourage earlier intervention in patients with impaired lung function or at risk of accelerated lung function decline.
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| 8. |
- Anchordoqui, Luis A., et al.
(författare)
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The Forward Physics Facility : Sites, experiments, and physics potential
- 2022
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Ingår i: Physics reports. - : Elsevier. - 0370-1573 .- 1873-6270. ; 968, s. 1-50
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Tidskriftsartikel (refereegranskat)abstract
- The Forward Physics Facility (FPF) is a proposal to create a cavern with the space and infrastructure to support a suite of far-forward experiments at the Large Hadron Collider during the High Luminosity era. Located along the beam collision axis and shielded from the interaction point by at least 100 m of concrete and rock, the FPF will house experiments that will detect particles outside the acceptance of the existing large LHC experiments and will observe rare and exotic processes in an extremely low-background environment. In this work, we summarize the current status of plans for the FPF, including recent progress in civil engineering in identifying promising sites for the FPF and the experiments currently envisioned to realize the FPF's physics potential. We then review the many Standard Model and new physics topics that will be advanced by the FPF, including searches for long-lived particles, probes of dark matter and dark sectors, high-statistics studies of TeV neutrinos of all three flavors, aspects of perturbative and non-perturbative QCD, and high-energy astroparticle physics.
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| 9. |
- Ariel, Gil, et al.
(författare)
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A multiscale method for stiff ordinary differential equations with resonance
- 2009
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Ingår i: Mathematics of Computation. - 0025-5718 .- 1088-6842. ; 78:266, s. 929-956
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Tidskriftsartikel (refereegranskat)abstract
- A multiscale method for computing the effective behavior of a class of stiff and highly oscillatory ordinary differential equations (ODEs) is presented. The oscillations may be in resonance with one another and thereby generate hidden slow dynamics. The proposed method relies on correctly tracking a set of slow variables whose dynamics is closed up to perturbation, and is sufficient to approximate any variable and functional that are slow under the dynamics of the ODE. This set of variables is detected numerically as a preprocessing step in the numerical methods. Error and complexity estimates are obtained. The advantages of the method is demonstrated with a few examples, including a commonly studied problem of Fermi, Pasta, and Ulam.
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| 10. |
- Ariel, Gil, et al.
(författare)
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A reversible multiscale integration method
- 2009
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Ingår i: Communications in Mathematical Sciences. - : Duke University Press. - 1539-6746 .- 1945-0796. ; 7:3, s. 595-610
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Tidskriftsartikel (refereegranskat)abstract
- A multiscale, time reversible method for computing the effective slow behavior of systems of highly oscillatory ordinary differential equations is presented. The proposed method relies on correctly tracking a set of slow variables that is sufficient to approximate any variable and functional that are slow under the dynamics of the system. The algorithm follows the framework of the heterogeneous multiscale method. The notion of time reversibility in the multiple time-scale setting is discussed. The algorithm requires nontrivial matching between the microscopic state variables and the macroscopic slow ones. Numerical examples show the efficiency of the multiscale method and the advantages of time reversibility.
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| 11. |
- Ariel, Gil, et al.
(författare)
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Gaussian Beam Decomposition of High Frequency Wave Fields Using Expectation-Maximization
- 2011
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Ingår i: Journal of Computational Physics. - : Elsevier. - 0021-9991 .- 1090-2716. ; 230:6, s. 2303-2321
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Tidskriftsartikel (refereegranskat)abstract
- A new numerical method for approximating highly oscillatory wave fields as a superposition of Gaussian beams is presented. The method estimates the number of beams and their parameters automatically. This is achieved by an expectation–maximization algorithm that fits real, positive Gaussians to the energy of the highly oscillatory wave fields and its Fourier transform. Beam parameters are further refined by an optimization procedure that minimizes the difference between the Gaussian beam superposition and the highly oscillatory wave field in the energy norm.
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| 12. |
- Ariel, Gil, et al.
(författare)
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Numerical multiscale methods for coupled oscillators
- 2009
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Ingår i: Multiscale Modeling & simulation. - : Society for Industrial & Applied Mathematics (SIAM). - 1540-3459 .- 1540-3467. ; 7:3, s. 1387-1404
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Tidskriftsartikel (refereegranskat)abstract
- A multiscale method for computing the effective slow behavior of a system of weakly coupled nonlinear planar oscillators is presented. The oscillators may be either in the form of a periodic solution or a stable limit cycle. Furthermore, the oscillators may be in resonance with one another and thereby generate some hidden slow dynamics. The proposed method relies on correctly tracking a set of slow variables that is sufficient to approximate any variable and functional that are slow under the dynamics of the ordinary differential equation. The technique is more efficient than existing methods, and its advantages are demonstrated with examples. The algorithm follows the framework of the heterogeneous multiscale method.
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| 13. |
- Ariel, G., et al.
(författare)
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Parareal multiscale methods for highly oscillatory dynamical systems
- 2016
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Ingår i: SIAM Journal on Scientific Computing. - : Society for Industrial and Applied Mathematics Publications. - 1064-8275 .- 1095-7197. ; 38:6, s. A3540-A3564
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Tidskriftsartikel (refereegranskat)abstract
- We introduce a new strategy for coupling the parallel in time (parareal) iterative methodology with multiscale integrators. Following the parareal framework, the algorithm computes a low-cost approximation of all slow variables in the system using an appropriate multiscale integrator, which is refined using parallel fine scale integrations. Convergence is obtained using an alignment algorithm for fast phase-like variables. The method may be used either to enhance the accuracy and range of applicability of the multiscale method in approximating only the slow variables, or to resolve all the state variables. The numerical scheme does not require that the system is split into slow and fast coordinates. Moreover, the dynamics may involve hidden slow variables, for example, due to resonances. We propose an alignment algorithm for almost-periodic solutions, in which case convergence of the parareal iterations is proved. The applicability of the method is demonstrated in numerical examples.
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| 14. |
- Atle, Andreas, 1972-
(författare)
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Approximations of Integral Equations for WaveScattering
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Wave scattering is the phenomenon in which a wave field interacts with physical objects. An incoming wave is scattered at the surface of the object and a scattered wave is produced. Common practical cases are acoustic, electromagnetic and elastic wave scattering. The numerical simulation of the scattering process is important, for example, in noise control, antenna design, prediction of radar cross sections and nondestructive testing.Important classes of numerical methods for accurate simulation of scattering are based on integral representations of the wave fields and theses representations require the knowledge of potentials on the surfaces of the scattering objects. The potential is typically computed by a numerical approximation of an integral equation that is defined on the surface. We first develop such numerical methods in time domain for the scalar wave equation. The efficiency of the techniques are improved by analytic quadrature and in some cases by local approximation of the potential.Most scattering simulations are done for harmonic or single frequency waves. In the electromagnetic case the corresponding integral equation method is called the method of moments. This numerical approximation is computationally very costly for high frequency waves. A simplification is suggested by physical optics, which directly gives an approximation of the potential without the solution of an integral equation. Physical optics is however only accurate for very high frequencies.In this thesis we improve the accuracy in the physical optics approximation of scalar waves by basing the computation of the potential on the theory of radiation boundary conditions. This theory describes the local coupling of derivatives in the wave field and if it is applied at the surface of the scattering object it generates an expression for the unknown potential. The full wave field is then computed as for other integral equation methods.The new numerical techniques are analyzed mathematically and their efficiency is established in a sequence of numerical experiments. The new on surface radiation conditions give, for example, substantial improvement in the estimation of the scattered waves in the acoustic case. This numerical experiment corresponds to radar cross-section estimation in the electromagnetic case.
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| 15. |
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| 16. |
- Chen, C., et al.
(författare)
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An implicit boundary integral method for interfaces evolving by Mullins-Sekerka dynamics
- 2017
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Ingår i: Springer Proceedings in Mathematics and Statistics. - Cham : Springer New York LLC. - 9783319667621 ; , s. 1-21
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Konferensbidrag (refereegranskat)abstract
- We present an algorithm for computing the nonlinear interface dynamics of the Mullins-Sekerka model for interfaces that are defined implicitly (e.g. by a level set function) using integral equations. The computation of the dynamics involves solving Laplace’s equation with Dirichlet boundary conditions on multiply connected and unbounded domains and propagating the interface using a normal velocity obtained from the solution of the PDE at each time step. Our method is based on a simple formulation for implicit interfaces, which rewrites boundary integrals as volume integrals over the entire space. The resulting algorithm thus inherits the benefits of both level set methods and boundary integral methods to simulate the nonlocal front propagation problem with possible topological changes. We present numerical results in both two and three dimensions to demonstrate the effectiveness of the algorithm.
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| 17. |
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| 18. |
- Chen, Hao Yu, et al.
(författare)
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Association of FADS1/2 Locus Variants and Polyunsaturated Fatty Acids With Aortic Stenosis
- 2020
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Ingår i: JAMA cardiology. - : American Medical Association (AMA). - 2380-6583 .- 2380-6591. ; 5:6, s. 694-702
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Tidskriftsartikel (refereegranskat)abstract
- Importance: Aortic stenosis (AS) has no approved medical treatment. Identifying etiological pathways for AS could identify pharmacological targets.Objective: To identify novel genetic loci and pathways associated with AS.Design, Setting, and Participants: This genome-wide association study used a case-control design to evaluate 44 703 participants (3469 cases of AS) of self-reported European ancestry from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort (from January 1, 1996, to December 31, 2015). Replication was performed in 7 other cohorts totaling 256 926 participants (5926 cases of AS), with additional analyses performed in 6942 participants from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Follow-up biomarker analyses with aortic valve calcium (AVC) were also performed. Data were analyzed from May 1, 2017, to December 5, 2019.Exposures: Genetic variants (615 643 variants) and polyunsaturated fatty acids (ω-6 and ω-3) measured in blood samples.Main Outcomes and Measures: Aortic stenosis and aortic valve replacement defined by electronic health records, surgical records, or echocardiography and the presence of AVC measured by computed tomography.Results: The mean (SD) age of the 44 703 GERA participants was 69.7 (8.4) years, and 22 019 (49.3%) were men. The rs174547 variant at the FADS1/2 locus was associated with AS (odds ratio [OR] per C allele, 0.88; 95% CI, 0.83-0.93; P = 3.0 × 10-6), with genome-wide significance after meta-analysis with 7 replication cohorts totaling 312 118 individuals (9395 cases of AS) (OR, 0.91; 95% CI, 0.88-0.94; P = 2.5 × 10-8). A consistent association with AVC was also observed (OR, 0.91; 95% CI, 0.83-0.99; P = .03). A higher ratio of arachidonic acid to linoleic acid was associated with AVC (OR per SD of the natural logarithm, 1.19; 95% CI, 1.09-1.30; P = 6.6 × 10-5). In mendelian randomization, increased FADS1 liver expression and arachidonic acid were associated with AS (OR per unit of normalized expression, 1.31 [95% CI, 1.17-1.48; P = 7.4 × 10-6]; OR per 5-percentage point increase in arachidonic acid for AVC, 1.23 [95% CI, 1.01-1.49; P = .04]; OR per 5-percentage point increase in arachidonic acid for AS, 1.08 [95% CI, 1.04-1.13; P = 4.1 × 10-4]).Conclusions and Relevance: Variation at the FADS1/2 locus was associated with AS and AVC. Findings from biomarker measurements and mendelian randomization appear to link ω-6 fatty acid biosynthesis to AS, which may represent a therapeutic target.
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| 19. |
- Chu, J., et al.
(författare)
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Volumetric variational principles for a class of partial differential equations defined on surfaces and curves : In memory of Heinz-Otto Kreiss
- 2018
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Ingår i: Research in Mathematical Sciences. - : Springer. - 2522-0144 .- 2197-9847. ; 5:2
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we propose simple numerical algorithms for partial differential equations (PDEs) defined on closed, smooth surfaces (or curves). In particular, we consider PDEs that originate from variational principles defined on the surfaces; these include Laplace–Beltrami equations and surface wave equations. The approach is to systematically formulate extensions of the variational integrals and derive the Euler–Lagrange equations of the extended problem, including the boundary conditions that can be easily discretized on uniform Cartesian grids or adaptive meshes. In our approach, the surfaces are defined implicitly by the distance functions or by the closest point mapping. As such extensions are not unique, we investigate how a class of simple extensions can influence the resulting PDEs. In particular, we reduce the surface PDEs to model problems defined on a periodic strip and the corresponding boundary conditions and use classical Fourier and Laplace transform methods to study the well-posedness of the resulting problems. For elliptic and parabolic problems, our boundary closure mostly yields stable algorithms to solve nonlinear surface PDEs. For hyperbolic problems, the proposed boundary closure is unstable in general, but the instability can be easily controlled by either adding a higher-order regularization term or by periodically but infrequently “reinitializing” the computed solutions. Some numerical examples for each representative surface PDEs are presented.
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| 20. |
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| 21. |
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| 22. |
- Engquist, Bjoern, et al.
(författare)
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Fast sweeping methods for hyperbolic systems of conservation laws at steady state II
- 2015
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Ingår i: Journal of Computational Physics. - : Elsevier BV. - 0021-9991 .- 1090-2716. ; 286, s. 70-86
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Tidskriftsartikel (refereegranskat)abstract
- The idea of using fast sweeping methods for solving stationary systems of conservation laws has previously been proposed for efficiently computing solutions with sharp shocks. We further develop these methods to allow for a more challenging class of problems including problems with sonic points, shocks originating in the interior of the domain, rarefaction waves, and two-dimensional systems. We show that fast sweeping methods can produce higher-order accuracy. Computational results validate the claims of accuracy, sharp shock curves, and optimal computational efficiency.
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| 23. |
- Figueiredo, I. N., et al.
(författare)
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Colonic Polyp Identification Using Pareto Depth Anomaly Detection Algorithm
- 2019
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Ingår i: Lecture Notes in Computational Vision and Biomechanics. - Cham : Springer Netherlands. ; , s. 3-11
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Konferensbidrag (refereegranskat)abstract
- Colon cancer prevention, diagnosis, and prognosis are directly related to the identification of colonic polyps, in colonoscopy video sequences. In addition, diagnosing colon cancer in the early stages improves significantly the chance of surviving and effective treatment. Due to the large number of images that come from colonoscopy, the identification of polyps needs to be automated for effciency. In this paper, we propose a strategy for automatic polyp recognition, based on a recent multi-objective anomaly detection concept, which itself is based on Pareto Depth Analysis (PDA). Clinically, in medical images, polyps are diagnosed based on a few criteria, such as texture, shape and color. Few works use multi-criteria classification in a systematic way for polyp detection. In the present paper we use a PDA approach, to act as a binary classifier for the identification of colonic polyps. The results obtained in a medical dataset, of conventional colonoscopy images, consisting of short videos from 34 different patients, and 34 different polyps, with a total of 1360 different polyp frames, confirm that the proposed method clearly outperforms the single performance of each criterion.
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| 24. |
- Figueiredo, Isabel N., et al.
(författare)
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Dissimilarity Measure of Consecutive Frames in Wireless Capsule Endoscopy Videos : a way of searching for abnormalities
- 2017
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Ingår i: 2017 IEEE 30TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS (CBMS). - : IEEE. - 9781538617106 ; , s. 702-707
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Konferensbidrag (refereegranskat)abstract
- In a previous work we have shown that the curve representing the dissimilarity measure between consecutive frames of a wireless capsule endoscopic video of the small bowel, obtained by means of an image registration method, can be regarded as a rough indicator of the speed of the capsule, and simultaneously, it is also a valuable auxiliary medical tool. In effect, this curve enables a global and fast interpretation of the video, in the sense that it clearly divides the video frames into two main categories: consecutive frames with similar content, which correspond to low values in the curve, and consecutive frames displaying abrupt changes in the image content, which are depicted by peaks, i.e. high values, in the curve. As the main goal of a wireless capsule video examination consists in searching for abnormal features in the images, the purpose of the present work is to analyse whether this curve can also be used to search, quickly, for abnormalities. The experiments performed focus on bleeding identification in small bowel images.
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| 25. |
- Figueiredo, Isabel N., et al.
(författare)
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Fast colonic polyp detection using a Hamilton-Jacobi approach to non-dominated sorting
- 2020
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Ingår i: Biomedical Signal Processing and Control. - : Elsevier. - 1746-8094 .- 1746-8108. ; 61
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes a novel method for fast colonic polyp detection in colonoscopy images. Firstly, polyp detection is formulated as a similarity-based anomaly detection method, which formally involves non-dominated sorting based on multiple objectives. The chosen objectives rely on the main physical and visible differences, observed in colonoscopy images, between regions containing colonic polyps and the surrounding normal mucosa. These differences are defined primarily according to the contrast in shape, texture, and color. Secondly, as non-dominated sorting is of combinatorial nature and is costly to compute, it is replaced by a fast algorithm that approximates the sorting in the continuum limit. The fast algorithm involves numerical solutions to a particular Hamilton-Jacobi equation. The proposed similarity-based anomaly detection is thus reformulated into a fast polyp detection method. Several experiments were conducted with a proprietary medical data set, containing 1640 instances of 41 different polyps. The results show that the proposed Hamilton-Jacobi approach to non-dominated sorting speeds up the non-dominated sorting procedure, by more than 500%, and, when compared with other existing methods, it is also faster without lost of accuracy. Moreover, the tests conducted for streaming data, reveal an outstanding performance, in terms of sensitivity and specificity, as well as, a fast auto-adaptability, which demonstrate the power of the proposed approach towards a real-time and automatic detection, undoubtedly beneficial for clinical practice.
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