| 1. |
- Kuehlewein, Laura, et al.
(författare)
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Clinical phenotype and course of PDE6A-associated retinitis pigmentosa disease, characterized in preparation for a gene supplementation trial
- 2020
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Ingår i: JAMA Ophthalmology. - : American Medical Association (AMA). - 2168-6165. ; 138:12, s. 1241-1250
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE Treatment trials require sound knowledge on the natural course of disease. OBJECTIVE To assess clinical features, genetic findings, and genotype-phenotype correlations in patients with retinitis pigmentosa (RP) associated with biallelic sequence variations in the PDE6A gene in preparation for a gene supplementation trial. DESIGN, SETTING, AND PARTICIPANTS This prospective, longitudinal, observational cohort study was conducted from January 2001 to December 2019 in a single center (Centre for Ophthalmology of the University of Tübingen, Germany) with patients recruited multinationally from 12 collaborating European tertiary referral centers. Patients with retinitis pigmentosa, sequence variants in PDE6A, and the ability to provide informed consent were included. EXPOSURES Comprehensive ophthalmological examinations; validation of compound heterozygosity and biallelism by familial segregation analysis, allelic cloning, or assessment of next-generation sequencing-read data, where possible. MAIN OUTCOMES AND MEASURES Genetic findings and clinical features describing the entire cohort and comparing patients harboring the 2 most common disease-causing variants in a homozygous state (c.304C>A;p.(R102S) and c.998 + 1G>A;p.?). RESULTS Fifty-seven patients (32 female patients [56%]; mean [SD], 40 [14] years) from 44 families were included. All patients completed the study. Thirty patients were homozygous for disease-causing alleles. Twenty-seven patients were heterozygous for 2 different PDE6A variants each. The most frequently observed alleles were c.304C>A;p.(R102S), c.998 + 1G>A;p.?, and c.2053G>A;p.(V685M). The mean (SD) best-corrected visual acuity was 0.43 (0.48) logMAR (Snellen equivalent, 20/50). The median visual field area with object III4e was 660 square degrees (5th and 95th percentiles, 76 and 11 019 square degrees; 25th and 75th percentiles, 255 and 3923 square degrees). Dark-adapted and light-adapted full-field electroretinography showed no responses in 88 of 108 eyes (81.5%). Sixty-nine of 108 eyes (62.9%) showed additional findings on optical coherence tomography imaging (eg, cystoid macular edema or macular atrophy). The variant c.998 + 1G>A;p.? led to a more severe phenotype when compared with the variant c.304C>A;p.(R102S). CONCLUSIONS AND RELEVANCE Seventeen of the PDE6A variants found in these patients appeared to be novel. Regarding the clinical findings, disease was highly symmetrical between the right and left eyes and visual impairment was mild or moderate in 90% of patients, providing a window of opportunity for gene therapy.
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| 2. |
- Al Abri, Seif, et al.
(författare)
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Tools to implement the World Health Organization End TB Strategy: Addressing common challenges in high and low endemic countries
- 2020
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Ingår i: International Journal of Infectious Diseases. - : ELSEVIER SCI LTD. - 1201-9712 .- 1878-3511. ; 92, s. S60-S68
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Tidskriftsartikel (refereegranskat)abstract
- Aim: The purpose of this viewpoint is to summarize the advantages and constraints of the tools and strategies available for reducing the annual incidence of tuberculosis (TB) by implementing the World Health Organization (WHO) End TB Strategy and the linked WHO TB Elimination Framework, with special reference to Oman. Methods: The case-study was built based on the presentations and discussions at an international workshop on TB elimination in low incidence countries organized by the Ministry of Health, Oman, which took place from September 5 to September 7, 2019, and supported by the WHO and European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Results: Existing tools were reviewed, including the screening of migrants for latent TB infection (LTBI) with interferon-gamma release assays, clinical examination for active pulmonary TB (APTB) including chest X-rays, organization of laboratory services, and the existing centres for mandatory health examination of pre-arrival or arriving migrants, including examination for APTB. The need for public-private partnerships to handle the burden of screening arriving migrants for active TB was discussed at length and different models for financing were reviewed. Conclusions: In a country with a high proportion of migrants from high endemic countries, screening for LTBI is of high priority. Molecular typing and the development of public-private partnerships are needed. (C) 2020 Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.
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| 3. |
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| 4. |
- Andersson Naesseth, Christian, et al.
(författare)
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Capacity estimation of two-dimensional channels using Sequential Monte Carlo
- 2014
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Ingår i: 2014 IEEE Information Theory Workshop. ; , s. 431-435
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Konferensbidrag (refereegranskat)abstract
- We derive a new Sequential-Monte-Carlo-based algorithm to estimate the capacity of two-dimensional channel models. The focus is on computing the noiseless capacity of the 2-D (1, ∞) run-length limited constrained channel, but the underlying idea is generally applicable. The proposed algorithm is profiled against a state-of-the-art method, yielding more than an order of magnitude improvement in estimation accuracy for a given computation time.
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| 5. |
- Andersson Naesseth, Christian, et al.
(författare)
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High-Dimensional Filtering Using Nested Sequential Monte Carlo
- 2019
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Ingår i: IEEE Transactions on Signal Processing. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1053-587X .- 1941-0476. ; 67:16, s. 4177-4188
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Tidskriftsartikel (refereegranskat)abstract
- Sequential Monte Carlo (SMC) methods comprise one of the most successful approaches to approximate Bayesian filtering. However, SMC without a good proposal distribution can perform poorly, in particular in high dimensions. We propose nested sequential Monte Carlo, a methodology that generalizes the SMC framework by requiring only approximate, properly weighted, samples from the SMC proposal distribution, while still resulting in a correctSMCalgorithm. This way, we can compute an "exact approximation" of, e. g., the locally optimal proposal, and extend the class of models forwhichwe can perform efficient inference using SMC. We showimproved accuracy over other state-of-the-art methods on several spatio-temporal state-space models.
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| 6. |
- Andersson Naesseth, Christian, 1986-
(författare)
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Machine learning using approximate inference : Variational and sequential Monte Carlo methods
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Automatic decision making and pattern recognition under uncertainty are difficult tasks that are ubiquitous in our everyday life. The systems we design, and technology we develop, requires us to coherently represent and work with uncertainty in data. Probabilistic models and probabilistic inference gives us a powerful framework for solving this problem. Using this framework, while enticing, results in difficult-to-compute integrals and probabilities when conditioning on the observed data. This means we have a need for approximate inference, methods that solves the problem approximately using a systematic approach. In this thesis we develop new methods for efficient approximate inference in probabilistic models.There are generally two approaches to approximate inference, variational methods and Monte Carlo methods. In Monte Carlo methods we use a large number of random samples to approximate the integral of interest. With variational methods, on the other hand, we turn the integration problem into that of an optimization problem. We develop algorithms of both types and bridge the gap between them.First, we present a self-contained tutorial to the popular sequential Monte Carlo (SMC) class of methods. Next, we propose new algorithms and applications based on SMC for approximate inference in probabilistic graphical models. We derive nested sequential Monte Carlo, a new algorithm particularly well suited for inference in a large class of high-dimensional probabilistic models. Then, inspired by similar ideas we derive interacting particle Markov chain Monte Carlo to make use of parallelization to speed up approximate inference for universal probabilistic programming languages. After that, we show how we can make use of the rejection sampling process when generating gamma distributed random variables to speed up variational inference. Finally, we bridge the gap between SMC and variational methods by developing variational sequential Monte Carlo, a new flexible family of variational approximations.
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| 7. |
- Andersson Naesseth, Christian, et al.
(författare)
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Nested Sequential Monte Carlo Methods
- 2015
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Ingår i: Proceedings of The 32nd International Conference on Machine Learning. - : Journal of Machine Learning Research (Online). - 9781510810587 ; , s. 1292-1301
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Konferensbidrag (refereegranskat)abstract
- We propose nested sequential Monte Carlo (NSMC), a methodology to sample from sequences of probability distributions, even where the random variables are high-dimensional. NSMC generalises the SMC framework by requiring only approximate, properly weighted, samples from the SMC proposal distribution, while still resulting in a correct SMC algorithm. Furthermore, NSMC can in itself be used to produce such properly weighted samples. Consequently, one NSMC sampler can be used to construct an efficient high-dimensional proposal distribution for another NSMC sampler, and this nesting of the algorithm can be done to an arbitrary degree. This allows us to consider complex and high-dimensional models using SMC. We show results that motivate the efficacy of our approach on several filtering problems with dimensions in the order of 100 to 1 000.
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| 8. |
- Andersson Naesseth, Christian, et al.
(författare)
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Sequential Monte Carlo for Graphical Models
- 2014
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Ingår i: Advances in Neural Information Processing Systems. ; , s. 1862-1870
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Konferensbidrag (refereegranskat)abstract
- We propose a new framework for how to use sequential Monte Carlo (SMC) algorithms for inference in probabilistic graphical models (PGM). Via a sequential decomposition of the PGM we find a sequence of auxiliary distributions defined on a monotonically increasing sequence of probability spaces. By targeting these auxiliary distributions using SMC we are able to approximate the full joint distribution defined by the PGM. One of the key merits of the SMC sampler is that it provides an unbiased estimate of the partition function of the model. We also show how it can be used within a particle Markov chain Monte Carlo framework in order to construct high-dimensional block-sampling algorithms for general PGMs.
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| 9. |
- Andersson, Viktoria, et al.
(författare)
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The In vitro Activity of Carbapenems Alone and in Combination with β-lactamase Inhibitors against Difficult-to-treat Mycobacteria; Mycobacterium tuberculosis, Mycobacterium abscessus, and Mycobacterium avium Complex: A Systematic Review
- 2023
-
Ingår i: INTERNATIONAL JOURNAL OF MYCOBACTERIOLOGY. - : WOLTERS KLUWER MEDKNOW PUBLICATIONS. - 2212-5531 .- 2212-554X. ; 12:3, s. 211-225
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Forskningsöversikt (refereegranskat)abstract
- Difficult-to-treat mycobacterial infections are increasing globally. There is an urgent need of new treatment alternatives for multidrug-resistant Mycobacterium tuberculosis (MTB), as well as nontuberculous mycobacteria such as the Mycobacterium abscessus complex (MABC) and Mycobacterium avium complex (MAC). Recently, new carbapenems and combinations of carbapenems with beta-lactamase inhibitors have become available, but activity data in vitro against mycobacteria are so far scarce. Therefore, we performed a systematic review collating the minimum inhibitory concentrations (MICs) of carbapenems, with or without a beta-lactamase inhibitors for MTB, MABC, and MAC. The databases PubMed and Web of Science were searched for the relevant articles in English up until September 21, 2022. Screening of studies was performed by two independent reviewers. MIC data by recommended methods with at least five individual MICs were included. Data were reported as MIC range, MIC50, modal MIC, and/or histograms when individual MICs were available. The study protocol was registered at PROSPERO (CRD42021258537). After screening, a total of 75 studies with MIC data for carbapenems with or without beta-lactamase inhibitors were included in the review. For MTB, the oral carbapenem tebipenem combined with the beta-lactamase inhibitor clavulanic acid resulted in the most significant reduction of MICs. For MABC, the addition of avibactam to tebipenem resulted in a 64-fold reduction of modal MIC. Data were insufficient for the analysis of MAC. Carbapenems, and in particular the novel oral compound tebipenem, in combination with clavulanic acid for MTB and avibactam for MABC may be an untapped potential for difficult-to-treat mycobacterial infections.
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| 10. |
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| 11. |
- Cohen, Adam, et al.
(författare)
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The global prevalence of latent tuberculosis: a systematic review and meta-analysis
- 2019
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Ingår i: European Respiratory Journal. - : EUROPEAN RESPIRATORY SOC JOURNALS LTD. - 0903-1936 .- 1399-3003. ; 54:3
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Forskningsöversikt (refereegranskat)abstract
- In 1999, the World Health Organization (WHO) estimated that one-third of the worlds population had latent tuberculosis infection (LTBI), which was recently updated to one-fourth. However, this is still based on controversial assumptions in combination with tuberculin skin test (TST) surveys. Interferon-gamma release assays (IGRAs) with a higher specificity than TST have since been widely implemented, but never used to estimate the global LTBI prevalence. We conducted a systematic review and meta-analysis of LTBI estimates based on both IGRA and TST results published between 2005 and 2018. Regional and global estimates of LTBI prevalence were calculated. Stratification was performed for low, intermediate and high TB incidence countries and a pooled estimate for each area was calculated using a random effects model. Among 3280 studies screened, we included 88 studies from 36 countries with 41 IGRA (n=67 167) and 67 TST estimates (n=284 644). The global prevalence of LTBI was 24.8% (95% CI 19.7-30.0%) and 21.2% (95% CI 17.9-24.4%), based on IGRA and a 10-mm TST cut-off, respectively. The prevalence estimates correlated well to WHO incidence rates (Rs=0.70, pamp;lt;0.001). In the first study of the global prevalence of LTBI derived from both IGRA and TST surveys, we found that one-fourth of the worlds population is infected. This is of relevance, as both tests, although imperfect, are used to identify individuals eligible for preventive therapy. Enhanced efforts are needed targeting the large pool of latently infected individuals, as this constitutes an enormous source of potential active tuberculosis.
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| 12. |
- Dahl, Victor Naestholt, et al.
(författare)
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Global trends of pulmonary infections with nontuberculous mycobacteria: a systematic review
- 2022
-
Ingår i: International Journal of Infectious Diseases. - : Elsevier. - 1201-9712 .- 1878-3511. ; 125, s. 120-131
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Forskningsöversikt (refereegranskat)abstract
- Objectives: To describe the global trends of pulmonary nontuberculous mycobacteria (NTM) infection and disease.Methods: A systematic review of studies including culture-based NTM data over time. Studies reporting on pulmonary NTM infection and/or disease were included. Information on the use of guideline-based criteria for disease were collected, in which, infection is defined as the absence of symptoms and radiological findings compatible with NTM pulmonary disease. The trends of change for incidence/prevalence were evaluated using linear regressions, and the corresponding pooled estimates were calculated.Results: Most studies reported increasing pulmonary NTM infection (82.1%) and disease (66.7%) trends. The overall annual rate of change for NTM infection and disease per 100,000 persons/year was 4.0% (95% confidence interval [CI]: 3.2-4.8) and 4.1% (95% CI: 3.2-5.0), respectively. For absolute numbers of NTM infection and disease, the overall annual change was 2.0 (95% CI: 1.6-2.3) and 0.5 (95% CI: 0.3-0.7), respectively. An increasing trend was also seen for Mycobacterium avium complex infection (n = 15/19, 78.9%) and disease (n = 10/12, 83.9%) and for Mycobacterium abscessus complex (n = 15/23, 65.2%) infection (n = 11/17, 64.7%) but less so for disease (n = 2/8, 25.0%).Conclusion: Our data indicate an overall increase in NTM worldwide for both infection and disease. The explanation to this phenomenon warrants further investigation.
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| 13. |
- Davies Forsman, Lina, et al.
(författare)
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Minimum Inhibitory Concentrations of Fluoroquinolones and Pyrazinamide Susceptibility Correlate to Clinical Improvement in Multidrug-resistant Tuberculosis Patients: A Nationwide Swedish Cohort Study Over 2 Decades
- 2019
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Ingår i: Clinical Infectious Diseases. - : OXFORD UNIV PRESS INC. - 1058-4838 .- 1537-6591. ; 69:8, s. 1394-1402
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Tidskriftsartikel (refereegranskat)abstract
- Background. Minimum inhibitory concentration (MIC) testing, unlike routine drug susceptibility testing (DST) at a single critical concentration, quantifies drug resistance. The association of MICs and treatment outcome in multidrug-resistant (MDR)-tuberculosis patients is unclear. Therefore, we correlated MICs of first- and second-line tuberculosis drugs with time to sputum culture conversion (tSCC) and treatment outcome in MDR-tuberculosis patients. Methods. Clinical and demographic data of MDR-tuberculosis patients in Sweden, including DST results, were retrieved from medical records from 1992 to 2014. MIC determinations were performed retrospectively for the stored individual Mycobacterium tuberculosis (Mtb) isolates using broth microdilution in Middlebrook 7H9. We fitted Cox proportional hazard models correlating MICs, DST results, and clinical variables to tSCC and treatment outcome. Results. Successful treatment outcome was observed in 83.5% (132/158) of MDR-tuberculosis patients. Increasing MICs of fluoroquinolones, diabetes, and age amp;gt;40 years were significantly associated with unsuccessful treatment outcome. Patients treated with pyrazinamide (PZA) had a significantly shorter tSCC compared to patients who were not (median difference, 27 days). Conclusions. Increasing MICs of fluoroquinolones were correlated with unsuccessful treatment outcome in MDR-tuberculosis patients. Further studies, including MIC testing and clinical outcome data to define clinical Mtb breakpoints, are warranted. PZA treatment was associated with shorter tSCC, highlighting the importance of PZA DST.
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| 14. |
- Froberg, Gabrielle, et al.
(författare)
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Towards clinical breakpoints for non-tuberculous mycobacteria-Determination of epidemiological cut off values for the Mycobacterium avium complex and Mycobacterium abscessus using broth microdilution
- 2023
-
Ingår i: Clinical Microbiology and Infection. - : ELSEVIER SCI LTD. - 1198-743X .- 1469-0691. ; 29:6, s. 758-764
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Tidskriftsartikel (refereegranskat)abstract
- Objective: For non-tuberculous mycobacteria (NTM), minimum inhibitory concentration (MIC) distri-butions of wild-type isolates have not been systematically evaluated despite their importance for establishing antimicrobial susceptibility testing (AST) breakpoints.Methods: We gathered MIC distributions for drugs used against the Mycobacterium avium complex (MAC) and Mycobacterium abscessus (MAB) obtained by commercial broth microdilution (SLOMYCOI and RAPMYCOI) from 12 laboratories. Epidemiological cut-off values (ECOFFs) and tentative ECOFFs (TEC-OFFs) were determined by EUCAST methodology including quality control (QC) strains.Results: The clarithromycin ECOFF was 16 mg/L for M. avium (n = 1271) whereas TECOFFs were 8 mg/L for M. intracellulare (n = 415) and 1 mg/L for MAB (n = 1014) confirmed by analysing MAB subspecies without inducible macrolide resistance (n = 235). For amikacin, the ECOFFs were 64 mg/L for MAC and MAB. For moxifloxacin, the WT spanned >8 mg/L for both MAC and MAB. For linezolid, the ECOFF and TECOFF were 64 mg/L for M. avium and M. intracellulare, respectively. Current CLSI breakpoints for amikacin (16 mg/L), moxifloxacin (1 mg/L) and linezolid (8 mg/L) divided the corresponding WT dis-tributions. For QC M. avium and M. peregrinum, >= 95% of MIC values were well within recommended QC ranges.Conclusion: As a first step towards clinical breakpoints for NTM, (T)ECOFFs were defined for several antimicrobials against MAC and MAB. Broad wild-type MIC distributions indicate a need for further method refinement which is now under development within the EUCAST subcommittee for anti-mycobacterial drug susceptibility testing. In addition, we showed that several CLSI NTM breakpoints are not consistent in relation to the (T)ECOFFs. Gabrielle Froeuroberg, Clin Microbiol Infect 2023;29:758 (c) 2023 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).
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| 15. |
- Gouignard, Nadège, et al.
(författare)
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Gene expression of the two developmentally regulated dermatan sulfate epimerases in the Xenopus embryo
- 2018
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Chondroitin sulfate (CS)/dermatan sulfate (DS) proteoglycans are abundant on the cell surface and in the extracellular matrix and have important functions in matrix structure, cell-matrix interaction and signaling. The DS epimerases 1 and 2, encoded by Dse and Dsel, respectively, convert CS to a CS/DS hybrid chain, which is structurally and conformationally richer than CS, favouring interaction with matrix proteins and growth factors. We recently showed that Xenopus Dse is essential for the migration of neural crest cells by allowing cell surface CS/DS proteoglycans to adhere to fibronectin. Here we investigate the expression of Dse and Dsel in Xenopus embryos. We show that both genes are maternally expressed and exhibit partially overlapping activity in the eyes, brain, trigeminal ganglia, neural crest, adenohypophysis, sclerotome, and dorsal endoderm. Dse is specifically expressed in the epidermis, anterior surface ectoderm, spinal nerves, notochord and dermatome, whereas Dsel mRNA alone is transcribed in the spinal cord, epibranchial ganglia, prechordal mesendoderm and myotome. The expression of the two genes coincides with sites of cell differentiation in the epidermis and neural tissue. Several expression domains can be linked to previously reported phenotypes of knockout mice and clinical manifestations, such as the Musculocontractural Ehlers-Danlos syndrome and psychiatric disorders.
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| 16. |
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| 17. |
- Lindsten, Fredrik, 1984-, et al.
(författare)
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Divide-and-Conquer With Sequential Monte Carlo
- 2017
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Ingår i: Journal of Computational And Graphical Statistics. - : AMER STATISTICAL ASSOC. - 1061-8600 .- 1537-2715. ; 26:2, s. 445-458
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Tidskriftsartikel (refereegranskat)abstract
- We propose a novel class of Sequential Monte Carlo (SMC) algorithms, appropriate for inference in probabilistic graphical models. This class of algorithms adopts a divide-and-conquer approach based upon an auxiliary tree-structured decomposition of the model of interest, turning the overall inferential task into a collection of recursively solved subproblems. The proposed method is applicable to a broad class of probabilistic graphical models, including models with loops. Unlike a standard SMC sampler, the proposed divide-and-conquer SMC employs multiple independent populations of weighted particles, which are resampled, merged, and propagated as the method progresses. We illustrate empirically that this approach can outperform standard methods in terms of the accuracy of the posterior expectation and marginal likelihood approximations. Divide-and-conquer SMC also opens up novel parallel implementation options and the possibility of concentrating the computational effort on the most challenging subproblems. We demonstrate its performance on a Markov random field and on a hierarchical logistic regression problem. Supplementary materials including proofs and additional numerical results are available online.
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| 18. |
- Lundquist, Christian, 1978-
(författare)
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Automotive Sensor Fusion for Situation Awareness
- 2009
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The use of radar and camera for situation awareness is gaining popularity in automotivesafety applications. In this thesis situation awareness consists of accurate estimates of theego vehicle’s motion, the position of the other vehicles and the road geometry. By fusinginformation from different types of sensors, such as radar, camera and inertial sensor, theaccuracy and robustness of those estimates can be increased.Sensor fusion is the process of using information from several different sensors tocompute an estimate of the state of a dynamic system, that in some sense is better thanit would be if the sensors were used individually. Furthermore, the resulting estimate isin some cases only obtainable through the use of data from different types of sensors. Asystematic approach to handle sensor fusion problems is provided by model based stateestimation theory. The systems discussed in this thesis are primarily dynamic and they aremodeled using state space models. A measurement model is used to describe the relationbetween the state variables and the measurements from the different sensors. Within thestate estimation framework a process model is used to describe how the state variablespropagate in time. These two models are of major importance for the resulting stateestimate and are therefore given much attention in this thesis. One example of a processmodel is the single track vehicle model, which is used to model the ego vehicle’s motion.In this thesis it is shown how the estimate of the road geometry obtained directly from thecamera information can be improved by fusing it with the estimates of the other vehicles’positions on the road and the estimate of the radius of the ego vehicle’s currently drivenpath.The positions of stationary objects, such as guardrails, lampposts and delineators aremeasured by the radar. These measurements can be used to estimate the border of theroad. Three conceptually different methods to represent and derive the road borders arepresented in this thesis. Occupancy grid mapping discretizes the map surrounding theego vehicle and the probability of occupancy is estimated for each grid cell. The secondmethod applies a constrained quadratic program in order to estimate the road borders,which are represented by two polynomials. The third method associates the radar measurementsto extended stationary objects and tracks them as extended targets.The approaches presented in this thesis have all been evaluated on real data from bothfreeways and rural roads in Sweden.
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| 19. |
- Lundquist, Christian, et al.
(författare)
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Estimation of the Free Space in Front of a Moving Vehicle
- 2009
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- There are more and more systems emerging making use of measurements from a forward looking radar and a forward looking camera. It is by now well known how to exploit this data in order to compute estimates of the road geometry, tracking leading vehicles, etc. However, there is valuable information present in the radar concerning stationary targets, that is typically not used. The present work shows how radar measurements of stationary targets can be used to provide a reliable estimate of the drivable space in front of a moving vehicle.In the present paper three conceptually different methods to estimate stationary objects or road borders are presented and compared. The first method considered is occupancy grid mapping, which discretizes the map surrounding the ego vehicle and the probability of occupancy is estimated for each grid cell. The second method applies a constrained quadratic program in order to estimate the road borders. The problem is stated as a constrained curve fitting problem. The third method associates the radar measurements to extended stationary objects and tracks them as extended targets.The required sensors, besides the standard proprioceptive sensors of a modern car, are a forward looking long range radar and a forward looking camera. Hence, there is no need to introduce any new sensors, it is just a matter of making better use of the sensor information that is already present in a modern car. The approach has been evaluated and tested on real data from highways and rural roads in Sweden and the results are very promising.
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| 20. |
- Lundquist, Christian, 1978-, et al.
(författare)
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Estimation of the Free Space in Front of a Moving Vehicle
- 2009
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Ingår i: Proceedings of the '09 SAE World Congress & Exhibition. - 400 Commonwealth Drive, Warrendale, PA, United States : SAE International. - 9780768021264
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Konferensbidrag (refereegranskat)abstract
- There are more and more systems emerging making use of measurements from a forward looking radar and a forward looking camera. It is by now well known how to exploit this data in order to compute estimates of the road geometry, tracking leading vehicles, etc. However, there is valuable information present in the radar concerning stationary objects, that is typically not used. The present work shows how radar measurements of stationary objects can be used to obtain a reliable estimate of the free space in front of a moving vehicle. The approach has been evaluated on real data from highways and rural roads in Sweden.
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| 21. |
- Lundquist, Christian, 1978-, et al.
(författare)
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Joint Ego-Motion and Road Geometry Estimation
- 2011
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Ingår i: Information Fusion. - : Elsevier. - 1566-2535 .- 1872-6305. ; 12:4, s. 253-263
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Tidskriftsartikel (refereegranskat)abstract
- We provide a sensor fusion framework for solving the problem of joint egomotion and road geometry estimation. More specifically we employ a sensor fusion framework to make systematic use of the measurements from a forward looking radar and camera, steering wheel angle sensor, wheel speed sensors and inertial sensors to compute good estimates of the road geometry and the motion of the ego vehicle on this road. In order to solve this problem we derive dynamical models for the ego vehicle, the road and the leading vehicles. The main difference to existing approaches is that we make use of a new dynamic model for the road. An extended Kalman filter is used to fuse data and to filter measurements from the camera in order to improve the road geometry estimate. The proposed solution has been tested and compared to existing algorithms for this problem, using measurements from authentic traffic environments on public roads in Sweden. The results clearly indicate that the proposed method provides better estimates.
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| 22. |
- Lundquist, Christian, 1978-, et al.
(författare)
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Recursive Identification of Cornering Stiffness Parameters for an Enhanced Single Track Model
- 2009
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Ingår i: Proceedings of the 15th IFAC Symposiumon System Identification. - Linköping : Linköping University Electronic Press. - 9783902661470 ; , s. 1726-1731
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Konferensbidrag (refereegranskat)abstract
- The current development of safety systems within the automotive industry heavily relies on the ability to perceive the environment. This is accomplished by using measurements from several different sensors within a sensor fusion framework. One important part of any system of this kind is an accurate model describing the motion of the vehicle. The most commonly used model for the lateral dynamics is the single track model, which includes the so called cornering stiffness parameters. These parameters describe the tire-road contact and are unknown and even time-varying. Hence, in order to fully make use of the single track model, these parameters have to be identified. The aim of this work is to provide a method for recursive identification of the cornering stiffness parameters to be used on-line while driving.
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| 23. |
- Lundquist, Christian, 1978-, et al.
(författare)
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Road Geometry Estimation and Vehicle Tracking using a Single Track Model
- 2008
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Ingår i: Proceedings of the 2008 IEEE Intelligent Vehicles Symposium. - Linköping : Linköping University Electronic Press. - 9781424425686 - 9781424425693 ; , s. 144-149
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Konferensbidrag (refereegranskat)abstract
- This paper is concerned with the, by now rather well studied, problem of integrated road geometry estimation and vehicle tracking. The main differences to the existing approaches are that we make use of an improved host vehicle model and a new dynamic model for the road. The problem is posed within a standard sensor fusion framework, allowing us to make good use of the available sensor information. The performance of the solution is evaluated using measurements from real and relevant traffic environments from public roads in Sweden. The experiments indicates that the gain in using the extended host vehicle model is most prominent when driving on country roads without any vehicles in front.
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| 24. |
- Lundquist, Christian, 1978-
(författare)
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Sensor Fusion for Automotive Applications
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mapping stationary objects and tracking moving targets are essential for many autonomous functions in vehicles. In order to compute the map and track estimates, sensor measurements from radar, laser and camera are used together with the standard proprioceptive sensors present in a car. By fusing information from different types of sensors, the accuracy and robustness of the estimates can be increased.Different types of maps are discussed and compared in the thesis. In particular, road maps make use of the fact that roads are highly structured, which allows relatively simple and powerful models to be employed. It is shown how the information of the lane markings, obtained by a front looking camera, can be fused with inertial measurement of the vehicle motion and radar measurements of vehicles ahead to compute a more accurate and robust road geometry estimate. Further, it is shown how radar measurements of stationary targets can be used to estimate the road edges, modeled as polynomials and tracked as extended targets.Recent advances in the field of multiple target tracking lead to the use of finite set statistics (FISST) in a set theoretic approach, where the targets and the measurements are treated as random finite sets (RFS). The first order moment of a RFS is called probability hypothesis density (PHD), and it is propagated in time with a PHD filter. In this thesis, the PHD filter is applied to radar data for constructing a parsimonious representation of the map of the stationary objects around the vehicle. Two original contributions, which exploit the inherent structure in the map, are proposed. A data clustering algorithm is suggested to structure the description of the prior and considerably improving the update in the PHD filter. Improvements in the merging step further simplify the map representation.When it comes to tracking moving targets, the focus of this thesis is on extended targets, i.e., targets which potentially may give rise to more than one measurement per time step. An implementation of the PHD filter, which was proposed to handle data obtained from extended targets, is presented. An approximation is proposed in order to limit the number of hypotheses. Further, a framework to track the size and shape of a target is introduced. The method is based on measurement generating points on the surface of the target, which are modeled by an RFS.Finally, an efficient and novel Bayesian method is proposed for approximating the tire radii of a vehicle based on particle filters and the marginalization concept. This is done under the assumption that a change in the tire radius is caused by a change in tire pressure, thus obtaining an indirect tire pressure monitoring system.The approaches presented in this thesis have all been evaluated on real data from both freeways and rural roads in Sweden.
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| 25. |
- Lundquist, Christian, 1978-, et al.
(författare)
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Situational Awareness and Road Prediction for Trajectory Control Applications
- 2012
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Ingår i: Handbook of Intelligent Vehicles. - London : Springer London. - 9780857290847 - 9780857290854 ; , s. 365-396
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Bokkapitel (refereegranskat)abstract
- The Handbook of Intelligent Vehicles provides a complete coverage of the fundamentals, new technologies, and sub-areas essential to the development of intelligent vehicles; it also includes advances made to date, challenges, and future trends. Significant strides in the field have been made to date; however, so far there has been no single book or volume which captures these advances in a comprehensive format, addressing all essential components and subspecialties of intelligent vehicles, as this book does. Since the intended users are engineering practitioners, as well as researchers and graduate students, the book chapters do not only cover fundamentals, methods, and algorithms but also include how software/hardware are implemented, and demonstrate the advances along with their present challenges. Research at both component and systems levels are required to advance the functionality of intelligent vehicles. This volume covers both of these aspects in addition to the fundamentals listed above.
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| 26. |
- Lundquist, Christian, 1978-, et al.
(författare)
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Tracking Stationary Extended Objects for Road Mapping using Radar Measurements
- 2009
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Ingår i: Proceedings of the '09 IEEE Intelligent Vehicle Symposium. - : IEEE. - 9781424435043 - 9781424435036 ; , s. 405-410
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Konferensbidrag (refereegranskat)abstract
- It is getting more common that premium cars areequipped with a forward looking radar and a forward looking camera. The data is often used to estimate the road geometry, tracking leading vehicles, etc. However, there is valuable information present in the radar concerning stationary objects, that is typically not used. The present work shows how stationary objects, such as guard rails, can be modeled and tracked as extended objects using radar measurements. The problem is cast within a standard sensor fusion framework utilizing the Kalman filter. The approach has been evaluated on real datafrom highways and rural roads in Sweden.
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| 27. |
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| 28. |
- Naesseth, Christian A., et al.
(författare)
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Elements of Sequential Monte Carlo
- 2019
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Ingår i: FOUNDATIONS AND TRENDS IN MACHINE LEARNING. - : NOW PUBLISHERS INC. - 1935-8237 .- 1935-8245. ; 12:3, s. 187-306
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Tidskriftsartikel (refereegranskat)abstract
- A core problem in statistics and probabilistic machine learning is to compute probability distributions and expectations. This is the fundamental problem of Bayesian statistics and machine learning, which frames all inference as expectations with respect to the posterior distribution. The key challenge is to approximate these intractable expectations. In this tutorial, we review sequential Monte Carlo (SMC), a random-sampling-based class of methods for approximate inference. First, we explain the basics of SMC, discuss practical issues, and review theoretical results. We then examine two of the main user design choices: the proposal distributions and the so called intermediate target distributions. We review recent results on how variational inference and amortization can be used to learn efficient proposals and target distributions. Next, we discuss the SMC estimate of the normalizing constant, how this can be used for pseudo-marginal inference and inference evaluation. Throughout the tutorial we illustrate the use of SMC on various models commonly used in machine learning, such as stochastic recurrent neural networks, probabilistic graphical models, and probabilistic programs.
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| 29. |
- Nilsson, Emil, et al.
(författare)
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Vehicle Motion Estimation Using an Infrared Camera
- 2011
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Ingår i: Proceedings of the 18th IFAC World Congress. - : Elsevier. - 9783902661937 ; , s. 12952-12957
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Konferensbidrag (refereegranskat)abstract
- This paper is concerned with vehicle motion estimation. The problem is formulated as a sensor fusion problem, where the vehicle motion is estimated based on the information from a far infrared camera, inertial sensors and the vehicle speed. This information is already present in premium cars. We are concerned with the off-line situation and the approach taken is to formulate the problem as a nonlinear least squares problem. In order to illustrate the performance of the proposed method experiments on rural roads in Sweden during night time driving have been performed. The results clearly indicates the efficacy of the approach.
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| 30. |
- Niward, Katarina, et al.
(författare)
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Susceptibility testing breakpoints for Mycobacterium tuberculosis categorize isolates with resistance mutations in gyrA as susceptible to fluoroquinolones : implications for MDR-TB treatment and the definition of XDR-TB
- 2016
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Ingår i: Journal of Antimicrobial Chemotherapy. - : Oxford University Press (OUP). - 0305-7453 .- 1460-2091. ; 71:2, s. 333-338
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Tidskriftsartikel (refereegranskat)abstract
- Fluoroquinolones (FQs) are important in the treatment of MDR-TB and in the definition of XDR-TB. Our objective was to investigate how discrepancies in the phenotypic and genotypic methods for antimicrobial susceptibility testing could affect the interpretation of antimicrobial susceptibility test results. We analysed MICs of ofloxacin and levofloxacin in Middlebrook 7H10 broth (7H10) as well as sequencing of the quinolone resistance-determining region of the gyrA gene and the MTBDRsl assay in 75 resistant isolates, including MDR and XDR strains of Mycobacterium tuberculosis. Among 75 resistant isolates, 27 had mutations associated with FQ resistance. Among isolates with resistance mutations in gyrA, 26% (seven of 27) were susceptible to levofloxacin and ofloxacin by phenotypic testing at 1 mg/L and 2 mg/L. The most common mutation was in codon 94 and these isolates had significantly increased MICs of levofloxacin (2-8 mg/L) compared with isolates with mutations in codon 90 (0.25-2 mg/L, PaEuroS < aEuroS0.05). The sensitivity and specificity for the MTBDRsl assay compared with gyrA sequencing were 96% and 98%, respectively. Current critical concentrations may classify up to 26% of isolates with gyrA mutations as susceptible to FQs due to a close relationship between susceptible and resistant populations. These results should be considered while improving clinical breakpoints for M. tuberculosis and may have an impact on the definition of XDR-TB.
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| 31. |
- Rudolf, Frauke, et al.
(författare)
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Increasing smear positive tuberculosis detection using a clinical score - A stepped wedge multicenter trial from Africa
- 2021
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Ingår i: International Journal of Infectious Diseases. - : Elsevier Science Ltd. - 1201-9712 .- 1878-3511. ; 113, s. S55-S62
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Bandim TBscore is a clinical score that predicts treatment outcome in Tuberculosis (TB) patients and proved useful as an indicator of which healthcare-seeking adults to refer for sputum smear microcopy. We aimed to test in a randomized trial if the TBscore could be used to enhance the detection of smear positive (SP) TB. Methods: We carried out a stepped wedge cluster-randomized trial at six health centers in Bissau, GuineaBissau, and Gondar, Ethiopia. The primary outcome was diagnostic yield for SP TB. Secondary outcomes were successful treatment and effect on overall 12 months mortality. The study was registered at the Pan African Clinical Trials Registry (PACTR201611001838365). Results: We included 3571 adults. Overall, there was no effect of the intervention on SP PTB detected (OR 1.39 (95%CI 0.75 - 2.56). Analysis stratified by country, showed that the TBscore increased case detection in Gondar (OR 4.05 (95%CI 1.67 - 9.85)) but no effect was found in Bissau (OR 0.47 (95%CI 0.22 - 1.05)) where take-up was much lower. Overall mortality decreased during the intervention (HR 0.31 (95%CI 0.13-0.72)). Conclusion: Using the TBscore for triage before smear microscopy may improve case detection and decrease mortality if there is sufficient laboratory capacity to increase sputum smears. (C) 2021 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.
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| 32. |
- Rudolf, Frauke, et al.
(författare)
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TBscore II: Refining and validating a simple clinical score for treatment monitoring of patients with pulmonary tuberculosis
- 2013
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Ingår i: Scandinavian Journal of Infectious Diseases. - : Informa Healthcare. - 0036-5548 .- 1651-1980. ; 45:11, s. 825-836
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Tidskriftsartikel (refereegranskat)abstract
- Background: The TBscore, based on simple signs and symptoms, was introduced to predict unsuccessful outcome in tuberculosis patients on treatment. A recent inter-observer variation study showed profound variation in some variables. Further, some variables depend on a physician assessing them, making the score less applicable. The aim of the present study was to simplify the TBscore. Methods: Inter-observer variation assessment and exploratory factor analysis were combined to develop a simplified score, the TBscore II. To validate TBscore II we assessed the association between start score and failure (i.e. death or treatment failure), responsiveness using Cohens effect size, and the relationship between severity class at treatment start and a decrease andlt; 25% in score from the start until the end of the second treatment month and subsequent mortality. Results: We analyzed data from 1070 Guinean (2003-2012) and 432 Ethiopian (2007-2012) pulmonary tuberculosis patients. For the refined score, items with less than substantial agreement (kappa andlt;= 0.6) and/or not associated with the underlying constructs were excluded. Items kept were: cough, dyspnea, chest pain, anemia, body mass index (BMI) andlt; 18 kg/m(2), BMI andlt; 16 kg/m(2), mid upper arm circumference (MUAC) andlt; 220 mm, and MUAC andlt; 200 mm. The effect sizes for the change between the start of treatment and the 2-month follow-up were 0.51 in Guinea-Bissau and 0.68 in Ethiopia, and for the change between the start of treatment and the end of treatment were 0.68 in Guinea-Bissau and 0.74 in Ethiopia. Severity class placement at treatment start predicted failure (p andlt; 0.001 Guinea-Bissau, p = 0.208 Ethiopia). Inability to decrease at least 25% in score was associated with a higher failure rate during the remaining 4 months of treatment (p = 0.063 Guinea-Bissau, p = 0.008 Ethiopia). Conclusion: The TBscore II could be a useful monitoring tool, aiding triage at the beginning of treatment and during treatment.
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| 33. |
- Sanders-Gutierrez, Oscar Alan, et al.
(författare)
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Molecular dynamics and DFT study of 38-atom coinage metal clusters
- 2022
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Ingår i: Computational Materials Science. - : Elsevier BV. - 0927-0256. ; 201
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Tidskriftsartikel (refereegranskat)abstract
- The thermal behavior of 38-atom mono-, bi-, and trimetallic clusters consisting of Cu, Ag, and Au atoms, is analyzed employing molecular dynamics simulations and DFT calculations for selected cluster compositions. Low-energy structures were singled out to perform NVT molecular dynamics simulations at several temperatures, using the Andersen thermostat for temperature control. The caloric curve is used to estimate the melting temperature and the specific heat. The pair distribution function g(r) of the solid and liquid-phase clusters is examined at different temperatures. When comparing the estimated melting points (Tm) among the monatomic clusters, the order becomes TmCu38>TmAg38>TmAu38. For bimetallic clusters, an increase of Tm is observed for Cu-Au compared to their monatomic counterparts, while the opposite occurs for Cu-Ag clusters. For trimetallic clusters, two low-energy isomers of the Cu36Ag1Au1 cluster are investigated. In this case, Tm is estimated to be 475 K, for the two isomers with the lowest-energy and second-to-lowest energy, respectively. For all the clusters studied, the pair distribution function g(r) shows that the first peak position is not shifted as an effect of temperature and its maximum value varies with composition, while the second peak essentially vanishes upon melting. The common-neighbor analysis (CNA) technique is used to analyze the local structural changes for the trimetallic clusters, again demonstrating a clear structural change upon melting. The HOMO-LUMO energy gap indicates that the trimetallic isomers' behavior is metallic, while the average binding energy show these clusters' energetic stability to be similar.
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| 34. |
- Schön, Thomas, et al.
(författare)
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Antimicrobial susceptibility testing of Mycobacterium tuberculosis complex isolates - the EUCAST broth microdilution reference method for MIC determination
- 2020
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Ingår i: Clinical Microbiology and Infection. - : ELSEVIER SCI LTD. - 1198-743X .- 1469-0691. ; 26:11, s. 1488-1492
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Tidskriftsartikel (refereegranskat)abstract
- Scope: Several methods are used worldwide for antibiotic susceptibility testing (AST) for the Mycobacterium tuberculosis complex (MTBC). The variability in the results obtained with these methods hampers setting epidemiological cut-off (ECOFF) values and clinical breakpoints according to EUCAST guidelines. Methods for susceptibility testing and determination of the minimal inhibitory concentrations (MICs) need to be standardized for MTBC isolates for old and new agents. Our objective was to establish a standardized reference method for MIC determination for MTBC. Methods: The EUCAST antimycobacterial susceptibility testing subcommittee (AMST) compared protocols of MIC determination with regard to medium, inoculum preparation, antituberculous agent preparation, incubation, reading of the results and interpretation. Recommendations: The EUCAST reference method of MIC determination for MTBC is the broth microdilution method in Middlebrook 7H9-10% OADC medium. The final inoculum is a 105 CFU/mL suspension, obtained from a 10(-2) dilution of a 0.5 McFarland suspension prepared after vortexing bacterial colonies with glass beads before suspending them in sterile water. The culture is maintained in a U-shaped 96well polystyrene microtitre sterile plate with a lid incubated at 36 degrees +/- 1 degrees C. Reading is done using an inverted mirror as soon as the 1:100 diluted control (i.e. 10(3) CFU/mL suspension) shows visual growth. The MIC, expressed in mg/L, is the lowest concentration that inhibits visual growth. Mycobacterium tuberculosis H37Rv ATCC 27294 is used as the reference strain and its targeted MIC values are within the range 0.03-0.12 for isoniazid, 0.12-0.5 for levofloxacin and 0.25-1 mg/L for amikacin. Conclusions: The EUCAST reference method for MTBC was endorsed by EUCAST after public consultation and will from now on be used to define EUCAST ECOFFs and clinical breakpoints. This reference method is not primarily intended to be used under routine conditions and the AST methods will need to be calibrated against this reference method to be used with EUCAST breakpoints. Thomas Sch_on, Clin Microbiol Infect 2020;26:1488 (c) 2020 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).
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| 35. |
- Schön, Thomas Bo, et al.
(författare)
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Sequential Monte Carlo Methods for System Identification
- 2015
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Ingår i: Proceedings of the 17th IFAC Symposium on System Identification.. - : Elsevier. ; , s. 775-786
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Konferensbidrag (refereegranskat)abstract
- One of the key challenges in identifying nonlinear and possibly non-Gaussian state space models (SSMs) is the intractability of estimating the system state. Sequential Monte Carlo (SMC) methods, such as the particle filter (introduced more than two decades ago), provide numerical solutions to the nonlinear state estimation problems arising in SSMs. When combined with additional identification techniques, these algorithms provide solid solutions to the nonlinear system identification problem. We describe two general strategies for creating such combinations and discuss why SMC is a natural tool for implementing these strategies.
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| 36. |
- Schön, Thomas, 1973-, et al.
(författare)
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Multicentre testing of the EUCAST broth microdilution reference method for MIC determination on Mycobacterium tuberculosis
- 2021
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Ingår i: Clinical Microbiology and Infection. - : Elsevier. - 1198-743X .- 1469-0691. ; 27:2, s. 288.e1-288.e4
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The first objective of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) subcommittee for antimycobacterial susceptibility testing (AMST), launched in 2016, was to set a reference method for determining the MICs of antituberculous agents, since many protocols are used worldwide and a consensus one is needed for the determination of microbiological breakpoints.METHODS: During 2017 and 2018, MIC determination protocols were evaluated prospectively in a multicentre study within the four AMST laboratories. MIC results were obtained for isoniazid, levofloxacin and amikacin on the reference strain Mycobacterium tuberculosis H37Rv ATCC 27294. Broth microdilution (BMD) in Middlebrook 7H9 and solid medium dilution (SMD) in Middlebrook 7H10 were performed using two inoculum concentrations. MICs were interpreted with regard to visual and 99% inhibition after 7, 14 or 21 days of incubation for BMD and 21 days for SMD.RESULTS: Following the EUCAST reference protocol, intra- and inter-assay agreements were within ±1 MIC dilution for >95% of the observations for the three drugs in both methods. MIC values, presented as MIC mode (range) for BMD and SMD respectively, were: 0.03 (0.015-0.06) mg/L and 0.12 (0.06-0.25) mg/L for isoniazid, 0.25 mg/L (0.25-0.5) and 0.5 mg/L (0.12-0.5) for levofloxacin, and 0.5 mg/L (0.5-1.0) and 0.5 mg/L (0.5-1.0) for amikacin.CONCLUSIONS: Both SMD and BMD were reproducible and eligible as a reference method for MIC determination of the Mycobacterium tuberculosis complex (MTBC). BMD was finally selected as the EUCAST reference method. From now on it will be used to set epidemiological cut-off values and clinical breakpoints of new and old antituberculous agents.
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| 37. |
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