| 1. |
- Aghanavesi, Somayeh, 1981-, et al.
(författare)
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A multiple motion sensors index for motor state quantification in Parkinson's disease
- 2020
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Ingår i: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 189
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Tidskriftsartikel (refereegranskat)abstract
- Aim: To construct a Treatment Response Index from Multiple Sensors (TRIMS) for quantification of motor state in patients with Parkinson's disease (PD) during a single levodopa dose. Another aim was to compare TRIMS to sensor indexes derived from individual motor tasks. Method: Nineteen PD patients performed three motor tests including leg agility, pronation-supination movement of hands, and walking in a clinic while wearing inertial measurement unit sensors on their wrists and ankles. They performed the tests repeatedly before and after taking 150% of their individual oral levodopa-carbidopa equivalent morning dose.Three neurologists blinded to treatment status, viewed patients’ videos and rated their motor symptoms, dyskinesia, overall motor state based on selected items of Unified PD Rating Scale (UPDRS) part III, Dyskinesia scale, and Treatment Response Scale (TRS). To build TRIMS, out of initially 178 extracted features from upper- and lower-limbs data, 39 features were selected by stepwise regression method and were used as input to support vector machines to be mapped to mean reference TRS scores using 10-fold cross-validation method. Test-retest reliability, responsiveness to medication, and correlation to TRS as well as other UPDRS items were evaluated for TRIMS. Results: The correlation of TRIMS with TRS was 0.93. TRIMS had good test-retest reliability (ICC = 0.83). Responsiveness of the TRIMS to medication was good compared to TRS indicating its power in capturing the treatment effects. TRIMS was highly correlated to dyskinesia (R = 0.85), bradykinesia (R = 0.84) and gait (R = 0.79) UPDRS items. Correlation of sensor index from the upper-limb to TRS was 0.89. Conclusion: Using the fusion of upper- and lower-limbs sensor data to construct TRIMS provided accurate PD motor states estimation and responsive to treatment. In addition, quantification of upper-limb sensor data during walking test provided strong results. © 2019
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| 2. |
- Aksteiner, S., et al.
(författare)
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New identities for linearized gravity on the Kerr spacetime
- 2019
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Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 99:4
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we derive a differential identity for linearized gravity on the Kerr spacetime and more generally on vacuum spacetimes of Petrov type D. We show that a linear combination of second derivatives of the linearized Weyl tensor can be formed into a complex symmetric 2-tensor M-ab which solves the linearized Einstein equations. The identity makes this manifest by relating M-ab to two terms solving the linearized Einstein equations by construction. The self-dual Weyl curvature of M-ab gives a covariant version of the Teukolsky-Starobinsky identities for linearized gravity which, in addition to the two classical identities for linearized Weyl scalars with extreme spin weights, includes three additional equations. In particular, they are not consequences of the classical Teukolsky-Starobinsky identities, but are additional integrability conditions for linearized gravity. The result has direct application in the construction of symmetry operators and also yields a set of nontrivial gauge invariants for linearized gravity.
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| 3. |
- Dalevi, Daniel, 1974, et al.
(författare)
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Expected Gene Order Distances and Model Selection in Bacteria
- 2008
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Ingår i: Bioinformatics. - Oxford, United Kingdom : Oxford University Press. - 1367-4803 .- 1367-4811. ; 24:11, s. 1332-1338
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: The evolutionary distance inferred from gene-order comparisons of related bacteria is dependent on the model. Therefore, it is highly important to establish reliable assumptions before inferring its magnitude. Results: We investigate the patterns of dotplots between species of bacteria with the purpose of model selection in gene-order problems. We find several categories of data which can be explained by carefully weighing the contributions of reversals, transpositions, symmetrical reversals, single gene transpositions and single gene reversals. We also derive method of moments distance estimates for some previously uncomputed cases, such as symmetrical reversals, single gene reversals and their combinations, as well as the single gene transpositions edit distance.
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| 4. |
- Eriksen, Niklas, 1974, et al.
(författare)
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Enumeration of derangements with descents in prescribed positions
- 2009
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Ingår i: Electronic Journal of Combinatorics. - : The Electronic Journal of Combinatorics. - 1077-8926 .- 1097-1440. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- We enumerate derangements with descents in prescribed positions. A generating function was given by Guo-Niu Han and Guoce Xin in 2007. We give a combinatorial proof of this result, and derive several explicit formulas. To this end, we consider fixed point $\lambda$-coloured permutations, which are easily enumerated. Several formulae regarding these numbers are given, as well as a generalisation of Euler's difference tables. We also prove that except in a trivial special case, if a permutation $\pi$ is chosen uniformly among all permutations on $n$ elements, the events that $\pi$ has descents in a set $S$ of positions, and that $\pi$ is a derangement, are positively correlated.
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| 5. |
- Eriksen, Niklas, 1974-
(författare)
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Expected number of breakpoints after t random reversals in genomes with duplicate genes
- 2008
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Ingår i: Discrete Applied Mathematics. - Amsterdam, Netherlands : Elsevier. - 0166-218X .- 1872-6771. ; 156:12, s. 2320-2335
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Tidskriftsartikel (refereegranskat)abstract
- In comparative genomics, one wishes to deduce the evolutionary distance between different species by studying their genomes. Using gene order information, we seek the number of times the gene order has changed between two species. One approach is to compute the method of moments estimate of this edit distance from a measure of dissimilarity called the breakpoint measure. In this paper, we extend formulae and bounds of this estimate on gene permutations to genomes with duplicate genes.
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| 6. |
- Eriksen, Niklas, 1974
(författare)
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Reversal and Transposition Medians
- 2007
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Ingår i: Theoretical Computer Science. - Amsterdam, Netherlands : Elsevier. ; 374:1-3, s. 111-126
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Tidskriftsartikel (refereegranskat)abstract
- In determining phylogenetic trees using gene order information, medians provide a powerful alternative to pairwise distances. On the other hand, both breakpoint and reversal medians are NP-hard to compute and the use of medians has been limited to relatively closely related genomes. In this paper, we show that in spite of the greater non-uniqueness of reversal medians, compared to breakpoint medians, medians of moderately distant genomes are often widely spread. This means that regardless of which approximation algorithms one may devise for computing reversal medians, the genomes need to be closely related for phylogenetic tree computations to be successful. To show this, we use results on transposition medians, which behave similarly, and also support our claims with simulations and a real data example with widely spread medians.
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| 7. |
- Eriksen, Niklas, 1974
(författare)
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The freshman's approach to Conway's napkin problem
- 2008
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Ingår i: The American mathematical monthly. - Washington, USA : Mathematical Association of America. - 0002-9890 .- 1930-0972. ; 115:6, s. 492-498
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Tidskriftsartikel (refereegranskat)abstract
- In the March 2006 issue of the MONTHLY, Claesson and Petersen gave a thorough solution to Conway's napkin problem. The problem is the following: Assume that n mathematicians arrive in random order at a conference dinner with a circular table, and that the napkins are placed exactly halfway between the plates so that the guests do not know whether they are supposed to use the right or the left napkin. Each guest prefers these napkins with probabilities p and 1-p, respectively, and tries her preferred alternative before trying the other, if the preferred napkin has been taken. Which proportion of guests is expected to sit down at a place where both adjacent napkins have been taken and thus be without a napkin? Claesson and Petersen use a system of generating functions to compute both the expectation and the variance of this proportion and to address similar questions, for instance regarding the number of guests who get a napkin though not the preferred one. However, these expectations can also be computed using purely elementary methods, such as the binomial theorem. We present the freshman's approach to the napkin problem and related problems, for instance the one with French diners mentioned, but not solved, by Claesson and Petersen.
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| 8. |
- Fagevik Olsén, Monika, 1964, et al.
(författare)
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Evaluation of Pressure Generated by Resistors From Different Positive Expiratory Pressure Devices
- 2015
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Ingår i: Respiratory Care. - : Daedalus Enterprises. - 0020-1324 .- 1943-3654. ; 60:10, s. 1418-1423
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Breathing exercises with positive expiratory pressure (PEP) are used to improve pulmonary function and airway clearance. Different PEP devices are available, but there have been no studies that describe the pressure generated by different resistors. The purpose of this study was to compare pressures generated from the proprietary resistor components of 4 commercial flow-dependent PEP valves with all other parameters kept constant. METHODS: Resistors from 4 flow-regulated PEP devices (Pep/Rmt system, Wellspect HealthCare; Pipe P breathing exerciser, Koo Medical Equipment; Mini-PEP, Philips Respironics [including resistors by Rusch]; and 15-mm endo-adapter, VBM Medizintechnik) were tested randomly by a blinded tester at constant flows of 10 and 18 L/min from an external gas system. All resistors were tested 3 times. RESULTS: Resistors with a similar diameter produced statistically significant different pressures at the same flow. The differences were smaller when the flow was 10 L/min compared with 18 L/min. The differences were also smaller when the diameter of the resistor was increased. The pressures produced by the 4 resistors of the same size were all significantly different when measuring 1.5- and 2.0-mm resistors at a flow of 10 L/min and 2.0-mm resistors at a flow of 18 L/min (P < .001). There were no significant differences between any of the resistors when testing sizes of 4.5 and 5.0 mm at either flow. The Mini-PEP and adapter resistors gave the highest pressures. CONCLUSIONS: Pressures generated by the different proprietary resistor components of 4 commercial PEP devices were not comparable, even though the diameter of the resistors is reported to be the same. The pressures generated were significantly different, particularly when using small-diameter resistors at a high flow. Therefore, the resistors may not be interchangeable. This is important information for clinicians, particularly when considering PEP for patients who do not tolerate higher pressures. (C) 2015 Daedalus Enterprises
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| 9. |
- Fredriksson, Johan, 1979, et al.
(författare)
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Diversity and dynamics of Archaea in an activated sludge wastewater treatment plant
- 2012
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The activated sludge process is one of the most widely used methods for treatment of wastewater and the microbial community composition in the sludge is important for the process operation. While the bacterial communities have been characterized in various activated sludge systems little is known about archaeal communities in activated sludge. The diversity and dynamics of the Archaea community in a full-scale activated sludge wastewater treatment plant were investigated by fluorescence in situ hybridization, terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes. RESULTS: The Archaea community was specialized and dominated by Methanosaeta-like species. During a 15 month period major changes in the community composition were only observed twice despite seasonal variations in environmental and operating conditions. Water temperature appeared to be the process parameter that affected the community composition the most. Several terminal restriction fragments also showed strong correlations with sludge properties and effluent water properties. The Archaea were estimated to make up 1.6-% of total cell numbers in the activated sludge and were present both as single cells and colonies of varying sizes. CONCLUSIONS: The results presented here show that Archaea can constitute a constant and integral part of the activated sludge and that it can therefore be useful to include Archaea in future studies of microbial communities in activated sludge.
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| 10. |
- Fredriksson, Johan, 1979, et al.
(författare)
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Impact of T-RFLP data analysis choices on assessments of microbial community structure and dynamics
- 2014
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 15:360
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Tidskriftsartikel (refereegranskat)abstract
- Background Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established there is no consensus on how to treat T-RFLP data to achieve the highest possible accuracy and reproducibility. This study focused on two critical steps in the T-RFLP data treatment: the alignment of the terminal restriction fragments (T-RFs), which enables comparisons of samples, and the normalization of T-RF profiles, which adjusts for differences in signal strength, total fluorescence, between samples. Results Variations in the estimation of T-RF sizes were observed and these variations were found to affect the alignment of the T-RFs. A novel method was developed which improved the alignment by adjusting for systematic shifts in the T-RF size estimations between the T-RF profiles. Differences in total fluorescence were shown to be caused by differences in sample concentration and by the gel loading. Five normalization methods were evaluated and the total fluorescence normalization procedure based on peak height data was found to increase the similarity between replicate profiles the most. A high peak detection threshold, alignment correction, normalization and the use of consensus profiles instead of single profiles increased the similarity of replicate T-RF profiles, i.e. lead to an increased reproducibility. The impact of different treatment methods on the outcome of subsequent analyses of T-RFLP data was evaluated using a dataset from a longitudinal study of the bacterial community in an activated sludge wastewater treatment plant. Whether the alignment was corrected or not and if and how the T-RF profiles were normalized had a substantial impact on ordination analyses, assessments of bacterial dynamics and analyses of correlations with environmental parameters. Conclusions A novel method for the evaluation and correction of the alignment of T-RF profiles was shown to reduce the uncertainty and ambiguity in alignments of T-RF profiles. Large differences in the outcome of assessments of bacterial community structure and dynamics were observed between different alignment and normalization methods. The results of this study can therefore be of value when considering what methods to use in the analysis of T-RFLP data.
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