| 1. |
- Galindo-Prieto, Beatriz, et al.
(författare)
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A new approach for variable influence on projection (VIP) in O2PLS models
- 2017
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Ingår i: Chemometrics and Intelligent Laboratory Systems. - : Elsevier. - 0169-7439 .- 1873-3239. ; 160, s. 110-124
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Tidskriftsartikel (refereegranskat)abstract
- A novel variable influence on projection approach for O2PLS® models, named VIPO2PLS, is presented in this paper. VIPO2PLS is a model-based method for judging the importance of variables. Its cornerstone is the 2-way formalism of the O2PLS models; i.e. the use of both predictive and orthogonal normalized loadings of the two modelled data matrices, and also a new weighting system based on the sum of squares of both data blocks (X, Y). The VIPO2PLS algorithm has been tested in one synthetic data set and two real cases, and the outcomes have been compared to the PLS-VIP, VIPOPLS, and i-PLS methods. The purpose is to achieve a sharper and enhanced model interpretation of O2PLS models by using the new VIPO2PLS method for assessing the importance of both X- and Y- variables.
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| 2. |
- Brunius, Carl, 1974, et al.
(författare)
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Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data
- 2017
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059 .- 1367-4811. ; 33:22, s. 3567-3574
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Tidskriftsartikel (refereegranskat)abstract
- Biobanks are important infrastructures for life science research. Optimal sample handling regarding e.g. collection and processing of biological samples is highly complex, with many variables that could alter sample integrity and even more complex when considering multiple study centers or using legacy samples with limited documentation on sample management. Novel means to understand and take into account such variability would enable high-quality research on archived samples. This study investigated whether pre-analytical sample variability could be predicted and reduced by modeling alterations in the plasma metabolome, measured by NMR, as a function of pre-centrifugation conditions (1-36 h pre-centrifugation delay time at 4 A degrees C and 22 A degrees C) in 16 individuals. Pre-centrifugation temperature and delay times were predicted using random forest modeling and performance was validated on independent samples. Alterations in the metabolome were modeled at each temperature using a cluster-based approach, revealing reproducible effects of delay time on energy metabolism intermediates at both temperatures, but more pronounced at 22 A degrees C. Moreover, pre-centrifugation delay at 4 A degrees C resulted in large, specific variability at 3 h, predominantly of lipids. Pre-analytical sample handling error correction resulted in significant improvement of data quality, particularly at 22 A degrees C. This approach offers the possibility to predict pre-centrifugation delay temperature and time in biobanked samples before use in costly downstream applications. Moreover, the results suggest potential to decrease the impact of undesired, delay-induced variability. However, these findings need to be validated in multiple, large sample sets and with analytical techniques covering a wider range of the metabolome, such as LC-MS.
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| 3. |
- Beier, Ulrika
(författare)
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Habitat use in fish communities : size- and environment-dependent mechanisms affecting biotic interactions and population regulation
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Through the influence of abiotic factors, the habitat use of organisms affects their metabolism as well as other species- and size-dependent individual-based rates. The habitat-specific performances of individuals interacting in different habitats thereby affect biotic interactions. Habitat use is thus central for the outcomes of biotic interactions that, in turn, regulate populations and communities. My aim is to investigate how individual processes are influenced by habitat-dependent abiotic factors, affecting biotic interactions to regulate habitat use and population structures in fish communities. I examined patterns of habitat distribution and population structures of perch (Perca fluviatilis L.), roach (Rutilus rutilus (L.)), and the zooplankton specialist vendace (Coregonus albula (L.)) using a database of standardised test fishing data in lakes. To clarify mechanisms, I experimentally studied predation from perch in pond enclosures as well as relative foraging abilities of the two competitors roach and vendace in aquaria with different temperature and light treatments. To test mechanisms in natural situations, I calculated species- and size-dependent net energy intake, incorporating temperature- and light-dependence, including metabolism, using field data from different habitats in lakes with and without vendace. I also developed and applied a stage-structured biomass model, considering a cold water species (vendace) using two habitats differing in temperature. I thereby studied how climate warming which acts differently on different lake habitats affected temperature-dependent individual-based processes, and results on the population level. Through multi-species studies, I found that a combination of size- and environment-dependent individual processes determining energy gain, rather than predation risk, could explain size- and species-specific habitat use. The single-species study showed that stage-specific intake rates in one habitat, altered by increased temperature, affected intraspecific competition in both habitats, through a mechanism of ‘inter-habitat subsidies’ which altered population structure through maturation and reproduction rates. My thesis shows how including size- and environment-dependent individual processes, and interactions across habitats, increases our understanding of population and community structure as well as effects of environmental change.
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| 4. |
- Malmberg, Filip, et al.
(författare)
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An efficient algorithm for exact evaluation of stochastic watersheds
- 2014
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Ingår i: Pattern Recognition Letters. - : Elsevier BV. - 0167-8655 .- 1872-7344. ; 47, s. 80-84
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Tidskriftsartikel (refereegranskat)abstract
- The stochastic watershed is a method for unsupervised image segmentation proposed by Angulo and Jeulin (2007). The method first computes a probability density function (PDF), assigning to each piece of contour in the image the probability to appear as a segmentation boundary in seeded watershed segmentation with randomly selected seeds. Contours that appear with high probability are assumed to be more important. This PDF is then post-processed to obtain a final segmentation. The main computational hurdle with the stochastic watershed method is the calculation of the PDF. In the original publication by Angulo and Jeulin, the PDF was estimated by Monte Carlo simulation, i.e., repeatedly selecting random markers and performing seeded watershed segmentation. Meyer and Stawiaski (2010) showed that the PDF can be calculated exactly, without performing any Monte Carlo simulations, but do not provide any implementation details. In a naive implementation, the computational cost of their method is too high to make it useful in practice. Here, we extend the work of Meyer and Stawiaski by presenting an efficient (quasi-linear) algorithm for exact computation of the PDF. We demonstrate that in practice, the proposed method is faster than any previously reported method by more than two orders of magnitude. The algorithm is formulated for general undirected graphs, and thus trivially generalizes to images with any number of dimensions.
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| 5. |
- Skarin, Anna
(författare)
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Modeling interdependent animal movement in continuous time
- 2016
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Ingår i: Biometrics. - : Wiley. - 0006-341X .- 1541-0420. ; 72, s. 315-324
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Tidskriftsartikel (refereegranskat)abstract
- This article presents a new approach to modeling group animal movement in continuous time. The movement of a group of animals is modeled as a multivariate Ornstein Uhlenbeck diffusion process in a high-dimensional space. Each individual of the group is attracted to a leading point which is generally unobserved, and the movement of the leading point is also an Ornstein Uhlenbeck process attracted to an unknown attractor. The Ornstein Uhlenbeck bridge is applied to reconstruct the location of the leading point. All movement parameters are estimated using Markov chain Monte Carlo sampling, specifically a Metropolis Hastings algorithm. We apply the method to a small group of simultaneously tracked reindeer, Rangifer tarandus tarandus, showing that the method detects dependency in movement between individuals.
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| 6. |
- Dublon, Ian
(författare)
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Superplot3d: an open source GUI tool for 3d trajectory visualisation and elementary processing
- 2013
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Ingår i: Source Code for Biology and Medicine. - : Springer Science and Business Media LLC. - 1751-0473. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- When acquiring simple three-dimensional (3d) trajectory data it is common to accumulate large coordinate data sets. In order to examine integrity and consistency of object tracking, it is often necessary to rapidly visualise these data. Ordinarily, to achieve this the user must either execute 3d plotting functions in a numerical computing environment or manually inspect data in two dimensions, plotting each individual axis. Superplot3d is an open source MATLAB script which takes tab delineated Cartesian data points in the form x,y,z and time and generates an instant visualization of the object’s trajectory in free-rotational three dimensions. Whole trajectories may be instantly presented, allowing for rapid inspection. Executable from the MATLAB command line (or deployable as a compiled standalone application) superplot3d also provides simple GUI controls to obtain rudimentary trajectory information, allow specific visualization of trajectory sections and perform elementary processing. Superplot3d thus provides a framework for non-programmers and programmers alike, to recreate recently acquired 3d object trajectories in rotatable 3d space. It is intended, via the use of a preference driven menu to be flexible and work with output from multiple tracking software systems. Source code and accompanying GUIDE .fig files are provided for deployment and further development.
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| 7. |
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| 8. |
- Ahmad, M. Rauf, et al.
(författare)
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Tests for high-dimensional covariance matrices using the theory of U-statistics
- 2015
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Ingår i: Journal of Statistical Computation and Simulation. - : Informa UK Limited. - 0094-9655 .- 1563-5163. ; 85:13, s. 2619-2631
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Tidskriftsartikel (refereegranskat)abstract
- Test statistics for sphericity and identity of the covariance matrix are presented, when the data are multivariate normal and the dimension, p, can exceed the sample size, n. Under certain mild conditions mainly on the traces of the unknown covariance matrix, and using the asymptotic theory of U-statistics, the test statistics are shown to follow an approximate normal distribution for large p, also when p >> n. The accuracy of the statistics is shown through simulation results, particularly emphasizing the case when p can be much larger than n. A real data set is used to illustrate the application of the proposed test statistics.
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| 9. |
- Cardilin, Tim, 1989, et al.
(författare)
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Tumor Static Concentration Curves in Combination Therapy
- 2017
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Ingår i: AAPS Journal. - : Springer Science and Business Media LLC. - 1550-7416. ; 19:2, s. 456-467
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Tidskriftsartikel (refereegranskat)abstract
- © 2016 The Author(s) Combination therapies are widely accepted as a cornerstone for treatment of different cancer types. A tumor growth inhibition (TGI) model is developed for combinations of cetuximab and cisplatin obtained from xenograft mice. Unlike traditional TGI models, both natural cell growth and cell death are considered explicitly. The growth rate was estimated to 0.006 h−1 and the natural cell death to 0.0039 h−1 resulting in a tumor doubling time of 14 days. The tumor static concentrations (TSC) are predicted for each individual compound. When the compounds are given as single-agents, the required concentrations were computed to be 506 μg · mL−1 and 56 ng · mL−1 for cetuximab and cisplatin, respectively. A TSC curve is constructed for different combinations of the two drugs, which separates concentration combinations into regions of tumor shrinkage and tumor growth. The more concave the TSC curve is, the lower is the total exposure to test compounds necessary to achieve tumor regression. The TSC curve for cetuximab and cisplatin showed weak concavity. TSC values and TSC curves were estimated that predict tumor regression for 95% of the population by taking between-subject variability into account. The TSC concept is further discussed for different concentration-effect relationships and for combinations of three or more compounds.
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| 10. |
- Nzabanita, Joseph, et al.
(författare)
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Bilinear regression model with Kronecker and linear structures for the covariance matrix
- 2015
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Ingår i: Afrika Statistika. - : Statistics and Probability African Society (SPAS). - 2316-090X. ; 10:2, s. 827-837
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, the bilinear regression model based on normally distributed random matrix is studied. For these models, the dispersion matrix has the so called Kronecker product structure and they can be used for example to model data with spatio-temporal relationships. The aim is to estimate the parameters of the model when, in addition, one covariance matrix is assumed to be linearly structured. On the basis of n independent observations from a matrix normal distribution, estimating equations in a flip-flop relation are established and the consistency of estimators is studied.
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