| 1. |
- Nilsson, Jenny A. U., et al.
(author)
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Observed and Modeled Global Ocean Turbulence Regimes as Deduced from Surface Trajectory Data
- 2013
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In: Journal of Physical Oceanography. - 0022-3670 .- 1520-0485. ; 43:11, s. 2249-2269
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Journal article (peer-reviewed)abstract
- A large-scale tool for systematic analyses of the dispersal and turbulent properties of ocean currents and the subsequent separation of dynamical regimes according to the prevailing trajectories taxonomy in a certain area was proposed by Rupolo. In the present study, this methodology has been extended to the analysis of model trajectories obtained by analytical computations of the particle advection equation using the Lagrangian open-source software package Tracing the Water Masses of the North Atlantic and the Mediterranean (TRACMASS), and intercomparisons have been made between the surface velocity fields from three different configurations of the global Nucleus for European Modelling of the Ocean (NEMO) ocean/sea ice general circulation model. Lagrangian time scales of the observed and synthetic trajectory datasets have been calculated by means of inverse Lagrangian stochastic modeling, and the influence of the model field spatial and temporal resolution on the analyses has been investigated. In global-scale ocean modeling, compromises are frequently made in terms of grid resolution and time averaging of the output fields because high-resolution data require considerable amounts of storage space. Here, the implications of such approximations on the modeled velocity fields and, consequently, on the particle dispersion, have been assessed through validation against observed drifter tracks. This study aims, moreover, to shed some light on the relatively unknown turbulent properties of near-surface ocean dynamics and their representation in numerical models globally and in a number of key regions. These results could be of interest for other studies within the field of turbulent eddy diffusion parameterization in ocean models or ocean circulation studies involving long-term coarse-grid model experiments.
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| 2. |
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| 3. |
- Wallin, Göran, et al.
(author)
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Energetics of activation of GTP hydrolysis on the ribosome
- 2013
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 1733-
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Journal article (peer-reviewed)abstract
- Several of the steps in protein synthesis on the ribosome utilize hydrolysis of guanosine triphosphate (GTP) as the driving force. This reaction is catalyzed by translation factors that become activated upon binding to the ribosome. The recently determined crystal structure of an elongation factor-Tuternary complex bound to the ribosome allows the energetics of GTP activation to be explored by computer simulations. A central problem regards the role of the universally conserved histidine, which has been proposed to act as a general base for guanosine triphosphate hydrolysis. Here we report a detailed energetic and structural analysis of different possible protonation states that could be involved in activation of the reaction. We show that the histidine cannot act as a general base, but must be protonated and in its active conformation to promote GTP hydrolysis. We further show that the sarcin-ricin loop of the ribosome spontaneously drives the histidine into the correct conformation for GTP activation.
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| 4. |
- Wallin, Gabriel, et al.
(author)
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Equating nonequivalent groups using propensity scores : model misspecification and sensitivity analysis
- 2021
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In: Quantitative psychology. - Cham : Springer. - 9783030747718 - 9783030747725 ; , s. 187-197
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Book chapter (peer-reviewed)abstract
- Equating test scores from nonequivalent groups requires to separate the effect of differences in ability from differences in test form difficulty between the test forms. The gold standard for this purpose is to use common items, however, not all testing programs have such items available. There might be other useful information available, and this paper studies the use of covariates in equating as a substitute for common items. To gain further insight about how to best incorporate covariates inequating this paper studies the propensity score, a scalar function of the covariates. The sensitivity of the propensity score as a proxy for ability is studied to investigate if bias is introduced in the estimated equated scores if the propensity score estimation model is misspecified. By considering an incorrect link function, leaving out a covariate and leaving out a second-order term from the estimation model, common misspecifications are studied. The results show that equating with respect to the propensity score is relatively robust to model misspecification, especially modeling nonlinearity with a linear model and leaving out second-order terms.
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| 7. |
- Henningsson, Susanne, 1977, et al.
(author)
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Detecting two-locus gene-gene effects using monotonisation of the penetrance matrix
- 2008
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In: Statistical Applications in Genetics and Molecular Biology. - 1544-6115. ; 7:1
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Journal article (peer-reviewed)abstract
- As more genetic loci are genotyped simultaneously and as the interest in effects of combinations of loci increases, the need for more powerful analysis methods is increased. In the present paper we present a method aimed at increasing the power of likelihood ratio tests for case-control studies investigating possible two-locus effects. The method is based on the notion that the expected effect pattern of one locus, as well as the expected pattern of a penetrance matrix representing the effect of two loci, is a monotone one. By using an algorithm for making the estimated penetrance matrix monotone, the alternative hypothesis is restricted to monotone penetrance matrices only. The evaluation of the likelihood ratio tests for several underlying monotone models shows that the power is substantially increased by using a monotone alternative as compared to when an unrestricted alternative is used.
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| 8. |
- Malm, Helena, et al.
(author)
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Transcriptional regulation of the miR-212/miR-132 cluster in insulin-secreting β-cells by cAMP-regulated transcriptional co-activator 1 and salt-inducible kinases.
- 2016
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In: Molecular and Cellular Endocrinology. - : Elsevier BV. - 1872-8057 .- 0303-7207. ; 424, s. 23-33
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Journal article (peer-reviewed)abstract
- MicroRNAs are central players in the control of insulin secretion, but their transcriptional regulation is poorly understood. Our aim was to investigate cAMP-mediated transcriptional regulation of the miR-212/miR-132 cluster and involvement of further upstream proteins in insulin secreting β-cells. cAMP induced by forskolin+IBMX or GLP-1 caused increased expression of miR-212/miR-132, and elevated phosphorylation of cAMP-response-element-binding-protein (CREB)/Activating-transcription-factor-1 (ATF1) and Salt-Inducible-Kinases (SIKs). CyclicAMP-Regulated Transcriptional Co-activator-1 (CRTC1) was concomitantly dephosphorylated and translocated to the nucleus. Silencing of miR-212/miR-132 reduced, and overexpression of miR-212 increased, glucose-stimulated insulin secretion. Silencing of CRTC1 expression resulted in decreased insulin secretion and miR-212/miR-132 expression, while silencing or inhibition of SIKs was associated with increased expression of the microRNAs and dephosphorylation of CRTC1. CRTC1 protein levels were reduced after silencing of miR-132, suggesting feed-back regulation. Our data propose cAMP-dependent co-regulation of miR-212/miR-132, in part mediated through SIK-regulated CRTC1, as an important factor for fine-tuned regulation of insulin secretion.
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| 9. |
- Svedman, Patrick, et al.
(author)
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Reduced Feedback SDMA Based on Subspace Packings
- 2009
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In: IEEE Transactions on Wireless Communications. - : IEEE. - 1536-1276 .- 1558-2248. ; 8:3, s. 1329-1339
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Journal article (peer-reviewed)abstract
- Herein, we treat Space Division Multiple Access (SDMA) based on partial channel state information and limited feedback. We propose a novel framework utilizing subspace packings, where beamforming, feedback, and scheduling are integrated. Advantages of the proposed framework are that the fed back supportable rates are based on the post-scheduling SINR and that the feedback implicitly contains information about the spatial compatibility of the users. The feasibility region of packings of different dimensions is indicated by the allocation outage probability which is derived. Grassmannian subspace packings, DFT-based packings, and non-orthogonal Grassmannian packings are formulated and studied as candidates. Numerical simulations show better performance for the proposed scheme compared to conventional channel quantization at the receiver with zero-forcing transmission in i.i.d. Rayleigh fading. Finally, we propose and evaluate a beam-graph method to further reduce the feedback load, that can be used in the context of tracking quantized beamformers.
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