| 1. |
- Botan, Alexandru, et al.
(författare)
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Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions
- 2015
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:49, s. 15075-15088
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Tidskriftsartikel (refereegranskat)abstract
- Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR. experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https://zenodo.org/collection/user-nmrlipids) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
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| 2. |
- Jensen, Evelyn L., et al.
(författare)
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Ancient and historical DNA in conservation policy
- 2022
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Ingår i: Trends in Ecology & Evolution. - : Elsevier. - 0169-5347 .- 1872-8383. ; 37:5, s. 420-429
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Forskningsöversikt (refereegranskat)abstract
- Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (N-e), and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.
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| 3. |
- Maaranen, Heikki, et al.
(författare)
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On initial populations of a genetic algorithm for continuous optimization problems
- 2007
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Ingår i: Journal of Global Optimization. - : Springer Science and Business Media LLC. - 0925-5001 .- 1573-2916. ; 37:3, s. 405-436
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Tidskriftsartikel (refereegranskat)abstract
- Genetic algorithms are commonly used metaheuristics for global optimization, but there has been very little research done on the generation of their initial population. In this paper, we look for an answer to the question whether the initial population plays a role in the performance of genetic algorithms and if so, how it should be generated. We show with a simple example that initial populations may have an effect on the best objective function value found for several generations. Traditionally, initial populations are generated using pseudo random numbers, but there are many alternative ways. We study the properties of different point generators using four main criteria: the uniform coverage and the genetic diversity of the points as well as the speed and the usability of the generator. We use the point generators to generate initial populations for a genetic algorithm and study what effects the uniform coverage and the genetic diversity have on the convergence and on the final objective function values. For our tests, we have selected one pseudo and one quasi random sequence generator and two spatial point processes: simple sequential inhibition process and nonaligned systematic sampling. In numerical experiments, we solve a set of 52 continuous test functions from 16 different function families, and analyze and discuss the results.
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| 4. |
- Marabita, Francesco, et al.
(författare)
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Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health
- 2022
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Ingår i: Cell Systems. - : Cell Press. - 2405-4712 .- 2405-4720. ; 13:3, s. 241-255.e7
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Tidskriftsartikel (refereegranskat)abstract
- We explored opportunities for personalized and predictive health care by collecting serial clinical measurements, health surveys, genomics, proteomics, autoantibodies, metabolomics, and gut microbiome data from 96 individuals who participated in a data-driven health coaching program over a 16-month period with continuous digital monitoring of activity and sleep. We generated a resource of >20,000 biological samples from this study and a compendium of >53 million primary data points for 558,032 distinct features. Multiomics factor analysis revealed distinct and independent molecular factors linked to obesity, diabetes, liver function, cardiovascular disease, inflammation, immunity, exercise, diet, and hormonal effects. For example, ethinyl estradiol, a common oral contraceptive, produced characteristic molecular and physiological effects, including increased levels of inflammation and impact on thyroid, cortisol levels, and pulse, that were distinct from other sources of variability observed in our study. In total, this work illustrates the value of combining deep molecular and digital monitoring of human health. A record of this paper's transparent peer review process is included in the supplemental information.
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| 5. |
- Martínez, Gerardo Santillán, et al.
(författare)
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Parameters selection in predictive online simulation
- 2017
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Ingår i: IEEE International Conference on Industrial Informatics (INDIN). - Piscataway, NJ : Institute of Electrical and Electronics Engineers (IEEE). - 9781509028702 ; , s. 726-729
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Konferensbidrag (refereegranskat)abstract
- Industrial applications with reliable predictive features are becoming increasingly important. A tracking simulator is an example of an online simulation system with great capabilities that fills the gap left by other predictive applications. In a tracking simulator, a simulation model is run in parallel with a physical process controlled by the process' control system. At the same time, a tracking mechanism is used to keep the state of the simulation model as close as possible to the real process by continually adjusting parameters of the model. The selection of these parameters impacts directly on the quality of the tracking simulation results and it is a complex task in processes with a big number of variables. This paper presents two case studies of tracking simulation where the controlled parameters are selected using different techniques. The first case study deals with a laboratory-scale hot water generation process where the parameters' selection is performed manually. The second case study deals with a combined heat and power production process with major uncertainties in the process structure. In this case, we focus on the variance decomposition method used to determine the most suitable controlled parameters. Conclusions and future work are finally presented.
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| 6. |
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| 7. |
- Miettinen, Arttu, et al.
(författare)
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Non-destructive automatic determination of aspect ratio and cross-sectional properties of fibres
- 2015
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Ingår i: Composites. Part A, Applied science and manufacturing. - : Elsevier. - 1359-835X .- 1878-5840. ; 77, s. 188-194
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Tidskriftsartikel (refereegranskat)abstract
- We propose a novel method for computerized estimation of the length/diameter distribution of fibres in short-fibre reinforced composite. Having its basis in X-ray micro-computed tomography, the method is non-destructive and does not require user intervention. In addition to the aspect ratio, the method is also capable of estimating other geometrical properties of fibre cross-sections. Based on results on specially fabricated model material, the accuracy and precision of the method seems to be reasonable. An application to the manufacturing process of wood fibre reinforced thermoplastic composite is also shown, indicating a significant decrease in the aspect ratio of fibres during the processing steps.
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| 8. |
- Tröstl, Jasmin, et al.
(författare)
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The role of low-volatility organic compounds in initial particle growth in the atmosphere
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 533:7604, s. 527-531
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Tidskriftsartikel (refereegranskat)abstract
- About half of present-day cloud condensation nuclei originate from atmospheric nucleation, frequently appearing as a burst of new particles near midday(1). Atmospheric observations show that the growth rate of new particles often accelerates when the diameter of the particles is between one and ten nanometres(2,3). In this critical size range, new particles are most likely to be lost by coagulation with pre-existing particles(4), thereby failing to form new cloud condensation nuclei that are typically 50 to 100 nanometres across. Sulfuric acid vapour is often involved in nucleation but is too scarce to explain most subsequent growth(5,6), leaving organic vapours as the most plausible alternative, at least in the planetary boundary layer(7-10). Although recent studies(11-13) predict that low-volatility organic vapours contribute during initial growth, direct evidence has been lacking. The accelerating growth may result from increased photolytic production of condensable organic species in the afternoon(2), and the presence of a possible Kelvin (curvature) effect, which inhibits organic vapour condensation on the smallest particles (the nano-Kohler theory)(2,14), has so far remained ambiguous. Here we present experiments performed in a large chamber under atmospheric conditions that investigate the role of organic vapours in the initial growth of nucleated organic particles in the absence of inorganic acids and bases such as sulfuric acid or ammonia and amines, respectively. Using data from the same set of experiments, it has been shown(15) that organic vapours alone can drive nucleation. We focus on the growth of nucleated particles and find that the organic vapours that drive initial growth have extremely low volatilities (saturation concentration less than 10(-4.5) micrograms per cubic metre). As the particles increase in size and the Kelvin barrier falls, subsequent growth is primarily due to more abundant organic vapours of slightly higher volatility (saturation concentrations of 10(-4.5) to 10(-0.5) micrograms per cubic metre). We present a particle growth model that quantitatively reproduces our measurements. Furthermore, we implement a parameterization of the first steps of growth in a global aerosol model and find that concentrations of atmospheric cloud concentration nuclei can change substantially in response, that is, by up to 50 per cent in comparison with previously assumed growth rate parameterizations.
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